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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    Frozen evolution of an RNA virus suggests accidental release as a potential cause of arbovirus re-emergence
    Pascall, David J. ; Nomikou, Kyriaki ; Bréard, Emmenuel ; Zientara, Stephan ; Silva Filipe, Ana da; Hoffmann, Bernd ; Jacquot, Maude ; Singer, Joshua B. ; Clercq, Kris De; Botner, Anette ; Sailleau, Corinne ; Viarouge, Cyril ; Batten, Carrie ; Puggioni, Giantonella ; Ligios, Ciriaco ; Savini, Giovanni ; Rijn, P.A. van; Mertens, Peter P.C. ; Biek, Roman ; Palmarini, Massimo - \ 2020
    PloS Biology (2020). - ISSN 1545-7885
    Measuring macroplastic in the Rhine
    Vriend, Paul - \ 2020
    Sturende factoren voor vissen in het beheersgebied van Waterschap Rijn & IJssel
    Kranenbarg, J. ; Peeters, E.T.H.M. ; Bruin, A. de; Groen, M. - \ 2019
    Nijmegen : Stichting RAVON (RAVON Rapport 2017.093) - 96
    The vegetable and potato sector in Nigeria : an overview of the present status
    Plaisier, Christine ; Dijkxhoorn, Youri ; Rijn, Fédes van; Bonnand, Johann ; Talabi, Olufolajimi - \ 2019
    Wageningen : Wageningen Economic Research (Wageningen Economic Research report 2019-119) - ISBN 9789463951876 - 76
    A living income for smallholder commodity farmers and protected forests and biodiversity: how can the private and public sectors contribute? : White Paper on sustainable commodity production
    Waarts, Y.R. ; Janssen, Valerie ; Ingram, V.J. ; Slingerland, M.A. ; Rijn, F.C. van; Beekman, G. ; Dengerink, Just ; Vliet, J.A. van; Arets, E.J.M.M. ; Sassen, M. ; Guijt, W.J. van; Vugt, S.M. van - \ 2019
    Wageningen : Wageningen Economic Research (Wageningen Economic Research 2019-122) - 26 p.
    Interventions and policies in the cocoa, tea and coffee sectors have failed to ensure that all smallholder commodity farmers earn more than the $1.90 World Bank poverty line or a living income, and they have not halted deforestation. Commodity farming is strongly associated with deforestation, in spite of interventions. For more than 50% of the cocoa and tea farmers in our datasets, household income would need to double in order for them to earn a living income. For those farmers, farming will never be a primary pathway out of poverty.
    Prospects of Next-Generation Vaccines for Bluetongue
    Rijn, P.A. van - \ 2019
    Frontiers in Veterinary Science 6 (2019). - ISSN 2297-1769
    Bluetongue (BT) is a haemorrhagic disease of wild and domestic ruminants with a huge economic worldwide impact on livestock. The disease is caused by BT-virus transmitted by Culicoides biting midges and disease control without vaccination is hardly possible. Vaccination is the most feasible and cost-effective way to minimize economic losses. Marketed BT vaccines are successfully used in different parts of the world. Inactivated BT vaccines are efficacious and safe but relatively expensive, whereas live-attenuated vaccines are efficacious and cheap but are unsafe because of under-attenuation, onward spread, reversion to virulence, and reassortment events. Both manufactured BT vaccines do not enable differentiating infected from vaccinated animals (DIVA) and protection is limited to the respective serotype. The ideal BT vaccine is a licensed, affordable, completely safe DIVA vaccine, that induces quick, lifelong, broad protection in all susceptible ruminant species. Promising vaccine candidates show improvement for one or more of these main vaccine standards. BTV protein vaccines and viral vector vaccines have DIVA potential depending on the selected BTV antigens, but are less effective and likely more costly per protected animal than current vaccines. Several vaccine platforms based on replicating BTV are applied for many serotypes by exchange of serotype dominant outer shell proteins. These platforms based on one BTV backbone result in attenuation or abortive virus replication and prevent disease by and spread of vaccine virus as well as reversion to virulence. These replicating BT vaccines induce humoral and T-cell mediated immune responses to all viral proteins except to one, which could enable DIVA tests. Most of these replicating vaccines can be produced similarly as currently marketed BT vaccines. All replicating vaccine platforms developed by reverse genetics are classified as genetic modified organisms. This implies extensive and expensive safety trails in target ruminant species, and acceptance by the community could be hindered. Nonetheless, several experimental BT vaccines show very promising improvements and could compete with marketed vaccines regarding their vaccine profile, but none of these next generation BT vaccines have been licensed yet.
    African Horse Sickness Virus
    Rijn, P.A. van - \ 2019
    In: Reference Module in Life Sciences Elsevier - ISBN 9780128096338
    African Horse Sickness is an infectious, non-contagious, arthropod-borne disease of Equidae caused by African horse sickness virus transmitted by biting culicoides midges. African Horse Sickness is endemic in Africa but outbreaks outside the African continent have been reported. The disease is characterized by changes in respiratory and circulatory functions and exhibits different forms. The mortality is >90% for naïve domestic horses. In contrast, infected zebra and African donkey display mild or no clinical signs and a mortality of 5%–10%. Nine serotypes of African horse sickness virus have been recognized showing no or poor cross-protection with each other.
    Vector competence is strongly affected by a small deletion or point mutations in bluetongue virus
    Gennip, René G.P. van; Drolet, Barbara S. ; Rozo Lopez, Paula ; Roost, Ashley J.C. ; Boonstra, Jan ; Rijn, Piet A. van - \ 2019
    Parasites & Vectors 12 (2019). - ISSN 1756-3305
    Arbovirus - Bluetongue virus - Culicoides - Feeding model - Midge - Vector competence - Virus propagation

    BACKGROUND: Transmission of vector-borne virus by insects is a complex mechanism consisting of many different processes; viremia in the host, uptake, infection and dissemination in the vector, and delivery of virus during blood-feeding leading to infection of the susceptible host. Bluetongue virus (BTV) is the prototype vector-borne orbivirus (family Reoviridae). BTV serotypes 1-24 (typical BTVs) are transmitted by competent biting Culicoides midges and replicate in mammalian (BSR) and midge (KC) cells. Previously, we showed that genome segment 10 (S10) encoding NS3/NS3a protein is required for virus propagation in midges. BTV serotypes 25-27 (atypical BTVs) do not replicate in KC cells. Several distinct BTV26 genome segments cause this so-called 'differential virus replication' in vitro. METHODS: Virus strains were generated using reverse genetics and their growth was examined in vitro. The midge feeding model has been developed to study infection, replication and disseminations of virus in vivo. A laboratory colony of C. sonorensis, a known competent BTV vector, was fed or injected with BTV variants and propagation in the midge was examined using PCR testing. Crossing of the midgut infection barrier was examined by separate testing of midge heads and bodies. RESULTS: A 100 nl blood meal containing ±105.3 TCID50/ml of BTV11 which corresponds to ±20 TCID50 infected 50% of fully engorged midges, and is named one Midge Alimentary Infective Dose (MAID50). BTV11 with a small in-frame deletion in S10 infected blood-fed midge midguts but virus release from the midgut into the haemolymph was blocked. BTV11 with S1[VP1] of BTV26 could be adapted to virus growth in KC cells, and contained mutations subdivided into 'corrections' of the chimeric genome constellation and mutations associated with adaptation to KC cells. In particular one amino acid mutation in outer shell protein VP2 overcomes differential virus replication in vitro and in vivo. CONCLUSION: Small changes in NS3/NS3a or in the outer shell protein VP2 strongly affect virus propagation in midges and thus vector competence. Therefore, spread of disease by competent Culicoides midges can strongly differ for very closely related viruses.

    Virus-induced autophagic degradation of STAT2 as a mechanism for interferon signaling blockade
    Avia, Miguel ; Rojas, Jose M. ; Miorin, Lisa ; Pascual, Elena ; Rijn, P.A. van; Martin, Veronica ; Garcia-Sastre, Adolfo ; Sevilla, Noemi - \ 2019
    Embo Reports 20 (2019)11. - ISSN 1469-221X - 15 p.
    The mammalian interferon (IFN) signaling pathway is a primary component of the innate antiviral response, and viral pathogens have evolved multiple mechanisms to antagonize this pathway and to facilitate infection. Bluetongue virus (BTV), an orbivirus of the Reoviridae family, is transmitted by midges to ruminants and causes a disease that produces important economic losses and restriction to animal trade and is of compulsory notification to the World Organization for Animal Health (OIE). Here, we show that BTV interferes with IFN‐I and IFN‐II responses in two ways, by blocking STAT1 phosphorylation and by degrading STAT2. BTV‐NS3 protein, which is involved in virion egress, interacts with STAT2, and induces its degradation by an autophagy‐dependent mechanism. This STAT2 degradative process requires the recruitment of an E3‐Ub‐ligase to NS3 as well as NS3 K63 polyubiquitination. Taken together, our study identifies a new mechanism by which a virus degrades STAT2 for IFN signaling blockade, highlighting the diversity of mechanisms employed by viruses to subvert the IFN response.
    Improved PCR diagnostics using up-to-date in silico validation: An F-gene RT-qPCR assay for the detection of all four lineages of peste des petits ruminants virus
    Flannery, John ; Rajko-Nenow, Paulina ; Arnold, Hannah ; Weezep, Erik van; Rijn, Piet A. van; Ngeleja, Chanasa ; Batten, Carrie - \ 2019
    Journal of Virological Methods 274 (2019). - ISSN 0166-0934
    In silico - PPRV - Rapid detection - RT-qPCR

    Peste des petits ruminants (PPR) is a globally significant disease of small ruminants caused by the peste des petits ruminants virus (PPRV) that is considered for eradication by 2030 by the United Nations Food and Agriculture Organisation (FAO). Critical to the eradication of PPR are accurate diagnostic assays. RT-qPCR assays targeting the nucleocapsid gene of PPRV have been successfully used for the diagnosis of PPR. We describe the development of an RT-qPCR assay targeting an alternative region (the fusion (F) gene) based on the most up-to-date PPRV sequence data. In silico analysis of the F-gene RT-qPCR assay performed using PCRv software indicated 98% sensitivity and 100% specificity against all PPRV sequences published in Genbank. The assay indicated the greatest in silico sensitivity in comparison to other previously published and recommended PPRV RT-qPCR assays. We evaluated the assay using strains representative of all 4 lineages in addition to samples obtained from naturally and experimentally-infected animals. The F-gene RT-qPCR assay showed 100% diagnostic specificity and demonstrated a limit of detection of 10 PPRV genome copies per μl. This RT-qPCR assay can be used in isolation or in conjunction with other assays for confirmation of PPR and should support the global efforts for eradication.

    Towards a sustainable sugarcane industry in India : mid-term results of the Solidaridad programme: Increasing water use efficiency in sugarcane growing in India through adoption of improved practices and technologies
    Plaisier, C. ; Janssen, V. ; Rijn, F. van - \ 2019
    Wageningen : Wageningen Economic Research (Wageningen Economic Research report 2019-032) - 55
    Towards a sustainable sugarcane industry in India appendices : Mid-term results on Solidaridad’s programme: Increasing water use efficiency in sugarcane growing in India
    Plaisier, C. ; Janssen, V. ; Rijn, F. van - \ 2019
    Wageningen : Wageningen Economic Research (Wageningen Economic Research report 2019-032b) - 52
    Achtergrondrapportage Programmeringsstudies Landbouw, Water en Voedsel: Noordzee en Visserij
    Smith, S. ; Steins, N.A. ; Bogaart, L. van den; Bos, O.G. ; Maarse, M. ; Rijn, J. van; Schadeberg, A. ; Tamis, J. ; Tatman, S. - \ 2019
    Yerseke : Wageningen Marine Research (Wageningen Marine Research rapport C075/19) - 153
    Duurzame Visserij: programmeringsstudie Landbouw, Water en Voedsel
    Smith, S.R. ; Bos, O.G. ; Steins, N.A. ; Schadeberg, Amanda ; Bogaart, Lisanne van den; Rijn, J. van; Tamis, J.E. ; Zaalmink, W. ; Ammerlaan, F.H.M. ; Elbersen, B.S. ; Vis, J.W. van de; Veraart, J.A. - \ 2019
    1928088 NS/IH
    Novel function of Bleutongue Virus NS3 Protein in Regulation of the MAPK/ERK Signaling Pathway
    Kundlacz, Cindy ; Pourcelot, Marie ; Fablet, Aurore ; Amaral Da Silva Moraes, Rayane ; Leger, Thibaut ; Morlet, Bastien ; Viarouge, Cyril ; Sailleau, C. ; Turpaud, Mathilde ; Gorlier, Axel ; Breard, Emmanuel ; Lecollinet, S. ; Rijn, P.A. van; Zientara, Stephan ; Vitour, Damien ; Caignard, Gregory - \ 2019
    Journal of Virology 93 (2019)16. - ISSN 0022-538X - 17 p.
    Bluetongue virus (BTV) is an arbovirus transmitted by blood-feeding midges to a wide range of wild and domestic ruminants. In this report, we showed that BTV, through its nonstructural protein NS3 (BTV-NS3), is able to activate the mitogen-activated protein kinase/extracellular signal-regulated kinase (MAPK/ERK) pathway, as assessed by phosphorylation levels of ERK1/2 and the translation initiation factor eukaryotic translation initiation factor 4E (eIF4E). By combining immunoprecipitation of BTV-NS3 and mass spectrometry analysis from both BTV-infected and NS3-transfected cells, we identified the serine/threonine-protein kinase B-Raf (BRAF), a crucial player in the MAPK/ERK pathway, as a new cellular interactor of BTV-NS3. BRAF silencing led to a significant decrease in the MAPK/ERK activation by BTV, supporting a model wherein BTV-NS3 interacts with BRAF to activate this signaling cascade. This positive regulation acts independently of the role of BTV-NS3 in counteracting the induction of the alpha/beta interferon response. Furthermore, the intrinsic ability of BTV-NS3 to bind BRAF and activate the MAPK/ERK pathway is conserved throughout multiple serotypes/strains but appears to be specific to BTV compared to other members of Orbivirus genus. Inhibition of MAPK/ERK pathway with U0126 reduced viral titers, suggesting that BTV manipulates this pathway for its own replication. Altogether, our data provide molecular mechanisms that unravel a new essential function of NS3 during BTV infection.
    Selectiviteitsoptimalisatie van de pulsvisserij
    Rijn, Jimmy van; Molenaar, Pieke - \ 2019
    IJmuiden : Wageningen Marine Research (Wageningen Marine Research rapport C072/19) - 42
    Viscous Liquid Threads with Inner Fluid Flow Inside Microchannels
    Molenaar, Jaap ; Heugten, Willem G.N. Van; Rijn, Cees J.M. Van - \ 2019
    ACS Omega 4 (2019)6. - ISSN 2470-1343 - p. 9800 - 9806.

    Forming droplets are often accompanied by an interconnecting liquid thread. It is postulated that this phenomenon can only exist as long as a pressure gradient exists within the thread, for instance, when a viscous liquid is conveyed via the liquid thread to the forming droplet. We have built a microfluidic setup to form and sustain a liquid thread, which after a length L ends in a droplet. To prevent the droplet from moving up too fast due to buoyancy, we force the droplet to shift along a tilted ceiling, which can be positioned at three different angles. This enables us to keep the gradual lengthening of the liquid thread under control. Based on the Navier-Stokes equation, we are able to predict the axial shape of such a liquid thread as a function of fluid mass density, initial thread radius, initial fluid velocity at the nozzle, fluid viscosity, and surface tension. Although an explicit solution of the governing differential equations is not known, we managed to find an explicit approximating expression for the shape function, which shows excellent agreement with both the measured and the numerically calculated shape functions. An intriguing phenomenon observed in the experiments is the breakup of the thread. This breakup always occurs close to the droplet. Using our approximating solution, we derive a relation that connects, for any time in the development of the thread, its length and the pressure gradient stemming from, among other effects, the shear at the interface of the liquid thread due to motion of the inner liquid. For relatively short thread lengths, this relation is linear on a log-log scale, due to the fact that in this regime, viscosity effects are dominant. However, if the thread length increases, this relation starts to deviate from linear behavior, due to surface tension effects. We show from the experimental results that the thread starts to show unstable behavior as soon as these capillary effects come into play. We show how to predict the thread length at which the capillary instability sets in for any liquid thread system. It is found that the predicted maximum dimensionless thread length is given by Lmax,pred ≈ 12Ca with Ca the capillary number.

    PCR diagnostics: In silico validation by an automated tool using freely available software programs
    Weezep, E. van; Kooi, Bart ; Rijn, P.A. van - \ 2019
    Journal of Virological Methods 270 (2019). - ISSN 0166-0934 - p. 106 - 112.
    PCR diagnostics are often the first line of laboratory diagnostics and are regularly designed to either differentiate between or detect all pathogen variants of a family, genus or species. The ideal PCR test detects all variants of the target pathogen, including newly discovered and emerging variants, while closely related pathogens and their variants should not be detected. This is challenging as pathogens show a high degree of genetic variation due to genetic drift, adaptation and evolution. Therefore, frequent re-evaluation of PCR diagnostics is needed to monitor its usefulness. Validation of PCR diagnostics recognizes three stages, in silico, in vitro and in vivo validation. In vitro and in vivo testing are usually costly, labour intensive and imply a risk of handling dangerous pathogens. In silico validation reduces this burden. In silico validation checks primers and probes by comparing their sequences with available nucleotide sequences. In recent years the amount of available sequences has dramatically increased by high throughput and deep sequencing projects. This makes in silico validation more informative, but also more computing intensive. To facilitate validation of PCR tests, a software tool named PCRv was developed. PCRv consists of a user friendly graphical user interface and coordinates the use of the software programs ClustalW and SSEARCH in order to perform in silico validation of PCR tests of different formats. Use of internal control sequences makes the analysis compliant to laboratory quality control systems. Finally, PCRv generates a validation report that includes an overview as well as a list of detailed results. In-house developed, published and OIE-recommended PCR tests were easily (re-) evaluated by use of PCRv. To demonstrate the power of PCRv, in silico validation of several PCR tests are shown and discussed.
    The Impacts of Cocoa Sustainability Initiatives in West Africa
    Ingram, V.J. ; Rijn, Fedes van; Waarts, Y.R. ; Gilhuis, Henk - \ 2019
    In: Public-Private Partnerships for Sustainable Development / Marx, Axel, Basel, Switzerland : MDPI - ISBN 9783038978329 - 248 p.
    Co-current crossflow microfiltration in a microchannel
    Amar, Levy I. ; Hill, Michael I. ; Faria, Monica ; Guisado, Daniela ; Rijn, Cees J.M. van; Leonard, Edward F. - \ 2019
    Biomedical Microdevices 21 (2019)1. - ISSN 1387-2176 - 1 p.
    Blood - Constant transmembrane pressure - Cross-flow - Erythrocytes - Microfiltration model - Microfluidics - Microsieve - Nanopores - Plasma - Sieve

    Steady state crossflow microfiltration (CMF) is an important and often necessary means of particle separation and concentration for both industrial and biomedical processes. The factors controlling the performance of CMF have been extensively reviewed. A major factor is transmembrane pressure (TMP). Because microchannels have small height, they tend to have high pressure gradients in the feed-flow direction. In the extreme, these gradients may even reverse the pressure across the membrane (inciting backflow). It is therefore desirable to compensate for the effect of feed-flow on the TMP, aiming at constant transmembrane pressure (cTMP) at a value which maximizes filtrate flux. This is especially critical during filtration of deformable particles (e.g. erythrocytes) through low intrinsic resistance membranes. Filtration flux is generally taken to be directly proportional to TMP, with pressure drop along the channel decreasing in the flow direction. A co-current flow of filtrate in a suitably designed filtrate collecting channel is shown to allow the TMP to remain constant and permit the sieving surface to perform optimally, permitting up to twice as much filtration over that of a naïve configuration. Manipulation of the filtrate channel may be even more beneficial if it prevents backflow that might otherwise occur at the end of a sufficiently long channel. Experiments with erythrocyte suspensions, reported here, validate these concepts.

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