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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    Derde externe audit van de Basisregistratie Kadaster : Rapportage en verklaring over de kwaliteit van de BRK
    Storm, Maarten ; Rip, Frans - \ 2019
    Wageningen : Wageningen Environmental Research (Wageningen Environmental Research rapport 2943) - 18
    De Kadasterwet stelt dat er elke drie jaar een externe audit moet plaatsvinden op de kwaliteit van de authentieke gegevens van de Basisregistratie Kadaster. In 2018/2019 heeft Wageningen Environmental Research deze audit voor de derde maal uitgevoerd d.m.v. interviews en een literatuurstudie. Dit rapport bevat de bevindingen en aanbevelingen van deze audit, inclusief een verklaring over de kwaliteit van de Basisregistratie Kadaster.
    LGN2018
    Rip, F.I. ; Hazeu, G.W. - \ 2019
    Geo-Info 16 (2019)5. - ISSN 1572-5464 - p. 38 - 39.
    Slechte data bestaan niet?
    Rip, F.I. - \ 2019
    Geo-Info 16 (2019)5. - ISSN 1572-5464 - p. 42 - 43.
    Redactioneel
    Rip, F.I. - \ 2019
    Geo-Info 16 (2019)2. - ISSN 1572-5464 - p. 1 - 1.
    Data over bomen voor planners en ontwerpers
    Rip, F. - \ 2019
    Studentenwaardering van geo-onderwijs
    Rip, F.I. - \ 2019
    Geo-Info 16 (2019)2. - ISSN 1572-5464 - p. 32 - 33.
    Technology in the Age of Innovation: Responsible Innovation as a New Subdomain Within the Philosophy of Technology
    Schomberg, Lucien von; Blok, Vincent - \ 2019
    Philosophy & Technology (2019). - ISSN 2210-5433
    History of innovation - Philosophy of innovation - Philosophy of technology - Responsible Research and Innovation - Techno-economic paradigm - Technological innovation

    Praised as a panacea for resolving all societal issues, and self-evidently presupposed as technological innovation, the concept of innovation has become the emblem of our age. This is especially reflected in the context of the European Union, where it is considered to play a central role in both strengthening the economy and confronting the current environmental crisis. The pressing question is how technological innovation can be steered into the right direction. To this end, recent frameworks of Responsible Innovation (RI) focus on how to enable outcomes of innovation processes to become societally desirable and ethically acceptable. However, questions with regard to the technological nature of these innovation processes are rarely raised. For this reason, this paper raises the following research question: To what extent is RI possible in the current age, where the concept of innovation is predominantly presupposed as technological innovation? On the one hand, we depart from a post-phenomenological perspective to evaluate the possibility of RI in relation to the particular technological innovations discussed in the RI literature. On the other hand, we emphasize the central role innovation plays in the current age, and suggest that the presupposed concept of innovation projects a techno-economic paradigm. In doing so, we ultimately argue that in the attempt to steer innovation, frameworks of RI are in fact steered by the techno-economic paradigm inherent in the presupposed concept of innovation. Finally, we account for what implications this has for the societal purpose of RI.

    Variable genome evolution in fungi after transposon-mediated amplification of a housekeeping gene
    Dhillon, Braham ; Kema, Gert H.J. ; Hamelin, Richard C. ; Bluhm, Burt H. ; Goodwin, Stephen B. - \ 2019
    Mobile DNA 10 (2019)1. - ISSN 1759-8753
    Fungal evolution - Genome evolution - Purifying selection - Transduplication

    Background: Transposable elements (TEs) can be key drivers of evolution, but the mechanisms and scope of how they impact gene and genome function are largely unknown. Previous analyses revealed that TE-mediated gene amplifications can have variable effects on fungal genomes, from inactivation of function to production of multiple active copies. For example, a DNA methyltransferase gene in the wheat pathogen Zymoseptoria tritici (synonym Mycosphaerella graminicola) was amplified to tens of copies, all of which were inactivated by Repeat-Induced Point mutation (RIP) including the original, resulting in loss of cytosine methylation. In another wheat pathogen, Pyrenophora tritici-repentis, a histone H3 gene was amplified to tens of copies with little evidence of RIP, leading to many potentially active copies. To further test the effects of transposon-Aided gene amplifications on genome evolution and architecture, the repetitive fraction of the significantly expanded genome of the banana pathogen, Pseudocercospora fijiensis, was analyzed in greater detail. Results: These analyses identified a housekeeping gene, histone H3, which was captured and amplified to hundreds of copies by a hAT DNA transposon, all of which were inactivated by RIP, except for the original. In P. fijiensis the original H3 gene probably was not protected from RIP, but most likely was maintained intact due to strong purifying selection. Comparative analyses revealed that a similar event occurred in five additional genomes representing the fungal genera Cercospora, Pseudocercospora and Sphaerulina. Conclusions: These results indicate that the interplay of TEs and RIP can result in different and unpredictable fates of amplified genes, with variable effects on gene and genome evolution.

    Geo en Agro
    Rip, F.I. - \ 2018
    Geo-Info 15 (2018)4. - ISSN 1572-5464 - p. 1 - 1.
    Met geo de boer op
    Rip, F.I. ; Postma, Sytske - \ 2018
    Geo-Info 15 (2018)4. - ISSN 1572-5464 - p. 48 - 50.
    Nederlandse geo-gereedheid daalt
    Rip, F.I. - \ 2018
    Geo-Info 15 (2018)2. - ISSN 1572-5464 - p. 44 - 45.
    GIMA MSc, al 15 jaar een wonder
    Rip, F.I. - \ 2018
    Geo-Info 15 (2018)3. - ISSN 1572-5464 - p. 30 - 30.
    Functional genetics and genomics of the banana black Sigatoka pathogen Pseudocercospora fijiensis
    Díaz Trujillo, Caucasella - \ 2018
    Wageningen University. Promotor(en): G.H.J. Kema; P.J.G.M. Wit, co-promotor(en): R.E. Arango. - Wageningen : Wageningen University - ISBN 9789463323642 - 247

    The hemibiotroph Pseudocercospora fijiensis is the causal agent of the black Sigatoka disease on bananas; present worldwide being the reason of large economical losses and subject to chemical control as the best control method nowadays. Nonetheless, this fungus has shown being able to become resistant to different chemical fungicides and thus a successful global threat to bananas. The biology of this fungus is largely unknown due to the missing –omics tools applied to this pathosystem. The only manner to counteract this fungus is to understand its biology of survival and pathogenicity.

    Chapter 1. Is the introduction to the fungus, it constitutes an update to the knowledge of its biology and epidemiology. It demonstrates the importance of generating more data and tools to understand this powerful pathogen.

    Chapter 2. Presents the P. fijiensis genome sequence, the analysis of its main characteristics compared with other close fungi. A new genetic map is included counting putative core and dispensable scaffolds, whose high polymorphism was observed by electrophoretic karyotyping within isolates from the same field population. It is shown the massive genome expansion mainly due to repetitive DNA, particularly by LTR-retrotransposons, and how this can affect close sequences. The effect of RIP on the genome is analyzed and compared to that on other closely related fungi. The location close to repetitive sequence from the effector Pfavr4 was discussed under the scope of its epidemiology and the protein employed helped to elucidate the first putative resistant cognate gene in the resistant banana cultivar Calcutta 4. Further analysis of strains originated from populations with and without fungicide selection pressure provided estimates of dispersal of strains and genetic flow that will help to predict spatial patterns of fungicide evolution under different management strategies.

    Chapter 3. Describes the protocol for Agrobacterium-mediated transformation of P. fijiensis for both random and targeted mutagenesis. This method was successfully applied to the gene Pfavr4 and the Pfku70. The former is the first effector described in P. fijiensis, and the latter is the gene codifier of the KU70 protein, the main point of the non-homologous end joining (NHEJ) pathway that has been related to an increase on homologous recombination in several fungi and other eukaryotes, providing important tools for further use. This method was additionally employed to swap the Pfcyp51 gene promoter that helped to decipher biology of azole resistance in P. fijiensis, as described in chapter 4.

    Chapter 4. The appearance of resistant strains to azoles has been mostly correlated with non- synonymous point mutations in the coding sequence Pfcyp51 gene. In this chapter, we identified a 19 base pairs (bp) repeat element in the promoter region of this gene, by a simple PCR analysis, showed that copy number correlates positively with increased resistance to azoles, as well as the exposure to azole fungicides. We swapped the promoter of a resistant strain into a susceptible strain, and thus demonstrated that presence of the repeat element proportionally upregulates Pfcyp51 expression as well as tolerance to azoles. Besides the knowledge on genetic mechanism for azole resistance in P. fijiensis, the present study might offer another tool for optimizing the use of azoles in the control of black Sigatoka.

    Chapter 5. A general discussion of the results obtained in this thesis is offered with a broader point of view. Implications in ecology, pathology and further expectations on the control of this fungus, together with insights on trending topics of molecular tools for future research are included.

    Terugblik ‘versnelde’ GeoBuzz
    Boer, A. den; Bosch, J. ; Rip, F.I. - \ 2018
    Geo-Info 15 (2018)1. - ISSN 1572-5464 - p. 30 - 37.
    Development of a Healthy Urban Route Planner for cyclists and pedestrians in Amsterdam
    Steeneveld, G.J. ; Vreugdenhil, L.C. ; Molen, M.K. van der; Ligtenberg, A. - \ 2017
    In: Societal Geo-innovation. Selected Papers of the 20th AGILE Conference on Geographic Information Science. - Cham : Springer - 3 p.
    Cities are hotspots of air pollution and heat stress, resulting in nuisance, health risks, medication costs, reduced labour productivity and sick leave for citizens. Yet the air pollution and heat stress are spatially and temporally unevenly distributed over the city, depending on pollutant emissions, street design and atmospheric turbulent mixing and radiation. If accurately forecasted, this spatiotemporal variation offers pedestrians and bikers alternative routes to minimize their exposure. We develop a route planner for bicyclists and pedestrians for Amsterdam (NL), that proposes routes based on model simulations of weather and air quality. We use the WRF-Chem atmosphere and air quality model at unprecedented grid spacing of 100-m (Ronda et al, 2015), with an underlying urban canopy model and NOx and PM10 emissions. The traffic emissions are based on observed traffic intensities and emission factors. WRF-Chem runs will be issued daily for a lead time of 48 hours, resulting in forecast maps of temperature and pollutant concentrations that will be uniquely expressed in a metric that combines both threats. The route planner that we build, using the open source routing library pgRouting and the OpenStreetMap network.
    GeoWijzer geeft grip op de organisatie rond de kwaliteit van geodata
    Vullings, L.A.E. ; Wessels, G. ; Rip, F.I. - \ 2017
    Geo-Info 14 (2017)5. - ISSN 1572-5464 - p. 22 - 23.
    Bij de omgang met geodata iskwaliteit een belangrijk aspect.Om die kwaliteit tot stand tebrengen en op peil te houdenmoet de bewerkingsketengoed georganiseerd zijn. Eenmethode om dat te bereiken isbenchmarking.
    Internationalisering
    Rip, F.I. - \ 2017
    Geo-Info 14 (2017)4. - ISSN 1572-5464 - p. 1 - 1.
    AGILE-conferentie 2017 in Wageningen
    Rip, F.I. - \ 2017
    Geo-Info 14 (2017)4. - ISSN 1572-5464 - p. 12 - 14.
    De AGILE-conferentie is de jaarlijkse toogdag van de vereniging van Europese laboratoria voor geografi sche informatie.
    De organisatie en invulling ervan zijn in alle opzichten internationaal van karakter. Dit verslag schetst wat facetten.
    Klaar voor geo? : Nederland in top 3
    Rip, F.I. - \ 2017
    Geo-Info 14 (2017)4. - ISSN 1572-5464 - p. 51 - 51.
    AHN en programma Beeldmateriaal samen verder
    Rip, F.I. ; Nobbe, Erik - \ 2017
    Geo-Info 14 (2017)3. - ISSN 1572-5464 - p. 10 - 12.
    Sinds 1992 is de nationale inwinning van hoogtegegevens sterk ontwikkeld, net als de beschikbaarstelling. Gaandeweg veranderde de maatschappelijke behoefte aan die gegevens. Klimaatverandering draagt daaraan bij, maar ook de toenemende verharding van het grondoppervlak. Ook techniek en organisatie van het inwinningsproces maken ontwikkelingen door. Nu wordt gewerkt aan AHN3 (Actueel Hoogtebestand Nederland), dat in 2019 af zal zijn. En daarna? Een gesprek met programmamanager Erik Nobbe van Het Waterschapshuis over hoe het verder gaat.
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