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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    Systems analysis of Mycoplasma hyopneumoniae to improve vaccine production
    Kamminga, Tjerko - \ 2017
    Wageningen University. Promotor(en): V.A.P. Martins dos Santos, co-promotor(en): P.J. Schaap; J.J.E. Bijlsma. - Wageningen : Wageningen University - ISBN 9789463436519 - 152
    interdisciplinary research - molecular biology - mycoplasma hyopneumoniae - vaccines - systems biology - systems analysis - pigs - pneumonia - animals - interdisciplinair onderzoek - moleculaire biologie - mycoplasma hyopneumoniae - vaccins - systeembiologie - systeemanalyse - varkens - longontsteking - dieren

    Mycoplasma hyopneumoniae (M. hyopneumoniae) is a bacterial pathogen that has evolved from a gram-positive ancestor and specifically colonizes the lower respiratory tract of pigs where it causes enzootic pneumonia and plays a major role in the development of respiratory disease in pigs. Whole-cell inactivated vaccines are available that lower the severity of disease and are widely applied in pig industry to prevent clinical signs and improve pig herd health. However, production of these vaccines is challenging because it is not known which bacterial components are needed for protection and complex cultivation media are needed because growth requirements are not completely understood. The aim of this thesis was to understand growth and survival strategies of M. hyopneumoniae during infection, to integrate this knowledge with metabolic modeling under conditions used for vaccine production and apply this knowledge to improve the current production process for M. hyopneumoniae vaccines.

    Chapter 1 provides a general introduction into the disease, treatment and prevention methods with a focus on vaccines. I then introduce the characteristics of the M. hyopneumoniae genome, transcriptome and review the current knowledge on infectious mechanisms and the response of the pig to infection and vaccination. Finally, I discuss the challenges related to vaccine production and introduce systems biology tools that will be applied in the thesis. In chapter 2 we define a strategy for risk-based process development of bacterial vaccines which provided the framework for future studies performed during this thesis. We propose to integrate the academic workflow for rational strain design with the industry standard for process design. Systems biology tools, especially genome-scale metabolic models, play an essential role in this strategy because application of these tools reduces process risks and increases process understanding. Therefore, in line with this strategy, we created a manually curated genome-scale metabolic model of M. hyopneumoniae which we applied to dynamically model the cultivation step in the vaccine production process (chapter 3). We found that only 16% of cellular energy in a standard fermentation was used for growth and 84% was used for non-growth associated maintenance. By model-driven experimentation we were able to increase the fraction of cellular energy used for growth by addition of pyruvate to the production medium, and showed in dedicated fermentor experiments that the improved process reached a 2.3 times higher biomass yield. Although the metabolic model helped to increase process yield, it did not allow prediction of a defined cultivation medium without components from porcine origin. Therefore, to better understand the dependency of M. hyopneumoniae on host derived components, we performed a functional comparison of 80 mycoplasma genomes and used multivariate and machine-learning algorithms to relate functional capability to the specific host and niche of mycoplasma species (chapter 4). This analysis allowed us to identify protein domains possibly needed for growth and survival in the pig lung. In addition, we found that protein domains expected to be essential for bacterial growth were not persistently present in mycoplasma genomes suggesting that alternative domain configurations exist that bypass their essentiality. To better understand whether the proteins we identified as possibly important for survival in pigs actually play a role during M. hyopneumoniae infection, we sequenced the bacterial mRNA during infection in chapter 5 and compared the in vivo transcriptome to that of broth grown mycoplasma. We found 22 up-regulated and 30 down-regulated genes during infection (FDR<0.01 and fold change >2LOG2) and identified differentially expressed ncRNAs. In chapter 6 we build upon our mycoplasma basis to further analyse the role of ncRNAs in bacterial genomes. We identified an exponential relationship between the AT content of genomes and the number of ncRNAs and propose that this relation is the result of spurious transcription, which is more likely to occur in AT rich genomes. This hypothesis is further substantiated by showing that spurious transcription demands minimal cellular energy and that overexpression of cis-binding ncRNAs in M. pneumoniae did not influence the level of proteins translated from their overlapping mRNAs. Finally, in chapter 7 I discuss four system strategies, identified in this thesis and derived from recent literature, and discuss how these strategies could be integrated in the metabolic model of M. hyopneumoniae. Lastly, I provide an outlook on the next steps needed for improvement of the production process for M. hyopneumoniae vaccines.

    In conclusion, this work provided novel insight in the metabolic capability of M. hyopneumoniae based on the proteome domain content, captured in a genome-scale metabolic model and studied under in vitro and in vivo conditions. Biomass yield of the cultivation step for vaccine production was increased and the basis was laid to further improve the production process for M. hyopneumoniae vaccines using model-based experimentation.

    Beschermde en bedreigde dieren en planten in de stad : een geografische analyse van geselecteerde Vogelrichtlijn-, Habitatrichtlijn-, en Rode Lijstsoorten
    Lahr, Joost ; Meeuwsen, Henk ; Lammertsma, Dennis ; Gooedhart, Paul ; Zee, Friso van der - \ 2016
    Wageningen : Wageningen Environmental Research (Wageningen Environmental Research rapport 2776) - 103
    bedreigde soorten - planten - dieren - stedelijke gebieden - vogelrichtlijn - habitatrichtlijn - biodiversiteit - geografische informatiesystemen - steden - endangered species - plants - animals - urban areas - birds directive - habitats directive - biodiversity - geographical information systems - towns
    Registreren in Falcoo
    Maurice - Van Eijndhoven, M.H.T. ; Oldenbroek, J.K. - \ 2016
    Zeldzaam huisdier 41 (2016)2. - ISSN 0929-905X - p. 12 - 13.
    registratie - computer software - stamboeken - dieren - registration - computer software - herdbooks - animals
    In de reeks over verschillende dierregistratiesystemen komt dit keer het softwareprogramma Falcoo aan bod. Dit systeem wordt in Nederland vooral gebruikt voor het registreren van schapen en geiten. We verkennen welke mogelijkheden Falcoo biedt voor het registreren van dieren.
    Het dier en de dood
    Stassen, Elsbeth - \ 2016
    animal ethics - killing of animals - moral values - lifespan - short life - pets - human-animal relationships - animals - animal welfare - animal health

    Elke dag worden in ons land duizenden dieren gedood. Het lijkt iets vanzelfsprekends.

    Maar dat is het niet, zegt hoogleraar Dier en samenleving

    Elsbeth Stassen. Dieren doden roept altijd vragen op. Vragen die moeilijk

    te beantwoorden zijn. Een nieuw boek helpt een handje.

    Impact of QTL properties on the accuracy of multi-breed genomic prediction
    Wientjes, Y.C.J. ; Calus, M.P.L. ; Goddard, M.E. ; Hayes, B.J. - \ 2015
    Genetics, Selection, Evolution 47 (2015). - ISSN 0999-193X
    dairy-cattle populations - residual feed-intake - complex traits - linkage disequilibrium - genotype imputation - data sets - selection - values - animals - reliability
    Background - Although simulation studies show that combining multiple breeds in one reference population increases accuracy of genomic prediction, this is not always confirmed in empirical studies. This discrepancy might be due to the assumptions on quantitative trait loci (QTL) properties applied in simulation studies, including number of QTL, spectrum of QTL allele frequencies across breeds, and distribution of allele substitution effects. We investigated the effects of QTL properties and of including a random across- and within-breed animal effect in a genomic best linear unbiased prediction (GBLUP) model on accuracy of multi-breed genomic prediction using genotypes of Holstein-Friesian and Jersey cows. Methods - Genotypes of three classes of variants obtained from whole-genome sequence data, with moderately low, very low or extremely low average minor allele frequencies (MAF), were imputed in 3000 Holstein-Friesian and 3000 Jersey cows that had real high-density genotypes. Phenotypes of traits controlled by QTL with different properties were simulated by sampling 100 or 1000 QTL from one class of variants and their allele substitution effects either randomly from a gamma distribution, or computed such that each QTL explained the same variance, i.e. rare alleles had a large effect. Genomic breeding values for 1000 selection candidates per breed were estimated using GBLUP modelsincluding a random across- and a within-breed animal effect. Results - For all three classes of QTL allele frequency spectra, accuracies of genomic prediction were not affected by the addition of 2000 individuals of the other breed to a reference population of the same breed as the selection candidates. Accuracies of both single- and multi-breed genomic prediction decreased as MAF of QTL decreased, especially when rare alleles had a large effect. Accuracies of genomic prediction were similar for the models with and without a random within-breed animal effect, probably because of insufficient power to separate across- and within-breed animal effects. Conclusions - Accuracy of both single- and multi-breed genomic prediction depends on the properties of the QTL that underlie the trait. As QTL MAF decreased, accuracy decreased, especially when rare alleles had a large effect. This demonstrates that QTL properties are key parameters that determine the accuracy of genomic prediction.
    The hybrid nature of pig genomes : unraveling the mosaic haplotype structure in wild and commercial Sus scrofa populations
    Bosse, M. - \ 2015
    Wageningen University. Promotor(en): Martien Groenen, co-promotor(en): Hendrik-Jan Megens; Ole Madsen. - Wageningen : Wageningen University - ISBN 9789462573000 - 253
    dieren - varkens - dierveredeling - genomen - hybridisatie - sus scrofa - haplotypen - genomica - populaties - genetische variatie - animals - pigs - animal breeding - genomes - hybridization - sus scrofa - haplotypes - genomics - populations - genetic variation - cum laude
    cum laude graduation
    Emotions on the loose: emotional contagion and the role of oxytocin in pigs
    Reimert, I. ; Bolhuis, J.E. ; Kemp, B. ; Rodenburg, T.B. - \ 2015
    Animal Cognition 18 (2015)2. - ISSN 1435-9448 - p. 517 - 532.
    social cognition - sus-scrofa - behavior - animals - empathy - humans - responses - welfare - slaughter - distress
    We studied emotional contagion, a simple form of empathy, and the role of oxytocin herein in pigs. Two training pigs per pen (n = 16 pens) were subjected to a positive treatment (pairwise access to a large compartment filled with peat, straw and some chocolate raisins) and a negative treatment (social isolation in a small compartment) in a test room using a within-subjects design. Thereafter, two naive pen mates joined the training pigs in the test room, but were not given access to the treatments. This allowed testing for emotional contagion. Subsequently, the naive pigs, serving as their own controls, were given 24 IU of oxytocin or a placebo intranasally 30 min before accompanying the training pigs, which were exposed to either the negative or positive treatment, to the test room. Behavioral differences found between the positive and negative treatments (e.g., play and “tail wagging” vs. standing alert, urinating, defecating and ears backward) show that the treatments induced a positive and negative emotional state in the training pigs, respectively. Changes in behaviors of the training pigs with and without naive pigs present (e.g., in ears backwards) and of the naive pigs with and without training pigs present (e.g., in standing alert) indicated that emotional contagion occurred, especially during the negative treatment. Oxytocin did not seem to affect the behavior of the treated naive pigs, but did affect behaviors (e.g., defecating) of the training pigs which had not received oxytocin. This suggests a role for oxytocin in pig communication, which merits further research.
    Evaluation of the sustainability of contrasted pig farming systems: integrated evaluation
    Bonneau, M. ; Klauke, T.N. ; Gonzalez, J. ; Rydhmer, L. ; Ilari-Antoine, E. ; Dourmad, J.Y. ; Greef, K.H. de; Houwers, H.W.J. ; Cinar, M.U. ; Fabrega, E. ; Zimmer, C. ; Hviid, M. ; Oever, B. van der; Edwards, S.A. - \ 2014
    Animal 8 (2014)12. - ISSN 1751-7311 - p. 2058 - 2068.
    management - animals
    The aim of this paper is to present an approach for an integrated evaluation of the sustainability of pig farming systems, taking into account the three classical pillars: economy, environment and society. Eight sustainability themes were considered: Animal Welfare (AW), Animal Health (AH), Breeding Programmes (BP), Environment (EN), Meat Safety (MS), Market Conformity (MC), Economy (EC) and Working Conditions (WC). A total of 37 primary indicators were identified and used for the evaluation of 15 much contrasted pig farming systems in five EU countries. The results show that the eight themes were not redundant and all contributed to the observed variation between systems. The tool was very robust for highlighting the strengths and weaknesses of the systems along the eight themes that were considered. The number of primary indicators could be reduced from 37 to 18 with limited impact on the strengths/weaknesses profile of the individual systems. Integrating the eight theme evaluations into a single sustainability score is based on hypotheses or presumptions on the relative weights that should be given to the eight themes, which are very dependent on the context and on the purpose of the users of the tool. Therefore, the present paper does not have the ambition to provide a ready-for-use tool, rather to suggest an approach for the integrated evaluation of the sustainability of pig farming systems.
    Accuracy of genomic prediction when combining two related crossbred populations
    Vallee, A.A.A. ; Arendonk, J.A.M. van; Bovenhuis, H. - \ 2014
    Journal of Animal Science 92 (2014)10. - ISSN 0021-8812 - p. 4342 - 4348.
    dairy-cattle breeds - beef-cattle - selection - performance - animals - values - uterine - traits - impact - gene
    Charolais bulls are selected for their crossbreed performance when mated to Montbéliard or Holstein dams. To implement genomic prediction, one could build a reference population for each crossbred population independently. An alternative could be to combine both crossbred populations into a single reference population to increase size and accuracy of prediction. The objective of this study was to investigate the accuracy of genomic prediction by combining different crossbred populations. Three scenarios were considered: 1) using 1 crossbred population as reference to predict phenotype of animals from the same crossbred population, 2) combining the 2 crossbred populations into 1 reference to predict phenotype of animals from 1 crossbred population, and 3) using 1 crossbred population as reference to predict phenotype of animals from the other crossbred population. Traits studied were bone thinness, height, and muscular development. Phenotypes and 45,117 SNP genotypes were available for 1,764 Montbéliard × Charolais calves and 447 Holstein × Charolais calves. The population was randomly spilt into 10 subgroups, which were assigned to the validation one by one. To allow fair comparison between scenarios, size of the reference population was kept constant for all scenarios. Breeding values were estimated with BLUP and genomic BLUP. Accuracy of prediction was calculated as the correlation between the EBV and the phenotypic values of the calves in the validation divided by the square root of the heritability. Genomic BLUP showed higher accuracies (between 0.281 and 0.473) than BLUP (between 0.197 and 0.452). Accuracies tended to be highest when prediction was within 1 crossbred population, intermediate when populations were combined into the reference population, and lowest when prediction was across populations. Decrease in accuracy from a prediction within 1 population to a prediction across populations was more pronounced for bone thinness (–27%) and height (–29%) than for muscular development (–14%). Genetic correlation between the 2 crossbred populations was estimated using pedigree relationships. It was 0.70 for bone thinness, 0.80 for height, and 0.99 for muscular development. Genetic correlation indicates the expected gain in accuracy of prediction when combining different populations into 1 reference population. The larger the genetic correlation is, the larger the benefit is to combine populations for genomic prediction.
    An experimental Toxoplasma gondii dose response challenge model to study therapeutic or vaccine efficacy in cats
    Cornelissen, J.B.W.J. ; Giessen, J.W.B. van der; Takumi, K. ; Teunis, P.F.M. ; Wisselink, H.J. - \ 2014
    PLoS ONE 9 (2014)9. - ISSN 1932-6203 - 9 p.
    crude rhoptry proteins - united-states - tissue cysts - oocysts - bradyzoites - infectivity - tachyzoites - outbreak - animals - humans
    High numbers of Toxoplasma gondii oocysts in the environment are a risk factor to humans. The environmental contamination might be reduced by vaccinating the definitive host, cats. An experimental challenge model is necessary to quantitatively assess the efficacy of a vaccine or drug treatment. Previous studies have indicated that bradyzoites are highly infectious for cats. To infect cats, tissue cysts were isolated from the brains of mice infected with oocysts of T. gondii M4 strain, and bradyzoites were released by pepsin digestion. Free bradyzoites were counted and graded doses (1000, 100, 50, 10), and 250 intact tissue cysts were inoculated orally into three cats each. Oocysts shed by these five groups of cats were collected from faeces by flotation techniques, counted microscopically and estimated by real time PCR. Additionally, the number of T. gondii in heart, tongue and brains were estimated, and serology for anti T. gondii antibodies was performed. A Beta-Poisson dose-response model was used to estimate the infectivity of single bradyzoites and linear regression was used to determine the relation between inoculated dose and numbers of oocyst shed. We found that real time PCR was more sensitive than microscopic detection of oocysts, and oocysts were detected by PCR in faeces of cats fed 10 bradyzoites but by microscopic examination. Real time PCR may only detect fragments of T. gondii DNA without the presence of oocysts in low doses. Prevalence of tissue cysts of T. gondii in tongue, heart and brains, and anti T. gondii antibody concentrations were all found to depend on the inoculated bradyzoite dose. The combination of the experimental challenge model and the dose response analysis provides a suitable reference for quantifying the potential reduction in human health risk due to a treatment of domestic cats by vaccination or by therapeutic drug application.
    The microbial eukaryote Blastocystis is a prevalent and diverse member of the healthy human gut microbiota
    Scanlan, P.D. ; Stensvold, C.R. ; Rajilic-Stojanovic, M. ; Heilig, H.G. ; Vos, W.M. de; O'Toole, P.W. ; Cotter, P.D. - \ 2014
    FEMS microbiology ecology 90 (2014)1. - ISSN 0168-6496 - p. 326 - 330.
    genetic diversity - cysteine proteases - subtypes - bacterial - insights - animals - fungi - cells
    To date, the majority of research into the human gut microbiota has focused on the bacterial fraction of the community. Inevitably, this has resulted in a poor understanding of the diversity and functionality of other intestinal microorganisms in the human gut. One such nonbacterial member is the microbial eukaryote Blastocystis, which has been implicated in the aetiology of a range of different intestinal and extra-intestinal diseases. However, prevalence data from different studies are conflicting, and crucially, there is limited information on its incidence and diversity in healthy individuals. Here, we survey the prevalence, genetic diversity and temporal stability of Blastocystis in a group of healthy adults (n = 105) using a sensitive PCR assay. Blastocystis was present in 56% of our sample set, which is much higher than previously reported from an industrialised county (Ireland). Moreover, a diversity of different subtypes (species) were detected, and Blastocystis was present in a subset of individuals sampled over a period of time between 6 and 10 years, indicating that it is capable of long-term host colonisation. These results show that Blastocystis is a common and diverse member of the healthy gut microbiota, thereby extending our knowledge of the microbial ecology of the healthy human intestine.
    Nutrient utilization, dietary preferences, and gastrointestinal development in veal calves : interactions between solid feed and milk replacer
    Berends, H. - \ 2014
    Wageningen University. Promotor(en): Wouter Hendriks, co-promotor(en): Walter Gerrits; Joost van den Borne. - Wageningen : Wageningen University - ISBN 9789462570436 - 239
    dieren - koeien - vleeskalveren - diervoeding - voedingsstoffen - groei - ontwikkeling - diervoedering - vaste voeding - melk - animals - cows - veal calves - animal nutrition - nutrients - growth - development - animal feeding - solid feeding - milk

    Solid feeds (SF), comprising roughages and concentrates, represent an increasingly important source of nutrients for veal calves. From a welfare and economic perspective, there is a strong incentive to replace a considerable portion of the milk replacer (MR) by SF in the diet. However, interactions between MR and SF complicate the prediction of the nutritional value of these ration components, and adverse effects on health may occur when combining MR and SF. To investigate these interactions, various combinations of MR, concentrates, and roughages were tested in a series of large-scale studies.

    When provided with unrestricted access to MR, concentrates, maize silage, hay, and straw over a 6-month period, calves markedly changed their preferences over time, and individual differences appeared very large. However, the ratio between digestible crude protein and digestible energy in the diet of choice appeared remarkably constant between calves. Another set of studies aimed at defining age-related changes in utilization efficiency of SF. It was demonstrated that stimulating early rumen development (before 12 wk of age) improves the nutritional value of each kg of SF in later life. In another study, it was shown that the nutritional value of SF increases with age. This effect is likely related to improved fermentation of fibrous SF. Increasing SF intake lead to an increase in the passage rates of concentrates and straw through the rumen.

    Compared to the feeding of MR alone, nitrogen (N) economy of veal calves can be improved by feeding a low-protein SF, creating a N shortage in the rumen. Urea-N, likely originating from the MR, was demonstrated to recycle back into the rumen for microbial protein production. In a subsequent study, it appeared that the feeding of a high-protein SF improved ruminal degradation of fibrous SF relative to a low-protein SF at equal protein intake, balanced via the MR. Urea recycling was demonstrated to be unable to completely compensate a N shortage in the rumen. An important interaction between MR and SF can be the influence of SF on the proportion of MR flowing in the rumen, where it is fermented and potentially causes health problems. The current standard to measure this so-called ‘ruminal drinking’ is the Co recovery method, which requires sacrificing the calves. Several non-terminal methods to quantify ruminal drinking were evaluated in three consecutive experiments. From a meta-analysis of Co recovery data, it was shown that on average 17% of the MR fed flows into the rumen instead of the abomasum. No associations with SF or MR intake related variables were found. Potential adverse effects of replacing MR by SF include abomasal damage, particularly in the pyloric area. This generally increases with the intake of SF, particularly in the presence of sharp, abrasive particles, and more so with a 20:80 than with a 50:50 mixture of roughage:concentrate. Results indicated that early rumen development can offer some protection in later life.

    In conclusion, when taking interactions between MR and SF into account, it appeared possible to replace a considerable portion of MR by SF without compromising calf performance and health.

    The development of a model for the prediction of feed intake and energy partitioning in dairy cows
    Zom, R.L.G. - \ 2014
    Wageningen University. Promotor(en): Wouter Hendriks, co-promotor(en): Ad van Vuuren. - Wageningen : Wageningen University - ISBN 9789462570443 - 176
    dieren - melkkoeien - melkveehouderij - voeropname - modelleren - verteerbare energie - animals - dairy cows - dairy farming - feed intake - modeling - digestible energy

    Balancing the supply of on-farm grown forages with the production targets of the dairy herd is a crucial aspect of the management of a dairy farm. Models which provides a rapid insight of the impact of the ration, feed quality and feeding management on feed intake and performance of dairy cows are indispensable to optimize feeding strategies, allocation of feeds and purchased concentrates, in order to find the best compromise between milk performance, nutrient use efficiency, manure excretion, gaseous emissions and profitability. This thesis describes the development of the Wageningen UR Dairy Cow Model (Wageningen DCM), a model for the prediction of feed intake and performance of dairy cows. The Wageningen DCM is constructed from two modules: a feed intake model and an energy partitioning model which describes the partitioning of the ingested net energy to milk energy output and body reserves. For the development of the feed intake model a calibration dataset was compiled with 38515 weekly records of ration feed composition, diet composition, individual feed intakes, milk yield and composition, parity, days in lactation and days pregnant from 1507 cows. The feed intake model predicts dry matter intake (DMI) from feed and animal characteristics. Data of standard feed analysis were used to estimate the satiety value (SV) of numerous feeds. The SV is the measure of the extent to which a feed limits intake. The cows’ ability to process the intake-limiting satiety value-units is expressed as the feed intake capacity (FIC). The FIC is estimated from parity, days in milk and days of pregnancy which are indicators of the size and physiological state of the cow. An evaluation of the feed intake model was performed using an independent dataset containing 8974 weekly means of DMI from 348 cows. On the basis of mean square prediction error (MSPE) and relative prediction error (RPE) as criteria, it was concluded that feed intake model was robust and can be applied to various diets and feeding management situations in lactating HF cows.

    A second model was developed to predict the partitioning of ingested net energy (NEL) to milk energy and body reserves. This energy partitioning model describes the baselines of daily NEL intake and milk energy output (MEO) during successive lactation cycles of a ‘reference’ cow. The MEO and change in body energy of a cow is estimated from deviation of NEL intake from the baseline. A NEL intake above the baselines results in a higher predicted MEO and reduced mobilization of body energy reserves. Whereas, a NEL intake below the baseline results in a lower predicted MEO and increased mobilization. The proportion of ingested NEL partitioned to MEO depends parity number, days in lactation and pregnant, reflecting the changes in priority in energy partitioning during successive lactation cycles of a dairy cow

    The feed intake model and energy partitioning model are integrated in the Wageningen DCM. Model simulations showed that the Wageningen DCM is able to simulate the effects of diet composition, nutritional strategies and effects of cow characteristics (parity, days in milk and pregnancy) on dry matter and nutrient intake, and the partitioning of ingested NEL into MEO and body energy. The Wageningen DCM requires easily available input data. Validation of the Wageningen DCM with external data indicated a good accuracy of the prediction of intake and milk energy output with relatively low prediction errors ≤ 0.1. The Wageningen DCM enables users to analyse and compare different feeding strategies, identify limitations of feeding strategies, formulate diets, calculate feed budgets and to develop economic and environmental sustainable feeding strategies.

    Dietary carbohydrates and denitrification in recirculating aquaculture systems
    Meriac, A. - \ 2014
    Wageningen University. Promotor(en): Johan Verreth. - Wageningen : Wageningen University - ISBN 9789462570351 - 129
    dieren - vissen - aquacultuur - koolhydraten - denitrificatie - aquacultuur en milieu - feces - vezels - recirculatie aquacultuur systemen - animals - fishes - aquaculture - carbohydrates - denitrification - aquaculture and environment - faeces - fibres - recirculating aquaculture systems

    Due to overfishing of global fish stocks and increasing fish meal prices, plant ingredients are being increasingly used as an alternative source of protein in fish feeds. However, the inclusion of unpurified plant ingredients will also increase the content of fibers in feeds. Fibers are nearly indigestible and will therefore increase solid waste production in aquaculture. This solid waste can be used to as a carbon source for denitrification to control nitrate levels in recirculating aquaculture systems (RAS), thereby reducing both solid and dissolved waste production. Additionally, fibers can change the recovery characteristics and lower the degradability of fecal waste. Therefore, this study investigates how changes in the dietary carbohydrate composition can affect waste production, system performance and denitrification in RAS. Furthermore, ultrasound treatment (to decrease particle size in fecal waste) and enzymatic conditioning (to increase fiber degradability) were tested as possible means to increase the bioavailability of carbon in fecal waste for denitrification.

    Comparing a high fiber (HNSP) and low fiber (LNSP) diet in RAS stocked with rainbow trout confirmed that the fibers in the HNSP diet increase fecal waste production. Although the HNSP diet produced more fecal waste than the LNSP diet, both diets produced the same amount of biodegradable fecal carbon. Since feces removal was higher in RAS using the HNSP diet, the load of degradable organic matter on the biofilters was lower with the HNSP diet than with the LNSP diet. Furthermore, fecal waste produced with the HNSP diet contained larger particles than feces of the LNSP diet, which could also improve the recovery of fecal waste with microscreens. Feces produced with the HNSP diet were also less degradable than feces produced with the LNSP diet. By using fecal waste as an internal carbon source for denitrification, solid and dissolved waste emissions from RAS could be reduced by ~50% for the HNSP diet. However, only approximately half of the supplied cellulose and hemicellulose were degraded in the denitrification reactors, whereas lignin was not degraded at all. Thus, the overall degradability of organic carbon in fecal waste was limited by fibers as hemicellulose, cellulose and lignin. Ultrasound and enzymatic conditioning did not sufficiently increase the degradability of fecal waste. Nonetheless, fibers originating from unpurified plant ingredients may also have beneficial effects on RAS performance by increasing fecal recovery. A more selective choice of feed ingredients could be used to increase the recovery and degradability of fecal waste in RAS.

    Mechanisms underlying disease transmission between spatially separated animals
    Bunnik, B.A.D. van - \ 2014
    Wageningen University. Promotor(en): Mart de Jong, co-promotor(en): Thomas Hagenaars; Gonnie Nodelijk. - Wageningen : Wageningen University - ISBN 9789461739537 - 150
    dieren - vleeskuikens - infectieziekten - ziekteoverdracht - gastheren (dieren, mensen, planten) - wiskundige modellen - epidemiologie - diergeneeskunde - animals - broilers - infectious diseases - disease transmission - hosts - mathematical models - epidemiology - veterinary science

    Transmission of infections between spatially separated hosts is a common problem, not only during major outbreaks of livestock diseases, but also in many other settings such as the transmission of infectious diseases between plants and crops or in healthcare settings. During the last major epidemics of livestock diseases in the Netherlands and abroad, disease transmission events occurred despite movement bans and other (bio-)security measures, implying that indirect transmission plays a major role. A better understanding of indirect transmission is necessary to put in place evidence based bio-security measures against neighbourhood (indirect) transmission. To gain more insight in the mechanisms underlying indirect transmission a series of experimental studies combined with mathematical modelling were conducted of which the results are presented in this thesis. First the effect of acidification of drinking water on the transmission parameters of direct and indirect transmission of Campylobacter jejuni (C. jejuni) between broilers was studied. It was shown that acidified drinking water has an effect on indirect transmission but not on direct transmission of C. jejuni between broilers. The sender and receiver sub-process of indirect transmission was then studied in more detail and it was shown that a significant negative interaction effect between acidification of the sender and receiver sub-processes exists, indicating that there is no additional effect of acidification of the drinking water on both sides of the transmission process compared to acidified drinking water only on one side. To study the transport of the pathogen in the environment in more detail, a series of indirect transmission experiments was carried out and a model framework was developed to study indirect transmission between spatially separated hosts. These studies showed that indirect transmission of C. jejuni between broilers is best described by a multistage environmental route from sending to receiving animal, suggesting that indirect transmission occurs through progressive (but slow) contamination of the environment surrounding the source. Indirect transmission experiments where repeated with both C. jejuni and Escherichia coli and the results showed that for C. jejuni it takes much longer for the first effective (viable) bacterium to cross the small distance of approximately 75 cm than it does for Escherichia coli. A new modelling approach to study indirect transmission was developed guided by these indirect transmission experiments. This model is capable of accurately describing the pathogen dispersal process by a diffusive transport mechanism which includes pathogen mortality. Lastly, a range of dose-response models were compared and tested how well these fitted to the data from a dose-response experiment. Here it was shown that for interpolation purposes two relatively simple models are best capable of describing the data from the dose-response experiment. For extrapolation purposes, however, it was shown that from the models that were studied a model that abides by the independent action hypothesis is best.

    Fear responses to novelty in testing environments are related to day-to-day activity in the home environment in dairy cattle
    MacKay, J.R.D. ; Haskell, M.J. ; Deag, J.M. ; Reenen, C.G. van - \ 2014
    Applied Animal Behaviour Science 152 (2014). - ISSN 0168-1591 - p. 7 - 16.
    individual-differences - beef-cattle - behavior - cows - humans - personality - animals - consistency - situations - boldness
    Behavioural tests for cattle take time to perform and can be stressful for the animals but are currently the only way of assessing behavioural reactions to fear-causing stimuli in a standardised manner. It may be possible to use behavioural data collected remotely in the home pen environment through the use of activity monitors and robotic milkers to identify fearful cattle without testing. In this study eighty five dairy cows were given a novel arena novel object (NANO) test and 79 of these were also human approach (HAP) tested, both thought to reflect fear. All animals had their activity recorded for 40 days prior to the testing period using a tri-axial accelerometer activity monitor. High numbers of novel object contacts in the test was associated with younger animals with fewer lying bouts per day and were less variable in their lying bout duration (Radj2=0.13, F 3,75 = 4.65, P = 0.005). Cows with a higher tolerance for human approach had fewer lying bouts per day, a shorter average standing bout duration and presented themselves to the robot milker more often (Radj2=0.08, F 3,69 = 3.12, P = 0.032). Personality traits constructed from a principle components analysis of the observed NANO behaviours were also associated with home pen activity. Cows which scored highly on the first component termed ‘neophobia’ were older, had more lying bouts and a greater variation in the duration of their average lying bout (Radj2=0.15, F 3,75 = 5.32, P = 0.002) while cows which scored highly on the second component termed ‘boldness’ were older cows with less variation in their average lying bout duration (Radj2=0.11, F2,75 = 5.63, P = 0.005). To conclude, significant relationships exist between behaviours in short-term personality tests and home pen activity recorded over several weeks. As fearfulness is reflected in spontaneous home pen behaviours, activity databases could be incorporated into models predicting fearfulness and welfare assessment protocols.
    Imputation of non-genotyped individuals based on genotyped relatives: assessing the imputation accuracy of a real case scenario in dairy cattle
    Bouwman, A.C. ; Hickey, J.M. ; Calus, M.P.L. ; Veerkamp, R.F. - \ 2014
    Genetics, Selection, Evolution 46 (2014). - ISSN 0999-193X - 11 p.
    genome-wide association - density genotypes - populations - selection - animals - pedigree - information - simulation - prediction - algorithm
    Background Imputation of genotypes for ungenotyped individuals could enable the use of valuable phenotypes created before the genomic era in analyses that require genotypes. The objective of this study was to investigate the accuracy of imputation of non-genotyped individuals using genotype information from relatives. Methods Genotypes were simulated for all individuals in the pedigree of a real (historical) dataset of phenotyped dairy cows and with part of the pedigree genotyped. The software AlphaImpute was used for imputation in its standard settings but also without phasing, i.e. using basic inheritance rules and segregation analysis only. Different scenarios were evaluated i.e.: (1) the real data scenario, (2) addition of genotypes of sires and maternal grandsires of the ungenotyped individuals, and (3) addition of one, two, or four genotyped offspring of the ungenotyped individuals to the reference population. Results The imputation accuracy using AlphaImpute in its standard settings was lower than without phasing. Including genotypes of sires and maternal grandsires in the reference population improved imputation accuracy, i.e. the correlation of the true genotypes with the imputed genotype dosages, corrected for mean gene content, across all animals increased from 0.47 (real situation) to 0.60. Including one, two and four genotyped offspring increased the accuracy of imputation across all animals from 0.57 (no offspring) to 0.73, 0.82, and 0.92, respectively. Conclusions At present, the use of basic inheritance rules and segregation analysis appears to be the best imputation method for ungenotyped individuals. Comparison of our empirical animal-specific imputation accuracies to predictions based on selection index theory suggested that not correcting for mean gene content considerably overestimates the true accuracy. Imputation of ungenotyped individuals can help to include valuable phenotypes for genome-wide association studies or for genomic prediction, especially when the ungenotyped individuals have genotyped offspring.
    A Bayesian Belief Network to Infer Incentive Mechanisms to Reduce antibiotic Use in Livestock Production
    Ge, L. ; Valeeva, N.I. ; Asseldonk, M.A.P.M. van; Hennen, W.H.G.J. ; Bergevoet, R.H.M. - \ 2014
    NJAS Wageningen Journal of Life Sciences 70-71 (2014). - ISSN 1573-5214 - p. 1 - 8.
    management - risk - resistance - framework - animals - pigs
    Efficient policy intervention to reduce antibiotic use in livestock production requires knowledge about potential causal factors of antibiotic use. Animal health status and management quality were considered the two most important factors that influence farmers’ decision-making concerning antibiotic use. The objective of this paper was to develop a Bayesian belief network (BBN) to analyze how these factors can directly and indirectly influence antibiotic use. Since both factors are not directly observable (i.e., latent), they were inferred from related observable variables (i.e., manifest variables). Using farm accounting data and registration data on antibiotic use and veterinary services in specialized finisher pig farms over the period 2007-2010, a confirmatory factor analysis was carried out to construct the two latent factors. Antibiotic use is quantified as the number of days per year in which an average pig is treated with antibiotics according to their standard daily dosages (NDD). Descriptive analysis on the data revealed that for the finisher pig farms, NDD averaged about 17 days, with substantial year-to-year variations and between-farm variations within the same year.The conditional probabilities for the BBN model were obtained through regression analysis between the constructed factors, NDD, and a number of technical and economic variables. The BBN model showed that antibiotic use was simultaneously influenced by the two latent factors, but in varying degrees depending on other variables. Therefore interventions targeting only to improve one factor are likely to lead to unsatisfactory outcomes of antibiotic use
    How superdiffusion gets arrested: ecological encounters explain shift from Lévy to Brownian movement
    Jager, M. de; Bartumeus, F. ; Kölzsch, A. ; Weissing, F.J. ; Hengeveld, G.M. ; Nolet, B.A. ; Herman, P.M.J. ; Koppel, J. van de - \ 2014
    Proceedings of the Royal Society. B: Biological Sciences 281 (2014)1774. - ISSN 0962-8452 - 8 p.
    power-law distributions - flight search patterns - environmental complexity - walks evolve - predators - dynamics - animals - mussels - success
    Ecological theory uses Brownian motion as a default template for describing ecological movement, despite limited mechanistic underpinning. The generality of Brownian motion has recently been challenged by empirical studies that highlight alternative movement patterns of animals, especially when foraging in resource-poor environments. Yet, empirical studies reveal animals moving in a Brownian fashion when resources are abundant. We demonstrate that Einstein's original theory of collision-induced Brownian motion in physics provides a parsimonious, mechanistic explanation for these observations. Here, Brownian motion results from frequent encounters between organisms in dense environments. In density-controlled experiments, movement patterns of mussels shifted from Lévy towards Brownian motion with increasing density. When the analysis was restricted to moves not truncated by encounters, this shift did not occur. Using a theoretical argument, we explain that any movement pattern approximates Brownian motion at high-resource densities, provided that movement is interrupted upon encounters. Hence, the observed shift to Brownian motion does not indicate a density-dependent change in movement strategy but rather results from frequent collisions. Our results emphasize the need for a more mechanistic use of Brownian motion in ecology, highlighting that especially in rich environments, Brownian motion emerges from ecological interactions, rather than being a default movement pattern
    Invasion Biology and Ecosystem Theory: Insights from a Continent in Transformation
    Prins, H.H.T. ; Gordon, I.J. - \ 2014
    Cambridge : Cambridge University Press - ISBN 9781107035812 - 530
    invasies - invasieve soorten - ecologie - ecosystemen - planten - dieren - australazië - invasions - invasive species - ecology - ecosystems - plants - animals - australasia
    Many conservationists argue that invasive species form one of the most important threats to ecosystems the world over, often spreading quickly through their new environments and jeopardising the conservation of native species. As such, it is important that reliable predictions can be made regarding the effects of new species on particular habitats. This book provides a critical appraisal of ecosystem theory using case studies of biological invasions in Australasia. Each chapter is built around a set of 11 central hypotheses from community ecology, which were mainly developed in North American or European contexts. The authors examine the hypotheses in the light of evidence from their particular species, testing their power in explaining the success or failure of invasion and accepting or rejecting each hypothesis as appropriate. The conclusions have far-reaching consequences for the utility of community ecology, suggesting a rejection of its predictive powers and a positive reappraisal of natural history.
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