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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    Green Challenges: plant en bodemweerbaarheidtegen ondergrondse ziekten
    Streminska, Marta ; Breeuwsma, Suzanne ; Huisman, Huei Ming ; Vos, Ric de; Eekelen, Henriette van; Stevens, Luc ; Salm, Caroline van der - \ 2020
    Bleiswijk : Stichting Wageningen Research, Wageningen Plant Research, Business unit Glastuinbouw (Rapport WPR 943) - 61
    Crops in soil-based and soilless greenhouse cultivation systems are susceptible to various soilborne diseases, such as foot and root rot and wilting, caused by pathogens as Fusarium and Pythium. The Grºeen Challenges project aims to reduce the use of chemical plant protection products and to develop new measures and strategies for disease and pest control through a system approach. This project investigated which measures can be taken to promote soil disease suppression and induced plant resistance against soilborne pathogens (Fusarium and Pythium) in different horticultural crops: vegetable crops (tomato and cucumber) and ornamental crop (lisianthus).
    Adherence to dietary guidelines in relation to visceral fat and liver fat in middle-aged men and women: the NEO study
    Eekelen, Esther van; Geelen, Anouk ; Alssema, Marjan ; Lamb, Hildo J. ; Roos, Albert de; Rosendaal, Frits R. ; Mutsert, Renée de - \ 2020
    International Journal of Obesity (2020)44. - ISSN 0307-0565 - p. 297 - 306.

    Background: It is unclear to what extent adherence to dietary guidelines may specifically affect visceral fat and liver fat. We aimed to study the association between the Dutch Healthy Diet Index (DHD-index) and total body fat, visceral adipose tissue (VAT) and hepatic triglyceride content (HTGC) in middle-aged men and women. Design: In this cross-sectional study, VAT was assessed by magnetic resonance imaging (MRI) in 2580 participants, and HTGC by proton-MR spectroscopy in 2083 participants. Habitual dietary intake and physical activity were estimated by questionnaire. Adherence to the current Dutch dietary guidelines was estimated by the 2015 DHD-index score based on the thirteen components (vegetables, fruit, wholegrain products, legumes, nuts, dairy, fish, tea, liquid fats, red meat, processed meat, sweetened beverages, and alcohol). The DHD-index ranges between 0 and 130 with a higher score indicating a healthier diet. We used linear regression to examine associations of the DHD-index with VAT and HTGC, adjusted for age, smoking, education, ethnicity, basal metabolic rate, energy restricted diet, menopausal state, physical activity, total energy intake, and total body fat. We additionally excluded the components one by one to examine individual contributions to the associations. Results: Included participants (43% men) had a mean (SD) age of 56 (6) years and DHD-index score of 71 (15). A 10-point higher DHD-index score was associated with 2.3 cm2 less visceral fat (95% CI; −3.5; −1.0 cm2) and less liver fat (0.94 times, 95% CI; 0.90; 0.98). Of all components, exclusion of dairy attenuated the associations with TBF and VAT. Conclusions: Adherence to the dietary guidelines as estimated by the DHD-index was associated with less total body fat, and with less visceral and liver fat after adjustment for total body fat. These findings might contribute to better understanding of the mechanisms underlying associations between dietary habits and cardiometabolic diseases.

    Beneficial and nature-based sediment use - Experiences from Dutch pilots
    Sittoni, Luca ; Boer, Jannes ; Star, Wouter R.L. Van Der; Heuvel, Marcel J.M. Van Den; Baptist, Martin J. ; Eekelen, Erik M.M. Van; Goot, Fokko Van Der; Nieboer, Henk E. ; Doets, Irena - \ 2019
    - p. 325 - 330.
    Beneficial use - Building with nature - Dredging - Sediment

    The natural sediment cycle is disrupted and impacted by human interventions world-wide, such as dams in rivers, port developments in estuaries, dredging activities for the maintenance of existing ports and waterways, and pollution from industrial activities. Coasts, shores, lakes and rivers suffer from an imbalance in sediment quantity and poor sediment quality. This impacts human industrial activities (e.g. navigation, logistic and tourism), life and safety (e.g. space for living, flood safety, food security and loss of productivity). In addition, shortage of sand cause by excessive sand mining or lack of sand in the environment in many locations of the world brings a special focus on fine and soft sediment, generally considered an unsuitable resource if not a contaminated waste. In line with this world-wide demand, EcoShape - Building with Nature is executing various pilots in the Netherlands and Indonesia to improve knowledge and demonstrate practical nature-based solutions regarding management, use and reuse of (fine and soft) sediments. These pilots are bonded in the EcoShape Living Lab for Mud initiative. These pilots cover the entire range from sediment in suspension to sediment as building material, embedding ecology, operations as well as socio-economic considerations. This presentation will focus on two of these pilots located in the Netherlands: the Mud Motor and de Kleirijperij (also part of the Eems-Dollard 2050 program). The Mud Motor explored potential for beneficial use of dredge sediments to feed salt marshes, through strategic disposal and optimal use of natural processes. The Kleirijperij studies the technical and financial feasibility of turning dredge sediments into clay-soil for dike construction. During the presentations we will focus on technical results as well as governance challenges and triggers critical for the realization of sustainable beneficial sediment use projects. These pilots and this presentation tight also to the 2017 CEDA and the 2018 PIANC working groups on Beneficial Sediment Use.

    The mud Motor: a beneficial use of dredged sediment to enhance salt marsh development
    Eekelen, E. van; Baptist, M.J. - \ 2019
    Terra et aqua 155 (2019). - ISSN 0376-6411 - p. 28 - 42.
    Consumption of Alcoholic and Sugar-Sweetened Beverages is Associated with Increased Liver Fat Content in Middle-Aged Men and Women
    Eekelen, Esther van; Beulens, Joline W.J. ; Geelen, Anouk ; Schrauwen-Hinderling, Vera B. ; Lamb, Hildo ; Roos, Albert de; Rosendaal, Frits ; Mutsert, Renée de - \ 2019
    The Journal of Nutrition 149 (2019)4. - ISSN 0022-3166 - p. 649 - 658.
    alcohol consumption - alcoholic beverages - liver fat - nonalcoholic beverages - substitution

    BACKGROUND: Fatty liver is the leading cause of chronic liver diseases and increases the risk of cardiovascular disease. Besides alcohol consumption, energy-containing nonalcoholic beverages may contribute to liver fat accumulation. OBJECTIVE: We aimed to study the consumption of alcoholic and nonalcoholic beverages and their mutual replacement in relation to hepatic triglyceride content (HTGC) in middle-aged men and women. METHODS: In this cross-sectional analysis, HTGC was assessed by proton magnetic resonance spectroscopy. Habitual consumption of alcoholic and nonalcoholic beverages was assessed using a validated food-frequency questionnaire. All beverages were converted to standard servings and to percentage of total energy intake (En%). We performed linear regression to examine the association of alcoholic and nonalcoholic beverages with HTGC, adjusted for age, sex, smoking, education, ethnicity, physical activity, total energy intake, and total body fat. We studied replacement of alcoholic beverages with nonalcoholic beverages per 1 serving/d and per 5 En%/d. RESULTS: After exclusion of individuals with missing values, 1966 participants (47% men) were analyzed, with a mean ± SD age of 55 ± 6 y, BMI of 26 ± 4 kg/m2, and HTGC of 5.7% ± 7.9%. Each extra alcoholic serving per day was associated with more liver fat (1.09 times; 95% CI: 1.05, 1.12). Replacing 5 En% of alcoholic beverages with milk was associated with less liver fat (0.89 times; 95% CI: 0.81, 0.98), whereas replacement with 5 En% of sugar-sweetened beverages was associated with liver fat to an extent similar to alcoholic beverages (1.00 times; 95% CI: 0.91, 1.09). CONCLUSION: In a population-based cohort, consumption of each extra daily alcoholic beverage was associated with more liver fat. In isocaloric replacement of alcoholic beverages, milk was associated with less liver fat, whereas sugar-sweetened beverages were equally associated with liver fat. This suggests that intake of alcohol and sugars may contribute to liver fat accumulation. This trial was registered at clinicaltrials.gov as NCT03410316.

    Pyrethric acid of natural pyrethrin insecticide: complete pathway elucidation and reconstitution in Nicotiana benthamiana
    Xu, H. ; Li, Wei ; Schilmiller, Anthony L. ; Eekelen, H.D.L.M. van; Vos, C.H. de; Jongsma, M.A. ; Pichersky, E. - \ 2019
    New Phytologist 223 (2019)2. - ISSN 0028-646X - p. 751 - 765.
    In the natural pesticides known as pyrethrins, which are esters produced in flowers of Tanacetum cinerariifolium (Asteraceae), the monoterpenoid acyl moiety is pyrethric acid or chrysanthemic acid.
    We show here that pyrethric acid is produced from chrysanthemol in six steps catalyzed by four enzymes, the first five steps occurring in the trichomes covering the ovaries and the last one occurring inside the ovary tissues.
    Three steps involve the successive oxidation of carbon 10 (C10) to a carboxylic group by TcCHH, a cytochrome P450 oxidoreductase. Two other steps involve the successive oxidation of the hydroxylated carbon 1 to give a carboxylic group by TcADH2 and TcALDH1, the same enzymes that catalyze these reactions in the formation of chrysanthemic acid. The ultimate result of the actions of these three enzymes is the formation of 10‐carboxychrysanthemic acid in the trichomes. Finally, the carboxyl group at C10 is methylated by TcCCMT, a member of the SABATH methyltransferase family, to give pyrethric acid. This reaction occurs mostly in the ovaries.
    Expression in N. benthamiana plants of all four genes encoding aforementioned enzymes, together with TcCDS, a gene that encodes an enzyme that catalyzes the formation of chrysanthemol, led to the production of pyrethric acid.
    Sweet Snacks Are Positively and Fruits and Vegetables Are Negatively Associated with Visceral or Liver Fat Content in Middle-Aged Men and Women
    Eekelen, Esther Van; Geelen, Anouk ; Alssema, Marjan ; Lamb, Hildo J. ; Roos, Albert De; Rosendaal, Frits R. ; Mutsert, Rencrossed De - \ 2019
    The Journal of Nutrition 149 (2019)2. - ISSN 0022-3166 - p. 304 - 313.
    food groups - liver fat - middle-aged men and women - obesity - visceral fat

    Visceral adipose tissue (VAT) and hepatic triglyceride content (HTGC) are major risk factors for cardiometabolic diseases. Objective: We aimed to investigate the association of dietary intake of the main food groups with VAT and HTGC in middle-aged men and women. Methods: We used data from the Netherlands Epidemiology of Obesity study, a population-based study including 6671 participants aged 45-65 y at baseline. In this cross-sectional analysis, VAT and HTGC were assessed by magnetic resonance imaging and spectroscopy, respectively, as the primary outcomes. Habitual intake of main food groups (dairy, meat, fish, fruits and vegetables, sweet snacks, and fats and oils) was estimated through the use of a food-frequency questionnaire. We examined associations of intake of different food groups with VAT and HTGC by linear regression analysis stratified by sex and adjusted for age, smoking, education, ethnicity, physical activity, basal metabolic rate, energy-restricted diet, menopausal state, and total energy intake. Results: In women, a 100-g/d higher intake of dairy was associated with 2.0 cm2 less VAT (95% CI: -3.4, -0.7 cm2) and a 0.95-fold lower HTGC (95% CI: 0.90-, 0.99-fold). Moreover, a 100-g/d higher intake of fruit and vegetables was associated with 1.6 cm2 less VAT (95% CI: -2.9, -0.2 cm2) in women. Fruit and vegetables were negatively associated (0.95; 95% CI: 0.91, 1.00) with HTGC, and sweet snacks were positively associated (1.29; 95% CI: 1.03, 1.63). Patterns were weaker but similar in men. Fish intake was not associated with VAT or HTGC and plant-based fat and oil intake were only associated with VAT after adjustment for total body fat. Conclusions: Despite some variation in the strength of the associations between men and women, dietary intake of sweet snacks was positively associated with HTGC, and fruit and vegetable intake were negatively associated with visceral and liver fat content. Prospective studies are needed to confirm these results. The Netherlands Epidemiology of Obesity study is registered at clinicaltrials.gov with identifier NCT03410316. J Nutr 2019;149:304-313.

    Epigenetic mapping of the Arabidopsis metabolome reveals mediators of the epigenotype-phenotype map
    Kooke, R. ; Morgado, L.N. ; Becker, F.F.M. ; Eekelen, H.D.L.M. van; Hazarika, Rashmi ; Zhang, Qunfeng ; Vos, C.H. de; Johannes, Frank ; Keurentjes, J.J.B. - \ 2019
    Genome Research 29 (2019)1. - ISSN 1088-9051 - p. 96 - 106.
    Identifying the sources of natural variation underlying metabolic differences between plants will enable a better understanding of plant metabolism and provide insights into the regulatory networks that govern plant growth and morphology. So far, however, the contribution of epigenetic variation to metabolic diversity has been largely ignored. In the present study, we utilized a panel of Arabidopsis thaliana epigenetic recombinant inbred lines (epiRILs) to assess the impact of epigenetic variation on the metabolic composition. Thirty epigenetic QTL (QTLepi) were detected, which partly overlap with QTLepi linked to growth and morphology. In an effort to identify causal candidate genes in the QTLepi regions or their putative trans-targets we performed in silico small RNA and qPCR analyses. Differentially expressed genes were further studied by phenotypic and metabolic analyses of knockout mutants. Three genes were detected that recapitulated the detected QTLepi effects, providing evidence for epigenetic regulation in cis and in trans. These results indicate that epigenetic mechanisms impact metabolic diversity, possibly via small RNAs, and thus aid in further disentangling the complex epigenotype-phenotype map.
    Beneficial use of dredged sediment to enhance salt marsh development by applying a ‘Mud Motor’
    Baptist, Martin J. ; Gerkema, T. ; Prooijen, B.C. van; Maren, D.S. van; Regteren, M. van; Schulz, K. ; Colosimo, I. ; Vroom, J. ; Kessel, T. van; Grasmeijer, B. ; Willemsen, P. ; Elschot, K. ; Groot, A.V. de; Cleveringa, J. ; Eekelen, E.M.M. van; Schuurman, F. ; Lange, H.J. de; Puijenbroek, M.E.B. van - \ 2019
    Ecological Engineering 127 (2019). - ISSN 0925-8574 - p. 312 - 323.
    Building with Nature - Nature-based solutions - Cohesive sediment - Dredging - Salt marshes - intertidal flats
    We test an innovative approach to beneficially re-use dredged sediment to enhance salt marsh development. A Mud Motor is a dredged sediment disposal in the form of a semi-continuous source of mud in a shallow tidal channel allowing natural processes to disperse the sediment to nearby mudflats and salt marshes. We describe the various steps in the design of a Mud Motor pilot: numerical simulations with a sediment transport model to explore suitable disposal locations, a tracer experiment to measure the transport fate of disposed mud, assessment of the legal requirements, and detailing the planning and technical feasibility. An extensive monitoring and research programme was designed to measure sediment transport rates and the response of intertidal mudflats and salt marshes to an increased sediment load. Measurements include the sediment transport in the tidal channel and on the shallow mudflats, the vertical accretion of intertidal mudflats and salt marsh, and the salt marsh vegetation cover and composition. In the Mud Motor pilot a total of 470,516 m 3
    of fine grained sediment (D50 of ∼10 μm) was disposed over two winter seasons, with an average of 22 sediment disposals per week of operation. Ship-based measurements revealed a periodic vertical salinity stratification that is inverted compared to a classical estuary and that is working against the asymmetric flood-dominated transport direction. Field measurements on the intertidal mudflats showed that the functioning of the Mud Motor, i.e. the successful increased mud transport toward the salt marsh, is significantly dependent on wind and wave forcing. Accretion measurements showed relatively large changes in surface elevation due to deposition and erosion of layers of
    watery mud with a thickness of up to 10 cm on a time scale of days. The measurements indicate notably higher sediment dynamics during periods of Mud Motor disposal. The salt marsh demonstrated significant vertical accretion though this has not yet led to horizontal expansion because there was more hydrodynamic stress than foreseen. In carrying out the pilot we learned that the feasibility of a Mud Motor depends on an assessment of additional travel time for the dredger, the effectiveness on salt marsh growth, reduced dredging volumes in a port, and many other practical issues. Our improved understanding on the transport processes in the channel and on the mudflats and salt marsh yields design lessons and guiding principles for future applications of sediment
    management in salt marsh development that include a Mud Motor approach
    QTL mapping of insect resistance components of Solanum galapagense
    Vosman, Ben ; Kashaninia, Atiyeh ; van’t Westende, Wendy ; Meijer-Dekens, Fien ; Eekelen, Henriëtte van; Visser, Richard G.F. ; Vos, Ric C.H. de; Voorrips, Roeland E. - \ 2019
    Theoretical and Applied Genetics 132 (2019)2. - ISSN 0040-5752 - p. 531 - 541.

    Key message: QTLs for insect resistance parameters, trichome type IV development, and more than 200 non-volatile metabolites, including 76 acyl sugars, all co-locate at the end of Chromosome 2 of Solanum galapagense. Abstract: Host plant resistance is gaining importance as more and more insecticides are being banned due to environmental concerns. In tomato, resistance towards insects is found in wild relatives and has been attributed to the presence of glandular trichomes and their specific phytochemical composition. In this paper, we describe the results from a large-scale QTL mapping of data from whitefly resistance tests, trichome phenotyping and a comprehensive metabolomics analysis in a recombinant inbred line population derived from a cross between the cultivated Solanum lycopersicum and the wild relative S. galapagense, which is resistant to a range of pest insects. One major QTL (Wf-1) was found to govern the resistance against two different whitefly species. This QTL co-localizes with QTLs for the presence of trichomes type IV and V, as well as all 76 acyl sugars detected and about 150 other non-volatile phytochemicals, including methyl esters of the flavonols myricetin and quercetin. Based on these results, we hypothesize that Wf-1 is regulating the formation of glandular trichome type IV on the leaf epidermis, enabling the production and accumulation of bioactive metabolites in this type of trichomes.

    Data from: Epigenetic mapping of the Arabidopsis metabolome reveals mediators of the epigenotype-phenotype map
    Kooke, R. ; Morgado, L.N. ; Becker, F.F.M. ; Eekelen, H.D.L.M. van; Hazarika, Rashmi ; Zhang, Qunfeng ; Johannes, Frank ; Keurentjes, J.J.B. - \ 2018
    Biometris
    Identifying the sources of natural variation underlying metabolic differences between plants will enable a better understanding of plant metabolism and provide insights into the regulatory networks that govern plant growth and morphology. So far, however, the contribution of epigenetic variation to metabolic diversity has been largely ignored. In the present study, we utilized a panel of Arabidopsis thaliana epigenetic recombinant inbred lines (epiRILs) to assess the impact of epigenetic variation on the metabolic composition. Thirty epigenetic QTL (QTLepi) were detected, which partly overlap with QTLepi linked to growth and morphology. In an effort to identify causal candidate genes in the QTLepi regions or their putative trans-targets we performed in silico small RNA and qPCR analyses. Differentially expressed genes were further studied by phenotypic and metabolic analyses of knockout mutants. Three genes were detected that recapitulated the detected QTLepi effects, providing evidence for epigenetic regulation in cis and in trans. These results indicate that epigenetic mechanisms impact metabolic diversity, possibly via small RNAs, and thus aid in further disentangling the complex epigenotype-phenotype map.
    Metabolite variation in the lettuce gene pool : towards healthier crop varieties and food
    Treuren, Rob van; Eekelen, Henriette D.L.M. van; Wehrens, Ron ; Vos, Ric C.H. de - \ 2018
    Metabolomics 14 (2018)11. - ISSN 1573-3882
    Crop improvement - Genetic resources - Lettuce - Phytochemical variation - Untargeted metabolomics - Vitamin C

    Introduction: Lettuce (Lactuca sativa L.) is generally not specifically acknowledged for its taste and nutritional value, while its cultivation suffers from limited resistance against several pests and diseases. Such key traits are known to be largely dependent on the ability of varieties to produce specific phytochemicals. Objectives: We aimed to identify promising genetic resources for the improvement of phytochemical composition of lettuce varieties. Methods: Phytochemical variation was investigated using 150 Lactuca genebank accessions, comprising a core set of the lettuce gene pool, and resulting data were related to available phenotypic information. Results: A hierarchical cluster analysis of the variation in relative abundance of 2026 phytochemicals, revealed by untargeted metabolic profiling, strongly resembled the known lettuce gene pool structure, indicating that the observed variation was to a large extent genetically determined. Many phytochemicals appeared species-specific, of which several are generally related to traits that are associated with plant health or nutritional value. For a large number of phytochemicals the relative abundance was either positively or negatively correlated with available phenotypic data on resistances against pests and diseases, indicating their potential role in plant resistance. Particularly the more primitive lettuces and the closely related wild relatives showed high levels of (poly)phenols and vitamin C, thus representing potential genetic resources for improving nutritional traits in modern crop types. Conclusion: Our large-scale analysis of phytochemical variation is unprecedented in lettuce and demonstrated the ample availability of suitable genetic resources for the development of improved lettuce varieties with higher nutritional quality and more sustainable production.

    Galapagos tomaat bron van resistentie tegen insecten
    Vosman, B. ; Vos, C.H. de; Eekelen, H.D.L.M. van - \ 2018

    Een wilde tomaat van de Galapagos eilanden blijkt een brede resistentie tegen verschillende soorten insecten te kennen. Het is een nauwe verwant van de cultuurtomaat. Daarom zal inkruisen van deze resistentie gemakkelijker verlopen dan het geval was bij al eerder bekende wilde resistenties, verwachten Wageningse onderzoekers.

    Broad spectrum insect resistance and metabolites in close relatives of the cultivated tomato
    Vosman, Ben ; van’t Westende, Wendy P.C. ; Henken, Betty ; Eekelen, Henriëtte D.L.M. van; Vos, Ric C.H. de; Voorrips, Roeland E. - \ 2018
    Euphytica 214 (2018)3. - ISSN 0014-2336
    Acyl sugars - Aphid - Caterpillar - Flavonoids - Lycopersicon group - Metabolomics - Thrips - Whitefly
    Wild relatives of tomato possess effective means to deal with several pests, among which are a variety of insects. Here we studied the presence of resistance components against Trialeurodes vaporariorum, Myzus persicae, Frankliniella occidentalis, and Spodoptera exigua in the Lycopersicon group of Solanum section Lycopersicon by means of bioassays and comprehensive metabolite profiling. Broad spectrum resistance was found in Solanum galapagense and a few accessions of S. pimpinellifolium. Resistance to the sap sucking insects may be based on the same mechanism, but different from the caterpillar resistance. Large and highly significant differences in the leaf metabolomes were found between S. galapagense, containing type IV trichomes, and its closest relative S. cheesmaniae, which lacks type IV trichomes. The most evident differences were the relatively high levels of different methylated forms of the flavonoid myricetin and many acyl sucrose structures in S. galapagense. Possible candidate genes regulating the production of these compounds were identified in the Wf-1 QTL region of S. galapagense, which was previously shown to confer resistance to the whitefly B. tabaci. The broad spectrum insect resistance identified in S. galapagense will be very useful to increase resistance in cultivated tomato.
    The living lab for mud: integrated sediment management based on Building with Nature concepts
    Eekelen, E.M.M. van; Sittoni, L. ; Groot, F. van der; Nieboer, H.E. ; Baptist, M.J. ; Boer, J. ; Tonneijck, F.H. - \ 2017
    - 8
    World-wide the turbidity of many rivers, estuaries and shallow seas is increasing, leading to degradation of water quality and growing siltation. Large volumes of dredged sediments are disposed and lost offshore, while coastal regions and river banks are eroding, exposing towns to more recurrent flooding. A huge amount of sediment is trapped in reservoirs behind dams, reducing their storage and flood mitigation capabilities. These are all indicators that smart and integrated sediment management is necessary. At the same time, coastal development activities demand for large quantities of sediment as building material, with many areas of the world characterized by fine sediments (mud), especially in large river delta regions. Integrated sediment management approaches leveraging on Building with Nature (BwN) concepts represents a potentially powerful solution to these enormous world-wide challenges and societal needs. With this in mind, EcoShape initiated the Living Lab for Mud (LLM), an initiative that aims to develop integrated knowledge and technologies to improve understanding and implementation of management, use and reuse of (fine and soft) sediments often linked to the reinforcement, safety and restoration of coastal ecosystems (e.g. salt marshes and mangroves) or land reclamation.The LLM consists of a series of pilot projects within and outside the Netherlands, which integrate the various aspects and processes of sediment management: from sedimentation and resuspension, to fate and transport, to consolidation and strength development. The LLM integrates these physical processes with biota and socio-economic aspects, in order to develop feasible, applicable and sustainable BwN based solutions. Pilots include strategic sediment disposal to naturally nourish coastal mudflats (i.e. Mud Motor, The Netherlands), enhancing sediment trapping to encourage mangroves restoration and coastal aggradation (i.e. Demak, Indonesia), and ripening of fine dredged sediments for production of building material (i.e. Kleirijperij, The Netherlands).This presentation will introduce the LLM initiative and give an overview of these pilot projects.
    Working with Nature in Wadden Sea Ports
    Baptist, M.J. ; Eekelen, E. van; Dankers, P.J.T. ; Grasmeijer, B. ; Kessel, T. van; Maren, D.S. van - \ 2017
    - 7
    Ecosystem services - working with Nature - cohesive sediment - harbour development - Wetland restoration
    Wadden Sea ports are situated at the border of the UNESCO World Heritage site Wadden Sea. Because of the protected status of this area, developing new economic activities is not straightforward. However, maintaining and developing port activities is needed to safeguard the economic viability of the Wadden Sea
    socio-economic region. In this paper we illustrate that sustainable port development is feasible when adopting a Working with Nature approach. This approach facilitates a design in which the proactive utilization and/or provision of ecosystem services serves as part of the engineering solution. We introduce four Working with Nature concepts that can be used in port designs, i.e. 1) optimising dredging strategies, 2) enhancing saltmarsh development, 3) creating estuarine gradients, and 4) optimising flow patterns. Based on these
    concepts, three case studies have been identified and pilot projects initiated. In the Port of Harlingen a pilot project has started in which an optimized dredging strategy is combined with saltmarsh development. Around the Port of Delfzijl an estuarine gradient is combined with the construction of a salt marsh and dredged
    sediment is used for dike strengthening. For the Port of Den Helder, a new design is proposed in which the concepts of enhancing salt marsh development, creating estuarine gradients and optimizing flow patterns are combined. Our conclusion is that even in a World Heritage site such as the Wadden Sea, port
    development is possible when ecosystem services are used and provided for, and when a Working with Nature concept is put at the heart of the design.
    Muddy waters and the Wadden Sea harbours
    Eekelen, E. van; Baptist, M.J. ; Dankers, P. ; Grasmeijer, B.T. ; Kessel, T. van; Maren, D.S. van - \ 2016
    - 11 p.
    ecosystem services - Building with nature - cohesive sediment - harbour development - Wetland restoration
    Several harbours along the Dutch Wadden Sea deal with large siltation rates and limited possibilities for developments. However, development of new harbour activities is needed for these harbours to be able to survive in the long run. As these harbours lie in or close to areas with a protected status, expansion is not straightforward. In this paper we illustrate that harbour development is possible when a Building with Nature approach is used. This approach facilitates a design in which the proactive utilization and/or provision of ecosystem services serves as part of the engineering solution. We introduce four Building with Nature concepts that can be used in harbour designs, i.e. 1) optimising dredging strategies, 2) enhancing saltmarsh development, 3) creating estuarine gradients, and 4) optimising flow patterns. Based on these concepts, three case studies have been identified and pilot projects initiated. In the Port of Harlingen a pilot has started in which an optimized dredging strategy is combined with saltmarsh development. Around the Port of Delfzijl an estuarine gradient is combined with a salt marsh. For the Port of Den Helder a new design was proposed in which the concepts of enhancing salt marsh development, creating estuarine gradients and optimizing flow patterns are combined. Our conclusion is that even in a UNESCO listed site such as the Wadden Sea, harbour development is possible when ecosystem services are used and provided for, and when a Building with Nature concept is put at the heart of an engineering design.
    Muddy Waters and the Wadden Sea Harbours
    Baptist, M.J. ; Eekelen, E. van; Dankers, P.J.T. ; Grasmeijer, B. ; Kessel, T. van; Maren, D.S. van - \ 2016
    Improved batch correction in untargeted MS-based metabolomics
    Wehrens, Ron ; Hageman, Jos A. ; Eeuwijk, Fred van; Kooke, Rik ; Flood, Pádraic J. ; Wijnker, Erik ; Keurentjes, Joost J.B. ; Lommen, Arjen ; Eekelen, Henriëtte D.L.M. van; Hall, Robert D. ; Mumm, Roland ; Vos, Ric C.H. de - \ 2016
    Metabolomics 12 (2016)5. - ISSN 1573-3882
    Arabidopsis thaliana - Batch correction - Mass spectrometry - Non-detects - Untargeted metabolomics

    Introduction: Batch effects in large untargeted metabolomics experiments are almost unavoidable, especially when sensitive detection techniques like mass spectrometry (MS) are employed. In order to obtain peak intensities that are comparable across all batches, corrections need to be performed. Since non-detects, i.e., signals with an intensity too low to be detected with certainty, are common in metabolomics studies, the batch correction methods need to take these into account. Objectives: This paper aims to compare several batch correction methods, and investigates the effect of different strategies for handling non-detects. Methods: Batch correction methods usually consist of regression models, possibly also accounting for trends within batches. To fit these models quality control samples (QCs), injected at regular intervals, can be used. Also study samples can be used, provided that the injection order is properly randomized. Normalization methods, not using information on batch labels or injection order, can correct for batch effects as well. Introducing two easy-to-use quality criteria, we assess the merits of these batch correction strategies using three large LC–MS and GC–MS data sets of samples from Arabidopsis thaliana. Results: The three data sets have very different characteristics, leading to clearly distinct behaviour of the batch correction strategies studied. Explicit inclusion of information on batch and injection order in general leads to very good corrections; when enough QCs are available, also general normalization approaches perform well. Several approaches are shown to be able to handle non-detects—replacing them with very small numbers such as zero seems the worst of the approaches considered. Conclusion: The use of quality control samples for batch correction leads to good results when enough QCs are available. If an experiment is properly set up, batch correction using the study samples usually leads to a similar high-quality correction, but has the advantage that more metabolites are corrected. The strategy for handling non-detects is important: choosing small values like zero can lead to suboptimal batch corrections.

    Combining an in vitro reporter gene assay with metabolomics to identify tomato phytochemicals responsible for inducing electrophile-responsive element (EpRE)-mediated gene transcription
    Eekelen, H.D.L.M. van; Gijsbers, L. ; Maliepaard, C.A. ; Vreeburg, R.A.M. ; Finkers, H.J. ; Tikunov, Y.M. ; Gomez Roldan, M.V. ; Haan, L.H.J. de; Vos, R.C.H. de; Aarts, J.M.M.J.G. ; Rietjens, I. ; Bovy, A.G. - \ 2015
    Metabolomics 11 (2015)2. - ISSN 1573-3882 - p. 302 - 311.
    solanum-lycopersicon - mass-spectrometry - fruit - expression - health - metabolism - flavonoids - lycopene - deglycosylation - polyphenols
    The electrophile-responsive element (EpRE) is a transcriptional enhancer involved in cancer-chemoprotective gene expression effects of certain dietary compounds. In this study we measured the ability of extracts of glycosidase treated tomato fruits from 97 different accessions to induce EpRE-mediated luciferase expression using EpRE-LUX reporter cells and analyzed the same extracts using LC–MSbased untargeted metabolomics profiling. We were able to pinpoint those tomato compounds that were most correlated with EpRE-mediated luciferase induction, by combining reporter gene assay data with the metabolic profiles of the same extracts. Flavonoids were the compounds showing the strongest positive correlation with EpRE-LUX activity. These results were validated using a transgenic tomato line accumulating high levels of flavonoids. Results obtained corroborated that flavonoids are an important determinant of the ability of tomato fruit extracts to induce EpRE-mediated beneficial health effects. Overall, these results indicate that combining untargeted metabolomics with reporter gene assays provides a powerful tool for nutritionists, plant breeders and food chemists towards identification of potential health-beneficial constituents of tomato fruits, as well as of other crops and products derived thereof.
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