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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Unexpected differential metabolic responses of Campylobacter jejuni to the abundant presence of glutamate and fucose
Hooft, Justin J.J. van der; Alghefari, Wejdan ; Watson, Eleanor ; Everest, Paul ; Morton, Fraser R. ; Burgess, Karl E.V. ; Smith, David G.E. - \ 2018
Metabolomics 14 (2018)11. - ISSN 1573-3882
Campylobacter jejuni - HILIC chromatography - Mass spectrometry fragmentation - Metabolomics - Sulphur metabolism

Introduction: Campylobacter jejuni is the leading cause of foodborne bacterial enteritis in humans, and yet little is known in regard to how genetic diversity and metabolic capabilities among isolates affect their metabolic phenotype and pathogenicity. Objectives: For instance, the C. jejuni 11168 strain can utilize both l-fucose and l-glutamate as a carbon source, which provides the strain with a competitive advantage in some environments and in this study we set out to assess the metabolic response of C. jejuni 11168 to the presence of l-fucose and l-glutamate in the growth medium. Methods: To achieve this, untargeted hydrophilic liquid chromatography coupled to mass spectrometry was used to obtain metabolite profiles of supernatant extracts obtained at three different time points up to 24 h. Results: This study identified both the depletion and the production and subsequent release of a multitude of expected and unexpected metabolites during the growth of C. jejuni 11168 under three different conditions. A large set of standards allowed identification of a number of metabolites. Further mass spectrometry fragmentation analysis allowed the additional annotation of substrate-specific metabolites. The results show that C. jejuni 11168 upon l-fucose addition indeed produces degradation products of the fucose pathway. Furthermore, methionine was faster depleted from the medium, consistent with previously-observed methionine auxotrophy. Conclusions: Moreover, a multitude of not previously annotated metabolites in C. jejuni were found to be increased specifically upon l-fucose addition. These metabolites may well play a role in the pathogenicity of this C. jejuni strain.

Addressing global ruminant agricultural challenges through understanding the rumen microbiome : Past, present, and future
Huws, Sharon A. ; Creevey, Christopher J. ; Oyama, Linda B. ; Mizrahi, Itzhak ; Denman, Stuart E. ; Popova, Milka ; Muñoz-Tamayo, Rafael ; Forano, Evelyne ; Waters, Sinead M. ; Hess, Matthias ; Tapio, Ilma ; Smidt, Hauke ; Krizsan, Sophie J. ; Yáñez-Ruiz, David R. ; Belanche, Alejandro ; Guan, Leluo ; Gruninger, Robert J. ; McAllister, Tim A. ; Newbold, C.J. ; Roehe, Rainer ; Dewhurst, Richard J. ; Snelling, Tim J. ; Watson, Mick ; Suen, Garret ; Hart, Elizabeth H. ; Kingston-Smith, Alison H. ; Scollan, Nigel D. ; Prado, Rodolpho M. Do; Pilau, Eduardo J. ; Mantovani, Hilario C. ; Attwood, Graeme T. ; Edwards, Joan E. ; McEwan, Neil R. ; Morrisson, Steven ; Mayorga, Olga L. ; Elliott, Christopher ; Morgavi, Diego P. - \ 2018
Frontiers in Microbiology 9 (2018)SEP. - ISSN 1664-302X
Diet - Host - Methane - Microbiome - Omics - Production - Rumen

The rumen is a complex ecosystem composed of anaerobic bacteria, protozoa, fungi, methanogenic archaea and phages. These microbes interact closely to breakdown plant material that cannot be digested by humans, whilst providing metabolic energy to the host and, in the case of archaea, producing methane. Consequently, ruminants produce meat and milk, which are rich in high-quality protein, vitamins and minerals, and therefore contribute to food security. As the world population is predicted to reach approximately 9.7 billion by 2050, an increase in ruminant production to satisfy global protein demand is necessary, despite limited land availability, and whilst ensuring environmental impact is minimized. Although challenging, these goals can be met, but depend on our understanding of the rumen microbiome. Attempts to manipulate the rumen microbiome to benefit global agricultural challenges have been ongoing for decades with limited success, mostly due to the lack of a detailed understanding of this microbiome and our limited ability to culture most of these microbes outside the rumen. The potential to manipulate the rumen microbiome and meet global livestock challenges through animal breeding and introduction of dietary interventions during early life have recently emerged as promising new technologies. Our inability to phenotype ruminants in a high-throughput manner has also hampered progress, although the recent increase in "omic" data may allow further development of mathematical models and rumen microbial gene biomarkers as proxies. Advances in computational tools, high-throughput sequencing technologies and cultivation-independent "omics" approaches continue to revolutionize our understanding of the rumen microbiome. This will ultimately provide the knowledge framework needed to solve current and future ruminant livestock challenges.

Global Carbon Budget 2017
Quéré, Corinne Le; Andrew, Robbie M. ; Friedlingstein, Pierre ; Sitch, Stephen ; Pongratz, Julia ; Manning, Andrew C. ; Ivar Korsbakken, Jan ; Peters, Glen P. ; Canadell, Josep G. ; Jackson, Robert B. ; Boden, Thomas A. ; Tans, Pieter P. ; Andrews, Oliver D. ; Arora, Vivek K. ; Bakker, Dorothee C.E. ; Barbero, Leticia ; Becker, Meike ; Betts, Richard A. ; Bopp, Laurent ; Chevallier, Frédéric ; Chini, Louise P. ; Ciais, Philippe ; Cosca, Catherine E. ; Cross, Jessica ; Currie, Kim ; Gasser, Thomas ; Harris, Ian ; Hauck, Judith ; Haverd, Vanessa ; Houghton, Richard A. ; Hunt, Christopher W. ; Hurtt, George ; Ilyina, Tatiana ; Jain, Atul K. ; Kato, Etsushi ; Kautz, Markus ; Keeling, Ralph F. ; Klein Goldewijk, Kees ; Körtzinger, Arne ; Landschützer, Peter ; Lefèvre, Nathalie ; Lenton, Andrew ; Lienert, Sebastian ; Lima, Ivan ; Lombardozzi, Danica ; Metzl, Nicolas ; Millero, Frank ; Monteiro, Pedro M.S. ; Munro, David R. ; Nabel, Julia E.M.S. ; Nakaoka, Shin Ichiro ; Nojiri, Yukihiro ; Padin, X.A. ; Peregon, Anna ; Pfeil, Benjamin ; Pierrot, Denis ; Poulter, Benjamin ; Rehder, Gregor ; Reimer, Janet ; Rödenbeck, Christian ; Schwinger, Jörg ; Séférian, Roland ; Skjelvan, Ingunn ; Stocker, Benjamin D. ; Tian, Hanqin ; Tilbrook, Bronte ; Tubiello, Francesco N. ; Laan-Luijkx, Ingrid T. van der; Werf, Guido R. van der; Heuven, Steven Van; Viovy, Nicolas ; Vuichard, Nicolas ; Walker, Anthony P. ; Watson, Andrew J. ; Wiltshire, Andrew J. ; Zaehle, Sönke ; Zhu, Dan - \ 2018
Earth System Science Data 10 (2018)1. - ISSN 1866-3508 - p. 405 - 448.
Accurate assessment of anthropogenic carbon dioxide (CO2) emissions and their redistribution among the atmosphere, ocean, and terrestrial biosphere-the "global carbon budget"-is important to better understand the global carbon cycle, support the development of climate policies, and project future climate change. Here we describe data sets and methodology to quantify the five major components of the global carbon budget and their uncertainties. CO2 emissions from fossil fuels and industry (EFF) are based on energy statistics and cement production data, respectively, while emissions from land-use change (ELUC), mainly deforestation, are based on land-cover change data and bookkeeping models. The global atmospheric CO2 concentration is measured directly and its rate of growth (GATM) is computed from the annual changes in concentration. The ocean CO2 sink (SOCEAN) and terrestrial CO2 sink (SLAND) are estimated with global process models constrained by observations. The resulting carbon budget imbalance (BIM), the difference between the estimated total emissions and the estimated changes in the atmosphere, ocean, and terrestrial biosphere, is a measure of imperfect data and understanding of the contemporary carbon cycle. All uncertainties are reported as ±1δ. For the last decade available (2007-2016), EFF was 9.4±0.5 GtC yr-1, ELUC 1.3±0.7 GtC yr-1, GATM 4.7±0.1 GtC yr-1, SOCEAN 2.4±0.5 GtC yr-1, and SLAND 3.0±0.8 GtC yr-1, with a budget imbalance BIM of 0.6 GtC yr-1 indicating overestimated emissions and/or underestimated sinks. For year 2016 alone, the growth in EFF was approximately zero and emissions remained at 9.9±0.5 GtC yr-1. Also for 2016, ELUC was 1.3±0.7 GtC yr-1, GATM was 6.1±0.2 GtC yr-1, SOCEAN was 2.6±0.5 GtC yr-1, and SLAND was 2.7±1.0 GtC yr-1, with a small BIM of-0.3 GtC. GATM continued to be higher in 2016 compared to the past decade (2007-2016), reflecting in part the high fossil emissions and the small SLAND consistent with El Ninõ conditions. The global atmospheric CO2 concentration reached 402.8±0.1 ppm averaged over 2016. For 2017, preliminary data for the first 6-9 months indicate a renewed growth in EFF of C2.0% (range of 0.8 to 3.0 %) based on national emissions projections for China, USA, and India, and projections of gross domestic product (GDP) corrected for recent changes in the carbon intensity of the economy for the rest of the world. This living data update documents changes in the methods and data sets used in this new global carbon budget compared with previous publications of this data set (Le Quéré et al., 2016, 2015b, a, 2014, 2013). All results presented here can be downloaded from https://doi.org/10.18160/GCP-2017 (GCP, 2017).
CRISPR-cas-mediated phage resistance enhances horizontal gene transfer by transduction
Watson, Bridget N.J. ; Staals, Raymond H.J. ; Fineran, Peter C. - \ 2018
MBio 9 (2018)1. - ISSN 2161-2129
Bacteriophages - CRISPR-Cas - Genomic islands - Horizontal gene transfer - Plasmids - Transduction

A powerful contributor to prokaryotic evolution is horizontal gene transfer (HGT) through transformation, conjugation, and transduction, which can be advantageous, neutral, or detrimental to fitness. Bacteria and archaea control HGT and phage infection through CRISPR-Cas (clustered regularly interspaced short palindromic repeats–CRISPR-associated proteins) adaptive immunity. Although the benefits of resisting phage infection are evident, this can come at a cost of inhibiting the acquisition of other beneficial genes through HGT. Despite the ability of CRISPR-Cas to limit HGT through conjugation and transformation, its role in transduction is largely overlooked. Transduction is the phage-mediated transfer of bacterial DNA between cells and arguably has the greatest impact on HGT. We demonstrate that in Pectobacterium atrosepticum, CRISPR-Cas can inhibit the transduction of plasmids and chromosomal loci. In addition, we detected phage-mediated transfer of a large plant pathogenicity genomic island and show that CRISPR-Cas can inhibit its transduction. Despite these inhibitory effects of CRISPR-Cas on transduction, its more common role in phage resistance promotes rather than diminishes HGT via transduction by protecting bacteria from phage infection. This protective effect can also increase transduction of phage-sensitive members of mixed populations. CRISPR-Cas systems themselves display evidence of HGT, but little is known about their lateral dissemination between bacteria and whether transduction can contribute. We show that, through transduction, bacteria can acquire an entire chromosomal CRISPR-Cas system, including cas genes and phage-targeting spacers. We propose that the positive effect of CRISPR-Cas phage immunity on enhancing transduction surpasses the rarer cases where gene flow by transduction is restricted. IMPORTANCE The generation of genetic diversity through acquisition of DNA is a powerful contributor to microbial evolution and occurs through transformation, conjugation, and transduction. Of these, transduction, the phage-mediated transfer of bacterial DNA, is arguably the major route for genetic exchange. CRISPR-Cas adaptive immune systems control gene transfer by conjugation and transformation, but transduction has been mostly overlooked. Our results indicate that CRISPR-Cas can impede, but typically enhances the transduction of plasmids, chromosomal genes, and pathogenicity islands. By limiting wild-type phage replication, CRISPR-Cas immunity increases transduction in both phage-resistant and -sensitive members of mixed populations. Furthermore, we demonstrate mobilization of a chromosomal CRISPR-Cas system containing phage-targeting spacers by generalized transduction, which might partly account for the uneven distribution of these systems in nature. Overall, the ability of CRISPR-Cas to promote transduction reveals an unexpected impact of adaptive immunity on horizontal gene transfer, with broader implications for microbial evolution.

Co- evolutionary planning theory: Evolutionary Governance Theory and its relatives
Assche, K.A.M. van; Beunen, R. ; Duineveld, M. - \ 2018
In: The Routledge Handbook of Planning Theory / Gunder, Michael, Madanipour, Ali, Watson, Vanessa, New York : Routledge - ISBN 9781138905016 - p. 221 - 233.
In a changing and often unpredictable globalized world, planning theory is core to understanding how planning and its practices both function and evolve. As illustrated in The Routledge Hand-book of Planning Theory, planning and its many roles have changed profoundly over the recent decades; so have the theories, both critical and explanatory, about its practices, values and knowledges. The handbook presents key contemporary themes in planning theory through the views of some of the most innovative thinkers in planning.
The Routledge Handbook of Planning Theory includes a chapter on Evolutionary Governance Theory. The chapters analyses the presence, the origins and the potential of co- evolutionary perspectives in planning theory. It pay particular attention to Evolutionary Governance Theory, as a comprehensive perspective on co- evolution in spatial planning and governance. The co- evolutionary approach to planning presents a middle ground between (social) engineering ap-proaches on the one hand and theories completely disqualifying planning and steering on the other. Both ends of the spectrum have often been criticized for respectively overestimating the steering possibilities of governments and the organizing capacities of markets. Planning theory embedded in governance theory can help to analyse and understand a particular governance context, to delineate the possibilities and limits of planning in that context, and to determine which planning efforts are most likely to have a positive impact. In a co-evolutionary perspec-tive, context as such, and governance context in particular, are never fixed, never stable: all elements and structures are continuously influencing each other.
The co-evolutionary perspective as developed in EGT opens up planning theory for a series of relevant concepts from different disciplines, relevant for the analysis of current and potential forms of planning in a community, while conversely giving theories and practices of planning a firm place within governance. The chapters shows how a co-evolutionary perspective is a very useful lens for both analysis and change, for the development of new planning perspectives or for the deliberate circumvention of a current planning system
Optimizing legume cropping : The policy questions
Kuhlman, Tom ; Helming, John ; Linderhof, Vincent - \ 2017
In: Legumes in Cropping Systems / Murphy-Bokern, D., Stoddard, F., Watson, C., CABI International - ISBN 9781780646749 - p. 226 - 243.
The cultivation of legumes is low in Europe. Public policy incentives and/or regulations have a role to play in changing this. This chapter examines six such policies. The CAPRI (Common Agricultural Policy Regional Impact) model, a partial equilibrium model for the agricultural sector, is used to simulate the effects of these policies and compare them to what would happen if no policy action were taken. Five of these policy scenarios are aimed at grain legumes (pulses and soybean), and one at forage legumes (in particular, clover). Three of the policies could be incorporated into the Common Agricultural Policy, whereas the other three are more general in nature: related to consumption, international trade and climate-change mitigation. It is the latter two that are likely to have the most significant effect on the cultivation of grain legumes.
Contribution of Dairy to Nutrient Intake in the Western Diet
Hettinga, Kasper ; Valenberg, Hein van - \ 2017
In: Nutrients in Dairy and Their Implications for Health and Disease / Watson, Ronald Ross, Collier, Robert J., Preedy, Victor R., Academic Press - ISBN 9780128097625 - p. 251 - 258.
Dairy - Dietary patterns - Minerals - Nutrient density - Omega-3 fatty acids - Protein quality - Vitamins

Milk and dairy products play an important role in providing nutrients in both Western and developing countries. Most research in this area focuses on the intake of individual nutrients from food products, like dairy products. However, nutrients are not consumed, and do not function, in isolation. Looking at nutrient intake from the perspective of whole food products, or even whole dietary patterns, may be a more suitable way to quantify the contribution of dairy to the intake of nutrients. A mathematical approach, the nutrient-rich food score, is explained and discussed in this chapter. Such models could in the future even be extended beyond nutrition (e.g., including sustainability or cost parameters) to even better guide healthy eating habits for consumers.

Positive biodiversity-productivity relationship predominant in global forests
Liang, J. ; Crowther, T.W. ; Picard, N. ; Wiser, S. ; Zhou, M. ; Alberti, G. ; Schulze, E.D. ; Mcguire, A.D. ; Bozzato, F. ; Pretzsch, H. ; Miguel, S. de; Paquette, A. ; Herault, B. ; Scherer-lorenzen, M. ; Barrett, C.B. ; Glick, H.B. ; Hengeveld, G.M. ; Nabuurs, Gert-Jan ; Pfautsch, S. ; Viana, H. ; Vibrans, A.C. ; Ammer, C. ; Schall, P. ; Verbyla, D. ; Tchebakova, N. ; Fischer, M. ; Watson, J.V. ; Chen, Han Y.H. ; Lei, X. ; Schelhaas, M.J. ; Lu, Huicui ; Gianelle, D. ; Parfenova, E.I. ; Salas, C. ; Lee, E. ; Lee, B. ; Kim, H.S. ; Bruelheide, H. ; Coomes, D.A. ; Piotto, D. ; Sunderland, T. ; Schmid, B. ; Gourlet-Fleury, S. ; Sonke, B. ; Tavani, R. ; Zhu, J. ; Brandl, S. ; Vayreda, J. ; Kitahara, F. ; Searle, E.B. ; Neldner, V.J. ; Ngugi, M.R. ; Baraloto, C. ; Frizzera, L. ; Ba Azy, R. ; Oleksyn, J. ; Zawila-Niedzwiecki, T. ; Bouriaud, O. ; Bussotti, F. ; Finer, L. ; Jaroszewicz, B. ; Jucker, T. ; Valladares, F. ; Jagodzinski, A.M. ; Peri, P.L. ; Gonmadje, C. ; Marthy, W. ; Obrien, T. ; Martin, E.H. ; Marshall, A.R. ; Rovero, F. ; Bitariho, R. ; Niklaus, P.A. ; Alvarez-Loayza, P. ; Chamuya, N. ; Valencia, R. ; Mortier, F. ; Wortel, V. ; Engone-Obiang, N.L. ; Ferreira, L.V. ; Odeke, D.E. ; Vasquez, R.M. ; Lewis, S.L. ; Reich, P.B. - \ 2016
Science 354 (2016)6309. - ISSN 0036-8075 - 15 p.
The biodiversity-productivity relationship (BPR) is foundational to our understanding of the global extinction crisis and its impacts on ecosystem functioning. Understanding BPR is critical for the accurate valuation and effective conservation of biodiversity. Using ground-sourced data from 777,126 permanent plots, spanning 44 countries and most terrestrial biomes, we reveal a globally consistent positive concave-down BPR, showing that continued biodiversity loss would result in an accelerating decline in forest productivity worldwide. The value of biodiversity in maintaining commercial forest productivity alone—US$166 billion to 490 billion per year according to our estimation—is more than twice what it would cost to implement effective global conservation. This highlights the need for a worldwide reassessment of biodiversity values, forest management strategies, and conservation priorities.
GO-FAANG meeting : a Gathering On Functional Annotation of Animal Genomes
Tuggle, Christopher K. ; Giuffra, Elisabetta ; White, Stephen N. ; Clarke, Laura ; Zhou, Huaijun ; Ross, Pablo J. ; Acloque, Hervé ; Reecy, James M. ; Archibald, Alan ; Bellone, Rebecca R. ; Boichard, Michèle ; Chamberlain, Amanda ; Cheng, Hans ; Crooijmans, Richard P.M.A. ; Delany, Mary E. ; Finno, Carrie J. ; Groenen, Martien A.M. ; Hayes, Ben ; Lunney, Joan K. ; Petersen, Jessica L. ; Plastow, Graham S. ; Schmidt, Carl J. ; Song, Jiuzhou ; Watson, Mick - \ 2016
Animal Genetics 47 (2016)5. - ISSN 0268-9146 - p. 528 - 533.
data coordination centre (DCC) - data sharing - Genomics - metanalysis

The Functional Annotation of Animal Genomes (FAANG) Consortium recently held a Gathering On FAANG (GO-FAANG) Workshop in Washington, DC on October 7–8, 2015. This consortium is a grass-roots organization formed to advance the annotation of newly assembled genomes of domesticated and non-model organisms (www.faang.org). The workshop gathered together from around the world a group of 100+ genome scientists, administrators, representatives of funding agencies and commodity groups to discuss the latest advancements of the consortium, new perspectives, next steps and implementation plans. The workshop was streamed live and recorded, and all talks, along with speaker slide presentations, are available at www.faang.org. In this report, we describe the major activities and outcomes of this meeting. We also provide updates on ongoing efforts to implement discussions and decisions taken at GO-FAANG to guide future FAANG activities. In summary, reference datasets are being established under pilot projects; plans for tissue sets, morphological classification and methods of sample collection for different tissues were organized; and core assays and data and meta-data analysis standards were established.

Changes in perceptions and motivators that influence the implementation of on-farm Salmonella control measures by pig farmers in England
Marier, Elizabeth ; Piers Smith, Richard ; Ellis-Iversen, Johanne ; Watson, Eamon ; Armstrong, Derek ; Hogeveen, Henk ; Cook, Alasdair J.C. - \ 2016
Preventive Veterinary Medicine 133 (2016). - ISSN 0167-5877 - p. 22 - 30.
Disease control - Motivators - Pig - Salmonella - Social epidemiology

This study presents British farmers’ perception of, and barriers to, implementing Salmonella control on pig farms. Four farms that had implemented interventions and their 33 close contacts (known to the intervention farmers) took part in interviews before (phase 1) and after (phase 2) intervention trials to assess the difference in perception over time. Their results were compared against those from nine randomly selected control farms. The hypothesis was that farms implementing interventions whether or not successful, would influence their close contacts’ opinion over time. Based on a ‘pathway to disease control’ model, three intrinsic factors known to influence motivation – attitudes, social norms and self-efficacy – were evaluated. Farmers mentioned that successful interventions on a farm would attract their attention. The use of an appropriate communication strategy is therefore recommended to stimulate farmers’ intent to implement control measures. Both before and after the intervention trials, all farmers had a positive attitude towards Salmonella control and felt that their peers and authorities were supportive of controlling Salmonella on farms. In phase 2, however, farmers were more likely to want to share the burden of control with other stakeholders along the food chain and their belief in self-efficacy had weakened. Whilst social norms were not associated with an intention to take action on control, a positive attitude towards Salmonella control and a belief in self-efficacy were more likely to result in an intent to control. In phase 2, farmers with an intent to implement an intervention appeared to have a greater, but not significant positive belief in self-efficacy (p = 0.108). This study confirmed that farmers recognised their responsibility for controlling Salmonella in pork – even though their confidence in their ability to control Salmonella decreased over time – and believed that responsibility should be shared with the rest of the production chain. It showed that farmers trusted their veterinarian as a source of advice to guide them during the process of implementing change, though an increase in farms’ Salmonella seroprevalence score (Zoonosis National Control Programme (ZNCP) score) especially for those with a low ZNCP score was also likely to influence their behaviour. Getting concrete feedback from customers or a tangible benefit from their action was a strong incentive especially for farms with a ZNCP score higher than 50%. The study also revealed a need to validate which measures are effective as farmers did not perceive that the current advised interventions were worth the additional effort.

Grain legume decline and potential recovery in European agriculture : a review
Zander, Peter ; Amjath-Babu, T.S. ; Preissel, Sara ; Reckling, Moritz ; Bues, Andrea ; Schläfke, Nicole ; Kuhlman, Tom ; Bachinger, Johann ; Uthes, Sandra ; Stoddard, Fred ; Murphy-Bokern, Donal ; Watson, Christine - \ 2016
Agronomy for Sustainable Development 36 (2016)2. - ISSN 1774-0746 - 20 p.
Diversification - Economic pressures - Land use change - Protein crops - Specialization - Sustainable land use

Sustainable development of agriculture is at the core of agricultural policy debates in Europe. There is a consensus that diversification of cropping would support sustainable development. However, a reduction in legume cultivation has been observed in the EU during the last decades. This decline has induced, in turn, a deficit of proteins and a reduction of ecosystem services provided by legumes. Therefore, we analysed the mechanisms that shape agricultural systems to identify leverage points for reviving European legume production. Specifically, we reviewed the factors that affect the market and non-market value of legumes and the relevant agricultural policies. We characterized the decline in legume cropping as an outcome of the dominance of economic forces that favour specialization of production systems over diversification. We found that the value of market outputs of legumes per unit area is relatively low and volatile, with a 25–78 % variation in pea gross margins, which reduces market competitiveness. We observed that the value of system-internal outputs of legumes such as the nitrogen fixed, of 130 to 153 kg N ha−1; crop protection services that reduce agrochemical costs, by 20–25 % in cereals; and yield enhancements of subsequent crops, of 0.2 to 1.6 t ha−1 in cereals, are often underestimated. In addition, markets fail to translate external effects of legumes such as biodiversity enhancement, reduction in emissions, of up to 50 % in N2O, and soil improvements into economic benefits. Current policies support legumes through selected mechanisms such as ecological focus areas, agri-environmental programmes and sparse coupled support measures. Domestic cultivation of legumes could be supported through trade policies such as import restrictions on genetically modified soybean or new mechanisms to appreciate non-market outputs including payments for ecosystem services and carbon markets. In addition, development of new value chains, niche markets, scaling-up of plant breeding efforts and dissemination of information is required.

FOODSECURE: The Future of Global Food and Nutrition Security : Brainstorming Lab at European Development Days 2015
Watson, Jill ; Achterbosch, T.J. - \ 2015
- 20 p.
Molucular Epidemiology and Evolution of Influenza Viruses Circulating within European Swine between 2009 and 2013
Watson, S.J. ; Langat, P. ; Reid, S. ; Lam, T. ; Cotten, M. ; Kelly, M. ; Reeth, K. Van; Qiu, Y. ; Simon, G. ; Bonin, E. ; Foni, E. ; Chiapponi, C. ; Larsen, L. ; Hjulsager, C. ; Markowska-Daniel, I. ; Urbaniak, K. ; Durrwald, R. ; Schlegel, M. ; Huovilainen, A. ; Davidson, I. ; Dan, A. ; Loeffen, W.L.A. ; Edwards, S. ; Bublot, M. ; Vila, T. ; Maldonado, J. ; Valls, L. ; Brown, I.H. ; Pybus, O.G. ; Kellam, P. - \ 2015
Journal of Virology 89 (2015)19. - ISSN 0022-538X - p. 9920 - 9931.
The emergence in humans of the A(H1N1)pdm09 influenza virus, a complex reassortant virus of swine origin, highlighted the importance of worldwide influenza virus surveillance in swine. To date, large-scale surveillance studies have been reported for southern China and North America, but such data have not yet been described for Europe. We report the first large-scale genomic characterization of 290 swine influenza viruses collected from 14 European countries between 2009 and 2013. A total of 23 distinct genotypes were identified, with the 7 most common comprising 82% of the incidence. Contrasting epidemiological dynamics were observed for two of these genotypes, H1huN2 and H3N2, with the former showing multiple long-lived geographically isolated lineages, while the latter had short-lived geographically diffuse lineages. At least 32 human-swine transmission events have resulted in A(H1N1)pdm09 becoming established at a mean frequency of 8% across European countries. Notably, swine in the United Kingdom have largely had a replacement of the endemic Eurasian avian virus-like (“avian-like”) genotypes with A(H1N1)pdm09-derived genotypes. The high number of reassortant genotypes observed in European swine, combined with the identification of a genotype similar to the A(H3N2)v genotype in North America, underlines the importance of continued swine surveillance in Europe for the purposes of maintaining public health. This report further reveals that the emergences and drivers of virus evolution in swine differ at the global level.
Long-term effects of nutrients on productivity and species-richness of grassland: the Ossekampen Grassland Experiment
Korevaar, H. ; Geerts, R.H.E.M. - \ 2015
In: Proceedings of the Conference Valuing long-term sites and experiments for agriculture and ecology. - Warwick, UK : Association of Applied Biologists - p. 253 - 256.
European surveillance network for influenza in pigs : Surveillance programs, diagnostic tools and swine influenza virus subtypes identified in 14 European countries from 2010 to 2013
Simon, Gaëlle ; Larsen, Lars E. ; Dürrwald, Ralf ; Foni, Emanuela ; Harder, Timm ; Reeth, Kristien Van; Markowska-Daniel, Iwona ; Reid, Scott M. ; Dan, Adam ; Maldonado, Jaime ; Huovilainen, Anita ; Billinis, Charalambos ; Davidson, Irit ; Agüero, Montserrat ; Vila, Thaïs ; Hervé, Séverine ; Breum, Solvej Østergaard ; Chiapponi, Chiara ; Urbaniak, Kinga ; Kyriakis, Constantinos S. ; Brown, Ian H. ; Loeffen, Willie ; Meulen, Karen Van der; Schlegel, Michael ; Bublot, Michel ; Kellam, Paul ; Watson, Simon ; Lewis, Nicola S. ; Pybus, Oliver G. ; Webby, Richard ; Chen, Hualan ; Vincent, Amy L. - \ 2014
PLoS One 9 (2014)12. - ISSN 1932-6203

Swine influenza causes concern for global veterinary and public health officials. In continuing two previous networks that initiated the surveillance of swine influenza viruses (SIVs) circulating in European pigs between 2001 and 2008, a third European Surveillance Network for Influenza in Pigs (ESNIP3, 2010-2013) aimed to expand widely the knowledge of the epidemiology of European SIVs. ESNIP3 stimulated programs of harmonized SIV surveillance in European countries and supported the coordination of appropriate diagnostic tools and subtyping methods. Thus, an extensive virological monitoring, mainly conducted through passive surveillance programs, resulted in the examination of more than 9 000 herds in 17 countries. Influenza A viruses were detected in 31% of herds examined from which 1887 viruses were preliminary characterized. The dominating subtypes were the three European enzootic SIVs: avian-like swine H1N1 (53.6%), human-like reassortant swine H1N2 (13%) and human-like reassortant swine H3N2 (9.1%), as well as pandemic A/H1N1 2009 (H1N1pdm) virus (10.3%). Viruses from these four lineages co-circulated in several countries but with very different relative levels of incidence. For instance, the H3N2 subtype was not detected at all in some geographic areas whereas it was still prevalent in other parts of Europe. Interestingly, H3N2-free areas were those that exhibited highest frequencies of circulating H1N2 viruses. H1N1pdm viruses were isolated at an increasing incidence in some countries from 2010 to 2013, indicating that this subtype has become established in the European pig population. Finally, 13.9% of the viruses represented reassortants between these four lineages, especially between previous enzootic SIVs and H1N1pdm. These novel viruses were detected at the same time in several countries, with increasing prevalence. Some of them might become established in pig herds, causing implications for zoonotic infections.

Intestinal permeability - a new target for disease prevention and therapy
Bischoff, S.C. ; Barbara, G. ; Buurman, W. ; Ockhuizen, T. ; Schulzke, J.D. ; Serino, M. ; Tilg, H. ; Watson, A. ; Wells, J.M. - \ 2014
BMC Gastroenterology 14 (2014). - ISSN 1471-230X - 25 p.
irritable-bowel-syndrome - placebo-controlled trial - enteropathogenic escherichia-coli - severe acute-pancreatitis - helicobacter-pylori caga - high-fat diet - clostridium-difficile infection - serotonin reuptake transporter - epithelial barrier function - apical
Data are accumulating that emphasize the important role of the intestinal barrier and intestinal permeability for health and disease. However, these terms are poorly defined, their assessment is a matter of debate, and their clinical significance is not clearly established. In the present review, current knowledge on mucosal barrier and its role in disease prevention and therapy is summarized. First, the relevant terms ‘intestinal barrier’ and ‘intestinal permeability’ are defined. Secondly, the key element of the intestinal barrier affecting permeability are described. This barrier represents a huge mucosal surface, where billions of bacteria face the largest immune system of our body. On the one hand, an intact intestinal barrier protects the human organism against invasion of microorganisms and toxins, on the other hand, this barrier must be open to absorb essential fluids and nutrients. Such opposing goals are achieved by a complex anatomical and functional structure the intestinal barrier consists of, the functional status of which is described by ‘intestinal permeability’. Third, the regulation of intestinal permeability by diet and bacteria is depicted. In particular, potential barrier disruptors such as hypoperfusion of the gut, infections and toxins, but also selected over-dosed nutrients, drugs, and other lifestyle factors have to be considered. In the fourth part, the means to assess intestinal permeability are presented and critically discussed. The means vary enormously and probably assess different functional components of the barrier. The barrier assessments are further hindered by the natural variability of this functional entity depending on species and genes as well as on diet and other environmental factors. In the final part, we discuss selected diseases associated with increased intestinal permeability such as critically illness, inflammatory bowel diseases, celiac disease, food allergy, irritable bowel syndrome, and – more recently recognized – obesity and metabolic diseases. All these diseases are characterized by inflammation that might be triggered by the translocation of luminal components into the host. In summary, intestinal permeability, which is a feature of intestinal barrier function, is increasingly recognized as being of relevance for health and disease, and therefore, this topic warrants more attention.
Smallholder inclusion in high value-adding supply chain by Food & Agribusiness Enterprises : A case study on black soybean in Java
Sjauw-Koen-Fa, A. ; Blok, V. ; Omta, S.W.F. - \ 2014
World agriculture faces increasing resource scarcity (land, water and phosphate) and growing environmental challenges (climate change effects, declining biodiversity, land degradation) and significant post-harvest food losses. As a consequence of a tighter and more volatile future food supply, global food insecurity will raise and conventional sourcing strategies of food and agribusiness enterprises will be affected. A growing number of private and public stakeholders are considering the crucial elements of an approach that meets the challenges of global food security and ecological responsible management of resources within a framework of inclusive business models. It is increasingly recognized that to guarantee global food supply, smallholder agriculture in developing and emerging economies needs to be integrated into high value adding local-, regional- but also international food supply chains. However, the inclusion of smallholders in high value supply chain, in particular in Asia and Africa, is highly complex. Small-scale farmers face major disadvantages in accessing high value supply chains. These include low volumes of produce to sell, variable quality, high transaction costs, poor functioning producer organizations and rural financial systems, and a limited ability to meet the high credence requirements of many high value outlets. They typically face a tilted playing field in terms of access to land, input, credit, technology and markets. The aspiration of food and agribusiness multinational enterprises (F&A MNEs) is to increase agricultural production by 20% while decreasing greenhouse gas emissions by 20% and reducing the prevalence of rural poverty by 20% each decade (WEF 2011). The WEF (2013, p. 4) reported that the initiatives taken by the public and private sector since the launching of ‘The New Vision of Agriculture’, will directly impact 12 million smallholder farmers in the next three to five years. The research question therefore arises: How can F&A MNEs be able to realise the so called 20/20/20 goals from a business perspective and therefore, how can they integrate smallholder supply in their core supply chains? Until now it is unclear how MNEs can realize smallholder inclusion in a manner that is both profitable and sustainable. Most pilot projects are supported and subsidized by governments, development agencies, NGOs or charitable organizations (i.e. Biénabe et al.,eds., 2011; Reardon et al.,2009). Smallholder inclusion pilot projects in which companies are involved, are often primarily CSR-driven. While this is how new experiences often begin prior to reaching mainstream corporate businesses and markets, the business perspective of investments in smallholders as supply source is still underrepresented in current research. In the present paper, we provide arguments for smallholder inclusion into high value supply chains from a business perspective. Based on an literature review, we identify potential keys to unlock smallholder agricultural production potential and elaborate on the challenges of smallholder inclusion in high value supply chains. A framework for an inclusive food strategy and an agenda for future research will be provided in the paper. This framework can help stakeholders along the food supply chain with the development of an inclusive food strategy in general, and F&A MNE’s in particular with the development of sustainable sourcing strategies. References Biénabe, E., Berdegué, J., Peppelenbos, L., and Belt, J., eds., 2011. Reconnecting Markets: Innovative Global Practices in connecting small-scale producers with dynamic food markets, Grower Publishing Limited, Farnham. Genier, C., Stamp, M. and Pfitzer, M., 2009. Corporate Social Responsibility for agro-industries development, Agro-industries for development, 223-252, FAO, UNIDO and CAB international, Rome. London, T. and Hart, S. L., eds. (2010). Next generation business strategies for the base of the pyramid. New approaches for building mutual value, Pearson Education, New Jersey. McIntyre, B.D., Herren, R.H., Wakhungu, J. and Watson, R.T., eds., 2009. Agriculture at a crossroad: Global report. IAASTD, Island Press, Washington. World Economic Forum, 2011. Realizing a new vision for agriculture: A road map for stakeholders, Geneva. World Economic Forum, 2013. Achieving the new vision for agriculture: New models for action, Geneva.
The impact of omega-3 fatty acids on quality of life
Rest, O. van de; Groot, C.P.G.M. de - \ 2014
In: Omega-3 Fatty Acids in Brain and Neurological Health / Watson, R.R., de Meester, F., San Diego : Elsevier - ISBN 9780124105270 - p. 81 - 85.
Improving quality of life (QoL) is becoming an increasingly important outcome in research into the elderly population and for studies in health promotion; generic outcomes are, next to disorder-specific outcomes, also very important. Current evidence indicates that low dietary intake and a low status of omega-3 fatty acids may be associated with mental health problems, which are among the leading causes of impaired QoL in old age. Some studies have also been performed that directly investigated the relationship between omega-3 fatty acids and QoL. In the current chapter these studies will be summarized and discussed. However, because the total number of studies is very limited (only two observational studies and only three intervention studies), no firm conclusions can yet be drawn. More research is warranted, for which some suggestions are provided in this chapter.
Induction and suppression of tick cell antiviral RNAi responses by tick-borne flaviviruses
Schnettler, E. ; Tykalova, H. ; Watson, M. ; Sharma, M. ; Sterken, M.G. ; Obbard, D.J. ; Lewis, S.H. ; McFarlane, M. ; Bell-Sakyi, L. ; Barry, G. ; Weisheit, S. ; Best, S.M. ; Kuhn, R.J. ; Pijlman, G.P. ; Chase-Topping, M.E. ; Gould, E.A. ; Grubhoffer, L. ; Fazakerley, J.K. ; Kohl, A. - \ 2014
Nucleic Acids Research 42 (2014)14. - ISSN 0305-1048 - p. 9436 - 9446.
forest-virus replicon - interferon antagonist - arbovirus infection - immunity - replication - drosophila - identification - alphavirus - mosquitos - origin
Arboviruses are transmitted by distantly related arthropod vectors such as mosquitoes (class Insecta) and ticks (class Arachnida). RNA interference (RNAi) is the major antiviral mechanism in arthropods against arboviruses. Unlike in mosquitoes, tick antiviral RNAi is not understood, although this information is important to compare arbovirus/host interactions in different classes of arbovirus vectos. Using an Ixodes scapularis-derived cell line, key Argonaute proteins involved in RNAi and the response against tick-borne Langat virus (Flaviviridae) replication were identified and phylogenetic relationships characterized. Analysis of small RNAs in infected cells showed the production of virus-derived small interfering RNAs (viRNAs), which are key molecules of the antiviral RNAi response. Importantly, viRNAs were longer (22 nucleotides) than those from other arbovirus vectors and mapped at highest frequency to the termini of the viral genome, as opposed to mosquito-borne flaviviruses. Moreover, tick-borne flaviviruses expressed subgenomic flavivirus RNAs that interfere with tick RNAi. Our results characterize the antiviral RNAi response in tick cells including phylogenetic analysis of genes encoding antiviral proteins, and viral interference with this pathway. This shows important differences in antiviral RNAi between the two major classes of arbovirus vectors, and our data broadens our understanding of arthropod antiviral RNAi.
The Socio-Political Conceptualization of Serengeti Landscapes in Europe: The Case of ‘Western Iberia’
Pellis, A. ; Felder, M. ; Duim, V.R. van der - \ 2013
In: Proceedings RMRS-P-74. - Fort Collins, USA : Department of Agriculture, Forest Service, Rocky Mountain Research Station - p. 21 - 27.
This paper reflects on the socio-political conceptualization of ‘Western Iberia’, one of Rewilding Europe’s first pilot areas. Drawing from Actor Network Theory and social theories discussing Politics of Scale, we illustrate how ‘Western Iberia’ is continuously being negotiated through practices in different sites within / outside its geographical boundaries. We identify five different versions of ‘Western Iberia’ for illustrative purposes to claim that there is not one ‘Western Iberia’ but many. We conclude that these multiple versions are contingent and produced in networks of actors, but also limited to unique social and material conditions. Through better understanding socio-political practice in constituting, approaching, arranging and representing ‘Western Iberia’, we aim to complement on-going ecological studies that traditionally reflect upon natural processes of rewilding. “
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