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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Comparison of ammonia emissions related to nitrogen use efficiency of livestock production in Europe
Groenestein, C.M. ; Hutchings, N.J. ; Haenel, H.D. ; Amon, B. ; Menzi, H. ; Mikkelsen, M.H. ; Misselbrook, T.H. ; Bruggen, C. van; Kupper, T. ; Webb, J. - \ 2019
Journal of Cleaner Production 211 (2019). - ISSN 0959-6526 - p. 1162 - 1170.
Ammonia emission intensity - Animal protein - Feed nitrogen - Manure management - Nitrogen use efficiency

The increasing global demand for food and the environmental effects of reactive nitrogen losses in the food production chain, increase the need for efficient use of nitrogen (N). Of N harvested in agricultural plant products, 80% is used to feed livestock. Because the largest atmospheric loss of reactive nitrogen from livestock production systems is ammonia (NH3), the focus of this paper is on N lost as NH3 during the production of animal protein. The focus of this paper is to understand the key factors explaining differences in Nitrogen Use Efficiency (NUE) of animal production among various European countries. Therefore we developed a conceptual framework to describe the NUE defined as the amount of animal-protein N per N in feed and NH3–N losses in the production of milk, beef, pork, chicken meat and eggs in The Netherlands, Switzerland, United Kingdom, Germany, Austria and Denmark. The framework describes how manure management and animal-related parameters (feed, metabolism) relate to NH3 emissions and NUE. The results showed that the animal product with the lowest NUE had the largest NH3 emissions and vice versa, which agrees with the reciprocal relationship between NUE and NH3 within the conceptual framework. Across animal products for the countries considered, about 20% of the N in feed is lost as NH3. The significant smallest proportion (12%) of NH3–N per unit of Nfeed is from chicken production. The proportions for other products are 17%, 19%, 20% and 22% for milk, pork, eggs and beef respectively. These differences were not significantly different due to the differences among countries. For all countries, NUE was lowest for beef and highest for chicken. The production of 1 kg N in beef required about 5 kg N in feed, of which 1 kg N was lost as NH3–N. For the production of 1 kg N in chicken meat, 2 kg N in feed was required and 0.2 kg was lost as NH3. The production of 1 kg N in milk required 4 kg N in feed with 0.6 kg NH3–N loss, the same as pork and eggs, but those needed 3 and 3.5 kg N in feed per kg N in product respectively. Except for beef, the differences among these European countries were mainly caused by differences in manure management practices and their emission factors, rather than by animal-related factors including feed and digestibility influencing the excreted amount of ammoniacal N (TAN). For beef, both aspects caused important differences. Based on the results, we encourage the expression of N losses as per N in feed or per N in product, in addition to per animal place, when comparing production efficiency and NUE. We consider that disaggregating emission factors into a diet/animal effect and a manure management effect would improve the basis for comparing national NH3 emission inventories.

Report on recommendations on future research and policy : deliverable D8.4
Hondo, Haris ; Kaunisto, Erik ; Ofei, Kwabena Titi ; Mikkelsen, Bent Egberg ; Zimmermann, K.L. ; Veer, P. van 't - \ 2018
EU - 32 p.
Inventory of types of consumer-generated food preparation data and data collection methodologies : deliverable D6.1
Klepacz, Naomi ; Maringer, Marcus ; Ekman, Susanne ; Normann, Anne ; Geelen, M.M.E.E. ; Raats, Monique ; Zimmermann, K.L. ; Mikkelsen, Bent Egberg - \ 2018
EU - 19 p.
Report on gaps and needs - WP6, Report on the potentials and limitations for the use of user-generated domestic food preparation data to answer questions regarding determinants of nutrition and eating : deliverable D6.5
Klepacz, Naomi ; Maringer, Marcus ; Ekman, Susanne ; Normann, Anne ; Geelen, M.M.E.E. ; Raats, Monique ; Zimmermann, K.L. ; Veer, P. van 't; Mikkelsen, Bent Egberg - \ 2018
EU - 16 p.
Report on the synthesis of the findings for WP8-10 : deliverable D4.3
Hodgkins, Charo ; Timotijevic, Lada ; Finglas, Paul ; Hieke, Sophie ; Mikkelsen, Bent Egberg ; Zimmermann, K.L. ; Veer, P. van 't - \ 2018
EU - 19 p.
Position and final paper of RICHFIELDS : deliverable D1.2
Bogaardt, M.J. ; Copani, Giacomo ; Cueva, Javier de la; Finglas, Paul ; Geelen, M.M.E.E. ; Hodgkins, Charo ; Korousic, Barbara ; Mikkelsen, Bent ; Poppe, K.J. ; Pour Abdollahian, Golboo ; Puttelaar, J. van den; Raats, Monique ; Selnes, T. ; Timotijevic, Lada ; Veen, H.B. van der; Veer, P. van 't; Zimmermann, K.L. - \ 2018
EU - 49 p.
Designing a research infrastructure on dietary intake and its determinants
Bogaardt, M.J. ; Geelen, A. ; Zimmermann, K. ; Finglas, P. ; Raats, M.M. ; Mikkelsen, B.E. ; Poppe, K.J. ; van't Veer, P. - \ 2018
Nutrition Bulletin 43 (2018)3. - ISSN 1471-9827 - p. 301 - 309.
big data - consumers - diet - food - public health - research infrastructure

Research on dietary intake and its determinants is crucial for an adequate response to the current epidemic of diet-related non-communicable chronic diseases. In order to respond to this challenge, the RICHFIELDS project was tasked with designing a research infrastructure (RI) that connects data on dietary intake of consumers in Europe, and its determinants, collected using apps and wearable sensors, from behavioural laboratories and experimental facilities and from other RIs. The main output of the project, an RI design, describes interfaces (portals) to collect data, a meta-database and a data-model to enable data linkage and sharing. The RICHFIELDS project comprises three phases, each consisting of three work packages, and an overarching methodological support work package. Phase 1 focused on data generated by consumers (e.g. collected by apps and sensors) relating to the purchase, preparation and consumption of food. Phase 2 focused on data generated by organisations such as businesses (e.g. retail data), government (e.g. procurement data) and experimental research facilities (e.g. virtual supermarkets). Phases 1 and 2 provided Phase 3 with insights on data types and design requirements, including the business models, data integration and management systems and governance and ethics. The final design will be used in the coming years to build an RI for the scientific research community, policy makers and businesses in Europe. The RI will boost interdisciplinary multi-stakeholder research through harmonisation and integration of data on food behaviour.

Small-scale coastal fisheries in European Seas are not what they were: Ecological, social and economic changes
Lloret, Josep ; Cowx, Ian G. ; Cabral, Henrique ; Castro, Margarida ; Font, Toni ; Gonçalves, Jorge M.S. ; Gordoa, Ana ; Hoefnagel, Ellen ; Matić-Skoko, Sanja ; Mikkelsen, Eirik ; Morales-Nin, Beatriz ; Moutopoulos, Dimitrios K. ; Muñoz, Marta ; Santos, Miguel Neves Dos; Pintassilgo, Pedro ; Pita, Cristina ; Stergiou, Konstantinos I. ; Ünal, Vahdet ; Veiga, Pedro ; Erzini, Karim - \ 2018
Marine Policy 98 (2018). - ISSN 0308-597X - p. 176 - 186.
Coastal, small-scale fisheries (SSF), whether artisanal (professional) or recreational, represent important socioeconomic activities across Europe that are currently undergoing a number of changes. This paper reviews and analyses the drivers of these changes, and makes recommendations for the future management of SSF. From the biological standpoint, the use of fishing gears that actively select certain species, sizes and sexes, the deployment of fishing gears on certain fragile habitats, the loss of fishing gears and the use of non-native species as bait are examples of how SSFs can threaten the sustainability of vulnerable coastal species and habitats. From a socioeconomic perspective, several factors are altering the traditional characteristics of coastal SSF. Among the most important is the growth of recreational fisheries in coastal waters and the disappearance of traditional low technology fisheries or their substitution by more mechanised, technical fisheries, which is leading to a loss of the traditional ecological knowledge held by artisanal fishers. On the other hand, the increasing competition between artisanal and recreational fisheries, and between them and commercial fishing operations, are also altering the classical features of coastal fisheries in some European countries. SSFs must adapt to the requirements of the new Common Fisheries Policy (CFP), namely management based on Maximum Sustainable Yield (MSY), multi-annual management plans and ecosystem based principles. It is concluded that it is necessary to integrate different assessment approaches (biological, social and economic), with active participation from stakeholders, governments and relevant research institutions, to better evaluate and manage coastal fisheries.
Integrated report of WP10 activities for Synthesis Report of Task 4.2 - Communicative exchange with consortium and stakeholders : deliverable D10.4
Hieke, Sophie ; Bucher, Tamara ; Mikkelsen, Bent E. ; Finglas, Paul ; Puttelaar, J. van den; Zimmermann, K.L. ; Poppe, K.J. - \ 2017
EU - 17 p.
Report on case studies : deliverable D8.1
Mikkelsen, Bent Egberg ; Ofei, Kwabena Titi ; Hondo, Haris ; Kaunisto, Erik ; Zimmermann, K.L. ; Veer, P. van 't - \ 2017
EU - 32 p.
Position document ‘Laboratories and research facilities in the field of food and health consumer behaviour and lifestyle’ : deliverable D10.1
Hieke, Sophie ; Bucher, Tamara ; Mikkelsen, Bent E. ; Finglas, Paul ; Puttelaar, J. van den; Zimmermann, K.L. ; Veer, P. van 't - \ 2017
EU - 33 p.
Paper on quality criteria and overview of criteria applied to available data/methods – WP5 (Report on the paper intended for publication, titled: “Food purchase data for mHealth research: A dynamic search inventory and analysis of applications”) : deliverable D5.4
Kaunisto, Erik ; Hondo, Haris ; Normann, Anne ; Zimmermann, K.L. ; Veer, P. van 't; Mikkelsen, Bent Egberg - \ 2017
EU - 23 p.
Vision document ‘Out of home consumption data and information for the RI Consumer Data Platform’ : deliverable D10.3
Bucher, Tamara ; Mikkelsen, Bent Egberg ; Ofei, Kwabena Titi ; Hieke, Sophie ; Zimmermann, K.L. ; Finglas, Paul - \ 2016
EU - 3 p.
List of quality criteria - Development of a Quality Evaluation Framework for Consumer-Generated Domestic Food Preparation Data : deliverable D6.3
Klepacz, Naomi ; Maringer, Marcus ; Ekman, Susanne ; Normann, Anne ; Verain, M.C.D. ; Geelen, M.M.E.E. ; Raats, Monique ; Zimmermann, K.L. ; Veer, P. van 't; Mikkelsen, Bent Egberg - \ 2016
EU - 31 p.
Linked Data Sharing to Foster Consumer Based Science Enabled by Richfields : A Research Infrastructure on Consumer Health and Food
Zimmermann, K.L. ; Verain, M.C.D. ; Bogaardt, M.J. ; Geelen, Anouk ; Finglas, Paul ; Raats, Monique ; Mikkelsen, B.E. ; Poppe, K.J. - \ 2016
In: Proceedings of Measuring Behavior 2016. - - 7 p.
Phylogeny of the viral hemorrhagic septicemia virus in European aquaculture
Cieslak, Michael ; Mikkelsen, Susie S. ; Skall, Helle F. ; Baud, Marine ; Diserens, Nicolas ; Engelsma, Marc Y. ; Haenen, Olga L.M. ; Mousakhani, Shirin ; Panzarin, Valentina ; Wahli, Thomas ; Olesen, Niels J. ; Schütze, Heike - \ 2016
PLoS ONE 11 (2016)10. - ISSN 1932-6203

One of the most valuable aquaculture fish in Europe is the rainbow trout, Oncorhynchus mykiss, but the profitability of trout production is threatened by a highly lethal infectious disease, viral hemorrhagic septicemia (VHS), caused by the VHS virus (VHSV). For the past few decades, the subgenogroup Ia of VHSV has been the main cause of VHS outbreaks in European freshwater-farmed rainbow trout. Little is currently known, however, about the phylogenetic radiation of this Ia lineage into subordinate Ia clades and their subsequent geographical spread routes. We investigated this topic using the largest Ia-isolate dataset ever compiled, comprising 651 complete G gene sequences: 209 GenBank Ia isolates and 442 Ia isolates from this study. The sequences come from 11 European countries and cover the period 1971-2015. Based on this dataset, we documented the extensive spread of the Ia population and the strong mixing of Ia isolates, assumed to be the result of the Europe-wide trout trade. For example, the Ia lineage underwent a radiation into nine Ia clades, most of which are difficult to allocate to a specific geographic distribution. Furthermore, we found indications for two rapid, large-scale population growth events, and identified three polytomies among the Ia clades, both of which possibly indicate a rapid radiation. However, only about 4% of Ia haplotypes (out of 398) occur in more than one European country. This apparently conflicting finding regarding the Europe-wide spread and mixing of Ia isolates can be explained by the high mutation rate of VHSV. Accordingly, the mean period of occurrence of a single Ia haplotype was less than a full year, and we found a substitution rate of up to 7.813 × 10-4 nucleotides per site per year. Finally, we documented significant differences between Germany and Denmark regarding their VHS epidemiology, apparently due to those countries' individual handling of VHS.

Backbone structures in human milk oligosaccharides: trans-glycosylation by metagenomic ß-N-acetylhexosaminidases
Nyffenegger, C. ; Nordvang, R.T. ; Zeuner, B. ; Lezyk, M. ; Difilippo, E. ; Logtenberg, M.J. ; Schols, H.A. ; Meyer, A.S. ; Mikkelsen, J.D. - \ 2015
Applied Microbiology and Biotechnology 99 (2015)19. - ISSN 0175-7598 - p. 7997 - 8009.
This paper describes the discovery and characterization of two novel ß-N-acetylhexosaminidases HEX1 and HEX2, capable of catalyzing the synthesis of human milk oligosaccharides (HMO) backbone structures with fair yields using chitin oligomers as ß-N-acetylglucosamine (GlcNAc) donor. The enzyme-encoding genes were identified by functional screening of a soil-derived metagenomic library. The ß-N-acetylhexosaminidases were expressed in Escherichia coli with an N-terminal His6-tag and were purified by nickel affinity chromatography. The sequence similarities of the enzymes with their respective closest homologues are 59 % for HEX1 and 51 % for HEX2 on the protein level. Both ß-N-acetylhexosaminidases are classified into glycosyl hydrolase family 20 (GH 20) are able to hydrolyze para-nitrophenyl-ß-N-acetylglucosamine (pNP-GlcNAc) as well as para-nitrophenyl-ß-N-acetylgalactosamine (pNP-GalNAc) and exhibit pH optima of 8 and 6 for HEX1 and HEX2, respectively. The enzymes are able to hydrolyze N-acetylchitooligosaccharides with a degree of polymerization of two, three, and four. The major findings were, that HEX1 and HEX2 catalyze trans-glycosylation reactions with lactose as acceptor, giving rise to the human milk oligosaccharide precursor lacto-N-triose II (LNT2) with yields of 2 and 8 % based on the donor substrate. In total, trans-glycosylation reactions were tested with the disaccharide acceptors ß-lactose, sucrose, and maltose, as well as with the monosaccharides galactose and glucose resulting in the successful attachment of GlcNAc to the acceptor in all cases.
Phylogeography and population dynamics of the white-sided dolphin (Lagenorhynchus acutus) in the North Atlantic
Banguera-Hinestroza, E. ; Evans, P.G.H. ; Mirimin, L. ; Reid, R.J. ; Mikkelsen, B. ; Couperus, A.S. ; Deaville, R. ; Rogan, E. ; Hoelzel, A.R. - \ 2014
Conservation Genetics 15 (2014)4. - ISSN 1566-0621 - p. 789 - 802.
Highly mobile species in the marine environment may be expected to show little differentiation at the population level, but this is often not the case. Instead cryptic population structure is common, and effective conservation will require an understanding of how these patterns evolve. Here we present an assessment from both sides of the North Atlantic of differentiation among populations of a dolphin species that inhabits mainly pelagic waters, the Atlantic white-sided dolphin. We compare eleven putative populations in the western and eastern North Atlantic at mtDNA and microsatellite DNA loci and find reduced nucleotide diversity and signals for historical bottlenecks and post-bottleneck expansions in all regions. We calculate expansion times to have occurred during the early Holocene, following the last glacial maximum (LGM). We find evidence for connectivity among populations from either side of the North Atlantic, and differentiation between putative populations in the far northeast compared with all other areas sampled. Some data suggest the possibility of separate refugia during the LGM explaining this pattern, although ongoing ecological processes may also be a factor. We discuss the implications for developing effective programs of conservation and management in the context of ongoing anthropogenic impact.
Characterisation of a novel endo-xyloglucanase (XcXGHA) from Xanthomonas that accommodates a xylosyl-substituted glucose at subsite -1
Feng, T. ; Yan, K.P. ; Mikkelsen, M.D. ; Meyer, A.S. ; Schols, H.A. ; Westereng, B. ; Mikkelsen, J.D. - \ 2014
Applied Microbiology and Biotechnology 98 (2014)23. - ISSN 0175-7598 - p. 9667 - 9679.
polysaccharide-degrading enzymes - geotrichum sp m128 - plant-cell walls - substrate-specificity - glycoside hydrolase - structural basis - oligosaccharides - expression - cloning - endo-beta-1,4-glucanase
A xyloglucan-specific endo-1,4ß-glucanase (XcXGHA) from Xanthomonas citri pv. mangiferaeindicae has been cloned, expressed in Escherichia coli, purified and characterised. The XcXGHA enzyme belongs to CAZy family GH74 and has catalytic site residues conserved with other xyloglucanases in this family. At its optimal reaction conditions, pH 7.0 and 40 °C, the enzyme has a k cat/K M value of 2.2¿×¿107 min-1 M-1 on a tamarind seed xyloglucan substrate. XcXGHA is relatively stable within a broad pH range (pH 4–9) and up to 50 °C (t 1/2, 50 °C of 74 min). XcXGHA is proven to be xyloglucan-specific, and a glycan microarray study verifies that XcXGHA catalyses cleavage of xyloglucan extracted from both monocot and dicot plant species. The enzyme catalyses hydrolysis of tamarind xyloglucan in a unique way by cleaving XXXG into XX and XG (X is xylosyl-substituted glucose; G is unsubstituted glucose), is able to degrade more complex xyloglucans and notably is able to cleave near more substituted xyloglucan motifs such as L [i.e. a-l-Fucp-(1¿¿¿2)-ß-d-Galp-(1¿¿¿2)-a-d-Xylp-(1¿¿¿6)-ß-d-Glcp]. LC-MS/MS analysis of product profiles of tamarind xyloglucan which had been catalytically degraded by XcXGHA revealed that XcXGHA has specificity for X in subsite -1. The 3D model suggests that XcXGHA consists of two seven-bladed ß-propeller domains with the catalytic center formed by the interface of these two domains, which is conserved in xyloglucanases in the GH74 family. However, the XcXGHA has two amino acids (D264 and R472) that differ from the conserved residues of other GH74 xyloglucanases. These two amino acids were predicted to be located on the opposite side of the active site pocket, facing each other and forming a closing surface above the active site pocket. These two amino acids may contribute to the unique substrate specificity of the XcXGHA enzyme.
Key indicators of air pollution and climate change impacts at forest supersites
Paoletti, E. ; Vries, W. de; Mikkelsen, T.N. ; Ibrom, A. ; Larsen, K.S. ; Tuovinen, J.P. ; Serengil, Y. ; Yurtseven, I. ; Wieser, G. ; Matyssek, R. - \ 2013
In: Climate Change, Air Pollution and Global Challenges: Understanding and Perspectives from Forest Research / Matyssek, R., Clarke, N., Cudlin, P., Mikkelsen, T.N., Tuovinen, J.P., Wieser, G., Paoletti, E., Oxford : Elsevier (Developments in Environmental Science 13) - ISBN 9780080983493 - p. 497 - 520.
Untangling the complex effects that different air pollution and climate change factors cause to forest ecosystems is challenging. Supersites, that is, comprehensive measurement sites where research and monitoring of the whole soil–plant–atmosphere system can be carried out, are suggested as a refinement of the current monitoring and research efforts in Europe. This chapter identifies and discusses key measurements to be carried out at such supersites, with a focus on four topical subjects: the carbon, nitrogen, ozone and water budgets. This kind of holistic approach is vital to a realistic translation of the ongoing changes in climate and air quality into research on the impacts on forest ecosystems. Such an integrated effort requires a considerable use of resources at highly instrumented measurement sites and can only be achieved by building on existing infrastructures.
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