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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    Naar werkbaar instrument bodemkwaliteit
    Haan, Janjo de - \ 2019
    Vleesconsumptie stijgt weer na jaren
    Dagevos, H. ; Verhoog, A.D. ; Horne, P.L.M. van; Hoste, R. - \ 2019
    Algen aan vooravond van opschaling
    Weide, Rommie van der - \ 2019
    Herfst? De haspels draaien nog steeds
    Timmer, Ruud - \ 2018
    Genetical genomics of quality related traits in potato tubers using proteomics
    Acharjee, A. ; Chibon, P.Y.F.R.P. ; Kloosterman, B.A. ; America, A.H.P. ; Renaut, J. ; Maliepaard, C.A. ; Visser, R.G.F. - \ 2018
    Wageningen University & Research
    genetical genomics - proteomics - protein QTL - potato quality traits
    Background Recent advances in ~omics technologies such as transcriptomics, metabolomics and proteomics along with genotypic profiling have permitted the genetic dissection of complex traits such as quality traits in non-model species. To get more insight into the genetic factors underlying variation in quality traits related to carbohydrate and starch metabolism and cold sweetening, we determined the protein content and composition in potato tubers using 2D–gel electrophoresis in a diploid potato mapping population. Upon analyzing we made sure that the proteins from the patatin family were excluded to ensure a better representation of the other proteins. Results We subsequently performed pQTL analyses for all other proteins with a sufficient representation in the population and established a relationship between proteins and 26 potato tuber quality traits (e.g. flesh colour, enzymatic discoloration) by co-localization on the genetic map and a direct correlation study of protein abundances and phenotypic traits. Over 1643 unique protein spots were detected in total over the two harvests. We were able to map pQTLs for over 300 different protein spots some of which co-localized with traits such as starch content and cold sweetening. pQTLs were observed on every chromosome although not evenly distributed over the chromosomes. The largest number of pQTLs was found for chromosome 8 and the lowest for chromosome number 10. For some 20 protein spots multiple QTLs were observed. Conclusions From this analysis, hotspot areas for protein QTLs were identified on chromosomes three, five, eight and nine. The hotspot on chromosome 3 coincided with a QTL previously identified for total protein content and had more than 23 pQTLs in the region from 70 to 80 cM. Some of the co-localizing protein spots associated with some of the most interesting tuber quality traits were identified, albeit far less than we had anticipated at the onset of the experiments.
    Genetical genomics of quality related traits in potato tubers using proteomics
    Acharjee, A. ; Chibon, P.Y.F.R.P. ; Kloosterman, B.A. ; America, A.H.P. ; Renaut, J. ; Maliepaard, C.A. ; Visser, R.G.F. - \ 2018
    BMC Plant Biology 18 (2018). - ISSN 1471-2229
    Background: Recent advances in ~omics technologies such as transcriptomics, metabolomics and proteomics along with genotypic profiling have permitted the genetic dissection of complex traits such as quality traits in non-model species. To get more insight into the genetic factors underlying variation in quality traits related to carbohydrate and starch metabolism and cold sweetening, we determined the protein content and composition in potato tubers using 2D-gel electrophoresis in a diploid potato mapping population. Upon analyzing we made sure that the proteins from the patatin family were excluded to ensure a better representation of the other proteins. Results: We subsequently performed pQTL analyses for all other proteins with a sufficient representation in the population and established a relationship between proteins and 26 potato tuber quality traits (e.g. flesh colour, enzymatic discoloration) by co-localization on the genetic map and a direct correlation study of protein abundances and phenotypic traits. Over 1643 unique protein spots were detected in total over the two harvests. We were able to map pQTLs for over 300 different protein spots some of which co-localized with traits such as starch content and cold sweetening. pQTLs were observed on every chromosome although not evenly distributed over the chromosomes. The largest number of pQTLs was found for chromosome 8 and the lowest for chromosome number 10. For some 20 protein spots multiple QTLs were observed. Conclusions: From this analysis, hotspot areas for protein QTLs were identified on chromosomes three, five, eight and nine. The hotspot on chromosome 3 coincided with a QTL previously identified for total protein content and had more than 23 pQTLs in the region from 70 to 80 cM. Some of the co-localizing protein spots associated with some of the most interesting tuber quality traits were identified, albeit far less than we had anticipated at the onset of the experiments.
    Integration of multi-omics data for prediction of phenotypic traits using random forest
    Acharjee, Animesh ; Kloosterman, Bjorn ; Visser, Richard G.F. ; Maliepaard, Chris - \ 2016
    BMC Bioinformatics 17 (2016)5. - ISSN 1471-2105
    Data integration - Genetical genomics - Networks - Random forest

    Background: In order to find genetic and metabolic pathways related to phenotypic traits of interest, we analyzed gene expression data, metabolite data obtained with GC-MS and LC-MS, proteomics data and a selected set of tuber quality phenotypic data from a diploid segregating mapping population of potato. In this study we present an approach to integrate these ~ omics data sets for the purpose of predicting phenotypic traits. This gives us networks of relatively small sets of interrelated ~ omics variables that can predict, with higher accuracy, a quality trait of interest. Results: We used Random Forest regression for integrating multiple ~ omics data for prediction of four quality traits of potato: tuber flesh colour, DSC onset, tuber shape and enzymatic discoloration. For tuber flesh colour beta-carotene hydroxylase and zeaxanthin epoxidase were ranked first and forty-fourth respectively both of which have previously been associated with flesh colour in potato tubers. Combining all the significant genes, LC-peaks, GC-peaks and proteins, the variation explained was 75%, only slightly more than what gene expression or LC-MS data explain by themselves which indicates that there are correlations among the variables across data sets. For tuber shape regressed on the gene expression, LC-MS, GC-MS and proteomics data sets separately, only gene expression data was found to explain significant variation. For DSC onset, we found 12 significant gene expression, 5 metabolite levels (GC) and 2 proteins that are associated with the trait. Using those 19 significant variables, the variation explained was 45%. Expression QTL (eQTL) analyses showed many associations with genomic regions in chromosome 2 with also the highest explained variation compared to other chromosomes. Transcriptomics and metabolomics analysis on enzymatic discoloration after 5min resulted in 420 significant genes and 8 significant LC metabolites, among which two were putatively identified as caffeoylquinic acid methyl ester and tyrosine. Conclusions: In this study, we made a strategy for selecting and integrating multiple ~ omics data using random forest method and selected representative individual peaks for networks based on eQTL, mQTL or pQTL information. Network analysis was done to interpret how a particular trait is associated with gene expression, metabolite and protein data.

    Addressing the risk of inadequate and excessive micronutrient intakes: traditional versus new approaches to setting adequate and safe micronutrient levels in foods
    Bruins, M.J. ; Mugambi, G.K. ; Verkaik-Kloosterman, J. ; Hoekstra, J. ; Kraemer, K. ; Osendarp, S.J.M. ; Melse, A. ; Gallagher, A.M. ; Verhagen, H. - \ 2015
    Food and Nutrition Research 59 (2015). - ISSN 1654-661X - 9 p.
    Fortification of foods consumed by the general population or specific food products or supplements designed to be consumed by vulnerable target groups is amongst the strategies in developing countries to address micronutrient deficiencies. Any strategy aimed at dietary change needs careful consideration, ensuring the needs of at-risk subgroups are met whilst ensuring safety within the general population. This paper reviews the key principles of two main assessment approaches that may assist developing countries in deciding on effective and safe micronutrient levels in foods or special products designed to address micronutrient deficiencies, that is, the cut-point method and the stepwise approach to risk–benefit assessment. In the first approach, the goal is to shift population intake distributions such that intake prevalences below the Estimated Average Requirement (EAR) and above the Tolerable Upper Intake Level (UL) are both minimized. However, for some micronutrients like vitamin A and zinc, a narrow margin between the EAR and UL exists. Increasing their intakes through mass fortification may pose a dilemma; not permitting the UL to be exceeded provides assurance about the safety within the population but can potentially leave a proportion of the target population with unmet needs, or vice versa. Risk–benefit approaches assist in decision making at different micronutrient intake scenarios by balancing the magnitude of potential health benefits of reducing inadequate intakes against health risks of excessive intakes. Risk–benefit approaches consider different aspects of health risk including severity and number of people affected. This approach reduces the uncertainty for policy makers as compared to classic cut-point methods.
    Nutritional impact of sodium reduction strategies on sodium intake from processed foods
    Hendriksen, M.A.H. ; Verkaik-Kloosterman, J. ; Noort, M.W.J. ; Raaij, J.M.A. van - \ 2015
    European Journal of Clinical Nutrition 69 (2015). - ISSN 0954-3007 - p. 805 - 810.
    salt reduction - choice questionnaire - consumption - bread
    Background/objectives: Sodium intake in the Netherlands is substantially above the recommended intake of 2400¿mg/day. This study aimed to estimate the effect of two sodium reduction strategies, that is, modification of the composition of industrially processed foods toward the technologically feasible minimum level or alteration of consumers’ behavior on sodium intake in the Netherlands. Subjects/methods: Data from the Dutch National Food Consumption Survey (2007–2010) and the Food Composition Table (2011) were used to estimate the current sodium intake. In the first scenario, levels in processed foods were reduced toward their technologically feasible minimum level (sodium reduction in processed foods scenario). The minimum feasible levels were based on literature searches or expert judgment. In the second scenario, foods consumed were divided into similar food (sub)groups. Subsequently, foods were replaced by low-sodium alternatives (substitution of processed foods scenario). Sodium intake from foods was calculated based on the mean of two observation days for the current food consumption pattern and the scenarios. Results: Sodium levels of processed foods could be reduced in most food groups by 50%, and this may reduce median sodium intake from foods by 38% (from 3042 to 1886¿mg/day in adult men). Substitution of foods may reduce sodium intake by 47% (from 3042 to 1627¿mg/day in adult men), owing to many low-sodium alternatives within food groups. Conclusions: In the Netherlands, reduction of sodium intake by modification of food composition or by alteration of behavior may substantially reduce the median sodium intake from foods below the recommended sodium intake.
    Population Tuber Expression profiling experiment
    Kloosterman, B.A. - \ 2014
    Wageningen UR
    E-MTAB-701 - Solanum tuberosum
    Transcript profiling of tuber samples of 94 genotypes deriving from a segregating diploid potato population
    Population LEAF Expression profiling experiment
    Kloosterman, B.A. - \ 2014
    Wageningen UR
    E-MTAB-808 - Solanum tuberosum
    Transcription profiling by array of leaf samples of 94 genotypes deriving from a segregating diploid potato population
    Tuber development
    Kloosterman, B. ; Bachem, C. - \ 2014
    In: The Potato: Botany, Production and Uses / Navarre, R., Pavek, M.J., Wallingford, UK : CABI - ISBN 9781780642802 - p. 45 - 63.
    During their life cycle, potato plants develop tuberous organs from underground stems called stolons, which allow the rapid development of daughter plants from sprouts at the beginning of the new growing season. The formation and growth of a potato tuber is a complex process that can be divided into separate physiological events. In recent years, several scientific breakthroughs in the signalling pathway of tuberization have revealed novel tuber identity genes and regulatory pathways. Different signalling pathways leading to tuber initiation either act independently or intersect, but all seem to be, at least in part, under the control of the circadian clock associated with phase transitions during the plant life cycle. This chapter integrates the different signalling pathways underlying the process of potato tuber initiation and subsequent tuber growth in relation to timing, tuber physiology, gene expression, and the hormonal changes impacting these processes.
    Long live the library! The Book Collections of the IISH, in Particular the KNAW Library
    Nederveen Meerkerk, E.J.V. van - \ 2014
    In: A Usable Collection: Essays in honour of Jaap Kloosterman on Collecting Social History / Blok, A., Lucassen, J., Sanders, H., Amsterdam : Amsterdam University Press - ISBN 9789089646880 - p. 264 - 273.
    The PIN family of proteins in potato and their putative role in tuberisation
    Roumeliotis, E. ; Kloosterman, B.A. ; Oortwijn, M.E.P. ; Visser, R.G.F. ; Bachem, C.W.B. - \ 2013
    Frontiers in Plant Science 4 (2013). - ISSN 1664-462X
    arabidopsis-thaliana - auxin biosynthesis - root gravitropism - tuber initiation - expression - transport - growth - identification - transformation - tissues
    The PIN family of trans-membrane proteins mediates auxin efflux throughout the plant and during various phases of plant development. In Arabidopsis thaliana, the PIN family comprised of 8 members, divided into ‘short’ and ‘long’ PINs according to the length of the hydrophilic domain of the protein. Based on sequence homology using the recently published potato genome sequence (Solanum tuberosum group Phureja) we identified ten annotated potato StPIN genes. Mining the publicly available gene expression data, we constructed a catalogue tissue specificity of StPIN gene expression, focusing on the process of tuberization. A total of four StPIN genes exhibited increased expression four days after tuber induction, prior to the onset of stolon swelling. For two PIN genes, StPIN4 and StPIN2, promoter sequences were cloned and fused to the GUS reporter protein to study tissue specificity in more detail. StPIN4 promoter driven GUS staining was detected in the flower stigma, in the flower style, below the ovary and petals, in the root tips, in the vascular tissue of the stolons and in the tuber parenchyma cells. StPIN2 promoter driven GUS staining was detected in flower buds, in the vascular tissue of the swelling stolons and in the storage parenchyma of the growing tubers. Based on our results, we postulate a role for the StPINs in redistributing auxin in the swelling stolon during early events in tuber development.
    Down regulation of StGA3ox genes in potato results in altered GA content and affect plant and tuber growth characteristics.
    Roumeliotis, E. ; Kloosterman, B.A. ; Oortwijn, M.E.P. ; Lange, Theo ; Visser, R.G.F. ; Bachem, C.W.B. - \ 2013
    Journal of Plant Physiology 170 (2013)14. - ISSN 0176-1617 - p. 1228 - 1234.
    gibberellin biosynthesis - overexpression - auxin - transformation - arabidopsis - 2-oxidases - metabolism - expression - confers - pea
    GA biosynthesis and catabolism has been shown to play an important role in regulating tuberization in potato. Active GAs are inactivated in the stolon tips shortly after induction to tuberization. Overexpression of a GA inactivation gene results in an earlier tuberization phenotype, while reducing expression of the same gene results in delayed tuberization. In addition, overexpression of genes involved in GA biosynthesis results in delayed tuberization, while decreased expression of those genes results in earlied tuberization. The final step in GA biosynthesis is catalysed by StGA3ox1 and StGA3ox2 activity, that convert inactive forms of GA into active GA1 and GA4. In this study we cloned StGA3ox2 gene in an RNAi construct and used this construct to transform potato plants. The StGA3ox2 silenced plants were smaller and had shorter internodes. In addition, we assayed the concentrations of various GAs in the transgenic plants and showed an altered GA content. No difference was observed on the time point of tuber initiation. However, the transgenic clones had increased number of tubers with the same yield, resulting in smaller average tuber weight. In addition, we cloned the promoter of StGA3ox2 to direct expression of the GUS reporter gene to visualize the sites of GA biosynthesis in the potato plant. Finally, we discuss how changes of several GA levels can have an impact on shoot, stolon and tuber development, as well as the possible mechanisms that mediate feed-forward and feed-back regulation loops in the GA biosynthetic pathway in potato.
    Replacement of meat and dairy by plant-derived foods: estimated effects on land use, iron and SFA intakes in young Dutch adult females
    Temme, E.H.M. ; Voet, H. van der; Thissen, J.T.N.M. ; Verkaik-Kloosterman, J. ; Donkersgoed, G. van; Nonhebel, S. - \ 2013
    Public Health Nutrition 16 (2013)10. - ISSN 1368-9800 - p. 1900 - 1907.
    consumption patterns - life-style - climate-change - consumers - health - diet - requirements - perspectives - vegetarians - energy
    Objective: Reduction in the current high levels of meat and dairy consumption may contribute to environmental as well as human health. Since meat is a major source of Fe, effects on Fe intake need to be evaluated, especially in groups vulnerable to negative Fe status. In the present study we evaluated the effects of replacing meat and dairy foods with plant-based products on environmental sustainability (land requirement) and health (SFA and Fe intakes) in women. Design: Data on land requirements were derived from existing calculation methods. Food composition data were derived from the Dutch Food Composition Table 2006. Data were linked to the food consumption of young Dutch women. Land requirements and nutrient intakes were evaluated at baseline and in two scenarios in which 30% (Scenario_30 %) or 100% (Scenario_100 %) of the dairy and meat consumption was randomly replaced by the same amount of plant-based dairy- and meat-replacing foods. Setting: The Netherlands. Subjects: Three hundred and ninety-eight young Dutch females. Results: Replacement of meat and dairy by plant-based foods benefited the environment by decreasing land use. The intake of SFA decreased considerably compared with the baseline situation. On average, total Fe intake increased by 2?5 mg/d, although most of the Fe intake was from a less bioavailable source. Conclusions: Replacement of meat and dairy foods by plant-based foods reduced land use for consumption and SFA intake of young Dutch females and did no compromise total Fe intake.
    Naturally occurring allele diversity allows potato cultivation in northern latitudes
    Kloosterman, B.A. ; Abelenda, J.A. ; Carretero Gomez, M. ; Oortwijn, M.E.P. ; Boer, J.M. de; Kowitwanich, K. ; Horvath, B.M. ; Eck, H.J. van; Smaczniak, C. ; Prat, S. ; Visser, R.G.F. ; Bachem, C.W.B. - \ 2013
    Nature 495 (2013)7440. - ISSN 0028-0836 - p. 246 - 250.
    flowering-time - arabidopsis - constans - tuberization - gene - plants - fkf1
    Potato (Solanum tuberosum L.) originates from the Andes and evolved short-day-dependent tuber formation as a vegetative propagation strategy. Here we describe the identification of a central regulator underlying a major-effect quantitative trait locus for plant maturity and initiation of tuber development. We show that this gene belongs to the family of DOF (DNA-binding with one finger) transcription factors1 and regulates tuberization and plant life cycle length, by acting as a mediator between the circadian clock and the StSP6A mobile tuberization signal2. We also show that natural allelic variants evade post-translational light regulation, allowing cultivation outside the geographical centre of origin of potato. Potato is a member of the Solanaceae family and isone of the world’s most important food crops. This annual plant originates from the Andean regions of South America3. Potato develops tubers from underground stems called stolons. Its equatorial origin makes potato essentially short-day dependent for tuberization and potato will not make tubers in the long-day conditions of spring and summer in the northern latitudes. When introduced in temperate zones, wild material will form tubers in the course of the autumnal shortening of day-length. Thus, one of the first selected traits in potato leading to a European potato type4 is likely to have been long-day acclimation for tuberization. Potato breeders can exploit the naturally occurring variation in tuberization onset and life cycle length, allowing varietal breeding for different latitudes, harvest times and markets.
    An appeal for the presentation of detailed human derived data for dose-response calculations in nutritional science
    Jong, N. de; Verkaik-Kloosterman, J. ; Verhagen, H. ; Boshuizen, H.C. ; Bokkers, B. ; Hoekstra, J. - \ 2013
    Food and Chemical Toxicology 54 (2013). - ISSN 0278-6915 - p. 43 - 49.
    continuous end-points - fish consumption - trend estimation - risk - stroke - metaanalysis - statement - quality - health - example
    If a diet, food or food constituent is recognised to have both health benefits and health risks, the benefits have to be compared with the risks to develop coherent scientific evidence-based dietary advice. This means that both risk and benefit assessment should follow a similar paradigm and that benefits and risks are expressed in a common currency. Dose–response functions are vital for that purpose. However, the construction of these functions is often of second interest in the currently available (epidemiological) literature. In order to bring forward the potential of epidemiological studies for the construction of the dose–response functions for benefit–risk purposes, the scientific (nutrition and health) community is asked to expand on their data presentation, either by presenting more detailed data focusing on dose–response necessities, and/or by sharing primary data
    Analytical standards for the measurement of nutrients in infant formula : macronutrients, minerals, carnitine, taurine and nucleotides
    Capuano, E. ; Alewijn, M. ; Ruth, S.M. van; Verkaik-Kloosterman, J. - \ 2012
    Wageningen : RIKILT Wageningen UR (Report / RIKILT Wageningen UR 2012.019) - 54
    flesvoedingsamenstelling - analytische methoden - globale analyse - macronutriënten - mineralen - taurine - carnitine - nucleotiden - voedingsstoffenbehoeften - recht - infant formulae - analytical methods - proximate analysis - macronutrients - minerals - taurine - carnitine - nucleotides - nutrient requirements - law
    Adequate methods with known performance characteristics for the assessment of the concentration of nutrients in infant and follow-on formula (referred to as "formula") are essential in the evaluation whether the composition deviates from the compositional provisions as laid down by law. Many standardized analytical methods for the analysis of nutrients in infant formula are internationally available.
    Modelling (flash) floods in a Dutch lowland catchment
    Brauer, C.C. ; Teuling, A.J. ; Overeem, A. ; Velde, Y. van der; Hazenberg, P. ; Kloosterman, P. ; Uijlenhoet, R. - \ 2012
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