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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    We will mail you new results for this query: keywords==Detection
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The relationship between the presence of antibodies and direct detection of Toxoplasma gondii in slaughtered calves and cattle in four European countries
Opsteegh, M. ; Spano, F. ; Aubert, D. ; Balea, A. ; Burrells, A. ; Cherchi, S. ; Cornelissen, J.B.W.J. ; Dam-Deisz, C. ; Guitian, J. ; Györke, A. ; Innes, E.A. ; Katzer, F. ; Limon, G. ; Possenti, A. ; Pozio, E. ; Schares, G. ; Villena, I. ; Wisselink, H.J. ; Giessen, J.W.B. van der - \ 2019
International Journal for Parasitology 49 (2019)7. - ISSN 0020-7519 - p. 515 - 522.
Cattle - Detection - Mouse bioassay - PCR - Serology - Toxoplasma gondii

In cattle, antibodies to Toxoplasma gondii infection are frequently detected, but evidence for the presence of T. gondii tissue cysts in cattle is limited. To study the concordance between the presence of anti-T. gondii IgG and viable tissue cysts of T. gondii in cattle, serum, liver and diaphragm samples of 167 veal calves and 235 adult cattle were collected in Italy, the Netherlands, Romania and the United Kingdom. Serum samples were tested for anti-T. gondii IgG by the modified agglutination test and p30 immunoblot. Samples from liver were analyzed by mouse bioassay and PCR after trypsin digestion. In addition, all diaphragms of cattle that had tested T. gondii-positive (either in bioassay, by PCR on trypsin-digested liver or serologically by MAT) and a selection of diaphragms from cattle that had tested negative were analyzed by magnetic capture quantitative PCR (MC-PCR). Overall, 13 animals were considered positive by a direct detection method: seven out of 151 (4.6%) by MC-PCR and six out of 385 (1.6%) by bioassay, indicating the presence of viable parasites. As cattle that tested positive in the bioassay tested negative by MC-PCR and vice-versa, these results demonstrate a lack of concordance between the presence of viable parasites in liver and the detection of T. gondii DNA in diaphragm. In addition, the probability to detect T. gondii parasites or DNA in seropositive and seronegative cattle was comparable, demonstrating that serological testing by MAT or p30 immunoblot does not provide information about the presence of T. gondii parasites or DNA in cattle and therefore is not a reliable indicator of the risk for consumers.

Novel TaqMan PCR screening methods for element cry3A and construct gat/T-pinII to support detection of both known and unknown GMOs
Prins, Theo W. ; Hoof, Richard A. van; Scholtens, Ingrid M.J. ; Kok, Esther J. - \ 2017
European Food Research and Technology 243 (2017)3. - ISSN 1438-2377 - p. 481 - 488.
Detection - Identification - PCR - qPCR - Real-time - Screening

The import and use of genetically modified organisms (GMOs) is strictly regulated in the European Union. In order to maintain the legislation on GMOs, a genetic element screening is generally applied as a first step to detect authorised as well as unauthorised GMOs. Subsequent identification of GMOs that relate to the detected elements is performed by the application of event-specific detection methods. However, as the diversity of GMOs on the world market is increasing, there is an ongoing need for methods for additional informative screening elements. Genes that are increasingly applied in GMOs are cry3A (including variants mcry3A and eCry3.1Ab) conferring resistance to Bt toxins, and gat, detoxifying glyphosate. Novel TaqMan PCR detection methods for element cry3A and construct gat/T-pinII were developed to support the identification of maize MIR604, 98140, 5307, canola 61061 and 73496, and soybean 356043. Also, other unknown (unauthorised) GMOs containing cry3A and/or gat/T-pinII can potentially be detected. Specificity, efficiency and sensitivity of the methods were evaluated.

A framework to measure the availability of engineered nanoparticles in soils : Trends in soil tests and analytical tools
Rodrigues, S.M. ; Trindade, T. ; Duarte, A.C. ; Pereira, E. ; Koopmans, G.F. ; Römkens, P.F.A.M. - \ 2016
TrAC : Trends in Analytical Chemistry 75 (2016). - ISSN 0165-9936 - p. 129 - 140.
Analysis - Availability - Detection - Extraction - Metal-based nanoparticles

In this study, the reactions of engineered nanoparticles (ENPs) in soils, with respect to their nanospecific properties, and observed effects of key soil properties (e.g. pH, ionic strength and natural colloids) on their stability in pore water are discussed. Key processes include aggregation and dissolution of ENPs, straining of ENPs in the solid matrix, stabilization of ENPs in pore water due to binding of molecules from dissolved organic matter (DOM) and inorganic colloids and the effect of artificial coatings. In view of these processes, this study provides guidance in the development of a framework to measure available and total soil contents of ENPs, via a set of extraction methods and advanced analytical tools. Particularly, the lack of effective extraction methods is thoroughly discussed regarding the identification of most relevant research gaps preventing an effective assessment of the availability, mobility and risks of exposure of sensitive receptors to ENPs in soils.

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.

A real-time TaqMan PCR assay to discriminate between pathotype 1 (D1) and non-pathotype 1 (D1) isolates of Synchytrium endobioticum
Bonants, P.J.M. ; Gent-Pelzer, M.P.E. van; Leeuwen, Gerard C.M. van; Lee, T.A.J. van der - \ 2015
European Journal of Plant Pathology 143 (2015)3. - ISSN 0929-1873 - p. 495 - 506.
Detection - Identification - Pathotype 1 (D1) - Potato wart disease - TaqMan PCR

Synchytrium endobioticum is a severe pathogen of potato causing wart disease. For this obligate fungus many pathotypes exist, which are pathogenic or non-pathogenic to different cultivars of potato. To determine to which pathotype an isolate belongs, two biological assays are used on a set of different potato cultivars: the Spieckermann and the Glynne-Lemmerzahl test. A differential set of cultivars has been recommended by EPPO (European Plant Protection Organization) for these tests. Drawbacks of these tests are that it can take up to several months to score the interaction and results are difficult to score and also often not conclusive. Therefore, possibilities were investigated to look for molecular markers for pathotype specificity. An extremely low level of diversity was observed in a set of eight isolates using CRoPS™ (Complexity Reduction of Polymorphic Sequences) technology. Only 191 sequence polymorphisms were found in 14,660 contigs representing approximately 195 Kb of sequence for eight isolates. Nine sequence polymorphisms could be related to pathotype specificity. Two of these polymorphisms were transferred into a real-time TaqMan PCR assay to discriminate between pathotype specific groups. Validation of the assays was performed using multiple isolates from different countries for which the bioassay had been performed.

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