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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Effect of meat processing on viability of Toxoplasma gondii: Towards replacement of mouse bioassay by in vitro testing
Opsteegh, M. ; Dam-Deisz, C. ; Boer, P. de; Fare, A. ; Hengeveld, P. ; Luiten, R. ; Smits, C.B. ; Verkleij, T. ; Giessen, Judith van der; Wisselink, H.J. - \ 2019
Felines are the definitive hosts of T. gondii and primary infection results in fecal shedding of infectious oocysts. Infected intermediate hosts will develop tissue cysts, which are infective to both cats and intermediate hosts. Meat containing viable tissue cysts is considered one of the main sources of human infection. In contrast to fresh meat, raw meat products usually undergo processing, including salting and mixing in additives such as acetate and lactate, which affects the viability of T. gondii. However, the experiments currently described in literature, are not always performed in line with the processing methods applied in industry. Therefore we aimed to study the effect of salting and additives according to the recipes used by commercial producers. Mouse or cat bioassay is the gold standard to demonstrate the presence of viable T. gondii. However, it is costly, time consuming and for ethical reasons not preferred for large-scale studies. Therefore, our second aim was to develop an alternative for mouse bioassay that can be used to determine the effect of processing on the viability of T. gondii tissue cysts. We focused on a tissue culture method to determine the parasite's ability to multiply, and a PMA-based assay to selectively detect DNA from live cells. Results with the PMA-based method were inconsistent and did not sufficiently discriminate between live and dead parasites. The tissue culture method showed promising results, but further optimization is needed before it can replace or reduce the number of mouse bioassays needed. Small scale experiments with minced meat incubated for 20h with low concentrations of salt, lactate and acetate showed a large but incomplete reduction of the number of infected mice. In future, in vitro methods are needed to allow more extensive testing of product-specific processing methods, thereby providing a better indication of the risk of T. gondii infection for consumers.
Clonal expansion of a virulent Streptococcus suis serotype 9 lineage distinguishable from carriage subpopulations
Willemse, Niels ; Ark, Kees C.H. van der; Stockhofe-Zurwieden, Norbert ; Smith, Hilde ; Picavet, Daisy I. ; Solt-Smits, Conny van; Wisselink, Henk J. ; Schultsz, Constance ; Greeff, Astrid de - \ 2019
Scientific Reports 9 (2019)1. - ISSN 2045-2322

Streptococcus suis is a porcine pathogen, causing severe invasive infections. S. suis serotype 9 is increasingly causing disease in Dutch and Chinese pig herds, but it is unknown whether all serotype 9 isolates are equally virulent and markers that can identify virulent strains are not available. Therefore, discrimination between virulent isolates and carriage isolates typically not associated with disease, is currently not possible. We collected tonsillar S. suis isolates from 6 herds not previously diagnosed with S. suis infections, and clinical S. suis isolates of previously diseased pigs. We confirmed the virulence of a virulent type strain and one representative clinical isolate, and the lack of virulence of two carriage isolates, in a pig infection model. Phylogenetic analysis of whole genome sequences of 124 isolates resulted in 10 groups, of which two were almost uniquely populated by clinical isolates. The population structure of S. suis serotype 9 appears highly diverse. However, analysis of the capsule loci sequences showed variation in a single region which fully correlated with a virulent genotype. Transmission electron microscopy suggested differences in capsule thickness between carriage and clinical genotypes. In conclusion, we found that that the S. suis serotype 9 population in the Netherlands is diverse. A distinct virulence-associated lineage was identified and could be discriminated based on the capsule locus sequence. Whilst the difference in virulence cannot be directly attributed to the DNA sequence, the correlation of capsule locus sequence with virulence could be used in the development of diagnostic tests to identify potential virulent S. suis serotype 9 in pigs.

Older adults’ active involvement in an undergraduate program in gerontology: Motives and meaning
Sliepenbeek, Marjan ; Smits, Carolien ; Spelt, Elisabeth J.H. ; Jukema, Jan S. - \ 2019
Gerontology and Geriatrics Education (2019). - ISSN 0270-1960
cocreation - Gerontological competences - older adults - undergraduate education - volunteers

Two Dutch undergraduate programs in applied gerontology have teamed up with older volunteers to educate students in collaborating with older adults in the field of age-friendly service development. The research question of this study was: What are the motives and meanings of the older volunteers concerning their participation in an undergraduate program? An explorative descriptive qualitative design was used to study the motives and meanings of the older volunteers through semi-structured interviews (n = 11) and a focus group interview (n = 4). Two themes and nine categories emerged: (1) Personal norms and values (categories: responsible life attitude, contribution, self-determination), (2) Personal gain (categories: intergenerational education, personal development, staying healthy, pleasure, feeling appreciated, feeling connected). Personal norms and values and personal gains are meaningful to older volunteers in applied gerontology education. Universities should respect these when designing measures for improving participation methods.

Successional Dynamics in the Gut Microbiome Determine the Success of Clostridium difficile Infection in Adult Pig Models
Jurburg, Stephanie D. ; Cornelissen, Jan J.B.W.J. ; Boer, Paulo de; Smits, Mari A. ; Rebel, Johanna M.J. - \ 2019
Frontiers in Cellular and Infection Microbiology 9 (2019). - ISSN 2235-2988 - 11 p.
animal models - bacteria - Clostridium difficile - microbiome - pig

Clostridium difficile infections (CDI) are a major cause of antibiotic-associated diarrhea. It is hypothesized that CDI develops due to the antibiotic-induced disruption of the intestinal microbial community structure, which allows C. difficile to flourish. Here, we pre-treated weaned pigs with the antibiotics Clindamycin or Ciprofloxacin for 1 day, and subsequently inoculated them with a human and pig enteropathogenic C. difficile strain 078 spores. Body temperature, clinical signs of disease, and the fecal microbiome were monitored daily for 15 days. Clindamycin had a stronger effect on the pigs than Ciprofloxacin, resulting in drastic shifts in the fecal microbiome, decreases in microbial diversity and significant increases in body temperature, even in the absence of C. difficile. Fecal shedding of C. difficile was detectable for 3 and 9 days in Ciprofloxacin and Clindamycin treated pigs inoculated with C. difficile, respectively, and in both cases decreased cell proliferation rates were detected in colon tissue. The timing of C. difficile shedding coincided with the decrease in a large cluster of Firmicutes following Clindamycin treatment, a pattern which was also independent of C. difficile inoculation. The observed community patterns suggest that successional dynamics following antibiotic treatment facilitate C. difficile establishment. The similarities between the microbiome responses observed in our study and those previously reported in CDI-infected humans further support the utility of adult pigs as models for the study of CDI.

The social license to operate of oil and gas development in Greenland
Smits, Coco C.A. - \ 2019
Wageningen University. Promotor(en): J.P.M. van Tatenhove, co-promotor(en): J. van Leeuwen. - Wageningen : Wageningen University - ISBN 9789463950459 - 221
Kun je je alvast wapenen tegen verkoudheid en griep?
Wichers, Harry - \ 2019
Circulaire economie en hergebruik van grondstoffen – de casus fosfaat
Kistenkas, F.H. ; Smits, M.J.W. - \ 2019
Landwerk 2019 (2019)3. - ISSN 1567-1844 - p. 18 - 22.
Akkermansia muciniphila Exerts Lipid-Lowering and Immunomodulatory Effects without Affecting Neointima Formation in Hyperlipidemic APOE*3-Leiden.CETP Mice
Katiraei, Saeed ; Vries, Margreet R. de; Costain, Alice H. ; Thiem, Kathrin ; Hoving, Lisa R. ; Diepen, Janna A. van; Smits, Hermelijn H. ; Bouter, Kristien E. ; Rensen, Patrick C.N. ; Quax, Paul H.A. ; Nieuwdorp, Max ; Netea, Mihai G. ; Vos, Willem M. de; Cani, Patrice D. ; Belzer, Clara ; Dijk, Ko Willems van; Berbée, Jimmy F.P. ; Harmelen, Vanessa van - \ 2019
Molecular Nutrition & Food Research (2019). - ISSN 1613-4125
Akkermansia muciniphila - atherosclerosis - immunity - lipid metabolism - mesenteric lymph nodes

Scope: Akkermansia muciniphila (A. muciniphila) is an intestinal commensal with anti-inflammatory properties both in the intestine and other organs. The aim is to investigate the effects of oral administration of A. muciniphila on lipid metabolism, immunity, and cuff-induced neointima formation in hyperlipidemic APOE*3-Leiden (E3L).CETP mice. Methods and results: Hyperlipidemic male E3L.CETP mice are daily treated with 2 × 108 CFU A. muciniphila by oral gavage for 4 weeks and the effects are determined on plasma lipid levels, immune parameters, and cuff-induced neointima formation and composition. A. muciniphila administration lowers body weight and plasma total cholesterol and triglycerides levels. A. muciniphila influences the immune cell composition in mesenteric lymph nodes, as evident from an increased total B cell population, while reducing the total T cell and neutrophil populations. Importantly, A. muciniphila reduces the expression of the activation markers MHCII on dendritic cells and CD86 on B cells. A. muciniphila also increases whole blood ex vivo lipopolysaccharide-stimulated IL-10 release. Finally, although treatment with A. muciniphila improves lipid metabolism and immunity, it does not affect neointima formation or composition. Conclusions: Four weeks of treatment with A. muciniphila exerts lipid-lowering and immunomodulatory effects, which are insufficient to inhibit neointima formation in hyperlipidemic E3L.CETP mice.

Experiences and views of older people on their participation in a nurse-led health promotion intervention: “community health consultation offices for seniors”
Marcus-Varwijk, Anne Esther ; Madjdian, Dónya S. ; Vet, Emely de; Mensen, Monique W.M. ; Visscher, Tommy L.S. ; Ranchor, Adelita V. ; Slaets, Joris P.J. ; Smits, Carolien H.M. - \ 2019
PLoS ONE 14 (2019)5. - ISSN 1932-6203

The growing number of community-dwelling older adults and the increased risks of adverse health events that accompany ageing, call for health promotion interventions. Nurses often lead these interventions. The views and experiences of older adults participating in these interventions have rarely been studied. To understand the views of targeted older adults, qualitative studies are essential. The aim of this study was to investigate the views and experiences of older adults on their participation in a nurse-led intervention, taking into account their views on healthy aging. Methods In a qualitative study, nineteen Dutch older adults aged 62 to 92 years participated in semi-structured interviews. These were transcribed verbatim and coded with the Qualitative Data Analysis Miner software program. The Qualitative Analysis Guide of Leuven was used for data analysis. Results Based on the analysis of the interviews, the following main themes emerged from the data reflecting the experiences of the participants: 1) awareness of aging, 2) experienced interaction with the nurse, and 3) perception of the consultations as a check-up and/or personal support. Conclusions This study underscores the importance of nurse-led interventions that match older adults’ personal views concerning healthy living, and their views and experiences concerning these interventions. Older adults’ holistic views of healthy living were not always assessed and valued by the nurses. Also, our study shows a wide variety of expectations, views and experiences among the participating older adults. This implies that health professionals should adjust their working and communication methods to the older adult’s views on life.

Multimodal Tracking of Controlled Staphylococcus aureus Infections in Mice
Welling, Mick M. ; Korne, Clarize M. De; Spa, Silvia J. ; Willigen, Danny M. Van; Hensbergen, Albertus W. ; Bunschoten, Anton ; Duszenko, Nikolas ; Smits, Wiep Klaas ; Roestenberg, Meta ; Leeuwen, Fijs W.B. Van - \ 2019
Bmc Infectious Diseases 5 (2019)7. - ISSN 1471-2334 - p. 1160 - 1168.
bacterial infection - cell-tracking - fluorescence - multimodal - SPECT - ubiquicidin

There is a need to develop diagnostic and analytical tools that allow noninvasive monitoring of bacterial growth and dissemination in vivo. For such cell-tracking studies to hold translational value to controlled human infections, in which volunteers are experimentally colonized, they should not require genetic modification, and they should allow tracking over a number of replication cycles. To gauge if an antimicrobial peptide tracer, 99m Tc-UBI 29-41 -Cy5, which contains both a fluorescent and a radioactive moiety, could be used for such in vivo bacterial tracking, we performed longitudinal imaging of a thigh-muscle infection with 99m Tc-UBI 29-41 -Cy5-labeled Staphylococcus aureus. Mice were imaged using SPECT and fluorescence-imaging modalities at various intervals during a 28 h period. Biodistribution analyses were performed to quantitate radioactivity in the abscess and other tissues. SPECT and fluorescence imaging in mice showed clear retention of the 99m Tc-UBI 29-41 -Cy5-labeled bacteria following inoculation in the thigh muscle. Despite bacterial replication, the signal intensity in the abscess only modestly decreased within a 28 h period: 52% of the total injected radioactivity per gram of tissue (%ID/g) at 4 h postinfection (pi) versus 44%ID/g at 28 h pi (15% decrease). After inoculation, a portion of the bacteria disseminated from the abscess, and S. aureus cultures were obtained from radioactive urine samples. Bacterial staining with 99m Tc-UBI 29-41 -Cy5 allowed noninvasive bacterial-cell tracking during a 28 h period. Given the versatility of the presented bacterial-tracking method, we believe that this concept could pave the way for precise imaging capabilities during controlled-human-infection studies.

De betekenis van mestverwerking in een circulaire economie
Woltjer, Geert ; Smits, Marie-José - \ 2019
Wageningen : Wageningen Economic Research (Wageningen Economic Research nota 2019-029) - 23
What is the role of manure processing in the transition to a circular economy? To this end, it is first of all important to get a clear picture of what manure processing is and how (manure) policy influences this. Current manure processing fits within a system that is primarily focused on solving current problems. However, the question is whether there is a role for manure processing if the transition to a circular economy is more advanced and, if so, what that role is.
Fluorescent imaging of bacterial infections and recent advances made with multimodal radiopharmaceuticals
Welling, Mick M. ; Hensbergen, Albertus W. ; Bunschoten, Anton ; Velders, Aldrik H. ; Scheper, Henk ; Smits, Wiep Klaas ; Roestenberg, Meta ; Leeuwen, Fijs W.B. van - \ 2019
Clinical and Translational Imaging 7 (2019)2. - ISSN 2281-5872 - p. 125 - 138.
Bacterial infection - Fluorescence imaging - Infectious diseases - Molecular imaging - Radioactivity

Background: Today, both radioactive SPECT and PET imaging radiopharmaceuticals are used for clinical diagnosis of bacterial infections. Due to the possible applications in image-guided surgery, fluorescent imaging of infections has gained interest. We here present the highlights and recent developments in the use of fluorescence imaging for bacterial infections. In this overview, we also include the latest developments in multimodal bacterial imaging strategies that combine radioactive and fluorescent imaging. Based on this literature, we present our future perspectives for the field including the translational potential. Methods: In the current review, we complement earlier reports with the most recent fluorescent and multimodal radiopharmaceuticals for bacterial infection imaging. Where possible, in this review, the chemical structure of the compounds and clinical images were shown. Results: A total of 35 out of 77 original articles on pre-clinical and clinical imaging of bacterial infections with fluorescent tracers and multimodality radiopharmaceuticals were included for reviewing. Conclusion: In our view, the highest translational potential lies with compounds that are based on targeting vectors that are specific for bacteria: e.g., fluorescently labelled UBI 29–41 , polymyxin B, vancomycin, ZnDPA and a M. tuberculosis-specific β-lactamase-cleavable linker CNIP800. Multimodal concepts using dually labelled UBI 29–41 , vancomycin, and ZnDPA help connect optical imaging to the more traditional use of radiopharmaceuticals in infectious diseases. Multimodal bacterial imaging is a promising strategy not only to diagnose bacterial infections but also to evaluate the effectivity of surgical treatment for infections.

Natuurinclusieve landbouw: van niches naar mainstream (fase 1)
Smits, Marie-José ; Polman, Nico ; Michels, Rolf ; Migchels, Gerard ; Schrijver, Raymond ; Sukkel, Wijnand ; Visser, Andries ; Vogelzang, Theo ; Kistenkas, Fred - \ 2019
Wageningen : Wageningen Economic Research (Wageningen Economic Research nota 2019-033) - 31
In deze studie wordt bekeken hoe natuurinclusieve landbouw op de middellange termijn kan uitgroeien van een niche naar de meest gangbare wijze van productie. Centraal staan de vragen: •Welke verdienmodellen zijn er denkbaar om opschaling van natuurinclusieve landbouw naar mainstream financieel mogelijk te maken?•Welk aandachtspunten zijn van belang om de transitie te faciliteren zodat op de middellange termijn natuurinclusieve landbouw kan uitgroeien van niche naar mainstream?
Cold chains in Hanoi and Bangkok: Changing systems of provision and practice
Rinkinen, Jenny ; Shove, E. ; Smits, M. - \ 2019
Journal of Consumer Culture 19 (2019)3. - ISSN 1469-5405 - p. 379 - 397.
social practice - systems of provision - urbanisation - refrigeration - food
We know that patterns of domestic consumption are situated within broader systems of provision and that home appliances like the fridge freezer bridge between practices of cooking, shopping and eating, on one hand, and increasingly global systems of food production, distribution and diet on the other. In analysing the uses of fridge freezers in Hanoi and Bangkok as expressions, in microcosm, of complex and evolving processes of urbanisation and food provisioning, this article provides new insight into how specific configurations, dependencies and patterns of consumption take hold and how they vary and change. Our analysis of systems and practices in flux has the dual function of showing how household strategies reflect and contribute to more extensive transformations, and of demonstrating how these are shaped by ongoing tensions and relations between new and established forms of urban food supply and associated concepts of freshness and safety. The result is a subtle account of the multiple routes through which consumer ‘needs’ evolve.
Prevalence of tick-borne viruses in Ixodes ricinus assessed by high-throughput real-time PCR
Gondard, Mathilde ; Michelet, Lorraine ; Nisavanh, Athinna ; Devillers, Elodie ; Delannoy, Sabine ; Fach, Patrick ; Aspan, Anna ; Ullman, Karin ; Chirico, Jan ; Hoffmann, Bernd ; Wal, Fimme Jan van der; Koeijer, Aline de; Solt-Smits, Conny van; Jahfari, Seta ; Sprong, Hein ; Mansfield, Karen L. ; Fooks, Anthony R. ; Klitgaard, Kirstine ; Bødker, Rene ; Moutailler, Sara - \ 2018
Pathogens and Disease 76 (2018)8. - ISSN 2049-632X
Europe - microfluidic analysis - molecular epidemiology - surveillance - tick borne viruses

Ticks are one of the principal arthropod vectors of human and animal infectious diseases. Whereas the prevalence of tick-borne encephalitis virus in ticks in Europe is well studied, there is less information available on the prevalence of the other tick-borne viruses (TBVs) existing worldwide. The aim of this study was to improve the epidemiological survey tools of TBVs by the development of an efficient high-throughput test to screen a wide range of viruses in ticks. In this study, we developed a new high-throughput virus-detection assay based on parallel real-time PCRs on a microfluidic system, and used it to perform a large scale epidemiological survey screening for the presence of 21 TBVs in 18 135 nymphs of Ixodes ricinus collected from five European countries. This extensive investigation has (i) evaluated the prevalence of four viruses present in the collected ticks, (ii) allowed the identification of viruses in regions where they were previously undetected. In conclusion, we have demonstrated the capabilities of this new screening method that allows the detection of numerous TBVs in a large number of ticks. This tool represents a powerful and rapid system for TBVs surveillance in Europe and could be easily customized to assess viral emergence.

Insights from the Circular Impacts case studies : Work package 4
Woltjer, G.B. ; Smits, M.J.W. ; Duin, Laurens ; Best, Aaron ; Hasenheit, Marius ; Drabik, Eleanor ; Rizos, Vasileios - \ 2018
EU - 61 p.
Phosphorus Recycling from manure – A Case Study on the Circular Economy : Work package 4
Smits, M.J.W. ; Woltjer, G.B. ; Luesink, H.H. ; Beekman, V. ; Koeijer, T.J. de; Daatselaar, C.H.G. ; Duin, Laurens - \ 2018
EU - 61 p.
Innovatieproject Hondsbossche Duinen
Ouwerkerk, Sonja ; Bodde, W. ; Smit, Marije ; Verheijen, Anne ; Leenders, Jakolien ; Wegman, Carolien ; Lagendijk, Georgette ; Scholl, Michaela ; Kuiters, A.T. ; Smits, N.A.C. ; Vries, Daisy de; Huiskes, H.P.J. ; Kramer, Henk ; Valk, Bert van der; IJff, Stéphanie - \ 2018
Ecoshape - 101 p.
Simulations of osmotic events in vitrification of equine oocytes and porcine embryos
Woelders, H. ; Guignot, Florence ; Oritiz-Escribano, Nerea ; Soom, A. van; Smits, Katrien - \ 2018
Holstein Friesian mid-lactation Milk Polar Metabolite Composition in relation to Dietary Fat Composition and DGAT1 Genotype
Pas, M.F.W. te; Vervoort, J. ; Kruijt, L. ; Calus, M.P.L. ; Smits, M. - \ 2018
BioRxiv
Background: The metabolite composition of cow milk is dependent on a large variety of animal associated factors including diet, genotype and gut microbiome composition. The objective of this study was to investigate changes in cow milk polar metabolite composition resulting from dietary and DGAT1 (Diacylglycerol O-acyltransferase 1) genotype perturbations. Methods and Results: Cows were fed a standard diet and a diet supplemented with (poly)unsaturated fatty acids (experimental diet) for ten weeks. Metabolite profiles were determined using 1H NMR (1-Hydrogen Nuclear magnetic resonance) technology. The results showed that the diet affected the polar metabolite composition of milk via the metabolism of the cow and via the metabolism of the gut and rumen microbiota. The experimental diet reduced the metabolic rate, especially the energy metabolism and the amino-sugar and amino acid metabolism, of the cows. Conclusion: Our results suggests the DGAT1 genotype affects both the diet related polar metabolite metabolism of the cow as well as that of the rumen microbiota. Milk metabolite levels in animals with more DGAT1 A-alleles were higher than milk metabolite levels in animals with more K-alleles.
Monitoringsrapportage 2017 : HPZ innovatieproject, document v0.1
Bodde, Willem ; Jansen, Maarten ; Smit, Marije ; Scholl, Michaela ; Lagendijk, Georgette ; Kuiters, Loek ; Vries, Daisy de; Kramer, Henk ; Smits, Nina ; Leenders, Jakolien - \ 2018
Den Haag : Rijkswaterstaat, Ministerie van Infrastructuur en Milieu - 84
Changes in Plasma Protein Expression Indicative of Early Diet-induced Metabolic Disease in Male Pigs (Sus scrofa).
Pas, M.F.W. te; Koopmans, Sietse Jan ; Kruijt, L. ; Boeren, J.A. ; Smits, M.A. - \ 2018
Comparative Medicine 68 (2018)4. - ISSN 1532-0820 - p. 286 - 293.
Recognition of the preclinical stages of metabolic diseases such as diabetes helps to prevent full development of the disease. In our research, we alter the diet composition of pigs to create a model of human metabolic disease. The objective of the current study was to identify plasma proteins and biologic mechanisms that differed in expression between pigs fed a 'cafeteria diet' (considered unhealthy; high in saturated fats) and those fed a 'Mediterranean diet' (considered healthy; high in unsaturated fats). Pigs fed the cafeteria diet showed increased plasma levels of proteins related to LDL ('bad cholesterol'), immune processes, blood clotting, and metal binding. The Mediterranean diet was associated with increased plasma quantities of proteins associated HDL particles ('good cholesterol'), binding of LDL particles, regulation of immune processes, and glycolysis. Pigs fed a cafeteria diet showed molecular signs of diabetes and atherosclerosis-even in the absence of clinical symptoms-which seemed to protect against the development of metabolic disorders. The current results suggest potential biomarkers of the early onset of metabolic syndromes. These biomarkers can help to reveal specific metabolic changes that precede the onset of diabetes, thus enabling the initiation of patient-specific interventions early during pathophysiologic development.
Verkenning potentiële bijdrage pacht natuurgrasland aan natuurinclusieve landbouw : Een modelmatige bedrijfseconomische analyse
Koeijer, Tanja de; Blokland, Pieter Willem ; Bos, Ernst ; Greijdanus, Auke ; Smits, Marie Jose - \ 2018
Wageningen : Wageningen Economic Research (Wageningen Economic Research rapport 2018-058) - ISBN 9789463434133 - 69
In the context of the development towards nature-inclusive agriculture, the relationship between the costs and benefits of management of natural areas by Staatsbosbeheer (national forest service) in conjunction with nature-inclusive measures on individual farmland areas was investigated. The analysis was completed for two representative dairy farms and a sample farm for suckler cows. The analysis reveals that, when the proportion of nature-inclusive agriculture increases, it becomes economically attractive for beef farmers to lease a larger area of natural grassland in order to compensate for the decrease of individual roughage production as a result of the nature-inclusive agricultural measures. Additionally, the factors of success or failure in the management of a profitable business were outlined in a qualitative analysis. Interviews support the insights gained from the model analysis in that the lease costs, the agricultural utility value, and the absent need for investment play an important role from a business economy standpoint in the optimum size of leased natural grassland in conjunction with nature-inclusive agriculture.
A Pig model to access the effect of nutritional interventions on intestinal Clostridium difficile expansion and the identification of a potential microbiome-based biomarker of CDI risks
Jurburg, S.D. ; Cornelissen, J.B.W.J. ; Boer, J.B.W.J. de; Smits, M.A. ; Rebel, J.M.J. - \ 2018
Can we solve it in the workshop? : Learning in river restoration and climate policy implementation
Rudberg, Peter M. - \ 2018
Wageningen University. Promotor(en): A.P.J. Mol, co-promotor(en): M. Smits. - Wageningen : Wageningen University - ISBN 9789463433808 - 212
Situating Electrification : Examples of infrastructure-practice dynamics from Thailand and Laos
Smits, M. - \ 2018
In: Infrastructures in Practice / Shove, Elizabeth, Trentmann, Frank, London : Routledge - ISBN 9781138476042 - p. 38 - 47.
Rapidly changing situations allow for insight into how infrastructures trigger the emergence, disappearance and transformation of specific practices, and of how these developments are, in turn, important for infrastructural configurations. This chapter explores features of this infrastructure-practice dynamic through two village-level case studies of rural electrification in Thailand and Laos. In both cases, different ‘layers’ of electricity infrastructure entered the villages in time frames of a few decades. In-depth fieldwork provides insight into how infrastructures, practices and demand co-evolved in these two cases. Specifically, the chapter examines the emergence and development of new and ‘electrified’ practices, such as watching television and lighting. The cases illustrate that the consequences of electrification are sometimes mediated by pre-existing material arrangements or by their absence, and that these consequences spill over into various aspects of life. By considering systems and politics of provision alongside shifting relations between variously electrified practices, the chapter bridges between concepts associated with socio-technical innovation, with political ecology, and with accounts of emerging complexes of social practice. It shows that systems and technologies of supply are not simply outcomes or expressions of ‘large’ political-economic forces, but are constituted and reproduced through the practices of different stakeholders.
IAG ring test animal proteins 2018
Raamsdonk, L.W.D. van; Hedemann, B. ; Smits, C.P.A.F. ; Vliege, J.J.M. - \ 2018
Wageningen : RIKILT Wageningen University & Research (RIKILT report 2018.008) - 33
Plant Selenium Hyperaccumulation Affects Rhizosphere: Enhanced Species Richness and Altered Species Composition
Cochran, Alyssa T. ; Bauer, Jemma ; Metcalf, Jessica L. ; Lovecka, Petra ; Jong, Martina S. de; Warris, S. ; Mooijman, P.J.W. ; Meer, I.M. van der; Knight, Rob ; Pilon-Smits, E.A.H. - \ 2018
Phytobiomes Journal 2 (2018)2. - ISSN 2471-2906 - p. 82 - 91.
Little is known about the microbiomes associated with plants with unusual properties, including plants that hyperaccumulate toxic elements such as selenium (Se). Se hyperaccumulators contain up to 1.5% of their dry weight in Se, concentrations shown to affect ecological interactions with herbivores, fungal pathogens and neighboring plants. Hyperaccumulators also enrich their surrounding soil with Se, which may alter the rhizobiome. To investigate whether plant Se affects rhizobacterial diversity and composition, we used a combination of culture-independent and culture-based approaches. Sequencing of 16S rRNA gene amplicons using the Illumina platform revealed that the rhizosphere microbiomes of Se hyperaccumulators were significantly different from nonaccumulators from the same site, with a higher average relative abundance of Pedobacter and Deviosa. Additionally, hyperaccumulators harbored a higher rhizobacterial species richness when compared with nonaccumulators from the same family on the same site. Independent from Se present at the site or in the host plant, the bacterial isolates were extremely resistant to selenate and selenite (up to 200 mM) and could reduce selenite to elemental Se. In conclusion, Se hyperaccumulation does not appear to negatively affect rhizobacterial diversity, and may select for certain taxa in the rhizosphere microbiome. Additionally, Se resistance in hyperaccumulator-associated bacteria and archaea may be widespread and not under selection by the host plant.
Learning-based intervention for river restoration: analyzing the lack of outcomes in the Ljusnan River basin, Sweden
Rudberg, P.M. ; Smits, M. - \ 2018
Ecology and Society 23 (2018)4. - ISSN 1708-3087 - 14 p.
hydropower - learning-based intervention - outcomes - river restoration - Sweden
We focus on a large and sustained stakeholder process for river restoration related to hydropower production that failed to reach any significant natural resource management outcomes. We explore to what extent the stakeholder process can be characterized as a learning-based intervention as well as the reasons for the lack of outcomes. The analysis draws on insights from existing literature of procedural and institutional factors identified to foster and hinder social learning in stakeholder processes. The analysis finds that the stakeholder process featured virtually all fostering procedural factors as well as various fostering institutional factors identified in the literature. The main hindering institutional element consisted of strong pre-existing water rights, granted by the legislation governing hydropower production and river restoration in Sweden. Existing legislation provided a key stakeholder with the power to successfully reach its objective through the unilateral action of exiting the stakeholder process. Our results demonstrate that various learning outcomes, including knowledge acquisition, trust building, and the creation of networks are possible in stakeholder processes that feature power imbalances. The results also suggest that, ultimately, the power imbalance limited the process from reaching significant natural resource management outcomes, both in the short and longer terms. Based on comparison with international cases, the results reveal the need to focus attention on the national scale to remediate power imbalances in stakeholder processes that arise from a share of stakeholders possessing strong prior rights to the use of natural resources. In such cases, sustainable management of natural resources could be better served by efforts to modify existing legislation, rather than investments in resource-intensive learning-based interventions.
Release of major peanut allergens from their matrix under various pH and simulated saliva conditions—Ara h2 and ara h6 are readily bio-accessible
Koppelman, Stef J. ; Smits, Mieke ; Tomassen, Monic ; Jong, Govardus A.H. De; Baumert, Joe ; Taylor, Steve L. ; Witkamp, Renger ; Veldman, Robert Jan ; Pieters, Raymond ; Wichers, Harry - \ 2018
Nutrients 10 (2018)9. - ISSN 2072-6643
Allergen - Arachis hypogaea - Bio-accessibility - Peanut - Saliva

The oral mucosa is the first immune tissue that encounters allergens upon ingestion of food. We hypothesized that the bio-accessibility of allergens at this stage may be a key determinant for sensitization. Light roasted peanut flour was suspended at various pH in buffers mimicking saliva. Protein concentrations and allergens profiles were determined in the supernatants. Peanut protein solubility was poor in the pH range between 3 and 6, while at a low pH (1.5) and at moderately high pHs (>8), it increased. In the pH range of saliva, between 6.5 and 8.5, the allergens Ara h2 and Ara h6 were readily released, whereas Ara h1 and Ara h3 were poorly released. Increasing the pH from 6.5 to 8.5 slightly increased the release of Ara h1 and Ara h3, but the recovery remained low (approximately 20%) compared to that of Ara h2 and Ara h6 (approximately 100% and 65%, respectively). This remarkable difference in the extraction kinetics suggests that Ara h2 and Ara h6 are the first allergens an individual is exposed to upon ingestion of peanut-containing food. We conclude that the peanut allergens Ara h2 and Ara h6 are quickly bio-accessible in the mouth, potentially explaining their extraordinary allergenicity.

Genome-based population structure analysis of the strawberry plant pathogen Xanthomonas fragariae reveals two distinct groups that evolved independently before its species description
Gétaz, Michael ; Krijger, M.C. ; Rezzonico, F. ; Smits, Theo ; Wolf, J.M. van der; Pothier, Joël F. - \ 2018
Microbial Genomics 2018 (2018)4. - ISSN 2057-5858
Xanthomonas fragariae is a quarantine organism in Europe, causing angular leaf spots on strawberry plants. It is spreading worldwide in strawberry-producing regions due to import of plant material through trade and human activities. In order to resolve the population structure at the strain level, we have employed high-resolution molecular typing tools on a comprehensive strain collection representing global and temporal distribution of the pathogen. Clustered regularly interspaced short palindromic repeat regions (CRISPRs) and variable number of tandem repeats (VNTRs) were identified within the reference genome of X. fragariae LMG 25863 as a potential source of variation. Strains from our collection were whole-genome sequenced and used in order to identify variable spacers and repeats for discriminative purpose. CRISPR spacer analysis and multiple-locus VNTR analysis (MLVA) displayed a congruent population structure, in which two major groups and a total of four subgroups were revealed. The two main groups were genetically separated before the first X. fragariae isolate was described and are potentially responsible for the worldwide expansion of the bacterial disease. Three primer sets were designed for discriminating CRISPR-associated markers in order to streamline group determination of novel isolates. Overall, this study describes typing methods to discriminate strains and monitor the pathogen population structure, more especially in the view of a new outbreak of the pathogen.
Supplementation of fructooligosaccharides to suckling piglets affects intestinal microbiota colonization and immune development
Schokker, Dirkjan ; Fledderus, Jan ; Jansen, Rutger ; Vastenhouw, Stephanie A. ; Bree, Freddy M. de; Smits, Mari A. ; Jansman, Alfons A.J.M. - \ 2018
Journal of Animal Science 96 (2018)6. - ISSN 0021-8812 - p. 2139 - 2153.
Emerging knowledge shows the importance of early life events in programming the intestinal mucosal immune system and development of the intestinal barrier function. These processes depend heavily on close interactions between gut microbiota and host cells in the intestinal mucosa. In turn, development of the intestinal microbiota is largely dependent on available nutrients required for the specific microbial community structures to expand. It is currently not known what the specificities are of intestinal microbial community structures in relation to the programming of the intestinal mucosal immune system and development of the intestinal barrier function. The objective of the present study was to investigate the effects of a nutritional intervention on intestinal development of suckling piglets by daily oral administration of fructooligosaccharides (FOS) over a period of 12 d (days 2–14 of age). At the microbiota community level, a clear “bifidogenic” effect of the FOS administration was observed in the colon digesta at day 14. The former, however, did not translate into significant changes of local gene expression in the colonic mucosa. In the jejunum, significant changes were observed for microbiota composition at day 14, and microbiota diversity at day 25. In addition, significant differentially expressed gene sets in mucosal tissues of the jejunum were identified at both days 14 and 25 of age. At the age of 14 d, a lower activity of cell cycle–related processes and a higher activity of extracellular matrix processes were observed in the jejunal mucosa of piglets supplemented with FOS compared with control piglets. At day 25, the lower activity of immune-related processes in jejunal tissue was seen in piglets supplemented with FOS. Villi height and crypt depth in the jejunum were significantly different at day 25 between the experimental and control groups, where piglets supplemented with FOS had greater villi and deeper crypts. We conclude that oral FOS administration during the early suckling period of piglets had significant bifidogenic effects on the microbiota in the colon and on gene expression in the jejunal mucosa by thus far unknown mechanisms.
Effect of vegan fecal microbiota transplantation on carnitine- and choline-derived trimethylamine-N-oxide production and vascular inflammation in patients with metabolic syndrome
Smits, Loek P. ; Kootte, Ruud S. ; Levin, Evgeni ; Prodan, Andrei ; Fuentes, Susana ; Zoetendal, Erwin G. ; Wang, Zeneng ; Levison, Bruce S. ; Cleophas, Maartje C.P. ; Kemper, E.M. ; Dallinga-Thie, Geesje M. ; Groen, Albert K. ; Joosten, Leo A.B. ; Netea, Mihai G. ; Stroes, Erik S.G. ; Vos, Willem M. de; Hazen, Stanley L. ; Nieuwdorp, Max - \ 2018
Journal of the American Heart Association 7 (2018)7. - ISSN 2047-9980
Atherosclerosis - Cardiovascular disease - Cardiovascular imaging - Inflammation - Metabolism
Background--Intestinal microbiota have been found to be linked to cardiovascular disease via conversion of the dietary compounds choline and carnitine to the atherogenic metabolite TMAO (trimethylamine-N-oxide). Specifically, a vegan diet was associated with decreased plasma TMAO levels and nearly absent TMAO production on carnitine challenge. Methods and Results--We performed a double-blind randomized controlled pilot study in which 20 male metabolic syndrome patients were randomized to single lean vegan-donor or autologous fecal microbiota transplantation. At baseline and 2 weeks thereafter, we determined the ability to produce TMAO from d6-choline and d3-carnitine (eg, labeled and unlabeled TMAO in plasma and 24-hour urine after oral ingestion of 250 mg of both isotope-labeled precursor nutrients), and fecal samples were collected for analysis of microbiota composition. 18F-fluorodeoxyglucose positron emission tomography/computed tomography scans of the abdominal aorta, as well as ex vivo peripheral blood mononuclear cell cytokine production assays, were performed. At baseline, fecal microbiota composition differed significantly between vegans and metabolic syndrome patients. With vegan-donor fecal microbiota transplantation, intestinal microbiota composition in metabolic syndrome patients, as monitored by global fecal microbial community structure, changed toward a vegan profile in some of the patients; however, no functional effects from vegan-donor fecal microbiota transplantation were seen on TMAO production, abdominal aortic 18Ffluorodeoxyglucose uptake, or ex vivo cytokine production from peripheral blood mononuclear cells. Conclusions--Single lean vegan-donor fecal microbiota transplantation in metabolic syndrome patients resulted in detectable changes in intestinal microbiota composition but failed to elicit changes in TMAO production capacity or parameters related to vascular inflammation.
Transitions to Energy and Climate Security in Southeast Asia? Civil Society Encounters with Illiberalism in Thailand and Myanmar
Simpson, Adam ; Smits, Mattijs - \ 2018
Society & Natural Resources 31 (2018)5. - ISSN 0894-1920 - p. 580 - 598.
Climate - energy - illiberalism - Myanmar - Thailand
All states, whether governed by liberal or illiberal regimes, face the prospect of momentous and potentially catastrophic environmental impacts due to climate change. Historically, energy policy has been directed towards simply achieving energy security. This goal has now been significantly complicated by the need to achieve it while minimizing greenhouse gas emissions. Environmental non governmental organizations (ENGOs) could play a crucial role in promoting the transition to energy and climate security but the relative (il)liberalism of the political regime they operate under influences their effectiveness. This article assesses how ENGOs have impacted on the transition to energy and climate security in Myanmar and Thailand, two Southeast Asian countries highly susceptible to climate impacts and characterized by illiberal rule. It finds that the impact of ENGOs was highly dependent on their strategies, tactics and operation, with community-level projects providing a key route to effect change under conditions of extreme illiberalism.
IAG ring test animal proteins 2017
Raamsdonk, L.W.D. van; Smits, C.P.A.F. ; Vliege, J.J.M. ; Pinckaers, V.G.Z. - \ 2018
Wageningen : RIKILT Wageningen University & Research (RIKILT report 2017.012) - 33
IAG ring test feed composition 2017
Raamsdonk, L.W.D. van; Smits, C.P.A.F. ; Vliege, J.J.M. ; Pinckaers, V.G.Z. - \ 2018
Wageningen : RIKILT Wageningen University & Research (RIKILT report 2017.011) - 31
An improved vitrification protocol for equine immature oocytes, resulting in a first live foal
Ortiz-Escribano, N. ; Bogado Pascottini, O. ; Woelders, H. ; Vandenberghe, L. ; Schauwer, C. De; Govaere, J. ; Abbeel, E. Van den; Vullers, T. ; Ververs, C. ; Roels, K. ; De Velde, M. Van; Soom, A. van; Smits, K. - \ 2018
Equine Veterinary Journal 50 (2018)3. - ISSN 0425-1644 - p. 391 - 397.
Cumulus cells - Horse - Oocytes - Vitrification
Background: The success rate for vitrification of immature equine oocytes is low. Although vitrified-warmed oocytes are able to mature, further embryonic development appears to be compromised. Objectives: The aim of this study was to compare two vitrification protocols, and to examine the effect of the number of layers of cumulus cells surrounding the oocyte during vitrification of immature equine oocytes. Study design: Experimental in vitro and in vivo trials. Methods: Immature equine oocytes were vitrified after a short exposure to high concentrations of cryoprotective agents (CPAs), or a long exposure to lower concentrations of CPAs. In Experiment 1, the maturation of oocytes surrounded by multiple layers of cumulus cells (CC oocytes) and oocytes surrounded by only corona radiata (CR oocytes) was investigated. In Experiment 2, spindle configuration was determined for CR oocytes vitrified using the two vitrification protocols. In Experiment 3, further embryonic development was studied after fertilisation and culture. Embryo transfer was performed in a standard manner. Results: Similar nuclear maturation rates were observed for CR oocytes vitrified using the long exposure and nonvitrified controls. Furthermore, a lower maturation rate was obtained for CC oocytes vitrified with the short exposure compared to control CR oocytes (P = 0.001). Both vitrification protocols resulted in significantly higher rates of aberrant spindle configuration than the control groups (P<0.05). Blastocyst development only occurred in CR oocytes vitrified using the short vitrification protocol, and even though blastocyst rates were significantly lower than in the control group (P<0.001), transfer of five embryos resulted in one healthy foal. Main limitations: The relatively low number of equine oocytes and embryo transfer procedures performed. Conclusions: For vitrification of immature equine oocytes, the use of 1) CR oocytes, 2) a high concentration of CPAs, and 3) a short exposure time may be key factors for maintaining developmental competence.
Exploring target-specific primer extension in combination with a bead-based suspension array for multiplexed detection and typing using Streptococcus suis as a model pathogen
Wal, F.J. van der; Achterberg, R.P. ; Smits, C.B. ; Bergervoet, J.H.W. ; Weerdt, M. de; Wisselink, H.J. - \ 2018
Journal of Veterinary Diagnostic Investigation 30 (2018)1. - ISSN 1040-6387 - p. 71 - 77.
We investigated the feasibility of an assay based on target-specific primer extension, combined with a suspension array, for the multiplexed detection and typing of a veterinary pathogen in animal samples, using Streptococcus suis as a model pathogen. A procedure was established for simultaneous detection of 6 S. suis targets in pig tonsil samples (i.e., 4 genes associated with serotype 1, 2, 7, or 9, the generic S. suis glutamate dehydrogenase gene [gdh], and the gene encoding the extracellular protein factor [epf]). The procedure was set up as a combination of protocols: DNA isolation from porcine tonsils, a multiplex PCR, a multiplex target-specific primer extension, and finally a suspension array as the readout. The resulting assay was compared with a panel of conventional PCR assays. The proposed multiplex assay can correctly identify the serotype of isolates and is capable of simultaneous detection of multiple targets in porcine tonsillar samples. The assay is not as sensitive as the current conventional PCR assays, but with the correct sampling strategy, the assay can be useful for screening pig herds to establish which S. suis serotypes are circulating in a pig population.
The Multidimensional Nature of Women's Empowerment : Beyond the Economic Approach
Bayissa, Fitsum W. ; Smits, Jeroen ; Ruben, Ruerd - \ 2018
Journal of International Development 30 (2018)4. - ISSN 0954-1748 - p. 661 - 690.
Economic dimension - Ethiopia - Multidimensional - Women's empowerment
Most interventions promoting women's empowerment focus on the economic dimension. Economic improvement is supposed to lead automatically to improvements in other dimensions. To test this assumption, we collected data from 508 women working in women groups in Addis Ababa. Besides the economic dimension, five other dimensions of empowerment were studied (familial, legal, psychological, political and socio-cultural). Findings show that the relationships between these six dimensions of empowerment are weak and that the psychological dimension is most central. The economic dimension is hardly connected to other dimensions. Hence, a broad package of interventions seems needed to achieve empowerment in all respects.
Ontwikkeling van een meetlat voor immuuncompetentie in varkens, vleeskuikens en vleeskalveren
Jansman, Alfons ; Schokker, Dirkjan ; Greeff, Astrid de; Krinpen, Marinus van; Hulst, Marcel ; Rebel, Annemarie ; Smits, Mari ; Kies, Arie ; Roubos, Petra ; Willems, Els ; Alderliesten, Evelien ; Wal, Eelke van der - \ 2017
Wageningen : Wageningen Livestock Research (Wageningen Livestock Research rapport 1097) - 48
Het doel van dit project is om een “meetlat” te ontwikkelen die de effecten van (voedings)interventies gericht op de verbetering van de immuuncompetentie van varkens, pluimvee en vleeskalveren kan vaststellen. Immuuncompetentie is binnen dit project gedefinieerd als het vermogen van dieren om effectieve responsen van het immuunsysteem te tonen op het moment dat de gezondheid van het dier onder druk wordt gezet. Een meetlat voor immuuncompetentie kan in de toekomst door de diervoedingssector gebruikt worden bij de ontwikkeling en evaluatie van nieuwe voerconcepten, ingrediënten en additieven gericht op de verbetering en ondersteuning van diergezondheid. Het is bekend dat de samenstelling van de voeding van jonge dieren invloed heeft op de functionele ontwikkeling van het maagdarmkanaal en op de samenstelling van de daarin aanwezige microbiota. De interacties tussen de microbiota en de weefsels van het darmkanaal (cross talk) hebben een belangrijke invloed op de ontwikkeling van immuuncompetentie. Daarom wordt in dit project gefocust op de effecten van (voedings)interventies op de microbiota, genexpressie veranderingen in darmweefsel, en morfologische en immunologische veranderen in de darm. De hier gepresenteerde meetlat voor immuuncompetentie is gebaseerd op de resultaten van onderzoek binnen het VDI programma van Feed4Foodure (projecten VDI-11; vleeskuikens, VDI-12; biggen, VDI- 13; gespeende biggen en kalveren) waarin m.b.v. model interventies de effecten van variatie in voersamenstelling op de microbiota samenstelling in het darmkanaal, de biologische responsen van darmweefsel en de zoötechnische dierprestaties zijn onderzocht. In de hier gepresenteerde meetlat worden gemeten effecten in deze studies aan elkaar gerelateerd en functioneel inzichtelijk gemaakt. Dit rapport beschrijft de ontwikkeling en totstandkoming van een eerste versie van de meetlat. Hierbij worden gemaakte keuzes, beperkingen en mogelijkheden van de meetlat bediscussieerd. Tenslotte wordt inzicht gegeven in de mogelijkheden tot verdere verfijningen en de toepasbaarheid van de meetlat.
Amine Metabolism Is Influenced by Dietary Protein Source
Kar, Soumya K. ; Jansman, Alfons J.M. ; Schokker, Dirkjan ; Kruijt, Leo ; Harms, Amy C. ; Wells, Jerry M. ; Smits, Mari A. - \ 2017
Frontiers in Nutrition 4 (2017). - ISSN 2296-861X
Growth in world population will inevitably leads to increased demand for protein for humans and animals. Protein from insects and blood plasma are being considered as possible alternatives, but more research on their nutritional quality and health effects is needed. Here, we studied the effect of dietary protein source on metabolism and metabolic amine profiles in serum and urine of mice. Groups of mice were fed semi-purified diets containing 300 g/kg of soybean meal, casein, partially delactosed whey powder, spray-dried plasma
protein, wheat gluten meal, and yellow mealworm. Feed and water intake as well as body weight gain were measured for 28 days. After 14 and 28 days, serum and urine samples were collected for measurement of a large panel of amine metabolites. MetaboAnalyst 3.0 was used for analysis of the raw metabolic data. Out of 68 targeted amine metabolites, we could detect 54 in urine and 41 in blood serum. Dietary protein sources were found to have profound effects on host metabolism, particularly in systemic amine profiles, considered here as an endophenotype. We recommend serum over urine to screen for the amine metabolic endophenotype based on partial least squares discriminant analysis. We concluded that metabolites like alpha-aminobutyric acid and methylhistidine are sensitive indicators of too much or too little availability of specific amino acids in the different protein diets. Furthermore, we concluded that amine metabolic profiles can be useful for assessing the nutritional quality of different protein sources.
Monitoringsrapportage : HPZ innovatieproject, groeidocument v0.1
Bodde, W. ; Groot, A.V. de; Smits, N.A.C. ; Huiskes, H.P.J. ; Vries, D. de; Kuiters, A.T. ; Leenders, J. ; Brandenburg, P. ; Wittebrood, Marloes ; Goessen, Petra - \ 2017
Ecoshape - 115 p.
Methods and means for determining treatment of subjects with exogenous somatotropin
Smits, N.G.E. ; Blokland, M.H. ; Nielen, M.W.F. - \ 2017
Octrooinummer: US2017354717, verleend: 2017-12-14.
Described are methods for determining whether a subject has been treated with exogenous somatotropin. The disclosure further relates to kits for determining whether a subject has been treated with exogenous somatotropin, and to the use of such kits for determining whether a subject has been treated with exogenous somatotropin.
Perturbation of microbiota in one-day old broiler chickens with antibiotic for 24 hours negatively affects intestinal immune development
Schokker, D. ; Jansman, A.J.M. ; Veninga, Gosse ; Bruin, Naomi de; Vastenhouw, S.A. ; Bree, F.M. de; Bossers, A. ; Rebel, J.M.J. ; Smits, M.A. - \ 2017
chicken - gut - microbiota - gene expression - immune development
Background Gut microbial colonization and development of immune competence are intertwined and are influenced by early-life nutritional, environmental, and management factors. Perturbation of the gut microbiome at young age affects the crosstalk between intestinal bacteria and host cells of the intestinal mucosa. Results We investigated the effect of a perturbation of the normal early life microbial colonization of the jejunum in 1-day old chickens. Perturbation was induced by administering 0.8Â mg amoxicillin per bird per day) via the drinking water for a period of 24Â h. Effects of the perturbation were measured by 16S rRNA profiling of the microbiome and whole genome gene expression analysis. In parallel to what has been observed for other animal species, we hypothesized that such an intervention may have negative impact on immune development. Trends were observed in changes of the composition and diversity of the microbiome when comparing antibiotic treated birds with their controls. in the jejunum, the expression of numerous genes changed, which potentially leads to changes in biological activities of the small intestinal mucosa. Validation of the predicted functional changes was performed by staining immune cells in the small intestinal mucosa and a reduction in the number of macrophage-like (KUL01+) cells was observed due to a direct or indirect effect of the antibiotic treatment. We provide evidence that a short, early life antibiotic treatment affects both the intestinal microbiota (temporarily) and mucosal gene expression over a period of 2Â weeks. Conclusion These results underscore the importance of early life microbial colonization of the gut in relation to immune development and the necessity to explore the capabilities of a variety of early life dietary and/or environmental factors to modulate the programming for immune competence in broilers.
The effects of a multispecies probiotic on migraine and markers of intestinal permeability-results of a randomized placebo-controlled study
Roos, N.M. De; Hemert, S. Van; Rovers, J.M.P. ; Smits, M.G. ; Witteman, B.J.M. - \ 2017
European Journal of Clinical Nutrition 71 (2017)12. - ISSN 0954-3007 - p. 1455 - 1462.
Background/Objectives:Migraine, associated with several gastrointestinal disorders, may result from increased intestinal permeability, allowing endotoxins to enter the bloodstream. We tested whether probiotics could reduce migraine through an effect on intestinal permeability and inflammation.Subjects/Methods:In total, 63 patients were randomly allocated to the probiotic (n=31) or the placebo group (n=32). Participants ingested a multispecies probiotic (5x10 9 colony-forming units) or placebo daily for 12 weeks. Migraine was assessed with the Migraine Disability Assessment Scale (MIDAS), the Headache Disability Inventory (HDI) and headache diaries. At baseline and 12 weeks, intestinal permeability was measured with the urinary lactulose/mannitol test and fecal and serum zonulin; inflammation was measured from interleukin (IL) -6, IL-10, tumor necrosis factor-α and C-reactive protein in serum.Results:The MIDAS migraine intensity score significantly decreased in both groups (P<0.001) and the HDI score significantly decreased in the probiotic group (P=0.032) and borderline in the placebo group (P=0.053). In the probiotics group, patients had a median of 6 migraine days in the first month, 4 in the second month (P=0.002) and 5 in the last month, which was not significantly different from the 5, 4, and 4 days in the placebo group. A ≤3/42day reduction in migraine days was seen in 12/31 patients in the probiotics group versus 7/29 in the placebo group (ns). Probiotic use did not significantly affect medication use, intestinal permeability or inflammation compared to placebo.Conclusions:In this study, we could not confirm significant benefit from a multispecies probiotic compared to a placebo on the outcome parameters of migraine and intestinal integrity.
Nutritional strategies to establish a responsible use of antibiotics in swine
Hartog, L.A. den; Hees, H. van; Ferguson, N. ; Smits, C. - \ 2017
In: Proceedings Banff Pork Seminar. - University of Alberta (Advances in Pork Production ) - p. 177 - 188.
Dietary protein sources differentially affect microbiota, mTOR activity and transcription of mTOR signaling pathways in the small intestine
Kar, Soumya K. ; Jansman, Alfons J.M. ; Benis, Nirupama ; Ramiro-Garcia, Javier ; Schokker, Dirkjan ; Kruijt, Leo ; Stolte, Ellen H. ; Taverne-Thiele, Johanna J. ; Smits, Mari A. ; Wells, Jerry M. - \ 2017
PLoS ONE 12 (2017)11. - ISSN 1932-6203
Dietary protein sources can have profound effects on host-microbe interactions in the gut that are critically important for immune resilience. However more knowledge is needed to assess the impact of different protein sources on gut and animal health. Thirty-six wildtype male C57BL/6J mice of 35 d age (n = 6/group; mean ± SEM body weight 21.9 ± 0.25 g) were randomly assigned to groups fed for four weeks with semi synthetic diets prepared with one of the following protein sources containing (300 g/kg as fed basis): soybean meal (SBM), casein, partially delactosed whey powder, spray dried plasma protein, wheat gluten meal and yellow meal worm. At the end of the experiment, mice were sacrificed to collect ileal tissue to acquire gene expression data, and mammalian (mechanistic) target of rapamycin (mTOR) activity, ileal digesta to study changes in microbiota and serum to measure cytokines and chemokines. By genome-wide transcriptome analysis, we identified fourteen high level regulatory genes that are strongly affected in SBM-fed mice compared to the other experimental groups. They mostly related to the mTOR pathway. In addition, an increased (P < 0.05) concentration of granulocyte colony-stimulating factor was observed in serum of SBM-fed mice compared to other dietary groups. Moreover, by 16S rRNA sequencing, we observed that SBM-fed mice had higher (P < 0.05) abundances of Bacteroidales family S24-7, compared to the other dietary groups. We showed that measurements of genome-wide expression and microbiota composition in the mouse ileum reveal divergent responses to diets containing different protein sources, in particular for a diet based on SBM.
Innovatieproject Hondsbossche en Pettemer Zeewiering (HPZ): monitoringsrapportage 2016
Smits, N.A.C. ; Huiskes, H.P.J. ; Vries, Daisy de; Kuiters, A.T. ; Scholl, M.M. - \ 2017
Wageningen Marine Research - 37 p.
Monitorings-rapportage: HPZ innovatieproject, groeidocument
Bodde, Willem ; Groot, A.V. de; Smits, N.A.C. ; Huiskes, H.P.J. ; Vries, Daisy de; Kuiters, A.T. ; Leenders, Jakolien ; Brandenbrug, Peter ; Wittebrood, Marloes ; Goessen, Petra - \ 2017
Wageningen Marine Research - 115 p.
Improvement of Insulin Sensitivity after Lean Donor Feces in Metabolic Syndrome Is Driven by Baseline Intestinal Microbiota Composition
Kootte, Ruud S. ; Levin, Evgeni ; Salojärvi, Jarkko ; Smits, Loek P. ; Hartstra, Annick V. ; Udayappan, Shanti D. ; Hermes, Gerben ; Bouter, Kristien E. ; Koopen, Annefleur M. ; Holst, Jens J. ; Knop, Filip K. ; Blaak, Ellen E. ; Zhao, Jing Hua ; Smidt, Hauke ; Harms, Amy C. ; Hankemeijer, Thomas ; Bergman, Jacques J.G.H.M. ; Romijn, Hans A. ; Schaap, Frank G. ; Olde Damink, Steven W.M. ; Ackermans, Mariette T. ; Dallinga-Thie, Geesje M. ; Zoetendal, Erwin ; Vos, Willem M. de; Serlie, Mireille J. ; Stroes, Erik S.G. ; Groen, Albert K. ; Nieuwdorp, Max - \ 2017
Cell Metabolism 26 (2017)4. - ISSN 1550-4131 - p. 611 - 619.e6.
fecal microbiota transplantation - insulin sensitivity - intestinal microbiota composition - plasma metabolites

The intestinal microbiota has been implicated in insulin resistance, although evidence regarding causality in humans is scarce. We therefore studied the effect of lean donor (allogenic) versus own (autologous) fecal microbiota transplantation (FMT) to male recipients with the metabolic syndrome. Whereas we did not observe metabolic changes at 18 weeks after FMT, insulin sensitivity at 6 weeks after allogenic FMT was significantly improved, accompanied by altered microbiota composition. We also observed changes in plasma metabolites such as γ-aminobutyric acid and show that metabolic response upon allogenic FMT (defined as improved insulin sensitivity 6 weeks after FMT) is dependent on decreased fecal microbial diversity at baseline. In conclusion, the beneficial effects of lean donor FMT on glucose metabolism are associated with changes in intestinal microbiota and plasma metabolites and can be predicted based on baseline fecal microbiota composition. Kootte et al. show that fecal microbiota transplantation from lean donors to obese patients with metabolic syndrome improves insulin sensitivity, a transient effect associated with changes in microbiota composition and fasting plasma metabolites. Baseline fecal microbiota composition in recipients predicts the response to lean donor fecal microbiota transplantation.

Alternatieve vloeren voor vleeskalveren
Heeres-van der Tol, Jetta ; Wolthuis, Maaike ; Bokma, Sjoerd ; Smits, Dolf ; Stockhofe, Norbert ; Vermeij, Izak ; Reenen, Kees van - \ 2017
Wageningen : Wageningen Livestock Research (Wageningen Livestock Research rapport 1056) - 103
dierenwelzijn - dierlijke productie - vleeskalveren - huisvesting - diergedrag - diergezondheid - animal welfare - animal production - veal calves - housing - animal behaviour - animal health
Natuurinclusief ondernemen : Overheid, graag meer bemoeienis!
Bos, E.J. ; Smits, M.J.W. - \ 2017
Landwerk 17 (2017)2. - ISSN 1567-1844 - p. 9 - 11.
Methodology for the case studies
Smits, M.J.W. ; Woltjer, G.B. - \ 2017
EU (Circular impacts ) - 19
economics - cycling - projects - renewable energy - recycling - sustainability - durability - politics - policy - environment - economie - kringlopen - projecten - hernieuwbare energie - recycling - duurzaamheid (sustainability) - duurzaamheid (durability) - politiek - beleid - milieu
This document is about the methodology and selection of the case studies. It is meant as a guideline for the case studies, and together with the other reports in this work package can be a source of inform ation for policy officers, interest groups and researchers evaluating or performing impact assessments of circular economy policies or specific circular economy projects. The methodology was developed to ensure that the case studies focus on the overall im pacts of the circular economy. The frame of the methodology is a s tep - by - step approach, which will be described in section s 3 and 4 of this document. In section 2 we describe the selection of the case studies.
Genome plasticity and polymorphisms in critical genes correlate with increased virulence of Dutch outbreak-related Coxiella burnetii strains
Kuley, Runa ; Kuijt, Eric ; Smits, Mari A. ; Roest, Hendrik I.J. ; Smith, Hilde E. ; Bossers, Alex - \ 2017
Frontiers in Microbiology 8 (2017). - ISSN 1664-302X
C. burnetii - Comparative genomics - Mutations - Orthologs - Q fever - Transposons - Virulence - Whole genome sequencing

Coxiella burnetii is an obligate intracellular bacterium and the etiological agent of Q fever. During 2007-2010 the largest Q fever outbreak ever reported occurred in The Netherlands. It is anticipated that strains from this outbreak demonstrated an increased zoonotic potential as more than 40,000 individuals were assumed to be infected. The acquisition of novel genetic factors by these C. burnetii outbreak strains, such as virulence-related genes, has frequently been proposed and discussed, but is not proved yet. In the present study, the whole genome sequence of several Dutch strains (CbNL01 and CbNL12 genotypes), a few additionally selected strains from different geographical locations and publicly available genome sequences were used for a comparative bioinformatics approach. The study focuses on the identification of specific genetic differences in the outbreak related CbNL01 strains compared to other C. burnetii strains. In this approach we investigated the phylogenetic relationship and genomic aspects of virulence and host-specificity. Phylogenetic clustering of whole genome sequences showed a genotype-specific clustering that correlated with the clustering observed usingMultiple Locus Variable-number TandemRepeat Analysis (MLVA). Ortholog analysis on predicted genes and single nucleotide polymorphism (SNP) analysis of complete genome sequences demonstrated the presence of genotype-specific gene contents and SNP variations in C. burnetii strains. It also demonstrated that the currently used MLVA genotyping methods are highly discriminatory for the investigated outbreak strains. In the fully reconstructed genome sequence of the Dutch outbreak NL3262 strain of the CbNL01 genotype, a relatively large number of transposon-linked genes were identified as compared to the other published complete genome sequences of C. burnetii. Additionally, large numbers of SNPs in its membrane proteins and predicted virulence-associated genes were identified in all Dutch outbreak strains compared to the NM reference strain and other strains of the CbNL12 genotype. The presence of large numbers of transposable elements and mutated genes, thereof most likely resulted in high level of genome rearrangements and genotype-specific pathogenicity of outbreak strains. Thus, the epidemic potential of Dutch outbreak strains could be linked to increased genome plasticity and mutations in critical genes involved in virulence and the evasion of the host immune system.

Sequence exchange between R genes converts virus resistance into nematode resistance, and vice versa
Slootweg, Erik J. ; Koropacka, K.B. ; Roosien, Jan ; Dees, Robert ; Overmars, Hein ; Klein Lankhorst, Rene ; Schaik, Casper van; Pomp, Rikus ; Bouwman-Smits, Liesbeth ; Helder, Hans ; Schots, Arjen ; Bakker, Jaap ; Smant, Geert ; Goverse, Aska - \ 2017
Plant Physiology 175 (2017). - ISSN 0032-0889 - p. 498 - 510.
Plants have evolved a limited repertoire of NB-LRR disease resistance (R) genes to protect themselves against a myriad of pathogens. This limitation is thought to be counterbalanced by the rapid evolution of NB-LRR proteins, as only few sequence changes have been shown to be sufficient to alter resistance specificities towards novel strains of a pathogen. However, little is known about the flexibility of NB-LRR genes to switch resistance specificities between phylogenetically unrelated pathogens. To investigate this, we created domain swaps between the close homologs Gpa2 and Rx1, which confer resistance in potato to the cyst nematode Globodera pallida and Potato virus X (PVX), respectively. The genetic fusion of the CC-NB-ARC of Gpa2 with the LRR of Rx1 (Gpa2CN/Rx1L) resulted in autoactivity, but lowering the protein levels restored its specific activation response including extreme resistance to PVX in potato shoots. The reciprocal construct (Rx1CN/Gpa2L) showed a loss-of-function phenotype, but exchange of the first 3 LRR repeats of Rx1 was sufficient to regain a wild type resistance response to G. pallida in the roots. These data demonstrate that exchanging the recognition moiety in the LRR is sufficient to convert extreme virus resistance in the leaves into mild nematode resistance in the roots, and vice versa. In addition, we show that the CC-NB-ARC can operate independently of the recognition specificities defined by the LRR domain, either above or belowground. These data show the versatility of NB-LRR genes to generate resistances to unrelated pathogens with completely different lifestyles and routes of invasion.
The new (Fragmented) geography of carbon market mechanisms : Governance challenges from Thailand and Vietnam
Smits, Mattijs - \ 2017
Global Environmental Politics 17 (2017)3. - ISSN 1526-3800 - p. 69 - 90.
Countries in the Global South—which are contributing an increasing share of global greenhouse gas emissions—are actively developing carbon market mechanisms, including emissions trading systems and (voluntary) offset mechanisms. This article analyzes past and emerging experiments with carbon market mechanisms in Thailand and Vietnam, in the context of their domestic political economies and the shifting dynamics of the global climate governance regime. Drawing from thirty-three in-depth interviews and document analysis, I show the changing roles of government, the private sector, civil society, and donor and multilateral actors in these countries. Moreover, the article identifies key factors that may play roles in the further—and more synergistic—development of carbon market mechanisms: the generation of domestic demand for carbon credits; building and keeping human capacity and adequate data; creating space for civil society; ensuring coordination within the government and between sectors, notably the energy sector; and establishing further linkages with regional (Asian) and global carbon market mechanisms, such as those in China, Japan, and South Korea. These findings suggest that market-based mechanisms with high social and environmental integrity are one of the options that countries in the Global South have to achieve low-carbon development in the post-Paris climate change regime.
Schistosome egg antigens, including the glycoprotein IPSE/alpha-1, trigger the development of regulatory B cells
Haeberlein, Simone ; Obieglo, Katja ; Ozir-Fazalalikhan, Arifa ; Chayé, Mathilde A.M. ; Veninga, Henrike ; Vlugt, Luciën E.P.M. van der; Voskamp, Astrid ; Boon, Louis ; Haan, Joke M.M. den; Westerhof, Lotte B. ; Wilbers, Ruud H.P. ; Schots, Arjen ; Schramm, Gabriele ; Hokke, Cornelis H. ; Smits, Hermelijn H. - \ 2017
PLoS Pathogens 13 (2017)7. - ISSN 1553-7366
Infection with the helminth Schistosoma (S.) mansoni drives the development of interleukin (IL)-10-producing regulatory B (Breg) cells in mice and man, which have the capacity to reduce experimental allergic airway inflammation and are thus of high therapeutic interest. However, both the involved antigen and cellular mechanisms that drive Breg cell development remain to be elucidated. Therefore, we investigated whether S. mansoni soluble egg antigens (SEA) directly interact with B cells to enhance their regulatory potential, or act indirectly on B cells via SEA-modulated macrophage subsets. Intraperitoneal injections of S. mansoni eggs or SEA significantly upregulated IL-10 and CD86 expression by marginal zone B cells. Both B cells as well as macrophages of the splenic marginal zone efficiently bound SEA in vivo, but macrophages were dispensable for Breg cell induction as shown by macrophage depletion with clodronate liposomes. SEA was internalized into acidic cell compartments of B cells and induced a 3-fold increase of IL-10, which was dependent on endosomal acidification and further enhanced by CD40 ligation. IPSE/alpha-1, one of the major antigens in SEA, was also capable of inducing IL-10 in naïve B cells, which was reproduced by tobacco plant-derived recombinant IPSE. Other major schistosomal antigens, omega-1 and kappa-5, had no effect. SEA depleted of IPSE/alpha-1 was still able to induce Breg cells indicating that SEA contains more Breg cell-inducing components. Importantly, SEA- and IPSE-induced Breg cells triggered regulatory T cell development in vitro. SEA and recombinant IPSE/alpha-1 also induced IL-10 production in human CD1d+B cells. In conclusion, the mechanism of S. mansoni-induced Breg cell development involves a direct targeting of B cells by SEA components such as the secretory glycoprotein IPSE/alpha-1.
Antibiotics in 16-day-old broilers temporarily affect microbial and immune parameters in the gut
Wisselink, H.J. ; Cornelissen, J.B.W.J. ; Mevius, D.J. ; Smits, M.A. ; Smidt, H. ; Rebel, Johanna M.J. - \ 2017
Poultry Science 96 (2017)9. - ISSN 0032-5791 - p. 3068 - 3078.
Animal health benefits from a stable intestinal homeostasis, for which proper development and functioning of the intestinal microbiota and immune system are essential. It has been established that changes in microbial colonization in early life (the first 2 wk post hatch) impacts the functioning of the adult gut and the associated crosstalk between microbiota and intestinal mucosal cells. The aim of the present study was to study the effect of the administration of antibiotics later in life (d 15 to 20 post hatch) on microbiota and immune parameters. For this purpose, chickens received from 15 d post hatch during 5 d amoxicillin or enrofloxacin through their drinking water. Before and at 6, 16, and 27 d after start of the administration of antibiotics, the composition of the microbiota in the jejunum was determined using a 16S ribosomal RNA gene-targeted DNA microarray, the CHICKChip. At 6 d after the start of the administration of the antibiotics, the composition and diversity of the microbiota were affected significantly (P < 0.05), but this change was small and observed only temporarily since differences disappeared at 16 d after initiating treatment with amoxillin and at 27 d after starting treatment with enrofloxacin. Intestinal morphology and development were not visibly affected since there were no differences between villus/crypt ratios and numbers of PAS+ and PCNA+ cells in the duodenum and jejunum at any time point. At 16 d after the start of antibiotic administration, the number of CD4+ T-cells and CD8+ T-cells in the duodenum was lower compared to the control animals; however, this difference was not significant. At some time points, significant differences (P < 0.05) were observed among the groups to locally expressed IL-8, IL-1β, IFN-γ, IL-2, and IL-4 mRNA. However, this effect was not long lasting, as differences that were observed at 16 d after starting the treatment had disappeared at 27 d after treatment was started. The results of this study indicate that later in the broiler's life, antibiotics only temporarily affect intestinal microbial and immune parameters.
Interactions and functionalities of the gut revealed by computational approaches
Benis, Nirupama - \ 2017
Wageningen University. Promotor(en): M.A. Smits; V.A.P. Martins dos Santos, co-promotor(en): D. Schokker; M. Suarez-Diez. - Wageningen : Wageningen University - ISBN 9789463434546 - 247
pigs - mice - digestive tract - digestive system - intestinal microorganisms - intestinal mucosa - computational science - immune system - feeds - animal nutrition - nutrition physiology - animal health - varkens - muizen - spijsverteringskanaal - spijsverteringsstelsel - darmmicro-organismen - darmslijmvlies - computational science - immuunsysteem - voer - diervoeding - voedingsfysiologie - diergezondheid

The gastrointestinal tract is subject of much research for its role in an organism’s health owing to its role as gatekeeper. The tissue acts as a barrier to keep out harmful substances like pathogens and toxins while absorbing nutrients that arise from the digestion of dietary components in in the lumen. There is a large population of microbiota that plays an important role in the functioning of the gut. All these sub-systems of the gastrointestinal tract contribute to the normal functioning of the gut. Due to its various functionalities, the gut is able to respond to different types of stimuli and bring the system back to homeostasis after perturbations.

The work done in this thesis uses several bioinformatic tools to improve our understanding of the functioning of the gut. This was achieved with data from model animals, mice and pigs which were subjected to changing environments before their gastrointestinal response was measured. Different types of stimuli were studied (eg, antibiotic exposure, changing diets and infection with pathogens) in order to understand the response of the gut to varying environments. This data was analysed using different data integration techniques that provide a holistic view of the gut response.

Vertical data integration techniques look for associations between different types of ~omics data to highlight possible interactions between the measured variables. Lateral integration techniques allow the study of one type of ~omics data over several time points or several experimental conditions. Using these techniques, we show proof of interactions between different sub-systems of the gut and the functional plasticity of the gut. Of the several hypotheses generated in this thesis we have validated several using existing literature and one using an in-vitro system. Further validation of these hypotheses will increase understanding of the responses of the gut and the interactions involved.

Multi-level integration of environmentally perturbed internal phenotypes reveals key points of connectivity between them
Benis, Nirupama ; Kar, Soumya K. ; Martins dos Santos, Vitor A.P. ; Smits, Mari A. ; Schokker, Dirkjan ; Suarez-Diez, Maria - \ 2017
Frontiers in Physiology 8 (2017). - ISSN 1664-042X - 11 p.
Data integration - Gastrointestinal tract - Internal phenotype - Metabolomics - Microbiota - Proteomics - Systems biology - Transcriptomics

The genotype and external phenotype of organisms are linked by so-called internal phenotypes which are influenced by environmental conditions. In this study, we used five existing -omics datasets representing five different layers of internal phenotypes, which were simultaneously measured in dietarily perturbed mice. We performed 10 pair-wise correlation analyses verified with a null model built from randomized data. Subsequently, the inferred networks were merged and literature mined for co-occurrences of identified linked nodes. Densely connected internal phenotypes emerged. Forty-five nodes have links with all other data-types and we denote them "connectivity hubs." In literature, we found proof of 6% of the 577 connections, suggesting a biological meaning for the observed correlations. The observed connectivities between metabolite and cytokines hubs showed higher numbers of literature hits as compared to the number of literature hits on the connectivities between the microbiota and gene expression internal phenotypes. We conclude that multi-level integrated networks may help to generate hypotheses and to design experiments aiming to further close the gap between genotype and phenotype. We describe and/or hypothesize on the biological relevance of four identified multi-level connectivity hubs.

Oil and gas development in Greenland: A social license to operate, trust and legitimacy in environmental governance
Smits, C. ; Leeuwen, J. van; Tatenhove, J.P.M. van - \ 2017
Resources Policy 53 (2017). - ISSN 0301-4207 - p. 109 - 116.
Greenland - oil and gas - trust - legitimacy - social license to operate
Since the turn of the century, Greenland has been examining the possibilities to develop its potential oil and gas resources. The large scale oil and gas activities will impact the small Greenlandic society, both positively and negatively. In this paper we employ the concept of a social license to operate to address the risks of an activity, represented by the acceptance or approval of an activity by societal actors. The focus of existing research is primarily on the interaction between local communities and companies. However, in an increasingly complex society, where the role of governments, companies and civil society is subject to constant change, social licenses to operate should be studied in an integrated way, to deal with all essential elements that influence the successful implementation of controversial activities.

This paper builds on the idea that successful implementation of an activity is determined by social, political and legal licenses. Trust and legitimacy are regarded as the fundamental principles on which all three licenses are based. This paper therefore adopts an integrated approach, in which the role of the political and legal licenses is taken into account as well as the social license. This approach provides for a more thorough analysis for different sources of personal and institutionalised trust as well as input, throughput and output legitimacy across the three licenses. The case study also illustrates the potential role of the government in co-shaping a social license to operate.
FeedOmics, an approach to evaluate the functional properties of protein containing feed ingredients
Kar, Soumya K. - \ 2017
Wageningen University. Promotor(en): M.A. Smits; J.M. Wells, co-promotor(en): A.J.M. Jansman; D. Schokker. - Wageningen : Wageningen University - ISBN 9789463434461 - 254
compound feeds - ingredients - protein sources - proteins - functional properties - metabolism - feed formulation - protein digestion - proteomics - digestive tract - nutrition physiology - animal nutrition - livestock feeding - mengvoer - ingrediënten - eiwitbronnen - eiwitten - functionele eigenschappen - metabolisme - voersamenstelling - eiwitvertering - eiwitexpressieanalyse - spijsverteringskanaal - voedingsfysiologie - diervoeding - veevoeding

This thesis presents FeedOmics approach as a toolkit, to evaluate (novel) protein containing feed ingredients of different origin considering both their nutritional and functional value in terms of their capacity to support or modify nutrient supply, the animal’s physiology, tissue development and functioning. Such knowledge may contribute to introduce novel and/or alternative protein containing feed ingredients in the diet of livestock, thus creating a sustainable food supply for growing human population.

Biological processes induced by ZnO, Amoxicillin, and Rye in cultured Intestinal Porcine Epithelial Cells (IPEC-J2)
Hulst, M.M. ; Hoekman, A.J.W. ; Smits, M.A. - \ 2017
Sus scrofa - GSE94139 - PRJNA369066
The objective of this study is to investigate to what extent gene expression data of dietary interventions generated in IPEC-J2 in vitro model overlap with in vivo data. Gene expression was recorded in IPEC-J2 cells upon exposure to three different dietary interventions commonly used in livestock. In a further step, we compared the results with mucosal gene expression responses, as measured in animals exposed to the same compounds via the diet. As compounds we used zinc oxide, rye and the antibiotic amoxicillin. The GEO accession numbers of the in vivo datasets are provided in the paper "Enrichment of in vivo determined transcription data from dietary intervention studies with in vitro data provides improved insight into gene regulation mechanisms" (submitted to "Genes and Nutrition").
Enrichment of in vivo transcription data from dietary intervention studies with in vitro data provides improved insight into gene regulation mechanisms in the intestinal mucosa
Hulst, Marcel ; Jansman, Alfons ; Wijers, Ilonka ; Hoekman, Arjan ; Vastenhouw, Stéphanie ; Krimpen, Marinus Van; Smits, Mari ; Schokker, Dirkjan - \ 2017
Genes & Nutrition 12 (2017). - ISSN 1555-8932 - 18 p.

Background

Gene expression profiles of intestinal mucosa of chickens and pigs fed over long-term periods (days/weeks) with a diet rich in rye and a diet supplemented with zinc, respectively, or of chickens after a one-day amoxicillin treatment of chickens, were recorded recently. Such dietary interventions are frequently used to modulate animal performance or therapeutically for monogastric livestock. In this study, changes in gene expression induced by these three interventions in cultured “Intestinal Porcine Epithelial Cells” (IPEC-J2) recorded after a short-term period of 2 and 6 hours, were compared to the in vivo gene expression profiles in order to evaluate the capability of this in vitro bioassay in predicting in vivo responses.


Methods

Lists of response genes were analysed with bioinformatics programs to identify common biological pathways induced in vivo as well as in vitro. Furthermore, overlapping genes and pathways were evaluated for possible involvement in the biological processes induced in vivo by datamining and consulting literature.


Results

For all three interventions, only a limited number of identical genes and a few common biological processes/pathways were found to be affected by the respective interventions. However, several enterocyte-specific regulatory and secreted effector proteins that responded in vitro could be related to processes regulated in vivo, i.e. processes related to mineral absorption, (epithelial) cell adherence and tight junction formation for zinc, microtubule and cytoskeleton integrity for amoxicillin, and cell-cycle progression and mucus production for rye.


Conclusions

Short-term gene expression responses to dietary interventions as measured in the in vitro bioassay have a low predictability for long-term responses as measured in the intestinal mucosa in vivo. The short-term responses of a set regulatory and effector genes, as measured in this bioassay, however, provided additional insight into how specific processes in piglets and broilers may be modulated by “early” signalling molecules produced by enterocytes. The relevance of this set of regulatory/effector genes and cognate biological processes for zinc deficiency and supplementation, gluten allergy (rye), and amoxicillin administration in humans is discussed.
What’s cooking? Unverified assumptions, overlooking of local needs and pro-solution biases in the solar cooking literature
Iessa, L. ; Vries, Y.A. de; Swinkels, C.E. ; Smits, M. ; Butijn, C.A.A. - \ 2017
Energy Research & Social Science 28 (2017). - ISSN 2214-6296 - p. 98 - 108.
solar cooking - review - development - practices
Solar cookers have been tested and studied in various settings, but despite their envisioned benefits – reduction of deforestation, economic benefits, improved health, and empowerment of women – results have been modest at best. This article performs a critical review of the literature on solar cooking (SC), to scrutinise the assumptions and methodological choices that may explain this conundrum. The literature review yielded 32 articles on solar cookers in Sub-Saharan Africa, where most SC projects can be found. Four recurrent types of issues stand out: local needs are often not sufficiently considered, existing cooking and fuelwood practices are seen as obstacles, many articles show a prosolution bias and there is a lack of methodologically sound impact studies. To overcome these issues, practice theory – which analyses the practice of cooking from the logic of the practice, rather than from an external point of view – is proposed to guide and focus future SC projects and studies. Furthermore, ethnographical methods can provide new and grounded evidence and allow for a stronger focus on local needs. These approaches can provide a fruitful evidence base to analyse the role of solar-cooking in achieving sustainable and long-term development benefits in the Global South.
Characterization of Coxiella burnetii outbreak strains
Kuley, Runa - \ 2017
Wageningen University. Promotor(en): M.A. Smits; J.M. Wells, co-promotor(en): A. Bossers. - Wageningen : Wageningen University - ISBN 9789463431514 - 226
coxiella burnetii - q fever - outbreaks - strains - characterization - pathogenesis - zoonoses - virulence - dna sequencing - polymerase chain reaction - livestock farming - netherlands - coxiella burnetii - q-koorts - uitbraken (ziekten) - stammen (biologisch) - karakterisering - pathogenese - zoönosen - virulentie - dna-sequencing - polymerase-kettingreactie - veehouderij - nederland

Q fever is a worldwide zoonotic infectious disease caused by the bacterium Coxiella burnetii. During 2007-2010, the largest Q fever outbreak was reported in The Netherlands, where more than 4000 human cases were registered showing a serious burden of the disease. During this outbreak, goats harboring predominantly the CbNL01 genotype strain were identified as the major source of disease in humans and drastic measures such as mass culling of infected goats were implemented to reduce the spread of the pathogen and control the disease. In order to minimize such complications in the future, it is crucial to have a thorough understanding of the disease causing pathogen and to develop effective Q fever vaccines. The causes of the large Dutch outbreak are not well-understood and one of the main reasons speculated were the hyper-virulent behavior of the circulating C. burnetii isolates. The research described in this thesis focuses on the characterization of C. burnetii outbreak strains isolated from infected goats, cattle, sheep and human clinical materials. Our studies were initiated to better understand the bacterial pathogenesis, virulence, evolution, adaptations in various environments, host immune responses and to identify pathogen related factors that have modulated the disease outbreak. We specifically aimed to identify the virulence factors and mechanisms that contributed to the increased zoonotic potential of the strain associated with the Dutch Q fever outbreak.

The studies presented in this thesis majorly applied Pathogenomic approaches at the genome and transcriptome level to decipher host-pathogen interactions and to develop new tools to study C. burnetii infections. A transcriptome analysis of the outbreak C. burnetii strain of the CbNL01 genotype grown under in vivo and in vitro conditions resulted in the identification of distinct metabolic adaptations and virulence mechanisms of the bacterium. Detailed comparative analysis of complete genome sequences of C. burnetii strains showed a high similarity between strains of the same genotype. Genome sequences of the Dutch outbreak CbNL01 genotype strains were more divergent than the genome sequences of the less prevalent CbNL12 genotype strains and the NM reference strain. The analysis also showed that the high virulence of the outbreak strains was not associated with acquiring novel virulence-related genes arguing against the idea that the Dutch outbreak was due to emergence of hyper-virulent strains though horizontal gene transfer. Among the prominent genetic differences in the CbNL01 outbreak strains compared to CbNL12 and NM, were the presence of several point mutations and increased transposon mediated genome plasticity, which might have contributed to its epidemic potential. Point mutations, especially in a large number of membrane proteins, could also have contributed to the increased zoonotic potential of CbNL01 strains allowing this clone to escape the host immune responses in goats and humans. In addition, mutations in critical genes involved in virulence and evasion of the host immune system could be potentially involved in the increased virulence of the CbNL01 outbreak strains. On the contrary, studies on host immune responses in an in vivo (experimental infections in mice) and an in vitro (human PBMC’s stimulation) model did not show any difference associated with the strain genotype. However, differences in immune responses were found to be associated with the host-origin of the C. burnetii strains. Among different host-origin strains, strains derived from goats and humans generated significantly lower innate and adaptive immune responses than strains derived from cattle, whereas no differences in immune responses were observed when strains were grouped based upon their genotype. These observations support immune evasions as a major virulence strategy of goat and human strains in hosts and further suggest that bacteria originating from goats have a greater potential to cause outbreaks in humans. This indicates that for Q fever prevention purposes goats should be efficiently monitored for the presence of C. burnetii. Taken together, the results described in this thesis suggest that the virulence potential of C. burnetii strains is not only based on genetic differences, but also on other host-adaptation mechanisms such as transposition of genomic elements and/or differential regulation of gene expression. Finally, the results from this thesis provide a framework for future studies in the development of vaccines and diagnostic tools for Q fever.

Production and glyco-engineering of immunomodulatory helminth glycoproteins in plants
Wilbers, Ruud H.P. ; Westerhof, Lotte B. ; Noort, Kim Van; Obieglo, Katja ; Driessen, Nicole N. ; Everts, Bart ; Gringhuis, Sonja I. ; Schramm, Gabriele ; Goverse, Aska ; Smant, Geert ; Bakker, Jaap ; Smits, Hermelijn H. ; Yazdanbakhsh, Maria ; Schots, Arjen ; Hokke, Cornelis H. - \ 2017
Scientific Reports 7 (2017). - ISSN 2045-2322
Helminth parasites control host-immune responses by secreting immunomodulatory glycoproteins. Clinical trials and mouse model studies have demonstrated the potential of helminth-derived glycoproteins for the treatment of immune-related diseases, like allergies and autoimmune diseases. Studies are however hampered by the limited availability of native parasite-derived proteins. Moreover, recombinant protein production systems have thus far been unable to reconstitute helminth-like glycosylation essential for the functionality of some helminth glycoproteins. Here we exploited the flexibility of the N-glycosylation machinery of plants to reconstruct the helminth glycoproteins omega-1 and kappa-5, two major constituents of immunomodulatory Schistosoma mansoni soluble egg antigens. Fine-tuning transient co-expression of specific glycosyltransferases in Nicotiana benthamiana enabled the synthesis of Lewis X (LeX) and LDN/LDN-F glycan motifs as found on natural omega-1 and kappa-5, respectively. In vitro and in vivo evaluation of the introduction of native LeX motifs on plant-produced omega-1 confirmed that LeX on omega-1 contributes to the glycoprotein’s Th2-inducing properties. These data indicate that mimicking the complex carbohydrate structures of helminths in plants is a promising strategy to allow targeted evaluation of therapeutic glycoproteins for the treatment of inflammatory disorders. In addition, our results offer perspectives for the development of effective anti-helminthic vaccines by reconstructing native parasite glycoprotein antigens.
Perturbation of microbiota in one-day old broiler chickens with antibiotic for 24 hours negatively affects intestinal immune development
Schokker, Dirkjan ; Jansman, Alfons J.M. ; Veninga, Gosse ; Bruin, Naomi de; Vastenhouw, Stephanie A. ; Bree, Freddy M. de; Bossers, Alex ; Rebel, Johanna M.J. ; Smits, Mari A. - \ 2017
BMC Genomics 18 (2017). - ISSN 1471-2164 - 14 p.
Background: Gut microbial colonization and development of immune competence are intertwined and are influenced by early-life nutritional, environmental, and management factors. Perturbation of the gut microbiome at young age affects the crosstalk between intestinal bacteria and host cells of the intestinal mucosa.
Results: We investigated the effect of a perturbation of the normal early life microbial colonization of the jejunum in 1-day old chickens. Perturbation was induced by administering 0.8 mg amoxicillin per bird per day) via the drinking water for a period of 24 h. Effects of the perturbation were measured by 16S rRNA profiling of the microbiome and whole genome gene expression analysis. In parallel to what has been observed for other animal species, we hypothesized that such an intervention may have negative impact on immune development.
Trends were observed in changes of the composition and diversity of the microbiome when comparing antibiotic treated birds with their controls. in the jejunum, the expression of numerous genes changed, which potentially leads to changes in biological activities of the small intestinal mucosa. Validation of the predicted functional changes was performed by staining immune cells in the small intestinal mucosa and a reduction in the number of macrophage-like (KUL01+) cells was observed due to a direct or indirect effect of the antibiotic treatment. We provide evidence that a short, early life antibiotic treatment affects both the intestinal microbiota (temporarily) and mucosal gene expression over a period of 2 weeks.
Conclusion: These results underscore the importance of early life microbial colonization of the gut in relation to immune development and the necessity to explore the capabilities of a variety of early life dietary and/or environmental factors to modulate the programming for immune competence in broilers.
The importance of endophenotypes to evaluate the relationship between genotype and external phenotype
Pas, Marinus F.W. te; Madsen, Ole ; Calus, Mario P.L. ; Smits, Mari A. - \ 2017
International Journal of Molecular Sciences 18 (2017)2. - ISSN 1661-6596
Bioinformatics - Genomic variation and environment - Integration - Livestock science - Metabolome - Methylome - Phenome - Proteome - Systems biology - Transcriptome

With the exception of a few Mendelian traits, almost all phenotypes (traits) in livestock science are quantitative or complex traits regulated by the expression of many genes. For most of the complex traits, differential expression of genes, rather than genomic variation in the gene coding sequences, is associated with the genotype of a trait. The expression profiles of the animal’s transcriptome, proteome and metabolome represent endophenotypes that influence/regulate the externally-observed phenotype. These expression profiles are generated by interactions between the animal’s genome and its environment that range from the cellular, up to the husbandry environment. Thus, understanding complex traits requires knowledge about not only genomic variation, but also environmental effects that affect genome expression. Gene products act together in physiological pathways and interaction networks (of pathways). Due to the lack of annotation of the functional genome and ontologies of genes, our knowledge about the various biological systems that contribute to the development of external phenotypes is sparse. Furthermore, interaction with the animals’ microbiome, especially in the gut, greatly influences the external phenotype. We conclude that a detailed understanding of complex traits requires not only understanding of variation in the genome, but also its expression at all functional levels.

Mimicking immunomodulatory helminth glycoproteins in plants to enable treatment of inflammatory diseases
Wilbers, R.H.P. ; Westerhof, L.B. ; Noort, Kim van; Obieglo, K. ; Driessen, N.N. ; Everts, B. ; Goverse, A. ; Smant, G. ; Bakker, J. ; Smits, H.H. ; Yazdanbakhsh, M. ; Schots, A. ; Hokke, C.H. - \ 2017
Helminth parasites control host-immune responses by secreting immunomodulatory glycoproteins. Clinical trials and mouse model studies have demonstrated the potential of helminths and helminth-derived glycoproteins for the treatment of immune-related diseases, like allergies and autoimmune diseases. Studies are however hampered by the limited availability of native parasite-derived proteins. Moreover, recombinant protein production systems have thus far been unable to reconstitute helminth-like glycosylation essential for the functionality of helminth glycoproteins. Here we exploited the flexibility of the N-glycosylation machinery of plants to reconstruct two helminth glycoproteins, omega-1 and kappa-5, major constituents of immunomodulatory Schistosoma mansoni soluble egg antigens. Fine-tuning transient co-expression of specific glycosyltransferases in Nicotiana benthamiana enabled the synthesis of Lewis X (LeX) and LDN/LDN-F glycan motifs as found on natural omega-1 and kappa-5, respectively. In vitro and in vivo evaluation of the introduction of native LeX motifs on plant-produced omega-1 confirmed that LeX on omega-1 contributes to the glycoprotein’s Th2-inducing properties. These data indicate that mimicking the complex carbohydrate structures of helminths in plants is a promising strategy to allow targeted evaluation of therapeutic glycoproteins for the treatment of inflammatory disorders. In addition, our results offer perspectives for the development of effective anti-helminthic vaccines by reconstructing native parasite glycoprotein antigens.
Gut microbial colonization in day old chicks
Woelders, H. ; Schokker, D. ; Smits, M.A. - \ 2017
International Hatchery Practice 31 (2017)1. - ISSN 0959-9363
Transitions to Energy and Climate Security in Thailand
Simpson, A. ; Smits, M. - \ 2017
In: Handbook of Transitions to Energy and Climate Security / Looney, Robert E., Abingdon : Routledge - ISBN 9781857437454 - p. 296 - 311.
Effects of a high level of dietary zinc over different post weaning periods on intestinal microbiota and mucosal gene expression in piglets
Jansman, A.J.M. ; Schokker, D. ; Gerritsen, R. ; Willems, E. ; Bree, F. de; Dekker, R.A. ; Smits, M.A. - \ 2016
Wageningen : Wageningen Livestock Research (Wageningen Livestock Research rapport 1001) - 48
Effects of a high level of dietary zinc as model intervention on intestinal microbiota and mucosal gene expression in piglets
Jansman, A.J.M. ; Schokker, D. ; Gerritsen, R. ; Bree, F. de; Hulst, M.M. ; Smits, M.A. - \ 2016
Wageningen : Wageningen Livestock Research (Wageningen Livestock Research rapport 1000) - 37
Effect of nutritional interventions with quercetin, oat hulls, β-glucans, lysozyme, and fish oil on immune competence related parameters of adult broiler
Krimpen, M.M. van; Torki, M. ; Schokker, D. ; Lensing, M. ; Vastenhouw, S. ; Bree, F.M. de; Bossers, A. ; Bruijn, N. de; Jansman, A.J.M. ; Rebel, J.M.J. ; Smits, M.A. - \ 2016
Wageningen : Wageningen Livestock Research (Wageningen Livestock Research report 977) - 50
The purpose of this experiment was to evaluate the effects of five nutritional interventions, provided during d 14 – 28, including inclusion of a plant extract (quercetin); an insoluble fiber (oat hulls); a prebiotic (β- glucan); an anti-microbial protein (lysozyme), and ω-3 fatty acids from fish oil, on growth performance, composition of the intestinal microbiota, and morphology and gene expression of small intestine of broilers. Despite the different types of interventions, parameters related to immune competence were only marginally affected by the tested products. It seemed that in this study inclusion of oat hulls, and probably β-glucans, had perspective to improve immune competence. It is recommended to revaluate some of the tested interventions, especially dietary inclusion of oat hulls and β-glucans, in broilers starting from day-old onward.
Intestinal development in two divergent chicken lines (X and Y)
Schokker, Dirkjan ; Vastenhouw, Stephanie ; Smits, Mari ; Rebel, Annemarie - \ 2016
Gallus gallus - GSE65042 - PRJNA272779
The objective of this study was to investigate the impact of genotypic variation on both early microbial colonization of the gut and functional development of intestinal tissue.
Effects of digested onion extracts on intestinal gene expression using rat intestine slices
Wit, N.J.W. de; Hulst, M.M. ; Govers, C.C.F.M. ; Meulen, J. van der; Hoef, A.M.A. van; Stoopen, G.M. ; Hamers, A.R.M. ; Hoekman, A.J.W. ; Vos, C.H. de; Bovee, T.F.H. ; Smits, M.A. ; Mes, J.J. ; Hendriksen, P.J.M. - \ 2016
Rattus norvegicus - GSE84179 - PRJNA328225
Rat small intestine precision cut slices were exposed for 6 hours to in vitro digested yellow (YOd) and white onion extracts (WOd) that was followed by transcriptomics analysis. The digestion was performed to mimic the digestion that in vivo takes place in the stomach and small intestine. The transcriptomics response of the rat small intestine precision cut slices was compared to that of human Caco-2 cells and the pig in-situ small intestinal segment perfusion. The microarray data for the human Caco-2 cells (GSE83893) and the pig in-situ small intestinal segment perfusion (GSE83908) have been submitted separately from the current data on rat intestine. The goal was to obtain more insight into to which extent mode of actions depend on the experimental model. A main outcome was that each of the three models pointed to the same mode of action: induction of oxidative stress and particularly the Keap1-Nrf2 pathway.
Effects of digested onion extracts on intestinal gene expression: an interspecies comparison using different intestine models
Hulst, M.M. ; Meulen, J. van der; Hoekman, A.J.W. ; Smits, M.A. - \ 2016
Sus scrofa - GSE83908 - PRJNA327381
Applicability of in vitro (human Caco-2 cells) and ex vivo intestine models (rat precision cut intestine slices and the pig in-situ small intestinal segment perfusion (SISP) technique) to study the effect of food compounds. In vitro digested yellow (YOd) and white onion extracts (WOd) were used as model food compounds and transcriptomics was applied to obtain more insight into which extent mode of actions depend on the model.
One-day old broilers exposed to amoxicillin
Schokker, D. ; Vastenhouw, S.A. ; Smits, M.A. ; Rebel, J.M.J. - \ 2016
Gallus gallus - GSE67452 - PRJNA279978
The objective of this study was to investigate the impact of short-term antibiotic treatment in early life on both early microbial colonization of the gut and functional development of intestinal tissue. From both control and antibiotic treated birds intestinal content samples were taken for microbiota analyzes and intestinal tissue samples were extracted for gene expression analyzes, both at three subsequent time-points (days 1, 5, and 14).
LPS challenge in jonge biggen : VDI-12: effect voerinterventie op biggen
Greeff, Astrid de; Allaart, Janneke ; Bruijn, Carlijn de; Schokker, Dirkjan ; Roubos, Petra ; Winkelman-Goedhart, Hélène ; Vastenhouw, Stéphanie ; Ruuls, Lisette ; Rebel, Johanna ; Smits, Mari - \ 2016
Wageningen : Wageningen Livestock Research (Wageningen Livestock Research rapport 1009) - 21
biggen - maatregel op voedingsgebied - adequate immuniteit - diergezondheid - lipopolysacchariden - varkenshouderij - dierhouderij - immunologie - piglets - nutritional intervention - immune competence - animal health - lipopolysaccharides - pig farming - animal husbandry - immunology
Het stimuleren van ondernemen met natuur: handelingsopties voor de overheid
Smits, M.J.W. ; Bos, E.J. - \ 2016
Wageningen : Wettelijke Onderzoekstaken Natuur & Milieu (WOt-technical report 83) - 90
natuur - ondernemingen - regering - overheidsbeleid - ondernemerschap - milieueconomie - nature - enterprises - government - government policy - entrepreneurship - environmental economics
De Rijksnatuurvisie wil ondernemers meer betrekken bij natuur. De ambitie is dat natuur altijd meegenomen wordt inhandelingen en beslissingen, ook van ondernemers. Dit wordt ‘natuurinclusief ondernemen’ genoemd. De vraag diecentraal staat in dit rapport is welke beleidsmaatregelen genomen kunnen worden om natuurinclusief ondernemen(verder) te stimuleren. Het antwoord op deze vraag wordt mede bepaald door de wisselwerking tussen publieke enprivate taken en verantwoordelijkheden voor natuur. Een tweede vraag is: in welke mate worden de kosten vannatuurinclusief ondernemen gedragen door de private sector en in welke mate door de publieke sector? Op basis vanvijftien interviews met personen uit het veld kwamen een aantal aandachtspunten en behoeften naar voren die vanbelang blijken voor het verder uitrollen van het concept ‘natuurinclusief ondernemen’. Zo is er behoefte aan duidelijkafgebakende experimenteerruimte om ondernemers het belang en de toepassing van natuurinclusief ondernemen telaten ervaren. Er leeft een gevoel van willekeur door verschillen in (lengte van) procedures tussen gemeenten enprovincies. Verder wordt een intermediair zoals voorheen de Dienst Landelijk Gebied wordt gemist voorgrondaanwerving, inrichting en voorfinanciering. Daarnaast is behoefte aan (ecologische) kennis bij ondernemers enaan ‘oplossingen’ voor de hoge grondprijs die natuurinclusieve landbouw belemmeren, en er werd gewezen op hetbelang van een gebiedsgerichte aanpak. En tot slot: natuurinclusief ondernemen impliceert vaak multifunctioneelgrondgebruik, maar dit stuit nogal eens op wetgeving gericht op bescherming van natuur. Hoewel aan de term‘natuurinclusief ondernemen’ het private belang ten grondslag ligt, blijkt een overheidsrol nog altijd onontbeerlijkhierbij. Zo wordt natuurinclusief ondernemen deels betaald met publiek geld, bijvoorbeeld via subsidies en fiscalevrijstelling. Ook al blijkt uit dit onderzoek de behoefte aan een overheidsrol, tegelijkertijd is duidelijkheid vereist.Wanneer kan natuur privaat opgepakt worden, en wanneer moet het publiek ondersteund worden? Een nieuwevenwicht tussen publieke en private inbreng bij beheer en behoud van natuur is nog niet gevonden---In its policy vision on nature, ‘The Natural Way Forward’ (2014), the government calls on entrepreneurs to take agreater interest in nature. The government’s ambition is for nature to be taken into account in all actions and decisions,including those by entrepreneurs. This is called ‘nature-inclusive enterprise’. The key research question in this report iswhich policy measures can be introduced to stimulate nature-inclusive enterprise. The answer to this question isdetermined in part by the interplay between public and private tasks and responsibilities for nature. A second questionis how the costs of nature-inclusive enterprise should be divided between the private and public sectors. Interviews with15 stakeholders revealed a number of issues and requirements that would help to roll out the concept of ‘natureinclusiveenterprise’ further. For example, there is a need for room to experiment, within clearly defined limits, to allowentrepreneurs to experience the value of nature-inclusive enterprise and how it can be put into practice. There is afeeling that the situation is somewhat arbitrary at the moment because of differences in the procedures, particularlytheir length, between municipalities and provinces. For land acquisition, landscape works and prefinancing, therespondents felt the need for an intermediary organisation like the former Government Service for Land and WaterManagement (DLG). In addition, entrepreneurs are in need of ecological expertise as well as ‘solutions’ to the high priceof land, which frustrates nature-inclusive farming. The importance of an area-based approach was also raised. Finally,nature-inclusive enterprise often implies multifunctional land use, but this tends to conflict with the nature conservationlegislation, which is geared more to protection. Although the term ‘nature-inclusive enterprise’ reflects the underlyingprivate sector interest, government still has an essential role to play. For one thing, nature-inclusive enterprise is stillpartly financed with public money, for example via grants and tax exemptions. The study also indicates that while thisgovernment intervention is welcomed, there is also a desire for certainty. When can nature be integrated into thebusiness case and when should it be supported by the public sector? A new balance between public and privateinvolvement in nature conservation has not yet been found.
Gut microbial colonization in day old chicks
Smits, Mari - \ 2016
Sustainable feed supply for worldwide poultry production
Hartog, L.A. den; Garcia Ruiz, I.A. ; Smits, C.H.M. ; Scott, T. - \ 2016
Hormones and β-Agonists
Ginkel, L.A. van; Bovee, T.F.H. ; Blokland, M.H. ; Sterk, S.S. ; Smits, N.G.E. ; Pleadin, Jelka ; Vulić, Ana - \ 2016
In: Chemical Analysis of Non-antimicrobial Veterinary Drug Residues in Food / Kay, Jack F., MacNeil, James D., Wang, Jian, Wiley - ISBN 9781118695074
This chapter provides some updated information on contemporary methods for hormone and β-agonist analyses. It deals with the classical approaches for the effective detection and identification of exogenous hormones. The chapter examines specific problems related to control strategies for natural hormones. These include both the traditional and generally recognized natural hormones as well as a series of androgenic steroids that can be present in biological samples obtained from a series of species. The fact that natural background concentrations can be present strongly complicates the analyses. The application of mass spectrometry (MS) in combination with gas chromatography (GC) or liquid chromatography (LC) is considered the "gold standard" for analytical methods in residue analysis. The chapter presents an overview of the available bio-based screening methods for the detection of hormones and ß-agonists, focusing on estrogens, androgens, progestogens, corticosteroids, thyroids, ß2-agonists, and growth hormones (GH).
Building pathway graphs from BioPAX data in R
Benis, N. ; Schokker, D. ; Kramer, F. ; Smits, Mari ; Suarez-Diez, M. - \ 2016
F1000 Research 5 (2016). - ISSN 2046-1402 - 13 p.

Biological pathways are increasingly available in the BioPAX format which uses an RDF model for data storage. One can retrieve the information in this data model in the scripting language R using the package rBiopaxParser, which converts the BioPAX format to one readable in R. It also has a function to build a regulatory network from the pathway information. Here we describe an extension of this function. The new function allows the user to build graphs of entire pathways, including regulated as well as non-regulated elements, and therefore provides a maximum of information. This function is available as part of the rBiopaxParser distribution from Bioconductor.
Delineating spatio-temporal processes in the gut mucosa of pigs
Hulsegge, B. ; Rebel, J.M.J. ; Schokker, D. ; Smits, M.A. - \ 2016
In: Book of Abstracts of the 67th Annual Meeting of the European Federation of Animal Science. - Wageningen : Wageningen Academic Publishers (Book of abstracts 22) - ISBN 9789086862849 - p. 542 - 542.
Quantification of viable campylobacter on chicken carcasses by pma real-time pcr and pma-isothermal amplifiaction
Cornelissen, J.B.W.J. ; Smits, C.B. ; Koene, M.G.J. - \ 2016
Procesindicatoren PAS : rapportage 2016
Smits, N.A.C. ; Mucher, C.A. ; Ozinga, W.A. ; Waal, R.W. de; Wamelink, G.W.W. - \ 2016
Wageningen : Wageningen Environmental Research (Wageningen Environmental Research rapport 2771) - 61
stikstof - indicatoren - monitoring - ecologisch herstel - habitats - vegetatie - nitrogen - indicators - ecological restoration - vegetation
In het kader van het Programma Aanpak Stikstof (PAS) is in 2016 doorgewerkt aan een aantal onderwerpen rondom de ecologische onderbouwing van het PAS, waaronder de procesindicatoren. Binnen de PAS-monitoring is afgesproken dat het proces van natuurherstel ook op korte termijn gevolgd wordt om zo snel mogelijk de effectiviteit van de herstelmaatregelen in kaart te brengen. Hiervoor zijn de PAS-procesindicatoren ontwikkeld. Deze procesindicatoren zijn vooral bedoeld om een indicatie van het herstelproces te geven. Deze procesindicatoren kunnen verschillen per habitattype en per maatregel, maar ook per gebied. Om die redenen is een flexibel systeem ontworpen met diverse parameters: luchtfoto’s, abiotische metingen, vegetatie en soorten. De huidige rapportage betreft de verslaglegging van de ontwikkelde systematiek van PAS-procesindicatoren.
MAGIC: Biobased alternative for sound- and vibration-reducing materials in railway fastening systems
Blaauw, R. ; Vogelzang, W. ; Knoop, J.R.I. ; Thiyagarajan, S. ; Es, D.S. van; Ridderikhoff, Hans ; Smits, Angela ; Honcoop, Erwin ; Houwen, Gerrien van der; Kerkhoven, Joost ; Koteris, Stefan - \ 2016
Wageningen UR Food & Biobased Research is working on the development of environmentally-friendly resins for elastic rail fastening systems for railway track. Currently the resins for these systems are petroleum-based polyurethanes. In the MAGIC project, Wageningen UR is working with Dutch companies edilon)(sedra and Croda.
Towards a Joint Maintenance Approach for floodplain management in the Netherlands: tensions and possibilities
Warner, Jeroen F. ; Fliervoet, Jan M. ; Smits, Antoine J.M. - \ 2016
In: The Challenges of Collaboration in Environmental Governance Edward Elgar Publishing Limited (New Horizons in Environmental Politics series ) - ISBN 9781785360404 - p. 290 - 314.
While multi-functional river rehabilitation has taken the limelight in today's water management, its follow-up phase, maintenance, has done so to a far lesser extent. A key challenge for today´s environmental management is the number and diversity of actors and sectors involved, each with their own perceptions, interests and resources. This chapter seeks to apply the gains made in the Joint Planning Approach (JPA), developed earlier at Radboud University, the Netherlands, to the maintenance stage of river planning. The application of that approach in the densely populated Netherlands is contrasted with an example of top-down, mono-functional maintenance in a floodplain area in the southwest. It is found that the approach brings considerable opportunities to integrate a fragmented field but that considerable challenges remain related to fragmented policies, building collaborative entities, and organizational constraints.
Beheeroptimalisatie Zuid-Limburgse hellingschraallanden : effecten van gefaseerde begrazing op bodem, vegetatie en fauna
Nijssen, Marijn ; Bobbink, Roland ; Geertsma, Marten ; Scherpenisse, Miriam ; Huiskes, Rik ; Kuper, Jan ; Smits, Nina ; Bohnen-Verbaarschot, Evi ; Verbeek, Peter ; Versluijs, Remco ; Wallis de Vries, Michiel ; Weijters, Maaike ; Wouters, Bart - \ 2016
Driebergen : VBNE, Vereniging van Bos- en Natuurterreineigenaren (Rapport / Vereniging van Bos- en Natuurterreineigenaren nr. OBN-209-HE) - 183
Effects of dietary protein sources on intestinal and systemic responses of pigs
Kar, S.K. ; Jansman, A.J.M. ; Schokker, D. ; Kruijt, L. ; Smits, M.A. - \ 2016
- 1 p.
Exploring the gut of 95 weeks old laying hens
Schokker, D. ; Woelders, H. ; Visscher, J. ; Rebel, Johanna M.J. ; Smits, M. - \ 2016
Feed additive strategies for replacement of antimicrobial growth promoters and a responsible use of antibiotics
Hartog, L.A. den; Smits, C.H.M. ; Hendriks, W.H. - \ 2016
Broadening Horizons (2016)34. - 5 p.
The rapid development of antimicrobial resistance (AMR) in human health care urges the need for effective strategies to reduce antibiotic use in animal production. The Netherlands and Denmark have already implemented successful strategies to reduce antibiotic usage in animal production. Part of the success of the reduction in antibiotic use may be attributed to the wide application of selected feed additives and combinations thereof targeting intestinal microbiota and immunity. Productivity and health responses can be obtained in animals similar to those reported for antimicrobial growth promoters by improving microbiological quality of drinking water and feed, stabilization of the intestinal microbiota and enforcement of the mucosal barrier of the host. Regulatory recognition of the prophylactic effects of feed additives in animal health should further facilitate the progress to reduce AMR.
Effects of digested onion extracts on intestinal gene expression: an interspecies comparison using different intestine models
Wit, N.J.W. de; Hulst, M.M. ; Govers, C.C.F.M. ; Meulen, J. van der; Hoef, A.M.A. van; Stoopen, G.M. ; Hamers, A.R.M. ; Hoekman, A.J.W. ; Vos, C.H. de; Bovee, T.F.H. ; Smits, M.A. ; Mes, J.J. ; Hendriksen, P.J.M. - \ 2016
PLoS ONE 11 (2016)9. - ISSN 1932-6203 - 18 p.
Human intestinal tissue samples are barely accessible to study potential health benefits of nutritional compounds. Numbers of animals used in animal trials, however, need to be minimalized. Therefore, we explored the applicability of in vitro (human Caco-2 cells) and ex vivo intestine models (rat precision cut intestine slices and the pig in-situ small intestinal segment perfusion (SISP) technique) to study the effect of food compounds. In vitro digested yellow (YOd) and white onion extracts (WOd) were used as model food compounds and transcriptomics was applied to obtain more insight into which extent mode of actions depend on the model. The three intestine models shared 9,140 genes which were used to compare the responses to digested onions between the models. Unsupervised clustering analysis showed that genes up- or down-regulated by WOd in human Caco-2 cells and rat intestine slices were similarly regulated by YOd, indicating comparable modes of action for the two onion species. Highly variable responses to onion were found in the pig SISP model. By focussing only on genes with significant differential expression, in combination with a fold change > 1.5, 15 genes showed similar onion-induced expression in human Caco-2 cells and rat intestine slices and 2 overlapping genes were found between the human Caco-2 and pig SISP model. Pathway analyses revealed that mainly processes related to oxidative stress, and especially the Keap1-Nrf2 pathway, were affected by onions in all three models. Our data fit with previous in vivo studies showing that the beneficial effects of onions are mostly linked to their antioxidant properties. Taken together, our data indicate that each of the in vitro and ex vivo intestine models used in this study, taking into account their limitations, can be used to determine modes of action of nutritional compounds and can thereby reduce the number of animals used in conventional nutritional intervention studies.
Protein, peptide, amino acid composition, and potential functional properties of existing and novel dietary protein sources for monogastrics
Kar, S.K. ; Jansman, A.J.M. ; Boeren, S. ; Kruijt, L. ; Smits, M.A. - \ 2016
Journal of Animal Science 94 (2016)7 supplement 3. - ISSN 0021-8812 - p. 30 - 39.
Amino acid - Bioactive peptide - Bioinformatics - Monogastric - Novel proteins - Peptides

Replacement of current protein resources for novel or alternative sources may be one of the solutions to abolish the expected scarcity of dietary protein for animal feeds. However, little is known about the nutritional, protein composition, and potential functional value of such novel or alternative protein sources. In the present study, we used advanced proteomic and bioinformatic approaches to characterize the protein component of 6 different protein sources and predicted the biofunctionalities of their in vivo digestion products. We used casein (CAS), partially delactosed whey powder (DWP), spray-dried porcine plasma (SDPP), soybean meal (SBM), wheat gluten meal (WGM), and yellow meal worm (YMW). We characterized and semiquantified the individual proteins present in these resources by nano-liquid chromatography–LTQ Orbitrap–mass spectrometry (nLCMS). Based on the data obtained, we calculated the AA composition of the proteins that constitute 90% of the total calculated protein content and compared this with the chemically deter-mined AA compositions of the corresponding protein sources. By the use of bioinformatic procedures, we predicted the bioactive properties of these protein sources after in silico digestion with monogastric proteolytic enzymes. We detected and semiquantified 37, 58, 85, 188, 113, and 33 different individual proteins in CAS, DWP, SDPP, SBM, WGM, and YMW, respectively. The calculated AA composition of the various protein sources was almost identical to the chemically determined composition, with correlation values ranging from 0.85 to 0.94. Furthermore, we revealed that the selected protein sources are potentially rich in bioactive peptides, in particular of angiotensin-converting enzyme inhibitors and peptides with antioxidative properties. We discuss the results in terms of the benefit of the applied nLCMS-based approach for analyzing protein feed ingredients and the use of these alternative sources of protein in animal feeds for monogastrics. Furthermore, we discuss new potential applications of this method in the area of (animal) nutrition.

Effect of dietary proteins on immunity and metabolism in mice
Kar, S.K. ; Kruijt, L. ; Jansman, A.J.M. ; Smits, M.A. - \ 2016
In: Energy and protein Metabolism and Nutrition. - Wageningen Academic Publishers (EAAP publication 137) - ISBN 9789086862863 - p. 175 - 175.
New market mechanism and its implication for carbon reduction in China
Gao, S. ; Smits, M. ; Mol, A.P.J. ; Wang, C. - \ 2016
Energy Policy 98 (2016). - ISSN 0301-4215 - p. 221 - 231.
new market mechanism - national operational framework - climate finance - climate change mitigation - China
This article presents a detailed review and analysis of the discussions around the new market mechanism (NMM) and explores its potential in China. It contributes to the current discussion of the NMM in three aspects. First, this article attempts to streamline ideas about the NMM. The term NMM is considered to be an umbrella concept for emission trading systems which all Parties can engage in on a voluntary basis in the implementation of their intended nationally determined contributions, and which need to satisfy three criteria: (i) having a large scale scope; (ii) aiming to facilitate a net emission reduction; (iii) allowing flexibility for the host country. We also present a framework to clarify the NMM. Based on this framework, major options with a high implementation potential are identified. Second, we argue that the national-level operational framework determines the chance of successful implementation of the NMM. We identify different options based on a literature survey and evaluate them with respect to effectiveness and efficiency. Third, we choose China, a highly influential country regarding climate change polices, as a case to analyze the potential contributions and challenges of the NMM and its implementation at different stages of national development
Effects of rye inclusion in diets on broiler performance, gut morphology and microbiota composition
Krimpen, M.M. van; Torki, Mehran ; Borgijink, S.M. ; Schokker, D. ; Vastenhouw, S.A. ; Bree, F.M. de; Bossers, A. ; Fabri, T. ; Bruijn, Naomi de; Jansman, A.J.M. ; Rebel, J.M.J. ; Smits, M.A. ; Emous, R.A. van - \ 2016
- 1 p.
It has been hypothesized that dietary inclusion of rye would increase viscosity of intestinal
digesta, consequently resulting in an effect on nutrient absorption, gut wall morphology,
composition of microbiota, and immunity-related processes in the gut wall, and it might be a
helpful model ingredient to investigate the negative effects of nutrition on immune competence
parameters of the birds. In this experiment the effects of dietary inclusion of three levels (0, 5,
and 10%) of rye between 14 and 28 days of age on gut health, digesta microbiota composition,
expression of genes in the small intestinal tissue and performance in broilers were investigated.
A total of 960 day-old male Ross 308 chicks were allocated to 24 pens (40 birds per pen).
Inclusion of 10% rye in the diet did not affect feed intake, but decreased body weight gain, and
increased feed conversion ratio. Litter quality was inversely related to the level of rye inclusion
in the diet. Providing rye-rich diets resulted in increased jejunal villus height and crypt depth
during the first week of provision, whereas the villus-crypt ratio was not affected. During the
second week of the experiment, however, the level of rye inclusion had no effect on jejunal
gut morphology. Inclusion of rye into the diet did not affect the number and size of jejunal
goblet cells. Dietary inclusion of rye did not affect the diversity of the jejunal microbiota,
as determined by the Shannon index, although specific microbial strains were affected by
rye inclusion. Lactobacillus species made about 75-80% of the jejunal microbiota, and rye
inclusion resulted in an exchange between the different lactobacillus species. At d28, the share
of Lactobacillus reuteri, Staphylococcus saporphyticus and Aerococcaceae in the microbiota in jejunal digesta decreased with increasing dietary rye. Dietary rye inclusion affected expression of genes in the small intestinal tissue involved in cell cycle processes of the epithelial cells, including proliferation, differentiation, motility, and survival, as well as in the complement and coagulation cascade. At 28 d of age, effects were more pronounced in birds fed the 10% rye diet, compared to birds fed the 5% rye diet. In conclusion, inclusion of 5% or 10% rye to the grower diet of broilers have limited effects on performance. Ileal gut morphology, microbiota composition of jejunal digesta, and gene expression profiles of jejunal tissue; however, were affected by dietary rye inclusion level.
Neonatal development of the gut of broilers is influenced by genetics and management
Schokker, D. ; Jansman, A.J.M. ; Smits, M.A. ; Rebel, J.M.J. - \ 2016
- 1 p.
Neonatal development of the gastro-intestinal tract is dependent on an interplay between gut microbiota and the host mucosal tissue. Several intrinsic and extrinsic factors have an effect on the interplay. Here, we demonstrate the impact of one internal and one external factor on gut microbiome development and immune status during neonatal development of broilers. To this end we used (1) broiler lines differing in their genetic background and (2) commercial birds that were treated with a therapeutic dose of an antibiotic at day 1 via the
drinking water. In genetically different broiler lines X and Y, kept under the same management conditions, microbiota composition in jejunum was significantly different over period of two weeks between the lines. Furthermore, by comparing the two lines, trends were observed in the microbiota data at the genus level. Different temporal intestinal gene expression patterns of the gut mucosal tissues were observed when comparing the genetically different broiler
lines. Birds from line X had higher expression of genes associated with immunological related processes at day 0. Genes related to cell cycle related processes showed higher expression over a period of two weeks in line Y. The early short antibiotic treatment of broilers affected both the microbiota composition in the intestinal tract, as well as the intestinal gene expression
over a period of at least two weeks. Significant differences were observed after functional analysis of the mucosal gene expression profiles in jejunum. Especially on day 5 lower activity of immune processes were observed in the antibiotic treated birds compared to their respective controls. To validate these functional changes, immune cells in the small intestinal mucosa were
stained and a significant lower number of KUL01+ cells were observed in the small intestinal tissue of antibiotic treated birds. The results indicate that both intrinsic factors (host genetics) and extrinsic factors (short antibiotic treatment) have an effect on the early life microbial colonization of the broiler gut and on the mucosal gene expression profiles. This suggest that also the interplay between microbiota and host mucosal cells is affected by these intrinsic and
extrinsic factors. We conclude that intestinal development is a complex process and that both genetic and (early life) management factors influence the interplay between the intestinal microbiome and host intestinal mucosal tissue. Therefore the interaction between genetic background and early life microbial colonization is a major driver of traits on performance and health of broilers.
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