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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    Effects of Dutch livestock production on human health and the environment
    Post, Pim M. ; Hogerwerf, Lenny ; Bokkers, Eddie A.M. ; Baumann, Bert ; Fischer, Paul ; Rutledge-Jonker, Susanna ; Hilderink, Henk ; Hollander, Anne ; Hoogsteen, Martine J.J. ; Liebman, Alex ; Mangen, Marie-Josée J. ; Manuel, Henk Jan ; Mughini-Gras, Lapo ; Poll, Ric van; Posthuma, Leo ; Pul, Addo van; Rutgers, Michiel ; Schmitt, Heike ; Steenbergen, Jim van; Sterk, Hendrika A.M. ; Verschoor, Anja ; Vries, Wilco de; Wallace, Robert G. ; Wichink Kruit, Roy ; Lebret, Erik ; Boer, Imke J.M. de - \ 2020
    Science of the Total Environment 737 (2020). - ISSN 0048-9697
    Animal production - Climate impact - Disability-adjusted life year (DALY) - Environmental impact - Livestock farming

    Observed multiple adverse effects of livestock production have led to increasing calls for more sustainable livestock production. Quantitative analysis of adverse effects, which can guide public debate and policy development in this area, is limited and generally scattered across environmental, human health, and other science domains. The aim of this study was to bring together and, where possible, quantify and aggregate the effects of national-scale livestock production on 17 impact categories, ranging from impacts of particulate matter, emerging infectious diseases and odor annoyance to airborne nitrogen deposition on terrestrial nature areas and greenhouse gas emissions. Effects were estimated and scaled to total Dutch livestock production, with system boundaries including feed production, manure management and transport, but excluding slaughtering, retail and consumption. Effects were expressed using eight indicators that directly express Impact in the sense of the Drivers-Pressures-State-Impact-Response framework, while the remaining 14 express Pressures or States. Results show that livestock production may contribute both positively and negatively to human health with a human disease burden (expressed in disability-adjusted life years) of up to 4% for three different health effects: those related to particulate matter, zoonoses, and occupational accidents. The contribution to environmental impact ranges from 2% for consumptive water use in the Netherlands to 95% for phosphorus transfer to soils, and extends beyond Dutch borders. While some aggregation across impact categories was possible, notably for burden of disease estimates, further aggregation of disparate indicators would require normative value judgement. Despite difficulty of aggregation, the assessment shows that impacts receive a different contribution of different animal sectors. While some of our results are country-specific, the overall approach is generic and can be adapted and tuned according to specific contexts and information needs in other regions, to allow informed decision making across a broad range of impact categories.

    Excreta emissions in progeny of low and high enteric methane yield selection line sheep fed pasture of different qualities
    Jonker, A. ; MacLean, S. ; Woyimo Woju, C. ; Garcia Rendon Calzada, M. ; Yu, W. ; Molano, G. ; Hickey, S. ; Pinares-Patiño, C.S. ; McEwan, J.C. ; Janssen, P.H. ; Sandoval, E. ; Lewis, S. ; Rowe, S. - \ 2019
    Animal Feed Science and Technology 257 (2019). - ISSN 0377-8401
    Animal variation - Breeding value - Greenhouse gas - Nitrous oxide - Repeatability - Urine

    Selection of sheep with low enteric methane (CH4) emissions is a greenhouse gas (GHG) mitigation option suitable for pastoral systems. However, the effect of breeding sheep with low enteric CH4 emissions on excreta output and associated CH4 and nitrous oxide (N2O) emissions and therefore total GHG emissions are not known. The objective of the current experiments were to determine excreta output, and estimate associated GHG emissions, from progeny of low and high enteric CH4 per unit of dry matter intake (DMI) selection line sheep (CH4/DMI). The animals were fed two qualities of cut perennial ryegrass-based pasture (very mature vs. vegetative, 12 animals per CH4/DMI line) in Exp. 1 and cut pasture in two repeated seasons (autumn and winter; 15 animals per CH4/DMI line × 2 seasons) in Exp. 2. Total faecal and urine output was determined on individual animals, followed by enteric CH4 emission measurements in respiration chambers. GHG emissions from urine (N2O) and faeces (CH4 and N2O) were estimated based on New Zealand Agricultural GHG Inventory methodology. There was no interaction between CH4/DMI selection line and diet quality in Exp. 1 or seasons in Exp.2. Total daily faecal output of DM, organic matter (OM) and neutral detergent fibre (NDF; all g/d) and associated calculated faecal CH4 emissions were greater for low compared to high CH4/DMI sheep in Exp. 1 (P < 0.05), while being similar between CH4/DMI selection lines in Exp. 2. Nitrogen (N) excretion and N partitioning into urine, faeces and body retention, and calculated excreta N emissions, were mostly similar between CH4/DMI selection line sheep in both experiments. Except, faecal N output (g/d and per unit of N intake) and associated calculated direct faecal N2O-N emissions (g/d) were greater in low compared to high CH4/DMI sheep in Exp. 1 (P < 0.05). Enteric CH4 emissions were numerically 8% less (P = 0.15) in Exp.1 and 10% less (P = 0.004) in Exp. 2 and total animal level GHG emissions (CH4 and N2O) were numerically 7% less (P = 0.21) in Exp. 1 and 8% less (P = 0.006) in Exp.2 for progeny of the low compared to the high CH4/DMI line sheep. In conclusion, the magnitude of difference in enteric CH4 (expressed as CO2-equivalent) between low and high CH4/DMI selection line sheep were still present when CH4 from faeces and N2O emissions from urine and faeces were also accounted for. The animal genetic traits were expressed independent of environmental factors, i.e. pasture quality and season.

    Large-Eddy Simulations of the Steady Wintertime Antarctic Boundary Layer
    Linden, Steven J.A. van der; Edwards, John M. ; Heerwaarden, Chiel C. van; Vignon, Etienne ; Genthon, Christophe ; Petenko, Igor ; Baas, Peter ; Jonker, Harmen J.J. ; Wiel, Bas J.H. van de - \ 2019
    Boundary-Layer Meteorology 173 (2019)2. - ISSN 0006-8314 - p. 165 - 192.
    Antarctic boundary layer - Large-eddy simulations - Long-lived stable boundary layer - Subsidence heating

    Observations of two typical contrasting weakly stable and very stable boundary layers from the winter at Dome C station, Antarctica, are used as a benchmark for two centimetre-scale-resolution large-eddy simulations. By taking the Antarctic winter, the effects of the diurnal cycle are eliminated, enabling the study of the long-lived steady stable boundary layer. With its homogeneous, flat snow surface, and extreme stabilities, the location is a natural laboratory for studies on the long-lived stable boundary layer. The two simulations differ only in the imposed geostrophic wind speed, which is identified as the main deciding factor for the resulting regime. In general, a good correspondence is found between the observed and simulated profiles of mean wind speed and temperature. Discrepancies in the temperature profiles are likely due to the exclusion of radiative transfer in the current simulations. The extreme stabilities result in a considerable contrast between the stable boundary layer at the Dome C site and that found at typical mid-latitudes. The boundary-layer height is found to range from approximately 50m to just 5m in the most extreme case. Remarkably, heating of the boundary layer by subsidence may result in thermal equilibrium of the boundary layer in which the associated heating is balanced by the turbulent cooling towards the surface. Using centimetre-scale resolutions, accurate large-eddy simulations of the extreme stabilities encountered in Antarctica appear to be possible. However, future simulations should aim to include radiative transfer and sub-surface heat transport to increase the degree of realism of these types of simulations.

    The Lemon Car Game Across Cultures: Evidence of Relational Rationality
    Hofstede, G.J. ; Jonker, Catholijn ; Verwaart, T. ; Yorke-Smith, Neil - \ 2019
    Group Decision and Negotiation 28 (2019)5. - ISSN 0926-2644 - p. 849 - 877.
    Negotiation - Culture - Experimental studies - Power distance - Long-term orientation - Lemon car
    In cross-cultural business negotiation, culture is known to influence negotiation processes. As a lens to study this effect we deployed the Lemon Car Game, an online negotiation game developed for this purpose (Hofstede et al. in: Proceedings of 39th international simulation and gaming association conference (ISAGA). Technologia, Kaunas, pp 39–46, 2009a; Hofstede et al. in: David, Sichman (eds) Multi-agent-based simulation IX, international workshop, MABS 2008, revised selected papers, LNAI 5269. Springer, Berlin, pp 1–16, 2009b). In this article we report the results from the game, obtained from over 800 players from more than 70 countries. We employ several complementary analyses in a mixed-methods approach.Our findings show that to make sense of the players’ actions during negotiation, economic rationality falls short. A pan-cultural individual-level analysis of actions and stated intentions also fails to yield a coherent picture. Within countries, however, actions and intentions do cohere, as shown by an ecological country-level factor analysis, from which three factors emerge for the sellers at country level: trustworthiness, opportunism, and fairness. We conclude from these findings that, in this game, players are driven by what we call relational rationality: they are rational from the perspective of the social world in which they live, with interpersonal relationships weighing heavily. Relational rationality changes players’ perspective of economic rationality, and thus their observed behaviour in negotiation. Based on this evidence, we extrapolate that relational rationality significantly influences negotiation processes in all cultures.
    Contribution of Eat1 and other alcohol acyltransferases to ester production in Saccharomyces cerevisiae
    Kruis, A.J. ; Gallone, Brigida ; Jonker, T. ; Mars, A.E. ; Rijswijck, I.M.H. van; Wolkers-Rooijackers, J.C.M. ; Smid, E.J. ; Steensels, Jan ; Verstrepen, Kevin J. ; Kengen, S.W.M. ; Oost, J. van der; Weusthuis, R.A. - \ 2018
    Frontiers in Microbiology 9 (2018). - ISSN 1664-302X - 11 p.
    Esters are essential for the flavor and aroma of fermented products, and are mainly produced by alcohol acyl transferases (AATs). A recently discovered AAT family named Eat (Ethanol acetyltransferase) contributes to ethyl acetate synthesis in yeast. However, its effect on the synthesis of other esters is unknown. In this study, the role of the Eat family in ester synthesis was compared to that of other Saccharomyces cerevisiae AATs (Atf1p, Atf2p, Eht1p, and Eeb1p) in silico and in vivo. A genomic study in a collection of industrial S. cerevisiae strains showed that variation of the primary sequence of the AATs did not correlate with ester production. Fifteen members of the EAT family from nine yeast species were overexpressed in S. cerevisiae CEN.PK2-1D and were able to increase the production of acetate and propanoate esters. The role of Eat1p was then studied in more detail in S. cerevisiae CEN.PK2-1D by deleting EAT1 in various combinations with other known S. cerevisiae AATs. Between 6 and 11 esters were produced under three cultivation conditions. Contrary to our expectations, a strain where all known AATs were disrupted could still produce, e.g., ethyl acetate and isoamyl acetate. This study has expanded our understanding of ester synthesis in yeast but also showed that some unknown ester-producing mechanisms still exist.
    Metabolic imaging of fatty kidney in diabesity : Validation and dietary intervention
    Jonker, Jacqueline T. ; Heer, Paul De; Engelse, Marten A. ; Rossenberg, Evelien H. Van; Klessens, Celine Q.F. ; Baelde, Hans J. ; Bajema, Ingeborg M. ; Koopmans, Sietse Jan ; Coelho, Paulo G. ; Streefland, Trea C.M. ; Webb, Andrew G. ; Dekkers, Ilona A. ; Rabelink, Ton J. ; Rensen, Patrick C.N. ; Lamb, Hildo J. ; Vries, Aiko P.J. De - \ 2018
    Nephrology Dialysis Transplantation 33 (2018)2. - ISSN 0931-0509 - p. 224 - 230.
    chronic kidney disease - fatty kidney - proton magnetic - renal triglyceride content - resonance spectroscopy - type 2 diabetes mellitus
    Background Obesity and type 2 diabetes have not only been linked to fatty liver, but also to fatty kidney and chronic kidney disease. Since non-invasive tools are lacking to study fatty kidney in clinical studies, we explored agreement between proton magnetic resonance spectroscopy (1 H-MRS) and enzymatic assessment of renal triglyceride content (without and with dietary intervention). We further studied the correlation between fatty kidney and fatty liver. Methods Triglyceride content in the renal cortex was measured by 1 H-MRS on a 7-Tesla scanner in 27 pigs, among which 15 minipigs had been randomized to a 7-month control diet, cafeteria diet (CAF) or CAF with low-dose streptozocin (CAF-S) to induce insulin-independent diabetes. Renal biopsies were taken from corresponding MRS-voxel locations. Additionally, liver biopsies were taken and triglyceride content in all biopsies was measured by enzymatic assay. Results Renal triglyceride content measured by 1 H-MRS and enzymatic assay correlated positively (r = 0.86, P < 0.0001). Compared with control diet-fed minipigs, renal triglyceride content was higher in CAF-S-fed minipigs (137 ± 51 nmol/mg protein, mean ± standard error of the mean, P < 0.05), but not in CAF-fed minipigs (60 ± 10 nmol/mg protein) compared with controls (40 ± 6 nmol/mg protein). Triglyceride contents in liver and kidney biopsies were strongly correlated (r = 0.97, P < 0.001). Conclusions Non-invasive measurement of renal triglyceride content by 1 H-MRS closely predicts triglyceride content as measured enzymatically in biopsies, and fatty kidney appears to develop parallel to fatty liver. 1 H-MRS may be a valuable tool to explore the role of fatty kidney in obesity and type 2 diabetic nephropathy in humans in vivo.
    Characterization of stem cell-derived liver and intestinal organoids as a model system to study nuclear receptor biology.
    Lange, Katja ; IJssennagger, Noortje ; Bijsmans, Ingrid T. ; Mil, Saskia W.C. van; Jonker, Johan W. ; Hooiveld, Guido - \ 2017
    Wageningen University
    GSE82111 - Mus musculus - GSE82111 - Mus musculus - PRJNA324071
    Nuclear receptors (NRs) are ligand-activated transcription factors regulating a large variety of processes involved in reproduction, development, and metabolism. NRs are ideal drug targets. Immortalized cell lines recapitulate NR biology very poorly and primary cultures are laborious and require a constant need for donor material. There is a clear need for development of novel preclinical model systems that better resemble human physiology since technical uncertainty early in drug development is the cause of many preclinical drugs not reaching the clinic. Here, we studied whether organoids, mini-organs derived from the respective tissue’s stem cells, can serve as a novel (preclinical) model system to study NR biology and targeteability. We characterized mRNA expression profiles of the NR superfamily in mouse liver, ileum, and colon organoids. NR mRNA expression patterns were similar to the respective tissues, indicating their suitability for NR research. Metabolic NRs Fxrα, Lxrα, Lxrβ, Pparα, and Pparγ were responsive to ligands in an NR-dependent fashion, as demonstrated by regulation of expression and binding to endogenous target genes. Transcriptome analyses of wildtype colonic organoids stimulated with Rosiglitazone showed that lipid metabolism was the highest significant changed function, greatly mimicking the known function of PPARs and Rosiglitazone in vivo. In conclusion, our results demonstrate that organoids constitutes a versatile and promising in vitro system to study NR biology and targeteability.
    Characterization of stem cell-derived liver and intestinal organoids as a model system to study nuclear receptor biology
    Bijsmans, Ingrid T.G.W. ; Milona, Alexandra ; Ijssennagger, Noortje ; Willemsen, Ellen C.L. ; Ramos Pittol, José M. ; Jonker, Johan W. ; Lange, Katja ; Hooiveld, Guido J.E.J. ; Mil, Saskia W.C. van - \ 2017
    Biochimica et Biophysica Acta. Molecular Basis of Disease 1863 (2017)3. - ISSN 0925-4439 - p. 687 - 700.
    Fxr - Ligands - Lxr - Nuclear receptors - Organoids - Ppar
    Nuclear receptors (NRs) are ligand-activated transcription factors regulating a large variety of processes involved in reproduction, development, and metabolism. NRs are ideal drug targets because they are activated by lipophilic ligands that easily pass cell membranes. Immortalized cell lines recapitulate NR biology poorly and generating primary cultures is laborious and requires a constant need for donor material. There is a clear need for development of novel preclinical model systems that better resemble human physiology. Uncertainty due to technical limitations early in drug development is often the cause of preclinical drugs not reaching the clinic. Here, we studied whether organoids, mini-organs derived from the respective mouse tissue's stem cells, can serve as a novel model system to study NR biology and targetability. We characterized mRNA expression profiles of the NR superfamily in mouse liver, ileum, and colon organoids. Tissue-specific expression patterns were largely maintained in the organoids, indicating their suitability for NR research. Metabolic NRs Fxrα, Lxrα, Lxrβ, Pparα, and Pparγ induced expression of and binding to endogenous target genes. Transcriptome analyses of wildtype colon organoids stimulated with Rosiglitazone showed that lipid metabolism was the highest significant changed function, greatly mimicking the PPARs and Rosiglitazone function in vivo. Finally, using organoids we identify Trpm6, Slc26a3, Ang1, and Rnase4, as novel Fxr target genes. Our results demonstrate that organoids represent a framework to study NR biology that can be further expanded to human organoids to improve preclinical testing of novel drugs that target this pharmacologically important class of ligand activated transcription factors.
    Mixture toxicity : Linking approaches from ecological and human toxicology
    Gestel, Cornelis A.M. van; Jonker, Martijs J. ; Kammenga, Jan E. ; Laskowski, Ryszard ; Svendsen, Claus - \ 2016
    CRC Press - ISBN 9781439830086 - 269 p.

    In the last decade and a half, great progress has been made in the development of concepts and models for mixture toxicity, both in human and environmental toxicology. However, due to their different protection goals, developments have often progressed in parallel but with little integration. Arguably the first book to clearly link ecotoxicology and classic human toxicology, Mixture Toxicity: Linking Approaches from Ecological and Human Toxicology incorporates extensive reviews of exposure to toxicants, toxicokinetics and toxicodynamics, toxicity of mixtures, and risk assessment. The book examines developments in both fields, compares and contrasts their current state of the art, and identifies where one field can learn from the other. Each chapter provides an essential overview of the state of the art in both human and ecotoxicological mixture risk assessment, focusing on the work published in the last fifteen years. The coverage progresses from exposure to risk assessment, at each step identifying the special complications typically raised by mixtures. Based on in-depth discussions among specialists representing different disciplines and approaches, the chapters each address: Exposure - how to quantify the amounts of chemicals that may enter the living organism. Kinetics, dynamics, and metabolism - how the chemicals enter an organism, travel within the organism, how they are metabolized and reach the target site, and explain development of toxicity with time. Toxicity - what are the chemicals' detrimental effects on the organism. Test design and complex mixture characterization - how chemicals interact, how to measure effects of mixtures, and how to identify responsible chemicals. Risk assessment - how to assess for risks in humans and the environment. An unusual combination of different points of view on exposure to and risk assessment of chemical mixtures, this book summarizes current knowledge on combined effects of toxicant mixtures, information that is generally only available in a very fragmented form as individual journal papers. It identifies possible crosslinks and includes recommendations for mutual developments that can improve the state of knowledge on mixture toxicity and ultimately lead to better and more integrated risk assessment.

    Erratum: Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range
    Henderson, Gemma ; Cox, Faith ; Ganesh, Siva ; Jonker, Arjan ; Young, Wayne ; Abecia, Leticia ; Angarita, Erika ; Aravena, Paula ; Nora Arenas, Graciela ; Ariza, Claudia ; Attwood, Graeme T. ; Mauricio Avila, Jose ; Avila-stagno, Jorge ; Bannink, André ; Barahona, Rolando ; Batistotti, Mariano ; Bertelsen, Mads F. ; Brown-Kav, Aya ; Carvajal, Andres M. ; Cersosimo, Laura ; Vieira Chaves, Alexandre ; Church, John ; Clipson, Nicholas ; Cobos-peralta, Mario A. ; Cookson, Adrian L. ; Cravero, Silvio ; Cristobal Carballo, Omar ; Crosley, Katie ; Cruz, Gustavo ; Cerón Cucchi, María ; Barra, Rodrigo de la; Menezes, Alexandre B. de; Detmann, Edenio ; Dieho, Kasper ; Dijkstra, Jan ; Reis, William L.S. Dos; Dugan, Mike E.R. ; Hadi Ebrahimi, Seyed ; Eythórsdóttir, Emma ; Nde Fon, Fabian ; Fraga, Martín ; Franco, Francisco ; Friedeman, Chris ; Fukuma, Naoki ; Gagić, Dragana ; Gangnat, Isabelle ; Javier Grilli, Diego ; Guan, Le Luo ; Heidarian Miri, Vahideh ; Hernandez-Sanabria, Emma ; Gomez, Alma Ximena Ibarra ; Isah, Olubukola A. ; Ishaq, Suzanne ; Jami, Elie ; Jelincic, Juan ; Kantanen, Juha ; Kelly, William J. ; Kim, Seon-Ho ; Klieve, Athol ; Kobayashi, Yasuo ; Koike, Satoshi ; Kopecny, Jan ; Nygaard Kristensen, Torsten ; Julie Krizsan, Sophie ; Lachance, Hannah ; Lachman, Medora ; Lamberson, William R. ; Lambie, Suzanne ; Lassen, Jan ; Leahy, Sinead C. ; Lee, Sang-Suk ; Leiber, Florian ; Lewis, Eva ; Lin, Bo ; Lira, Raúl ; Lund, Peter ; Macipe, Edgar ; Mamuad, Lovelia L. ; Cuquetto Mantovani, Hilário ; Marcoppido, Gisela Ariana ; Márquez, Cristian ; Martin, Cécile ; Martinez, Gonzalo ; Eugenia Martinez, Maria ; Lucía Mayorga, Olga ; McAllister, Tim A. ; McSweeney, Chris ; Mestre, Lorena ; Minnee, Elena ; Mitsumori, Makoto ; Mizrahi, Itzhak ; Molina, Isabel ; Muenger, Andreas ; Muñoz, Camila ; Murovec, Bostjan ; Newbold, John ; Nsereko, Victor ; O’donovan, Michael ; Okunade, Sunday ; O’neill, Brendan ; Ospina, Sonia ; Ouwerkerk, Diane ; Parra, Diana ; Pereira, Luiz Gustavo Ribeiro ; Pinares-patiño, Cesar ; Pope, Phil B. ; Poulsen, Morten ; Rodehutscord, Markus ; Rodriguez, Tatiana ; Saito, Kunihiko ; Sales, Francisco ; Sauer, Catherine ; Shingfield, Kevin ; Shoji, Noriaki ; Simunek, Jiri ; Stojanović-Radić, Zorica ; Stres, Blaz ; Sun, Xuezhao ; Swartz, Jeffery ; Liang Tan, Zhi ; Tapio, Ilma ; Taxis, Tasia M. ; Tomkins, Nigel ; Ungerfeld, Emilio ; Valizadeh, Reza ; Adrichem, Peter van; Hamme, Jonathan van; Hoven, Woulter van; Waghorn, Garry ; Wallace, John R. ; Wang, Min ; Waters, Sinéad M. ; Keogh, Kate ; Witzig, Maren ; Wright, Andre-Denis G. ; Yamano, Hidehisa ; Yan, Tianhai ; Yáñez-ruiz, David R. ; Yeoman, Carl J. ; Zambrano, Ricardo ; Zeitz, Johanna ; Zhou, Mi ; Wei Zhou, Hua ; Xia Zou, Cai ; Zunino, Pablo ; Janssen, Peter H. - \ 2016
    Scientific Reports 6 (2016). - ISSN 2045-2322 - 2 p.
    How does temperature affect the acute toxicity of oil at sea?
    Heuvel-Greve, M.J. van den; Puts, Isolde ; Frederiks, Ben ; Rijk, Arnoud ; Foekema, E.M. ; Sneekes, A.C. ; Jonker, Chiel ; Murk, Albertinka J. - \ 2016
    - 1 p.
    Een dubbele kijk op co-creatie
    Bakker, H.C.M. de; Dagevos, H. - \ 2016
    Bestuurskunde 25 (2016)1. - ISSN 0927-3387 - p. 90 - 99.
    This essay review discusses three publications on co-creation: ‘We, the government’ by Davied van Berlo (2012), ‘Co-creation of innovation’ by Corry Ehlen (2015), and ‘New Business Models’ by Jan Jonker et al. (2014). The theme of this essay is the specific character of co-creation compared to other buzzwords (e.g. participation, co-production, social responsibility) that can be heard in the search for a new balance between the state and civil society. We suggest that the distinctive character of co-creation lies in the active engagement of parties who work together to co-create. Co-creation means raising the bar of collaboration and dialogue. Openness, trust, equality and reciprocity are emphasised as essential elements in the process. It is literally about collectively creating multiple values in which there should be plenty of room for creativity and sharing ideas. Following on the publications of Ehlen and Jonker a dual vision on co-creation arises. In general terms, the potential of co-creation depends on the know-how, commitment and values of the actors involved (microscopic perspective) and on the social capital in the wider environment that they can draw upon to bolster the co-creation process (macroscopic perspective).
    Multi-platform metabolomics analyses of a broad collection of fragrant and non-fragrant rice varieties reveals the high complexity of grain quality characteristics
    Mumm, R. ; Hageman, J.A. ; Calingacion, M.N. ; Vos, C.H. de; Jonker, H.H. ; Erban, A. ; Kopka, J. ; Hansen, T.H. ; Laursen, K.H. ; Schjoerring, J.K. ; Ward, J.L. ; Beale, M.H. ; Jongee, S. ; Rauf, A. ; Habibi, F. ; Indrasari, S.D. ; Sakhan, S. ; Ramli, A. ; Romero, M. ; Reinke, R. ; Ohtsubo, K. ; Boualaphanh, C. ; Fitzgerald, M.A. ; Hall, R.D. - \ 2016
    Metabolomics 12 (2016)2. - ISSN 1573-3882 - 19 p.
    The quality of rice in terms not only of its nutritional value but also in terms of its aroma and flavour is becoming increasingly important in modern rice breeding
    where global targets are focused on both yield stability and grain quality. In the present paper we have exploited advanced, multi-platform metabolomics approaches to determine the biochemical differences in 31 rice varieties from a diverse range of genetic backgrounds and origin. All were grown under the specific local conditions for which they have been bred and all aspects of varietal identification and sample purity have been guaranteed by local experts from each country. Metabolomics analyses using 6 platforms have revealed the extent of biochemical differences (and similarities) between the chosen rice genotypes.
    Comparison of fragrant rice varieties showed a difference in the metabolic profiles of jasmine and basmati varieties. However with no consistent separation of the germplasm class. Storage of grains had a significant effect on the
    metabolome of both basmati and jasmine rice varieties but changes were different for the two rice types. This shows how metabolic changes may help prove a causal relationship with developing good quality in basmati rice or
    incurring quality loss in jasmine rice in aged grains. Such metabolomics approaches are leading to hypotheses on the potential links between grain quality attributes, biochemical composition and genotype in the context of breeding for improvement. With this knowledge we shall establish a
    stronger, evidence-based foundation upon which to build targeted strategies to support breeders in their quest for improved rice varieties.
    Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range
    Henderson, G. ; Cox, F. ; Ganesh, S. ; Jonker, A. ; Young, W. ; Janssen, P.H. ; Bannink, A. ; Dieho, K. ; Dijkstra, J. - \ 2015
    Scientific Reports 5 (2015). - ISSN 2045-2322 - 13 p.
    Ruminant livestock are important sources of human food and global greenhouse gas emissions. Feed degradation and methane formation by ruminants rely on metabolic interactions between rumen microbes and affect ruminant productivity. Rumen and camelid foregut microbial community composition was determined in 742 samples from 32 animal species and 35 countries, to estimate if this was influenced by diet, host species, or geography. Similar bacteria and archaea dominated in nearly all samples, while protozoal communities were more variable. The dominant bacteria are poorly characterised, but the methanogenic archaea are better known and highly conserved across the world. This universality and limited diversity could make it possible to mitigate methane emissions by developing strategies that target the few dominant methanogens. Differences in microbial community compositions were predominantly attributable to diet, with the host being less influential. There were few strong co-occurrence patterns between microbes, suggesting that major metabolic interactions are non-selective rather than specific.
    Collapse of turbulence in stably stratified channel flow: a transient phenomenon
    Donda, J.M.M. ; Hooijdonk, I.G.S. ; Moene, A.F. ; Jonker, J.J. ; Heijst, G.J.F. van; Clercx, H.J.H. ; Wiel, B.J.H. van de - \ 2015
    Quarterly Journal of the Royal Meteorological Society 141 (2015)691. - ISSN 0035-9009 - p. 2137 - 2147.
    The collapse of turbulence in a pressure-driven, cooled channel flow is studied by using 3D direct numerical simulations (DNS) in combination with theoretical analysis using a local similarity model. Previous studies with DNS reported a definite collapse of turbulence in cases when the normalized surface cooling h/L (with h the channel depth and L the Obukhov length) exceeded a value of 0.5. A recent study by the present authors succeeded in explaining this collapse using the so-called maximum sustainable heat flux (MSHF) theory. This states that collapse may occur when the ambient momentum of the flow is too weak to transport enough heat downward to compensate for the surface cooling. The MSHF theory predicts that, in pressure-driven flows, acceleration of the fluid after collapse will eventually cause a regeneration of turbulence, in contrast with the aforementioned DNS results. It also predicts that the flow should be able to survive ‘supercritical’ cooling rates, in cases when sufficient momentum is applied to the initial state. Here, both predictions are confirmed using DNS simulations. It is also shown that in DNS a recovery of turbulence will occur naturally, provided that perturbations of finite amplitude are imposed on the laminarized state and provided that sufficient time for flow acceleration is allowed. As such, we conclude that the collapse of turbulence in this configuration is a temporary, transient phenomenon for which a universal cooling rate does not exist. Finally, in the present work a one-to-one comparison between a parametrized, local similarity model and the turbulence-resolving model (DNS) is made. Although local similarity originates from observations that represent much larger Reynolds numbers than those covered by our DNS simulations, both methods appear to predict very similar mean velocity (and temperature) profiles. This suggests that in-depth analysis with DNS can be an attractive complementary tool with which to study atmospheric physics, in addition to tools that are able to represent high Reynolds number flows like large-eddy simulations.
    Comprehensive metabolomics to evaluate the impact of industrial processing on the phytochemical composition of vegetable purees
    Lopez-Sanchez, P. ; Vos, R.C.H. de; Jonker, H.H. ; Mumm, R. ; Hall, R.D. ; Bialek, L. ; Leenman, R. ; Strassburg, K. ; Vreeken, R. ; Hankemeier, T. ; Schumm, S. ; Duynhoven, J.P.M. van - \ 2015
    Food Chemistry 168 (2015). - ISSN 0308-8146 - p. 348 - 355.
    mass-spectrometry - plant metabolomics - thermal treatments - vitamin-c - broccoli - tomato - fruit - antioxidant - cancer - l.
    The effects of conventional industrial processing steps on global phytochemical composition of broccoli, tomato and carrot purees were investigated by using a range of complementary targeted and untargeted metabolomics approaches including LC–PDA for vitamins, 1H NMR for polar metabolites, accurate mass LC–QTOF MS for semi-polar metabolites, LC–MRM for oxylipins, and headspace GC–MS for volatile compounds. An initial exploratory experiment indicated that the order of blending and thermal treatments had the highest impact on the phytochemicals in the purees. This blending-heating order effect was investigated in more depth by performing alternate blending-heating sequences in triplicate on the same batches of broccoli, tomato and carrot. For each vegetable and particularly in broccoli, a large proportion of the metabolites detected in the purees was significantly influenced by the blending-heating order, amongst which were potential health-related phytochemicals and flavour compounds like vitamins C and E, carotenoids, flavonoids, glucosinolates and oxylipins. Our metabolomics data indicates that during processing the activity of a series of endogenous plant enzymes, such as lipoxygenases, peroxidases and glycosidases, including myrosinase in broccoli, is key to the final metabolite composition and related quality of the purees.
    Staphylococcus aureus ST398 gene expression profiling during ex vivo colonization of porcine nasal epithelium
    Tulinski, P. ; Duim, B. ; Wittink, F.R. ; Jonker, M.J. ; Breit, T.M. ; Putten, J.P. van; Wagenaar, J.A. ; Fluit, A.C. - \ 2014
    BMC Genomics 15 (2014). - ISSN 1471-2164
    clumping factor-b - methicillin-resistant - carriage - model - adherence - humans - proteinases - determinant - infections - cells
    Background: Staphylococcus aureus is a common human and animal opportunistic pathogen. In humans nasal carriage of S. aureus is a risk factor for various infections. Methicillin-resistant S. aureus ST398 is highly prevalent in pigs in Europe and North America. The mechanism of successful pig colonization by MRSA ST398 is poorly understood. Previously, we developed a nasal colonization model of porcine nasal mucosa explants to identify molecular traits involved in nasal MRSA colonization of pigs. Results: We report the analysis of changes in the transcription of MRSA ST398 strain S0462 during colonization on the explant epithelium. Major regulated genes were encoding metabolic processes and regulation of these genes may represent metabolic adaptation to nasal mucosa explants. Colonization was not accompanied by significant changes in transcripts of the main virulence associated genes or known human colonization factors. Here, we documented regulation of two genes which have potential influence on S. aureus colonization; cysteine extracellular proteinase (scpA) and von Willebrand factor-binding protein (vWbp, encoded on SaPIbov5). Colonization with isogenic-deletion strains (Delta vwbp and Delta scpA) did not alter the ex vivo nasal S. aureus colonization compared to wild type. Conclusions: Our results suggest that nasal colonization with MRSA ST398 is a complex event that is accompanied with changes in bacterial gene expression regulation and metabolic adaptation.
    Production of digital terrain models for the Dutch Caribbean : implication for Saba & St. Eustatius
    Mücher, C.A. ; Jonker, D. ; Stuiver, H.J. ; Kramer, H. ; Meesters, H.W.G. - \ 2014
    Wageningen UR Alterra (Alterra-rapport 2569) - 39
    luchtfotografie - interpolatie - digitaal terreinmodel - inventarisaties - eilanden - caribisch gebied - aerial photography - interpolation - digital elevation model - inventories - islands - caribbean
    De BES eilanden behoren sinds oktober 2010 tot de Nederlandse gemeenten. Het opstellen van natuurbeleidsplannen behoren tot de nieuwe taken. Gedetailleerde hoogtekaarten zijn daarbij van belang. Met name voor Saba en St. Eustatius, met een zeer gevarieerd en complex reliëf, zijn accurate hoogtekaarten van groot belang.
    Metabolomic variation of brassica rapa var. rapa (var. raapstelen) and raphanus sativus l. at different developmental stages
    Jahangir, M. ; Abdel-Farid, I.B. ; Vos, C.H.R. de; Jonker, H.H. ; Choi, Y.H. ; Verpoorte, R. - \ 2014
    Pakistan Journal of Botany 46 (2014)4. - ISSN 0556-3321 - p. 1445 - 1452.
    antioxidant activity - plant metabolomics - growth - vegetables - phenolics - genomics - radish
    Brassica rapa (var. raapstelen) and Raphanus sativus (red radish) are being used as food and fodder while also known as model in recent plant research due to the diversity of metabolites as well as genetic resemblance to Arabidopsis. This study explains the change in metabolites (amino acids, organic acids, chlorophyll, carotenoids, tocopherols, ascorbic acid, sucrose, phenylpropanoids and glucosinolates) during plant development. In present study the metabolomic variation in relation to plant growth has been evaluated, for Brassica rapa (var. raapstelen) and red radish (Raphanus sativus) at three different developmental stages. A non-targeted and targeted metabolomic approach by NMR and HPLC in combination with Principal component analysis (PCA) of the data was used to identify phytochemicals being influenced by plant growth. The results lead to the better understanding of metabolic changes during plant development and show the importance of plant age with respect to the metabolomic profile of vegetables.
    The minimum wind speed for sustainable turbulence in the nocturnal boundary layer
    Wiel, B.J.H. van de; Donda, J.M.M. ; Hooijdonk, I.G.S. ; Baas, P. ; Moene, A.F. ; Jonker, H.J.J. ; Heijst, G.J.F. van; Clercx, H.J.H. ; Sun, J. - \ 2014
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