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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    Open brief aan ministers van LNV en Milieu en Wonen
    Bakker, Martha ; Boersma, Hidde ; haar, Bernard ter; Hennink, Michiel ; Rabbinge, Rudy ; Veerman, Cees ; Winsemius, Pieter ; Zeeuw, Friso de; Kasteren, Joost van - \ 2020
    Open brief aan ministers van LNV en Milieu en Wonen
    An invitation for more research on transnational corporations and the biosphere
    Folke, Carl ; Österblom, Henrik ; Jouffray, Jean Baptiste ; Lambin, Eric F. ; Adger, Neil ; Scheffer, Marten ; Crona, Beatrice I. ; Nyström, Magnus ; Levin, Simon A. ; Carpenter, Stephen R. ; Anderies, John M. ; Chapin, Stuart ; Crépin, Anne Sophie ; Dauriach, Alice ; Galaz, Victor ; Gordon, Line J. ; Kautsky, Nils ; Walker, Brian H. ; Watson, James R. ; Wilen, James ; Zeeuw, Aart de - \ 2020
    Nature Ecology & Evolution 4 (2020). - ISSN 2397-334X
    Dissection of cell division orientation control in Arabidopsis thaliana
    Zeeuw, Thijs A.J. de - \ 2020
    Wageningen University. Promotor(en): D. Weijers. - Wageningen : Wageningen University - ISBN 9789463952248 - 237

    Land plants can grow to exceptional body sizes, with the most complex specialized structures. Directional cell division has a fundamental role throughout the tremendous plant growth processes, yet its molecular regulation is still largely unknown. Chapter 1 of this thesis discusses mechanisms and sub-cellular structures known to be involved in plant cell division orientation control, and explores tools used for dissection of this complex mechanism.

    Dissecting the complex plant cell division control mechanisms requires a simple and highly predictable in vivo model system. The highly predictable a relatively simple development of the Arabidopsis embryo makes it suitable for studying plant cell division regulation. In Chapter 2, we explore the cellular basis -, cell division patterns -, and regulatory pathways underlying early plant embryogenesis. We describe previous research showing that most cell divisions in the Arabidopsis embryo divide according a geometry- based “shortest-wall” principle, except for formative, asymmetric divisions. When auxin- signalling is disabled by overexpression of the dominant negative response inhibitor BODENLOS (BDL; bdl-mutant) all divisions in the embryo switch to “shortest-wall” divisions, suggesting auxin-signalling based control of oriented cell divisions.

    Since the microtubule (MT) cytoskeleton is a possible factor regulating cell division orientation downstream of auxin, dissecting its dynamics and regulatory mechanisms is crucial to understand cell division regulation. Combining high-resolution imaging of cell walls and MTs with a modelling strategy for MT organisation, in Chapter 3, we show that the cortical MT array is crucial for division plane orientation control in de Arabidopsis embryo. In our model, MT-dynamics are confined by cell shape -, MT stability at cell edges-, and local MT stability by auxin. Additionally, comparison of cell-biology in wild-type - and bdl-mutant embryos in Chapter 4 reveals that F-actin organisation and cell expansion are affected in the mutant. These results suggest a function for the cytoskeleton and cell shape regulation in plant cell division orientation control downstream of BDL-mediated auxin-signalling.

    Transcripts of factors regulating cytoskeletal structures and cell shape downstream of auxin should be differentially expressed in the bdl-mutant background. To allow for  the identification of these factors, in Chapter 5, we establish and optimize a pipeline to generate high-quality embryo transcriptomes for the earliest embryonic stages. As a proof of concept, we use this pipeline to generate a reference transcriptome for early Arabidopsis embryogenesis which can be used as a tool in future developmental embryonic research.

    Since the role of auxin-signalling in cell division control is inferred from overexpression of a dominant response inhibitor, it is not clear if endogenous auxin truly regulates division orientation. In Chapter 6, we show that the segregating tir1/afb hexuple – and bdl-mutant embryos have similar division plane defects, suggesting that cell division regulation is regulated by auxin. However, we were not able to verify an overlap in transcriptomic regulation between the two auxin-insensitive mutants, possibly due to the small number of true mutants in the tir1/afb-mutant. Using the bdl-mutant transcriptome we identified IQ-domain 6 as a possible target of BDL-mediated auxin-signalling involved in cell division plane control. We show that the IQD6-8 protein family subclade localizes to MTs, and IQD6 binds cytoskeletal structures and calmodulins, in vivo. Loss of function of the IQD6-8 subclade results in skewed division planes in the embryo and roots, suggesting a role in cell division control, possible through Ca2+-mediated cytoskeletal regulation.

    Finally, in Chapter 7, we discuss future challenges in research focused on plant cell division orientation control, and the most important findings of this thesis are placed in a broader cell biological – and plant developmental framework.

    Quantification of nitrogen oxides emissions from build-up of pollution over Paris with TROPOMI
    Lorente, A. ; Boersma, K.F. ; Eskes, H.J. ; Veefkind, J.P. ; Geffen, J.H.G.M. van; Zeeuw, M.B. de; Denier van der Gon, H.A.C. ; Beirle, S. ; Krol, M.C. - \ 2019
    Scientific Reports 9 (2019)1. - ISSN 2045-2322

    Nitrogen dioxide (NO2) is a regulated air pollutant that is of particular concern in many cities, where concentrations are high. Emissions of nitrogen oxides to the atmosphere lead to the formation of ozone and particulate matter, with adverse impacts on human health and ecosystems. The effects of emissions are often assessed through modeling based on inventories relying on indirect information that is often outdated or incomplete. Here we show that NO2 measurements from the new, high-resolution TROPOMI satellite sensor can directly determine the strength and distribution of emissions from Paris. From the observed build-up of NO2 pollution, we find highest emissions on cold weekdays in February 2018, and lowest emissions on warm weekend days in spring 2018. The new measurements provide information on the spatio-temporal distribution of emissions within a large city, and suggest that Paris emissions in 2018 are only 5–15% below inventory estimates for 2011–2012, reflecting the difficulty of meeting NOx emission reduction targets.

    Tomatenziekte aangetroffen in Westland
    Vlugt, Rene van der - \ 2019
    Discounting in the presence of scarce ecosystem services
    Zhu, Xueqin ; Smulders, Sjak ; Zeeuw, Aart de - \ 2019
    Journal of Environmental Economics and Management 98 (2019). - ISSN 0095-0696
    Consumption value - Discount rate - Ecosystem services - Growth rate - Production value - Ramsey balanced growth

    The discount rate for cost-benefit analysis has to take account of future scarcity of ecosystem services in consumption and production. Previous literature focuses on the first aspect and shows the importance of the relative price effect, for given growth rates of consumption and ecosystem services. This paper focuses on intermediate ecosystem services in production and shows that for limited substitutability and a low growth rate of these ecosystem services, the growth rate of consumption, and thus the discount rate, declines towards a low value. Using a Ramsey growth model, the paper distinguishes three cases. If ecosystem services can be easily substituted, the discount rate converges to the usual value in the long term. Secondly, if ecosystem services can be easily substituted in production but not in consumption, the relative price effect is important. Finally, and most interestingly, if ecosystem services cannot be easily substituted in production, the discount rate declines towards a low value and the relative price effect is less important. Another part of the previous literature has shown that a declining discount rate is the result of introducing several forms of uncertainty, but this paper reaches that conclusion from an endogenous effect on the growth rate of the economy.

    Transnational corporations and the challenge of biosphere stewardship
    Folke, Carl ; Österblom, Henrik ; Jouffray, Jean Baptiste ; Lambin, Eric F. ; Adger, W.N. ; Scheffer, Marten ; Crona, Beatrice I. ; Nyström, Magnus ; Levin, Simon A. ; Carpenter, Stephen R. ; Anderies, John M. ; Chapin, Stuart ; Crépin, Anne Sophie ; Dauriach, Alice ; Galaz, Victor ; Gordon, Line J. ; Kautsky, Nils ; Walker, Brian H. ; Watson, James R. ; Wilen, James ; Zeeuw, Aart de - \ 2019
    Nature Ecology & Evolution 3 (2019)10. - ISSN 2397-334X - p. 1396 - 1403.

    Sustainability within planetary boundaries requires concerted action by individuals, governments, civil society and private actors. For the private sector, there is concern that the power exercised by transnational corporations generates, and is even central to, global environmental change. Here, we ask under which conditions transnational corporations could either hinder or promote a global shift towards sustainability. We show that a handful of transnational corporations have become a major force shaping the global intertwined system of people and planet. Transnational corporations in agriculture, forestry, seafood, cement, minerals and fossil energy cause environmental impacts and possess the ability to influence critical functions of the biosphere. We review evidence of current practices and identify six observed features of change towards 'corporate biosphere stewardship', with significant potential for upscaling. Actions by transnational corporations, if combined with effective public policies and improved governmental regulations, could substantially accelerate sustainability efforts.

    A Plausible Microtubule-Based Mechanism for Cell Division Orientation in Plant Embryogenesis
    Chakrabortty, Bandan ; Willemsen, Viola ; Zeeuw, Thijs de; Liao, Che Yang ; Weijers, Dolf ; Mulder, Bela ; Scheres, Ben - \ 2018
    Current Biology 28 (2018)19. - ISSN 0960-9822 - p. 3031 - 3043.e2.
    arabidopsis - auxin - cell shape - computational modeling - cytokinesis - division orientation - embryogenesis - microtubules - systems biology

    Oriented cell divisions are significant in plant morphogenesis because plant cells are embedded in cell walls and cannot relocate. Cell divisions follow various regular orientations, but the underlying mechanisms have not been clarified. We propose that cell-shape-dependent self-organization of cortical microtubule arrays is able to provide a mechanism for determining planes of early tissue-generating divisions and may form the basis for robust control of cell division orientation in the embryo. To show this, we simulate microtubules on actual cell surface shapes, from which we derive a minimal set of three rules for proper array orientation. The first rule captures the effects of cell shape alone on microtubule organization, the second rule describes the regulation of microtubule stability at cell edges, and the third rule includes the differential effect of auxin on local microtubule stability. These rules generate early embryonic division plane orientations and potentially offer a framework for understanding patterned cell divisions in plant morphogenesis. Chakrabortty et al. show that a computational model for dynamic self-organization of cortical microtubules on experimentally extracted cell shapes provides a plausible molecular mechanism for division plane orientation in the first four divisions of early stage A. thaliana embryos, in WT as well as two developmental mutants bodenlos and clasp.

    Host- and stage-dependent secretome of the arbuscular mycorrhizal fungus Rhizophagus irregularis
    Zeng, Tian ; Holmer, Rens ; Hontelez, Jan ; Lintel-Hekkert, Bas te; Marufu, Lucky ; Zeeuw, Thijs de; Wu, Fangyuan ; Schijlen, Elio ; Bisseling, Ton ; Limpens, Erik - \ 2018
    The Plant Journal 94 (2018)3. - ISSN 0960-7412 - p. 411 - 425.
    Arbuscular mycorrhizal fungi form the most wide‐spread endosymbiosis with plants. There is very little host‐specificity in this interaction, however host preferences as well as varying symbiotic efficiencies have been observed. We hypothesize that secreted proteins (SPs) may act as fungal effectors to control symbiotic efficiency in a host‐dependent manner. Therefore, we studied whether AM fungi adjust their secretome in a host‐ and stage‐dependent manner to contribute to their extremely wide host‐range. We investigated the expression of SP‐encoding genes of Rhizophagus irregularis in three evolutionary distantly‐related plant species, Medicago truncatula, Nicotiana benthamiana and Allium schoenoprasum. In addition we used laser microdissection in combination with RNAseq to study SP expression at different stages of the interaction in Medicago. Our data indicate that most expressed SPs show roughly equal expression levels in the interaction with all three host plants. In addition, a subset shows significant differential expression depending on the host plant. Furthermore, SP expression is controlled locally in the hyphal network in response to host dependent cues. Overall, this study presents a comprehensive analysis of the R. irregularis secretome, which now offers a solid basis to direct functional studies on the role of fungal SPs in AM symbiosis.
    Technology for Rooftop Greenhouses
    Montero, Juan I. ; Baeza, Esteban ; Muñoz, Pere ; Sanyé-Mengual, Esther ; Stanghellini, Cecilia - \ 2017
    In: Rooftop Urban Agriculture / Orsini, F., Dubbeling, M., de Zeeuw, H., Gianquinto, G., Springer (Rooftop Urban Agriculture ) - ISBN 9783319577197 - p. 83 - 101.
    Rooftop greenhouses (RTGs) can generate significant advantages provided RTGs and buildings are connected in terms of energy, water and CO2 flows. Beyond the production of high-value crops, environmental benefits such as re-use of waste water, application of residual heat and absorption of carbon dioxide are derived from urban RTGs. Social benefits viz the creation of employment, social cohesion and so on are also important assets of RTGs. This chapter is focussed on RTGs technology. RTG share many common aspects with conventional greenhouses, but at the same time RTGs show attributes that should be discussed separately. Synergies such as using residual heat, rain water for irrigation, CO2 exchange, etc. are part of the common metabolism greenhouse-building. This chapter will concentrate on the available technology from conventional greenhouses which is more suitable for RTGs, particularly concerning greenhouse structure, covering materials, climate control and soilless cultivation systems.
    Tissue and Organ Initiation in the Plant Embryo : A First Time for Everything
    Palovaara, Joakim ; Zeeuw, Thijs de; Weijers, Dolf - \ 2016
    Annual Review of Cell and Developmental Biology 32 (2016). - ISSN 1081-0706 - p. 47 - 75.
    Apical-basal axis - Asymmetric cell division - Cell specification - Meristems - Plant embryogenesis - Radial patterning - Stem cells

    Land plants can grow to tremendous body sizes, yet even the most complex architectures are the result of iterations of the same developmental processes: organ initiation, growth, and pattern formation. A central question in plant biology is how these processes are regulated and coordinated to allow for the formation of ordered, 3D structures. All these elementary processes first occur in early embryogenesis, during which, from a fertilized egg cell, precursors for all major tissues and stem cells are initiated, followed by tissue growth and patterning. Here we discuss recent progress in our understanding of this phase of plant life. We consider the cellular basis for multicellular development in 3D and focus on the genetic regulatory mechanisms that direct specific steps during early embryogenesis.

    Plant organogenesis : Rules of order
    Zeeuw, Thijs De; Weijers, Dolf - \ 2016
    Current Biology 26 (2016)4. - ISSN 0960-9822 - p. R157 - R159.

    Plant lateral roots have a defined developmental pattern and shape, but a key question is whether strict regulation underlies observed regularity. A new study uses long-term in toto live imaging and simulations to show that organogenesis rather follows self-organizing principles.

    Urban food systems
    Wiskerke, J.S.C. - \ 2015
    In: Cities and Agriculture / de Zeeuw, Henk, Drechsel, Pay, Routledge (Earthscan Food and Agriculture ) - ISBN 9781138860582 - p. 1 - 25.
    Meer aandacht nodig voor ui
    PPO Akkerbouw, Groene Ruimte en Vollegrondsgroente, - \ 2015
    Boerderij 100 (2015)30. - ISSN 0006-5617 - p. 58 - 58.
    akkerbouw - uien - proeven op proefstations - gewasbescherming - plantenziekteverwekkende schimmels - economische samenwerking - arable farming - onions - station tests - plant protection - plant pathogenic fungi - economic cooperation
    Akkerbouwer Jaap de Zeeuw is voorzitter van het Platform Nederlandse Uientelers. Hier en daar duikt de naam van deze organisatie op, onder meer als participant in het koprotonderzoek met PPO.
    COMMENTARY: Climate engineering reconsidered
    Barrett, S. ; Lenton, T.M. ; Millner, A. ; Tavoni, A. ; Carpenter, S. ; Anderies, J.M. ; Chapin, F.S. ; Crepin, A.S. ; Daily, G. ; Ehrlich, P. ; Folke, C. ; Galaz, V. ; Hughes, T. ; Kautsky, N. ; Lambin, E.F. ; Naylor, R. ; Nyborg, K. ; Polasky, S. ; Scheffer, M. ; Wilen, J. ; Xepapadeas, A. ; Zeeuw, A. de - \ 2014
    Nature Climate Change 4 (2014)7. - ISSN 1758-678X - p. 527 - 529.
    injections
    Does aquaculture add resilience to the global food system?
    Troell, M. ; Naylor, R.L. ; Metian, M. ; Beveridge, M. ; Tyedmers, P.H. ; Folke, C. ; Arrow, K.J. ; Barrett, S. ; Crepin, A.S. ; Ehrlich, P. ; Gren, R. ; Kautsky, N. ; Levin, S.A. ; Nyborg, K. ; Osterblom, H. ; Polasky, S. ; Scheffer, M. ; Walker, B.H. ; Xepapadeas, T. ; Zeeuw, A. de - \ 2014
    Proceedings of the National Academy of Sciences of the United States of America 111 (2014)37. - ISSN 0027-8424 - p. 13257 - 13263.
    fish - nutrition - impacts - prices - era
    Aquaculture is the fastest growing food sector and continues to expand alongside terrestrial crop and livestock production. Using portfolio theory as a conceptual framework, we explore how current interconnections between the aquaculture, crop, livestock, and fisheries sectors act as an impediment to, or an opportunity for, enhanced resilience in the global food system given increased resource scarcity and climate change. Aquaculture can potentially enhance resilience through improved resource use efficiencies and increased diversification of farmed species, locales of production, and feeding strategies. However, aquaculture's reliance on terrestrial crops and wild fish for feeds, its dependence on freshwater and land for culture sites, and its broad array of environmental impacts diminishes its ability to add resilience. Feeds for livestock and farmed fish that are fed rely largely on the same crops, although the fraction destined for aquaculture is presently small (~4%). As demand for high-value fed aquaculture products grows, competition for these crops will also rise, as will the demand for wild fish as feed inputs. Many of these crops and forage fish are also consumed directly by humans and provide essential nutrition for low-income households. Their rising use in aquafeeds has the potential to increase price levels and volatility, worsening food insecurity among the most vulnerable populations. Although the diversification of global food production systems that includes aquaculture offers promise for enhanced resilience, such promise will not be realized if government policies fail to provide adequate incentives for resource efficiency, equity, and environmental protection.
    Structuurvisie Vianen : Toetsingsadvies over het mileueffectrapport
    Broekmeyer, M.E.A. ; Eck, M. van; Tas, M.A.J. van der; Termorshuizen, J. ; Zeeuw, J.H. de - \ 2012
    Utrecht : MER, commissie voor de mileueffectrapportage - ISBN 9789042136021 - 9 p.
    Immunomodulatory effects of potential probiotics in a mouse peanut sensitization model
    Meijerink, M. ; Wells, J. ; Taverne, N. ; Zeeuw Brouwer, M.L. de; Hilhorst, B. ; Venema, K. ; Bilsen, J. van - \ 2012
    FEMS Immunology and Medical Microbiology 65 (2012)3. - ISSN 0928-8244 - p. 488 - 496.
    lactic-acid bacteria - placebo-controlled trial - regulatory t-cells - blood mononuclear-cells - atopic-dermatitis - dendritic cells - food allergy - lactobacillus-rhamnosus - cytokine production - responses
    Peanut allergy accounts for the majority of severe food-related allergic reactions and there is a need for new prevention and treatment strategies. Probiotics may be considered for treatment on the basis of their immunomodulating properties. Cytokine profiles of probiotic strains were determined by in vitro co-culture with human PBMCs. Three strains were selected to investigate their prophylactic potential in a peanut sensitization model by analysing peanut-specific antibodies, mast cell degranulation and ex vivo cytokine production by splenocytes. The probiotic strains induced highly variable cytokine profiles in PBMCs. L. salivarius HMI001, L. casei Shirota (LCS) and L. plantarum WCFS1 were selected for further investigation owing to their distinct cytokine patterns. Prophylactic treatment with both HMI001 and LCS attenuated the Th2 phenotype (reduced mast cell responses and ex vivo IL-4 and/or IL-5 production). In contrast, WCFS1 augmented the Th2 phenotype (increased mast cell and antibody responses and ex vivo IL-4 production). In vitro PBMC screening was useful in selecting strains with anti-inflammatory and Th1 skewing properties. In case of HMI001 (high IL-10/IL-12 ratio) and LCS (high interferon- and IL-12), partial protection was seen in a mouse peanut allergy model. Strikingly, certain strains may worsen the allergic reaction as shown in the case of WCFS1.
    Structuurvisie Vianen Advies over reikwijdte en detailniveau van het milieueffectrapport
    Broekmeyer, M.E.A. ; Spel, D. ; Tas, M.A.J. van der; Termorshuizen, J.J. ; Zeeuw, J.H. de - \ 2011
    Utrecht, The Netherlands : MER - ISBN 9789042132993 - 8
    bestemmingsplannen - milieueffectrapportage - gemeenten - utrecht - zoning plans - environmental impact reporting - municipalities - utrecht
    Met het vaststellen van de structuurvisie 2030 wil de gemeente Vianen op hoofdlijnen richting geven aan en samenhang brengen in de ruimtelijke ontwikkelingen op het grondgebied die voortkomen uit rijks-, provinciaal en gemeentelijk beleid. Het MER zal inzicht moeten geven in de ontwikkelingen die de structuurvisie maximaal mogelijk maakt, voor zover deze relevant zijn voor het voorspellen van de milieueffecten
    Structuurvisie gemeente Heemskerk, Toetsingsadvies over het milieueffectrapport
    Broekmeyer, M.E.A. ; Kerkhoff, R.J. van; Korf, G. ; Tommel, D.K.J. ; Zeeuw, J.H. de - \ 2011
    Utrecht : Commissie voor de Milieueffectrapportage (rapportnummer 2548–47) - ISBN 9789042133198 - 8
    natura 2000 - regionale planning - milieueffectrapportage - gemeenten - kennemerland - natura 2000 - regional planning - environmental impact reporting - municipalities - kennemerland
    De gemeente Heemskerk wil een nieuwe structuurvisie voor haar gehele grondgebied vaststellen. Daarmee wordt de bestaande structuurvisie uit 2003 geactualiseerd. De structuurvisie is kaderstellend voor activiteiten die mogelijk significante gevolgen hebben voor het Natura 2000-gebied ‘Noordhollands Duinreservaat’
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