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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    Emissies naar lucht uit de landbouw,1990-2018 : Berekeningen met het model NEMA
    Bruggen, C. van; Bannink, A. ; Groenestein, C.M. ; Huijsmans, J.F.M. ; Lagerwerf, L.A. ; Luesink, H.H. ; Velthof, G.L. ; Vonk, J. - \ 2020
    Wageningen : Wettelijke Onderzoekstaken Natuur & Milieu (WOt-technical report 178) - 224
    In the Netherlands, agricultural activities are a major source of gaseous emissions of ammonia (NH3), nitrogen oxide (NO), nitrous oxide (N2O), methane (CH4), non-methane volatile organic compounds (NMVOC), CO2 from lime fertilisers and particulate matter (PM10 and PM2.5). The emissions were calculated using the National Emission Model for Agriculture (NEMA). In 2018, NH3 emissions from livestock manure, fertiliser and other sources on farms and hobby farms, from private use and from manure application in terrestrial ecosystems amounted to 118.0 million kg NH3, 2.2 million kg less than in 2017. This decrease was due mainly to the reduction in the size of the dairy herd. Emissions of N2O in 2018 were 20.5 million kg, 0.5 million kg less than in 2017. NO emissions in 2018 amounted to 22.3 million kg, 0.6 million kg less than in 2017. CH4 emissions decreased from 503 to 484 million kg due to the smaller dairy herd. Emissions of NMVOC amounted to 93 million kg in 2018, down from 98 million kg in 2017. Emissions of particulate matter PM10 decreased in 2018 from 6.2 to 5.9 million kg. PM2.5 emissions remained constant at 0.6 million kg. Based on new data for several factors which are described in this report, emission figures have been updated for a number of years in the time series since 1990. NH3 emissions from livestock manure have fallen by two thirds since 1990, mainly as a result of lower nitrogen excretion rates of livestock and the introduction of low-emission manure application. Emissions of N2O and NO decreased over this period by 40% and 33% respectively, less markedly than the NH3 reduction because of higher emissions from manure injection (compared with surface spreading manure) and a shift from excretion on pasture to excretion in animal houses. CH4 emissions decreased by 18% between 1990 and 2018 due to a decrease in livestock numbers and increased feed use efficiency of dairy cattle. PM10 emissions increased by 19% in the same period due to laying poultry farms switching from housing systems with liquid manure to systems with solid manure.
    Lactate formation and subsequent chain elongation in repeated-batch food waste fermentation
    Contreras Davila, Carlos ; Carrión, Víctor J. ; Vonk, Vincent R. ; Buisman, Cees ; Strik, David - \ 2020
    Wageningen University & Research
    PRJEB33791 - ERP116611 - metagenome - lactate - n-caproate - food waste - fermentation
    The production of biochemicals, materials and biofuels from renewables through biorefinery processes is important to reduce the anthropogenic impact on the environment. Chain elongation processes based on open microbiomes have been successfully developed to produce medium-chain fatty acids (versatile platform products) from organic waste streams. Yet, the sustainability of chain elongation can still be improved by reducing the use of electron donors and reducing chemicals use. This work aimed to in situ produce the electron donor lactate coupled to subsequent chain elongation for n-caproate production with decreased chemicals use for pH control. Food waste was used as substrate in repeated-batch fermentation experiments.
    Greenhouse gas emissions in the Netherlands 1990-2018 : National Inventory Report 2020
    Ruyssenaars, P.G. ; Coenen, P.W.H.G. ; Rienstra, J.D. ; Zijlema, P.J. ; Arets, E.J.M.M. ; Baas, K. ; Dröge, R. ; Geilenkirchen, G. ; Hoen, M. 't; Honig, E. ; Huet, B. van; Huis, E.P. van; Koch, W.W.R. ; Lagerwerf, L.L. ; Molder, R.A. te; Montfoort, J.A. ; Vonk, J. ; Zanten, M.C. van - \ 2020
    Bilthoen : National Institute for Public Health and the Environment (RIVM) - 528 p.
    Total greenhouse gas (GHG) emissions in the Netherlands in 2018 decreased by approximately 2.7 percent, in comparison with 2017 emissions. This decrease was mainly the result of decreased coal combustion for energy and heat production.In 2018, total GHG emissions (including indirect CO2 emissions and excluding emissions from Land use, land use change and forestry (LULUCF)) in the Netherlands amounted to 188.2 Tg CO2 eq. This is approximately 15.1 percent below the emissions in the base year 1990 (221.7 Tg CO2 eq.).CO2 emissions in 2018 were 1.6 percent below the level in the base year. The total of the emissions of methane, nitrous oxide and fluorinated gases (CH4, N2O and F-gases) was reduced by more than 50% over this period.This report documents the Netherlands’ annual submission for 2020 of its GHG emissions inventory in accordance with the 2006 IPCC Guidelines for National Greenhouse Gas Inventories (IPCC, 2006) prescribed by the United Nations Framework Convention on Climate Change (UNFCCC), the Kyoto Protocol (KP) and the European Union’s Greenhouse Gas Monitoring Mechanism.This report includes explanations of observed trends in emissions, an assessment of the sources with the highest contribution to total national emissions (key sources) and a description of the uncertainty in the emissions es timates. Estimation methods, data sources and emission factors (EFs) are described for each source category, and there is also a description of the quality assurance system and the verification activities performed on the data. The report also describes changes in methodologies since the previous submission (NIR 2019), the results of recalculations and planned improvements.
    Epigenome-wide meta-analysis of blood DNA methylation in newborns and children identifies numerous loci related to gestational age
    Merid, Simon Kebede ; Novoloaca, Alexei ; Sharp, Gemma C. ; Küpers, Leanne K. ; Kho, Alvin T. ; Roy, Ritu ; Gao, Lu ; Annesi-Maesano, Isabella ; Jain, Pooja ; Plusquin, Michelle ; Kogevinas, Manolis ; Allard, Catherine ; Vehmeijer, Florianne O. ; Kazmi, Nabila ; Salas, Lucas A. ; Rezwan, Faisal I. ; Zhang, Hongmei ; Sebert, Sylvain ; Czamara, Darina ; Rifas-Shiman, Sheryl L. ; Melton, Phillip E. ; Lawlor, Debbie A. ; Pershagen, Göran ; Breton, Carrie V. ; Huen, Karen ; Baiz, Nour ; Gagliardi, Luigi ; Nawrot, Tim S. ; Corpeleijn, Eva ; Perron, Patrice ; Duijts, Liesbeth ; Nohr, Ellen Aagaard ; Bustamante, Mariona ; Ewart, Susan L. ; Karmaus, Wilfried ; Zhao, Shanshan ; Page, Christian M. ; Herceg, Zdenko ; Jarvelin, Marjo Riitta ; Lahti, Jari ; Baccarelli, Andrea A. ; Anderson, Denise ; Kachroo, Priyadarshini ; Relton, Caroline L. ; Bergström, Anna ; Eskenazi, Brenda ; Soomro, Munawar Hussain ; Vineis, Paolo ; Snieder, Harold ; Bouchard, Luigi ; Jaddoe, Vincent W. ; Sørensen, Thorkild I.A. ; Vrijheid, Martine ; Arshad, S.H. ; Holloway, John W. ; Håberg, Siri E. ; Magnus, Per ; Dwyer, Terence ; Binder, Elisabeth B. ; Demeo, Dawn L. ; Vonk, Judith M. ; Newnham, John ; Tantisira, Kelan G. ; Kull, Inger ; Wiemels, Joseph L. ; Heude, Barbara ; Sunyer, Jordi ; Nystad, Wenche ; Munthe-Kaas, Monica C. ; Raïkkönen, Katri ; Oken, Emily ; Huang, Rae Chi ; Weiss, Scott T. ; Antó, Josep Maria ; Bousquet, Jean ; Kumar, Ashish ; Söderhäll, Cilla ; Almqvist, Catarina ; Cardenas, Andres ; Gruzieva, Olena ; Xu, Cheng Jian ; Reese, Sarah E. ; Kere, Juha ; Brodin, Petter ; Solomon, Olivia ; Wielscher, Matthias ; Holland, Nina ; Ghantous, Akram ; Hivert, Marie France ; Felix, Janine F. ; Koppelman, Gerard H. ; London, Stephanie J. ; Melén, Erik - \ 2020
    Genome Medicine 12 (2020)1. - ISSN 1756-994X
    Development - Epigenetics - Gestational age - Preterm birth - Transcriptomics

    Background: Preterm birth and shorter duration of pregnancy are associated with increased morbidity in neonatal and later life. As the epigenome is known to have an important role during fetal development, we investigated associations between gestational age and blood DNA methylation in children. Methods: We performed meta-analysis of Illumina's HumanMethylation450-array associations between gestational age and cord blood DNA methylation in 3648 newborns from 17 cohorts without common pregnancy complications, induced delivery or caesarean section. We also explored associations of gestational age with DNA methylation measured at 4-18 years in additional pediatric cohorts. Follow-up analyses of DNA methylation and gene expression correlations were performed in cord blood. DNA methylation profiles were also explored in tissues relevant for gestational age health effects: Fetal brain and lung. Results: We identified 8899 CpGs in cord blood that were associated with gestational age (range 27-42 weeks), at Bonferroni significance, P < 1.06 × 10-7, of which 3343 were novel. These were annotated to 4966 genes. After restricting findings to at least three significant adjacent CpGs, we identified 1276 CpGs annotated to 325 genes. Results were generally consistent when analyses were restricted to term births. Cord blood findings tended not to persist into childhood and adolescence. Pathway analyses identified enrichment for biological processes critical to embryonic development. Follow-up of identified genes showed correlations between gestational age and DNA methylation levels in fetal brain and lung tissue, as well as correlation with expression levels. Conclusions: We identified numerous CpGs differentially methylated in relation to gestational age at birth that appear to reflect fetal developmental processes across tissues. These findings may contribute to understanding mechanisms linking gestational age to health effects.

    BENEFIT Partnership - 2019 annual report : Bilateral Ethiopian-Netherlands effort for food, income and trade partnership
    Alemu, Dawit ; Koomen, Irene ; Schaap, Mirjam ; Ayana, Amsalu ; Borman, Gareth ; Elias, Eyasu ; Smaling, Eric ; Getaw, Helen ; Becx, Gertjan ; Sopov, Monika ; Terefe, Geremew ; Schrader, Ted ; Tafere, Tewodros ; Vonk, Remko - \ 2020
    Wageningen : Wageningen Centre for Development Innovation (Report / Wageningen Centre for Development Innovation WCDI-20-094) - 211
    Referentieraming van emissies naar de lucht uit landbouw en landgebruik tot 2030 : Achtergronddocument bij de Klimaat-en Energieverkenning 2019, met ramingen van emissies van methaan, lachgas, ammoniak, stikstofoxide, fijnstof en NMVOS uit de landbouw en kooldioxide en lachgas door landgebruik
    Velthof, G.L. ; Bruggen, C. van; Arets, E. ; Groenestein, C.M. ; Helming, J.F.M. ; Luesink, H.H. ; Schelhaas, M.J. ; Huijsmans, J.F.M. ; Lagerwerf, L.A. ; Vonk, J. - \ 2019
    Wageningen : Wageningen Environmental Research (Wageningen Environmental Research rapport 2970) - ISBN 9789463952156 - 113
    In het kader van de Klimaat- en Energieverkenning (KEV) zijn ramingen gemaakt voor 2020, 2025 en 2030 van i) niet aan energie gerelateerde emissies uit de landbouw naar de lucht, in de vorm van methaan (CH4), lachgas (N2O), ammoniak (NH3), stikstofoxide (NOx), fijnstof (PM10 en PM2,5) en NMVOS (niet-methaan vluchtige organische stoffen) en ii) emissies van kooldioxide (CO2) en N2O door landgebruik, landgebruiksveranderingen en bosbouw (LULUCF). Het jaar 2017 is het basisjaar in de ramingen. De ramingen gaan uit van vastgesteld beleid en van naleving van onderliggende wet- en regelgeving. De peildatum voor het vastgestelde beleid in de raming is 1 mei 2019. De onzekerheden zijn in beeld gebracht voor de factoren met een groot effect op de emissies in 2030. In de raming is de CH4-emissie in 2030 met ruim 32 miljoen kg CH4 afgenomen ten opzichte van 2017 (6,4%). Deze afname wordt veroorzaakt door een afname van het aantal melkkoeien en jongvee. De geraamde N2O-emissie in 2030 is bijna 1 miljoen kg lager (4,5%) dan die in 2017. De grootste afname in N2O- emissie is zichtbaar bij bemesting met kunstmest en bij beweiding. De ammoniakemissie uit de landbouw neemt af van 114 miljoen kg in 2017 naar 109 miljoen kg in 2020 en 101 miljoen kg in 2030. Deze daling hangt samen met meer emissiearme stallen en minder melkkoeien, jongvee en varkens. De NOx-emissie (uitgedrukt in NO) is in 2030 0,7 miljoen kg lager dan in 2017. De emissie van fijnstof (PM10) neemt af van 6,2 miljoen kg in 2017 naar 5,1 miljoen kg in 2030 en die van de fijnere fractie van fijnstof (PM2,5) neemt af van 0,60 miljoen kg in 2017 naar 0,52 miljoen kg in 2030. De totale geraamde emissies uit de LULUCF-sector liggen in de periode 2020-2030 tussen de 5339 miljoen kg en 5707 miljoen kg CO2-equivalenten. Toepassing van de regels uit de LULUCF-verordening van de EU, om de prestaties van lidstaten te beoordelen op de emissies en verwijderingen van CO2 voor de tijdreeks 2020-2030, resulteert in een nettotekort van 316 miljoen kg CO2-equivalenten in 2025 en 258 miljoen kg CO2-equivalenten in 2030. Als prestaties voor de vijfjarige periodes 2021-2025 en 2026-2030 in het kader van LULUCF afgerekend worden, komt dat op een nettotekort van 1500 miljoen kg CO2-equivalent in de eerste periode en van 1200 miljoen kg CO2 equivalent in de tweede periode.
    Whole Grain Wheat Consumption Affects Postprandial Inflammatory Response in a Randomized Controlled Trial in Overweight and Obese Adults with Mild Hypercholesterolemia in the Graandioos Study
    Hoevenaars, Femke P.M. ; Esser, Diederik ; Schutte, Sophie ; Priebe, Marion G. ; Vonk, Roel J. ; Brink, Willem J. van den; Kamp, Jan Willem van der; Stroeve, Johanna H.M. ; Afman, Lydia A. ; Wopereis, Suzan - \ 2019
    The Journal of Nutrition 149 (2019)12. - ISSN 0022-3166 - p. 2133 - 2144.
    (compromised) healthy subjects - challenge test - composite biomarkers - inflammation - liver - metabolic health - phenotypic flexibility - resilience - whole grain wheat

    BACKGROUND: Whole grain wheat (WGW) consumption is associated with health benefits in observational studies. However, WGW randomized controlled trial (RCT) studies show mixed effects. OBJECTIVES: The health impact of WGW consumption was investigated by quantification of the body's resilience, which was defined as the "ability to adapt to a standardized challenge." METHODS: A double-blind RCT was performed with overweight and obese (BMI: 25-35 kg/m2) men (n = 19) and postmenopausal women (n = 31) aged 45-70 y, with mildly elevated plasma total cholesterol (>5 mmol/L), who were randomly assigned to either 12-wk WGW (98 g/d) or refined wheat (RW). Before and after the intervention a standardized mixed-meal challenge was performed. Plasma samples were taken after overnight fasting and postprandially (30, 60, 120, and 240 min). Thirty-one biomarkers were quantified focusing on metabolism, liver, cardiovascular health, and inflammation. Linear mixed-models evaluated fasting compared with postprandial intervention effects. Health space models were used to evaluate intervention effects as composite markers representing resilience of inflammation, liver, and metabolism. RESULTS: Postprandial biomarker changes related to liver showed decreased alanine aminotransferase by WGW (P = 0.03) and increased β-hydroxybutyrate (P = 0.001) response in RW. Postprandial changes related to inflammation showed increased C-reactive protein (P = 0.001), IL-6 (P = 0.02), IL-8 (P = 0.007), and decreased IL-1B (P = 0.0002) in RW and decreased C-reactive protein (P < 0.0001), serum amyloid A (P < 0.0001), IL-8 (P = 0.02), and IL-10 (P < 0.0001) in WGW. Health space visualization demonstrated diminished inflammatory (P < 0.01) and liver resilience (P < 0.01) by RW, whereas liver resilience was rejuvenated by WGW (P < 0.05). CONCLUSIONS: Twelve-week 98 g/d WGW consumption can promote liver and inflammatory resilience in overweight and obese subjects with mildly elevated plasma cholesterol. The health space approach appeared appropriate to evaluate intervention effects as composite markers. This trial was registered at www.clinicaltrials.gov as NCT02385149.

    Repeated-batch food waste fermentation for n-caproate production with reduced hydroxide use and no external electron donor addition
    Contreras Davila, Carlos ; Carrión, Víctor J. ; Vonk, Vincent R. ; Buisman, C.J.N. ; Strik, D.P.B.T.B. - \ 2019
    Wageningen University & Research
    microbial chain elongation - medium-chain fatty acids - n-caproate - anaerobic digestion
    Fed-batch food waste fermentation was done without pH control for n-caproate production in an open microbiome. Acidification was steered towards lactate and, subsequently, chain elongation to n-butyrate and n-caproate was observed. Lactate was a key electron donor and its consumption during chain elongation helped to reduce the chemicals use for pH control.
    Emissies naar lucht uit de landbouw in 2017 : Berekeningen met het model NEMA
    Bruggen, C. van; Bannink, A. ; Groenestein, C.M. ; Huijsmans, J.F.M. ; Lagerwerf, L.A. ; Luesink, H.H. ; Sluis, S.M. van der; Velthof, G.L. ; Vonk, J. - \ 2019
    Wageningen : Wettelijke Onderzoekstaken Natuur & Milieu (WOt-technical report 147) - 131
    Agricultural activities are in the Netherlands a major source of gaseous emission as ammonia (NH3), nitrogen oxide (NO),nitrous oxide (N2O), methane (CH4) and non-methane volatile organic compounds (NMVOC) and particulate matter (PM10 andPM2.5). The emissions in 2017 were calculated using the National Emission Model for Agriculture (NEMA). The method calculatesthe NH3 emission from livestock manure based on the total ammonia nitrogen (TAN) content in manure. In 2017 NH3 emissionsfrom livestock manure, fertilizer and other sources in agriculture, from hobby farms, private parties and manure application onnature areas amounted to 120.5 million kg NH3, 3.9 million kg more than in 2016. Nitrogen excretion increased due to a largerfeed requirement for dairy cows and higher nitrogen levels in roughage. N2O emissions in 2017 were 21.3 million kg, slightlyabove the level of 2016 (20.7 million kg). The NO emission in 2017 amounted to 23.1 million kg compared to 22.5 million kg in2016. The CH4 emission decreased due to the shrinking of the dairy herd from 508 to 503 million kg. NMVOC emissionsamounted to 98 million kg in 2017 compared to 99 million kg in 2016. Emissions of particulate matter PM10 and PM2.5, 6.2 and0.6 million kg respectively, hardly changed compared to 2016. Some figures in the time series 1990-2016 were revised onbasis of new insights. NH3 emissions from livestock manure in the Netherlands dropped by two thirds since 1990, mainly as aresult of lower nitrogen excretion rates by livestock and low emission manure application. Emissions of N2O and NO alsodecreased over the same period, but less strongly (38% and 31% respectively), due to higher emissions from manure injectioninto the soil and the shift from poultry housing systems with slurry manure towards solid manure systems. CH4 emissions reducedby 14% between 1990 and 2017, caused by a decrease in livestock numbers and increased feed efficiency of dairy cattle.
    A predictive strategy for mapping locations where future MOSSFA events are expected
    Murk, A.J. ; Hollander, D.J. ; Chen, S. ; Hu, C. ; Liu, Y. ; Vonk, S.M. ; Schwing, Patrick T. ; Gilbert, S. ; Foekema, E.M. - \ 2019
    In: Scenarios and Responses to Future Deep Oil Spills / Murawski, S.A., Ainsworth, C.H., Gilbert, S., Hollander, D.J., Paris, C.B., Schlueter, M., Wetzel, D.L., Springer Nature Switzerland - ISBN 9783030129620 - p. 355 - 368.
    A MOSSFA (marine oil snow sedimentation and flocculent accumulation) event was the reason that substantial amounts of the spilled oil were transported to the seafloor during the Deepwater Horizon (DWH) oil well blowout. The region-wide sinking and flocculent accumulation of marine oil snow on the sediment surface changed redox conditions, slowed down the biodegradation of the oil, and increased the spatial and temporal impacts on the benthic community and habitat suitability. Recent field research has confirmed that, in addition to the DWH MOSSFA event in the northern Gulf of Mexico (nGoM), another extensive MOSSFA event occurred in a biologically sensitive area in the southern Gulf of Mexico (sGoM) during the 1979 - 1980 Ixtoc I oil well blowout. Thus, MOSSFA events are not unexpected and have the potential to not only alter sediment chemical conditions but also to extend, expand, and intensify the ecological impact of an oil spill. Consequently this risk should be taken into consideration when preparing response...
    Novel ecosystems in urbanized areas under multiple stressors: Using ecological history to detect and understand ecological processes of an engineered ecosystem (lake Markermeer)
    Riel, M.C. van; Vonk, J.A. ; Noordhuis, R. ; Verdonschot, P.F.M. - \ 2019
    Wageningen : Freshwater ecosystems, Wageningen Environmental Research - ISBN 9789463950183 - 34
    Greenhouse gas emissions in the Netherlands 1990-2017 : National inventory report 2019
    Ruyssenaars, P.G. ; Coenen, P.W.H.G. ; Zijlema, P.J. ; Arets, E.J.M.M. ; Baas, K. ; Dröge, R. ; Geilenkirchen, G. ; Hoen, M. 't; Honig, E. ; Huet, B. van; Huis, E.P. van; Koch, W.W.R. ; Lagerwerf, L.L. ; Molder, R.A. te; Montfoort, J.A. ; Peek, C.J. ; Vonk, J. ; Zanten, M.C. van - \ 2019
    RIVM - 420 p.
    Meta-analysis of epigenome-wide association studies in neonates reveals widespread differential DNA methylation associated with birthweight
    Küpers, Leanne K. ; Monnereau, Claire ; Sharp, Gemma C. ; Yousefi, Paul ; Salas, Lucas A. ; Ghantous, Akram ; Page, Christian M. ; Reese, Sarah E. ; Wilcox, Allen J. ; Czamara, Darina ; Starling, Anne P. ; Novoloaca, Alexei ; Lent, Samantha ; Roy, Ritu ; Hoyo, Cathrine ; Breton, Carrie V. ; Allard, Catherine ; Just, Allan C. ; Bakulski, Kelly M. ; Holloway, John W. ; Everson, Todd M. ; Xu, Cheng Jian ; Huang, Rae Chi ; Plaat, Diana A. van der; Wielscher, Matthias ; Merid, Simon Kebede ; Ullemar, Vilhelmina ; Rezwan, Faisal I. ; Lahti, Jari ; Dongen, Jenny van; Langie, Sabine A.S. ; Richardson, Tom G. ; Magnus, Maria C. ; Nohr, Ellen A. ; Xu, Zongli ; Duijts, Liesbeth ; Zhao, Shanshan ; Zhang, Weiming ; Plusquin, Michelle ; DeMeo, Dawn L. ; Solomon, Olivia ; Heimovaara, Joosje H. ; Jima, Dereje D. ; Gao, Lu ; Bustamante, Mariona ; Perron, Patrice ; Wright, Robert O. ; Hertz-Picciotto, Irva ; Zhang, Hongmei ; Karagas, Margaret R. ; Gehring, Ulrike ; Marsit, Carmen J. ; Beilin, Lawrence J. ; Vonk, Judith M. ; Jarvelin, Marjo Riitta ; Bergström, Anna ; Örtqvist, Anne K. ; Ewart, Susan ; Villa, Pia M. ; Moore, Sophie E. ; Willemsen, Gonneke ; Standaert, Arnout R.L. ; Håberg, Siri E. ; Sørensen, Thorkild I.A. ; Taylor, Jack A. ; Räikkönen, Katri ; Yang, Ivana V. ; Kechris, Katerina ; Nawrot, Tim S. ; Silver, Matt J. ; Gong, Yun Yun ; Richiardi, Lorenzo ; Kogevinas, Manolis ; Litonjua, Augusto A. ; Eskenazi, Brenda ; Huen, Karen ; Mbarek, Hamdi ; Maguire, Rachel L. ; Dwyer, Terence ; Vrijheid, Martine ; Bouchard, Luigi ; Baccarelli, Andrea A. ; Croen, Lisa A. ; Karmaus, Wilfried ; Anderson, Denise ; Vries, Maaike de; Sebert, Sylvain ; Kere, Juha ; Karlsson, Robert ; Arshad, Syed Hasan ; Hämäläinen, Esa ; Routledge, Michael N. ; Boomsma, Dorret I. ; Feinberg, Andrew P. ; Newschaffer, Craig J. ; Govarts, Eva ; Moisse, Matthieu ; Fallin, M.D. ; Melén, Erik ; Prentice, Andrew M. ; Kajantie, Eero ; Almqvist, Catarina ; Oken, Emily ; Dabelea, Dana ; Boezen, H.M. ; Melton, Phillip E. ; Wright, Rosalind J. ; Koppelman, Gerard H. ; Trevisi, Letizia ; Hivert, Marie France ; Sunyer, Jordi ; Munthe-Kaas, Monica C. ; Murphy, Susan K. ; Corpeleijn, Eva ; Wiemels, Joseph ; Holland, Nina ; Herceg, Zdenko ; Binder, Elisabeth B. ; Davey Smith, George ; Jaddoe, Vincent W.V. ; Lie, Rolv T. ; Nystad, Wenche ; London, Stephanie J. ; Lawlor, Debbie A. ; Relton, Caroline L. ; Snieder, Harold ; Felix, Janine F. - \ 2019
    Nature Communications 10 (2019)1. - ISSN 2041-1723

    Birthweight is associated with health outcomes across the life course, DNA methylation may be an underlying mechanism. In this meta-analysis of epigenome-wide association studies of 8,825 neonates from 24 birth cohorts in the Pregnancy And Childhood Epigenetics Consortium, we find that DNA methylation in neonatal blood is associated with birthweight at 914 sites, with a difference in birthweight ranging from −183 to 178 grams per 10% increase in methylation (P Bonferroni < 1.06 x 10 −7 ). In additional analyses in 7,278 participants, <1.3% of birthweight-associated differential methylation is also observed in childhood and adolescence, but not adulthood. Birthweight-related CpGs overlap with some Bonferroni-significant CpGs that were previously reported to be related to maternal smoking (55/914, p = 6.12 x 10 −74 ) and BMI in pregnancy (3/914, p = 1.13x10 −3 ), but not with those related to folate levels in pregnancy. Whether the associations that we observe are causal or explained by confounding or fetal growth influencing DNA methylation (i.e. reverse causality) requires further research.

    BENEFIT Partnership – 2018 annual report : Bilateral Ethiopian-Netherlands Effort for Food, Income and Trade Partnership
    Alemu, Dawit ; Koomen, Irene ; Ayana, Amsalu ; Borman, Gareth ; Elias, Eyasu ; Smaling, Eric ; Getaw, Helen ; Becx, Gertjan ; Sopov, Monika ; Terefe, Geremew ; Schrader. Ted, ; Terefa, Tewodros ; Vonk, Remko - \ 2019
    Wageningen : Wageningen Centre for Development Innovation (Report / WDCI 19-053) - 199
    Methodology for estimating emissions from agriculture in the Netherlands : Calculations of CH4, NH3, N2O, NOx, NMVOC, PM10, PM2.5 and CO2 with the National Emission Model for Agriculture (NEMA), Update 2019
    Lagerwerf, L.A. ; Bannink, A. ; Bruggen, C. van; Groenestein, C.M. ; Huijsmans, J.F.M. ; Kolk, J.W.H. van der; Luesink, H.H. ; Sluis, S.M. van der; Velthof, G.L. ; Vonk, J. - \ 2019
    Wageningen : Statutory Research Tasks Unit for Nature & the Environment (WOt technical report 148) - 215
    The National Emission Model for Agriculture (NEMA) is used to calculate emissions to air from agricultural activities in the Netherlands on a national scale. Emissions of ammonia (NH3) and other N compounds (NOx and N2O) are calculated for animal housing, manure storage, manure application and grazing using a flow model for total ammoniacal nitrogen (TAN). Emissions from the application of inorganic N fertilizer, compost and sewage sludge, cultivation of organic soils, crop residues, and ripening of crops are calculated as well. The NEMA is also used to estimate emissions of methane (CH4) from enteric fermentation and manure management, nonmethane volatile organic compounds (NMVOC) and particulate matter (PM) from manure management and agricultural soils, as well as for carbon dioxide (CO2) from liming. Emissions are calculated in accordance with the criteria of international guidelines and reported in an annual Informative Inventory Report (IIR; for air pollutants) and National Inventory Report (NIR; for greenhouse gases). This methodology report provides an outline of and describes the background to the calculation of emissions according to the NEMA.
    Megaherbivores may impact expansion of invasive seagrass in the Caribbean
    Christianen, Marjolijn J.A. ; Smulders, Fee O.H. ; Engel, M.S. ; Nava, Mabel I. ; Willis, Sue ; Debrot, Adolphe O. ; Palsbøll, Per J. ; Vonk, J.A. ; Becking, Leontine E. - \ 2019
    Journal of Ecology 107 (2019)1. - ISSN 0022-0477 - p. 45 - 57.
    1. Our knowledge of the functional role of large herbivores is rapidly expanding, and the impact of grazing on species co‐existence and non‐native species expansion has been studied across ecosystems. However, experimental data on large grazer impacts on plant invasion in aquatic ecosystems are lacking. 2. Since its introduction in 2002, the seagrass species Halophila stipulacea has rapidly expanded across the Eastern Caribbean, forming dense meadows in green turtle (Chelonia mydas) foraging areas. We investigate the changes in seagrass species co‐existence and the impacts of leaf grazing by green turtles on non‐native seagrass expansion in Lac Bay (Bonaire, Caribbean Netherlands). 3. Green turtle grazing behavior changed after the introduction of non‐native seagrass to Lac Bay in 2010. Field observations, together with time‐lapse satellite images over the last four decades, showed initiation of new grazing patches (65 ha, an increase of 72%). The sharp border between grazed and ungrazed seagrass patches moved in the direction of shallower areas with native seagrass species that had previously (1970‐2010) been ungrazed. Green turtles deployed with Fastloc‐GPS transmitters confirmed high site fidelity to these newly cropped patches. In addition, cafeteria experiments indicated selective grazing by green turtles on native species. These native seagrass species had significantly higher nutritional values compared to the non‐native species. In parallel, exclosure‐experiments showed that non‐native seagrass expanded more rapidly in grazed canopies compared to ungrazed canopies. Finally, in six years from 2011‐2017, H. stipulacea underwent a significant expansion, invading 20 to 49 fixed monitoring locations in Lac Bay, increasing from 6% to 20% in total occurrence. During the same period, native seagrass Thalassia testudinum occurrence decreased by 33%. 4. Synthesis. Our results provide first‐time evidence of large scale replacement of native seagrasses by rapidly colonising H. stipulacea in the Caribbean and add a mechanistic explanation for this invasiveness. We conclude that green turtle leaf grazing may modify the rate and spatial extent of this invasive species’ expansion, due to grazing preferences, and increased space for settlement. This work shows how large herbivores play an important but unrecognized role in species co‐existence and plant invasions of aquatic ecosystems.
    Captivity
    Bovenkerk, Bernice ; Keulartz, Jozef - \ 2018
    In: Encyclopedia of Animal Cognition and Behavior / Vonk, Jennifer, Shackelford, Todd, Springer International Publishing - ISBN 9783319478296 - 10 p.
    Animals are kept in captivity for many different purposes, such as recreation or entertainment, for their products, for medical experimentation and scientific research and education, for companionship, for their labor, and for their own benefit (in particular sheltering and treating lost and sick animals). Many of these animals have been domesticated, and this domestication process raises ethical questions of its own, but here we will focus on wild animals in zoos and the question of under what circumstances it is morally justified to keep them in captivity.
    A 12-wk whole-grain wheat intervention protects against hepatic fat : the Graandioos study, a randomized trial in overweight subjects
    Schutte, Sophie ; Esser, Diederik ; Hoevenaars, Femke P.M. ; Hooiveld, Guido J.E.J. ; Priebe, Marion G. ; Vonk, Roel J. ; Wopereis, Suzan ; Afman, Lydia A. - \ 2018
    American Journal of Clinical Nutrition 108 (2018)6. - ISSN 0002-9165 - p. 1264 - 1274.

    Background: Whole-grain wheat (WGW) is described as nutritionally superior to refined wheat (RW) and thus advocated as the healthy choice, although evidence from intervention studies is often inconsistent. The liver, as the central organ in energy metabolism, might be an important target organ for WGW interventions. Objective: The aim of this study was to investigate the potential benefits of WGW consumption compared with RW consumption on liver health and associated parameters. Design: We performed a double-blind, parallel trial in which 50 overweight 45- to 70-y-old men and postmenopausal women were randomly allocated to a 12-wk intervention with either WGW (98 g/d) or RW (98 g/d) products. Before and after the intervention we assessed intrahepatic triglycerides (IHTGs) and fat distribution by proton magnetic resonance spectroscopy/magnetic resonance imaging, fecal microbiota composition, adipose tissue gene expression, and several fasting plasma parameters, as well as postprandial plasma lipids after a mixed meal. Results: Fasting plasma cholesterol, triglycerides, nonesterified fatty acids, and insulin were not affected by RW or WGW intervention. We observed a substantial increase of 49.1% in IHTGs in the RW when compared with the WGW group (P = 0.033). Baseline microbiota composition could not predict the increase in IHTGs after RW, but gut microbiota diversity decreased in the RW group when compared with the WGW group (P = 0.010). In the WGW group, we observed increased postprandial triglyceride levels compared with the RW group (P = 0.020). In addition, the WGW intervention resulted in a trend towards lower fasting levels of the liver acute-phase proteins serum amyloid A (P = 0.057) and C-reactive protein (P = 0.064) when compared to the RW intervention. Conclusions: A 12-wk RW intervention increases liver fat and might contribute to the development of nonalcoholic fatty liver disease, whereas a 12-wk 98-g/d WGW intervention prevents a substantial increase in liver fat. Our results show that incorporating feasible doses of WGW in the diet at the expense of RW maintains liver health. The study was registered at clinicaltrials.gov as NCT02385149.

    Balans van de Leefomgeving 2018 : Nederland duurzaam vernieuwen
    Egmond, Petra van; Elzenga, Hans ; Buitelaar, Edwin ; Eerdt, Martha van; Eskinasi, Martijn ; Franken, Ron ; Gaalen, Frank van; Hanemaaijer, Aldert ; Hilbers, Hans ; Hollander, Guus de; Nijland, Hans ; Ritsema van Eck, Jan ; Ros, Jan ; Schilder, Frans ; Spoon, Martijn ; Uitbeijerse, Gabrielle ; Wouden, Ries van der; Vonk, Marijke ; Vugteveen, Pim ; Goossen, Martijn ; Blom, Wim ; Bredenoord, Hendrien ; Brink, Thelma van den; Evers, David ; Doren, Didi van; Grinsven, Hans van; Hinsberg, Arjen van; Muilwijk, Hanneke ; Oorschot, Mark van; Peeters, Jeroen ; Puijenbroek, Peter van; Raspe, Otto ; Rijn, Frank van; Schijndel, Marian van; Sluis, Sietske van der; Sorel, Niels ; Timmerhuis, Jacqueline ; Verwest, Femke ; Westhoek, Henk ; Sanders, Marlies ; Dirkx, Joep - \ 2018
    Den Haag : Planbureau voor de Leefomgeving - 284
    Emissies naar lucht uit de landbouw in 2016 : Berekeningen met het model NEMA
    Bruggen, C. van; Bannink, A. ; Groenestein, C.M. ; Huijsmans, J.F.M. ; Luesink, H.H. ; Sluis, S.M. van der; Velthof, G.L. ; Vonk, J. - \ 2018
    Wageningen : Wettelijke Onderzoekstaken Natuur & Milieu (WOt technical report 119) - 124
    Agricultural activities are in the Netherlands a major source of ammonia (NH3), nitrogen oxide (NO), nitrous oxide (N2O), methane (CH4) and particulate matter (PM10 and PM2.5). The emissions in 2016 were calculated using the National Emission Model for Agriculture (NEMA). Some figures in the time series 1990-2015 were revised. The method calculates the NH3 emission from livestock manure based on the total ammonia nitrogen (TAN) content in manure. In 2016 NH3 emissions from livestock manure, fertilizer and other sources in agriculture, from hobby farms, private parties and manure disposal in nature areas amounted to 116.8 million kg NH3, 1.3 million kg more than in 2015. Nitrogen excretion increased due to expansion of the dairy herd, but because of a larger share of low emission housing and more manure exports outside agriculture, the increase in NH3 emission remained limited. N2O emissions in 2016 were 21.1 million kg at virtually the same level as in 2015(21.2). NO emissions in 2016 totaled 22.8 million kg compared to 22.6 million kg in 2015. CH4 emissions increased from 496 to512 million kg due to the expansion of the dairy herd. Emissions of particulate matter PM10 and PM2.5, 6.5 and 0.6 million kg respectively, did not change compared to 2015. NH3 emissions from livestock manure in the Netherlands dropped by almost two thirds since 1990, mainly as a result of lower nitrogen excretion rates by livestock and low emission manure application. Emissions of N2O and NO also decreased over the same period, but less strongly (38% and 31% respectively), due to higher emissions from manure injection into the soil and the shift from poultry housing systems with liquid manure towards solid manure systems. CH4 emissions reduced by 13% between 1990 and 2016 caused by a decrease in livestock numbers and increased feed efficiency of dairy cattle.
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