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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    Distribution maps of cetacean and seabird populations in the North‐East Atlantic
    Waggitt, J.J. ; Evans, P.G.H. ; Andrade, J. ; Banks, A.N. ; Boisseau, O. ; Bolton, M. ; Bradbury, G. ; Brereton, T. ; Camphuysen, C.J. ; Durinck, J. ; Felce, T. ; Fijn, R.C. ; Garcia‐Baron, I. ; Garthe, S. ; Geelhoed, S.C.V. ; Gilles, A. ; Goodall, M. ; Haelters, J. ; Hamilton, S. ; Hartny‐Mills, L. ; Hodgins, N. ; James, K. ; Jessopp, M. ; Kavanagh, A.S. ; Leopold, M. ; Lohrengel, K. ; Louzao, M. ; Markones, N. ; Martinez‐Cediera, J. ; O’Cadhla, O. ; Perry, S.I. ; Pierce, G.J. ; Ridoux, V. ; Robinson, K.P. ; Santos, M.B. ; Saavedra, C. ; Skov, H. ; Stienen, E.W.M. ; Sveegaard, S. ; Thompson, P. ; Vanermen, N. ; Wall, D. ; Webb, A. ; Wilson, J. ; Wanless, S. ; Hiddink, J.G. - \ 2020
    Journal of Applied Ecology 57 (2020)2. - ISSN 0021-8901 - p. 253 - 269.
    Distribution maps of cetaceans and seabirds at basin and monthly scales are needed for conservation and marine management. These are usually created from standardised and systematic aerial and vessel surveys, with recorded animal densities interpolated across study areas. However, distribution maps at basin and monthly scales have previously not been possible because individual surveys have restricted spatial and temporal coverage. This study develops an alternative approach consisting of: (1) collating diverse survey data to maximise spatial and temporal coverage, (2) using detection functions to estimate variation in the surface area covered (km2) among these surveys, standardising measurements of effort and animal densities, and (3) developing species distribution models (SDM) that overcome issues with heterogeneous and uneven coverage. 2.68 million km of survey data in the North‐East Atlantic between 1980 and 2018 were collated and standardised. SDM using Generalized Linear Models and General Estimating Equations in a hurdle approach were developed. Distribution maps were then created for 12 cetacean and 12 seabird species at 10 km and monthly resolution. Qualitative and quantitative assessment indicated good model performance. Synthesis and applications. This study provides the largest ever collation and standardisation of diverse survey data for cetaceans and seabirds, and the most comprehensive distribution maps of these taxa in the North‐East Atlantic. These distribution maps have numerous applications including the identification of important areas needing protection, and the quantification of overlap between vulnerable species and anthropogenic activities. This study demonstrates how the analysis of existing and diverse survey data can meet conservation and marine management needs.
    Data from: Distribution maps of cetacean and seabird populations in the North-East Atlantic
    Waggitt, J.J. ; Evans, P.G.H. ; Andrade, Jose ; Banks, A.N. ; Boisseau, O. ; Bolton, M. ; Bradbury, G. ; Brereton, T. ; Camphuysen, Kees ; Durinck, J. ; Felce, T. ; Fijn, R.C. ; Garcia‐Baron, I. ; Garthe, S. ; Geelhoed, Steve ; Gilles, A. ; Goodall, M. ; Leopold, Mardik - \ 2019
    Dryad
    species distribution models - detection function - North Sea - Celtic Sea - Bay of Biscay - English Channel - Irish Sea - Hebrides
    Persistence of dissolved organic matter explained by molecular changes during its passage through soil
    Roth, Vanessa Nina ; Lange, Markus ; Simon, Carsten ; Hertkorn, Norbert ; Bucher, Sebastian ; Goodall, Timothy ; Griffiths, Robert I. ; Mellado-Vázquez, Perla G. ; Mommer, Liesje ; Oram, Natalie J. ; Weigelt, Alexandra ; Dittmar, Thorsten ; Gleixner, Gerd - \ 2019
    Nature Geoscience 12 (2019). - ISSN 1752-0894 - p. 755 - 761.

    Dissolved organic matter affects fundamental biogeochemical processes in the soil such as nutrient cycling and organic matter storage. The current paradigm is that processing of dissolved organic matter converges to recalcitrant molecules (those that resist degradation) of low molecular mass and high molecular diversity through biotic and abiotic processes. Here we demonstrate that the molecular composition and properties of dissolved organic matter continuously change during soil passage and propose that this reflects a continual shifting of its sources. Using ultrahigh-resolution mass spectrometry and nuclear magnetic resonance spectroscopy, we studied the molecular changes of dissolved organic matter from the soil surface to 60 cm depth in 20 temperate grassland communities in soil type Eutric Fluvisol. Applying a semi-quantitative approach, we observed that plant-derived molecules were first broken down into molecules containing a large proportion of low-molecular-mass compounds. These low-molecular-mass compounds became less abundant during soil passage, whereas larger molecules, depleted in plant-related ligno-cellulosic structures, became more abundant. These findings indicate that the small plant-derived molecules were preferentially consumed by microorganisms and transformed into larger microbial-derived molecules. This suggests that dissolved organic matter is not intrinsically recalcitrant but instead persists in soil as a result of simultaneous consumption, transformation and formation.

    Antibiotic research and development: business as usual?
    Harbarth, S. ; Theuretzbacher, U. ; Hackett, J. ; Adriaenssens, N. ; Anderson, J. ; Antonisse, A. ; Ardal, C. ; Baillon-Plot, N. ; Baraldi, E. ; Bhatti, T. ; Bradshaw, D. ; Brown, N. ; Carmeli, Y. ; Cars, O. ; Charbonneau, C. ; Cheng, S. ; Ciabuschi, F. ; Cirino, J. ; Clift, C. ; Colson, A. ; Dane, A. ; De-Lima, N. ; Dooa, M. ; Drabik, D. ; Eisenstein, B. ; Farquhar, R. ; Fidan, D. ; Galli, F. ; Gilchrist, K. ; Gilman, S. ; Goeschl, T. ; Goodall, J. ; Goossens, H. ; Gouglas, D. ; Guise, T. ; Gyssens, I. ; Hallerback, P. ; Heymann, D. ; Hoffman, S. ; Howell, J. ; Hulscher, M. ; Hunt, T. ; Huttner, B. ; Jantarada, F. ; Lindgren, E. ; Nolet, B. ; Schouten, J. ; Vink, P. ; Wesseler, J. - \ 2015
    Journal of Antimicrobial Chemotherapy 70 (2015)6. - ISSN 0305-7453 - p. 1604 - 1607.
    The global burden of antibiotic resistance is tremendous and, without new anti-infective strategies, will continue to increase in the coming decades. Despite the growing need for new antibiotics, few pharmaceutical companies today retain active antibacterial drug discovery programmes. One reason is that it is scientifically challenging to discover new antibiotics that are active against the antibiotic-resistant bacteria of current clinical concern. However, the main hurdle is diminishing economic incentives. Increased global calls to minimize the overuse of antibiotics, the cost of meeting regulatory requirements and the low prices of currently marketed antibiotics are strong deterrents to antibacterial drug development programmes. New economic models that create incentives for the discovery of new antibiotics and yet reconcile these incentives with responsible antibiotic use are long overdue. DRIVE-AB is a €9.4 million public–private consortium, funded by the EU Innovative Medicines Initiative, that aims to define a standard for the responsible use of antibiotics and to develop, test and recommend new economic models to incentivize investment in producing new anti-infective agents.
    Do Farmers reduce genetic diversity when they domesticate tropical trees? a case study from Amazonia.
    Hollingsworth, P.M. ; Dawson, I.K. ; Goodall-Copestake, W.P. ; Richardson, J.E. ; Weber, J.C. ; Sotelo Montes, C. ; Pennington, R.T. - \ 2005
    Molecular Ecology 14 (2005)2. - ISSN 0962-1083 - p. 497 - 501.
    conservation - leguminosae - bottlenecks - richness - markers
    Agroforestry ecosystems may be an important resource for conservation and sustainable use of tropical trees, but little is known of the genetic diversity they contain. Inga edulis, a widespread indigenous fruit tree in South America, is used as a model to assess the maintenance of genetic diversity in five planted vs. five natural stands in the Peruvian Amazon. Analysis of five SSR (simple sequence repeat) loci indicated lower allelic variation in planted stands [mean corrected allelic richness 31.3 (planted) and 39.3 (natural), P = 0.009]. Concerns regarding genetic erosion in planted Amazonian tree stands appear valid, although allelic variation on-farm is still relatively high
    ABC transporters of the wheat pathogen Mycosphaerella graminicola function as protectants against biotic and xenobiotic toxic compounds
    Zwiers, L.H. ; Stergiopoulos, I. ; Gielkens, M.M.C. ; Goodall, S.D. ; Waard, M.A. de - \ 2003
    Molecular Genetics and Genomics 269 (2003). - ISSN 1617-4615 - p. 499 - 507.
    atp-binding cassette - pleiotropic drug-resistance - saccharomyces-cerevisiae - phytoalexin resveratrol - pseudomonas-fluorescens - septoria-tritici - b resistance - gene encodes - in-vivo - efflux
    We have studied the role of five ABC transporter genes (MgAtr to MgAtr5) from the wheat pathogen Mycosphaerella graminicola in multidrug resistance (MDR). Complementation of Saccharomyces cerevisiae mutants with the ABC transporter genes from M. graminicola showed that all the genes tested encode proteins that provide protection against chemically unrelated compounds, indicating that their products function as multidrug transporters with distinct but overlapping substrate specificities. Their substrate range in yeast includes fungicides, plant metabolites, antibiotics, and a mycotoxin derived from Fusarium graminearum (diacetoxyscirpenol). Transformants of M. graminicola in which individual ABC transporter genes were deleted or disrupted did not exhibit clear-cut phenotypes, probably due to the functional redundancy of transporters with overlapping substrate specificity. Independently generated MgAtr5 deletion mutants of M. graminicola showed an increase in sensitivity to the putative wheat defence compound resorcinol and to the grape phytoalexin resveratrol, suggesting a role for this transporter in protecting the fungus against plant defence compounds. Bioassays with antagonistic bacteria indicated that MgAtr2 provides protection against metabolites produced by Pseudomonas fluorescens and Burkholderia cepacia. In summary, our results show that ABC transporters from M. graminicola play a role in protection against toxic compounds of natural and artificial origin.
    Functional analysis of transporters in the wheat pathogen Mycosphaerella graminicola
    Stergiopoulos, I. ; Zwiers, L.H. ; Gielkens, M.M.C. ; Goodall, S.D. ; Venema, K. ; Waard, M.A. De - \ 2002
    In: Modern fungicides and antifungal compounds III, 13th International Reinhardbrunn Symposium, 14-18 May 2001 / Dehne, H.W., Gisi, U., Kuck, K.H., Russell, P.E., Lyr, H., Thuringia, Germany : - ISBN 9783786201441 - p. 177 - 186.
    Molecular cloning and characterisation of three new ATP-binding cassette transporter genes from the wheat pathogen Mycosphaerella graminicola
    Stergiopoulos, I. ; Gielkens, M.M.C. ; Goodall, S.D. ; Venema, K. ; Waard, M.A. De - \ 2002
    Gene 289 (2002). - ISSN 0378-1119 - p. 141 - 149.
    Three single copy ATP-binding cassette (ABC) transporter encoding genes, designated MgAtr3, MgAtr4, and MgAtr5, were cloned and sequenced from the plant pathogenic fungus Mycosphaerella graminicola. The encoded ABC proteins all exhibit the [NBD-TMS6]2 configuration and can be classified as novel members of the pleiotropic drug resistance (PDR) class of ABC transporters. The three proteins are highly homologous to other fungal and yeast, ABC proteins involved in multidrug resistance or plant pathogenesis. MgAtr4 and MgAtr5 possess a conserved ABC motif at both the N- and C-terminal domain of the protein. In contrast, the Walker A motif in the N-terminal and the ABC signature in the C-terminal domain of MgAtr3, deviate significantly from the consensus sequence found in other members of the PDR class of ABC transporters. Expression of MgAtr3 could not be detected under any of the conditions tested. However, MgAtr4 and MgAtr5 displayed distinct expression profiles when treated with a range of compounds known to be either substrates or inducers of ABC transporters. These included synthetic fungitoxic compounds, such as imazalil and cyproconazole, natural toxic compounds, such as the plant defence compounds eugenol and psoralen, and the antibiotics cycloheximide and neomycin. The expression pattern of the genes was also dependent on the morphological state of the fungus. The findings suggest a role for MgAtr4 and MgAtr5 during plant pathogenesis and in protection against toxic compounds.
    ABC transporters in the wheat pathogen Mycosphaerella graminicola
    Stergiopoulos, I. ; Gielkens, M.M.C. ; Goodall, S.D. ; Venema, K. ; Zwiers, L.H. ; Waard, M.A. De - \ 2001
    In: Book of Abstracts 3rd FEBS Advanced Lecture Course ATP-binding cassette (ABC) proteins: from genetic disease to multidrug resistance, Grosau, Austria, 3-10 March 2001. - Grosau, Austria : [s.n.], 2001 - p. 118 - 118.
    Functional analysis of ABC transporters in the wheat pathogen Mycosphaerella graminicola
    Stergiopoulos, I. ; Gielkens, M.M.C. ; Goodall, S.D. ; Venema, K. ; Zwiers, L.H. ; Waard, M.A. De - \ 2001
    In: Book of Abstracts 13th International Reinhardsbrunn Symposium, Friedrichroda, Germany, 14-18 May 2001 Friedrichroda, Germany : - p. 59 - 59.
    ATP-binding cassette (ABC)transporters from the wheat pathogen Mycosphaerella graminicola
    Waard, M.A. De; Gielkens, M.M.C. ; Goodall, S.D. ; Stergiopoulos, I. ; Venema, K. ; Zwiers, L.H. - \ 2001
    In: Book of Abstracts XXI Fungal Genetics Conference, Asilomar, USA, 13-18 March 2001 Asilomar, USA : - p. 97 - 97.
    Identification of two major virion protein genes of white spot syndrome virus of shrimp
    Hulten, M.C.W. van; Westenberg, M. ; Goodall, S.D. ; Vlak, J.M. - \ 2000
    Virology 266 (2000). - ISSN 0042-6822 - p. 227 - 236.
    White Spot Syndrome Virus (WSSV) is an invertebrate virus, causing considerable mortality in shrimp. Two structural proteins of WSSV were identified. WSSV virions are enveloped nucleocapsids with a bacilliform morphology with an approximate size of 275 x 120 nm, and a tail-like extension at one end. The double-stranded viral DNA has an approximate size 290 kb. WSSV virions, isolated from infected shrimps, contained four major proteins: 28 kDa (VP28), 26 kDa (VP26), 24 kDa (VP24), and 19 kDa (VP19) in size, respectively. VP26 and VP24 were found associated with nucleocapsids; the others were associated with the envelope. N-terminal amino acid sequences of nucleocapsid protein VP26 and the envelope protein VP28 were obtained by protein sequencing and used to identify the respective genes (vp26 and vp28) in the WSSV genome. To confirm that the open reading frames of WSSV vp26 (612) and vp28 (612) are coding for the putative major virion proteins, they were expressed in insect cells using baculovirus vectors and analyzed by Western analysis. A polyclonal antiserum against total WSSV virions confirmed the virion origin of VP26 and VP28. Both proteins contained a putative transmembrane domain at their N terminus and many putative N- and O-glycosylation sites. These major viral proteins showed no homology to baculovirus structural proteins, suggesting, together with the lack of DNA sequence homology to other viruses, that WSSV may be a representative of a new virus family, Whispoviridae.
    Three major structural proteins of White Spot Syndrome Virus have evolved by gene duplication
    Hulten, M.C.W. van; Zandbergen, F. ; Westenberg, M. ; Goodall, S.D. ; Vlak, J.M. - \ 2000
    In: 33rd Annual Meeting of the Society for Invertebrate Pathology Guanajuato : - p. 96 - 96.
    An economic model to estimate farm-specific losses due to Bovine Respiratory Diseases in dairy heifers
    Fels-Klerx, H.J. van der; Jalvingh, A.W. ; Huirne, R.B.M. ; Dijkhuizen, A.A. - \ 2000
    In: Proceedings of a meeting held at the University of Edinburgh on the 29th, 30th and 31st o March 2000 : Society for Veterinary Epidemiology and Preventive Medicine, Edinburg, 2000 / M.V. Thrusfield and E.A. Goodall. - Edinburgh : [s.n.], 2000. - ISBN 0 948073 44 6 - p. 163 - 170.
    ABC transporters in the wheat pathogen Mycosphaerella graminicola
    Stergiopoulos, I. ; Gielkens, M.M.C. ; Goodall, S.D. ; Venema, K. ; Zwiers, L.H. ; Waard, M.A. de - \ 2000
    In: Abstract book Autumnschool 2000 : Interactions between plants and attacking organisms; mechanisms, genetics, ecology and evolution, Wageningen, the Netherlands, 16-18 October 2000 Wageningen : Graduate Schools EPS and PE&RC - p. 34 - 34.
    Simulation of two different emergency vaccination campaigns with marker vaccine in the control of the Dutch CSF epidemic in 1997/98
    Mangen, M.M.J. ; Nielen, M. ; Jalvingh, A.W. ; Dijkhuizen, A.A. - \ 2000
    In: Proceedings of a meeting held at the University of Edinburgh on the 29th, 30th and 31st of March 2000 : Society for Veterinary Epidemiology and Preventive Medicine, Edinburgh, 2000 / Thrusfield, M.V., Goodall, E.A., - p. 48 - 59.
    Risk of animal movements for the introduction of contagious animal diseases into densely populated livestock areas of the European Union
    Vos, C.J. de; Horst, H.S. ; Dijkhuizen, A.A. - \ 2000
    In: Proceedings of a meeting held at the University of Edinburgh on the 29th, 30th and 31st of March 2000 : Society for Veterinary Epidemilogy and Preventive Medicine, Edinburgh, 2000 / Thrusfield, M.V., Goodall, E.A., Edinburgh : - ISBN 9780948073441 - p. 124 - 136.
    ABC transporters in the wheat pathogen Mycosphaerella graminicola
    Zwiers, L.H. ; Gielkens, M.M.C. ; Goodall, S.D. ; Stergiopoulos, I. ; Venema, K. ; Waard, M.A. de - \ 1999
    Fungal Genetics Newsletter 46 (1999)supplement. - ISSN 0895-1942 - p. 122 - 122.
    ABC transporters in the wheat pathogen Mycosphaerella graminicola
    Zwiers, L.H. ; Gielkens, M. ; Goodall, S. ; Stergiopoulos, I. ; Venema, K. ; Waard, M. de - \ 1999
    In: Book of abstracts : 9th International Congress on Molecular Plant-Microbe Interactions, Amsterdam, the Netherlands, 25-30 July 1999. - [S.l.] : [s.n.], 1999 - p. 73 - 73.
    Economic analysis of animal welfare aspects in the broiler production chain
    Maurice, H. ; Horst, H.S. ; Horne, P.L.M. van; Dijkhuizen, A.A. - \ 1999
    In: Society for Veterinary Epidemiology and Preventive Medicine : Proceedings of a meeting held at the University of Bristol, March 24 - 26, 1999 / E.A. Goodall, M.V. Thrusfield - ISBN: 0-948073-39 X - p. 182 - 196.
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