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
University. Promotor(en): Vitor Martins dos Santos, co-promotor(en): Peter 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 - 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 - 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.
The hybrid nature of pig genomes : unraveling the mosaic haplotype structure in wild and commercial Sus scrofa populations
Bosse, M. - \ 2015
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 - haplotypes - genomics - populations - genetic variation - cum laude
cum laude graduation
Nutrient utilization, dietary preferences, and gastrointestinal development in veal calves : interactions between solid feed and milk replacer
Berends, H. - \ 2014
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
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
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
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.

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.
Ethiek, emoties en ophef over dieren in de natuur : theorie en praktijk van maatschappelijke discussies omtrent beheermaatregelen gericht op in het wild levende dieren
Langers, F. ; Mattijssen, T.J.M. ; Buijs, A.E. ; Steingröver, E.G. ; Westerink - Petersen, J. - \ 2013
Wageningen : Alterra (Alterra-rapport 2441) - 63
dierenwelzijn - wilde dieren - ethiek - natuurbeheer - fauna - dieren - ganzen - dolfijnen - opinies - dierethiek - animal welfare - wild animals - ethics - nature management - animals - geese - dolphins - opinions - animal ethics
De afgelopen jaren is gebleken dat veel maatschappelijk debat kan ontstaan over het beheer van in het wild levende dieren. Het ministerie van EZ wil handvatten om mogelijke maatschappelijke discussies rondom faunabeheer tijdig te herkennen. Alterra heeft hiertoe een state of the art studie uitgevoerd van theorievorming rondom ethiek en emoties van burgerreacties in relatie tot in het wild levende dieren, en deze toegepast op twee actuele casussen: orka Morgan en de ganzenproblematiek in Nederland. De state of the art studie maakte duidelijk dat burgers voornamelijk vanuit waarden en emoties redeneren, waar beleidsmakers en natuurbeheerders de focus leggen op kennis. Inzicht in elkaars taal is essentieel om nader tot elkaar te komen. Of een voorgenomen maatregel commotie veroorzaakt is sterk afhankelijk van het dier dat het betreft, de schade die het dier veroorzaakt en de impact van de voorgenomen maatregel. Voorts speelt mee of er partijen zijn die zich hard maken. In de discussie over de orka Morgan is het biocentrisme dominant: debatten gaan vooral over het welzijn van Morgan. In de ganzendiscussie zijn het vooral biocentrische en antropocentrische visies die tegenover elkaar staan in de twee dominante discoursen.
In vitro fermentation capacity of hindgut microbiota in pigs in relation to dietary fibre
Sappok, M.A. - \ 2012
University. Promotor(en): Martin Verstegen; Wouter Hendriks, co-promotor(en): Wilbert Pellikaan. - S.l. : s.n. - ISBN 9789461733153 - 132
dieren - varkens - fermentatie - diervoeding - einddarm - microbiota van het spijsverteringskanaal - voedingsvezels - zeugen - animals - pigs - fermentation - animal nutrition - hindgut - gastrointestinal microbiota - dietary fibres - sows

As pigs compete with humans for high quality feed ingredients such as grains, alternative feed sources need to be found. These alternative feed ingredients are usually high in indigestible carbohydrates, consisting mainly of non-starch polysaccharides (NSP) and are less suitable for human consumption. In order to find the most suitable feed ingredients for pig nutrition, they need to be well characterized regarding their nutritional value. This is possible with in vitro methods which mimic the hindgut degradation of these mainly indigestible feed ingredients. These in vitro methods either use enzymes or faecal inocula to incubate the feed ingredient to be tested. However, there is a lack of information on some general aspects of in vitro methods with pigs, such as the number of animals to use for inocula preparation, influence of enzymatic pre-digestion of feed ingredients, repeatability of fermentation results, adaptation time of donor animals etc.
The studies described in this thesis describe a number of experiments which were designed to test some of these above mentioned aspects in order to improve the in vitro procedure and therefore the predictability of feeding values of new feed ingredients (in the following called substrates). The first study compared two in vitro methods; one using enzymes and using inocula for fermentation and a combination of the two. The results showed a similar ranking order. Nonetheless, a combination of enzymatic pre-digestion with subsequent fermentation seems most suitable to best predict the nutrient availability of the tested substrate. The second study determined if 19 days of adaptation of donor animals is adequate to adapt them to a new diet, either high or low in NSP. The adaptation to the new diet was not completed and had the biggest influence on the slow fermentable substrate cellulose. The third study revealed that the results of a single fermentation run can be representative for the fermentation capacity of the donor animals. However, the optimal number of donor animals remains to be determined in order to receive results with a low variation coefficient. The last study compared the fermentation capacity of pigs raised on different organic farms. The results showed that animals across organic farms had a relatively similar and high fermentation capacity despite the different rations fed on single farms and varying farm management. This might be caused by the animals’ lifelong exposure to a high variety of fibre.
The results of this thesis show that in vitro fermentation methods can be further improved and need further attention regarding the optimal number of donor animals and their nutrition. It would be of special interest to compare the differences of fermentation capacity and energy yield between animals that are fed diets either high or low in NSP. Pig diets based on an improved in vitro methodology have the potential to increase economic profit for feed industry and farmers, but also to increase animal health and welfare.

Fatty acid digestion, synthesis and metabolism in broiler chickens and pigs
Smink, W. - \ 2012
University. Promotor(en): Martin Verstegen; Wouter Hendriks, co-promotor(en): Walter Gerrits. - S.l. : s.n. - ISBN 9789461733061 - 141
dieren - diervoeding - vetzuren - spijsvertering - metabolisme - varkens - vleeskuikens - animals - animal nutrition - fatty acids - digestion - metabolism - pigs - broilers

The impact of variation in the composition of dietary fat on digestion, metabolism and synthesis of fatty acids was studied in broiler chickens and in pigs. In young broiler chickens, digestion of unsaturated fatty acids was substantially higher compared with that of saturated fatty acids. Positional distribution appeared important. Particularly digestion of saturated fatty acids, e.g. palmitic acid (C16:0), esterified at the sn-1 and -3 position of the glycerol backbone was lower (51%) compared with that observed at the sn-2 position (90%). Based on these observations, an equation was developed predicting the digestion of dietary fat sources in broiler chickens and pigs, taking fatty acid composition, the positioning, and the proportion of free fatty acids into account. The deposition of fat, especially of monounsaturated fatty acids in body tissues, increased in broilers by feeding saturated fats in comparison with unsaturated fats caused by both a reduced ß-oxidation and an increased rate of de novo synthesis of fatty acids. In a feeding trial with pigs, starch, saturated and unsaturated fatty acid sources were compared at similar intakes of net energy. Growth performance and backfat thickness were unaffected by dietary energy source. Intramuscular fat content, however, tended to be increased in starch fed pigs when compared with pigs fed the saturated fatty acid source. To study the interactions between dietary linoleic acid (LA; C18:2 n-6) and -linolenic acid (ALA; C18:3 n-3) and their impact on the synthesis of long-chain polyunsaturated fatty acids (LC-PUFA) in both the n-3 and n-6 chains, a trial was designed in which identical increments in the intake of ALA and LA were fed to growing pigs. Generally, dietary LA inhibited the synthesis of n-3 LC-PUFA in the liver. Dietary ALA increased the content of eicosapentaenoic acid (EPA; C20:5 n-3) but decreased that of docosahexaenoic acid (DHA; C22:6 n-3) in the liver. DHA levels in brain were hardly affected by both dietary LA and ALA. It was concluded that in addition to Δ6 desaturase, elongase 2 might be a rate-limiting enzyme in the formation of DHA. The impact of these findings on the potential of contribution of feeding LA and ALA to pigs to meet human dietary requirements for LC-PUFA by meat products was investigated by analysing the fatty acid composition of muscle and fat tissues. It appeared impossible to attain substantial improvements in tissue DHA contents by feeding different combinations of LA and ALA. However, EPA of intramuscular fat can be increased by feeding ALA, particularly when restricting LA intake. In addition, docosapentaenoic acid (DPA; C22:5 n-3) was increased in both muscle and backfat by dietary ALA. DPA might have comparable biological effects as EPA. The potential of meat products to supply DPA in food is considerable and therefore of interest.

Geochemische bodematlas van Nederland
Mol, G. ; Spijker, J.H. ; Gaans, P. van; Römkens, P.F.A.M. - \ 2012
Wageningen : Wageningen Academic Publishers - ISBN 9789086861866 - 276
bodemchemie - geochemie - bodem - metaalelementen - kaarten - planten - dieren - risico - bodemkwaliteit - nederland - soil chemistry - geochemistry - soil - metallic elements - maps - plants - animals - risk - soil quality - netherlands
Deze Geochemische bodematlas geeft een uniek overzicht van de chemische samenstelling van de bodem in Nederland. Bodemmonsters van meer dan 350 locaties zijn geanalyseerd op meer dan 40 chemische elementen. De atlas geeft niet alleen informatie over de door de mens beïnvloede toplaag van de bodem, maar ook over de dieper gelegen C-horizont die nog niet of nauwelijks door de mens is beïnvloed. De lijst van elementen omvat uiteraard bekende metalen als cadmium, koper en lood en relevante meststoffen als fosfor en kalium. Daarnaast geeft de atlas ook inzicht in gehalten van elementen waarvan minder bekend is, zoals thallium, uranium en lithium. Totaalgehalten alleen geven onvoldoende inzicht in de beschikbaarheid of het risico van chemische elementen voor planten, dieren, en mensen. Daarom presenteert deze atlas ook meetresultaten van aanvullende bepalingen die de 'reactieve' en de 'beschikbare' fracties van de elementen in de bodemmonsters benaderen.
TRIM proteins and CXS chemokines : evolutionary dynamics and functional characterization of two large protein families in teleost fish
Aa, L.M. van der - \ 2012
University. Promotor(en): Huub Savelkoul, co-promotor(en): Lidy van Kemenade; P. Boudinot. - [S.l. : s.n. - ISBN 9789461731203 - 224
chemokinen - teleostei - immuunsysteem - immuniteit - virussen - eiwitten - dieren - antiviruseigenschappen - chemokines - immune system - immunity - viruses - proteins - animals - antiviral properties

Two large protein families with roles in the immune system were the subject of this thesis. In part one of the thesis, TRIM proteins were studied, which are part of an ancient intracellular immune system. In mammals, TRIM proteins were recently found to play an important role in the antiviral immune response as they can restrict multiple viruses. To better understand the evolution of the TRIM protein family, TRIM proteins were investigated in teleost fish, which emerged early during vertebrate evolution. A detailed description of the entire TRIM gene family in fish was made and it was discovered that certain TRIM genes have undergone a radical expansion, giving rise to three multigene families. Experimental studies indicated a role for trout TRIM proteins in antiviral immunity and demonstrated that they have E3 ubiquitin ligase activity. As it recently became evident that ubiquitination is an important mode to control the activity of proteins of innate immune pathways, possibly TRIM proteins in fish have a similar activity.

In part two of this thesis, inflammatory CXC chemokines were studied, for which limited functional data was available in fish at the start of the thesis project. CXC chemokines are specialized cytokines that direct leukocyte migration during inflammation. In zebrafish and carp, two CXC lineages were identified that resemble mammalian CXCL8, a similar diversification was observed for chemokines that resemble mammalian CXCL9, CXCL10, CXCL11chemokines. A characterization of the functions for cyprinid CXCL8-like and CXCL9-11-like (named CXCb) chemokines was made by in vitro and in vivo gene expression studies. By preparation of recombinant proteins it was demonstrated that carp chemokines of the CXCL8-like and CXCb subsets are both chemotactic for fish leukocytes. Chemokines of the CXCL8-like and CXCb subsets appeared to be functionally distinct, as they have a different effect on phagocyte activation and act during different phases of the inflammatory response. These results indicate that CXC chemokines have already specialized functions in fish.

Dierenwelzijnsbeleid: hoe blijf je bij de tijd?
Hopster, H. - \ 2011
Lectoraat Dierenwelzijn
dierenwelzijn - beleid - gemeenten - dierethiek - verantwoordelijkheid - opvoeding - dieren - animal welfare - policy - municipalities - animal ethics - responsibility - child rearing practices - animals
Presentatie gemeentelijk dierenwelzijnsbeleid
Systems Biology and Livestock Science
Pas, M.F.W. te; Woelders, H. ; Bannink, A. - \ 2011
Chichester, UK : John Wiley and Sons - ISBN 9780813811741 - 332
dieren - systeembiologie - vee - computers - moleculaire biologie - animals - systems biology - livestock - molecular biology
Systems Biology is an interdisciplinary approach to the study of life made possible through the explosion of molecular data made available through the genome revolution and the simultaneous development of computational technologies that allow us to interpret these large data sets. Systems Biology has changed the way biological science views and studies life and has been implemented in research efforts across the biological sciences. Systems Biology and Livestock Science will be the first book to review the latest advances using this research methodology in efforts to improve the efficiency, health, and quality of livestock production. Systems Biology and Livestock Science opens with useful introductory chapters explaining key systems biology principles. The chapters then progress to look at specific advances in fields across livestock science. Coverage includes, but is not limited to, chapters on systems biology approaches to animal nutrition, reproduction, health and disease, and animal physiology. Written by leading researchers in the field, Systems Biology and Livestock Science, will be an invaluable resource to researchers, professionals, and advance students working in this rapidly developing discipline.
Ammoniakemissie uit dierlijke mest en kunstmest in 2009 : berekeningen met het Nationaal emissiemodel voor Ammoniak (NEMA)
Bruggen, C. van; Groenestein, C.M. ; Haan, B.J. de; Hoogeveen, M.W. ; Huijsmans, J.F.M. ; Sluis, S.M. ; Velthof, G.L. - \ 2011
Wageningen : Wettelijke Onderzoekstaken Natuur & Milieu (WOt-werkdocument 251) - 34
dieren - dierlijke meststoffen - ammoniakemissie - modellen - emissie - dierhouderij - landbouw en milieu - kunstmeststoffen - landbouwstatistieken - animals - animal manures - ammonia emission - models - emission - animal husbandry - agriculture and environment - fertilizers - agricultural statistics
De landbouw is de belangrijkste bron van ammoniak (NH3) in Nederland. De ammoniakemissie in 2009 is berekend met het Nationaal Emissiemodel voor Ammoniak (NEMA). Deze rekenmethodiek gaat bij de berekening van emissie uit stallen en mestopslagen tijdens beweiding en bij mesttoediening uit van de hoeveelheid totaal ammoniakaal stikstof (TAN) in de mest. Met het NEMA-model is de ammoniakemissie berekend voor de periode 1990-2009. De ammoniakemissie in 2009 is vrijwel gelijk aan de emissie in 2008. Sinds 1990 is de ammoniakemissie uit de landbouw met tweederde gedaald. Deze afname is voor een groot deel het gevolg van de verminderde stikstofexcretie door landbouwhuisdieren, waardoor de emissies uit stallen, mestopslagen, beweiding en mestaanwending zijn verminderd. De emissie door aanwending van dierlijke mest is met bijna 80% verminderd in 2009 ten opzichte van 1990.
Natuur in Nederland
Berendse, F. - \ 2011
Zeist : KNNV - ISBN 9789050113762 - 304
natuur - landschap - planten - dieren - beekdalen - veengebieden - polders - kustgebieden - steden - nederland - nature - landscape - plants - animals - brook valleys - peatlands - coastal areas - towns - netherlands
Dit boek presenteert in één uitgave alles wat je wilt weten over de Nederlandse natuur: planten, dieren en landschappen, samenhang en ontstaansgeschiedenis, landgebruik en wandelmogelijkheden. De auteur schreef dit boek in de traditie van de klassieker Wilde Planten. Ook hij behandelt de natuur per landschapstype. Maar hij richt zich zowel op planten als op vogels, vlinders en paddenstoelen. Er wordt een beschrijving gegeven van tien Nederlandse landschappen, van de Drentse hoogvenen tot de duinen, van de Gelderse beekdalen tot de polders en van het rivierenland tot de Limburgse heuvels. Ook de steden passeren de revue.
Gewapende vrede : beschouwingen over plant-dierrelaties
Schaminée, J.H.J. ; Janssen, J.A.M. ; Weeda, E.J. - \ 2011
Zeist : KNNV uitgeverij (Vegetatiekundige Monografieën 3) - ISBN 9789050113526 - 191
plant-dier interacties - dieren - planten - ecologie - vogels - lepidoptera - biocenose - aquatisch milieu - terrestrische ecologie - plant-animal interactions - animals - plants - ecology - birds - biocoenosis - aquatic environment - terrestrial ecology
Planten en dieren hebben elkaar nodig, maar staan ook op gespannen voet met elkaar. Dieren worden door planten aangetrokken voor bestuiving en het verspreiden van zaden, maar tegelijkertijd moeten deze laatste zich beschermen tegen overmatige vraat en fysiek geweld. Daarover gaat dit boek, een reeks beschouwingen over het fascinerende samenspel van plant en dier in de natuur. Aan bod komen onderwerpen als de relaties tussen een enkele plantensoort en zijn dierlijke partners, het functioneren van levensgemeenschappen in water of op land en de co-evolutie van grassen en grazers. Is er nog toekomst voor weidevogels in ons land en wat zal het effect zijn van klimaatverandering op onze dagvlinders? Welke methoden staan de bioloog ter beschikking om meer inzicht te verkrijgen in de samenhang tussen vegetatie en de daarvan afhankelijke fauna?
De rozeschildluis Aulacaspis rosae
Pijnakker, J. ; Leman, A. ; Ramakers, P.M.J. - \ 2011
aulacaspis rosae - rozen - cymbidium - verspreiding - wind - dieren - roses - dispersal - animals
Informatieposter over de rozeschildluis Aulacaspis rosae
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