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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    Meerwaarde voor vis
    Zaalmink, W. ; Verweij, M. - \ 2015
    Den Haag : LEI Wageningen UR (LEI publicatie 2015-035 ) - 47
    visserij - nederland - belgië - denemarken - circuits - duurzaamheid (sustainability) - agro-industriële ketens - bedrijfsresultaten in de landbouw - coöperaties - elektronische handel - winkels - consumenten - handel - fisheries - netherlands - belgium - denmark - circuits - sustainability - agro-industrial chains - farm results - cooperatives - electronic commerce - shops - consumers - trade
    Deze brochure beschrijft inspirerende voorbeelden van enkele niet-alledaagse afzetmogelijkheden van vis, Het doel is visserijondernemers te stimuleren tot het ontwikkelen van economisch en ecologisch rendabele visketens.
    Rapid BAC selection for tol2-mediated transgenesis in zebrafish
    Bussmann, J. ; Schulte-Merker, S. - \ 2011
    Development 138 (2011)19. - ISSN 0950-1991 - p. 4327 - 4332.
    bacterial artificial chromosomes - fluorescent protein - expression - embryos - gene - integration - circuits - tol2 - mice
    The generation of zebrafish transgenic lines that express specific fluorophores in a cell-or tissue-specific manner is an important technique that takes full advantage of the optical clarity of the embryo. Identifying promoter fragments that faithfully recapitulate endogenous expression patterns and levels is often difficult and using large genomic DNA fragments, such as bacterial artificial chromosomes (BACs), makes the process of transgenesis less reliable. Here we provide a detailed protocol that allows for BAC selection and subsequent rapid modification through recombineering in Escherichia coli, resulting in BACs that can be injected into zebrafish embryos and, aided by tol2-mediated transgenesis, reliably yield stable transgenic lines. A number of BACs can be prepared in parallel, and injection of the BACs containing CFP/YFP/RFP or Gal4 cassettes allows for immediate testing of whether a particular BAC will yield the desired result. Furthermore, since injected embryos often show widespread expression, recombineered BACs provide an alternative to two-color in situ hybridizations: BACs injected into embryos of a different transgenic reporter line thus enable in vivo colocalization studies. Using this protocol, we have generated 66 stable lines for 23 different genes, with an average transgenesis rate above 10%. Importantly, we provide evidence that BAC size shows no apparent correlation to the transgenesis rate achieved and that there are no severe position effects.
    Modeling and analysis of the dynamic behavior of the XlnR regulon in Aspergillus niger
    Omony, J. ; Graaff, L.H. de; Straten, G. van; Boxtel, A.J.B. van - \ 2011
    BMC Systems Biology 5 (2011)Suppl. 1. - ISSN 1752-0509 - 14 p.
    gene-expression - transcriptional regulation - regulatory networks - time delays - systems - oscillations - circuits - endoglucanase - approximation - degradation
    Background: In this paper the dynamics of the transcription-translation system for XlnR regulon in Aspergillus niger is modeled. The model is based on Hill regulation functions and uses ordinary differential equations. The network response to a trigger of D-xylose is considered and stability analysis is performed. The activating, repressive feedback, and the combined effect of the two feedbacks on the network behavior are analyzed. Results: Simulation and systems analysis showed significant influence of activating and repressing feedback on metabolite expression profiles. The dynamics of the D-xylose input function has an important effect on the profiles of the individual metabolite concentrations. Variation of the time delay in the feedback loop has no significant effect on the pattern of the response. The stability and existence of oscillatory behavior depends on which proteins are involved in the feedback loop. Conclusions: The dynamics in the regulation properties of the network are dictated mainly by the transcription and translation degradation rate parameters, and by the D-xylose consumption profile. This holds true with and without feedback in the network. Feedback was found to significantly influence the expression dynamics of genes and proteins. Feedback increases the metabolite abundance, changes the steady state values, alters the time trajectories and affects the response oscillatory behavior and stability conditions. The modeling approach provides insight into network behavioral dynamics particularly for small-sized networks. The analysis of the network dynamics has provided useful information for experimental design for future in vitro experimental work
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