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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    Wildlife roadkill patterns in a fragmented landscape of the Western Amazon
    Filius, Jonathan ; Hoek, Yntze van der; Jarrín-V, Pablo ; Hooft, Pim van - \ 2020
    Ecology and Evolution 10 (2020)13. - ISSN 2045-7758 - p. 6623 - 6635.
    Amazon - herpetofauna - hotspots - road ecology - roadkill - spatial patterns

    One of the most evident and direct effects of roads on wildlife is the death of animals by vehicle collision. Understanding the spatial patterns behind roadkill helps to plan mitigation measures to reduce the impacts of roads on animal populations. However, although roadkill patterns have been extensively studied in temperate zones, the potential impacts of roads on wildlife in the Neotropics have received less attention and are particularly poorly understood in the Western Amazon. Here, we present the results of a study on roadkill in the Amazon region of Ecuador; a region that is affected by a rapidly increasing development of road infrastructure. Over the course of 50 days, in the wet season between September and November 2017, we searched for road-killed vertebrates on 15.9 km of roads near the city of Tena, Napo province, for a total of 1,590 surveyed kilometers. We recorded 593 dead specimens, predominantly reptiles (237 specimens, 40%) and amphibians (190, 32%), with birds (102, 17%) and mammals (64, 11%) being less common. Recorded species were assigned to three functional groups, based on their movement behavior and habitat use (“slow,” “intermediate,” and “fast”). Using Ripley's K statistical analyses and 2D HotSpot Identification Analysis, we found multiple distinct spatial clusters or hotspots, where roadkill was particularly frequent. Factors that potentially determined these clusters, and the prevalence of roadkill along road segments in general, differed between functional groups, but often included land cover variables such as native forest and waterbodies, and road characteristics such as speed limit (i.e., positive effect on roadkill frequency). Our study, which provides a first summary of species that are commonly found as roadkill in this part of the Amazon region, contributes to a better understanding of the negative impacts of roads on wildlife and is an important first step toward conservation efforts to mitigate these impacts.

    High-Speed Super-Resolution Imaging Using Protein-Assisted DNA-PAINT
    Filius, Mike ; Cui, Tao Ju ; Ananth, Adithya N. ; Docter, Margreet W. ; Hegge, Jorrit W. ; Oost, John van der; Joo, Chirlmin - \ 2020
    Nano Letters 20 (2020)4. - ISSN 1530-6984 - p. 2264 - 2270.
    Ago-PAINT - Argonaute - DNA origami - DNA-PAINT - single-molecule FRET - super-resolution microscopy

    Super-resolution imaging allows for the visualization of cellular structures on a nanoscale level. DNA-PAINT (DNA point accumulation in nanoscale topology) is a super-resolution method that depends on the binding and unbinding of DNA imager strands. The current DNA-PAINT technique suffers from slow acquisition due to the low binding rate of the imager strands. Here we report on a method where imager strands are loaded into a protein, Argonaute (Ago), which allows for faster binding. Ago preorders the DNA imager strand into a helical conformation, allowing for 10 times faster target binding. Using a 2D DNA origami structure, we demonstrate that Ago-assisted DNA-PAINT (Ago-PAINT) can speed up the current DNA-PAINT technique by an order of magnitude, while maintaining the high spatial resolution. We envision this tool to be useful for super-resolution imaging and other techniques that rely on nucleic acid interactions.

    Uitverkoop van de ruimtelijke ordening en planologie in Nederland?
    Pleijte, M. - \ 2009
    In: Plandag 2009, Tussen Droom en Werkelijkheid, Brussels, Belgium 07 May 2009. - Delft : Stichting Planologische Discussiedagen - ISBN 9789080854574 - p. 215 - 221.
    Modeling the binding of fulvic acid by goethite: The speciation of adsorbed FA molecules
    Filius, J.D. ; Meeussen, J.C.L. ; Hiemstra, T. ; Riemsdijk, W.H. van - \ 2003
    Geochimica et Cosmochimica Acta 67 (2003)8. - ISSN 0016-7037 - p. 1463 - 1474.
    natural organic-matter - nica-donnan model - humic substances - surface complexation - competitive adsorption - proton binding - hydrous oxides - ion-binding - iron-oxide - charge
    Under natural conditions, the adsorption of ions at the solid-water interface may be strongly influenced by the adsorption of organic matter. In this paper, we describe the adsorption of fulvic acid (FA) by metal (hydr)oxide surfaces with a heterogeneous surface complexation model, the ligand and charge distribution (LCD) model. The model is a self-consistent combination of the nonideal competitive adsorption (NICA) equation and the CD-MUSIC model. The LCD model can describe simultaneously the concentration, pH, and salt dependency of the adsorption with a minimum of only three adjustable parameters. Furthermore, the model predicts the coadsorption of protons accurately for an extended range of conditions. Surface speciation calculations show that almost all hydroxyl groups of the adsorbed FA molecules are involved in outer sphere complexation reactions. The carboxylic groups of the adsorbed FA molecule form inner and outer sphere complexes. Furthermore, part of the carboxylate groups remain noncoordinated and deprotonated. Copyright (C) 2003 Elsevier Science Ltd.
    Financial analysis of sustained forest management for timber: perspectives for application of the CELOS management system in Brazilian Amazonia
    Graaf, N.R. de; Filius, A.M. ; Huesca Santos, A.R. - \ 2003
    Forest Ecology and Management 177 (2003). - ISSN 0378-1127 - p. 287 - 299.
    Sustained management of the Terra Firme Forest in Amazonia is financially analysed for an integrated forest management and timber processing industry. Two scenarios are studied, one with reduced impact logging (RIL) and sparing of reserves without silvicultural follow-up in a 100-year harvesting cycle, and another one inclusive of silviculture after RIL, liberating reserves in a 25-year cycle. Cycle lengths are based on CELOS research in Suriname. Acquisition of land is assumed to be complete at the beginning, the 100-year cycle option needing four times as much land as the 25-year cycle option. A cash flow analysis over a 100-year period for both options with a 8% discount rate shows that the total costs in the land-intensive option (25 years) with silviculture are considerably less than in the land-extensive option; the lower cost of infrastructure, log transportation and land acquisition offset the cost of silviculture. Because the annual revenues from timber sale are the same in both options, the NPV of the intensive option is also much higher. A sensitivity analysis shows that the land-intensive option is expected to give still a positive NPV in less favourable situations. The relatively small forest area in the land-intensive option together with the organisational setting, which includes integration with the processing industry, favours a sustainable development. More intensive management gives signals to settlers that helps prevent their encroachment. In addition, the higher annual increment in this option facilitates a contribution to regional development and makes a larger area available for strict nature reserves. (C) 2002 Elsevier Science B.V. All rights reserved.
    Transport of humic and fulvic acid in an acid sandy soil
    Weng, L. ; Fest, E. ; Filius, J. ; Temminghoff, E.J.M. ; Riemsdijk, W.H. van - \ 2002
    In: Humic substances: natures̕ most versatile materials : Proceedings of the 20th Anniversary Conference of the International Humic Substances Society ; July 21 - 26, 2002, Northeastern University, Boston, Massachusetts, United States of America. - Boston : IHSS - p. 168 - 171.
    Transport of humic and fulvic acids in relation to metal mobility in a copper-contaminated acid sandy soil
    Weng, L. ; Fest, E.P.M.J. ; Filius, J. ; Temminghoff, E.J.M. ; Riemsdijk, W.H. van - \ 2002
    Environmental Science and Technology 36 (2002). - ISSN 0013-936X - p. 1699 - 1704.
    The transport of inorganic and organic pollutants in water and soil can be strongly influenced by the mobility of natural dissolved organic matter (DOM). In this paper, the transport of a humic acid (HA) and a fulvic acid (FA) in a copper-contaminated acid sandy soil was studied. The data showed that the transport behavior of HA differed from that of FA. The breakthrough curves (BTCs) of HA were characterized by a rapid relatively sharp front followed by a plateau at a lower HA concentration than in the influent solution. The increase of the Ca concentration decreased the HA concentration further. Compared to HA, the BTCs of FA were retarded and showed an extended tailing, approaching complete breakthrough. The increase of the Ca concentration decreased the FA concentration only temporarily. On the basis of our model calculation, the characterization of HA transport could be explained by the coagulation of HA largely upon the binding of Al. The increase of the Ca concentration resulted in further coagulation of HA because of the increased Ca adsorption, which occurred mainly in the Donnan phase. For FA, the adsorption to the soil matrix was more likely the process that controls its solubility and mobility. The mobility of Al and Cu in the soil column was closely related to the solubility and transport of the DOM in soil solution. The concentration of Ca in the effluent was lower than in the influent because Ca was retained in the soil due to the retardation of HA and FA and due to the compensation of the other cations released from the soil to the solution
    Communicatie volgens Ko de Boswachter; studie naar de rol van communicatie bij de vervreemding tussen bosbezoekers en bosbeheerder in Nederland
    Bezemer, V. ; Verbij, E.E.M. ; Filius, P. - \ 2001
    Wageningen : Alterra (Alterra-rapport 212) - 75
    bossen - recreatie - bosbedrijfsvoering - taxatie - communicatie - begrazing - herbivoren - geïntroduceerde soorten - nederland - forests - recreation - forest management - valuation - communication - grazing - herbivores - introduced species - netherlands
    In deze studie wordt de rol van communicatie in het proces van vervreemding tussen bosgebruikers en bosbeheerders verder uitgediept. Hierbij gaat het om de rol die communicatie nu speelt en in de toekomst kan spelen om het proces van vervreemding bij te sturen in de gewenste richting. Aan de hand van de thematische casussen exoten en grote grazers wordt het communicatietraject omtrent deze onderwerpen op een systematische wijze geanalyseerd. Gekeken wordt naar de kern van het probleem, de doelgroepenvan communicatie, de inhoud van de boodschap, de communicatiemiddelen en de organisatie en logistiek. Een belangrijke conclusie is om in de communicatie in te spelen op de waarden die belangrijk worden gevonden door de doelgroep, in dit geval de bosbezoekers.
    Modeling the adsorption of weak organic acids on goethite : the ligand and charge distribution model
    Filius, J.D. - \ 2001
    Wageningen University. Promotor(en): W.H. Van Riemsdijk; J.C.L. Meeussen. - S.l. : S.n. - ISBN 9789058084545 - 183
    organische zuren - goethiet - adsorptie - biologische beschikbaarheid - transportprocessen - organic acids - goethite - adsorption - bioavailability - transport processes

    A detailed study is presented in which the CD-MUSIC modeling approach is used in a new modeling approach that can describe the binding of large organic molecules by metal (hydr)oxides taking the full speciation of the adsorbed molecule into account. Batch equilibration experiments were performed using the iron (hydr)oxide goethite to determine the adsorption of a series of weak organic acids (e.g. lactic acid, oxalic acid, malonic acid, phthalic acid, citric acid, and fulvic acid). In order to develop the new modeling approach, the binding of weak organic acids with a well-defined structure and charging behavior is first described using the classical CD-MUSIC model approach. The adsorption can be described accurately with a limited number of surface species, which differ in the degree of protonation and in the number of inner sphere and outer sphere complexes formed between the reactive groups of the organic molecule and the oxide surface. For the formation of inner and outer sphere complexes, a constant distribution of charge over the solid/water interface is assumed. With the same charge distribution for inner and outer sphere complexes, the adsorption of FA is described with the CD-MUSIC model using a small set of discrete surface species. This approach is not fully satisfactory since it does not take the full speciation of the adsorbed weak organic acids into account as can be inferred from spectroscopic data. In order to take the full possible speciation of the adsorbed organic molecule into account, a new model concept was developed. In the ligand and charge distribution (LCD) model concept, the number of inner sphere, outer sphere and proton complexes of the reactive groups of one adsorbed organic molecule is calculated using the NICCA equation. From the resulting speciation of the adsorbed molecule, the main input parameters of the CD-MUSIC model are obtained. The new model concept is successfully tested on the adsorption and infrared data of benzenecarboxylic acid adsorption on goethite by Boily et al. (2000a,b). The LCD model was extended for the surface complexation of the phenolic groups in order to describe the previously determined data of FA adsorption by goethite. Simultaneously, the concentration, pH, and salt dependency of the FA adsorption are described well. Furthermore, the co-adsorption of protons upon the adsorption of FA by goethite is predicted accurately. The developed model approach offers new insights in the fundamental understanding of ion adsorption under natural conditions.

    Modeling the binding of benzenecarboxylates by goethite: The ligand and charge distribution model
    Filius, J.D. ; Meeussen, J.C.L. ; Hiemstra, T. ; Riemsdijk, W.H. van - \ 2001
    Journal of Colloid and Interface Science 244 (2001). - ISSN 0021-9797 - p. 31 - 42.
    A heterogeneous complexation model approach has been developed to describe the adsorption of large organic molecules by goethite taking the full speciation of the adsorbed molecules into account. The essence of the model is the calculation of the mean mode of an adsorbed organic molecule, defined by an overall affinity, charge distribution, and reaction stoichiometry. The calculation of the mean mode of the adsorbed organic molecule is based on the pH-dependent interaction of a functional group for binding a proton or forming an inner or outer sphere complex with specific surface sites. The distribution of the organic molecules over the solid and solution phases is calculated using the CD-MUSIC model with parameters obtained from the mean mode of the adsorbed molecule. The mean mode of the adsorbed molecule is calculated using the competitive Langmuir or NICCA equation in combination with an electrostatic model comprising charge distribution, taking the competitive binding of functional groups with protons or surface sites into account. The new model is applied to the adsorption data of a series of benzenecarboxylic acids. The model approach can describe simultaneously the concentration, pH, and salt dependency of the benzenecarboxylate adsorption. Furthermore, the model is applied to describe data obtained from IR spectroscopy. The new approach predicts the data reasonably well using only three adjustable parameters in case of the NICCA-CD-MUSIC approach. The average stoichiometry of the overall reaction is not an input parameter of the model but is an output parameter. In future work the new model will be applied to the adsorption of larger organic acids, e.g., fulvic acid
    Natuurbeleving door doelgroepen; waarden en wensen van jagers, sportvissers, vogelwerkgroepleden en vrijwilligers in het landschapsbeheer
    Filius, P. ; Buijs, A.E. ; Goossen, C.M. - \ 2000
    Wageningen : Alterra (Alterra-rapport 104) - 63
    landschap - milieubeheer - perceptie - openluchtrecreatie - attitudes - jagen - vis vangen - nederland - vogels kijken - kennis - natuur - landscape - environmental management - perception - outdoor recreation - attitudes - hunting - fishing - netherlands - birdwatching - knowledge - nature
    Aan de hand van een schriftelijke enqulte onder groepen van elk ongeveer veertig jagers, vissers, vogelwerkgroepleden en vrijwilligers in het landschapsbeheer wordt de relatie met de natuur beschreven van intensief bij de natuur betrokken doelgroepen.Vanwege de intensiteit waarmee deze groepen de natuur bezoeken en de rol die de groepen spelen bij draagvlak en uitvoering van natuurbeleid, is het van belang rekening te houden met hun wensen en voorkeuren voor beheer en inrichting van de groene omgeving. Een belangrijke conclusie uit het onderzoek is dat (kleinschalige) cultuurlandschappen voor alle groepen in dit onderzoek belangrijk zijn. Bij communicatie met deze groepen is het van belang zich te verplaatsen in hun gedachtewereld. De verschillen tussen jagers en leden van de vogelwerkgroep zijn het meest opvallend. Jagers kenmerken zich door een meer antropocentrische grondhouding ten aanzien van de natuur en een breed natuurbeeld, waarbij aanwezigheid en ingrijpen van de mens vaak als onderdeel van de natuur worden gezien. Leden van de vogelwerkgroep hebben een meer ecocentrische grondhouding ten aanzien van de natuur en een smaller natuurbeeld, waarin de nadruk ligt op grootschalige en autonome natuur.
    Vertegenwoordigers in beleidsprocessen; manoeuvreren tussen beleid en achterban
    Verbij, E.E.M. ; Bervaes, J.C.A.M. ; Filius, P. - \ 2000
    Wageningen : Alterra (Alterra-rapport 105) - 51
    beleid - grondbeleid - overheidsbeleid - structuurbeleid - participatie - participatief management - belangengroepen - policy - land policy - government policy - structural policy - participation - participative management - interest groups
    De overheid streeft ernaar maatschappelijke partners meer te betrekken bij het totstandkomen en uitvoeren van beleid. Vertegenwoordigers van maatschappelijke organisaties en overheid spelen daarbij een belangrijke rol. In de praktijk moeten vertegenwoordigers zowel opkomen voor de belangen van hun achterban, als op een constructieve wijze deelnemen aan planvorming. In deze studie is de rol van vertegenwoordigers in beeld gebracht aan de hand van een casestudie van de processen rond de planvorming voor landinrichting in de Gooi en Vechtstreek. Gebleken is dat vertegenwoordigers niet alleen moeten beschikken over veel kennis van de beleidsomgeving, goede communicatieve vaardigheden en veel tijd, ook moeten zij hun onderhandelingsstijl kunnen aanpassenaan verschillende fasen in de planvorming. Vertegenwoordigers van de overheid en maatschappelijke organisaties kunnen alleen goed functioneren als zij onderhandelingsruimte hebben gekregen van hun achterban. Hiërarchische manieren van sturing, waarbij beleid van bovenaf wordt opgelegd, bieden geen onderhandelingsruimte.
    Adsorption of fulvic acid on goethite
    Filius, J.D. ; Lumsdon, D.G. ; Meeussen, J.C.L. ; Hiemstra, T. ; Riemsdijk, W.H. van - \ 2000
    Geochimica et Cosmochimica Acta 64 (2000). - ISSN 0016-7037 - p. 51 - 60.
    Etudes Économiques
    Filius, A.M. - \ 2000
    In: Elaboration du Plan d'Aménagement du Site du Programme Tropenbos Cameroon : Séminaire Atelier "Elaboration du Plan d'Aménagement du Site du Programme Tropenbos Cameroon" , Kribi, 1996 / O. Eyog Matig, P. Schmidt, B. Foahom. - Kribi, Kameroen : Tropenbos - Cameroon Programme, 2000. (Tropenbos-Cameroon Reports 00-4) - p. 30 - 35.
    Infrastructurele projecten en recreatiekwaliteit; een verkennende studie naar de gevolgen, samenhang en kansen
    Apell, C.A.M. ; Seegeren, A.H.J. ; Filius, P. - \ 1999
    Wageningen : IBN-DLO (IBN-rapport 415) - 78 p.
    The Netherlands
    Schmidt, P. ; Kuiler, E. ; Wiersum, F. ; Filius, B. - \ 1999
    In: Forestry in changing societies in Europe; Information for teaching module - Study book, Part II: Forestry in changing societies in Europe / Pelkonen, P., Pitkänen, A., Schmidt, P., Oesten, G., Piussie, P., Rojas, E., - p. 229 - 253.
    Transport of malonate in a goethite-silica sand system
    Filius, J.D. ; Meeussen, J.C.L. ; Riemsdijk, W.H. van - \ 1999
    Colloids and Surfaces. A: Physicochemical and Engineering Aspects 151 (1999). - ISSN 0927-7757 - p. 245 - 253.
    Synthesis and significance of the results of the research in management and economics for the design of a forest management plan
    Eba'a Atyi, R. ; Filius, A.M. - \ 1999
    In: Forest management related studies of the Tropenbos-Cameroon Programme, Wageningen, 1 october 1998. / W.B.J. Jonkers, M. Wessel (eds.). - Wageningen, Tropenbos-Cameroon Programme, 1999. (Tropenbos-Cameroon Reports; 99-1) - p. 69 - 78.
    Natuurbeelden in de praktijk : de invloed van natuurbeelden en natuurvisies op gedrag en mening over het beleid
    Buijs, A.E. ; Filius, P. - \ 1998
    Wageningen : DLO-Staring Centrum [etc.] (Rapport / DLO-Staring Centrum 623) - 86
    natuurbescherming - overheidsbeleid - perceptie - samenleving - attitudes - nature conservation - government policy - perception - society - attitudes
    Graadmeters sociaal draagvlak en beleving
    Buijs, A.E. ; Coeterier, J.F. ; Filius, P. ; Schöne, M.B. - \ 1998
    [Wageningen] : DLO-Staringcentrum (Werkdocument / DLO Natuurplanbureau-onderzoek 1998/07) - 98 p.
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