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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    Light availability and land-use history drive biodiversity and functional changes in forest herb layer communities
    Depauw, Leen ; Perring, Michael P. ; Landuyt, Dries ; Maes, Sybryn L. ; Blondeel, Haben ; Lombaerde, Emiel De; Brūmelis, Guntis ; Brunet, Jörg ; Closset-Kopp, Déborah ; Czerepko, Janusz ; Decocq, Guillaume ; Ouden, Jan den; Gawryś, Radosław ; Härdtle, Werner ; Hédl, Radim ; Heinken, Thilo ; Heinrichs, Steffi ; Jaroszewicz, Bogdan ; Kopecký, Martin ; Liepiņa, Ilze ; Macek, Martin ; Máliš, František ; Schmidt, Wolfgang ; Smart, Simon M. ; Ujházy, Karol ; Wulf, Monika ; Verheyen, Kris - \ 2020
    Journal of Ecology 108 (2020)4. - ISSN 0022-0477 - p. 1411 - 1425.
    atmospheric depositions - biodiversity measures - climate change - forest canopy features - functional signature - post-agricultural forests - resurvey

    A central challenge of today's ecological research is predicting how ecosystems will develop under future global change. Accurate predictions are complicated by (a) simultaneous effects of different drivers, such as climate change, nitrogen deposition and management changes; and (b) legacy effects from previous land use. We tested whether herb layer biodiversity (i.e. richness, Shannon diversity and evenness) and functional (i.e. herb cover, specific leaf area [SLA] and plant height) responses to environmental change drivers depended on land-use history. We used resurvey data from 192 plots across nineteen European temperate forest regions, with large spatial variability in environmental change factors. We tested for interactions between land-use history, distinguishing ancient and recent (i.e. post-agricultural) forests and four drivers: temperature, nitrogen deposition, and aridity at the regional scale and light dynamics at the plot-scale. Land-use history significantly modulated global change effects on the functional signature of the herb layer (i.e. cover, SLA and plant height). Light availability was the main environmental driver of change interacting with land-use history. We found greater herb cover and plant height decreases and SLA increases with decreasing light availability in ancient than in recent forests. Furthermore, we found greater decreases in herb cover with increased nitrogen deposition in ancient forests, whereas warming had the strongest decreasing effect on the herb cover in recent forests. Interactive effects between land-use history and global change on biodiversity were not found, but species evenness increased more in ancient than in recent forests. Synthesis. Our results demonstrate that land-use history should not be overlooked when predicting forest herb layer responses to global change. Moreover, we found that herb layer composition in semi-natural deciduous forests is mainly controlled by local canopy characteristics, regulating light levels at the forest floor, and much less by environmental changes at the regional scale (here: warming, nitrogen deposition and aridity). The observed disconnect between biodiversity and functional herb layer responses to environmental changes demonstrates the importance of assessing both types of responses to increase our understanding of the possible impact of global change on the herb layer.

    The impact of probiotics and prebiotics on the immune system.
    Klaenhammer, T.R. ; Kleerebezem, M. ; Kopp, M.V. ; Rescigno, M. - \ 2012
    Nature Reviews. Immunology 12 (2012)10. - ISSN 1474-1733 - p. 728 - 734.
    placebo-controlled trial - lactobacillus-rhamnosus gg - randomized controlled-trial - 1st 6 months - irritable-bowel-syndrome - t-regulatory cells - double-blind - lipoteichoic acid - atopic-dermatitis - experimental colitis
    Probiotics and prebiotics are increasingly being added to foodstuffs with claims of health benefits. Probiotics are live microorganisms that are thought to have beneficial effects on the host, whereas prebiotics are ingredients that stimulate the growth and/or function of beneficial intestinal microorganisms. But can these products directly modulate immune function and influence inflammatory diseases? Here, Nature Reviews Immunology asks four experts to discuss these issues and provide their thoughts on the future application of probiotics as a disease therapy
    Development of a framework based on an ecosystem services approach for deriving specific protection goals for environmental risk assessment of pesticides
    Nienstedt, K.M. ; Brock, T.C.M. ; Wensem, J. van; Montforts, M.H.M.M. ; Hart, A. ; Aagaard, A. ; Alix, A. ; Boesten, J.J.T.I. ; Bopp, S.K. ; Brown, C. ; Capri, E. ; Forbes, V. ; Kopp, H. ; Liess, M. ; Luttik, R. ; Maltby, L. ; Sousa, J.P. ; Streissl, F. ; Hardy, R.H. - \ 2012
    Science of the Total Environment 415 (2012). - ISSN 0048-9697 - p. 31 - 38.
    ecological risk - models
    General protection goals for the environmental risk assessment (ERA) of plant protection products are stated in European legislation but specific protection goals (SPGs) are often not precisely defined. These are however crucial for designing appropriate risk assessment schemes. The process followed by the Panel on Plant Protection Products and their Residues (PPR) of the European Food Safety Authority (EFSA) as well as examples of resulting SPGs obtained so far for environmental risk assessment (ERA) of pesticides is presented. The ecosystem services approach was used as an overarching concept for the development of SPGs, which will likely facilitate communication with stakeholders in general and risk managers in particular. It is proposed to develop SPG options for 7 key drivers for ecosystem services (microbes, algae, non target plants (aquatic and terrestrial), aquatic invertebrates, terrestrial non target arthropods including honeybees, terrestrial non-arthropod invertebrates, and vertebrates), covering the ecosystem services that could potentially be affected by the use of pesticides. These SPGs need to be defined in 6 dimensions: biological entity, attribute, magnitude, temporal and geographical scale of the effect, and the degree of certainty that the specified level of effect will not be exceeded. In general, to ensure ecosystem services, taxa representative for the key drivers identified need to be protected at the population level. However, for some vertebrates and species that have a protection status in legislation, protection may be at the individual level. To protect the provisioning and supporting services provided by microbes it may be sufficient to protect them at the functional group level. To protect biodiversity impacts need to be assessed at least at the scale of the watershed/landscape.
    Exploring high-end scenarios for local sea level rise to develop flood protection strategies for a lowlying delta-the Netherlands as an example
    Katsman, C.A. ; Sterl, A. ; Beersma, H.W. ; Brink, H.W. van den; Church, J.A. ; Hazeleger, W. ; Kopp, R.E. ; Kroon, D. ; Kwadijk, J. ; Lammersen, R. ; Lowe, J. ; Oppenheimer, M. ; Plag, H.P. ; Ridley, J. ; Storch, H. von; Vaughan, D.G. ; Vellinga, P. ; Vermeersen, L.L.A. ; Wal, R.S.W. ; Weise, R. - \ 2011
    Climatic Change 109 (2011)3-4. - ISSN 0165-0009 - p. 617 - 645.
    hoogwaterbeheersing - zeespiegelschommelingen - kustbeheer - flood control - sea level fluctuations - coastal management - greenland ice-sheet - last interglacial period - pine island glacier - climate-change - mass-balance - thermohaline circulation - antarctic peninsula - northeast atlantic - west antarctica - acceleration
    Sea level rise, especially combined with possible changes in storm surges and increased river discharge resulting from climate change, poses a major threat in low-lying river deltas. In this study we focus on a specific example of such a delta: the Netherlands. To evaluate whether the country’s flood protection strategy is capable of coping with future climate conditions, an assessment of low-probability/high-impact scenarios is conducted, focusing mainly on sea level rise. We develop a plausible high-end scenario of 0.55 to 1.15 m global mean sea level rise, and 0.40 to 1.05 m rise on the coast of the Netherlands by 2100 (excluding land subsidence), and more than three times these local values by 2200. Together with projections for changes in storm surge height and peak river discharge, these scenarios depict a complex, enhanced flood risk for the Dutch delta.
    Optimization and prevalidation of the in vitro ER alpha CALUX method to test estrogenic and antiestrogenic activity of compounds
    Burg, B. van der; Winter, R. ; Weimer, M. ; Berckmans, P. ; Suzuki, G. ; Gijsbers, L. ; Jonas, A. ; Linden, S. van der; Witters, H. ; Aarts, J.M.M.J.G. ; Legler, J. ; Kopp-Schneider, A. ; Bremer, S. - \ 2010
    Reproductive Toxicology 30 (2010)1. - ISSN 0890-6238 - p. 73 - 80.
    cell-line - transactivation assay - endocrine disruptors - bioassays - androgen - chemicals - panel - beta
    Estrogenicity of chemicals has received significant attention and is linked to endocrine-disrupting activities. However, there is a paucity of validated methods to assess estrogenicity in vitro. We have established a robust method to test estrogenic and antiestrogenic activity of compounds in vitro, as an alternative to using animal models such as the uterotrophic assay. To this end we optimized protocols to be used in combination with CALUX reporter gene assays and carried out an in house prevalidation, followed by two rounds of tests to establish transferability. Problems in the initial test with transferability were solved by isolation of a novel cell clone of the ER alpha CALUX line with greatly improved stability and luciferase levels. This cell line proved to be a very suitable and reliable predictor of estrogenicity of chemicals and was able to readily rank a range of chemicals on the basis of their EC50 values.
    Exploring high-end climate change scenarios for flood protection of the Netherlands
    Vellinga, P. ; Katsman, C. ; Sterl, A. ; Beersma, J.J. ; Hazeleger, W. ; Church, J. ; Kopp, R. ; Kroon, D. ; Oppenheimer, M. ; Plag, H.P. ; Rahmstorf, S. ; Lowe, J. ; Ridley, J. ; Storch, H. von; Vaughan, D. ; Wal, R. van der; Weisse, R. ; Kwadijk, J. ; Lammersen, R. ; Marinova, N.A. - \ 2009
    De Bilt : KNMI (KNMI scientific report / Royal Netherlands Meteorological Institute WR 2009-05)
    zeespiegelschommelingen - klimaatverandering - kustgebieden - sea level fluctuations - climatic change - coastal areas
    This international scientific assessment has been carried out at the request of the Dutch Delta Committee. The "Deltacommissie" requested that the assessment explore the high-end climate change scenarios for flood protection of the Netherlands. It is a state-of–the art scientific assessment of the upper bound values and longer term projections (for sea level rise up to 2200) of climate induced sea level rise, changing storm surge conditions and peak discharge of river Rhine. It comprises a review of recent studies, model projections and expert opinions of more than 20 leading climate scientists from different countries around the North Sea, Australia and the USA
    Conceptual model for improving the link between exposure and effects in the aquatic risk assessment of pesticides
    Boesten, J.J.T.I. ; Köpp, H. ; Adriaanse, P.I. ; Brock, T.C.M. ; Forbes, V.E. - \ 2007
    Ecotoxicology and Environmental Safety 66 (2007)3. - ISSN 0147-6513 - p. 291 - 308.
    macrophyte-dominated mesocosms - active ingredient linuron - pulsed treatment - responses
    Assessment of risks to aquatic organisms is important in the registration procedures for pesticides in industrialised countries. This risk assessment consists of two parts: (i) assessment of effects to these organisms derived from ecotoxicological experiments (=effect assessment), and (ii) assessment of concentration levels in relevant environmental compartments resulting from pesticide application (=exposure assessment). Current procedures lack a clear conceptual basis for the interface between the effect and exposure assessments which may lead to a low overall scientific quality of the risk assessment. This interface is defined here as the type of concentration that gives the best correlation to ecotoxicological effects and is called the ecotoxicologically relevant concentration (ERC). Definition of this ERC allows the design of tiered effect and exposure assessments that can interact flexibly and efficiently. There are two distinctly different exposure estimates required for pesticide risk assessment: that related to exposure in ecotoxicological experiments and that related to exposure in the field. The same type of ERC should be used consistently for both types of exposure estimates. Decisions are made by comparing a regulatory acceptable concentration (=RAC) level or curve (i.e., endpoint of the effect assessment) with predicted environmental concentration (=PEC) levels or curves (endpoint of the exposure assessment). For decision making based on ecotoxicological experiments with time-variable concentrations a tiered approach is proposed that compares (i) in a first step single RAC and PEC levels based on conservative assumptions, (ii) in a second step graphically RAC and PEC curves (describing the time courses of the RAC and PEC), and (iii) in a third step time-weighted average RAC and PEC levels.
    Electron microscopy of brain amyloid plaques from a patient with new variant Creutzfeldt-Jakob disease
    Fournier, J.G. ; Kopp, N. ; Streichenberger, N. ; Escaig-Haye, F. ; Langeveld, J. ; Brown, P. - \ 2000
    Acta Neuropathologica 99 (2000). - ISSN 0001-6322 - p. 637 - 642.
    Comparative structural analysis and substrate specificity engineering of the hyperthermostable b-glucosidase CelB from Pyrococcus furiosus
    Kaper, T. ; Lebbink, J.H.G. ; Pouwels, J. ; Kopp, J. ; Schulz, G.E. ; Oost, J. van der; Vos, W.M. de - \ 2000
    Biochemistry 39 (2000). - ISSN 0006-2960 - p. 4963 - 4970.
    The substrate specificity of the -glucosidase (CelB) from the hyperthermophilic archaeon Pyrococcus furiosus, a family 1 glycosyl hydrolase, has been studied at a molecular level. Following crystallization and X-ray diffraction of this enzyme, a 3.3 Å resolution structural model has been obtained by molecular replacement. CelB shows a homo-tetramer configuration, with subunits having a typical ()8-barrel fold. Its active site has been compared to the one of the previously determined 6-phospho--glycosidase (LacG) from the mesophilic bacterium Lactococcus lactis. The overall design of the substrate binding pocket is very well conserved, with the exception of three residues that have been identified as a phosphate binding site in LacG. To verify the structural model and alter its substrate specificity, these three residues have been introduced at the corresponding positions in CelB (E417S, M424K, F426Y) in different combinations: single, double, and triple mutants. Characterization of the purified mutant CelB enzyme revealed that F426Y resulted in an increased affinity for galactosides, whereas M424K gave rise to a shifted pH optimum (from 5.0 to 6.0). Analysis of E417S revealed a 5-fold and a 3-fold increase of the efficiency of hydrolyzing o-nitrophenol--D-galactopyranoside-6-phosphate, in the single and triple mutants, respectively. In contrast, their activity on nonphosphorylated sugars was largely reduced (30-300-fold). The residue at position E417 in CelB seems to be the determining factor for the difference in substrate specificity between the two types of family 1 glycosidases.
    Submicroscopic immunodetection of PrP in the brain of a patient with a new-variant of Creutzfeldt-Jakob disease
    Grigoriev, V. ; Escaig-Haye, F. ; Streichenberger, N. ; Kopp, N. ; Langeveld, J. ; Brown, P. ; Fournier, J.G. - \ 1999
    Neuroscience Letters 263 (1999). - ISSN 0304-3940 - p. 1 - 4.
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