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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Exploring the use of wild relatives in potato breeding through integrated cytogenetic and genomic approaches
Gaiero Guadagna, Paola - \ 2018
Wageningen University. Promotor(en): Hans de Jong, co-promotor(en): Eric Schranz. - Wageningen : Wageningen University - ISBN 9789463433464 - 193
Genetic variation of wildlife in a human-dominated landscape : Genome-wide SNP analysis of wild boar (Sus scrofa) en red deer (Cervus elaphus) from the European continent
Jong, Joost F. de - \ 2018
Wageningen University. Promotor(en): Herbert Prins, co-promotor(en): Pim van Hooft; Sip van Wieren; Hendrik-Jan Megens. - Wageningen : Wageningen University - ISBN 9789463433792 - 202
IgE Cross-Reactivity of Cashew Nut Allergens
Bastiaan-Net, Shanna ; Reitsma, Marit ; Cordewener, Jan H.G. ; Valk, Johanna P.M. van der; America, Twan A.H.P. ; Dubois, Anthony E.J. ; Gerth van Wijk, Roy ; Savelkoul, Huub F.J. ; Jong, Nicolette W. de; Wichers, Harry J. - \ 2018
International Archives of Allergy and Immunology (2018). - ISSN 1018-2438 - 14 p.
Allergenicity - Cashew nut - Food allergy - IgE cross-reactivity - Immunoblotting - Tree nut allergy

Background: Allergic sensitisation towards cashew nut often happens without a clear history of eating cashew nut. IgE cross-reactivity between cashew and pistachio nut is well described; however, the ability of cashew nut-specific IgE to cross-react to common tree nut species and other Anacardiaceae, like mango, pink peppercorn, or sumac is largely unknown. Objectives: Cashew nut allergic individuals may cross-react to foods that are phylogenetically related to cashew. We aimed to determine IgE cross-sensitisation and cross-reactivity profiles in cashew nut-sensitised subjects, towards botanically related proteins of other Anacardiaceae family members and related tree nut species. Method: Sera from children with a suspected cashew nut allergy (n = 56) were assessed for IgE sensitisation to common tree nuts, mango, pink peppercorn, and sumac using dot blot technique. Allergen cross-reactivity patterns between Anacardiaceae species were subsequently examined by SDS-PAGE and immunoblot inhibition, and IgE-reactive allergens were identified by LC-MS/MS. Results: From the 56 subjects analysed, 36 were positive on dot blot for cashew nut (63%). Of these, 50% were mono-sensitised to cashew nuts, 19% were co-sensitised to Anacardiaceae species, and 31% were co-sensitised to tree nuts. Subjects co-sensitised to Anacardiaceae species displayed a different allergen recognition pattern than subjects sensitised to common tree nuts. In pink peppercorn, putative albumin- and legumin-type seed storage proteins were found to cross-react with serum of cashew nut-sensitised subjects in vitro. In addition, a putative luminal binding protein was identified, which, among others, may be involved in cross-reactivity between several Anacardiaceae species. Conclusions: Results demonstrate the in vitro presence of IgE cross-sensitisation in children towards multiple Anacardiaceae species. In this study, putative novel allergens were identified in cashew, pistachio, and pink peppercorn, which may pose factors that underlie the observed cross-sensitivity to these species. The clinical relevance of this widespread cross-sensitisation is unknown.

Quantitative Assessment Of The Health Risk For Livestock When Animal Viruses Are Applied in Human Oncolytic Therapy: A Case Study for Seneca Valley Virus
Schijven, Jack ; Brizee, Sabrina ; Teunis, Peter ; Vos-de Jong, C.J. de; Eble, P.L. ; Rutjes, Saskia - \ 2018
Risk Analysis (2018). - ISSN 0272-4332
Some viruses cause tumor regression and can be used to treat cancer patients; these viruses are called oncolytic viruses. To assess whether oncolytic viruses from animal origin excreted by patients pose a health risk for livestock, a quantitative risk assessment (QRA) was performed to estimate the risk for the Dutch pig industry after environmental release of Seneca Valley virus (SVV). The QRA assumed SVV excretion in stool by one cancer patient on Day 1 in the Netherlands, discharge of SVV with treated wastewater into the river Meuse, downstream intake of river water for drinking water production, and consumption of this drinking water by pigs. Dose–response curves for SVV infection and clinical disease in pigs were constructed from experimental data. In the worst scenario (four log10 virus reduction by drinking water treatment and a farm with 10,000 pigs), the infection risk is less than 1% with 95% certainty. The risk of clinical disease is almost seven orders of magnitude lower. Risks may increase proportionally with the numbers of treated patients and days of virus excretion. These data indicate that application of wild‐type oncolytic animal viruses may infect susceptible livestock. A QRA regarding the use of oncolytic animal virus is, therefore, highly recommended. For this, data on excretion by patients, and dose–response parameters for infection and clinical disease in livestock, should be studied.
INNOVA Ezine 2 – Valencia Region, Droughts and Agricultural Interests in a Metropolitan Area in Spain
Timmermans, W. ; Jong, F. de; Martín, Adrià Rubio ; Bruijn, Daphne de; Harsema, H. - \ 2018
Wageningen : Blauwdruk
In the metropolitan area of Valencia the water use is intense and the region suffers from frequent droughts due to climate conditions. Valencia is surrounded by an agricultural landscape with deep cultural significance and with a multi-sectoral structure in which irrigated agriculture plays an important role in the consumption of water. The Albufera Natural Park, less than 10 km south of Valencia, is a freshwater lagoon and its surroundings rice plots. Given the predicted adverse effects of climate change, it is important for the City of Valencia to develop adaptation strategies for the future climate. The mandate for the INNOVA project is to develop a climate service that satisfies the water use needs to support the distribution of potable water to its users.

The second INNOVA e-zine shows the climate and adaptation challenges the Valencia region is facing. The first issue showed the Mirror Waal project in the Nijmegen area (NL).

From awareness of upcoming flooding risks, via complex planning and design efforts into the final result. Whereas Nijmegen is far in the Adaptation Cycle; the Valencia metropolitan area is between the steps of identifying adaptation options (Step 3) and assessing these options (Step 4).
INNOVA: Innovation in Climate Service Provision
Jong, F. de; Cellier, Louis ; Manez, Maria - \ 2018
Manual for FOCUS_TOXSWA v5.5.3 and for expert use of TOXSWA kernel v3.3 : User’s Guide version 5
Beltman, W.H.J. ; Horst, M.M.S. ter; Adriaanse, P.I. ; Jong, A. de - \ 2018
Wageningen : Statutory Research Tasks Unit for Nature & the Environment (WOt-technical report 126) - 148
The FOCUS_TOXSWA model calculates exposure concentrations of pesticides and their metabolites in watercourses and ponds, of the so-called FOCUS surface water scenarios. These concentrations are used in the pesticide registration procedure at EU level. The model concepts of TOXSWA are described briefly. The procedure for using the TOXSWA kernel (i.e. expert use) and related input files and output files are described. Concerning FOCUS_TOXSWA, the use of the graphical user interface to access the input and output is described. Input data are stored in a database. Pesticide entries resulting from drainage or runoff/erosion are accessed from separate files generated by FOCUS_MACRO and FOCUS_PRZM. Substance properties are accessed from the SPIN tool/database. Instructions for simulating a water-sediment study and a multi-year run are given.
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.
A retrospective analysis to identify the contribution of the breeder on health and performance of broiler chickens
Jong, I.C. de; Riel, J.W. van - \ 2018
In: The XVth European Poultry Conference: Conference Information and Proceedings. - Zagreb : - ISBN 9789082915709 - p. 146 - 146.
Broiler, Data analysis, Health, Performance
Data on performance and health are routinely collected in the various stages of the broiler production chain. In The Netherlands, routinely collected data are usually stored and solely used by the owner(s), and the various databases are not connected. Connecting databases may however provide insight to improve the quality of the chain. We were interested in the contribution of the parent stock to the performance of the broiler flock, as transgenerational effects have been reported and variation in performance and health between breeder farms and flocks exist. Broiler flock data at depopulation, collected by the slaughter plant (growth, uniformity, rejections, first week and total mortality) and from a national database (antibiotic treatments) were linked to breeder flocks and farms by unique identifiers for the period between 2011-2016.
This resulted in 2174 broiler flock records (at house level). Within these records, 74 broiler farms, 88 breeder farms, and 209 breeder flocks were identified. A mixed model analysis was used to simultaneously estimate effects of season, parent flock age, time, and the variance components that determine the contribution of the chain phase to the broiler performance parameters. Results showed no systematic effects of the breeder farm on the various parameters at broiler level. Systematic effects of breeder flock were relatively small; the largest effect was found on rejections in the broiler flock (estimated contribution to the variance component: 7%). The largest contributions to the variance
component were found for broiler farm: 14% (antibiotic treatment) to 59% (growth index). Also the phase between egg laying at the breeder farm and chick placement at the broiler farm (here called: chick delivery) had a large contribution to the variance component: rejections: 27%, first week mortality: 52%). Negligible effects were found for house at broiler farm and specific breeder-broiler farm combinations. A moderate effect of broiler house within a chick delivery was found. It can be concluded that systematic effects of breeder flock and farm on broiler performance and health could not be found, and that broiler farm and chick delivery had a large contribution on the variation in broiler performance and health. This does not exclude that transgenerational
effects exist, but these may be relatively short lasting, and thus could not be found in the present analysis, or might be overruled by more influential factors after egg laying at the breeder farm.
Identification of risk factors and prevalence of injuries at different stages of the broiler slaughter process
Jong, I.C. de; Gerritzen, Marien ; Reimert, H.G.M. ; Lohman, T. - \ 2018
In: The XVth European Poultry Conference: Conference Information and Proceedings / Prukner-Radovčić, Estella, Medić, Helga, Zagreb : - ISBN 9789082915709 - p. 240 - 240.
Broiler, Handling, Injuries, Slaughter, Welfare
Transport and handling of broilers during the (pre)slaughter process are risk factors for welfare. The impact of preslaughter treatments on injuries and thus the effect on welfare is poorly known. Moreover, it is unclear which proportion of carcass damage can be attributed to the conscious phase, and affects welfare, and which proportion of carcass damage can be attributed to handling after stunning and killing of birds and is related to product quality. We first analysed routinely collected data of a Dutch slaughter plant to identify risk factors for carcass damage. It was included whether or not prevalence of carcass damage was related to flock welfare status. Data collected in 2014-2016 from five farms with low foot pad dermatitis (FPD) score (<40 points) and five farms with high FPD score (>80 points) were analysed (N=771 flocks), assuming that FPD score was indicative of flock welfare status. A regression model was applied. The model showed positive associations between live body weight (P=0.000; B=0.001), number of dead-on-arrival (P=0.001; B=0.004), and wing damage. A negative association was found between wing damage and number of broilers per tray (P=0.037; B=-0.015). No relation between FPD score and carcass damage was found. Second, prevalence of injuries or damage during the slaughter process was determined in 20 flocks. Wing, leg and breast bruises, wing dislocations, and wing and leg fractures were scored between lairage and post-plucking. An increase in wing fractures from lairage (0,99%), post-shackling (1.67%), post-stunning (2.73%) and post-plucking (5.02%) was found (P=0.000 between all stages). Medium and large breast bruises increased between lairage and post-plucking (P=0.000). Small wing bruises decreased between lairage and post-plucking (P=0.047). This study showed that flock welfare status was not related to injuries, and that weight and crate density could be identified as risk factors for wing damage. Injuries and damage do mainly occur during the slaughter process. However, it was difficult to determine whether or not carcass damage originated from handling live animals, and thus is an animal welfare problem, or after stunning and therefore is a product quality issue. It is advised to develop an accuratebruise and damage scoring system that can be used to determine whether or not carcassdamage was caused in live animals.
INNOVA Ezine1 – Nijmegen, the EU Green Capital 2018 and Room for the River Waal
Timmermans, W. ; Jong, F. de; Ginkel, M. van; Martinez, G. ; Bruijn, D. de; Harsema, H. - \ 2018
The Dutch city of Nijmegen is becoming well-known because of its planning approach that combines large scale climate adaptation measures with a strong emphasis on spatial quality. Nijmegen is situated along the Waal river, one of Europe’s largest transport and ecological corridors. More than 250M euro has been spent on a new bypass of the Waal, called the Mirror Waal, one of the major urban examples of the Dutch Room for the River project. This e-zine shows the Mirror Waal project. From awareness of upcoming flooding risks, via complex planning and design efforts into the final result, including innovative ecological engineering, new sport activities and spontaneous festivals. The e-zine is presented by the INNOVA project. It is the first e-zine out of ten. INNOVA is a research project aiming to facilitate the use of climate data and projections, scientifically known as climate services, in adaptation efforts by urban governments. The project focuses on three European cities, and a small island state. These are: Kiel Bay in Germany, Nijmegen in The Netherlands, Valencia in Spain, and finally, the French West-Indies Islands of Guadeloupe & Martinique.
Comparison of performance, health and welfare aspects between commercially housed hatchery-hatched and on-farm hatched broiler flocks
Jong, I.C. de; Gunnink, H. ; Hattum, T. van; Riel, J.W. van; Raaijmakers, M.M.P. ; Zoet, E.S. ; Brand, H. van den - \ 2018
Animal (2018). - ISSN 1751-7311 - 9 p.
broiler - early feeding - on-farm hatching - performance - welfare

On-farm hatching systems for broiler chicks are increasingly used in practice. We studied whether or not performance, health and welfare aspects differed between commercial flocks hatched on-farm or in a hatchery (control). In two successive production cycles on seven farms, a total of 16 on-farm hatched flocks were paired to 16 control flocks, housed at the same farm. Paired flocks originated from the same batch of eggs and were subjected to similar on-farm management. On-farm hatched and control flocks only differed with respect to hatching conditions, with on-farm hatched flocks not being exposed to, for example, chick handling, post-hatch feed and water deprivation and transport, in contrast to control flocks that were subjected to standard hatchery procedures, subsequently transported and placed in the poultry house. Day-old chick quality (navel and hock scores), 1st week mortality, total mortality, BW at day (d) 0, d7 and at depopulation, and (total) feed conversion ratio were determined. Prevalence of footpad dermatitis, hock burn, breast discoloration/blisters and cleanliness, litter quality and gait score were determined at d21 of age and around depopulation (d39 on average). Gross pathology and gut morphology were examined at depopulation age in a sample of birds of five flocks per treatment. On-farm hatching resulted in a higher BW at d0 (=5.4 g) and d7 (=11.5 g) (P<0.001), but day-old chick quality as measured by navel (P=0.003) and hock (P=0.01) quality was worse for on-farm hatched compared to control birds. Body weight, 1st week and total mortality, and feed conversion ratio at slaughter age were similar for both on-farm hatched and control flocks. On-farm hatched flocks had less footpad dermatitis (P=0.05), which indicated a better welfare. This was likely related to a tendency for better litter quality in on-farm hatched flocks at 21 days of age in comparison to control flocks (P=0.08). No major differences in gross pathology or in intestinal morphology at depopulation age were found between treatments. In conclusion, on-farm hatching resulted in better 1st week broiler performance and better welfare compared to conventional hatching in a hatchery.

Effects of experimental light at night on extra-pair paternity in a songbird
Jong, Maaike de; Lamers, Koosje P. ; Eugster, Mark ; Ouyang, Jenny Q. ; Silva, Arnaud Da; Mateman, A.C. ; Grunsven, Roy H.A. van; Visser, Marcel E. ; Spoelstra, Kamiel - \ 2018
Journal of Experimental Zoology Part A: Ecological and Integrative Physiology 329 (2018)8-9. - ISSN 2471-5638 - p. 441 - 448.
artificial light at night - extra-pair paternity - great tit - light color - light pollution - Parus major

Light pollution is increasing worldwide and significantly affects animal behavior. In birds, these effects include advancement of morning activity and onset of dawn song, which may affect extra-pair paternity. Advanced dawn song of males may stimulate females to engage in extra-pair copulations, and the earlier activity onset may affect the males’ mate guarding behavior. Earlier work showed an effect of light at night on extra-pair behavior, but this was in an area with other anthropogenic disturbances. Here, we present a two-year experimental study on effects of light at night on extra-pair paternity of great tits (Parus major). Previously dark natural areas were illuminated with white, red, and green LED lamps and compared to a dark control. In 2014, the proportion of extra-pair young in broods increased with distance to the red and white lamps (i.e., at lower light intensities), but decreased with distance to the poles in the dark control. In 2013, we found no effects on the proportion of extra-pair young. The total number of offspring sired by a male was unaffected by artificial light at night in both years, suggesting that potential changes in female fidelity in pairs breeding close to white and red light did not translate into fitness benefits for the males of these pairs. Artificial light at night might disrupt the natural patterns of extra-pair paternity, possibly negates potential benefits of extra-pair copulations and thus could alter sexual selection processes in wild birds.

Welzijn vleeskuikens onder de loep
Jong, I.C. de - \ 2018
Wageningen : Wageningen Livestock Research - 2 p.
Innovatieve vleeskuikenproductieketen
Jong, I.C. de - \ 2018
Wageningen : Wageningen Livestock Research - 2 p.
Big Data in de vleeskuikenhouderij
Jong, I.C. de - \ 2018
Wageningen : Wageningen Livestock Research - 2 p.
Broiler welfare under scrutiny
Jong, I.C. de - \ 2018
Wageningen : Wageningen Livestock Research - 2 p.
Big Data in broiler farming
Jong, I.C. de - \ 2018
Wageningen : Wageningen Livestock Research - 2 p.
A new model to Calibrate a Reference Standard for bovine tuberculin purified protein derivative in the target species
Frankena, Klaas ; Jacobs, Liesbeth ; Dijk, Tonny van; Good, Margaret ; Duignan, Anthony ; Jong, Mart C.M. de - \ 2018
Frontiers in Veterinary Science 5 (2018)OCT. - ISSN 2297-1769
Bovine international standard - Cattle - Guinea pigs - Mycobacterium bovis - New reference standard - Potency estimation - Tuberculin

Since 1986, use of a Bovine International Standard (BIS) for bovine tuberculin has been required to ensure national and international uniformity regarding the potency designation of bovine tuberculin Purified Protein Derivative (PPDb) preparations produced by multiple manufacturers. The BIS is the unique golden standard in the guinea pig potency assay, representing 100% potency, where potencies of production batches are calculated as relative potencies in comparison with the potency of the BIS which was set at 32,500 international Unit (IU) per mg. The stock supply and lifetime of the BIS is limited.The aim of this study was to develop a model to determine the potency of a newly produced in-house Reference Standard (RS) for PPDb with great accuracy in the target species (cattle) and to prove its precision and accuracy in the guinea pig potency test. First simulations were done to estimate the required number of cattle needed. Then, 30 naturally bTB infected cattle were subjected to a tuberculin skin test using multiple injections of both the RS and the BIS. Both were applied randomly in the same volume and concentration (1 dose). The potency of the RS against the BIS was directly derived from the least square means (LSMEANS) and was estimated as 1.067 (95% CI: 1.025-1.109), equal to a potency of 34,700 ± 1,400 IU/mg. In six guinea pig potency assays the RS was used to assign potencies to production batches of PPDb. Here, precision and accuracy of the RS was determined according to the parallel-line assay. Relative potencies were estimated by exponentiation of the common slope. The corresponding 95% confidence intervals were obtained according to Fieller's theorem. In sensitized guinea pigs, the relative potency of the RS against the BIS was 1.115 (95% CI: 0.871-1.432), corresponding to an absolute potency of 36,238 IU/mg (95% CI: 28,308-46,540).In conclusion: the method used to determine the potency of the RS against the BIS in naturally bTB infected cattle, resulted in a highly accurate potency estimate of the RS. The RS can be used in the guinea pig test to assign potencies to PPDb production batches with high precision and accuracy.

Gereedschapskist klimaatslim bosbeheer : Voorstudie en projectplannen modules bosbeheer, bosaanleg, landschappelijke beplantingen, stedelijk groen en agroforestry
Boosten, Martijn ; Jong, J.J. de; Schelhaas, M. ; Nabuurs, G.J. ; Borgman, David ; Kremers, Jasprina - \ 2018
Wageningen : Stichting Probos - 60 p.
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