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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    The ecology of infrastructure decommissioning in the North Sea: what we need to know and how to achieve it
    Fowler, A.M. ; Jørgensen, A.M. ; Coolen, J.W.P. ; Jones, D.O.B. ; Svendsen, J.C. ; Brabant, R. ; Rumes, B. ; Degraer, S. - \ 2020
    ICES Journal of Marine Science 77 (2020)3. - ISSN 1054-3139 - p. 1109 - 1126.
    artificial reefs - biodiversity - conservation - decommissioning - ecosystem - marine policy - North Sea - offshore infrastructure - platform - sustainability - wind farm
    As decommissioning of oil and gas (O&G) installations intensifies in the North Sea, and worldwide, debate rages regarding the fate of these novel habitats and their associated biota—a debate that has important implications for future decommissioning of offshore wind farms (OWFs). Calls to relax complete removal requirements in some circumstances and allow part of an O&G installation to be left in the marine environment are increasing. Yet knowledge regarding the biological communities that develop on these structures and their ecological role in the North Sea is currently insufficient to inform such decommissioning decisions. To focus debate regarding decommissioning policy and guide ecological research, we review environmental policy objectives in the region, summarize existing knowledge regarding ecological aspects of decommissioning for both O&G and OWF installations, and identify approaches to address knowledge gaps through science–industry collaboration. We find that in some cases complete removal will conflict with other policies regarding protection and restoration of reefs, as well as the conservation of species within the region. Key ecological considerations that are rarely considered during decommissioning decisions are: (i) provision of reef habitat, (ii) productivity of offshore ecosystems, (iii) enhancement of biodiversity, (iv) protection of the seabed from trawling, and (v) enhancement of connectivity. Knowledge gaps within these areas will best be addressed using industry infrastructure and vessels for scientific investigations, re-analysis of historical data held by industry, scientific training of industry personnel, joint research funding opportunities, and trial decommissioning projects.
    PLATFORM policy brief No. 3. The role of the ERA-NET instrument in fostering inclusiveness
    Turk, K. ; Greimel, M. ; Bunthof, C.J. ; Kuzniar-van der Zee, B. - \ 2017
    H2020 Platform of bioeconomy ERA-NET Actions (PLATFORM) - 4 p.
    platform - policy brief - policy - ERA-NET instrument - ERA-NET - inclusiveness - PLATFORM - policy brief - Policy - ERA-NET instrument - ERA-NET - inclusiveness
    Perspective Document on Inclusiveness - Fostering Inclusiveness
    Turk, K. ; Bunthof, C.J. - \ 2016
    H2020 Platform of bioeconomy ERA-NET Actions (PLATFORM) - 31 p.
    inclusiveness - platform - bioeconomy - ERA-NET - bioeconomy - ERA-NET - inclusiveness - PLATFORM - fostering
    Poster PLATFORM DB - Bioeconomy P2P partnerships database - An online web resource on bioeconomy Public-to-Public Partnerships, joint calls and research projects
    Kuzniar-van der Zee, B. - \ 2016
    H2020 Platform of bioeconomy ERA-NET Actions (PLATFORM) - 1 p.
    platform - database - p2p partnerships - public-to-public partnerships - bioeconomy - joint calls - research projects - PLATFORM - P2P - p2p partnerships - Bioeconomy - Database - public-to-public partnerships - joint calls - research projects - Platform db
    Report PLATFORM Master Class on Inclusiveness, 10-11 May 2016, Vienna
    Greimel, M. ; Turk, K. ; Bunthof, C.J. - \ 2016
    H2020 Platform of bioeconomy ERA-NET Actions (PLATFORM) - 14 p.
    platform - bioeconomy - ERA-NET - inclusiveness - PLATFORM - bioeconomy - ERA-NET - inclusiveness - Master Class
    PLATFORM Policy Brief No. 2. Co-creation of a Global Bioeconomy
    Kwant, K. ; Lampel, S. ; Bunthof, C.J. ; Kuzniar-van der Zee, B. - \ 2016
    H2020 Platform of bioeconomy ERA-NET Actions (PLATFORM) - 4 p.
    platform - policy brief - policy - co-creation - global - bioeconomy - PLATFORM - ERA-NET - Bioeconomy - global bioeconomy - policy - policy brief
    Using RNA-Seq to assemble a rose transcriptome with more than 13,000 full-length expressed genes and to develop the WagRhSNP 68k Axiom SNP array for rose (Rosa L.)
    Koning, C.F.S. ; Esselink, G. ; Vukosavljev, M. ; Westende, W.P.C. van 't; Gitonga, V.W. ; Krens, F.A. ; Voorrips, R.E. ; Weg, W.E. van de; Schulz, D. ; Debener, T. ; Maliepaard, C.A. ; Arens, P.F.P. ; Smulders, M.J.M. - \ 2015
    Frontiers in Plant Science 6 (2015). - ISSN 1664-462X - 10 p.
    powdery mildew - markers - tool - identification - resistance - genome - diversity - sequences - platform - plant
    In order to develop a versatile and large SNP array for rose, we set out to mine ESTs from diverse sets of rose germplasm. For this RNA-Seq libraries containing about 700 million reads were generated from tetraploid cut and garden roses using Illumina paired-end sequencing, and from diploid Rosa multiflora using 454 sequencing. Separate de novo assemblies were performed in order to identify single nucleotide polymorphisms (SNPs) within and between rose varieties. SNPs among tetraploid roses were selected for constructing a genotyping array that can be employed for genetic mapping and marker-trait association discovery in breeding programs based on tetraploid germplasm, both from cut roses and from garden roses. In total 68,893 SNPs were included on the WagRhSNP Axiom array. Next, an orthology-guided assembly was performed for the construction of a non-redundant rose transcriptome database. A total of 21,740 transcripts had significant hits with orthologous genes in the strawberry (Fragaria vesca L.) genome. Of these 13,390 appeared to contain the full-length coding regions. This newly established transcriptome resource adds considerably to the currently available sequence resources for the Rosaceae family in general and the genus Rosa in particular.
    Opportunities and challenges for seaweed in the biobased economy
    Hal, J.W. van; Huijgen, W.J.J. ; Lopez Contreras, A.M. - \ 2014
    Trends in Biotechnology 32 (2014)5. - ISSN 0167-7799 - p. 231 - 233.
    marine macroalgae - platform - acetone - butanol
    The unique chemical composition of seaweeds and their fast growth rates offer many opportunities for biorefining. In this article we argue that cascading biorefinery valorization concepts are viable alternatives to only using seaweeds as carbohydrate sources for the fermentative production of biofuels. However, many challenges remain with respect to use of seaweeds for chemical production, such as the large seasonal variation in the chemical composition of seaweeds.
    WormQTL—public archive and analysis web portal for natural variation data in Caenorhabditis spp
    Snoek, L.B. ; Velde, K.J. van der; Arends, D. ; Li, Y. ; Beyer, A. ; Elvin, M. ; Fisher, J. ; Hajnal, A. ; Hengartner, M. ; Poulin, G. ; Rodriguez Sanchez, M. ; Schmid, T. ; Schrimpf, S. ; Xue, F. ; Jansen, R.C. ; Kammenga, J.E. ; Swertz, M.A. - \ 2013
    Nucleic acids research 41 (2013)D1. - ISSN 0305-1048 - p. D738 - D743.
    life-history traits - c. elegans - systems biology - qtl - polymorphism - genotype - environment - plasticity - platform - genome
    Here, we present WormQTL (, an easily accessible database enabling search, comparative analysis and meta-analysis of all data on variation in Caenorhabditis spp. Over the past decade, Caenorhabditis elegans has become instrumental for molecular quantitative genetics and the systems biology of natural variation. These efforts have resulted in a valuable amount of phenotypic, high-throughput molecular and genotypic data across different developmental worm stages and environments in hundreds of C. elegans strains. WormQTL provides a workbench of analysis tools for genotype–phenotype linkage and association mapping based on but not limited to R/qtl ( All data can be uploaded and downloaded using simple delimited text or Excel formats and are accessible via a public web user interface for biologists and R statistic and web service interfaces for bioinformaticians, based on open source MOLGENIS and xQTL workbench software. WormQTL welcomes data submissions from other worm researchers.
    SPICY: towards automated phenotyping of large pepper plants in the greenhouse
    Heijden, G.W.A.M. van der; Song, Y. ; Horgan, G. ; Polder, G. ; Dieleman, J.A. ; Bink, M.C.A.M. ; Palloix, A. ; Eeuwijk, F.A. van; Glasbey, C. - \ 2012
    Functional Plant Biology 39 (2012)11. - ISSN 1445-4408 - p. 870 - 877.
    complex traits - platform - cereals - qtl
    Most high-throughput systems for automated plant phenotyping involve a fixed recording cabinet to which plants are transported. However, important greenhouse plants like pepper are too tall to be transported. In this research we developed a system to automatically measure plant characteristics of tall pepper plants in the greenhouse. With a device equipped with multiple cameras, images of plants are recorded at a 5 cm interval over a height of 3 m. Two types of features are extracted: (1) features from a 3D reconstruction of the plant canopy; and (2) statistical features derived directly from RGB images. The experiment comprised 151 genotypes of a recombinant inbred population of pepper, to examine the heritability and quantitative trait loci (QTL) of the features. Features extracted from the 3D reconstruction of the canopy were leaf size and leaf angle, with heritabilities of 0.70 and 0.56 respectively. Three QTL were found for leaf size, and one for leaf angle. From the statistical features, plant height showed a good correlation (0.93) with manual measurements, and QTL were in accordance with QTL of manual measurements. For total leaf area, the heritability was 0.55, and two of the three QTL found by manual measurement were found by image analysis
    From the cover: the micro-petri dish, a million-well growth chip for the culture and high-throughput screening of microorganisms
    Ingham, C.J. ; Sprenkels, A. ; Bomer, J. ; Molenaar, D. ; Berg, Aad van den; Hylckama Vlieg, J.E.T. van; Vos, W.M. de - \ 2007
    Proceedings of the National Academy of Sciences of the United States of America 104 (2007)46. - ISSN 0027-8424 - p. 18217 - 18222.
    sp-nov. - bacteria - microfluidics - galactosidase - platform - future - cells
    A miniaturized, disposable microbial culture chip has been fabricated by microengineering a highly porous ceramic sheet with up to one million growth compartments. This versatile culture format, with discrete compartments as small as 7 x 7 µm, allowed the growth of segregated microbial samples at an unprecedented density. The chip has been used for four complementary applications in microbiology. (i) As a fast viable counting system that showed a dynamic range of over 10,000, a low degree of bias, and a high culturing efficiency. (ii) In high-throughput screening, with the recovery of 1 fluorescent microcolony in 10,000. (iii) In screening for an enzyme-based, nondominant phenotype by the targeted recovery of Escherichia coli transformed with the plasmid pUC18, based on expression of the lacZ reporter gene without antibiotic-resistance selection. The ease of rapid, successive changes in the environment of the organisms on the chip, needed for detection of -galactosidase activity, highlights an advantageous feature that was also used to screen a metagenomic library for the same activity. (iv) In high-throughput screening of >200,000 isolates from Rhine water based on metabolism of a fluorogenic organophosphate compound, resulting in the recovery of 22 microcolonies with the desired phenotype. These isolates were predicted, on the basis of rRNA sequence, to include six new species. These four applications suggest that the potential for such simple, readily manufactured chips to impact microbial culture is extensive and may facilitate the full automation and multiplexing of microbial culturing, screening, counting, and selection.
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