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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An alternative bioassay for Synchytrium endobioticum demonstrates the expression of potato wart resistance in aboveground plant parts
Vossenberg, Bart van de; Gent-Pelzer, Marga van; Boerma, M. ; Gouw, Lucas P. van der; Lee, Theo van der; Vossen, Jack - \ 2019
Wageningen University and Research
PRJEB30662 - ERP113139 - Synchytrium endobioticum
The obligate biotrophic chytrid species Synchytrium endobioticum is the causal agent of potato wart disease. Currently 39 pathotypes have been described based on their interaction with a differential set of potato varieties. Wart resistance and pathotyping is performed using bioassays in which etiolated tuber sprouts are inoculated. Here we describe an alternative method in which aboveground plant parts are inoculated. Susceptible plants produced typical wart symptoms in developing, but not in fully expanded, aboveground organs. Colonization of the host by S endobioticum was verified by screening for resting spores by microscopy and by molecular techniques using TaqMan PCR and RNAseq analysis. When applied to resistant plants, none of these symptoms were detectable. Recognition of S. endobioticum pathotypes by differentially resistant potato varieties was identical in aboveground plant parts and the tuber-based bioassays. This suggests that S. endobioticum resistance genes are expressed both in etiolated “belowground” sprouts and green aboveground organs. RNAseq analysis demonstrated that the symptomatic aboveground materials contain less contaminants compared to resting spores extracted from tuber-based assays. This reduced microbial contamination in the aboveground bioassay could be an important advantage to study this obligate biotrophic plant-pathogen interaction. As wart resistance is active in both below and above ground organs, the aboveground bioassay can potentially speed up screening for S. endobioticum resistance in potato breeding programs as it omits the requirement for tuber formation. In addition, possibilities arise to express S. endobioticum effectors in potato leaves through agroinfiltration, thereby providing additional phenotyping tools for research and breeding.
An Alternative Bioassay for Synchytrium endobioticum Demonstrates the Expression of Potato Wart Resistance in Aboveground Plant Parts
Vossenberg, B.T.L.H. van de; Gent-Pelzer, M.P.E. van; Boerma, M. ; Gouw, L.P. van der; Lee, T.A.J. van der; Vossen, J.H. - \ 2019
Phytopathology 109 (2019)6. - ISSN 0031-949X - p. 1043 - 1052.
Genetics and resistance - Molecular verification - Mycology - Pathogen proliferation - Plant–pathogen interaction - RNAseq - Species richness - Techniques

The obligate biotrophic chytrid species Synchytrium endobioticum is the causal agent of potato wart disease. Currently, 39 pathotypes have been described based on their interaction with a differential set of potato varieties. Wart resistance and pathotyping is performed using bioassays in which etiolated tuber sprouts are inoculated. Here, we describe an alternative method in which aboveground plant parts are inoculated. Susceptible plants produced typical wart symptoms in developing but not in fully expanded aboveground organs. Colonization of the host by S. endobioticum was verified by screening for resting spores by microscopy and by molecular techniques using TaqMan polymerase chain reaction and RNAseq analysis. When applied to resistant plants, none of these symptoms were detectable. Recognition of S. endobioticum pathotypes by differentially resistant potato varieties was identical in axillary buds and the tuber-based bioassays. This suggests that S. endobioticum resistance genes are expressed in both etiolated “belowground” sprouts and green aboveground organs. RNAseq analysis demonstrated that the symptomatic aboveground materials contain less contaminants compared with resting spores extracted from tuber-based assays. This reduced microbial contamination in the aboveground bioassay could be an important advantage to study this obligate biotrophic plant–pathogen interaction. Because wart resistance is active in both below- and aboveground organs, the aboveground bioassay can potentially speed up screening for S. endobioticum resistance in potato breeding programs because it omits the requirement for tuber formation. In addition, possibilities arise to express S. endobioticum effectors in potato leaves through agroinfiltration, thereby providing additional phenotyping tools for research and breeding.

Tracking outbreak populations of the pepper weevil Anthonomus eugenii (Coleoptera; Curculionidae) using complete mitochondrial genomes
De Vossenberg, Bart T.L.H. Van; Warbroek, Tim ; Ingerson-Mahar, Joseph ; Waalwijk, Cees ; Gouw, Lucas P. Van Der; Eichinger, Bernadette ; Loomans, Antoon J.M. - \ 2019
PLoS ONE 14 (2019)8. - ISSN 1932-6203

The pepper weevil, Anthonomus eugenii, is a major pest on Capsicum species. Apart from natural spread, there is a risk of spread via international pepper trade. In the Netherlands, a pepper weevil outbreak occurred in 2012 and affected six greenhouses producing different sweet pepper varieties. The following year, a pepper weevil outbreak occurred in Italy. To trace the origin of the Dutch outbreak and to establish if the Dutch and Italian outbreaks were linked, we determined the mitogenomes of A. eugenii specimens collected at outbreak locations, and compared these with specimens from the native area, and other areas where the pest was introduced either by natural dispersal or via trade. The circular 17,257 bp A. eugenii mitogenome comprises thirteen mitochondrial genes typically found in insect species. Intra-species variation of these mitochondrial genes revealed four main mitochondrial lineages encompassing 41 haplotypes. The highest diversity was observed for specimens from its presumed native area (i.e. Mexico). The Dutch outbreak specimens represented three highly similar haplotypes, suggesting a single introduction of the pest. The major Dutch haplotype was also found in two specimens from New Jersey. As the Netherlands does not have pepper trade with New Jersey, it is likely that the specimens sampled in New Jersey and those sampled in the Netherlands originate from a shared source that was not included in this study. In addition, our analysis shows that the Italian and Dutch outbreaks were not linked. The mitochondrial genome is a useful tool to trace outbreak populations and the methodology presented in this paper could prove valuable for other invasive pest species, such as the African fruit moth Thaumatotibia leucotreta and emerald ash borer Agrilus planipennis.

Metaproteomic and 16S rRNA Gene Sequencing Analysis of the Infant Fecal Microbiome
Cortes, Laetitia ; Wopereis, Harm ; Tartiere, Aude ; Piquenot, Julie ; Gouw, Joost W. ; Tims, Sebastian ; Knol, Jan ; Chelsky, Daniel - \ 2019
International Journal of Molecular Sciences 20 (2019)6. - ISSN 1661-6596
fecal - infants - intestinal - mass spectrometry - metabolism - metacluster - microbiome

A metaproteomic analysis was conducted on the fecal microbiome of eight infants to characterize global protein and pathway expression. Although mass spectrometry-based proteomics is now a routine tool, analysis of the microbiome presents specific technical challenges, including the complexity and dynamic range of member taxa, the need for well-annotated metagenomic databases, and high inter-protein sequence redundancy and similarity. In this study, an approach was developed for assessment of biological phenotype and metabolic status, as a functional complement to DNA sequence analysis. Fecal samples were prepared and analysed by tandem mass spectrometry and a homology-based meta-clustering strategy was used to combine peptides from multiple species into representative proteins. In total, 15,250 unique peptides were sequenced and assigned to 2154 metaclusters, which were then assigned to pathways and functional groups. Differences were noted in several pathways, consistent with the dominant genera observed in different subjects. Although this study was not powered to draw conclusions from the comparisons, the results obtained demonstrate the applicability of this approach and provide the methods needed for performing semi-quantitative comparisons of human fecal microbiome composition, physiology and metabolism, as well as a more detailed assessment of microbial composition in comparison to 16S rRNA gene sequencing.

The landscape setting of bog bodies: Interdisciplinary research into the site location of Yde Girl, The Netherlands
Beek, R. van; Candel, J.H.J. ; Quik, C. ; Bos, J.A.A. ; Gouw-Bouman, M.T.I.J. ; Makaske, A. ; Maas, G.J. - \ 2019
Holocene 29 (2019)7. - ISSN 0959-6836 - p. 1206 - 1222.
Past studies of archaeological bog finds, such as bog bodies, wooden trackways and a wide variety of other materials, are characterized by a strong focus on material culture. Their original environmental and cultural context has received far less attention. This paper centres on the original landscape setting of bog bodies. Interdisciplinary reconstructions of the physical and cultural landscape at the time of deposition can lead to significant new and more detailed insights into the context and meaning of this remarkable phenomenon. We aim to show the value of such interdisciplinary research by reconstructing the original physical and cultural landscape setting of the most iconic bog body of The Netherlands: Yde Girl. This approximately 16-year-old girl was killed about 2000 years ago and deposited in a bog south of the modern-day village of Yde (province of Drenthe). Our interdisciplinary research team used a combination of research methods from physical geography, geomorphology, palynology and archaeology to analyse both the site itself and its wider environment. This kind of integrated, detailed landscape research on bog bodies has hardly been done yet. We expect that our research design, methodology and results may also be applied in future research of other bog bodies. Furthermore, they may inspire research on other types of archaeological find categories from peatlands.
Holocene drift-sand activity in the Netherlands
Pierik, Harm J. ; Lanen, Rowin J. van; Gouw-Bouman, Marjolein T.I.J. ; Groenewoudt, Bert J. ; Wallinga, J. ; Hoek, Wim Z. - \ 2018
drift sand activity - stuifzandvoorkomen
This dataset contains a new national overview of the occurrence of drift sand activity in the Netherlands from ca. 5000 BC to AD 1700. The dataset has been compiled from overview studies, field studies and new data.
Controls on late-Holocene drift-sand dynamics : The dominant role of human pressure in the Netherlands
Pierik, Harm J. ; Lanen, Rowin J. van; Gouw-Bouman, Marjolein T.I.J. ; Groenewoudt, Bert J. ; Wallinga, Jakob ; Hoek, Wim Z. - \ 2018
Holocene 28 (2018)9. - ISSN 0959-6836 - p. 1361 - 1381.
chronology - climate - drift-sand activity - Holocene - human impact - vegetation development

Holocene drift-sand activity in the northwest European sand belt is commonly directly linked to population pressure (agricultural activity) or to climate change (e.g. storminess). In the Pleistocene sand areas of the Netherlands, small-scale Holocene drift-sand activity began in the Mesolithic, whereas large-scale sand drifting started during the Middle Ages. This last phase not only coincides with the intensification of farming and demographic pressure but also is commonly associated with a colder climate and enhanced storminess. This raises the question to what extent drift-sand activity can be attributed to either human activities or natural forcing factors. In this study, we compare the spatial and temporal patterns of drift-sand occurrence for the four characteristic Pleistocene sand regions in the Netherlands for the period between 1000 BC and AD 1700. To this end, we compiled a new supra-regional overview of drift-sand activity based on age estimates (14C, optically stimulated luminescence (OSL), archaeological and historical ages). The occurrence of sand drifting was then compared in time and space with historical-route networks, relative vegetation openness and climate. Results indicate a constant but low drift-sand activity between 1000 BC and AD 1000, interrupted by a remarkable decrease in activity around the BC/AD transition. It is evident that human pressure on the landscape was most influential on initiating sand drifting: this is supported by more frequent occurrences close to routes and the uninterrupted increase of drift-sand activity from AD 900 onwards, a period of high population density and large-scale deforestation. Once triggered by human activities, this drift-sand development was probably further intensified several centuries later during the cold and stormier ‘Little Ice Age’ (LIA; AD 1570–1850).

Impact of dust, formaldehyde and delayed feeding after hatch
Gouw, P. de; Ven, L.F.J. van de; Lourens, A. ; Kemp, B. ; Brand, H. van den - \ 2017
Poultry World
During the hatch window the early birds are exposed up to 36 hours to the hatchers environment. Depending on circumstances dust, formaldehyde and feed deprivation negatively influences the chicks start.
Effects of dust, formaldehyde and delayed feeding on early postnatal development of broiler chickens
Gouw, P. de; Ven, L.J.F. van de; Lourens, A. ; Kemp, B. ; Brand, H. van den - \ 2017
Research in Veterinary Science 112 (2017). - ISSN 0034-5288 - p. 201 - 207.
Hatching environment - Hatch window - Chicken quality - Perinatal development - Immunological development
We investigated effects of perinatal exposure to dust or formaldehyde and the moment of first feed intake after hatching on broiler chicken development during the first week of life. Four environmental treatments were used from 468 until 512 h of incubation: control (CONT), heat treated dust (HTD), untreated dust (UTD) or formaldehyde disinfection (FORM). After hatching, all chickens were assigned to 1 of 2 feeding treatments: early feeding (EF; feed and water available in the hatcher) or delayed feeding (DF). After 512 h of incubation (day 0), chickens were reared until day 7 of age. In DF chickens, body weight (BW), yolk free body mass (YFBM) and relative liver weight did not differ among environmental treatments at day 0. However, in EF chickens BW at day 0 was greater in HTD chickens than in UTD and FORM chickens. YFBM in EF chickens at day 0 was greater when chickens were exposed to HTD compared to the other environmental treatments. In EF chickens, relative liver weight was greater in HTD chickens than in FORM. In DF chickens, BW at day 0 was positively related with hatching time (HT). In EF chickens, YFBM was positively related to HT. Residual yolk weight at day 0 was positively related with HT, whereas relative liver weight and microbicidal capacity were negatively related with HT. This study demonstrated that formaldehyde and dust during the hatching phase affect broiler chicken development at pulling from the incubator, but not at day 7.
Welfare assessment of broiler chicken flocks from different hatching systems
Jong, I.C. de; Gunnink, H. ; Gouw, P. de; Leijten, F. ; Raaijmakers, Mariël ; Zoet, Lisa ; Ven, L.J.F. van de; Brand, H. van den - \ 2016
In: Welfare quality network seminar. - Finland : University of Helsinki - 1 p.
On-farm hatching of broiler chickens is increasingly applied in The Netherlands. Eggs are transported to the farm at E18 and chicks are provided with feed and water immediately after hatching, in contrast to chickens hatched at the hatchery. The aim of the study was to assess the welfare of broilers hatched on-farm as compared to hatchery hatched broilers. Sixteen broiler flocks hatched on-farm in the X-treck system (X) were paired to 16 control flocks (C) from the same parent stock, reared in identical houses on the same farm and subjected to similar management. Welfare indicators, based on the Welfare Quality broiler assessment protocol, were measured at d21 and slaughter age. In addition, behavioural observations were carried out and technical performance was registered. Analysis of variance was used to test effects of treatment and age; data were transformed if necessary. X broilers had a lower incidence of foot pad dermatitis at d21 and at slaughter (p<0.05) and had numerically better hock burn scores at slaughter age than C broilers (P=0.56). X broilers were more dirty at d21 and at slaughter age than C broilers (p=0.08). Litter quality was better in Xhouses than in C houses at d21 (P=0.07), which seems to be in contradiction to bird cleanliness but in agreement with foot and hock scores. An age x treatment interaction was found for gait score, with X broilers having worse scores at d21 but having better scores at slaughter age than C broilers. Significant differences in behaviour were found at d21 and slaughter age, indicating that X broilers were less active than C broilers. Although technical performance of X broilers was better during the first weeks as compared to C broilers, no significant differences were found at slaughter age. This study indicates that on-farm hatching may positively affect broiler welfare.
The complete picture: combining palynological, cultural and landscape data to reconstruct palaeovegetation patterns
Beek, Roy van; Gouw-Bouman, M.T.I.J. ; Bos, J.A.A. ; Pierik, H.J. - \ 2016
Effect of hatching conditions on indicators of welfare and health in broiler chickens
Jong, I.C. de; Gunnink, H. ; Gouw, P. de; Leijten, F. ; Raaijmakers, Mariël ; Zoet, Lisa ; Wolfs, E. ; Ven, L.F.J. van de; Brand, H. van den - \ 2016
- p. 182 - 182.
On-farm hatching of broiler chickens is increasingly applied, because farmers report improved performance compared to broilers hatched at the hatchery. However, there is little scientific evidence for these effects. Aim of the study was to find evidence for long-lasting effects of hatching conditions on performance and welfare of broiler chickens. Broilers hatched at the hatchery (n=16 control flocks) or on-farm (X-treck system, n=16 flocks). Each X-treck flock was paired to a control flock from similar parent stock, reared in identical houses and subjected to similar management. In the X-treck, eggs are transferred to the stable at d18 of incubation and hatch in the stable. Chicks have immediate access to feed and water. Chicks from the hatchery received their first feed and water when they arrived at the farm. Indicators of welfare were measured at d0 (arrival of hatchery chicks), d21 and just before slaughter. Analysis of variance was used to test effects of treatment and age; data were transformed if necessary. X-treck broilers were heavier at d0 compared to control broilers (P<0.01) due to immediate access to feed and water after hatching. Quality of X-treck chicks was impaired compared to control chicks, as indicated by on average a worse navel and leg quality (P=0.01), which might be due to selection of chicks at the hatchery, which did not happen in the X-treck system. Control chicks showed a more stressful response (more vocalisations) in a novel environment test at d0 compared to X-treck chicks (P<0.01), but there were no treatment differences at d21. No treatment differences in gait score at d21 and at slaughter age were found, indicating that hatching conditions did not affect lameness. X-treck broilers had less foot pad dermatitis at d21 and slaughter age (P<0.05) and had numerically better hock burn scores at slaughter age than control broilers (P=0.56). X-treck broilers were more dirty at d21 and at slaughter age than control broilers (P=0.08). Litter quality was better in X-treck houses than in control houses, which seems to be in contradiction to bird cleanliness but in agreement with foot and hock scores. Farm records of the majority of flocks indicated a lower rejection rate at slaughter and a lower mortality for X-treck flocks compared to control flocks, although these figures need to be confirmed in the final analysis. Thus, first results of this study indicate that effects of hatching conditions on welfare of broiler chickens may indeed be long-lasting.
Environmental conditions in commercial hatcheries: consequences for broiler chicken health
Gouw, Pieter de - \ 2015
Environmental conditions in commercial hatcheries: consequences for broiler chicken health
Gouw, P. de; Ven, L.J.F. van de; Kemp, B. ; Brand, H. van den - \ 2015
In: Proceedings of the WIAS Science Day 2015 - Facing the Future. - WIAS - p. 27 - 27.
Uitbroeden op het vleeskuikenbedrijf geeft sterkere kuikens
Gouw, Pieter de - \ 2014
Environmental conditions in commercial hatcheries: consequences for broiler chicken health
Gouw, P. de; Ven, L.J.F. van de; Heetkamp, M.J.W. ; Kemp, B. ; Brand, H. van den - \ 2014
In: Proceedings of the XIVth European Poultry Conference. - - p. 470 - 470.
Effects of hatching environment on physiological and immunological developement of broiler chickens
Gouw, P. de; Ven, L.J.F. van de; Kemp, B. ; Brand, H. van den - \ 2014
In: Proceedings of the Incubation and Fertility Research Group Meeting. - - p. 5 - 5.
Effects of hatching environment on physiological and immunological developement of broiler chickens
Gouw, Pieter de - \ 2014
Environmental conditions in commercial hatcheries: consequences for broiler chicken health
Gouw, Pieter de - \ 2014
Zonder groen-blauwe samenhang geen ruimtelijke kwaliteit
Opdam, P.F.M. - \ 2006
In: Van polderen naar verbinden; de collectieve winst van vernieuwend ruimtegebruik / de Gouw, P., Hillebrand, H., Zantinge, R., Gouda : Habiforum - p. 28 - 29.
landschapsecologie - regionale planning - landscape ecology - regional planning
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