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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Plasma metabolites associated with colorectal cancer : A discovery-replication strategy
Geijsen, Anne J.M.R. ; Brezina, Stefanie ; Keski-Rahkonen, Pekka ; Baierl, Andreas ; Bachleitner-Hofmann, Thomas ; Bergmann, Michael M. ; Boehm, Juergen ; Brenner, Hermann ; Chang-Claude, Jenny ; Duijnhoven, Fränzel J.B. van; Gigic, Biljana ; Gumpenberger, Tanja ; Hofer, Philipp ; Hoffmeister, Michael ; Holowatyj, Andreana N. ; Karner-Hanusch, Judith ; Kok, Dieuwertje E. ; Leeb, Gernot ; Ulvik, Arve ; Robinot, Nivonirina ; Ose, Jennifer ; Stift, Anton ; Schrotz-King, Petra ; Ulrich, Alexis B. ; Ueland, Per Magne ; Kampman, Ellen ; Scalbert, Augustin ; Habermann, Nina ; Gsur, Andrea ; Ulrich, Cornelia M. - \ 2019
International Journal of Cancer (2019). - ISSN 0020-7136
colorectal cancer - discovery-replication approach - metabolomics - UHPLC-QTOF-MS

Colorectal cancer is known to arise from multiple tumorigenic pathways; however, the underlying mechanisms remain not completely understood. Metabolomics is becoming an increasingly popular tool in assessing biological processes. Previous metabolomics research focusing on colorectal cancer is limited by sample size and did not replicate findings in independent study populations to verify robustness of reported findings. Here, we performed a ultrahigh performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UHPLC-QTOF-MS) screening on EDTA plasma from 268 colorectal cancer patients and 353 controls using independent discovery and replication sets from two European cohorts (ColoCare Study: n = 180 patients/n = 153 controls; the Colorectal Cancer Study of Austria (CORSA) n = 88 patients/n = 200 controls), aiming to identify circulating plasma metabolites associated with colorectal cancer and to improve knowledge regarding colorectal cancer etiology. Multiple logistic regression models were used to test the association between disease state and metabolic features. Statistically significant associated features in the discovery set were taken forward and tested in the replication set to assure robustness of our findings. All models were adjusted for sex, age, BMI and smoking status and corrected for multiple testing using False Discovery Rate. Demographic and clinical data were abstracted from questionnaires and medical records.

Nutrimetabolomics: An Integrative Action for Metabolomic Analyses in Human Nutritional Studies
Ulaszewska, Marynka M. ; Weinert, Christoph H. ; Trimigno, Alessia ; Portmann, Reto ; Andres Lacueva, Cristina ; Badertscher, René ; Brennan, Lorraine ; Brunius, Carl ; Bub, Achim ; Capozzi, Francesco ; Cialiè Rosso, Marta ; Cordero, Chiara E. ; Daniel, Hannelore ; Durand, Stéphanie ; Egert, Bjoern ; Ferrario, Paola G. ; Feskens, Edith J.M. ; Franceschi, Pietro ; Garcia-Aloy, Mar ; Giacomoni, Franck ; Giesbertz, Pieter ; González-Domínguez, Raúl ; Hanhineva, Kati ; Hemeryck, Lieselot Y. ; Kopka, Joachim ; Kulling, Sabine E. ; Llorach, Rafael ; Manach, Claudine ; Mattivi, Fulvio ; Migné, Carole ; Münger, Linda H. ; Ott, Beate ; Picone, Gianfranco ; Pimentel, Grégory ; Pujos-Guillot, Estelle ; Riccadonna, Samantha ; Rist, Manuela J. ; Rombouts, Caroline ; Rubert, Josep ; Skurk, Thomas ; Sri Harsha, Pedapati S.C. ; Meulebroek, Lieven Van; Vanhaecke, Lynn ; Vázquez-Fresno, Rosa ; Wishart, David ; Vergères, Guy - \ 2018
Molecular Nutrition & Food Research 63 (2018)1. - ISSN 1613-4125
GC–MS - LC–MS - metabolomics - NMR - nutrition
The life sciences are currently being transformed by an unprecedented wave of developments in molecular analysis, which include important advances in instrumental analysis as well as biocomputing. In light of the central role played by metabolism in nutrition, metabolomics is rapidly being established as a key analytical tool in human nutritional studies. Consequently, an increasing number of nutritionists integrate metabolomics into their study designs. Within this dynamic landscape, the potential of nutritional metabolomics (nutrimetabolomics) to be translated into a science, which can impact on health policies, still needs to be realized. A key element to reach this goal is the ability of the research community to join, to collectively make the best use of the potential offered by nutritional metabolomics. This article, therefore, provides a methodological description of nutritional metabolomics that reflects on the state-of-the-art techniques used in the laboratories of the Food Biomarker Alliance (funded by the European Joint Programming Initiative “A Healthy Diet for a Healthy Life” (JPI HDHL)) as well as points of reflections to harmonize this field. It is not intended to be exhaustive but rather to present a pragmatic guidance on metabolomic methodologies, providing readers with useful “tips and tricks” along the analytical workflow.
Age and Sex Effects on Plasma Metabolite Association Networks in Healthy Subjects
Vignoli, Alessia ; Tenori, Leonardo ; Luchinat, Claudio ; Saccenti, Edoardo - \ 2018
Journal of Proteome Research 17 (2018)1. - ISSN 1535-3893 - p. 97 - 107.
differential network analysis - metabolism - metabolomics - network inference - NMR
In the era of precision medicine, the analysis of simple information like sex and age can increase the potential to better diagnose and treat conditions that occur more frequently in one of the two sexes, present sex-specific symptoms and outcomes, or are characteristic of a specific age group. We present here a study of the association networks constructed from an array of 22 plasma metabolites measured on a cohort of 844 healthy blood donors. Through differential network analysis we show that specific association networks can be associated with sex and age: Different connectivity patterns were observed, suggesting sex-related variability in several metabolic pathways (branched-chain amino acids, ketone bodies, and propanoate metabolism). Reduction in metabolite hub connectivity was also found to be associated with age in both sex groups. Network analysis was complemented with standard univariate and multivariate statistical analysis that revealed age- and sex-specific metabolic signatures. Our results demonstrate that the characterization of metabolite-metabolite association networks is a promising and powerful tool to investigate the human phenotype at a molecular level.
Disentangling hexaploid genetics : towards DNA-informed breeding for postharvest performance in chrysanthemum
Geest, Geert van - \ 2017
Wageningen University. Promotor(en): Richard Visser, co-promotor(en): Uulke van Meeteren; Paul Arens. - Wageningen : Wageningen University - ISBN 9789463436427 - 142
chrysanthemum - plant breeding - postharvest quality - hexaploidy - polyploidy - quantitative trait loci - phenotypes - linkage mapping - metabolomics - polymorphism - dna - plantenveredeling - kwaliteit na de oogst - hexaploïdie - polyploïdie - loci voor kwantitatief kenmerk - fenotypen - koppelingskartering - metabolomica - polymorfisme

DNA-informed selection can strongly improve the process of plant breeding. It requires the detection of DNA polymorphisms, calculation of genetic linkage, access to reliable phenotypes and methods to detect genetic loci associated with phenotypic traits of interest. Cultivated chrysanthemum is an outcrossing hexaploid with an unknown mode of inheritance. This complicates the development of resources and methods that enable the detection of trait loci. Postharvest performance is an essential trait in chrysanthemum, but is difficult to measure. This makes it an interesting but challenging trait to phenotype and detect associated genetic loci. In this thesis I describe the development of resources and methods to enable phenotyping for postharvest performance, genetic linkage map construction and detection of quantitative trait loci in hexaploid chrysanthemum.

Postharvest performance is a complicated trait because it is related to many different disorders that reduce quality. One of these disorders in chrysanthemum is disk floret degreening, which occurs after long storage. In chapter 2, we show that degreening can be prevented by feeding the flower heads with sucrose, suggesting carbohydrate starvation plays a role in the degreening process. To investigate the response to carbohydrate starvation of genotypes with different sensitivity to disk floret degreening, we investigated the metabolome of sugar-fed and carbohydrate-starved disk florets by 1H-NMR and HPAEC. We show that the metabolome is severely altered at carbohydrate starvation. In general, starvation results in an upregulation of amino acid and secondary metabolism. Underlying causes of genotypic differences explaining variation in disk floret degreening in the three investigated genotypes remained to be elucidated, but roles of regulation of respiration rate and camphor metabolism were posed as possible candidates.

In chapter 3, disk floret degreening was found to be the most important postharvest disorder after 3 weeks of storage among 44 white chrysanthemum cultivars. To investigate the inheritance of disk floret degreening, we crossed two genotypes with opposite phenotypic values of both disk floret degreening and carbohydrate content to obtain a population segregating for disk floret degreening. To phenotype the cultivar panel and the bi-parental population precisely and in a high throughput manner, we developed a method that quantified colour of detached capitula over time. This method was validated with visual observations of disk floret degreening during vase life tests. In a subset of the bi-parental population we measured carbohydrate content of the disk florets at harvest. The amount of total carbohydrates co-segregated with sensitivity to degreening, which shows that the difference in disk floret degreening sensitivity between the parents could be explained by their difference in carbohydrate content. However, the correlation was rather weak, indicating carbohydrate content is not the only factor playing a role.

In order to develop resources for DNA-informed breeding, one needs to be able to characterize DNA polymorphisms. In chapter 4, we describe the development of a genotyping array containing 183,000 single nucleotide polymorphisms (SNPs). These SNPs were acquired by sequencing the transcriptome of 13 chrysanthemum cultivars. By comparing the genomic dosage based on the SNP assay and the dosage as estimated by the read depth from the transcriptome sequencing data, we show that alleles are expressed conform the genomic dosage, which contradicts to what is often found in disomic polyploids. In line with this finding, we conclusively show that cultivated chrysanthemum exhibits genome-wide hexasomic inheritance, based on the segregation ratios of large numbers of different types of markers in two different populations.

Tools for genetic analysis in diploids are widely available, but these have limited use for polyploids. In chapter 5, we present a modular software package that enables genetic linkage map construction in tetraploids and hexaploids. Because of the modularity, functionality for other ploidy levels can be easily added. The software is written in the programming language R and we named it polymapR. It can generate genetic linkage maps from marker dosage scores in an F1 population, while taking the following steps: data inspection and filtering, linkage analysis, linkage group assignment and marker ordering. It is the first software package that can handle polysomic hexaploid and partial polysomic tetraploid data, and has advantages over other polyploid mapping software because of its scalability and cross-platform applicability.

With the marker dosage scores of the bi-parental F1 population from the genotyping array and the developed methods to perform linkage analysis we constructed an integrated genetic linkage map for the hexaploid bi-parental population described in chapter 3 and 4. We describe this process in chapter 6. With this integrated linkage map, we reconstructed the inheritance of parental haplotypes for each individual, and expressed this as identity-by-descent (IBD) probabilities. The phenotypic data on disk floret degreening sensitivity that was acquired as described in chapter 3, was used in addition to three other traits to detect quantitative trait loci (QTL). These QTL were detected based on the IBD probabilities of 1 centiMorgan intervals of each parental homologue. This enabled us to study genetic architecture by estimating the effects of each separate allele within a QTL on the trait. We showed that for many QTL the trait was affected by more than two alleles.

In chapter 7, the findings in this thesis are discussed in the context of breeding for heterogeneous traits, the implications of the mode of inheritance for breeding and the advantages and disadvantages of polyploidy in crop breeding. In conclusion, this thesis provides in general a significant step for DNA-informed breeding in polysomic hexaploids, and for postharvest performance in chrysanthemum in particular.

Dual herbivore attack and herbivore density affect metabolic profiles of Brassica nigra leaves
Ponzio, Camille ; Papazian, Stefano ; Albrectsen, Benedicte R. ; Dicke, Marcel ; Gols, Rieta - \ 2017
Plant, Cell & Environment 40 (2017)8. - ISSN 0140-7791 - p. 1356 - 1367.
Brevicoryne brassicae - dual herbivory - induced defence - metabolomics - Pieris brassicae - 017-4026

Plant responses to dual herbivore attack are increasingly studied, but effects on the metabolome have largely been restricted to volatile metabolites and defence-related non-volatile metabolites. However, plants subjected to stress, such as herbivory, undergo major changes in both primary and secondary metabolism. Using a naturally occurring system, we investigated metabolome-wide effects of single or dual herbivory on Brassica nigra plants by Brevicoryne brassicae aphids and Pieris brassicae caterpillars, while also considering the effect of aphid density. Metabolomic analysis of leaf material showed that single and dual herbivory had strong effects on the plant metabolome, with caterpillar feeding having the strongest influence. Additionally, aphid-density-dependent effects were found in both the single and dual infestation scenarios. Multivariate analysis revealed treatment-specific metabolomic profiles, and effects were largely driven by alterations in the glucosinolate and sugar pools. Our work shows that analysing the plant metabolome as a single entity rather than as individual metabolites provides new insights into the subcellular processes underlying plant defence against multiple herbivore attackers. These processes appear to be importantly influenced by insect density.

Identification of metabolites involved in heat stress response in different tomato genotypes
Paupière, Marine J. - \ 2017
Wageningen University. Promotor(en): Richard Visser, co-promotor(en): Arnaud Bovy; Yury Tikunov. - Wageningen : Wageningen University - ISBN 9789463431842 - 168
solanum lycopersicum - tomatoes - genotypes - heat stress - heat tolerance - pollen - metabolomes - metabolites - metabolomics - tomaten - genotypen - warmtestress - hittetolerantie - stuifmeel - metabolomen - metabolieten - metabolomica

Tomato production is threatened by climate change. High temperatures lead to a decrease of fruit set which correlates with a decrease of pollen fertility. The low viability of tomato pollen under heat stress was previously shown to be associated with alterations in specific metabolites. In this thesis, we used untargeted metabolomics approaches to broaden the identification of metabolites affected by heat stress. We assessed the suitability of pollen isolation methods for metabolomics analysis and considered the pitfalls for our further analysis. We explored the developmental metabolomes of pollen and anthers of different tomato genotypes under control and high temperature conditions and identified that microsporogenesis is a critical developmental stage for the production of mature and fertile pollen grain under heat stress. Several metabolites were putatively associated with tolerance to high temperature such as specific flavonoids, polyamines and alkaloids. These metabolites can be further used as markers in breeding programs to develop new genotypes tolerant to high temperatures.

Entropy-Based Network Representation of the Individual Metabolic Phenotype
Saccenti, Edoardo ; Menichetti, Giulia ; Ghini, Veronica ; Remondini, Daniel ; Tenori, Leonardo ; Luchinat, Claudio - \ 2016
Journal of Proteome Research 15 (2016)9. - ISSN 1535-3893 - p. 3298 - 3307.
metabolite modules - metabolite-metabolite association networks - metabolomics - network multiplex

We approach here the problem of defining and estimating the nature of the metabolite-metabolite association network underlying the human individual metabolic phenotype in healthy subjects. We retrieved significant associations using an entropy-based approach and a multiplex network formalism. We defined a significantly over-represented network formed by biologically interpretable metabolite modules. The entropy of the individual metabolic phenotype is also introduced and discussed.

Metabolomics meets functional assays: coupling LC-MS and microfluidic cell-based receptor-ligand analyses
Henquet, M.G.L. ; Roelse, M. ; Vos, R.C.H. de; Schipper, A. ; Polder, G. ; Ruijter, N.C.A. de; Hall, R.D. ; Jongsma, M.A. - \ 2016
Metabolomics 12 (2016). - ISSN 1573-3882
metabolomics
Introduction

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

Objective

We aimed to combine LC–MS metabolomics with a cell based receptor assay. This combination could increase the understanding of biological processes and may provide novel opportunities for functional metabolomics.

Methods

We developed a flow through biosensor with human cells expressing both the TRPV1, a calcium ion channel which responds to capsaicin, and the fluorescent intracellular calcium ion reporter, YC3.6. We have analysed three contrasting Capsicum varieties. Two were selected with contrasting degrees of spiciness for characterization by HPLC coupled to high mass resolution MS. Subsequently, the biosensor was then used to link individual pepper compounds with TRPV1 activity.

Results

Among the compounds in the crude pepper fruit extracts, we confirmed capsaicin and also identified both nordihydrocapsaicin and dihydrocapsaicin as true agonists of the TRPV1 receptor. Furthermore, the biosensor was able to detect receptor activity in extracts of both Capsicum fruits as well as a commercial product. Sensitivity of the biosensor to this commercial product was similar to the sensory threshold of a human sensory panel.

Conclusion

Our results demonstrate that the TRPV1 biosensor is suitable for detecting bioactive metabolites. Novel opportunities may lie in the development of a continuous functional assay, where the biosensor is directly coupled to the LC–MS.
Regulation of cucumber (Cucumis sativus) induced defence against the two-spotted spider mite (Tetranychus urticae
He, J. - \ 2016
Wageningen University. Promotor(en): Harro Bouwmeester; Marcel Dicke, co-promotor(en): Iris Kappers. - Wageningen : Wageningen University - ISBN 9789462576810 - 211 p.
cucumis sativus - cucumbers - induced resistance - plant pests - tetranychus urticae - mites - defence mechanisms - herbivore induced plant volatiles - herbivory - metabolomics - terpenoids - genomics - komkommers - geïnduceerde resistentie - plantenplagen - mijten - verdedigingsmechanismen - herbivoor-geinduceerde plantengeuren - herbivorie - metabolomica - terpenen - genomica

Plants have evolved mechanisms to combat herbivory. These mechanisms can be classified as direct defences which have a negative influence on the herbivores and indirect defence that attracts natural enemies of the attacking herbivores. Both direct and indirect defences can be constantly present or induced upon attack. This study, using cucumber (Cucumis sativus) and the two-spotted spider mite (Tetranychus urticae) as model, aimed to reveal the molecular mechanisms underlying the induced defence during herbivory, with emphasis on transcriptional changes and the involved TFs, the enzymatic function of the genes associated with volatile biosynthesis, and their promoters which regulate their expression.

Big data dringen door in de tuinbouw. Naar een volledig begrip van plantgedrag en productkwaliteit
Kierkels, T. ; Zedde, H.J. van de - \ 2015
Onder Glas 12 (2015)11. - p. 24 - 25.
tuinbouw - glastuinbouw - innovaties - landbouwkundig onderzoek - kunstmatige intelligentie - gewaskwaliteit - plantenveredeling - sorteren - kwaliteit - teeltsystemen - 3d analyse - metabolomica - genomica - transcriptomica - horticulture - greenhouse horticulture - innovations - agricultural research - artificial intelligence - crop quality - plant breeding - sorting - quality - cropping systems - 3d analysis - metabolomics - genomics - transcriptomics
Vijftien onderzoeksgroepen van Wageningen UR hebben de handen ineengeslagen om te komen tot het beter meten, begrijpen en voorspellen van plantgedrag en productkwaliteit. Het vakgebied heet ‘Plant phenomics’ en maakt gebruik van innovatieve technieken en sensoren. Het doel is een betere beheersing van teelt- en veredelingsproces en productkwaliteit. Toepassingen voor de praktijk liggen nog vooral op het terrein van sorteren en automatische kwaliteitsbeoordeling.
Effect of temperature on biomass allocation in seedlings of two contrasting genotypes of the oilseed crop Ricinus communis
Ribeiro de Jesus, P.R. ; Zanotti, R.F. ; Deflers, C. ; Fernandez, L.G. ; Castro, R.D. De; Ligterink, W. ; Hilhorst, H.W.M. - \ 2015
Journal of Plant Physiology 185 (2015). - ISSN 0176-1617 - p. 31 - 39.
abiotic stress tolerance - plant-responses - heat-stress - castor-oil - acid gaba - growth - metabolomics - arabidopsis - pathways - moisture
Ricinus communis is becoming an important crop for oil production, and studying the physiological and biochemical aspects of seedling development may aid in the improvement of crop quality and yield. The objective of this study was to assess the effect of temperature on biomass allocation in two R. communis genotypes. Biomass allocation was assessed by measuring dry weight of roots, stems, and cotyledons of seedlings grown at three different temperatures. Root length of each seedling was measured. Biomass allocation was strongly affected by temperature. Seedlings grown at 25 ¿C and 35 ¿C showed greater biomass than seedlings grown at 20 ¿C. Cotyledon and stem dry weight increased for both genotypes with increasing temperature, whereas root biomass allocation showed a genotype-dependent behavior. Genotype MPA11 showed a continuous increase in root dry weight with increasing temperature, while genotype IAC80 was not able to sustain further root growth at higher temperatures. Based on metabolite and gene expression profiles, genotype MPA11 increases its level of osmoprotectant molecules and transcripts of genes encoding for antioxidant enzymes and heat shock proteins to a higher extent than genotype IAC80. This might be causal for the ability to maintain homeostasis and support root growth at elevated temperatures in genotype MPA11.
Correlating composition and functionality of soy protein hydrolysates used in animal cell cultures
Gupta, A.J. - \ 2015
Wageningen University. Promotor(en): Harry Gruppen, co-promotor(en): Peter Wierenga; J.W. Boots. - Wageningen : Wageningen University - ISBN 9789462573208 - 127
sojaeiwit - eiwithydrolysaten - functionele eigenschappen - warmtebehandeling - celculturen - chemische samenstelling - metabolomica - soya protein - protein hydrolysates - functional properties - heat treatment - cell cultures - chemical composition - metabolomics

Abstract

Soy protein hydrolysates are often supplemented to chemically defined (CD) media in cell cultures, but there is little understanding of the effect of their composition on their functionality (viable cell density, total immunoglobulin (IgG), and specific IgG production). To identify the key parameters (e.g. compound classes) that determine their functionality, hydrolysates were prepared from different starting materials (meal, concentrates, and isolate) and from soybean meal that was heated for different time periods. The functionality of these hydrolysates were compared to those of industrial hydrolysates. From the comparison, it was shown that the variation in industrial and experimental processes of hydrolysate production induced larger variation in the functionality than the variation in starting materials. Moreover, it was observed that the correlations between the functionality and compositional parameters observed in one experiment were absent in the other experiments. During the study, it became apparent that the variations in other factors, like CD media and temperature during culturing also resulted in variation in functionality. The extent of variations in the functionality due to variation in CD media and temperature during culturing was equivalent to the variation caused by varying the hydrolysate composition. The functionality data of the different experiments were fitted with a model that described the relation between specific IgG production and viable cell density. Using the model, the maximum achievable total IgG production could be calculated for a culture condition. This information can provide directions for further optimization of hydrolysates to maximize total IgG production.

Mapping in the era of sequencing: high density genotyping and its application for mapping TYLCV resistance in Solanum pimpinellifolium
Viquez-Zamora, M. ; Caro Rios, C.M. ; Finkers, H.J. ; Tikunov, Y.M. ; Bovy, A.G. ; Visser, R.G.F. ; Bai, Y. ; Heusden, A.W. van - \ 2014
BMC Genomics 15 (2014). - ISSN 1471-2164 - 10 p.
leaf-curl-virus - recombinant inbred lines - mass-spectrometry - lycopersicon-pimpinellifolium - tomato - infection - genes - metabolomics - inheritance - population
Background A RIL population between Solanum lycopersicum cv. Moneymaker and S. pimpinellifolium G1.1554 was genotyped with a custom made SNP array. Additionally, a subset of the lines was genotyped by sequencing (GBS). Results A total of 1974 polymorphic SNPs were selected to develop a linkage map of 715 unique genetic loci. We generated plots for visualizing the recombination patterns of the population relating physical and genetic positions along the genome. This linkage map was used to identify two QTLs for TYLCV resistance which contained favourable alleles derived from S. pimpinellifolium. Further GBS was used to saturate regions of interest, and the mapping resolution of the two QTLs was improved. The analysis showed highest significance on Chromosome 11 close to the region of 51.3 Mb (qTy-p11) and another on Chromosome 3 near 46.5 Mb (qTy-p3). Furthermore, we explored the population using untargeted metabolic profiling, and the most significant differences between susceptible and resistant plants were mainly associated with sucrose and flavonoid glycosides. Conclusions The SNP information obtained from an array allowed a first QTL screening of our RIL population. With additional SNP data of a RILs subset, obtained through GBS, we were able to perform an in silico mapping improvement to further confirm regions associated with our trait of interest. With the combination of different¿~¿omics platforms we provide valuable insight into the genetics of S. pimpinellifolium-derived TYLCV resistance.
Regulatory Network of Secondary Metabolism in Brassica rapa: Insight into the Glucosinolate Pathway
Pino del Carpio, D. ; Kumar, R. ; Arends, D. ; Lin, K. ; Vos, R.C.H. de; Muth, D. ; Kodde, J. ; Boutilier, K.A. ; Bucher, J. ; Wang, X. ; Jansen, R.C. ; Bonnema, G. - \ 2014
PLoS ONE 9 (2014)9. - ISSN 1932-6203 - 11 p.
arabidopsis-thaliana - mass-spectrometry - coexpression networks - genomics approach - genetic genomics - biosynthesis - metabolomics - identification - plants - fruit
Brassica rapa studies towards metabolic variation have largely been focused on the profiling of the diversity of metabolic compounds in specific crop types or regional varieties, but none aimed to identify genes with regulatory function in metabolite composition. Here we followed a genetical genomics approach to identify regulatory genes for six biosynthetic pathways of health-related phytochemicals, i.e carotenoids, tocopherols, folates, glucosinolates, flavonoids and phenylpropanoids. Leaves from six weeks-old plants of a Brassica rapa doubled haploid population, consisting of 92 genotypes, were profiled for their secondary metabolite composition, using both targeted and LC-MS-based untargeted metabolomics approaches. Furthermore, the same population was profiled for transcript variation using a microarray containing EST sequences mainly derived from three Brassica species: B. napus, B. rapa and B. oleracea. The biochemical pathway analysis was based on the network analyses of both metabolite QTLs (mQTLs) and transcript QTLs (eQTLs). Colocalization of mQTLs and eQTLs lead to the identification of candidate regulatory genes involved in the biosynthesis of carotenoids, tocopherols and glucosinolates. We subsequently focused on the well-characterized glucosinolate pathway and revealed two hotspots of co-localization of eQTLs with mQTLs in linkage groups A03 and A09. Our results indicate that such a large-scale genetical genomics approach combining transcriptomics and metabolomics data can provide new insights into the genetic regulation of metabolite composition of Brassica vegetables.
Control of anthocyanin and non-flavonoid compounds by anthocyanin-regulating MYB and bHLH transcription factors in Nicotiana benthamiana leaves
Outchkourov, N.S. ; Carollo, C.A. ; Gomez Roldan, M.V. ; Vos, C.H. de; Bosch, H.J. ; Hall, R.D. ; Beekwilder, M.J. - \ 2014
Frontiers in Plant Science 5 (2014). - ISSN 1664-462X - 9 p.
r2r3-myb gene family - mass-spectrometry - tomato fruit - arabidopsis-thaliana - biosynthesis - tobacco - accumulation - metabolomics - plants - health
Coloration of plant organs such as fruit, leaves and flowers through anthocyanin production is governed by a combination of MYB and bHLH type transcription factors (TFs). In this study we introduced Rosea1 (ROS1, a MYB type) and Delila (DEL, a bHLH type), into Nicotiana benthamiana leaves by agroinfiltration. ROS1 and DEL form a pair of well-characterized TFs from Snapdragon (Antirrhinum majus), which specifically induce anthocyanin accumulation when expressed in tomato fruit. In N. benthamiana, robust induction of a single anthocyanin, delphinidin-3-rutinoside (D3R) was observed after expression of both ROS1 and DEL. Surprisingly in addition to D3R, a range of additional metabolites were also strongly and specifically up-regulated upon expression of ROS1 and DEL. Except for the D3R, these induced compounds were not derived from the flavonoid pathway. Most notable among these are nornicotine conjugates with butanoyl, hexanoyl, and octanoyl hydrophobic moieties, and phenylpropanoid-polyamine conjugates such as caffeoyl putrescine. The defensive properties of the induced molecules were addressed in bioassays using the tobacco specialist lepidopteran insect Manduca sexta. Our study showed that the effect of ROS1 and DEL expression in N. benthamiana leaves extends beyond the flavonoid pathway. Apparently the same transcription factor may regulate different secondary metabolite pathways in different plant species.
Self-organising maps: a versatile tool for the automatic analysis of untargeted metabolomic imaging datasets
Franceschi, P. ; Wehrens, H.R.M.J. - \ 2014
Proteomics 14 (2014)7-8. - ISSN 1615-9853 - p. 853 - 861.
identification - metabolomics - exchange
MS-based imaging approaches allow for location-specific identification of chemical components in biological samples, opening up possibilities of much more detailed understanding of biological processes and mechanisms. Data analysis, however, is challenging, mainly because of the sheer size of such datasets. This article presents a novel approach based on self-organizing maps, extending previous work in order to be able to handle the large number of variables present in high-resolution mass spectra. The key idea is to generate prototype images, representing spatial distributions of ions, rather than prototypical mass spectra. This allows for a two-stage approach, first generating typical spatial distributions and associated m/z bins, and later analyzing the interesting bins in more detail using accurate masses. The possibilities and advantages of the new approach are illustrated on an in-house dataset of apple slices.
Assessment of pleiotropic transcriptome perturbations in Arabidopsis engineered for indirect insect defence
Houshyani Hassanzadeh, B. ; Krol, A.R. van der; Bino, R.J. ; Bouwmeester, H.J. - \ 2014
BMC Plant Biology 14 (2014). - ISSN 1471-2229
global gene-expression - metabolomics - thaliana - gm - biosynthesis - metabolism - emission - synthase - crops - wheat
Background: Molecular characterization is an essential step of risk/safety assessment of genetically modified (GM) crops. Holistic approaches for molecular characterization using omics platforms can be used to confirm the intended impact of the genetic engineering, but can also reveal the unintended changes at the omics level as a first assessment of potential risks. The potential of omics platforms for risk assessment of GM crops has rarely been used for this purpose because of the lack of a consensus reference and statistical methods to judge the significance or importance of the pleiotropic changes in GM plants. Here we propose a meta data analysis approach to the analysis of GM plants, by measuring the transcriptome distance to untransformed wild-types. Results: In the statistical analysis of the transcriptome distance between GM and wild-type plants, values are compared with naturally occurring transcriptome distances in non-GM counterparts obtained from a database. Using this approach we show that the pleiotropic effect of genes involved in indirect insect defence traits is substantially equivalent to the variation in gene expression occurring naturally in Arabidopsis. Conclusion: Transcriptome distance is a useful screening method to obtain insight in the pleiotropic effects of genetic modification.
Physiological and molecular adaptations of Lactococcus lactis to near-zero growth conditions
Ercan, O. - \ 2014
Wageningen University. Promotor(en): Michiel Kleerebezem, co-promotor(en): Eddy Smid. - Wageningen : Wageningen University - ISBN 9789462570719 - 206
lactococcus lactis - adaptatiefysiologie - voedselmicrobiologie - groeitempo - groeispanning - transcriptomica - metabolomica - adaptation physiology - food microbiology - growth rate - growth stress - transcriptomics - metabolomics

Lactococcus lactis is an important lactic acid bacteria (LAB) species that is used for the manufacture of dairy products, such as cheese, buttermilk, and other fermented products. The predominant function of this bacterium in dairy fermentation is the production of lactic acid, as its major fermentation end-product that contributes to preservation and microbial safety of the product. Moreover, L. lactis is frequently encountered in natural ecosystems such as in (rotting) plant material.

Due to restricted energy source availability, natural microbial communities commonly live in a situation that can be characterized as ‘hunger’, which is different from strict nutrient-starvation. As a consequence, environmental microbes commonly grow at very low-growth rates as compared to laboratory cultures. Analogously, microorganisms can experience such nutrient-poor conditions in diverse industrial fermentation applications. For example, LAB encounter extreme low or no energy source availability during the extended ripening process of cheeses or dry sausages, which can take months. Despite these harsh environmental conditions, many LAB are able to remain viable in these processes for months and sustain a low-level metabolic activity, which plays an important role in their contribution to flavor and aroma formation in the product matrix.

In this thesis, the quantitative physiology of L. lactis at near-zero specific growth rates was studies, employing both metabolic and genome-wide transcriptome studies in an experimental set-up of carbon-limited retentostat cultivation. Chapter 2 describes how retentostat cultivation enables uncoupling of growth and non-growth related processes in L. lactis, allowing the quantitative analysis of the physiological adaptations of this bacterium to near-zero growth rates. In chapter 3, transcriptome and metabolome analyses were integrated to understand the molecular adaptation of L. lactis to near-zero specific growth rate, and expand the studies in chapter 2 towards gene regulations patterns that play a profound role in zero-growth adaptation. Chapter 4 describes the enhanced robustness to several stress conditions of L. lactis after its adaptation to extremely low-specific growth rate by carbon-limited retentostat cultivation. In this chapter correlations were modelled that quantitatively and accurately describe the relationships between growth-rate, stress-robustness, and stress-gene expression levels, revealing correlation coefficients for each of the varieties involved. Chapter 5 evaluates the distinction between the transcriptome responses to extended carbon-limited growth and severe starvation conditions, where the latter condition was elicited by switching off the medium supply of the retentostat cultures described in chapter 1. Chapter 6 highlights the comparison of the physiological and molecular adaptations of industrially important microorganisms towards carbon-limited retentostat conditions. In conclusion, this thesis describes the quantitative physiological, metabolic, and genome-wide transcriptional adaptations of L. lactis at near-zero specific growth rates induced by carbon source limited retentostat cultivation, and compares these molecular adaptations to those elicited by strict carbon-starvation conditions.

Plant metabolomics and the golden age of Dutch painting
Hall, R.D. - \ 2014
Wageningen : Wageningen University, Wageningen UR - ISBN 9789461739735 - 24
metabolomica - plantensamenstelling - fytochemie - schilderijen - geschiedenis - nederland - metabolomics - plant composition - phytochemistry - paintings - history - netherlands
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.
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