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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Construction of Genetic Linkage Maps in Multiparental Populations
Zheng, Chaozhi ; Boer, Martin P. ; Eeuwijk, Fred A. van - \ 2019
Genetics 212 (2019)4. - ISSN 0016-6731 - p. 1031 - 1044.
cross-pollinated (CP) - genetic map construction - hidden Markov model (HMM) - MPP - multiparent advanced generation intercross (MAGIC) - multiparental populations - nested association mapping (NAM)

Construction of genetic linkage maps has become a routine step for mapping quantitative trait loci (QTL), particularly in animal and plant breeding populations. Many multiparental populations have recently been produced to increase genetic diversity and QTL mapping resolution. However, few software packages are available for map construction in these populations. In this paper, we build a general framework for the construction of genetic linkage maps from genotypic data in diploid populations, including bi- and multiparental populations, cross-pollinated (CP) populations, and breeding pedigrees. The framework is implemented as an automatic pipeline called magicMap, where the maximum multilocus likelihood approach utilizes genotypic information efficiently. We evaluate magicMap by extensive simulations and eight real datasets: one biparental, one CP, four multiparent advanced generation intercross (MAGIC), and two nested association mapping (NAM) populations, the number of markers ranging from a few hundred to tens of thousands. Not only is magicMap the only software capable of accommodating all of these designs, it is more accurate and robust to missing genotypes and genotyping errors than commonly used packages.

Development of a welfare assessment protocol for dairy calves from birth through to weaning
Barry, J. ; Kennedy, E. ; Sayers, R. ; Boer, I.J.M. De; Bokkers, E.A.M. - \ 2019
Animal Welfare 28 (2019)3. - ISSN 0962-7286 - p. 331 - 344.
Animal welfare - Behaviour - Dairy calves - Health - Housing - Management

The aim of this study was to develop a welfare assessment protocol using different indicators, for pre-weaned dairy calves, that is feasible and time efficient. To this end, the protocol had to combine animal-based indicators (measurements on physiology, general appearance and behaviour) providing the basis for welfare assessment, with resource-based indicators (measurements on management and the environment) providing the basis for identifying risk factors. Indicators, both animal- and resource-based, were selected by a review of existing literature and a process of expert consultation. Following the formulation phase, the protocol was then applied on five Irish dairy farms to develop further for completeness and on-farm feasibility. After each on-farm application, the protocol was critically evaluated, and modifications were made accordingly. Upon completion of the on-farm application phase, a feasible, reliable and time-efficient protocol was produced.

Een eerlijke prijs voor de boer bestaat niet
Vijn, M.P. - \ 2019
Wageningen : Wageningen Economic Research
Linking Probabilistic Exposure and Pharmacokinetic Modeling to Assess the Cumulative Risk from the Bisphenols BPA, BPS, BPF, and BPAF for Europeans
Karrer, Cecile ; Boer, Waldo De; Delmaar, Christiaan ; Cai, Yaping ; Crépet, Amélie ; Hungerbühler, Konrad ; Goetz, Natalie Von - \ 2019
Environmental Science and Technology 53 (2019)15. - ISSN 0013-936X - p. 9181 - 9191.

The bisphenols S, F, and AF (BPS, BPF, and BPAF) are used to replace the endocrine disrupting chemical bisphenol A (BPA) while exerting estrogenic effects of comparable potency. We assessed the cumulative risk for the aforementioned BPs in Europe and compared the risk before and after the year 2011, which was when the first BPA restrictions became effective. For this, we probabilistically modeled external exposures from food, personal care products (PCPs), thermal paper, and dust (using the tools MCRA and PACEM for exposures from food and PCPs, respectively). We calculated internal concentrations of unconjugated BPs with substance-specific PBPK models and cumulated these concentrations normalized by estrogenic potency. The resulting mean internal cumulative exposures to unconjugated BPs were 3.8 and 2.1 ng/kg bw/day before and after restrictions, respectively. This decline was mainly caused by the replacement of BPA by BPS in thermal paper and the lower dermal uptake of BPS compared to BPA. However, the decline was not significant: the selected uncertainty intervals overlapped (P2.5-P97.5 uncertainty intervals of 2.7-4.9 and 1.3-6.3 ng/kg bw/day before and after restrictions, respectively). The upper uncertainty bounds for cumulative exposure were higher after restrictions, which reflects the larger uncertainty around exposures to substitutes compared to BPA.

A network approach to prioritize conservation efforts for migratory birds
Xu, Yanjie ; Si, Yali ; Takekawa, John ; Liu, Qiang ; Prins, Herbert H.T. ; Yin, Shenglai ; Prosser, Diann J. ; Gong, Peng ; Boer, Willem F. de - \ 2019
Conservation Biology (2019). - ISSN 0888-8892
bird migration - connectivity - conservation designation - habitat loss - network

Habitat loss can trigger migration network collapse by isolating migratory bird breeding grounds from nonbreeding grounds. Theoretically, habitat loss can have vastly different impacts depending on the site's importance within the migratory corridor. However, migration-network connectivity and the impacts of site loss are not completely understood. We used GPS tracking data on 4 bird species in the Asian flyways to construct migration networks and proposed a framework for assessing network connectivity for migratory species. We used a node-removal process to identify stopover sites with the highest impact on connectivity. In general, migration networks with fewer stopover sites were more vulnerable to habitat loss. Node removal in order from the highest to lowest degree of habitat loss yielded an increase of network resistance similar to random removal. In contrast, resistance increased more rapidly when removing nodes in order from the highest to lowest betweenness value (quantified by the number of shortest paths passing through the specific node). We quantified the risk of migration network collapse and identified crucial sites by first selecting sites with large contributions to network connectivity and then identifying which of those sites were likely to be removed from the network (i.e., sites with habitat loss). Among these crucial sites, 42% were not designated as protected areas. Setting priorities for site protection should account for a site's position in the migration network, rather than only site-specific characteristics. Our framework for assessing migration-network connectivity enables site prioritization for conservation of migratory species.

Upcycling food leftovers and grass recources through farm animals
Hal, O. van; Boer, I.J.M. de; Muller, A. ; Vries, S. de; Erb, K. ; Schader, Christian ; Zanten, H.H.E. van - \ 2019
In: Book of Abstracts of the 70th Annual Meeting of the European Federation of Animal Science. - Wageningen Academic Publishers (EAAP book of abstracts ) - ISBN 9789086863396 - p. 316 - 316.
How to handle trade-offs and synergies in our search towards a sustainable food system?
Boer, I.J.M. de; Linden, A. van der; Olde, E.M. de - \ 2019
In: Book of Abstracts of the 70th Annual Meeting of the European Federation of Animal Science. - Wageningen Academic Publishers (EAAP books of abstracts ) - ISBN 9789086863396 - p. 345 - 345.
Sustainability performance of grass-based beef production systems in the Bourbonnais area of France
Linden, A. van der; Olde, E.M. de; Mornier, C. ; Pineau, C. ; Tichit, M. ; Boer, I.J.M. de - \ 2019
In: Book of Abstracts of the 70th Annual Meeting of the European Federation of Animal Science. - Wageningen Academic Publishers (EAAP books of abstracts ) - ISBN 9789086863396 - p. 346 - 346.
How thirsty is our beef? : understanding water use for feed production
Ran, Ylva - \ 2019
Wageningen University. Promotor(en): Imke de Boer, co-promotor(en): Corina van Middelaar; M. Herrero. - Wageningen : Wageningen University - ISBN 9789463439930 - 174
Erfgesprekken over klimaatrobuuste beekdalen
Westerink, Judith ; Boer, Tineke de; Vogelzang, Theo - \ 2019
Wageningen : Wageningen Environmental Research - 20
De partners in Agrifood Capital denken na over het klimaatrobuust maken van beekdallandschappen in Noordoost Brabant. In dat kader zijn erfgesprekken gevoerd met landgebruikers in de benedenstroomse delen van de beekdalen van de Aa en van de Dommel, onder meer om inzicht te krijgen in wat meespeelt in hun overwegingen over gewenste en mogelijke aanpassing van het landgebruik. De landgebruikers hebben immers een centrale rol in een transitie naar klimaatrobuuste beekdalen, zowel qua inrichting als qua gebruik. Het ging om kwalitatief onderzoek. Er zijn groepsgesprekken en individuele gesprekken gevoerd met in totaal 21 grondeigenaren en grondgebruikers, waaronder 17 boeren. Voor diverse boeren is klimaatverandering iets ongrijpbaars. Ze zien nog weinig gevolgen van klimaatverandering en geloven niet dat het nodig is om aanpassingen te doen aan het landgebruik. Water moet kunnen worden vastgehouden en zo nodig snel weer worden afgevoerd. Diverse mogelijke maatregelen zijn besproken. De meesten zien meer in technische oplossingen zoals stuwen en drains dan in bijvoorbeeld het opnieuw laten meanderen van beken. Het verhogen van het organische stofgehalte in de bodem heeft brede steun en veel boeren werken daar al aan. Over het algemeen zijn respondenten best bereid om na te denken over aanpassingen op hun grond. Zelfs waterberging is bespreekbaar. Het gaat vooral om wederkerigheid. Het is belangrijk dat de landgebruikers erop vooruit kunnen gaan en dat er perspectief wordt geboden. Beschikbaarheid van grond is daarin van grote invloed. Daarnaast zal samenwerking gezocht moeten worden om te komen tot integrale gebiedsontwikkeling. Vanwege de grote verschillen in situatie en overtuigingen is het van belang om iedere grondgebruiker ook individueel te benaderen.
Postnatal effects of colostrum quality and management, and hygiene practises, on immunity and mortality in Irish dairy calves
Barry, John ; Bokkers, Eddie ; Berry, Donagh P. ; Boer, Imke de; McClure, Jennifer ; Kennedy, Emer - \ 2019
In: Animal lives worth living. - Wageningen Academic Publishers - ISBN 9789086863389 - p. 90 - 90.
Do grazing management practices influence the behaviour of dairy cows at pasture?
Crossley, Robin E. ; Kennedy, Emer ; Boer, Imke J.M. de; Bokkers, Eddie A.M. ; Conneely, Muireann - \ 2019
In: Animal lives worth living. - Wageningen Academic Publishers - ISBN 9789086863389 - p. 111 - 111.
Associating cow characteristics with mobility scores in pasture-based dairy cows
O'Connor, A.H. ; Bokkers, E.A.M. ; Boer, I.J.M. de; Hogeveen, H. ; Sayers, R. ; Byrne, N. ; Ruelle, E. ; Shalloo, L. - \ 2019
Journal of Dairy Science 102 (2019)9. - ISSN 0022-0302 - p. 8332 - 8342.
body condition - claw disorder - grass-based system - lameness - parity

The quality of dairy cow mobility can have significant welfare, economic, and environmental consequences that have yet to be extensively quantified for pasture-based systems. The objective of this study was to characterize mobility quality by examining associations between specific mobility scores, claw disorders (both the type and severity), body condition score (BCS), and cow parity. Data were collected for 6,927 cows from 52 pasture-based dairy herds, including mobility score (0 = optimal mobility; 1, 2, or 3 = increasing severities of suboptimal mobility), claw disorder type and severity, BCS, and cow parity. Multinomial logistic regression was used for analysis. The outcome variable was mobility score, and the predictor variables were BCS, type and severity of claw disorders, and cow parity. Three models were run, each with 1 reference category (mobility score 0, 1, or 2). Each model also included claw disorders (overgrown claw, sole hemorrhage, white line disease, sole ulcer, and digital dermatitis), BCS, and cow parity as predictor variables. The presence of most types of claw disorders had odds ratios >1, indicating an increased likelihood of a cow having suboptimal mobility. Low BCS (BCS <3.00) was associated with an increased risk of a cow having suboptimal mobility, and relatively higher parity was also associated with an increased risk of suboptimal mobility. These results confirm an association between claw disorders, BCS, cow parity, and dairy cow mobility score. Therefore, mobility score should be routinely practiced to identify cows with slight deviations from the optimal mobility pattern and to take preventive measures to keep the problem from worsening.

Predicting hydrological impacts of the Yangtze-to-Huaihe Water Diversion Project on habitat availability for wintering waterbirds at Caizi Lake
Li, Chunlin ; Li, Haifeng ; Zhang, Yong ; Zha, D. ; Zhao, Binbin ; Yang, Sen ; Zhang, Baowei ; Boer, Willem F. de - \ 2019
Journal of Environmental Management 249 (2019). - ISSN 0301-4797
Hydrological regime - Water project - Waterbird conservation - Wetland management - Yangtze

Quantifying the relationship between hydrological regime and habitat availability is the first step to predict potential impacts of water engineering projects on waterbirds, particularly in periodically flooded wetlands. The proposed Yangtze-to-Huaihe Water Diversion Project (YHWD) cuts through Caizi Lake, which is of international importance for wintering waterbirds. In order to explore the potential impacts of the project on habitat availability for the wintering waterbirds, we first built linear models to fit relationships between land cover patterns and water level dynamics in the lake, and then used generalized linear mixed models to test effects of habitat variables (water area, grassland area and mudflat area) on bird abundances of different functional groups. The avian habitat use differed among guilds, and was correlated with the land cover pattern, which was strongly dependent on seasonal water level fluctuations. Following water recession in autumn, the exposure of riparian habitats was more prominent in the eastern part of the lake, where the channel of the proposed YHWD project is located. This part of the lake is also where we located most of the important bird areas. Compared to the current situation, 54.3% of the grassland and 60.5% of the mudflats are predicted to be lost during winter due to the projected water level rise, resulting in reduced habitat availability for grass foragers, invertebrate eaters and tuber feeders. In order to mitigate potential impacts of the YHWD project, we suggest habitat compensations by construction of artificial habitats, and maintenance of water level regime at the whole lake by restoring similarity in water level fluctuations between Xizi Lake and Caizi Lake.

Pathogen suppression by microbial volatile organic compounds in soils
Boer, Wietse de; Li, Xiaogang ; Meisner, Annelein ; Garbeva, Paolina - \ 2019
FEMS microbiology ecology 95 (2019)8. - ISSN 0168-6496
disease suppression - fungistasis - microbial interactions - soil atmosphere - soil microbial community - sustainable management strategies - volatile organic compounds

There is increasing evidence that microbial volatile organic compounds (mVOCs) play an important role in interactions between microbes in soils. In this minireview, we zoom in on the possible role of mVOCs in the suppression of plant-pathogenic soil fungi. In particular, we have screened the literature to see what the actual evidence is that mVOCs in soil atmospheres can contribute to pathogen suppression. Furthermore, we discuss biotic and abiotic factors that influence the production of suppressive mVOCs in soils. Since microbes producing mVOCs in soils are part of microbial communities, community ecological aspects such as diversity and assembly play an important role in the composition of produced mVOC blends. These aspects have not received much attention so far. In addition, the fluctuating abiotic conditions in soils, such as changing moisture contents, influence mVOC production and activity. The biotic and abiotic complexity of the soil environment hampers the extrapolation of the production and suppressing activity of mVOCs by microbial isolates on artificial growth media. Yet, several pathogen suppressive mVOCs produced by pure cultures do also occur in soil atmospheres. Therefore, an integration of lab and field studies on the production of mVOCs is needed to understand and predict the composition and dynamics of mVOCs in soil atmospheres. This knowledge, together with the knowledge of the chemistry and physical behaviour of mVOCs in soils, forms the basis for the development of sustainable management strategies to enhance the natural control of soil-borne pathogens with mVOCs. Possibilities for the mVOC-based control of soil-borne pathogens are discussed.

Treatment of Severe Protein Malnutrition After Bariatric Surgery
Kuin, Carlijn ; Ouden, Floor den; Brandts, Hans ; Deden, Laura ; Hazebroek, Eric ; Borren, Marcel van; Boer, Hans de - \ 2019
Obesity Surgery (2019). - ISSN 0960-8923
Bariatric surgery - Hyperammonemia - Hypoalbuminemia - Nutrition - Pancreatic enzymes - Tube feeding

Background: Severe protein malnutrition, with a serum albumin < 25 g/L, is one of the complications that may develop after bariatric surgery. It is associated with increased morbidity and mortality and requires timely diagnosis and appropriate treatment to prevent rapid clinical deterioration. However, evidence-based recommendations for a specific treatment approach are currently not available. The present study describes the efficacy of a newly developed treatment regimen for post-bariatric patients presenting with severe hypoalbuminemia. Methods: A single-centre, retrospective analysis of eleven post-bariatric patients presenting with severe hypoalbuminemia, treated with continuous 24 h nasal-jejunal tube feeding of a medium chain triglyceride (MCT) formulation in combination with pancreatic enzyme supplementation every 3 h. Results: Duration of tube feeding ranged from 25 to 156 days (median 64 days) and pancreatic enzyme was supplemented for 22–195 days (median 75 days). An increase in serum albumin levels of 5 g/L and 10 g/L was achieved after a median period of 20 (range 6–26 days) and 36 days (range 21–57 days), respectively. Albumin levels were > 35 g/L after a median period of 58 days (range 44–171 days). Conclusion: In this case series, a continuous 24-h nasal-jejunal MCT tube feed combined with frequent pancreatic enzyme supplementation was effective in all patients presenting with severe post-bariatric hypoalbuminemia and was not associated with adverse effects.

The role of farm animals in a circular food system
Zanten, Hannah H.E. Van; Ittersum, Martin K. Van; Boer, Imke J.M. De - \ 2019
Global Food Security 21 (2019). - ISSN 2211-9124 - p. 18 - 22.
Bio-economy - Circularity - Climate - Fish - Food production - Land use - Livestock - Sustainable diets

If we use farm animals for what they are good at - converting by-products from the food system and grass resources into valuable food and manure - they can contribute significantly to human food supply, while at the same time reducing the environmental impact of the entire food system. By converting these so-called low-opportunity-cost feeds, farm animals recycle biomass and nutrients into the food system that would otherwise be lost to food production. Rearing animals under this circular paradigm, however, requires a transition from our current linear food system towards a circular one. Here we present a biophysical concept for the role of farm animals in a circular food system, essential for meeting dietary recommendations within the boundaries of our planet.

Reading soils : using easily obtainable soil information to assess soil functioning
Leeuwen, Maricke Maria Wilhelmina Johanna van - \ 2019
Wageningen University. Promotor(en): Jakob Wallinga; Imke de Boer, co-promotor(en): Cathelijne Stoof; Jos van Dam. - Wageningen : Wageningen University - ISBN 9789463439428 - 170
In vivo assessment of muscle mitochondrial function in healthy, young males in relation to parameters of aerobic fitness
Lagerwaard, Bart ; Keijer, Jaap ; McCully, Kevin K. ; Boer, Vincent C.J. de; Nieuwenhuizen, Arie G. - \ 2019
European Journal of Applied Physiology 119 (2019)8. - ISSN 1439-6319 - p. 1799 - 1808.
EPOC - Mitochondrial capacity - Muscle mitochondria - NIRS - Oxidative metabolism

Purpose: The recovery of muscle oxygen consumption (mV˙ O2) after exercise provides a measure of skeletal muscle mitochondrial capacity, as more and better-functioning mitochondria will be able to restore mV˙ O2 faster to the pre-exercise state. The aim was to measure muscle mitochondrial capacity using near-infrared spectroscopy (NIRS) within a healthy, normally active population and relate this to parameters of aerobic fitness, investigating the applicability and relevance of using NIRS to assess muscle mitochondrial capacity non-invasively. Methods: Mitochondrial capacity was analysed in the gastrocnemius and flexor digitorum superficialis (FDS) muscles of eight relatively high-aerobic fitness (V˙ O2peak ≥ 57 mL/kg/min) and eight relatively low-aerobic fitness male subjects (V˙ O2peak ≤ 47 mL/kg/min). Recovery of whole body V˙ O2, i.e. excess post-exercise oxygen consumption (EPOC) was analysed after a cycling protocol. Results: Mitochondrial capacity, as analysed using NIRS, was significantly higher in high-fitness individuals compared to low-fitness individuals in the gastrocnemius, but not in the FDS (p = 0.0036 and p = 0.20, respectively). Mitochondrial capacity in the gastrocnemius was significantly correlated with V˙ O2peak (R2 = 0.57, p = 0.0019). Whole body V˙ O2 recovery was significantly faster in the high-fitness individuals (p = 0.0048), and correlated significantly with mitochondrial capacity in the gastrocnemius (R2 = 0.34, p = 0.028). Conclusion: NIRS measurements can be used to assess differences in mitochondrial muscle oxygen consumption within a relatively normal, healthy population. Furthermore, mitochondrial capacity correlated with parameters of aerobic fitness (V˙ O2peak and EPOC), emphasising the physiological relevance of the NIRS measurements.

Estimating the impact of clinical mastitis in dairy cows on greenhouse gas emissions using a dynamic stochastic simulation model: A case study
Mostert, P.F. ; Bokkers, E.A.M. ; Boer, I.J.M. De; Middelaar, C.E. Van - \ 2019
Animal (2019). - ISSN 1751-7311
carbon footprint - disease - environmental impact - health - modeling

The increasing attention for global warming is likely to contribute to the introduction of policies or other incentives to reduce greenhouse gas (GHG) emissions related to livestock production, including dairy. The dairy sector is an important contributor to GHG emissions. Clinical mastitis (CM), an intramammary infection, results in reduced milk production and fertility, increases culling and mortality of cows and, therefore, has a negative impact on the efficiency (output/input) of milk production. This may increase GHG emissions per unit of product. Our objective was to estimate the impact of CM in dairy cows on GHG emissions of milk production for the Dutch situation. A dynamic stochastic simulation model was developed to simulate the dynamics and losses of CM for individual lactations. Cows receive a parity (1 to 5+), a milk production and a calving interval (CI). Based on the parity, cows have a risk of CM, with a maximum of three cases in a lactation. Pathogens causing CM were classified as gram-positive bacteria, gram-negative bacteria, or other. Based on the parity and pathogen combinations, cows had a reduced milk production, discarded milk, prolonged CI and a risk of removal (culling and mortality) that reduce productivity of dairy cows and therefore increase GHG emissions per unit of product. Using life cycle assessment, emissions of GHGs were estimated from cradle to farm gate for processes along the milk production chain that are affected by CM. Processes included were feed production, enteric fermentation, and manure management. Emissions of GHGs were expressed as kg CO2 equivalents per ton of fat-and-protein-corrected milk (kg CO2e/t FPCM). Emissions of cows with CM increased on average by 57.5 (6.2%) kg CO2e/t FPCM compared with cows without CM. This increase was caused by removal (39%), discarded milk (38%), reduced milk production (17%) and prolonged CI (6%). The GHG emissions increased by 48 kg CO2e/t FPCM for cows with one case of CM, by 69 kg CO2e/t FPCM for cows with two cases of CM and by 92 kg CO2e/t FPCM for cows with three cases of CM compared with cows without CM. Preventing CM can be an effective strategy for farmers to reduce GHG emissions and can contribute to sustainable development of the dairy sector, because this also can improve the income of farmers and the welfare of cows. The impact of CM on GHG emissions, however, will vary between farms due to environmental conditions and management practices.

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