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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    Integrative pangenome analysis of the Pectobacterium genus
    Jonkheer, Eef ; Brankovics, Balázs ; Houwers, I.M. ; Wolf, J.M. van der; Bonants, P.J.M. ; Vreeburg, R.A.M. ; Sheikhizadeh Anari, S. ; Ridder, D. de; Smit, S. ; Lee, T.A.J. van der - \ 2019
    Borgen van maatregelen om ammoniakemissie te reduceren
    Migchels, Gerard ; Joosten, Leo ; Leeuwen, Marieke van; Ferwerda, Reina ; Wim Houwers, Wim - \ 2019
    Wageningen : Wageningen Livestock Research (Rapport / Wageningen Livestock Research 1196) - 42
    Development and evaluation of a triplex TaqMan assay and Next Generation Sequence Analysis for improved detection of Xylella in plant material
    Bonants, P.J.M. ; Griekspoor, Y. ; Houwers, I.M. ; Krijger, M.C. ; Zouwen, P.S. van der; Lee, T.A.J. van der; Wolf, J.M. van der - \ 2019
    Plant Disease 103 (2019)4. - ISSN 0191-2917 - 36 p.
    Xylella fastidiosa is a heterogenous gram-negative bacterial plant pathogen with a wide host range covering over 300 plant species. Since 2013, in Europe, the presence of the pathogen is increasing in a part of the Mediterranean area, but causes in particular severe disease problems in olive orchards in the Southern part of Italy. Various subspecies of the pathogen were also diagnosed in natural outbreaks and intercepted ornamental plants in Europe, among them Olea europaea, Coffea arabica and Nerium oleander. The host range of the pathogen can vary, depending on the subspecies and even the strain. The availability of fast and reliable diagnostic tools are indispensable in management strategies to control diseases caused by X. fastidiosa. To improve the reliability of the TaqMan assay, currently widely used in surveys, a triplex TaqMan assay was developed in which two specific and sensitive TaqMan assays, previously designed for X. fastidiosa, were combined with an internal control. The triplex assay exhibited the same diagnostic sensitivity as the simplex assays. In addition, the usefulness of a metagenomic approach using next generation sequencing (NGS) was demonstrated, in which total DNA extracted from plant material was sequenced. DNA extracts from plant material free of X. fastidiosa, from artificially inoculated hosts plants or from naturally infected plants sampled in France, Spain and Italy, or intercepted in Austria and The Netherlands, were analysed for the presence of X. fastidiosa using the metagenomic approach. In all samples, even in samples with a low infection level, but not in the pathogen-free samples, DNA reads were detected specific for X. fastidiosa. In most cases, the pathogen could be identified up to the subspecies level and for one sample even the whole genome could be assembled and the sequence type could be determined. All results of NGS analysed samples were confirmed with the triplex TaqMan PCR and LAMP.
    Pangenome analysis and its application on Pectobacterium
    Jonkheer, Eef ; Smit, S. ; Ridder, D. de; Brankovics, Balázs ; Houwers, I.M. ; Wolf, J.M. van der; Bonants, P.J.M. ; Vreeburg, R.A.M. ; Lee, T.A.J. van der - \ 2018
    Use of whole genome sequencing data in the taxonomy and diagnostics of plant pathogenic Ralstonia species.
    Kurm, V. ; Mendes, O. ; Bonants, P.J.M. ; Wolf, J.M. van der; Coipan, E.C. ; Houwers, I.M. ; Waalwijk, C. - \ 2018
    KNPV Werkgroep Phytobacteriën
    Towards improved methods for detection of Xylella fastidiosa in plant material using triplex TaqMan PCR and NGS analysis
    Bonants, P.J.M. ; Griekspoor, Y. ; Houwers, I.M. ; Krijger, M.C. ; Zouwen, P.S. van der; Lee, T.A.J. van der; Wolf, J.M. van der - \ 2018
    Innovative detection methods to support plant health diagnostics
    Bonants, P.J.M. ; Houwers, I.M. ; Dullemans, A.M. ; Griekspoor, Y. ; Mendes, O. ; Gent-Pelzer, M.P.E. van; Vlugt, R.A.A. van der; Bergervoet, J.H.W. ; Schoen, C.D. ; Wolf, J.M. van der; Lee, T.A.J. van der - \ 2018
    Benchmarking of Dairy Processors’ Associations : actors and their activities in The Netherlands, Zambia and South Africa
    Houwers, Wim ; Lee, Jan van der - \ 2018
    Wageningen : Wageningen Livestock Research (Wageningen Livestock Research report 1096) - 33
    This report describes a study of dairy processors’ associations in three countries. As the dairy sectors in these countries are at different stages of development, the challenges these associations face are very different indeed, and so are their functions and structures. Learnings from these cases are drawn for the situation in Kenya.
    The use of Next Generation Sequence Technolgy to evaluate the presence of plant pathogens in tomato seeds : What’s in a Pipeline ?
    Bonants, P.J.M. ; Dullemans, A.M. ; Houwers, I.M. ; Verstappen, E.C.P. ; Lee, T.A.J. van der - \ 2017
    Global Engage’s 4Bio summit hosts the 5th qPCR and Digital PCR Congress, 4th Synthetic Biology and Gene Editing Congress, 3rd Microfluidics Congress: Europe and NGS Tech & Applications Congress.
    Houwers, Ilse - \ 2017
    Next Generation Sequence Technology to evaluate the presence of plant pathogens in tomato seeds: What’s in a Pipeline?
    Bonants, P.J.M. ; Verstappen, E.C.P. ; Houwers, I.M. ; Dullemans, A.M. ; Lee, T.A.J. van der - \ 2017
    Evaluatie van parkhuisvesting van vleeskonijnen : Verschillen de parksystemen in hygiëne en reinigbaarheid?
    Rommers, J.M. ; Houwers, H.W.J. ; Greef, K.H. de - \ 2017
    Konijnenwijzer 35 (2017). - p. 13 - 17.
    evaluatie - groepshuisvesting - vleeskonijnen - parkhuisvesting - parksystemen - hygiene - reinigbaarheid
    In het najaar 2015 zijn drie parksystemen voor vleeskonijnen met elkaar
    vergeleken. Er is gekeken of de drie systemen voldeden aan de
    behoeften van konijnen, en of de systemen onderling verschilden in
    productie resultaten (eindgewichten en uitval), hygiëne en
    reinigbaarheid en arbeidsgemak. In een viertal opeenvolgende artikelen
    in dit blad wordt verslag gedaan van dit onderzoek. In dit artikel wordt
    ingegaan op de hygiëne en reinigbaarheid van de verschillende parken.
    Improvement of detection of Xylella fastidiosa using triplex TaqMan PCR and Next Generation Sequence (NGS)
    Bonants, P.J.M. ; Griekspoor, Y. ; Houwers, I.M. ; Krijger, M.C. ; Zouwen, P.S. van der; Lee, T.A.J. van der; Wolf, J.M. van der - \ 2017
    Benchmarking Dairy Processor Associations - What can experiences elsewhere tell us in Kenya?
    Houwers, H.W.J. ; Lee, J. van der - \ 2017
    Evaluatie van parkhuisvesting voor vleeskonijnen
    Rommers, Jorine ; Jong, Ingrid de; Houwers, Wim ; Hattum, Theo van - \ 2017
    Wageningen : Wageningen Livestock Research (Wageningen Livestock Research rapport 1018)
    konijnen - slachtdieren - groepshuisvesting - dierenwelzijn - mestresultaten - schoonmaken - dierlijke productie - huisvesting, dieren - rabbits - meat animals - group housing - animal welfare - fattening performance - cleaning - animal production - animal housing
    In dit rapport wordt verslag gedaan van een onderzoek dat is uitgevoerd op een konijnen praktijkbedrijf en waarbij drie verschillende parksystemen voor vleeskonijnen zijn vergeleken. Gelet is of de systemen voldoen aan de behoefte van konijnen, de productiviteit is gemeten en de hygiëne, de reinigbaarheid en het arbeidsgemak zijn in kaart gebracht.
    Fodder Cultivation and Conservation:Practice and experiences in different setting
    Haan, Gjalt de; Houwers, H.W.J. - \ 2016
    Cooperation of Colombian and Netherlands public and private partners in capacity and business development in the dairy sector
    Houwers, H.W.J. - \ 2016
    - 37 p.
    Goed ogende konijnen uit slechte nesten, wat doen we ermee in parkhuisvesting?
    Rommers, J.M. ; Greef, K.H. de; Houwers, H.W.J. ; Hattum, T.G. van - \ 2016
    Konijnenwijzer 34 (2016)mei. - p. 10 - 12.
    NGS applications in plant pathogen diagnostics
    Dullemans, Annette - \ 2015
    NGS applications in plant pathogen diagnosticsDullemans Annette, Verstappen Els, Houwers Ilse, Verbeek Martin, Van der Lee Theo, Van der Vlugt René and Bonants Peter. Wageningen UR, BU Biointeractions & Plant Health, PO. Box 16, 6700 AA Wageningen, The Netherlands, annette.dullemans@wur.nlRoutine diagnostics of plant pathogens often involve methods such as ELISA and real-time (TaqMan) PCR. These methods only detect known pathogens. Next Generation Sequencing (NGS) is a valuable method to identify new pathogens. We developed a (semi) automated pipeline to use HiSeq Illumina Sequencing to detect pathogens in different hosts. Total DNA or RNA was isolated from symptomatic plant tissue to generate sequence libraries. Individual samples were labelled with tags to pool multiple samples in one run. The sequence reads generated from a single sample were analyzed in a CLC Genomics Work Bench pipeline. Host reads were removed and the remaining reads were used in a de novo assembly. The resulting contig sequences were compared with sequences in public and in-house databases to identify the origin of the non-host sequences. General knowledge on plant pathogens is essential to identify the pathogen contigs. The read coverage of the pathogen genomes expressed as the Reads per Kb per million reads, and therefore the analytical sensitivity, depends on number of reads, genome size, and the abundance of the pathogen in the host. To investigate whether NGS can be a useful tool in routine screening, RNA samples from an inspection service were sequenced. Samples infected with known pathogens, detected by real-time (Taqman) PCR could be confirmed by NGS. Several examples of NGS will be presented.
    Sri Lanka fodder study; An overview of potential, bottlenecks and improvements to meet the rising demand for quality fodder in Sri Lanka
    Houwers, H.W.J. ; Wouters, A.P. ; Vernooij, A.G. - \ 2015
    Wageningen : Livestock Research Wageningen UR (Report / Wageningen UR Livestock Research 924)
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