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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    On-site detectiemethoden voor verbetering van plantgezondheid en fytosanitaire inspectie
    Schoen, Cor - \ 2020
    On-site plant pathogen detection methods
    Schoen, Cor - \ 2020
    A loop-mediated isothermal amplification (LAMP) assay based on unique markers derived from genotyping by sequencing data for rapid in planta diagnosis of Panama disease caused by Tropical Race 4 in banana
    Ordóñez, N. ; Salacinas, M. ; Mendes, O. ; Seidl, M.F. ; Meijer, H.J.G. ; Schoen, C.D. ; Kema, G.H.J. - \ 2019
    Plant Pathology 68 (2019)9. - ISSN 0032-0862 - p. 1682 - 1693.
    DArTseq - field diagnostic - Fusarium odoratissimum - LAMP - Musa - Tropical Race 4

    The socio-economic impact of Fusarium odoratissimum, which is colloquially called tropical race 4 (TR4), is escalating as this fungal pathogen spreads to new banana-growing areas. Hence, the development of simple, reliable and rapid detection technologies is indispensable for implementing quarantine measures. Here, a versatile loop-mediated isothermal amplification (LAMP) assay has been developed that is applicable under field and laboratory conditions. DNA markers unique to TR4 isolates were obtained by diversity arrays technology sequencing (DArTseq), a genotyping by sequencing technology that was conducted on 27 genotypes, comprising 24 previously reported vegetative compatibility groups (VCGs) and three TR4 isolates. The developed LAMP TR4 assay was successfully tested using 22 TR4 isolates and 45 non-target fungal and bacterial isolates, as well as on infected plants under greenhouse and field conditions. The detection limit was 1 pg µL−1 pure TR4 DNA or 102 copies plasmid-localized TR4 unique sequence (SeqA) per reaction, which was not affected by background DNA in complex samples. The LAMP TR4 assay offers a powerful tool for the routine and unambiguous identification of banana plants infected with TR4, contributing to advanced diagnosis in field situations and monitoring of fusarium wilt.

    Genotyping by sequencing to identify diagnostic regions in Fusarium oxysporum f. sp. cubense Tropical Race 4 and applications in disease epidemiology
    Salacinas, Maricar ; Ordonez, N. ; Mendes, O. ; Schoen, C.D. ; Seidl, M.F. ; Meijer, H.J.G. ; Kema, G.H.J. - \ 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
    Automated DNA purification and multiplexed lamp assay preparation on a centrifugal microfluidic 'Lab-on-a-Disc' platform
    Kinahan, David J. ; Julius, Lourdes A.N. ; Schoen, Cor ; Dreo, Tanja ; Ducree, Jens - \ 2018
    In: 2018 IEEE Micro Electro Mechanical Systems, MEMS 2018. - Institute of Electrical and Electronics Engineers Inc. - ISBN 9781538647820 - p. 1134 - 1137.
    This work presents a rotational-pulse actuated micro-fluidic cartridge enabling automated detection of plant pathogens on a compact device towards point-of-use monitoring of food safety. This highly integrated 'Lab-on-a-Disc' (LoaD) system first runs the sample over a stationary phase of silica beads, followed by ethanol (EtOH) wash and final elution of DNA. The eluate is then homogenized using 'shake mode' agitation, accurately metered and then mixed with reagents for loop-mediated isothermal amplification (LAMP). We successfully purify plant DNA and demonstrate on-disc quantitative LAMP amplification.
    Loop-mediated isothermal amplification (LAMP) shield for Arduino DNA detection
    Velders, Aldrik H. ; Schoen, Cor ; Saggiomo, Vittorio - \ 2018
    BMC Research Notes 11 (2018). - ISSN 1756-0500
    Arduino instruments - Loop mediated isothermal amplification - Nucleic acid detection - Portable
    Objective: Loop-mediated isothermal amplification (LAMP) of DNA is gaining relevance as a method to detect nucleic acids, as it is easier, faster, and more powerful than conventional Polymerase Chain Reaction. However, LAMP is still mostly used in laboratory settings, because of the lack of a cheap and easy, one-button device that can perform LAMP experiments. Results: Here we show how to build and program an Arduino shield for a LAMP and detection of DNA. The here described Arduino Shield is cheap, easy to assemble, to program and use, it is battery operated and the detection of DNA is done by naked-eye so that it can be used in field.
    Fungal communities including plant pathogens in near surface air are similar across northwestern Europe
    Nicolaisen, Mogens ; West, Jonathan S. ; Sapkota, Rumakanta ; Canning, Gail G.M. ; Schoen, Cor ; Justesen, Annemarie F. - \ 2017
    Frontiers in Microbiology 8 (2017)SEP. - ISSN 1664-302X
    Air sampling - Airborne - Metabarcoding - Plant pathogen - Urban
    Information on the diversity of fungal spores in air is limited, and also the content of airborne spores of fungal plant pathogens is understudied. In the present study, a total of 152 air samples were taken from rooftops at urban settings in Slagelse, DK, Wageningen NL, and Rothamsted, UK together with 41 samples from above oilseed rape fields in Rothamsted. Samples were taken during 10-day periods in spring and autumn, each sample representing 1 day of sampling. The fungal content of samples was analyzed by metabarcoding of the fungal internal transcribed sequence 1 (ITS1) and by qPCR for specific fungi. The metabarcoding results demonstrated that season had significant effects on airborne fungal communities. In contrast, location did not have strong effects on the communities, even though locations were separated by up to 900 km. Also, a number of plant pathogens had strikingly similar patterns of abundance at the three locations. Rooftop samples were more diverse than samples taken above fields, probably reflecting greater mixing of air from a range of microenvironments for the rooftop sites. Pathogens that were known to be present in the crop were also found in air samples taken above the field. This paper is one of the first detailed studies of fungal composition in air with the focus on plant pathogens and shows that it is possible to detect a range of pathogens in rooftop air samplers using metabarcoding.
    Highly scalable combinatorial mixing of samples with target-specific primers for rapid pathogen detection on a centrifugal platform
    Chung, D.W.Y. ; Kinahan, D.J. ; Schoen, C. ; Dreo, T. ; Ducrée, J. - \ 2016
    In: 20th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2016. - Chemical and Biological Microsystems Society - ISBN 9780979806490 - p. 848 - 849.

    In application areas such as crop genotyping, plant diagnostics, pharmaceuticals and forensics, screening a large number of M samples for specific responses to a library of N active agents in a time- and cost-efficient manner is of critical importance. Parameters of interest include response of cells to a specific drug compound, identification of specific genes or plant pathogens in crops using DNA markers and DNA traceability for food safety. The cost of reagents as well as the liquid handling ro-botics required to perform the enormous number of pipetting steps severely hamper the proliferation of such key technologies into smaller laboratories.

    Development and application of loop-mediated isothermal amplification (LAMP) for detection of Plasmopara viticola
    Kong, X. ; Qin, W. ; Xiaoqing, X. ; Kong, F. ; Schoen, C.D. ; Feng, J. ; Wang, Z. ; Zhang, H. - \ 2016
    Scientific Reports 6 (2016). - ISSN 2045-2322 - 9 p.
    Microbiology techniques
    A rapid LAMP (loop-mediated isothermal amplification) detection method was developed on the basis of the ITS sequence of P. viticola, the major causal agent of grape downy mildew. Among the 38 fungal and oomycete species tested, DNA isolated exclusively from P. viticola resulted in a specific product after LAMP amplification. This assay had high sensitivity and was able to detect the presence of less than 33 fg of genomic DNA per 25-μL reaction within 30 min. The infected leaves may produce sporangia that serve as a secondary inoculum. The developed LAMP assay is efficient for estimating the latent infection of grape leaves by P. viticola. When combined with the rapid and simple DNA extraction method, this assay’s total detection time is shortened to approximately one hour; therefore it is suitable for on-site detection of latent infection in the field. The sporangia levels in the air are strongly associated with disease severity. The LAMP method was also demonstrated to be able to estimate the level of sporangia released in the air in a certain period. This assay should make disease forecasting more accurate and rapid and should be helpful in decision-making regarding the control of grape downy mildew.
    Multiplex detection and identification of Phytophthora spp. using target-specific primer extension and Luminex xTAG technology
    Kostov, K. ; Verstappen, E.C.P. ; Bergervoet, J.H.W. ; Weerdt, M. de; Schoen, C.D. ; Slavov, S. ; Bonants, P.J.M. - \ 2016
    Plant Pathology 65 (2016)6. - ISSN 0032-0862 - p. 1008 - 1021.
    Detection - Identification - Luminex - Multiplex - Phytophthora - TSPE

    There are more than 100 species that belong to the fungus-like genus Phytophthora, many of which can cause severe damage to plants in both natural and agricultural ecosystems. The availability of techniques for detection and identification are crucial for monitoring and control of these pathogens. In recent years, new methods using molecular approaches have been developed. However, the majority of them are designed to detect single Phytophthora species. Techniques that are able to target multiple species in one sample would offer advantages, especially for the assessment of Phytophthora diversity in the environment. This paper describes a multiplex assay for simultaneous detection and identification of 26 members of Phytophthora down to species level and another 22 to clade or subclade level through target-specific primer extension (TSPE) and the Luminex xTAG array detection system. The assay starts with PCR amplification of two genomic regions, ITS and coxI, followed by a multiplex TSPE reaction with clade-, subclade- and species-specific probes. As a result, biotin-dCTP labelled products are generated and subsequently detected through hybridization with a set of anti-TAG coupled, colour-coded paramagnetic beads. The specificity of the method has been tested using DNA extracts from over 400 isolates representing 110 Phytophthora species and subspecies. The sensitivity and robustness have been determined by the use of DNA mixtures, dilution series and environmental samples. Thus the developed technique allows simultaneous identification of multiple Phytophthora species, particularly useful for the detection of these pathogens in environmental samples such as soil, water and plant tissue.

    Nematocure : kennisconcept voor duurzame wering van nematoden in agroproductiesystemen
    Overbeek, L.S. van; Elberse, I. ; Korthals, G.W. ; Molendijk, L.P.G. ; Nijhuis, E.H. ; Os, G.J. van; Schoen, C.D. ; Visser, J.H.M. ; Wurff, A.W.G. van der - \ 2015
    In: Kennisbasisprogramma Duurzaam Agroketens Wageningen UR - p. 33 - 38.
    Plantenziektenkundig laboratorium voor elke glastuinbouwteler : On-site detectie voor snel opsporen pathogenen
    Bezemer, J. ; Schoen, C.D. - \ 2015
    Onder Glas 12 (2015)3. - p. 24 - 25.
    glastuinbouw - groenten - tomaten - afwijkingen, planten - tests - testinstallaties - innovaties - detectie - technieken - greenhouse horticulture - vegetables - tomatoes - plant disorders - tests - test rigs - innovations - detection - techniques
    Een teler heeft een virus in de kas, maar hij weet niet welk virus precies? Hij heeft last van een aaltje en wil uitzoeken welk aaltje het is? Zijn de vlekjes veroorzaakt door Botrytis of door meeldauw? Binnenkort zorgen telers zelf voor antwoorden op deze vragen. Snel en goedkoop, in de kas.
    Rapid identification and detection of pathogenic Fungi by padlock probes
    Tsui, C.K.M. ; Wang, B. ; Schoen, C.D. ; Hamelin, R.C. - \ 2013
    In: Laboratory Protocols in Fungal Biology / Kumar Gupta, Vijai, Tuohy, Maria G., Ayyachamy, Manimaran, Turner, Kevin M., O'Donovan, Anthonia, New York : Springer Science + Business Media (Fungal Biology ) - ISBN 9781461423553 - p. 505 - 517.
    Fungi are important pathogens of human diseases, as well as to agricultural crop and trees. Molecular diagnostics can detect diseases early, and improve identification accuracy and follow-up disease management. The use of padlock probe is effective to facilitate these detections and pathogen identification quickly and accurately. In this chapter we describe three diagnostic assays that utilize padlock probes in combination with various technologies for the detection of pathogenic fungi.
    Teler kan ziekteverwekkers ter plekke identificeren
    Schoen, C.D. - \ 2013
    Vakblad voor de Bloemisterij 68 (2013)51/52. - ISSN 0042-2223 - p. 46 - 47.
    Wetenschappers hebben een methode ontwikkeld waarmee ook telers eenvoudig ter plekke kunnen vaststellen of een bepaalde ziekteverwekker in verdachte monsters aanwezig is. De methode werkt snel. Zo kan een teler binnen vijftien minuten de aanwezigheid van een ziekteverwekker in zijn kas vaststellen. Voor de identificatie hoeft hij geen specifieke kennis te hebben.
    Iedereen kan ziekteverwekkers ter plekke identificeren
    Schoen, C.D. - \ 2013
    Groenten & Fruit (2013)18. - ISSN 0925-9708 - p. 20 - 21.
    Plant Research International heeft met internationale partners een methode ontwikkeld waarmee telers en inspecteurs eenvoudig ter plekke vast kunnen stellen of een bepaalde ziekteverwekker in verdachte monsters aanwezig is. Deze LAMP-methode werkt snel.
    Multiplex detection and identification of bacterial pathogens causing potato blackleg and soft rot in Europe, using padlock probes
    Slawiak, M. ; Doorn, R. van; Szemes, M. ; Speksnijder, A.G.C.L. ; Waleron, M. ; Wolf, J.M. van der; Lojkowska, E. ; Schoen, C.D. - \ 2013
    Annals of Applied Biology 163 (2013)3. - ISSN 0003-4746 - p. 378 - 393.
    fragment-length-polymorphism - carotovora ssp-atroseptica - erwinia-carotovora - pectobacterium-carotovorum - sp-nov. - oligonucleotide-microarray - dickeya-chrysanthemi - genetic diversity - pectin lyase - new-zealand
    The objective of this study was to develop a multiplex detection and identification protocol for bacterial soft rot coliforms, namely Pectobacterium wasabiae (Pw), Pectobacterium atrosepticum (Pba) and Dickeya spp., responsible for potato blackleg and tuber soft rot. The procedures were derived from the phylogenetic relationships of these and other Enterobacteriaceae based on recA sequences. The group of Pw strains was highly homogeneous and could be distinguished from the other species. A ligation-based method for detection of Pw was developed. Five padlock probes (PLPs) were designed, targeting recA sequences to identify the Pw, Pba or Dickeya spp., whereas a sixth probe recognised recA sequences of all soft rot coliforms including Pectobacterium carotovorum subsp. carotovorum (Pcc). Two PLP-based applications were developed: one using real-time PCR and one using universal microarrays. Assay sensitivity and specificity were demonstrated using 71 strains of Pw, Pcc, Pba and Dickeya spp. Both multiplex methods can be potentially used for seed testing and in ecological studies, but further validation is required
    A Universal Microarray Detection Method for Identification of Multiple Phytophthora spp. Using Padlock Probes
    Sikora, K. ; Verstappen, E.C.P. ; Mendes, O. ; Schoen, C.D. ; Ristaino, J. ; Bonants, P.J.M. - \ 2012
    Phytopathology 102 (2012)6. - ISSN 0031-949X - p. 635 - 645.
    polymerase-chain-reaction - internal transcribed spacer - real-time pcr - ribosomal dna - phylogenetic-relationships - natural ecosystems - plant-pathogens - reaction assay - ramorum - quantification
    The genus Phytophthora consists of many species that cause important diseases in ornamental, agronomic, and forest ecosystems worldwide. Molecular methods have been developed for detection and identification of one or several species of Phytophthora in single or multiplex reactions. In this article, we describe a padlock probe (PLP)-based multiplex method of detection and identification for many Phytophthora spp. simultaneously. A generic TaqMan polymerase chain reaction assay, which detects all known Phytophthora spp., is conducted first, followed by a species-specific PLP ligation. A 96-well-based microarray platform with colorimetric readout is used to detect and identify the different Phytophthora spp. PLPs are long oligonucleotides containing target complementary sequence regions at both their 5' and 3' ends which can be ligated on the target into a circular molecule. The ligation is point mutation specific; therefore, closely related sequences can be differentiated. This circular molecule can then be detected on a microarray. We developed 23 PLPs to economically important Phytophthora spp. based upon internal transcribed spacer-1 sequence differences between individual Phytophthora spp. Tests on genomic DNA of many Phytophthora isolates and DNA from environmental samples showed the specificity and utility of PLPs for Phytophthora diagnostics.
    Multiplex detection of Phytophthora: Padlock probe based Universal detection Multiplex Array (PUMA)
    Bonants, P.J.M. ; Gaszczyk, K. ; Mendes, O. ; Verstappen, E.C.P. ; Schoen, C.D. - \ 2011
    Molecular techniques for pathogen identification and fungus detection in the Environment
    Tsui, C.K.M. ; Woodhall, J. ; Chen, W. ; Lévesque, C.A. ; Lau, A. ; Schoen, C.D. ; Baschien, C. ; Najafzadeh, M.J. ; Hoog, G.S. de - \ 2011
    IMA fungus 2 (2011)2. - ISSN 2210-6340 - p. 177 - 189.
    Many species of fungi can cause disease in plants, animals and humans. Accurate and robust detection and quantification of fungi is essential for diagnosis, modeling and surveillance. Also direct detection of fungi enables a deeper understanding of natural microbial communities, particularly as a great many fungi are difficult or impossible to cultivate. In the last decade, effective amplification platforms, probe development and various quantitative PCR technologies have revolutionized research on fungal detection and identification. Examples of the latest technology in fungal detection and differentiation are discussed here
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