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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    The handbook for standardized field and laboratory measurements in terrestrial climate change experiments and observational studies (ClimEx)
    Halbritter, Aud H. ; Boeck, Hans J. De; Eycott, Amy E. ; Reinsch, Sabine ; Robinson, David A. ; Vicca, Sara ; Berauer, Bernd ; Christiansen, Casper T. ; Estiarte, Marc ; Grünzweig, José M. ; Gya, Ragnhild ; Hansen, Karin ; Jentsch, Anke ; Lee, Hanna ; Linder, Sune ; Marshall, John ; Peñuelas, Josep ; Kappel Schmidt, Inger ; Stuart-Haëntjens, Ellen ; Wilfahrt, Peter ; Vandvik, Vigdis ; Abrantes, Nelson ; Almagro, María ; Althuizen, Inge H.J. ; Barrio, Isabel C. ; Beest, Mariska Te; Beier, Claus ; Beil, Ilka ; Carter Berry, Z. ; Birkemoe, Tone ; Bjerke, Jarle W. ; Blonder, Benjamin ; Blume-Werry, Gesche ; Bohrer, Gil ; Campos, Isabel ; Cernusak, Lucas A. ; Chojnicki, Bogdan H. ; Cosby, Bernhard J. ; Dickman, Lee T. ; Djukic, Ika ; Filella, Iolanda ; Fuchslueger, Lucia ; Gargallo-Garriga, Albert ; Gillespie, Mark A.K. ; Goldsmith, Gregory R. ; Gough, Christopher ; Halliday, Fletcher W. ; Hegland, Stein Joar ; Ploeg, Martine van der; Verbruggen, Erik - \ 2020
    Methods in Ecology and Evolution 11 (2020)1. - ISSN 2041-210X - p. 22 - 37.
    best practice - coordinated experiments - data management and documentation - ecosystem - experimental macroecology - methodology - open science - vegetation

    Climate change is a world-wide threat to biodiversity and ecosystem structure, functioning and services. To understand the underlying drivers and mechanisms, and to predict the consequences for nature and people, we urgently need better understanding of the direction and magnitude of climate change impacts across the soil–plant–atmosphere continuum. An increasing number of climate change studies are creating new opportunities for meaningful and high-quality generalizations and improved process understanding. However, significant challenges exist related to data availability and/or compatibility across studies, compromising opportunities for data re-use, synthesis and upscaling. Many of these challenges relate to a lack of an established ‘best practice’ for measuring key impacts and responses. This restrains our current understanding of complex processes and mechanisms in terrestrial ecosystems related to climate change. To overcome these challenges, we collected best-practice methods emerging from major ecological research networks and experiments, as synthesized by 115 experts from across a wide range of scientific disciplines. Our handbook contains guidance on the selection of response variables for different purposes, protocols for standardized measurements of 66 such response variables and advice on data management. Specifically, we recommend a minimum subset of variables that should be collected in all climate change studies to allow data re-use and synthesis, and give guidance on additional variables critical for different types of synthesis and upscaling. The goal of this community effort is to facilitate awareness of the importance and broader application of standardized methods to promote data re-use, availability, compatibility and transparency. We envision improved research practices that will increase returns on investments in individual research projects, facilitate second-order research outputs and create opportunities for collaboration across scientific communities. Ultimately, this should significantly improve the quality and impact of the science, which is required to fulfil society's needs in a changing world.

    Patterns of local, intercontinental and interseasonal variation of soil bacterial and eukaryotic microbial communities
    Gruyter, Johan De; Weedon, James T. ; Bazot, Stéphane ; Dauwe, Steven ; Fernandez-Garberí, Pere Roc ; Geisen, Stefan ; La Motte, Louis Gourlez De; Heinesch, Bernard ; Janssens, Ivan A. ; Leblans, Niki ; Manise, Tanguy ; Ogaya, Romà ; Löfvenius, Mikaell Ottosson ; Peñuelas, Josep ; Sigurdsson, Bjarni D. ; Vincent, Gaëlle ; Verbruggen, Erik - \ 2019
    FEMS microbiology ecology 96 (2019)3. - ISSN 0168-6496
    microbial ecology - protists - soil biogeography - soil microbial communities - spatio-temporal variability

    Although ongoing research has revealed some of the main drivers behind global spatial patterns of microbial communities, spatio-temporal dynamics of these communities still remain largely unexplored. Here, we investigate spatio-temporal variability of both bacterial and eukaryotic soil microbial communities at local and intercontinental scales. We compare how temporal variation in community composition scales with spatial variation in community composition, and explore the extent to which bacteria, protists, fungi and metazoa have similar patterns of temporal community dynamics. All soil microbial groups displayed a strong correlation between spatial distance and community dissimilarity, which was related to the ratio of organism to sample size. Temporal changes were variable, ranging from equal to local between-sample variation, to as large as that between communities several thousand kilometers apart. Moreover, significant correlations were found between bacterial and protist communities, as well as between protist and fungal communities, indicating that these microbial groups change in tandem, potentially driven by interactions between them. We conclude that temporal variation can be considerable in soil microbial communities, and that future studies need to consider temporal variation in order to reliably capture all drivers of soil microbiome changes.

    Protein and the Adaptive Response With Endurance Training: Wishful Thinking or a Competitive Edge?
    Knuiman, P. ; Hopman, Maria ; Verbruggen, Conor ; Mensink, M.R. - \ 2018
    Frontiers in Physiology 9 (2018). - ISSN 1664-042X - 8 p.
    The significance of carbohydrates for endurance training has been well established, whereas the role of protein and the adaptive response with endurance training is unclear. Therefore, the aim of this perspective is to discuss the current evidence on the role of dietary protein and the adaptive response with endurance training. On a metabolic level, a single bout of endurance training stimulates the oxidation of several amino acids.
    Although the amount of amino acids as part of total energy expenditure during exercise is relatively low compared to other substrates (e.g., carbohydrates and fat), it may depress the rates of skeletal muscle protein synthesis, and thereby have a negative effect on training adaptation. A low supply of amino acids relative to that of carbohydrates may also have negative effects on the synthesis of capillaries, synthesis and turn-over of mitochondrial proteins and proteins involved in oxygen transport including hamoglobin and myoglobin. Thus far, the scientific evidence demonstrating the significance of dietary protein is mainly derived from research with resistance exercise training regimes. This is
    not surprising since the general paradigm states that endurance training has insignificant effects on skeletal muscle growth. This could have resulted in an underappreciation of the role of dietary protein for the endurance athlete. To conclude, evidence of the role of protein on endurance training adaptations and performance remains scarce and is mainly derived from acute exercise studies. Therefore, future human intervention studies must unravel whether dietary protein is truly capable of augmenting endurance training adaptations and ultimately performance.
    Responsibility in EU food law
    Meulen, B.M.J. van der - \ 2017
    In: Hybridization of Food Governance / Verbruggen, Paul, Havinga, Tetty, Cheltenham : Edward Elgar - ISBN 9781785361692 - p. 121 - 136.
    Modern food governance is increasingly hybrid, involving not only government, but also industry and civil society actors. This book analyzes the unfolding interplay between public and private actors in global and local food governance. How are responsibilities and risks allocated in hybrid governance arrangements, how is legitimacy ensured, and what effects do these arrangements have on industry or government practices? The expert contributors draw on law, economics, political science and sociology to discuss these questions through rich empirical cases.
    Stadium Coltan : artisanal mining, reforms and social change in eastern Democratic Republic of Congo
    Wakenge, Claude Iguma - \ 2017
    Wageningen University. Promotor(en): D.J.M. Hilhorst, co-promotor(en): K. Vlassenroot; J.G.R. Cuvelier. - Wageningen : Wageningen University - ISBN 9789463434560 - 210
    mining - conflict - economic sociology - cooperatives - reconstruction - poverty - rural sociology - workers - feedstocks - minerals - congo democratic republic - central africa - mijnbouw - conflict - economische sociologie - coöperaties - reconstructie - armoede - rurale sociologie - werkers - industriële grondstoffen - mineralen - democratische republiek kongo - centraal-afrika

    In the Democratic Republic of Congo (DRC), the mining sector has the potential to play a pivotal role in post-conflict reconstruction (World Bank, 2008), and artisanal mining sustains the livelihoods of millions people in the country (PACT, 2010). However, in the last 15 years, minerals from this artisanal mining have been ill-reputed. Eastern DRC has often been characterised by chronic instability and violent conflicts (Autesserre, 2010; Stearns, 2011) because it is widely believed that minerals in this region have attracted the greed of national and foreign armed groups, who benefit from the mining business.

    Although this ‘greed hypothesis’ has been criticised for its inconsistent performance in explaining resource-related conflicts (Le Billon, 2010; Ross, 2006), various national and international reform initiatives have gained momentum (Verbruggen et al., 2011). These initiatives aim to make the Congolese artisanal mining sector more transparent and to prevent ‘conflict minerals’ from entering the international market. In 2014, 13 reform initiatives—10 focusing on 3T (tantalum, tin and tungsten) and three on gold—were operational in eastern DRC (Cuvelier et al. 2014: 5). The implicit assumptions are that mining reforms will fully ‘clean’ artisanal mining of violence and corruption and that this will contribute to sustaining people’s livelihoods (Garrett and Mitchell, 2009: 12).

    This study investigated initiatives intended to ‘formalise’ artisanal mining in DRC—in other words, they aimed to bring mining under state control. The study especially focuses on the effects of one among these initiatives—the ITRI Tin Supply Chain Initiative (iTSCi)—on two groups of actors: miners (creuseurs) and middlemen (négociants). This thesis thus presents a fine-grained case study of the iTSCi. Designed by the International Tin Research Institute in 2009, iTSCi provides a means of determining the origin of 3T and documenting the trading chain for these minerals by ‘tagging and bagging’ the loads of 3T near miners’ shafts (at postes d’achat/selling points or buying stations), at counting offices (comptoirs) and in mineral depots, before the minerals are exported through the international market.

    This is a qualitative study undertaken at three coltan mining sites of northern Katanga: Kahendwa, Kisengo and Mai-Baridi. Coltan has been extracted at these sites since 2007. From March 2013 to September 2014, data were collected using participant observation of people’s practices (extraction/sale of coltan and various types of interactions between trading houses, cooperatives, mineworkers (creuseurs) and middlemen (négociants), as well as detailed in-depth interviews with creuseurs, négociants and their households. Data were also collected from the staff of mining cooperatives, trading houses, state authorities and civil servants—predominantly of the Service d’Assistance et d’Encadrement du Small-Scale Mining (SAESSCAM) and the Division des Mines. The last group of informants were a group of clandestine coltan négociants (known as hiboux—literally, ‘owls’), who were followed in the study.

    The purpose of this research is to study the micro-dynamics of changes after the reforms following the implementation of iTSCi. The study thus provides insights into how iTSCi is concretely implemented and how it has altered the organisation of mining and the trade of coltan. The study also aims to examine how this organisation affected creuseurs and négociants. The main research question of this study is as follows:

    How have initiatives to reform artisanal mining (iTSCi in particular) affected institutional change, how does this relate to changes in patterns of coltan production and trade, how were creuseurs and négociants affected by these changes, and how did these groups respond in the coltan mining areas of Kahendwa, Kisengo and Mai Baridi (northern Katanga) from 2009 to 2014?

    Analytically, the study adopted three main theoretical perspectives. First, an actor-oriented approach was taken, building on the premise that individual actors have the agency, knowledge and experience to reflect upon their situation and to respond to changes in their surrounding context (Giddens, 1984). Although the examined mining reforms consist predominantly of ‘ready-made’ techniques such as iTSCi’s ‘tagging and bagging’, analysing reforms with an actor orientation helps to highlight people’s reactions and responses. This includes how reform policies are applied in institutions (e.g. mining cooperatives), how they interact, how they are assigned meaning and how they are negotiated by social actors (Christoplos and Hilhorst, 2009).

    Second, the study builds on the sociology of economic life, which holds that economic action is a form of social action that is socially ‘embedded’, meaning that it is linked with or dependent on actions and institutions (such as social networks) that are noneconomic in content, goals and processes (Granovetter, 2005). This perspective facilitates the analysis of the livelihoods of négociants, including mechanisms of smuggling minerals into and beyond the mining areas where iTSCi is in force.

    Third, this thesis introduced the original concept of ‘enclaves of regulations’. These enclaves refer to the mining areas where iTSCi or other reforms are in force. This thesis has shown that, although these ‘enclaves’ appear to be ‘closed’ and insulated from the environment in terms of the locally applied rules for the mining and trading of minerals (e.g. ‘tagging and bagging’), in reality, such closure is not complete. This thesis has demonstrated that it would therefore be more appropriate to consider these ‘enclaves’ as semi-autonomous fields with porous boundaries.

    Apart from the introduction and the concluding chapters, this thesis is composed of five chapters. Chapter 2 explores the evolution of the mineral sector in the Katanga province. It analyses the history of mining, the initiation of artisanal mining and how the ongoing reforms have been informed by this history. In this chapter, it is shown that there is a long history of the organisation of mining in the Katangese province. The reforms therefore did not enter into a stage of anarchy, or an institutional void, but they added a layer to already existing forms of organisation.

    Chapter 3 focuses on mining cooperatives as newly introduced institutions aimed at governing the artisanal mining sites. Through a single case study, the chapter analyses how these cooperatives —especially the Coopérative des Artisanaux Miniers du Congo, CDMC—were introduced into the mining areas and how they interacted and blended with pre-existing miners’ organisations. This chapter demonstrates that cooperatives have been an emergent—rather than durable—solution in terms of representing the interests of artisanal miners.

    In Chapter 4, I provide a different perspective on ‘conflict minerals’. I thus introduce the notion of ‘reform conflicts’ to emphasise that, although ongoing reforms aim to sever the supposed linkages between the artisanal mining business and violent conflicts, these reforms have become a driving force behind the emergence of new conflicts over property rights and access to minerals.

    Chapter 5 is about livelihoods. It analyses how the reforms have influenced the livelihoods and socioeconomic position of négociants. This chapter also explores what kind of opportunities the reforms have offered to this group of mineral brokers often considered powerful in the mineral supply chain and explains what kind of constraints the négociants have confronted and why they have opted to diversify their livelihood portfolios. The chapter has shown that the reforms have affected this group of mineral brokers in different ways. Some négociants were well off, whereas others have been excluded from the mineral commodity chain. These findings contradict the widespread opinion that négociants are always abusive brokers in the mineral production and commodity chain.

    Chapter 6 analyses the responses of creuseurs and négociants to iTSCi. Although the mining sites where iTSCi is in force appear to be ‘enclaves of regulations’, I explore the strategies of creuseurs and négociants to bypass iTSCi and the reforms, especially around the coltan trade. This chapter demonstrates that coltan smuggling is a deeply rooted practice. Despite the reforms, smuggling continues in different forms.

    All of the elements highlighted above suggest that mining reforms have undergone a major shift, from addressing the initial problems associated with ‘conflict minerals’ to creating or reinforcing various types of problems, such as the influence of ‘big men’ in the mining business, coltan smuggling and the emergence of new conflicts over accessing minerals. This means that reform initiatives such as iTSCi should be based on knowledge about the actual situation. Thus, understanding and addressing these new types of problems calls for a comprehensive approach at both local and broader levels.

    The total cost of rearing a heifer on Dutch dairy farms : Calculated versus perceived cost
    Mohd Nor, N. ; Steeneveld, W. ; Derkman, T.H.J. ; Verbruggen, M.D. ; Evers, A.G. ; Haan, M.H.A. De; Hogeveen, H. - \ 2015
    Irish Veterinary Journal 68 (2015)1. - ISSN 2046-0481
    Costs - Dairy - Economics - Young stock

    Background: As farmers do not often keep a record of the expenditures for rearing, an economic tool that provides insight into the cost of rearing is useful. In the Netherlands, an economic tool (Jonkos) has been developed that can be used by farmers to obtain insight into the cost of rearing on their farm. The first objective of this study is to calculate the total cost of rearing young stock in Dutch dairy herds using Jonkos. The second objective is to compare the calculated total cost of rearing with the farmers' own estimation of the cost of rearing (the perceived cost). Findings: Information was available for 75 herds that reared their own young stock and who had used the Jonkos tool. The perceived cost of rearing young stock was only available for 36 herds. In the 75 herds, the average herd size was 100 dairy cows. The average calculated total cost of rearing a heifer was €1,790. The average perceived total cost of rearing a heifer (including labour and housing costs) was €1,030. Conclusion: Most Dutch farmers in the study underestimated the total cost of rearing. The Jonkos economic tool has the advantage that herd-specific information can be entered as input values. The output of the tool can improve the awareness of farmers about the total costs of rearing. This awareness can lead to a higher priority of young stock rearing and consequently to an improved quality of young stock rearing.

    Of Monkeys and Men: A Metabolomic Analysis of Static and Dynamic Urinary Metabolic Phenotypes in Two Species
    Saccenti, E. ; Tenori, L. ; Verbruggen, P. ; Timmerman, M.E. ; Bouwman, J. ; Greef, J. de; Luchinat, C. ; Smilde, A.K. - \ 2014
    PLoS ONE 9 (2014)9. - ISSN 1932-6203
    multilevel component analysis - time - creatinine - evolution - pathways - humans - diet
    Background Metabolomics has attracted the interest of the medical community for its potential in predicting early derangements from a healthy to a diseased metabolic phenotype. One key issue is the diversity observed in metabolic profiles of different healthy individuals, commonly attributed to the variation of intrinsic (such as (epi)genetic variation, gut microbiota, etc.) and extrinsic factors (such as dietary habits, life-style and environmental conditions). Understanding the relative contributions of these factors is essential to establish the robustness of the healthy individual metabolic phenotype. Methods To assess the relative contribution of intrinsic and extrinsic factors we compared multilevel analysis results obtained from subjects of Homo sapiens and Macaca mulatta, the latter kept in a controlled environment with a standardized diet by making use of previously published data and results. Results We observed similarities for the two species and found the diversity of urinary metabolic phenotypes as identified by nuclear magnetic resonance (NMR) spectroscopy could be ascribed to the complex interplay of intrinsic factors and, to a lesser extent, of extrinsic factors in particular minimizing the role played by diet in shaping the metabolic phenotype. Moreover, we show that despite the standardization of diet as the most relevant extrinsic factor, a clear individual and discriminative metabolic fingerprint also exists for monkeys. We investigate the metabolic phenotype both at the static (i.e., at the level of the average metabolite concentration) and at the dynamic level (i.e., concerning their variation over time), and we show that these two components sum up to the overall phenotype with different relative contributions of about 1/4 and 3/4, respectively, for both species. Finally, we show that the great degree diversity observed in the urinary metabolic phenotype of both species can be attributed to differences in both the static and dynamic part of their phenotype
    Plant science: the key to preventing slow cadmium poisoning
    Clemens, S. ; Aarts, M.G.M. ; Thomine, S. ; Verbruggen, N. - \ 2013
    Trends in Plant Science 18 (2013)2. - ISSN 1360-1385 - p. 92 - 99.
    quantitative trait locus - rice oryza-sativa - shoot cd translocation - heavy-metal atpase - grain cadmium - wheat cultivars - accumulating cd - potato-tubers - durum-wheat - arabidopsis
    Practically all human populations are environmentally exposed to cadmium (Cd), mostly through plant-derived food. A growing body of epidemiological evidence suggests that there is no margin of safety between current Cd exposure levels and the threshold for adverse health effects and, hence, there is an urgent need to lower human Cd intake. Here we review recent studies on rice (Oryza sativa) and Cd-hyperaccumulating plants that have led to important insights into the processes controlling the passage of Cd from the soil to edible plant organs. The emerging molecular understanding of Cd uptake, root retention, root-to-shoot translocation and grain loading will enable the development of low Cd-accumulating crops
    Prenylated isoflavonoids from plants as selective estrogen receptor modulators (phytoSERMs)
    Simons, R. ; Gruppen, H. ; Bovee, T.F.H. ; Verbruggen, M.A. ; Vincken, J.P. - \ 2012
    Food & Function 3 (2012)8. - ISSN 2042-6496 - p. 810 - 827.
    hops humulus-lupulus - breast-cancer cells - ionization mass-spectrometry - human liver-microsomes - glycyrrhiza-glabra l - in-vitro - dietary phytoestrogens - antiestrogenic activities - human urine - postmenopausal women
    Isoflavonoids are a class of secondary metabolites, which comprise amongst others the subclasses of isoflavones, isoflavans, pterocarpans and coumestans. Isoflavonoids are abundant in Leguminosae, and many of them can bind to the human estrogen receptor (hER) with affinities similar to or lower than that of estradiol. Dietary intake of these so-called phytoestrogens has been associated with positive effects on menopausal complaints, hormone-related cancers, and osteoporosis. Therefore, phytoestrogens are used as nutraceuticals in functional foods or food supplements. Most of the isoflavonoids show agonistic activity towards both hERa and hERß, the extent of which is modulated by the substitution pattern of their skeleton (i.e.-OH, -OCH(3)). Interestingly, substitutions consisting of a five-carbon prenyl group often seem to result in an antiestrogenic activity. There is growing evidence that the action of some of these prenylated isoflavonoids is tissue-specific, suggesting that they act like selective estrogen receptor modulators (SERMs), such as the well-known chemically synthesized raloxifene and tamoxifen. These so-called phytoSERMS might have high potential for realizing new food and pharma applications. In this review, the structural features of isoflavonoids (i.e. the kind of skeleton and prenylation (e.g. chain or pyran), position of the prenyl group on the skeleton, and the extent of prenylation (single, double)) are discussed in relation to their estrogenic activity. Anti-estrogenic and SERM activity of isoflavonoids was always associated with prenylation, but these activities did not seem to be confined to one particular kind/position of prenylation or isoflavonoid subclass. Few estrogens with agonistic activity were prenylated, but these were not tested for antagonistic activity; possibly, these molecules will turn out to be phytoSERMs as well. Furthermore, the data on the dietary occurrence, bioavailability and metabolism of prenylated isoflavonoids are discussed.
    Nutraceutical composition obtained from fungus-challenged soy seedlings
    Verbruggen, M.A. ; Simons, R. ; Niessen, H. ; Vincken, J.P. ; Gruppen, H. - \ 2012
    Octrooinummer: WO2012006750, gepubliceerd: 2012-01-19.
    Soybean seedlings and therefrom extractable compositions are described. Such compositions comprise prenylated isoflavones and at least one isoflavonoid, said isoflavonoid being selected from one of the chemical classes of isoflavones, coumestans and pterocarpans. Such compositions usually comprise at least 5 % prenylated isoflavones, in particular prenylated isoflavones selected from prenylated daidzein, prenylated hydroxydaidzein, prenylated glycitein, prenylated hydroxygenistein, and prenylated genistein. Such compositions also comprise pterocarpans, preferably in amounts of at least 20 %, and with a novel ratio of glyceollin I to glyceollin II to glyceollin III to glyceollin IV. Also described is a production method comprising the step of fermenting the soybeans under stress, in particular in the presence of cultures of fungi, preferably in the presence of Rhizopus microsporus Var. oryzae.
    Energieopslag maakt duurzame energie voorspelbaar
    Terbijhe, A. ; Verbruggen, T. ; Veth, J. de; Pukala, P. - \ 2012
    Lelystad : Praktijkonderzoek Plant & Omgeving B.V. ACRRES - 68
    duurzame energie - opslag - energie - kosten-batenanalyse - rentabiliteit - proeven op proefstations - accu's - uitrusting - windenergie - zonne-energie - sustainable energy - storage - energy - cost benefit analysis - profitability - station tests - batteries - equipment - wind power - solar energy
    De verdiencapaciteit van de WindAccu zit in de electriciteitsmarkt (APX/ENDEX en PV/Onbalans) en transportvoordeel of besparing op energiebelasting, afhankelijk van de situatie. Er zijn 2 cases uitgewerkt in dit rapport. Het eerste betreft het akkerbouwbedrijf van familie de Jong, met zonpv en wind, de ander de onderzoekslocatie van Wageningen UR in Lelystad. Na een grondige analyse van de (markt) mogelijkheden is de conclusie helaas de volgende. Batterijen voor opslag van elektrische energie zijn zonder uitzondering nog te duur om zonder aanvullende inkomsten rendabel te zijn. Stel dat de kostendaling die zich in de PV-sector heeft voorgedaan, exemplarisch is voor de kostendaling van batterijen, dan is er voldoende verdiencapaciteit in de electriciteitsmarkt en kostenbesparing om bij de juiste randvoorwaarden duurzame energie rendabeler te maken.
    The curse of the black box
    Cortois, R. ; Deyn, G.B. de - \ 2012
    Plant and Soil 350 (2012)1-2. - ISSN 0032-079X - p. 27 - 33.
    arbuscular mycorrhizal fungi - plant-soil feedbacks - biodiversity - diversity - agroecosystems - productivity - management - community - maize - biota
    Background Soil is a foremost provider of (agro-)ecosystem services, making plant-soil interactions pivotal in agriculture research. The functioning of soils entails complex interactions between soil biota and the abiotic soil environment and is therefore often considered as a ‘black box’. The study of Verbruggen et al. (this volume) tries to crack the black box open by examining the role of soil microbial communities from conventional and organic farming fields for the growth of Zea mays and phosphorous retention in the soil. Scope In this commentary on the paper of Verbruggen et al. (2011) we use the study to illustrate that investigating soils, and specifically the role of soil biota in ecosystem functioning, is not straightforward, given the overwhelming soil biodiversity and the complexity of soil as a habitat. We discuss the key elements that need to be considered in order to translate results of highly controlled experiments with inoculated soil biota to their functioning in the field. Conclusions Verbruggen et al. contribute to our understanding of the functional role of AMF in agro-ecosystems. Yet the results only allow us to merely speculate about the realized functional role of AMF communities in the field, a very interesting avenue for future research.
    Agonistic and antagonistic estrogens in licorice root (Glycyrrhiza glabra)
    Simons, R. ; Vincken, J.P. ; Mol, L.A.M. ; The, S.A.M. ; Bovee, T.F.H. ; Luijendijk, T.J.C. ; Verbruggen, M.A. ; Gruppen, H. - \ 2011
    Analytical and Bioanalytical Chemistry 401 (2011)1. - ISSN 1618-2642 - p. 305 - 313.
    breast-cancer cells - antiestrogenic activities - receptor-alpha - phenolic-compounds - in-vitro - constituents - mcf-7 - flavonoids - tissues - protein
    The roots of licorice (Glycyrrhiza glabra) are a rich source of flavonoids, in particular, prenylated flavonoids, such as the isoflavan glabridin and the isoflavene glabrene. Fractionation of an ethyl acetate extract from licorice root by centrifugal partitioning chromatography yielded 51 fractions, which were characterized by liquid chromatography–mass spectrometry and screened for activity in yeast estrogen bioassays. One third of the fractions displayed estrogenic activity towards either one or both estrogen receptors (ERs; ERa and ERß). Glabrene-rich fractions displayed an estrogenic response, predominantly to the ERa. Surprisingly, glabridin did not exert agonistic activity to both ER subtypes. Several fractions displayed higher responses than the maximum response obtained with the reference compound, the natural hormone 17ß-estradiol (E2). The estrogenic activities of all fractions, including this so-called superinduction, were clearly ER-mediated, as the estrogenic response was inhibited by 20–60% by known ER antagonists, and no activity was found in yeast cells that did not express the ERa or ERß subtype. Prolonged exposure of the yeast to the estrogenic fractions that showed superinduction did, contrary to E2, not result in a decrease of the fluorescent response. Therefore, the superinduction was most likely the result of stabilization of the ER, yeast-enhanced green fluorescent protein, or a combination of both. Most fractions displaying superinduction were rich in flavonoids with single prenylation. Glabridin displayed ERa-selective antagonism, similar to the ERa-selective antagonist RU 58668. Whereas glabridin was able to reduce the estrogenic response of E2 by approximately 80% at 6¿×¿10-6 M, glabrene-rich fractions only exhibited agonistic responses, preferentially on ERa.
    Increasing Soy Isoflavonoid Content and Diversity by Simultaneous Malting and Challenging by a Fungus to Modulate Estrogenicity
    Simons, R. ; Vincken, J.P. ; Roidos, N. ; Bovee, T.F.H. ; Iersel, M. van; Verbruggen, H. ; Gruppen, H. - \ 2011
    Journal of Agricultural and Food Chemistry 59 (2011)12. - ISSN 0021-8561 - p. 6748 - 6758.
    ionization mass-spectrometry - antiestrogenic activities - prenylated pterocarpans - electrospray-ionization - phytophthora-megasperma - fusarium-solani - accumulation - glyceollin - roots - biosynthesis
    Soybeans were germinated on a kilogram-scale, by the application of malting technology used in the brewing industry, and concomitantly challenged with Rhizopus microsporus var. oryzae. In a time-course experiment, samples were taken every 24 h for 10 days, and the isoflavonoid profile was analyzed by RP-UHPLC-MS. Upon induction with R. microsporus, the isoflavonoid composition changed drastically with the formation of phytoalexins belonging to the subclasses of the pterocarpans and coumestans and by prenylation of the various isoflavonoids. The pterocarpan content stabilized at 2.24 mg of daidzein equivalents (DE) per g after 9 days. The levels of the less common glyceofuran, glyceollin IV, and V/VI ranged from 0.18 to 0.35 mg DE/g and were comparable to those of the more commonly reported glyceollins I, II, and III (0.22–0.32 mg DE/g) and glycinol (0.42 mg DE/g). The content of prenylated isoflavones after the induction process was 0.30 mg DE/g. The total isoflavonoid content increased by a factor of 10–12 on DW basis after 9 days, which was suggested to be ascribable to de novo synthesis. These changes were accompanied by a gradual increase in agonistic activity of the extracts toward both the estrogen receptor a (ERa) and ERß during the 10-day induction, with a more pronounced activity toward ERß. Thus, the induction process yielded a completely different spectrum of isoflavonoids, with a much higher bioactivity toward the estrogen receptors. This, together with the over 10-fold increase in potential bioactives, offers promising perspectives for producing more, novel, and higher potency nutraceuticals by malting under stressed conditions.
    Identification of prenylated pterocarpans and other isoflavonoids in Rhizopus spp. elicited soya bean seedlings by electrospray ionisation mass spectrometry
    Simons, R. ; Vincken, J.P. ; Bohin, M.C. ; Kuijpers, T.F.M. ; Verbruggen, M.A. ; Gruppen, H. - \ 2011
    Rapid Communications in Mass Spectrometry 25 (2011)1. - ISSN 0951-4198 - p. 55 - 65.
    phytoalexin synthesis - root extracts - lupinus-angustifolius - liquid-chromatography - cell-cultures - glyceollin - induction - biosynthesis - aglycones - flavonol
    Phytoalexins from soya are mainly characterised as prenylated pterocarpans, the glyceollins. Extracts of non-soaked and soaked soya beans, as well as that of soya seedlings, grown in the presence of Rhizopus microsporus var. oryzae, were screened for the presence of prenylated flavonoids with a liquid chromatography/mass spectrometry (LC/MS)-based screening method. The glyceollins I–III and glyceollidins I–II, belonging to the isoflavonoid subclass of the pterocarpans, were tentatively assigned. The formation of these prenylated pterocarpans was accompanied by that of other prenylated isoflavonoids of the subclasses of the isoflavones and the coumestans. It was estimated that approx. 40% of the total isoflavonoid content in Rhizopus-challenged soya bean seedlings were prenylated pterocarpans, whereas 7% comprised prenylated isoflavones and prenylated coumestans. The site of prenylation (A-ring or B-ring) of the prenylated isoflavones was tentatively annotated using positive-ion mode MS by comparing the 1,3AR retro-Diels-Alder (RDA) fragments of prenylated and non-prenylated isoflavones. Furthermore, the fragmentation pathways of the five pterocarpans in negative-ion (NI) mode were proposed, which involved the cleavage of the C-ring and/or D-ring. The absence of the ring-closed prenyl (pyran or furan) gave exclusively -H2Ox,yRDA fragments, whereas its presence gave predominantly the common RDA fragments.
    Review of recent literature concerning mixture toxicity of pesticides to aquatic organisms
    Verbruggen, E.M.J. ; Brink, P.J. van den - \ 2010
    Bilthoven : RIVM (RIVM report / National Institute for Public Health and the Environment 601400001/2010) - 34
    toxiciteit - pesticiden - mengsels - literatuuroverzichten - waterorganismen - risicoschatting - aquatische toxicologie - ecotoxicologie - toxicity - pesticides - mixtures - literature reviews - aquatic organisms - risk assessment - aquatic toxicology - ecotoxicology
    De eenvoudigste manier om effecten van mengsels van bestrijdingsmiddelen te beoordelen is om de effecten van de individuele stoffen bij elkaar op te tellen (concentratieadditie). In het algemeen laten experimenten zien dat de stoffen elkaars werking niet versterken (geen synergisme). Als er toch sprake is van versterking, is dat effect doorgaans gering. Het concept concentratieadditie is daarom geschikt om de schadelijke effecten van mengsels van bestrijdingsmiddelen te schatten. Dit blijkt uit een overzicht van recente literatuur over de toxiciteit van mengsels van bestrijdingsmiddelen dat het RIVM met het kennisinstituut Alterra heeft gemaakt. De inventarisatie is een update van een analyse uit 2000 en bevestigt het beeld van toen. Het ministerie van VROM wilde als opdrachtgever in kaart brengen welke ontwikkelingen spelen op het gebied van het beoordelen van mengsels van bestrijdingsmiddelen. De studie beschrijft daarom ook methodologische vernieuwingen die de risicoschatting van mengsels kunnen verfijnen.
    Intraspecific variation of seed floating ability in Sparganium emersum suggests a bimodal dispersal strategy
    Pollux, B.J.A. ; Verbruggen, E. ; Groenendael, J.M. Van; Ouborg, N.J. - \ 2009
    Aquatic Botany 90 (2009)2. - ISSN 0304-3770 - p. 199 - 203.
    Buoyancy - Cryptic seed heteromorphism - Germination - Hydrochory - Long-distance dispersal - Seed mass

    Water-mediated spread of seeds (hydrochory) plays an important role in the dispersal of aquatic plants. In this study we investigate intraspecific variation in floating ability and germination capacity of Sparganium emersum seeds in relation to seed mass, within three natural populations along the Rur River (the Netherlands-Germany). Our results suggest that S. emersum produces two types of seeds: (i) short-floating seeds (SFS) that sink within 4 weeks (approximately 71% of all seeds), and (ii) long-floating seeds (LFS) that float at least for 6 months (approximately 28% of all seeds). Our study further shows that short-floating seeds display a significantly higher germination (%) (SFS = 89.9% vs LFS = 32.6%), a faster germination rate (SFS = 8.71 ± 3.3 vs LFS = 9.32 ± 3.1 days to germination) and a higher mean seed mass (SFS = 15.17 ± 4.5 vs LFS = 11.25 ± 3.8 mg), compared to long-floating seeds. It is argued that the production of these two types of seeds by S. emersum plants, each type with a different potential for water-mediated dispersal, represents a bimodal hydrochoric dispersal strategy.

    A rapid screening method for prenylated flavonoids with ultra-high-performance liquid chromatography/electrospray ionisation mass spectrometry in licorice root extracts
    Simons, R. ; Vincken, J.P. ; Bakx, E.J. ; Verbruggen, M.A. ; Gruppen, H. - \ 2009
    Rapid Communications in Mass Spectrometry 23 (2009)19. - ISSN 0951-4198 - p. 3083 - 3093.
    glycyrrhiza-glabra - isoprenylated flavonoids - phenolic constituents - humulus-lupulus - aglycones - flavanone - cultures
    Due to their substitution with an isoprenoid group, prenylated flavonoids have an increased affinity for biological membranes and target proteins, enhancing their potential bioactivity. Although many prenylated flavonoids have been described, there are no methods that specifically screen for their presence in complex mixtures, prior to purification. We describe a method based on ultra-high-performance liquid chromatography (UHPLC) with electrospray ionisation mass spectrometry (ESI-MS) that allows rapid screening for prenylated flavonoids in multi-component plant extracts. Identification of the prenylated flavonoids is based on screening for neutral losses of 42 u and 56 u in the positive-ion mode MS2 and MS3 spectra within the MS chromatograms. In addition, this method discriminates between a prenyl chain and a ring-closed prenyl (pyran ring), based on the ratio of the relative abundances of the ions that lose 42 u and 56 u (42:56). The application of this screening method on a 70% aq. ethanol, ethanol and ethyl acetate extract of the roots of Glycyrrhiza glabra indicated the presence of 70 mono- and di-prenylated flavonoids. In addition, of each prenylated flavonoid the type of prenylation, chain or pyran ring was determined.
    Digital Dematerialization: Economic Mechanisms Behind the Net Impact of ICT on Materials Use
    Bergh, J.C.J.M. van den; Verbruggen, H. ; Linderhof, V.G.M. - \ 2009
    In: Climate Change And Sustainable Development New Challenges for Poverty Reduction / Salih, M.A.M., Cramer, J., Box, L., Cheltengham, UK : Edward Elgar Publishing - ISBN 9781848444096 - p. 192 - 213.
    European food law handbook
    Meulen, B.M.J. van der; Velde, M. van der; Szajkowska, A. ; Verbruggen, R. - \ 2008
    Wageningen : Wageningen Academic Publishers (European Institute for Food Law series no. 2) - ISBN 9789086860821 - 632
    voedsel - voedingsmiddelenwetgeving - voedselproducten - etiketteren - voedseladditieven - nieuwe voedingsmiddelen - voedselhygiëne - eu regelingen - handboeken - europese unie - europa - tracking en tracing - food - food legislation - food products - labelling - food additives - novel foods - food hygiene - eu regulations - handbooks - european union - europe - tracking and tracing
    This handbook analyses and explains the institutional, substantive and procedural elements of EU food law, taking the General Food Law as a focus point. Principles are discussed as well as specific rules addressing food as a product, the processes related to food and communication about food through labelling. These rules define requirements on subjects like market approval for food additives, novel foods and genetically modified foods; food hygiene, tracking & tracing, withdrawal & recall.
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