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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    Implementation of PROMETHEUS 4‐step approach for evidence use in EFSA scientific assessments: benefits, issues, needs and solutions
    Aiassa, Elisa ; Martino, Laura ; Barizzone, Fulvio ; Ciccolallo, Laura ; Garcia, Ana ; Georgiadis, Marios ; Guajardo, Irene Muñoz ; Tomcikova, Daniela ; Alexander, Jan ; Calistri, Paolo ; Gundert‐remy, Ursula ; Hart, Andrew David ; Hoogenboom, Ron Laurentius ; Messean, Antoine ; Naska, Androniki ; Navarro, Maria Navajas ; Noerrung, Birgit ; Ockleford, Colin ; Wallace, Robert John ; Younes, Maged ; Abuntori, Blaize ; Alvarez, Fernando ; Aryeetey, Monica ; Baldinelli, Francesca ; Barrucci, Federica ; Bau, Andrea ; Binaglia, Marco ; Broglia, Alessandro ; Castoldi, Anna Federica ; Christoph, Eugen ; Sesmaisons‐Lecarré, Agnes De; Georgiadis, Nikolaos ; Gervelmeyer, Andrea ; Istace, Frederique ; López‐Gálvez, Gloria ; Manini, Paola ; Maurici, Daniela ; Merten, Caroline ; Messens, Winy ; Mosbach‐Schulz, Olaf ; Putzu, Claudio ; Bordajandi, Luisa Ramos ; Smeraldi, Camilla ; Tiramani, Manuela ; Martínez, Silvia Valtueña ; Sybren, Vos ; Hardy, Anthony Richard ; Hugas, Marta ; Kleiner, Juliane ; Seze, Guilhem De - \ 2018
    EFSA Supporting Publications 15 (2018)4. - ISSN 2397-8325
    In 2014, the European Food Safety Authority (EFSA) started the PROMETHEUS (PROmoting METHods for Evidence Use in Scientific assessments) project to improve further and increase the consistency of the methods it uses in its scientific assessments. The project defined a set of principles for the scientific assessment process and a 4‐step approach (plan/carry out/verify/report) for their fulfilment, which was tested in ten case studies, one from each EFSA panel. The present report describes the benefits, issues, needs and solutions related to the implementation of the 4‐step approach in EFSA, identified in a dedicated workshop in October 2017. The key benefits of the approach, which was deemed applicable to all types of EFSA scientific assessment including assessments of regulated products, are: 1) increased ‘scientific value’ of EFSA outputs, i.e. the extent of impartiality, methodological rigour, transparency and engagement; 2) guarantee of fitness‐for‐purpose, as it implies tailoring the methods to the specificities of each assessment; 3) efficiency gain, since preparing a protocol for the assessment upfront helps more streamlined processes throughout the implementation phase; 4) innovation, as the approach promotes the pioneering practice of ‘planning before doing’ (well established in primary research) for broad scientific assessments in regulatory science; and 5) increased harmonisation and consistency of EFSA assessments. The 4‐step approach was also considered an effective system for detecting additional methodological and/or expertise needs and a useful basis for further defining a quality management system for EFSA's scientific processes. The identified issues and solutions related to the implementation of the approach are: a) lack of engagement and need for effective communication on benefits and added value; b) need for further advances especially in the field of problem formulation/protocol development, evidence appraisal and evidence integration; c) need for specialised expertise in the previous aspects; and specific needs for d) assessments of regulated products and e) outsourced projects.
    Isolation and validation of microsatellite markers from a depleted South African sciaenid species, the dusky kob (Argyrosomus japonicus), by means of the FIASCO/454 approach
    Mirimin, L. ; Ruiz Guajardo, J.C. ; Vervalle, J. ; Bester-Van der Merwe, Aletta ; Kerwath, S. ; Macey, B. ; Bloomer, P. ; Roodt-Wilding, R. - \ 2013
    Conservation Genetics Resources 5 (2013)3. - ISSN 1877-7252 - p. 841 - 844.
    454 GS-FLX - Argyrosomus spp - FIASCO - Microsatellites - Sciaenid

    The dusky kob (Argyrosomus japonicus) is a large, estuarine-dependent sciaenid fish that has been severely depleted in South African waters and that, in recent years, has received considerable attention from the local fish farming industry. Discovery and application of appropriate molecular markers is necessary to improve the understanding of wild population structure, assist the effectiveness of broodstock and breeding programmes, and ensure monitoring of potential interactions between wild and farmed fish. The present study uses a recently tested approach that combines the FIASCO enrichment protocol with 454 GS-FLX Next Generation Sequencing, to identify large numbers of microsatellite-containing sequences at a low cost and high discovery rate from the dusky kob genome. Following the FIASCO enrichment (targeting specifically tetranucleotide repeats), 2,355 potential tetranucleotide microsatellites (perfect repeat motifs including eight or more repeat units flanked by regions for primer design) were identified from 1/5th of a single 454 lane. From these sequences, a test panel of 60 potential markers was selected for validation. A total of eight (13 %) markers were successfully amplified from a test sample of wild dusky kob individuals and showed high levels of polymorphism (observed heterozygosity per locus ranging between 0.375 and 0.905). Cross-species amplification of seven of these markers was also successfully carried out in another closely related and commercially important South African sciaenid species, the silver kob (A. inodorus). The microsatellite markers developed in the present study are readily available tools suitable to address genetic variability of Argyrosomus species of southern Africa.

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