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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    Volatilome-Genome-Wide Association Study on Wholemeal Maize Flour
    Alves, Mara Lisa ; Bento-Silva, Andreia ; Gaspar, Daniel ; Paulo, Manuel ; Brites, Cláudia ; Mendes-Moreira, Pedro ; Rosário Bronze, Maria do; Malosetti, Marcos ; Eeuwijk, Fred van; Vaz Patto, Maria Carlota - \ 2020
    Journal of Agricultural and Food Chemistry 68 (2020)29. - ISSN 0021-8561 - p. 7809 - 7818.
    aldehydes - candidate genes - Portuguese maize germplasm - volatiles - Zea mays L.

    Odor and aroma, resulting from the perception of volatiles by the olfactory receptors, are important in consumer food acceptance. To develop more efficient molecular breeding tools to improve the odor/aroma on maize (Zea mays L.), a staple food crop, increasing the knowledge on the genetic basis of maize volatilome is needed. In this work, we conducted a genome-wide association study on a unique germplasm collection to identify genomic regions controlling maize wholemeal flour's volatilome. We identified 64 regions on the maize genome and candidate genes controlling the levels of 15 volatiles, mainly aldehydes. As an example, the Zm00001d033623 gene was within a region associated with 2-octenal (E) and 2-nonenal (E), two byproducts of linoleic acid oxidation. This gene codes for linoleate 9S-lipoxygenase, an enzyme responsible for oxidizing linoleic acid. This knowledge can now support the development of molecular tools to increase the selection efficacy/efficiency of these volatiles within maize breeding programs.

    The genetic and functional analysis of flavor in commercial tomato : the FLORAL4 gene underlies a QTL for floral aroma volatiles in tomato fruit
    Tikunov, Yury M. ; Roohanitaziani, Raana ; Meijer-Dekens, Fien ; Molthoff, Jos ; Paulo, Joao ; Finkers, Richard ; Capel, Iris ; Carvajal Moreno, Fatima ; Maliepaard, Chris ; Nijenhuis-de Vries, Mariska ; Labrie, Caroline W. ; Verkerke, Wouter ; Heusden, Adriaan W. van; Eeuwijk, Fred van; Visser, Richard G.F. ; Bovy, Arnaud G. - \ 2020
    The Plant Journal (2020). - ISSN 0960-7412
    2-phenylethanol - aroma - flavor - quantitative trait loci - Solanum lycopersicum - tomato - volatiles

    Tomato (Solanum lycopersicum L.) has become a popular model for genetic studies of fruit flavor in the last two decades. In this article we present a study of tomato fruit flavor, including an analysis of the genetic, metabolic and sensorial variation of a collection of contemporary commercial glasshouse tomato cultivars, followed by a validation of the associations found by quantitative trait locus (QTL) analysis of representative biparental segregating populations. This led to the identification of the major sensorial and chemical components determining fruit flavor variation and detection of the underlying QTLs. The high representation of QTL haplotypes in the breeders’ germplasm suggests that there is great potential for applying these QTLs in current breeding programs aimed at improving tomato flavor. A QTL on chromosome 4 was found to affect the levels of the phenylalanine-derived volatiles (PHEVs) 2-phenylethanol, phenylacetaldehyde and 1-nitro-2-phenylethane. Fruits of near-isogenic lines contrasting for this locus and in the composition of PHEVs significantly differed in the perception of fruity and rose-hip-like aroma. The PHEV locus was fine mapped, which allowed for the identification of FLORAL4 as a candidate gene for PHEV regulation. Using a gene-editing-based (CRISPR-CAS9) reverse-genetics approach, FLORAL4 was demonstrated to be the key factor in this QTL affecting PHEV accumulation in tomato fruit.

    Biological activities associated with the volatile compound 2,5-bis(1-methylethyl)-pyrazine
    Janssens, Thierry K.S. ; Tyc, Olaf ; Besselink, Harrie ; Boer, Wietse de; Garbeva, Paolina - \ 2019
    FEMS Microbiology Letters 366 (2019)3. - ISSN 0378-1097
    Burkholderia - Paenibacillus - mode of action - pyrazine - toxicity - transcriptional reporter assays - volatiles

    Pyrazines are 1,4-diazabenzene-based volatile organic compounds and known for their broad-spectrum antimicrobial activity. In the present study, we assessed the antimicrobial activity of 2,5-bis(1-methylethyl)-pyrazine, produced by Paenibacillus sp. AD87 during co-culture with Burkholderia sp. AD24. In addition, we were using transcriptional reporter assays in E. coli and mammalian cells to decipher the possible mode of action. Bacterial and mammalian luciferase reporter strains were deployed to elucidate antimicrobial and toxicological effects of 2,5-bis(1-methylethyl)-pyrazine. At high levels of exposure, 2,5-bis(1-methylethyl)-pyrazine exerted strong DNA damage response. At lower concentrations, cell-wall damage response was observed. The activity was corroborated by a general toxicity reporter assay in E. coli ΔampD, defective in peptidoglycan turnover. The maximum E. coli cell-wall stress activity was measured at a concentration close to the onset of the mammalian cytotoxicity, while other adverse outcome pathways, such as the activation of aryl hydrocarbon and estrogenic receptor, the p53 tumour suppressor and the oxidative stress-related Nrf2 transcription factor, were induced at elevated concentrations compared to the response of mammalian cells. Because of its broad-spectrum antimicrobial activity at lower concentrations and the relatively low mammalian toxicity, 2,5-bis(1-methylethyl)-pyrazine is a potential bio-based fumigant with possible applications in food industry, agriculture or logistics.

    Thrips advisor : Exploiting thrips-induced defences to combat pests on crops
    Steenbergen, Merel ; Abd-El-Haliem, Ahmed ; Bleeker, Petra ; Dicke, Marcel ; Escobar-Bravo, Rocio ; Cheng, Gang ; Haring, Michel A. ; Kant, Merijn R. ; Kappers, Iris ; Klinkhamer, Peter G.L. ; Leiss, Kirsten A. ; Legarrea, Saioa ; Macel, Mirka ; Mouden, Sanae ; Pieterse, Corné M.J. ; Sarde, Sandeep J. ; Schuurink, Robert C. ; Vos, Martin De; Wees, Saskia C.M. Van; Broekgaarden, Colette - \ 2018
    Journal of Experimental Botany 69 (2018)8. - ISSN 0022-0957 - p. 1837 - 1848.
    Cell-content feeder - effectors - herbivorous insect - phytohormone signalling - plant defence - specialized metabolites - thrips - virus - volatiles

    Plants have developed diverse defence mechanisms to ward off herbivorous pests. However, agriculture still faces estimated crop yield losses ranging from 25% to 40% annually. These losses arise not only because of direct feeding damage, but also because many pests serve as vectors of plant viruses. Herbivorous thrips (Thysanoptera) are important pests of vegetable and ornamental crops worldwide, and encompass virtually all general problems of pests: they are highly polyphagous, hard to control because of their complex lifestyle, and they are vectors of destructive viruses. Currently, control management of thrips mainly relies on the use of chemical pesticides. However, thrips rapidly develop resistance to these pesticides. With the rising demand for more sustainable, safer, and healthier food production systems, we urgently need to pinpoint the gaps in knowledge of plant defences against thrips to enable the future development of novel control methods. In this review, we summarize the current, rather scarce, knowledge of thrips-induced plant responses and the role of phytohormonal signalling and chemical defences in these responses. We describe concrete opportunities for breeding resistance against pests such as thrips as a prototype approach for next-generation resistance breeding.

    Isoprene emission by poplar is not important for the feeding behaviour of poplar leaf beetles
    Müller, A. ; Kaling, M. ; Faubert, P. ; Gort, G. ; Smid, H.M. ; Loon, J.J.A. van; Dicke, M. ; Kanawati, B. ; Schmitt-Kopplin, P. ; Polle, A. ; Schnitzler, J.P. ; Rosenkranz, M. - \ 2015
    BMC Plant Biology 15 (2015)1. - ISSN 1471-2229 - 16 p.
    organic-compound emissions - chrysomela-populi - phratora-vitellinae - plant interactions - emitting poplars - volatiles - biosynthesis - caterpillars - performance - trichocarpa
    Background Chrysomela populi (poplar leaf beetle) is a common herbivore in poplar plantations whose infestation causes major economic losses. Because plant volatiles act as infochemicals, we tested whether isoprene, the main volatile organic compound (VOC) produced by poplars (Populus x canescens), affects the performance of C. populi employing isoprene emitting (IE) and transgenic isoprene non-emitting (NE) plants. Our hypothesis was that isoprene is sensed and affects beetle orientation or that the lack of isoprene affects plant VOC profiles and metabolome with consequences for C. populi feeding. Results Electroantennographic analysis revealed that C. populi can detect higher terpenes, but not isoprene. In accordance to the inability to detect isoprene, C. populi showed no clear preference for IE or NE poplar genotypes in the choice experiments, however, the beetles consumed a little bit less leaf mass and laid fewer eggs on NE poplar trees in field experiments. Slight differences in the profiles of volatile terpenoids between IE and NE genotypes were detected by gas chromatography - mass spectrometry. Non-targeted metabolomics analysis by Fourier Transform Ion Cyclotron Resonance Mass Spectrometer revealed genotype-, time- and herbivore feeding-dependent metabolic changes both in the infested and adjacent undamaged leaves under field conditions. Conclusions We show for the first time that C. populi is unable to sense isoprene. The detected minor differences in insect feeding in choice experiments and field bioassays may be related to the revealed changes in leaf volatile emission and metabolite composition between the IE and NE poplars. Overall our results indicate that lacking isoprene emission is of minor importance for C. populi herbivory under natural conditions, and that the lack of isoprene is not expected to change the economic losses in poplar plantations caused by C. populi infestation.
    Fitness consequences of indirect plant defence in the annual weed, Sinapis arvensis
    Gols, R. ; Wagenaar, R. ; Poelman, E.H. ; Kruidhof, H.M. ; Loon, J.J.A. van; Harvey, J.A. - \ 2015
    Functional Ecology 29 (2015)8. - ISSN 0269-8463 - p. 1019 - 1025.
    pieris-brassicae - herbivory - tolerance - evolution - volatiles - insects - parasitoids - strategies - selection - ecology
    Plant traits that enhance the attraction of the natural enemies of their herbivores have been postulated to function as an 'indirect defence'. An important underlying assumption is that this enhanced attraction results in increased plant fitness due to reduced herbivory. This assumption has been rarely tested. We investigated whether there are fitness consequences for the charlock mustard Sinapis arvensis, a short-lived outcrossing annual weedy plant, when exposed to groups of large cabbage white (Pieris brassicae) caterpillars parasitized by either one of two wasp species, Hyposoter ebeninus and Cotesia glomerata, that allow the host to grow during parasitism. Hyposoter ebeninus is solitary and greatly reduces host growth compared with healthy caterpillars, whereas C. glomerata is gregarious and allows the host to grow approximately as large as unparasitized caterpillars. Both healthy and parasitized P. brassicae caterpillars initially feed on the foliage, but later stages preferentially consume the flowers. In a garden experiment, plants damaged by parasitized caterpillars produced more seeds than conspecific plants damaged by unparasitized caterpillars. Reproductive potential (germination success multiplied by total seed number) was similar for plants that were not exposed to herbivory and those that were damaged by parasitized caterpillars and lower for plants that were damaged by healthy unparasitized caterpillars. However, these quantitative seed traits negatively correlated with the qualitative seed traits, individual seed size and germination success, suggesting a trade-off between these two types of traits. We show that parasitism of insect herbivores that feed on reproductive plant tissues may have positive fitness consequences for S. arvensis. The extent to which plant fitness may benefit depends on parasitoid lifestyle (solitary or gregarious), which is correlated with the amount of damage inflicted on these tissues by the parasitized host
    Understanding the long-lasting attraction of malaria mosquitoes to odor baits
    Mweresa, C.K. ; Otieno, B. ; Omusula, P. ; Weldegergis, B.T. ; Verhulst, N.O. ; Dicke, M. ; Loon, J.J.A. van; Takken, W. ; Mukabana, W.R. - \ 2015
    PLoS ONE 10 (2015)3. - ISSN 1932-6203 - 16 p.
    gambiae-sensu-stricto - human skin emanations - anopheles-gambiae - human pathogen - aedes-aegypti - human sweat - identification - culicidae - volatiles - behavior
    The use of odor baits for surveillance and control of malaria mosquitoes requires robust dispensing tools. In this study, the residual activity of a synthetic mosquito attractant blend dispensed from nylon or low density polyethylene (LDPE) sachets was evaluated at weekly intervals for one year without re-impregnation. The potential role of bacteria in modulating the attraction of mosquitoes to odor-treated nylon that had been used repeatedly over the one year study period, without re-impregnation, was also investigated. Significantly higher proportions of female Anopheles gambiae sensu stricto mosquitoes were consistently attracted to treated nylon strips than the other treatments, up to one year post-treatment. Additional volatile organic compounds and various bacterial populations were found on the treated nylon strips after one year of repeated use. The most abundant bacteria were Bacillus thuringiensis and Acinetobacter baumannii. Autoclaving of treated nylon strips prior to exposure had no effect on trap collections of laboratory-reared female An. Gambiae (P = 0.17) or wild female An. Gambiae sensu lato (P = 0.26) and Mansonia spp. (P = 0.17) mosquitoes. Trap catches of wild female An. Funestus (P <0.001) and other anophelines (P <0.007) were higher when treated strips had been autoclaved prior to deployment as opposed to when the treated nylon strips were not autoclaved. By contrast, wild female Culex mosquitoes were more strongly attracted to non-autoclaved compared to autoclaved treated nylon strips (P <0.042). This study demonstrates the feasibility of using odor baits for sampling and surveillance of malaria as well as other mosquito vectors over prolonged periods of time. Preliminary evidence points towards the potential role of bacteria in sustaining prolonged use of nylon material for dispensing synthetic attractant odorants for host-seeking malaria and other mosquito vectors but further investigations are required.
    A New Method to Infer Causal Phenotype Networks Using QTL and Phenotypic Information
    Wang, H. ; Eeuwijk, F. van - \ 2014
    PLoS ONE 9 (2014)8. - ISSN 1932-6203
    quantitative trait loci - bayesian networks - tomato fruits - multi-trait - environment - model - accumulation - volatiles - genomics
    In the context of genetics and breeding research on multiple phenotypic traits, reconstructing the directional or causal structure between phenotypic traits is a prerequisite for quantifying the effects of genetic interventions on the traits. Current approaches mainly exploit the genetic effects at quantitative trait loci (QTLs) to learn about causal relationships among phenotypic traits. A requirement for using these approaches is that at least one unique QTL has been identified for each trait studied. However, in practice, especially for molecular phenotypes such as metabolites, this prerequisite is often not met due to limited sample sizes, high noise levels and small QTL effects. Here, we present a novel heuristic search algorithm called the QTL+phenotype supervised orientation (QPSO) algorithm to infer causal directions for edges in undirected phenotype networks. The two main advantages of this algorithm are: first, it does not require QTLs for each and every trait; second, it takes into account associated phenotypic interactions in addition to detected QTLs when orienting undirected edges between traits. We evaluate and compare the performance of QPSO with another state-of-the-art approach, the QTL-directed dependency graph (QDG) algorithm. Simulation results show that our method has broader applicability and leads to more accurate overall orientations. We also illustrate our method with a real-life example involving 24 metabolites and a few major QTLs measured on an association panel of 93 tomato cultivars. Matlab source code implementing the proposed algorithm is freely available upon request.
    Effect of belowground herbivory on parasitoid associative learning of plant odours
    Kruidhof, H.M. ; Rijk, M. de; Hoffmann, D. ; Harvey, J.A. ; Vet, L.E.M. ; Soler Gamborena, R. - \ 2013
    Oikos 122 (2013)7. - ISSN 0030-1299 - p. 1094 - 1100.
    aboveground multitrophic interactions - infochemical use - natural enemies - root herbivores - quality - behavior - wasps - performance - preference - volatiles
    Root herbivores can influence both the performance and the behaviour of parasitoids of aboveground insect herbivores through changes in aboveground plant quality and in the composition of the plant's odour blend. Here we show that root herbivory by Delia radicum larvae did not influence the innate preferences for plant odours of the two closely related parasitoid species Cotesia glomerata and C. rubecula, but did affect their learned preferences, and did so in an opposite direction. While C. glomerata learned to prefer the odour of plants with intact roots, C. rubecula learned to prefer the odour of root-infested plants. The learned preference of C. glomerata for the odour of plants with intact roots matches our previously published result of its better performance when developing in P. brassicae hosts feeding on this plant type. In contrast, the relatively stronger learned preference of C. rubecula for the odour of root-infested plants cannot be merely explained by its performance, as the results of our present study indicate that D. radicum root herbivory did not influence the performance of C. rubecula nor of its host P. rapae. Our results stress the importance of assessing the influence of root herbivores on both innate and learned responses of parasitoids to plant odours.
    Induced plant responses to microbes and insects
    Pieterse, C.M.J. ; Poelman, E.H. ; Wees, S.C.M. van; Dicke, M. - \ 2013
    Frontiers in Plant Science 4 (2013). - ISSN 1664-462X - 3 p.
    induced resistance - arabidopsis - volatiles - susceptibility - pathways - immunity - defense - stress - growth - acid
    Plants are members of complex communities and interact both with antagonists and beneficial organisms. An important question in plant defense-signaling research is how plants integrate signals induced by pathogens, insect herbivores and beneficial microbes into the most appropriate adaptive response. Molecular and genomic tools are now being used to uncover the complexity of the induced defense signaling networks that have evolved during the arms races between plants and the other organisms with which they intimately interact. To understand the functioning of the complex defense signaling network in nature, molecular biologists and ecologists have joined forces to place molecular mechanisms of induced plant defenses in an ecological perspective. In this Research Topic, we aim to provide an on-line, open-access snapshot of the current state of the art of the field of induced plant responses to microbes and insects, with a special focus on the translation of molecular mechanisms to ecology and vice versa. We will collect Original Research and Review papers on the topic, but also other article types, such as Methods and Opinions are welcome.
    NON-SMOKY GLYCOSYLTRANSFERASE1 Prevents the Release of Smoky Aroma from Tomato Fruit
    Tikunov, Y.M. ; Molthoff, J.W. ; Vos, R.C.H. de; Beekwilder, M.J. ; Houwelingen, A.M.M.L. van; Hooft, J.J.J. van der; Nijenhuis-de Vries, M.A. ; Labrie, C.W. ; Verkerke, W. ; Geest, H.C. van de; Víquez Zamora, A.M. ; Presa, S. ; Rambla Nebot, J.L. ; Granell, A. ; Hall, R.D. ; Bovy, A.G. - \ 2013
    The Plant Cell 25 (2013)8. - ISSN 1040-4651 - p. 3067 - 3078.
    mass spectrometry - small molecules - salicylic-acid - key enzyme - flavor - volatiles - biosynthesis - components - odor - gene
    Phenylpropanoid volatiles are responsible for the key tomato fruit (Solanum lycopersicum) aroma attribute termed “smoky.” Release of these volatiles from their glycosylated precursors, rather than their biosynthesis, is the major determinant of smoky aroma in cultivated tomato. Using a combinatorial omics approach, we identified the NON-SMOKY GLYCOSYLTRANSFERASE1 (NSGT1) gene. Expression of NSGT1 is induced during fruit ripening, and the encoded enzyme converts the cleavable diglycosides of the smoky-related phenylpropanoid volatiles into noncleavable triglycosides, thereby preventing their deglycosylation and release from tomato fruit upon tissue disruption. In an nsgt1/nsgt1 background, further glycosylation of phenylpropanoid volatile diglycosides does not occur, thereby enabling their cleavage and the release of corresponding volatiles. Using reverse genetics approaches, the NSGT1-mediated glycosylation was shown to be the molecular mechanism underlying the major quantitative trait locus for smoky aroma. Sensory trials with transgenic fruits, in which the inactive nsgt1 was complemented with the functional NSGT1, showed a significant and perceivable reduction in smoky aroma. NSGT1 may be used in a precision breeding strategy toward development of tomato fruits with distinct flavor phenotypes.
    Jasmonate and ethylene signaling mediate whitefly-induced interference with indirect plant defense in Arabidopsis thaliana
    Zhang, P.J. ; Broekgaarden, C. ; Zheng, S.J. ; Snoeren, T.A.L. ; Loon, J.J.A. van; Gols, R. ; Dicke, M. - \ 2013
    New Phytologist 197 (2013)4. - ISSN 0028-646X - p. 1291 - 1299.
    salicylic-acid - transcriptome changes - feeding guilds - tomato plants - herbivores - volatiles - insect - responses - gene - involvement
    Upon herbivore attack, plants activate an indirect defense, that is, the release of a complex mixture of volatiles that attract natural enemies of the herbivore. When plants are simultaneously exposed to two herbivore species belonging to different feeding guilds, one herbivore may interfere with the indirect plant defense induced by the other herbivore. However, little is understood about the mechanisms underlying such interference. Here, we address the effect of herbivory by the phloem-feeding whitefly Bemisia tabaci on the induced indirect defense of Arabidopsis thaliana plants to Plutella xylostella caterpillars, that is, the attraction of the parasitoid wasp Diadegma semiclausum. Assays with various Arabidopsis mutants reveal that B. tabaci infestation interferes with indirect plant defense induced by P. xylostella, and that intact jasmonic acid and ethylene signaling are required for such interference caused by B. tabaci. Chemical analysis of plant volatiles showed that the composition of the blend emitted in response to the caterpillars was significantly altered by co-infestation with whiteflies. Moreover, whitefly infestation also had a considerable effect on the transcriptomic response of the plant to the caterpillars. Understanding the mechanisms underlying a plant’s responses to multiple attackers will be important for the development of crop protection strategies in a multi-attacker context.
    Evaluation of low density polyethylene and nylon for delivery of synthetic mosquito attractants.
    Mukabana, W.R. ; Mweresa, C.K. ; Omusula, P. ; Orindi, B.O. ; Smallegange, R.C. ; Loon, J.J.A. van; Takken, W. - \ 2012
    Parasites & Vectors 5 (2012). - ISSN 1756-3305 - 18 p.
    vector anopheles-gambiae - sensu-stricto diptera - human skin microbiota - semifield conditions - carbon-dioxide - traps - odor - behavior - culicidae - volatiles
    BACKGROUND: Synthetic odour baits present an unexploited potential for sampling, surveillance and control of malaria and other mosquito vectors. However, application of such baits is impeded by the unavailability of robust odour delivery devices that perform reliably under field conditions. In the present study the suitability of low density polyethylene (LDPE) and nylon strips for dispensing synthetic attractants of host-seeking Anopheles gambiae mosquitoes was evaluated. METHODS: Baseline experiments assessed the numbers of An. gambiae mosquitoes caught in response to low density polyethylene (LDPE) sachets filled with attractants, attractant-treated nylon strips, control LDPE sachets, and control nylon strips placed in separate MM-X traps. Residual attraction of An. gambiae to attractant-treated nylon strips was determined subsequently. The effects of sheet thickness and surface area on numbers of mosquitoes caught in MM-X traps containing the synthetic kairomone blend dispensed from LDPE sachets and nylon strips were also evaluated. Various treatments were tested through randomized 4¿×¿4 Latin Square experimental designs under semi-field conditions in western Kenya. RESULTS: Attractant-treated nylon strips collected 5.6 times more An. gambiae mosquitoes than LDPE sachets filled with the same attractants. The attractant-impregnated nylon strips were consistently more attractive (76.95%; n¿=¿9,120) than sachets containing the same attractants (18.59%; n¿=¿2,203), control nylon strips (2.17%; n¿=¿257) and control LDPE sachets (2.29%; n¿=¿271) up to 40¿days post-treatment (P¿
    MetAlign 3.0: performance enhancement by efficient use of advances in computer hardware
    Lommen, A. ; Kools, H.J. - \ 2012
    Metabolomics 8 (2012)4. - ISSN 1573-3882 - p. 719 - 726.
    metabolomics approach - mass-spectrometry - lc-ms - identification - arabidopsis - metabolites - volatiles
    A new, multi-threaded version of the GC-MS and LC-MS data processing software, metAlign, has been developed which is able to utilize multiple cores on one PC. This new version was tested using three different multi-core PCs with different operating systems. The performance of noise reduction, baseline correction and peak-picking was 8-19 fold faster compared to the previous version on a single core machine from 2008. The alignment was 5-10 fold faster. Factors influencing the performance enhancement are discussed. Our observations show that performance scales with the increase in processor core numbers we currently see in consumer PC hardware development.
    MSClust: a tool for unsupervised mass spectra extraction of chromatography-mass spectrometry ion-wise aligned data
    Tikunov, Y.M. ; Laptenok, S. ; Hall, R.D. ; Bovy, A.G. ; Vos, C.H. de - \ 2012
    Metabolomics 8 (2012)4. - ISSN 1573-3882 - p. 714 - 718.
    metabolomics approach - plant metabolomics - peak alignment - tomato - ms - metabolism - volatiles
    Mass peak alignment (ion-wise alignment) has recently become a popular method for unsupervised data analysis in untargeted metabolic profiling. Here we present MSClust—a software tool for analysis GC–MS and LC–MS datasets derived from untargeted profiling. MSClust performs data reduction using unsupervised clustering and extraction of putative metabolite mass spectra from ion-wise chromatographic alignment data. The algorithm is based on the subtractive fuzzy clustering method that allows unsupervised determination of a number of metabolites in a data set and can deal with uncertain memberships of mass peaks in overlapping mass spectra. This approach is based purely on the actual information present in the data and does not require any prior metabolite knowledge. MSClust can be applied for both GC–MS and LC–MS alignment data sets
    Penalized regression techniques for modeling relationships between metabolites and tomato taste attributes
    Menendez, P. ; Eilers, P. ; Tikunov, Y.M. ; Bovy, A.G. ; Eeuwijk, F. van - \ 2012
    Euphytica 183 (2012)3. - ISSN 0014-2336 - p. 379 - 387.
    lycopersicon-esculentum - nonvolatile components - organoleptic quality - selection - flavor - volatiles - lasso - identification - cultivars - traits
    The search for models which link tomato taste attributes to their metabolic profiling, is a main challenge within the breeding programs that aim to enhance tomato flavor. In this paper, we compared such models calculated by the traditional statistical approach, stepwise regression, with models obtained by the new generation of regression techniques, known as penalized regression or regularization methods. In addition, for penalized regression, different scenarios and various model selection criteria were discussed to conclude that classical crossvalidation, selects models with many superfluous variables whereas model selection criteria such as Bayesian information criterion, seem to be more suitable, when the goal is to find parsimonious models, to explain tomato taste attributes based on metabolic information. An exhaustive comparison of the discussed methodology was done for six sensory traits, showing that the most important covariates were identified by the stepwise regression as well as by some of the penalized regression methods, despite the general disagreement on the size of the regression coefficients between them. In particular, for stepwise regression the coefficients are inflated due to their high variance which is not the case with penalized regression, showing that this new methodology, can be an alternative to obtain more accurate models.
    Characterization of the natural variation in Arabidopsis thaliana metabolome by the analysis of metabolic distance
    Houshyani Hassanzadeh, B. ; Kabouw, P. ; Muth, D. ; Vos, R.C.H. de; Bino, R.J. ; Bouwmeester, H.J. - \ 2012
    Metabolomics 8 (2012)suppl. 1. - ISSN 1573-3882 - p. 131 - 145.
    genomic diversity - mass-spectrometry - functional genomics - mildew resistance - plants - tomato - biosynthesis - pathogens - volatiles - defense
    Metabolite fingerprinting is widely used to unravel the chemical characteristics of biological samples. Multivariate data analysis and other statistical tools are subsequently used to analyze and visualize the plasticity of the metabolome and/or the relationship between those samples. However, there are limitations to these approaches for example because of the multi-dimensionality of the data that makes interpretation of the data obtained from untargeted analysis almost impossible for an average human being. These limitations make the biological information that is of prime importance in untargeted studies be partially exploited. Even in the case of full exploitation, current methods for relationship elucidation focus mainly on between groups variation and differences. Therefore, a measure that is capable of exploiting both between- and within-group biological variation would be of great value. Here, we examined the natural variation in the metabolome of nine Arabidopsis thaliana accessions grown under various environmental conditions and established a measure for the metabolic distance between accessions and across environments. This data analysis approach shows that there is just a minor correlation between genetic and metabolic diversity of the nine accessions. On the other hand, it delivers so far in Arabidopsis unexplored chemical information and is shown to be biologically relevant for resistance studies.
    Effects of a botanical larvicide derived from Azadirachta indica (the neem tree) on oviposition behaviour in Anopheles gambiae s.s. mosquitoes
    Howard, A.F.V. ; Adongo, E.A. ; Vulule, J. ; Githure, J. - \ 2011
    Journal of Medicinal Plants Research 5 (2011)10. - ISSN 1996-0875 - p. 1948 - 1954.
    malaria vector mosquitos - western kenya - body-size - diptera-culicidae - culex mosquitos - sensu-stricto - giles - volatiles - stephensi - fecundity
    More focus is given to mosquito larval control due to the necessity to use several control techniques together in integrated vector management programmes. Botanical products are thought to be able to provide effective, sustainable and cheap mosquito larval control tools. However, bio-larvicides like Azadirachta indica (neem) could repel adult mosquitoes from laying their eggs in the treated larval habitats. In this study the response of Anopheles gambiae s.s. mosquitoes towards varying doses of crude aqueous neem extracts was examined. Non-choice oviposition tests were used to measure the proportion of mosquitoes laying on the first or second night, or not laying at all, when compared to the control. For each individual mosquito, the number of eggs laid and/or retained in the ovary was counted to determine the relationship between wing length and egg production. Larger female mosquitoes produced larger egg batches. The results show that at a dose of 0.1 g/l, a concentration previously found to be effective at controlling mosquito larvae, the oviposition behaviour of adult female mosquitoes was not significantly affected. The results indicate that the mosquitoes would expose progeny to this neem control tool, making the use of these simple neem wood extracts effective and potentially sustainable.
    Parasitoid-specific induction of plant responses to parasitized herbivores affects colonization by subsequent herbivores
    Poelman, E.H. ; Zheng, S.J. ; Zhang, Z. ; Heemskerk, N.M. ; Cortesero, A.M. ; Dicke, M. - \ 2011
    Proceedings of the National Academy of Sciences of the United States of America 108 (2011)49. - ISSN 0027-8424 - p. 19647 - 19652.
    insect attack - volatiles - defense - elicitors - larvae - specialist - selection - pathogen - leaves - wasps
    Plants are exposed to a suite of herbivorous attackers that often arrive sequentially. Herbivory affects interactions between the host plants and subsequently attacking herbivores. Moreover, plants may respond to herbivory by emitting volatile organic compounds (VOCs) that attract carnivorous natural enemies of the herbivores. However, information borne by VOCs is ubiquitous and may attract carnivores, such as parasitoids, that differ in their effectiveness at releasing the plant from its herbivorous attackers. Furthermore, the development of parasitoids within their herbivorous hosts, attacking a given host plant, may influence the elicitation of defensive reactions in the host plant. This may, in turn, affect the behavior of subsequent herbivores attacking the host plant. Here, we show that the species identity of a parasitoid had a more significant effect on defense responses of Brassica oleracea plants than the species identity of the herbivorous hosts of the parasitoids. Consequently, B. oleracea plants that were damaged by caterpillars (Pieris spp.) parasitized by different parasitoid species varied in the degree to which diamondback moths (Plutella xylostella) selected the plants for oviposition. Attracting parasitoids in general benefitted the plants by reducing diamondback moth colonization. However, the species of parasitoid that parasitized the herbivore significantly affected the magnitude of this benefit by its species-specific effect on herbivore–plant interactions mediated by caterpillar regurgitant. Our findings show that information-mediated indirect defense may lead to unpredictable consequences for plants when considering trait-mediated effects of parasitized caterpillars on the host plant and their consequences because of community-wide responses to induced plants.
    Temporal dynamics of herbivore-induced responses in Brassica juncea and their effect on generalist and specialist herbivores
    Mathur, V. ; Ganta, S. ; Raaijmakers, C.E. ; Reddy, A.S. ; Vet, L.E.M. ; Dam, N.M. van - \ 2011
    Entomologia Experimentalis et Applicata 139 (2011)3. - ISSN 0013-8703 - p. 215 - 225.
    plant defense syndromes - black mustard - oilseed rape - wild radish - glucosinolate - volatiles - induction - insect - performance - population
    Herbivore feeding may induce an array of responses in plants, and each response may have its own temporal dynamics. Precise timing of these plant responses is vital for them to have optimal effect on the herbivores feeding on the plant. This study measured the temporal dynamics of various systemically induced responses occurring in Brassica juncea (L.) Czern. (Brassicaceae) leaves after insect herbivory in India and The Netherlands. Morphological (trichomes, leaf size) and chemical (glucosinolates, amino acids, sugars) responses were analysed. The effects of systemic responses were assessed using a specialist [Plutella xylostella L. (Lepidoptera: Plutellidae)] and a generalist [Spodoptera litura Fabricius (Lepidoptera: Noctuidae)] herbivore. We tested the hypotheses that morphological responses were slower than chemical responses and that generalist herbivores would be more affected by induced responses than specialists. Glucosinolates and trichomes were found to increase systemically as quickly as 4 and 7 days after herbivore damage, respectively. Amino acids, sugars, and leaf size remained unaffected during this period. The generalist S. litura showed a significant feeding preference for undamaged leaves, whereas the specialist herbivore P. xylostella preferred leaves that were damaged 9 days before. Performance bioassays on generalist S. litura revealed that larvae gained half the weight on leaves from damaged plants as compared to larvae feeding on leaves from undamaged plants. These studies show that although morphological responses are somewhat slower than chemical responses, they also contribute to induced plant resistance in a relatively short time span. We argue that before considering induced responses as resistance factors, their effect should be assessed at various points in time with both generalist and specialist herbivores.
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