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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Three stars for animal welfare
Bos, Bram - \ 2017
animal welfare - animal production - poultry - fowls - animal housing - animal behaviour - animal health
De voordelen van integreren : Jelmer Zandbergen onderzocht voor zijn MSc studie het houden van kippen in een boomgaard
Zandbergen, Jelmer - \ 2017
Ekoland (2017)3. - ISSN 0926-9142 - p. 22 - 23.
fruitteelt - kippen - boomgaarden - biologische landbouw - pluimveehouderij - uitloop - diergedrag - fruit growing - fowls - orchards - organic farming - poultry farming - outdoor run - animal behaviour
Als onderdeel van een MSc studie Organic Agriculture aan de WUR heeft Jelmer Zandbergen een onderzoeksproject uitgevoerd op de Fruittuin van West. De Fruittuin van West is een bedrijf van 6 hectare in Amsterdam Nieuw-West, in 2014 opgezet door Wil Sturkenboom. Er worden meer dan 20 soorten fruit geteeld en er lopen kippen in de boomgaard.
Cockerels back on the menu
Leenstra, Ferry - \ 2016
animal welfare - animal production - poultry - animal ethics - fowls
Ontwikkeling pluimveehouderij met focus op dierenwelzijn - Dierenwelzijn in beeld
Ruis, M.A.W. - \ 2016
You Tube
pluimvee - dierlijke productie - dierenwelzijn - diergedrag - huisvesting, dieren - diervoeding - diergezondheid - dierethiek - domesticatie - kippen - pluimveehouderij - lesmaterialen - poultry - animal production - animal welfare - animal behaviour - animal housing - animal nutrition - animal health - animal ethics - domestication - fowls - poultry farming - teaching materials
De hedendaagse kip is ontstaan uit vier wilde rassen. Het Bankivahoen uit Zuid-Oost Azie is hiervan de belangrijkste. Vanaf 1.500 vóór Christus verspreidde het hoen zich door heel Zuid-Oost Azië, China en Japan. In Noordwest Europa is de kip vermoedelijk rond 200 voor Christus geïntroduceerd door de Grieken en Romeinen. In de jaren ’50 van de vorige eeuw werd in Nederland op grote schaal geïnvesteerd in innovaties en verschenen de grote broedmachines en de eerste volautomatische legbatterijen. Ook kwamen begin jaren ’50 verschillende ‘merken’ hybride kippen - kruisingen van zuivere lijnen of rassen - op de markt. Hieruit ontstonden de hoogproductieve leghennen en vleeskuikens.

Halverwege de jaren ’60 dringt in de maatschappij het besef door dat er weinig oog is voor het welzijn van kippen. Decennia later heeft dit geleid tot een aantal veranderingen en verboden. Vanaf 2012 is het in heel Europa verboden om leghennen in legbatterijen te houden, en het aantal vleeskuikens per vierkante meter is in Europa aan banden gelegd. Een ander voorbeeld is de aankomende plicht om leghennen, en vermeerderingsdieren voor de vleessector, met hele snavels te houden. De pluimveesector is de uitdaging aangegaan om vlees en eieren duurzamer te produceren.
Learning to live with bird flu
Bouwstra, Ruth ; Poel, Wim van der - \ 2015
animal welfare - animal production - poultry - animal health - avian influenza - fowls
Eggshell colour and disease resistance may be linked
Berghof, Tom - \ 2015
fowls - disease resistance - selection

Selection for ‘natural antibodies’ might have an effect on eggshell colour, researchers say.

Researchers at Wageningen University have found that selection for ‘natural antibodies’, a recently discovered immune characteristic, is a potential strategy to improve general disease resistance in laying hens. Selection for this immune characteristic has minimal negative consequences on production they say, but might have an effect on eggshell colour. Their findings are published in PLoS ONE and Poultry Science.

Naar gezonde kalveren en kippen
Ruis, Markus - \ 2015
calves - fowls - animal welfare - animal health - zoonoses - care of animals - animal production - poultry - cattle - animal housing
Radio en kleurige overalls helpen tegen verenpikken
Rodenburg, T.B. - \ 2015
WageningenWorld (2015)2. - ISSN 2210-7908 - p. 7 - 7.
hennen - kippen - verenpikken - diergedrag - stressfactoren - dierenwelzijn - geluiden - radio - kleur - diergezondheid - dierlijke productie - pluimvee - hens - fowls - feather pecking - animal behaviour - stress factors - animal welfare - sounds - colour - animal health - animal production - poultry
Wageningen University heeft samen met de Universiteit Utrecht en de Rijksuniversiteit Groningen manieren gevonden om verenpikken bij leghennen tegen te gaan. Dat biedt perspectief bij het verbod op snavelkappen dat in 2018 van kracht wordt.
Activation and evasion of the type I Interferon response by infectious bronchitis virus : roles of the accessory proteins
Kint, J. - \ 2015
Wageningen University. Promotor(en): Geert Wiegertjes; Huub Savelkoul, co-promotor(en): Maria Forlenza. - Wageningen : Wageningen University - ISBN 9789462573376 - 138
interferon - coronavirus - infectieus bronchitisvirus - coronaviridae - immuniteitsreactie - kippen - kippenziekten - pluimveeziekten - vaccinontwikkeling - kwantitatieve methoden - eiwit - virale inmenging - infectious bronchitis virus - immune response - fowls - fowl diseases - poultry diseases - vaccine development - quantitative methods - protein - viral interference

SUMMARY

Viruses are intracellular parasites that exploit the machinery of the host cell to replicate. To defend themselves against invading viruses, animal cells have evolved an anti-viral mechanism, known as the type I interferon response. Through natural selection viruses have in turn evolved mechanisms to counteract or evade the type I IFN response. Coronaviruses are a large group of positive-stranded RNA viruses that cause a range of human and veterinary diseases. Infectious bronchitis virus (IBV) is a member of the genus Gammacoronavirus and it is the causative agent of a highly contagious respiratory disease of poultry. To date, only few studies have investigated the interaction between IBV and the type I IFN response.

In this thesis, we describe for the first time the activation of the type I interferon response (IFN response) by the Gammacoronavirus IBV, and the repressive role of accessory proteins therein. In Chapter 1 I provide a general introduction into coronaviruses in general and the Gammacoronavirus IBV in particular. I also introduce the IFN response, and highlight differences between the mammalian and chicken IFN response. Finally, I review current knowledge on the roles of coronavirus accessory proteins in counteraction of the IFN response. In Chapter 2 we describe our studies which demonstrated that activation of the IFN response by IBV is dependent on the intracellular double-stranded RNA sensor MDA5. We show that detection of IBV-infection by MDA5 is delayed with respect to the peak of viral replication, and demonstrate that this delay is not due to inhibition of dsRNA detection by IBV. Using mutant viruses that cannot express accessory proteins (null viruses), we found that accessory proteins 3a and 3b of IBV mediate transcription and translation of Ifnβ mRNA.

The observation that IBV delays the activation of the IFN response, prompted us to investigate the sensitivity of IBV to IFN treatment in Chapter 3. Here we show that IBV is relatively resistant to treatment with type I IFN, as relatively high doses of type I IFN are required to decrease propagation of the virus. Next, we studied which viral protein(s) contribute to resistance of IBV to type I IFN and found that absence of accessory proteins 3a and 3b increased sensitivity of IBV to type I IFN, via a presently unknown mechanism. In addition, we observed that independent of accessory proteins 3a and 3b, IBV blocks signaling of IFN by inhibiting phosphorylation and translocation of the transcription factor STAT1. To explain the delayed kinetics of IFN production observed in Chapter 2, we investigated whether delayed protein production was restricted to IFN, or whether IBV, like Alpha- and Betacoronaviruses, inhibits general translation of host proteins (i.e. induces host shutoff). In Chapter 4 we demonstrate that IBV-induced transcription of Ifnβ mRNA leads to the production of relatively little IFN protein. We discovered that limited production of IFN protein by IBV-infected cells is the result of general inhibition of host translation, confirming that IBV induces a shutoff of host-protein production. This finding indicates that evasion of the innate immune system by Gammacoronaviruses may be more similar to that of Alpha- and Betacoronaviruses than previously thought. Using accessory protein null viruses we discovered that accessory protein 5b of IBV is essential for the inhibition of host-protein synthesis by IBV. In Chapter 5 and Chapter 6 we describe the methods used in this thesis to quantify the number of infectious virus particles of IBV as well as methods used to quantify the activation of the type I IFN response in chicken cells. Although the studies described in this thesis have answered several questions about the interaction of IBV with the type I IFN response of its host, they have also raised new questions to be addressed in future research. In the final Chapter of this thesis (Chapter 7), I discuss a number of remaining questions and future perspectives regarding evasion of the IFN response by IBV. Finally, I explore the possible implications of our findings on the in vivo pathogenicity of IBV and on the rational design of attenuated IBV vaccines.

In conclusion, the work described in this thesis demonstrates for the first time how IBV evades, activates, and antagonises the IFN response. Also, this thesis comprises the first study that describes a function for the accessory proteins of IBV and shows that these poorly understood proteins play an important role in antagonism of the type I IFN response.

Genetic improvement in indigenous chicken of Ethiopia
Woldegiorgiss, W.E. - \ 2015
Wageningen University. Promotor(en): Johan van Arendonk, co-promotor(en): Liesbeth van der Waaij; T. Dessie. - Wageningen : Wageningen University - ISBN 9789462573161 - 130
kippen - pluimvee - inheems vee - genetische verbetering - houding van boeren - perceptie - kippenrassen - prestatieniveau - dierveredeling - ethiopië - fowls - poultry - native livestock - genetic improvement - farmers' attitudes - perception - fowl breeds - performance - animal breeding - ethiopia

Abstract

Wondmeneh Esatu Woldegiorgiss (2015). Genetic improvement in indigenous chicken of Ethiopia. PhD thesis, Wageningen University, the Netherlands

This thesis considered various approaches to study the potential for improvement of village poultry production system using improved indigenous chicken. The approaches were structured survey questionnaire, village poultry simulation model (VIPOSIM), Heckman two-step model (econometric model), and experiments involving laboratory and field. First factors that determine the probability and intensity of adoption of exotic chickens were assessed. The probability of adopting exotic chickens was found to be positively affected by access to an off-farm income and negatively by livestock income. The intensity of adoption was negatively affected by being male household head, having a larger farm size, and having livestock income. Then, perceptions of farmers towards village poultry and impacts of interventions on flock and economic performance were assessed. Farmers’ perceptions affected their decisions about implementation of interventions, and interventions increased productivity but only in a few cases the increased revenues outweighed the additional costs. Subsequently, the evaluation of the breeds was conducted by comparing the natural antibody and productivity of improved indigenous chicken with crossbred, commercial and unimproved indigenous chickens. The results revealed that not only the NAb levels but also the effect of NAbs on survival differ between indigenous and improved breeds. NAb levels are associated with survival in commercial layer breed, but reduced survival in indigenous chickens placed in confinement. Improved indigenous chickens showed higher performance than unimproved one for all traits measured on-station, but remains lighter and developed more into a laying type than meat through the short-term selective breeding program. Overall, the present studies indicate that interventions need to be tailored towards the local situation to ensure that they lead not only to improved productivity but also to improved income.

Breeding program for indigenous chicken in Kenya
Ngeno, K. - \ 2015
Wageningen University. Promotor(en): Johan van Arendonk, co-promotor(en): Liesbeth van der Waaij; A.K. Kahi. - Wageningen : Wageningen University - ISBN 9789462572775 - 154
kippen - pluimvee - inheems vee - dierveredeling - veredelingsprogramma's - genetische diversiteit - ecotypen - genomen - genetische verbetering - kenya - fowls - poultry - native livestock - animal breeding - breeding programmes - genetic diversity - ecotypes - genomes - genetic improvement

Abstract

Ngeno, K. (2015). Breeding program for indigenous chicken in Kenya. Analysis of diversity in indigenous chicken populations. PhD thesis, Wageningen University, the Netherlands

The objective of this research was to generate knowledge required for the development of an indigenous chicken (IC) breeding program for enhanced productivity and improved human livelihood in Kenya. The initial step was to review five questions; what, why and how should we conserve IC in an effective and sustainable way, who are the stakeholders and what are their roles in the IC breeding program. The next step of the research focused on detecting distinctive IC ecotypes through morphological and genomic characterization. Indigenous chicken ecotypes were found to be populations with huge variability in the morphological features. Molecular characterization was carried out using microsatellite markers and whole genome re-sequenced data. The studied IC ecotypes are genetically distinct groups. The MHC-linked microsatellite markers divided the eight IC ecotypes studied into three mixed clusters, composing of individuals from the different ecotypes whereas non-MHC markers grouped ICs into two groups. Analysis revealed high genetic variation within the ecotype with highly diverse MHC-linked alleles which are known to be involved in disease resistance. Whole genome re-sequencing revealed genomic variability, regions affected by selection, candidate genes and mutations that can explain partially the phenotypic divergence between IC and commercial layers. Unlike commercial chickens, IC preserved a high genomic variability that may be important in addressing present and future challenges associated with environmental adaptation and farmers’ breeding goals. Lastly, this study showed that there is an opportunity to improve IC through selection within the population. Genetic improvement utilizing within IC selection requires setting up a breeding program. The study described the systematic and logical steps in designing a breeding program by focusing on farmers’ need, how to improve IC to fit the farming conditions, and management regimes.

IAG ring test feed composition 2014
Raamsdonk, L.W.D. van; Pinckaers, V.G.Z. ; Vliege, J.J.M. - \ 2014
Wageningen : RIKILT Wageningen UR (RIKILT report 2014.010) - 21
voersamenstelling - pluimveevoeding - ringtest - microanalyse - microscopie - kippen - feed formulation - poultry feeding - ring test - microanalysis - microscopy - fowls
A ring test was organized for the microscopic determination of composition in animal feed in the framework of the annual ring tests of the IAG – International Association for Feeding stuff Analysis, Section Feeding stuff Microscopy. The aim of the ring study was to provide the participants information on the performance of the local implementation of the method for composition analysis of feed.
The Isolated Chicken Eye test to replace the Draize test in rabbits : from development to implementation: “The long and winding road”
Prinsen, M.K. - \ 2014
Wageningen University. Promotor(en): Ruud Woutersen; C.F.M. Hendriksen, co-promotor(en): C.A.M. Krul. - Wageningen : Wageningen University - ISBN 9789462570030 - 184
ogen - konijnen - kippen - laboratoriumdieren - alternatieven voor dierproeven - dierproeven - toxiciteit - toxicologie - histopathologie - dierenwelzijn - eyes - rabbits - fowls - laboratory animals - animal testing alternatives - animal experiments - toxicity - toxicology - histopathology - animal welfare
Dit proefschrift beschrijft de ontwikkeling, optimalisatie, validatie (binnen TNO) en toepassing van een alternatieve test met geïsoleerde ogen van kippen (de Isolated Chicken Eye, kortweg de ICE test) en in bredere zin de internationale validatie en acceptatie van de ICE test door overheidsinstanties.
Offspring sex ratio bias and sex related characteristics of eggs in chicken
Aslam, M.A. - \ 2014
Wageningen University. Promotor(en): Mari Smits; T.G.G. Groothuis, co-promotor(en): Henri Woelders. - Wageningen : Wageningen University - ISBN 9789462570757 - 192
kippen - eieren - geslachtsverhouding - karakteristieken - nageslacht - toewijzing - polymerase-kettingreactie - hormonen - voedselbeperking - dierveredeling - fowls - eggs - sex ratio - characteristics - progeny - allocation - polymerase chain reaction - hormones - food restriction - animal breeding

Understanding the factors influencing sex of egg and sex ratio in laying chicken may lead to finding potential solutions for the problem of killing of day old male chicks, which is the current practice in breeding of laying hens. In studies described in this thesis, it was investigated if the sex of the chicken egg can be predicted by measurable differences in male and female eggs at unincubated stage and if the female primary sex ratio can be induced in laying chicken using different experimental conditions such as feed restriction and corticosterone feeding. The method of sex determination in unincubated chicken eggs using PCR targeted to CHD1 gene was first developed. This method was subsequently used to study the primary sex ratio bias as well as relationship between egg sex and yolk hormones. No significant relationship of the sex of egg with concentrations of several hormones (testosterone, estradiol, androstenedione, progesterone, dihydrotestosterone) and glucose in yolk as well as of egg parameters (mass, width and length) was found. Effect of feed availability on sex ratio was tested in two separate studies. In one study, the rate of change of hen body mass between day of laying and day of laying minus 2 days (encompass time of meiosis completion) was a significant predictor for the sex of that egg, suggesting meiotic drive as mechanism of sex ratio bias. This relationship was not found in the later study. The difference in results could be due to the reason that hens decreased in body mass much less in the later study as compared to earlier study. Blood corticosterone concentrations were associated with sex ratio per hen in the earlier study. Effect of egg mass on egg sex was studied during the later experiment of feed restriction. The egg sex ratio per hen was negatively associated with the average egg mass per hen in the feed restriction group. Two groups of hens were selected from the feed restriction group i.e. male biased hens with low egg mass and female biased hens with high egg mass for microarray analysis of gene expression in the germinal disc of collected F1 follicle. The results did not show differential expression of genes between the groups. However, gene set enrichment analysis showed that a number of processes related to cell cycle progression, mitotic/meiotic apparatus and chromosomal movement were differently enriched between the groups, supporting meiotic drive as potential mechanisms underlying sex ratio determination. In another experiment, blood circulating levels of corticosterone in hens were increased by feeding corticosterone mixed feed under ad libitum. The blood levels of corticosterone were significantly higher in treated hens but these levels were not associated with sex ratio. Treatment did not affect the overall sex ratio, but affected the sex ratio in interaction with hen body mass. In the corticosterone group, sex ratio, laying rate, and fertility rate per hen were decreased in heavy hens. These results suggest that three parameters (sex ratio, laying rate and fertility rate) are connected at the level of ovarian physiology. Interference with meiosis have been shown to affect these three parameters, suggesting the involvement of meiotic drive as mechanism of sex ratio bias.

Laag pathogene aviaire influenza virus infecties op pluimveebedrijven in Nederland
Goot, J.A. van der; Verhagen, J. ; Gonzales, J. ; Backer, J.A. ; Bongers, J.H. ; Boender, G.J. ; Fouchier, R.A.M. ; Koch, G. - \ 2013
Tijdschrift voor Diergeneeskunde 138 (2013)6. - ISSN 0040-7453 - p. 24 - 27, 29.
pluimveehouderij - pluimveeziekten - aviaire influenza - hennen - kippen - ziekte-incidentie - huisvesting, dieren - agrarische productiesystemen - uitloop - risicofactoren - poultry farming - poultry diseases - avian influenza - hens - fowls - disease incidence - animal housing - agricultural production systems - outdoor run - risk factors
Dit artikel is een samenvatting van het rapport "Laag pathogene aviaire influenza virus iInfecties op pluimveebedrijven in Nederland" (CVI 2012). Dit rapport is geschreven naar aanleiding van vragen van het toenmalige Ministerie van Economische zaken, Landbouw en Innovatie. De vragen die werden gesteld zijn: - hebben pluimveebedrijven met vrije uitloop een grotere kans op introductie van LPAI virus infecties?; - is de kans op introductie gerelateerd aan wilde vogels?; - is er een periode in het jaar waarin het risico op infectie groter is? - kunnen er factoren geidentificeerd worden die de kans op introductie verminderen?
Multistage carbon dioxide gas stunning of broilers
Gerritzen, M.A. ; Reimert, H.G.M. ; Hindle, V.A. ; Verhoeven, M.T.W. ; Veerkamp, W.B. - \ 2013
Poultry Science 92 (2013). - ISSN 0032-5791 - p. 41 - 50.
behavioral-responses - gaseous stimulation - chickens - mixtures - welfare - euthanasia - exposure - aversion - fowls
The stunning quality of animals for slaughter remains under constant scrutiny. In response to previous research showing low stunning efficiency in poultry, the conventional water bath will be phased out in the Netherlands. Presently, the main practical alternative to water bath stunning of poultry is a 2-phased gas stunning method. Gas stunning methods are recognized by governments and animal welfare organizations across Europe. In this study, 3 sets of experiments were conducted on gas stunning methods using CO2 in 2 phases. Two methods were examined to identify potential effects on bird behavior and investigate their practical implications: a 5-stage incremental CO2 scheme lasting 6 min (treatment 1) and a 4-stage incremental CO2 scheme lasting 4 min (treatment 2). The onset and duration of unconsciousness were specifically tested in experiment 2 by using 25 birds equipped with electrodes monitoring brain and heart activity. Behavioral responses were observed on 15 non-instrument-monitored birds kept in the same cages at that time. Results in all 3 sets of the experiments showed that multistage gas stunning was stable and consistent, and increases in CO2 concentrations were rapid and reliable. Ambient temperatures and RH of the air remained within acceptable levels at all times. Induction of unconsciousness occurred below 40% CO2 and did not significantly differ between treatments. Conscious birds were never exposed to high CO2 concentrations (>40% CO2), yet some birds showed signs of distress (e.g., head shaking, wing flapping) before losing consciousness. Discomfort experienced during exposure to low (
Laying hens : a practical guide for layer focused management
Bestman, M.W.P. ; Ruis, M.A.W. - \ 2012
Zutphen [etc.] : Roodbont [etc.] (Poultry signals ) - ISBN 9789087401245 - 119 p.
dierlijke productie - pluimvee - hennen - kippen - dierenwelzijn - diergezondheid - huisvesting, dieren - pluimveehouderij - animal production - poultry - hens - fowls - animal welfare - animal health - animal housing - poultry farming
Maatregelen t.b.v. een betere groei van opfokhennen
Wagenaar, J.P. ; Verwer, C. - \ 2012
Wageningen : Wageningen UR - 31 p.
hennen - kippen - pluimveehouderij - biologische landbouw - stress - vaccinatie - dierenwelzijn - pluimvee - dierlijke productie - hens - fowls - poultry farming - organic farming - vaccination - animal welfare - poultry - animal production
In dit project is gekeken welke maatregelen genomen kunnen worden om de groei van biologische opfokhennen te verbeteren, gegeven een huidig toegepast vaccinatieschema. Het gaat hierbij om maatregelen die al toegepast worden en om nieuwe maatregelen die in potentie een positief effect op de groei en ontwikkeling van opfokhennen hebben. Naast een literatuurstudie is ook samen met de praktijk gekeken naar geschikte maatregelen.
Moederlijk testosteron in eierdooiers
Slijkhuis, H. - \ 2012
Kleindier magazine 126 (2012)5. - p. 57 - 58.
pluimvee - kippen - testosteron - pluimveehouderij - poultry - fowls - testosterone - poultry farming
In 1993 ontdekten onderzoekers in de dooier van eieren van vogels een goed te metem hoeveelheid van het hormoon testosteron.
Chicken intestinal development in health and disease : transcriptomic and modeling approaches
Schokker, D.J. - \ 2012
Wageningen University. Promotor(en): Mari Smits, co-promotor(en): Annemarie Rebel. - S.l. : s.n. - ISBN 9789462575325 - 225
fowls - intestines - biological development - gene expression - transcriptomics - animal health - poultry diseases - intestinal physiology - immunology - mathematical models - kippen - darmen - biologische ontwikkeling - genexpressie - transcriptomica - diergezondheid - pluimveeziekten - darmfysiologie - immunologie - wiskundige modellen

Intestinal health is an important condition for sustainable animal production. Since it is known that there is significant variation in intestinal health and functionality, there is much to gain in this respect. However, to fully exploit the biological potential of the animal’s gastro-intestinal tract, the mechanism and regulation of major intestinal processes need to be unraveled first. In addition, identification of key components and processes involved in intestinal adaptation mechanisms may help to identify internal and external factors that influence the health and functioning of the gut. Improved knowledge in this area may contribute in defining rational strategies to improve sustainable animal production.
Traditionally research used reductionist approaches and focused on specific components or isolated processes related to intestinal functioning. However, the recent developments in the areas of genomics and computational sciences provide tools and methods that allow studying the system of the gut as a whole. In this thesis we have set first steps in the use of such Systems Biology approaches towards the identification of the key components and processes involved in intestinal functioning and health. We investigated molecular processes associated with gut development in chickens under two extreme contrasting conditions. We used an infection with Salmonella immediately after hatch and control animals to create the two contrasting phenotypic conditions. We used microarray-based genome-wide mRNA profiling to identify patterns of gene expression and cellular processes associated with each conditions. Comparisons between the two conditions and the application of modeling approaches revealed genes, groups of genes, molecular pathways, gene networks, and high level regulators of system behavior. We also used a mathematical modeling approach to describe the dynamics of cellular components of the immune system and their corresponding interactions under the same two contrasting conditions.
We identified different temporal gene expression profiles associated with morphological, functional and immunological processes. Several of these processes differed between the two contrasting conditions, whereas others were not affected be the experimental treatments. By inferring gene association networks, we observed that an infection with Salmonella considerably changes the behavior of intestinal tissue as well as the regulation of the underlying molecular processes. For each contrasting condition, we identified a specific set of potential high-level regulator genes (hubs). We hypothesize that these hubs are steering systems behavior. Bioinformatic analysis of the hubs suggested that the disturbance with Salmonella is associated with a shift from transcriptional regulation in the non-disturbed tissue to cell-cell communication in the disturbed tissue. Furthermore, the generated mathematical model describes the dynamics of the cellular components of the immune system as well as the dynamics of the invading pathogen well. The model was able to predict the cellular immune response of the host against an invading pathogen.
We developed basic knowledge of (molecular) processes that are associated with different physiological conditions of intestinal tissue and we acquired global views on adaptation mechanisms of the intestine, including the regulation thereof. This information can be used to formulate new hypotheses about behavioral aspects of the gut, for the discovery of new biological mechanisms, and ultimately for the development of tools and rational strategies to improve intestinal functionality and health, either via diet and/or the host genotype. Such developments are urgently required to diminish the incidence and impact of intestinal diseases in farm animal species and to reduce the use of antibiotics in animal husbandry.

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