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.

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Betekenis van greppel plas-dras als habitat voor weidevogelkuikens
Visser, Tim ; Melman, T.C.P. - \ 2018
De Levende Natuur 119 (2018)3. - ISSN 0024-1520 - p. 114 - 118.
Ontwatering in de agrarische bedrijfsvoering is één van de grootste hinderpalen voor het habitat van weidevogels. Zou het op kleine schaal creëren van vochtige/natte omstandigheden hiervoor een oplossing kunnen zijn, bijvoorbeeld in de vorm van ‘greppel plas-dras’. Dit artikel beschrijft de resultaten van onderzoek in de Eempolders naar het effect van greppel plas-dras op de kwaliteit van het grasland als foerageerhabitat voor weidevogelkuikens, aan de hand van de biomassa, openheid (doorwaadbaarheid) en structuurvariatie van de vegetatie, de insectenrijkdom en de mate waarin weidevogelgezinnen gebruik maken van percelen met een greppel plas-dras.
Mitochondrial dynamics in cancer-induced cachexia
Ende, Miranda van der; Grefte, Sander ; Plas, Rogier ; Meijerink, Jocelijn ; Witkamp, Renger F. ; Keijer, Jaap ; Norren, Klaske van - \ 2018
Biochimica et Biophysica Acta - Reviews on Cancer 1870 (2018)2. - ISSN 0304-419X - p. 137 - 150.
Animal models - Cancer-induced cachexia - Mitochondria - Mitochondrial dynamics - Muscle

Cancer-induced cachexia has a negative impact on quality of life and adversely affects therapeutic outcomes and survival rates. It is characterized by, often severe, loss of muscle, with or without loss of fat mass. Insight in the pathophysiology of this complex metabolic syndrome and direct treatment options are still limited, which creates a research demand. Results from recent studies point towards a significant involvement of muscle mitochondrial networks. However, data are scattered and a comprehensive overview is lacking. This paper aims to fill existing knowledge gaps by integrating published data sets on muscle protein or gene expression from cancer-induced cachexia animal models. To this end, a database was compiled from 94 research papers, comprising 11 different rodent models. This was combined with four genome-wide transcriptome datasets of cancer-induced cachexia rodent models. Analysis showed that the expression of genes involved in mitochondrial fusion, fission, ATP production and mitochondrial density is decreased, while that of genes involved ROS detoxification and mitophagy is increased. Our results underline the relevance of including post-translational modifications of key proteins involved in mitochondrial functioning in future studies on cancer-induced cachexia.

Greppel plas-dras voor weidevogels : betekenis als habitatonderdeel voor weidevogelkuikens
Visser, Tim ; Melman, Dick ; Buij, Ralph ; Schotman, Alex - \ 2017
Wageningen : Wageningen Environmental Research (Wageningen Environmental Research rapport 2845) - 67
Welke waarde hebben percelen met greppel plas-dras voor kuikens van de grutto?
Land reform in South Africa : Beneficiary participation and impact on land use in the Waterberg District
Netshipale, Avhafunani J. ; Oosting, Simon J. ; Raidimi, Edzisani N. ; Mashiloane, Majela L. ; Boer, Imke J.M. de - \ 2017
NJAS Wageningen Journal of Life Sciences 83 (2017). - ISSN 1573-5214 - p. 57 - 66.
Beneficiary participation - Change in policy - Land reform - Land use - South Africa
National challenges of food insecurity and unemployment in South Africa prompted an increase in expectations for agricultural land acquired through land reform programmes to make meaningful contributions. Embedded in these expectations is the need for understanding the situation in reformed farms. This study reviewed policies and literature on land reform, and analyzed beneficiary participation in reformed farms and the impact of land reform on land use in land restitution and land redistribution farms in the Waterberg District Municipality. Data were collected through individual surveys, key informants interviews and stakeholder workshop. Beneficiary participation levels were significantly lower in restitution farms (18% per farm) than in redistribution farms (65% per farm). The changes in land redistribution policy over time resulted in significant differences in beneficiary participation among land redistribution models, with participation levels increasing with time. Land redistribution model SLAG had the lowest beneficiary participation level (19% per farm) while the latest model PLAS had the highest (100% per farm). The changes in land redistribution policy over time resulted in significant differences in extent of land used among land redistribution models, though the trend was not systemic. On average, redistribution farms under SLAG and LRAD2 models used ≤70% of the farm land, while farms under LRAD1 and PLAS models used more than 90% of the farm land. The research approach used in this study found similar results in beneficiary participation to those in literature where case studies approach was used in restitution farms. On the contrary, in redistribution farms the research approach resulted in findings that differed from case study literature and revealed the needs for representative sample and time if conclusive recommendations were to be reached.
Hoe de Plas van Bruil zichzelf reguleert
Duineveld, Martijn - \ 2017
Plasmodel voorspelt ammoniakemissie van vloer
Snoek, J.W. - \ 2016
Agrabeton (2016). - ISSN 0167-3246
ammoniakemissie - plasmodel - stalvloer
Onderzoeker Dennis Snoek van Wageningen UR heeft een model ontwikkeld waarmee bepaald kan worden wat de invloed is van de urineplas op de ammoniakemissie van een nieuwe stalvloer voor melkkoeien.

01 plasmodel2
Voor de ontwikkeling van het plasmodel wordt gebruik gemaakt van een thermische camera.

01 plasmodel
De thermische camera laat ook zien hoe snel de urine op de vloer wordt afgevoerd.

De urineplas is het belangrijkste onderdeel in het huidige ammoniakemissiemodel. Het plasmodel van Snoek is een methode om invulling te geven aan de variabele 'plasoppervlakte' in dit ammoniakemissiemodel.
Voor de ontwikkeling van het plasmodel wordt gebruik gemaakt van een thermische camera. De camera laat zien hoe groot de warme plas is direct na het urineren en laat ook zien hoe snel de urine op de vloer wordt afgevoerd. Aan de hand hiervan is te bepalen in welke mate een stalvloer kan bijdragen aan het beperken van de ammoniakemissie. Immers, hoe sneller de urine wordt afgevoerd, hoe minder de urine zal reageren met de vaste mest en hoe minder ammoniakvorming er optreedt op het vloeroppervlak.

Snel resultaat

Het voordeel van het plasmodel is dat er al een meetstrategie ontwikkeld kan worden voor het bestaande ammoniakemissiemodel voordat de stal gebouwd is. Nu worden er proefstallen gebouwd en geldt er een uitgebreid jaarrond meetprotocol waarbij de binnenkomende en uitgaande stallucht worden gemeten. Onderzoeker Snoek denkt dat een kleine proeflocatie de beste optie is om nieuwe vloertypen te testen en te vergelijken voordat er een volledig proefstal gebouwd wordt.
Naast de plasoppervlakte heeft Snoek ook meetmethoden ontwikkeld voor andere invoervariabelen in het ammoniakemissiemodel, zoals: urine pH, plasdikte en urine-ureum. Uiteindelijk wil de onderzoeker een meetmodel ontwikkelen dat een combinatie is van het bestaande ammoniakemissiemodel en de ontwikkelde nieuwe meetstrategie.
Zodra een proefstal gebouwd is, kan de nieuw ontwikkelde meetmethode toegepast worden om op korte termijn inzicht te krijgen in de daadwerkelijke ammoniakemissie. Dit is in principe al mogelijk nog voordat er aan de huidige minimum koebezetting wordt voldaan. De resultaten kunnen snel beschikbaar zijn.

Lagere kosten

Bijkomend voordeel is dat de kosten van het meten aanzienlijk beperkt kunnen worden. Op dit moment kost het meten van een vloer tussen de 50 tot 100 duizend euro. Meten volgens het plasmodel zal deze kosten aanzienlijk reduceren. Snoek rondt zijn promotieonderzoek in oktober 2016 af. Hierna wil hij zijn opgedane ervaring en kennis openbaar maken zodat producenten van welzijnsvloeren en andere stallenbouwers hier gebruik van kunnen maken.
Biological control of fireblight of apple by combined application of two phages.
Köhl, J. ; Plas, C.H. ; Molhoek, W.M.L. ; Hagens, S. ; Nuboer, W. ; Wolf, J.M. van der - \ 2016
A full-body transcriptome and proteome resource for the European common carp
Kolder, I.C.R.M. ; Plas-Duivesteijn, S.J. van der; Tan, G. ; Wiegertjes, G.F. ; Forlenza, M. ; Guler, A.T. ; Travin, D.Y. ; Nakao, M. ; Moritomo, T. ; Irnazarow, I. ; Dunnen, J.T. den; Anvar, S.Y. ; Jansen, H.J. ; Dirks, R.P. ; Palmblad, M. ; Lenhard, B. ; Henkel, C.V. ; Spaink, H.P. - \ 2016
BMC Genomics 17 (2016)1. - ISSN 1471-2164
Cyprinus carpio - Genome - Proteomics - RNA-Seq - Transcriptomics tissue-specific expression

Background: The common carp (Cyprinus carpio) is the oldest, most domesticated and one of the most cultured fish species for food consumption. Besides its economic importance, the common carp is also highly suitable for comparative physiological and disease studies in combination with the animal model zebrafish (Danio rerio). They are genetically closely related but offer complementary benefits for fundamental research, with the large body mass of common carp presenting possibilities for obtaining sufficient cell material for advanced transcriptome and proteome studies. Results: Here we have used 19 different tissues from an F1 hybrid strain of the common carp to perform transcriptome analyses using RNA-Seq. For a subset of the tissues we also have performed deep proteomic studies. As a reference, we updated the European common carp genome assembly using low coverage Pacific Biosciences sequencing to permit high-quality gene annotation. These annotated gene lists were linked to zebrafish homologs, enabling direct comparisons with published datasets. Using clustering, we have identified sets of genes that are potential selective markers for various types of tissues. In addition, we provide a script for a schematic anatomical viewer for visualizing organ-specific expression data. Conclusions: The identified transcriptome and proteome data for carp tissues represent a useful resource for further translational studies of tissue-specific markers for this economically important fish species that can lead to new markers for organ development. The similarity to zebrafish expression patterns confirms the value of common carp as a resource for studying tissue-specific expression in cyprinid fish. The availability of the annotated gene set of common carp will enable further research with both applied and fundamental purposes.

Differentiating samples and experimental protocols by direct comparison of tandem mass spectra
Plas-Duivesteijn, Suzanne J. Van Der; Wulff, Tune ; Klychnikov, Oleg ; Keijzer, Jeroen De; Nessen, Merel A. - \ 2016
Rapid Communications in Mass Spectrometry 30 (2016)6. - ISSN 0951-4198 - p. 731 - 738.

Rationale Peptide tandem mass spectra can be analyzed by a number of means. They can be compared against predicted spectra of peptides derived from genome sequences, compared against previously acquired and identified spectra, or - sometimes - sequenced de novo. We recently introduced another method which compares spectra between liquid chromatography/tandem mass spectrometry (LC/MS/MS) datasets to determine the shared spectral content, and demonstrated how this can be applied in a molecular phylogenetic study using sera from human and non-human primates. We will here explore if such a method have other, serendipitous uses. Methods We used the existing compareMS2 algorithm without modification on a diverse set of experiments. Results First we conducted a small phylogenetic study, using (mammalian) bone samples to study old material, and human pathogens aiming to distinguish clinically important strains. Although not as straightforward as primate sera analysis, the method shows significant promise for all these applications. We also used the algorithm to compare 24 different protocols for extraction of proteins from muscle tissue. The results provided useful information in comparing protocols. Finally, we applied compareMS2 aiming for quality control of two traceable protein reference standards (troponin) used in clinical chemistry assays, by analysing the effect of storage conditions. Conclusions The results illustrate a broad applicability of the metric based on shared tandem mass spectra between LC/MS/MS datasets for analysing protein digests in different types of experiments. There is no reason to assume that our instance of this method is optimal in any of these situations, as it makes limited or no use of accurate mass and chromatographic retention time. We propose that with further improvement and refinement, this type of analysis can be applied as a simple but informative first step in many pipelines for bottom-up tandem mass spectrometry data analysis in proteomics and other fields, comparing or analysing large numbers of samples or datasets.

Nu al 'wolken' muggen gesignaleerd bij plas Cattenbroek
Vliet, Arnold van - \ 2015
Nu al 'wolken' muggen gesignaleerd bij plas Cattenbroek
Vliet, Arnold van - \ 2015
Inoculum sources of the post-harvest pathogens Neofabraea spp. and Cadophora spp. in Dutch apple and pear orchards
Köhl, J. ; Wenneker, M. ; Haas, L. de; Anbergen, R.H.N. ; Plas, C.H. ; Kastelein, P. - \ 2015
Optimaliseren herinrichting van diepe plassen : Technisch achtergronddocument bij de MCA Verondiepen, een multicriteria-instrument om locatiekeuze en inrichtingsvariant te optimaliseren
Lange, H.J. de; Gylstra, R. ; Huijsmans, T. ; Huijsmans, T. ; Sluiter, H. ; Timmermans, F. ; Besse-Lototskaya, A.A. ; Brink, N.W. van den - \ 2015
Alterra, Wageningen-UR (Stowa rapport 2015-40) - 48 p.
plassen - zandafgravingen - publieke participatie - baggerspeciedepots - natuurontwikkeling - waterkwaliteit - ponds - sand pits - public participation - spoil banks - nature development - water quality
Het nuttig toepassen van grond of baggerspecie kan als kans worden gezien in gebiedsontwikkeling of natuurontwikkeling in en rond een diepe plas. Om een optimale keuze voor inrichting en functie te kunnen maken, moeten verschillende aspecten worden afgewogen. Hiervoor is de MCA Verondiepen ontwikkeld, een multicriteria-instrument om stakeholders op een gestructureerde wijze een analyse te kunnen doen van de huidige functie en kwaliteit, impact van herinrichting, en mogelijke nieuwe functie en kwaliteit. De toepassing van de MCA Verondiepen wordt geïllustreerd aan de hand van verschillende praktijkvoorbeelden. Dit document bevat achtergrondinformatie bij een excelinstrument.
Inoculum sources of the post-harvest pathogens Neofabraea spp. and Cadophora spp. in Dutch apple and pear orchards
Köhl, J. ; Wenneker, M. ; Haas, B.H. de; Anbergen, R.H.N. ; Plas, C.H. ; Kastelein, P. - \ 2015
Post-harvest diseases of apple and pear cause significant economic losses during long storage. Quiescent infections by fungal
pathogens such as Neofabraea alba, N. perennans, Neonectria galligena, Phytophthora spp., Alternaria spp., Fusarium spp.,
Cadophora spp. and Stemphylium vesicarium can occur in Dutch orchards and lead to post-harvest fruit rots in storage.
Knowledge on the occurrence of the different post-harvest diseases and their epidemiology is very limited. The objective of the
study was to identify the inoculum sources of main post-harvest pathogens and to gain insight into their population dynamics.
Samples of various necrotic residues and tree parts were collected in 10 apple and 10 pear orchards during the growing season
2012 monthly from May until September and in December from 4 replicate plots in each orchard. Species-specific primers and
probes were developed for N. alba, N. perennans and C. luteo-olivacea. TaqMan-PCR assays were used to quantify the amount
of DNA of each of the three pathogens in the environmental samples from the orchards.
N. perennans was found only in few samples whereas N. alba and C. luteo-olivacea were abundantly present on necrotic tissues
of apple and pear such as mummies, cankers and dead leaves. Interestingly, these pathogens were also found in varying
amounts on necrotic tissues of other plant species present on the orchard floors such as various weeds and grasses. The
concentration of pathogen DNA in the various substrate types varied during the growing season. Population dynamics also
differed between individual orchards indicating that orchard characteristics and management strategies may influence the
development of the pathogen populations.
The new knowledge on the major inoculum sources of fruit rot pathogens in apple and pear orchards is essential for the
development of preventative sanitation measures which reduce the risk of pre-harvest infections by the pathogens followed by
post-harvest losses. The inoculum load can be reduced by physical removal of the sources, enhancing decomposition or
application of competitive biological control agents. The new knowledge on the variation of populations dynamics between but
also within orchards can be used to identify major factors affecting pathogen survival and multiplication during the growing
season.
Editorial: Ever-growing data sets pose (new) challenges to genomic prediction models
Calus, M.P.L. ; Plas, J. van den; Napel, J. ten - \ 2015
Journal of Animal Breeding and Genetics 132 (2015)6. - ISSN 0931-2668 - p. 407 - 408.
Alg groeit goed op plas en poep van NIOO
Sikkema, A. ; Lamers, P.P. - \ 2015
Resource: weekblad voor Wageningen UR 10 (2015)8. - ISSN 1874-3625
afvalwater - afvalwaterbehandeling - nieuwe sanitatie - biobased economy - algen - chlorella sorokiniana - organische meststoffen - algenteelt - waste water - waste water treatment - new sanitation - algae - organic fertilizers - algae culture
Chlorella sorokiniana reinigt geconcentreerd wc-water. Resultaat: schoon water én meststof
Effects of Land Redistribution on Land Entitlement and Use in Limpopo Province, RSA
Netshipale, A.J. ; Oosting, S.J. ; Raidimi, E.N. ; Mashiloane, M.L. ; Boer, I.J.M. de - \ 2015
In: Book of Abstracts Tropentag: Management of land use systems for enhanced food security. - - p. 36 - 36.
Four models of the South African land redistribution programme were distinguishable i.e. model A (SLAG: 1995 – 2000), model B (LRAD1: 2001 – 2007), model C (LRAD2: 2008 – 2010) and model D (PLAS: 2006 to 2012). The models differed in emphasis given to social and economic objectives of land reform, which was influenced by the national needs at the time of model conceptualization and implementation. The earlier model, SLAG, was social oriented while the later models had economic viability as the main objective. This study investigated the socio-economic outcomes during the evolution of the land redistribution programme. Sixty farms that represented evolution models of the land redistribution programme were selected. Socio-economic data were collected from farm representatives by means of semi-structured questionnaires. Additional data were collected from stakeholders through key-informants interviews. In time, land redistribution had decreasing social contributions: There were 57 households benefitting per farm on average during model A with level of participation in land administration and/or use at 20% and the beneficiary numbers decreased with time to an average of 3 individuals in model D with levels of participation at 100%. The proportional land usage per farm improved from 60% under model A to 100% under model D. The type of land being reformed and planned agricultural sector developments of the area contributed to variations in land use. The evolution affected beneficiary numbers negatively and participation levels positively, confirming the shift from social to economic objective. Other factors had more influence on land use than the evolution of the redistribution programme. Keywords: land redistribution, model, evolution, beneficiaries, land use, Limpopo Province.
Sources of Neofabraea spp. and Cadophora spp. in Dutch apple and pear orchards
Köhl, J. ; Wenneker, M. ; Haas, B.H. de; Anbergen, R. ; Lombaers-van der Plas, C.H. ; Kastelein, P. - \ 2015
In: Proceedings of Meeting IOBC-WPRS Working group "Integrated Plant Protection in Fruit Crops’, Sub group ‘Pome Fruit Diseases". - IOBC - ISBN 9789290672937 - p. 143 - 145.
Post-harvest diseases of apple and pear result in significant economic losses during long storage. Pathogens causing quiescent infections in the orchard leading to late post-harvest losses in The Netherlands are Neofabraea alba (Lenticel spot disease), N. perennans (Bull eye rot), Neonectria galligena (Nectria rot), Phytophthora spp., Alternaria spp., Fusarium spp., Cadophora spp. (Phialophora spp.) and Stemphylium vesicarium. Knowledge on the occurrence of the different post-harvest diseases and their epidemiology is very limited. The objectives of our project were to develop tools for the quantitative species-specific detection of pathogens in environmental samples; to study the population dynamics of pathogens in orchards; and to identify major inoculum sources of the different pathogens. Species-specific primers and probes have been developed for three main pathogens N. alba, N. perennans and Cadophora luteo-olivacea. The amount of DNA of each of the three pathogens can now be quantified in environmental samples using TaqMan-PCR assays. Samples of various necrotic plant residues and tree parts were collected in 10 apple and 10 pear orchards during the growing season 2012 to investigate their role as potential inoculum source. In all orchard samples were taken monthly from May until September and in December 2012 from 4 plots (replicates). Neofabraea alba and C. luteo-olivacea were found in all orchards whereas N. perennans occurred only occasionally. Neofabraea alba and C. luteo-olivacea were present on necrotic tissues of apple and pear such as mummies, cankers, and dead leaves. Interestingly, the pathogens were also found in varying amounts on necrotic tissues of other plant species present on the orchard floors. The concentration of pathogen DNA showed a differential pattern on different substrate types. Based on the new knowledge on major inoculum sources of the different pathogens, preventative measures will be developed to reduce the risk of late post-harvest losses
Hoe kan er zo'n rijk onderwaterleven verstopt zitten in onze grauwe Noordzee?
Lindeboom, H.J. - \ 2015
Universiteit van Nederland
noordzee - soortenrijkdom - soortendiversiteit - productiviteit - voedingsstoffen - eutrofiëring - lesmaterialen - north sea - species richness - species diversity - productivity - nutrients - eutrophication - teaching materials
De Noordzee is een gebied dat rijk is aan leven. Hoe kan het dat er in die troebele plas water zoveel verschillende dieren leven? Hoe zorgde die diversiteit en rijkdom voor oorlogen? En waarom is het schadelijk dat we de zee door onze welvaart vol fosfaat pompen? Die vragen en meer behandelt prof. dr. Han Lindeboom van de Wageningen UR in dit college.
Analysis of microbial taxonomical groups present in maize stalks suppressive to colonization by toxigenic Fusarium spp.: A strategy for the identification of potential antagonists
Köhl, J. ; Lombaers-van der Plas, C.H. ; Moretti, A. ; Bandyopadhyay, R. ; Somma, S. ; Kastelein, P. - \ 2015
Biological Control 83 (2015). - ISSN 1049-9644 - p. 20 - 28.
biological-control - rhizosphere microbiome - quantitative detection - microdochium-bolleyi - acremonium-strictum - fungal antagonists - idriella-bolleyi - seed treatment - head blight - durum-wheat
Pink ear rot of maize caused by Fusarium verticillioides, Fusariumproliferatum and Fusariumgraminearumcan lead to severe yield losses and contamination of grain with a range of mycotoxins. Maize stalks colonized by Fusarium spp. are the main primary inoculum source for Fusarium incited epidemics in maize or other susceptible crops grown in rotation. The colonization of individual maize stalks originating from fields in The Netherlands, Italy and Nigeria byFusarium spp. was quantified using specific TaqMan-PCR assays. Highest values were found for F. graminearum and Fusariumavenaceum in Dutch samples, for F. graminearum and FUM producing species (F. verticillioides and F. proliferatum) in Italian samples and FUM producing Fusarium spp. in Nigerian samples. The increase in Fusarium spp. colonization under field conditions during a period of 3–6 months after harvest of the maize crops varied considerably between individual stalks. The fungal and bacterial diversity was analyzed for sub-sets of stalks with high versus low increase of Fusariumcolonization. Bacterial taxonomic groups such as Bacillus, Curtobacterium, Erwinia, Flavobacterium,Novosphingobium, Pantoea, Sphingomonas, Rahnella and Staphylococcus and fungal taxonomic groups such as Acremomium sp., Cryptococcus flavescens, Cryptococcus zeae, Leptosphaeria sp. andMicrodochium bolleyi were more abundant in the stalks with lower increase in pathogen colonization. Such fungal and bacterial groups associated with ‘suppressive stalks’ may be antagonistic to Fusarium spp. and a source of candidate strains for the selection of new biological control agents
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