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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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 (2019). - 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 insugarcane 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
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, Engbert A. ; 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.

The Impact of Innovation Platform Diversity in Agricultural Network Formation and Technology Adoption : Evidence from Sub-Saharan Africa
Pamuk, Haki ; Rijn, Fedes Van - \ 2019
Journal of Development Studies 55 (2019)6. - ISSN 0022-0388 - p. 1240 - 1252.
This study investigates the diversity in impact of innovation platforms (IPs) on agricultural networks and technology adoption among 1200 households in nine sub-Saharan Africa countries. We explore the extent to which the 32 IPs implemented adopted the Integrated Agricultural Research for Development Approach (IAR4D). We find that IPs implemented according to the IAR4Dness principles are better at promoting networks of households with other farmers within villages. We find that IPs with more active members were more successful in promoting agricultural technologies, while IPs with many different stakeholders were less successful in promoting agricultural technologies.
Beroepsvisserijenquête IJsselmeer en Markermeer : Praktijkkennis over de toestand van commerciële visbestanden in het jaar 2017 gebundeld
Rijn, J. van; Beier, U. ; Steenbergen, J. - \ 2018
IJmuiden : Wageningen Marine Research (Wageningen Marine Research rapport C107/18) - 91
Naast het formele advies over de biologische toestand van vier schubvissoorten, aal en spiering, vindt er sinds 2016 een enquête plaats onder beroepsvissers. Het doel van de zogenaamde beroepsvisserij enquête is het formeel inzichtelijk maken van het praktijkperspectief over de biologische toestand van belangrijke commerciële vissoorten op het IJsselmeer en Markermeer, te weten: aal, baars, snoekbaars, blankvoorn, brasem, Chinese wolhandkrab, bot en spiering. Daarnaast worden er algemene vragen over de visser, bijvangst per tuig en de bedrijfssituatie gesteld. In de enquête van 2017 zijn de respondenten gevraagd een onderscheid te maken tussen de biologische toestand van de visbestanden in het IJssel- en Markermeer. Met de feedback van drie vissers en de opdrachtgever is de enquête in december 2017 gefinaliseerd en verzonden naar vissers die volgens de logboekregistratie actief zijn geweest in 2017. Van de 56 verstuurde enquêtes zijn er 25 exemplaren teruggestuurd, hiermee is een responspercentage van 45% behaald. Van deze respondenten zijn er 24 die voltijd vissen. De voltijdvissers hebben gemiddeld 32 jaar ervaring en visten in 2017 gemiddeld 37 weken. De visserij op de acht soorten vindt verdeeld over alle gebieden plaats waarbij het zuidelijk deel van het Markermeer, IJmeer en de wateren rond Flevoland duidelijk minder vaak gebruikt worden voor visserij. Uit het aantal soorten dat er per respondent bevist wordt, lijkt er een verdeling te zijn tussen meer specialistische vissers die gericht op 2-3 soorten vissen en wat meer de generalisten die gericht op 5-7 soorten vissen. Op aal, snoekbaars en wolhandkrab vindt er een duidelijk gerichte visserij plaats. Baars en blankvoorn worden zowel gevangen in gerichte visserij als door bijvangst. Bij de vragen over de biologische toestand in 2017 vergeleken met 2016 viel op dat de respondenten voor de meeste soorten gematigd positief waren over de hoeveelheid maatse en ondermaatse individuen. Over aal en spiering is men duidelijk positief en over bot is men iets negatiever dan gemiddeld. Van brasem ziet men vooral kleine individuen en voor blankvoorn vooral grote, terwijl men voor de overige soorten alle maten individuen ziet. Wat opvalt is dat men voor aal, in beide meren, een lagere natuurlijke sterfte ziet ten opzichte van 2016 en voor het Markermeer bij baars en snoekbaars juist een hogere natuurlijke sterfte dan in 2016. Bij de voorspelling van de hoeveelheid volwassen vis in 2018 t.o.v. 2017 valt het op dat men erg optimistisch is over aal, spiering, baars (in het IJsselmeer) en Chinese wolhandkrab (in het Markermeer). Zonder de vergelijking te maken met 2017 was de respondenten hun voorspelling over de marktwaardige individuen overwegend optimistisch met uitzondering van bot, brasem en snoekbaars in het IJsselmeer. De niet-marktwaardige bijvangst lijkt overwegend lager te zijn dan vorig jaar voor de twee soorten fuiken en onveranderd voor de staand want en hoekwant visserij. Over de bedrijfssituatie is men erg optimistisch. Er bleek volgens de respondenten geen duidelijk onderscheid in de biologische toestand van de bestanden tussen de twee meren. In het vervolg is dit onderscheid duidelijker te bevragen door een open vraag per soort te stellen in plaats van de huidige dubbele vraagstelling. Om de kwaliteit van de resultaten te waarborgen is het aan te raden vooraf een verkorte proef enquête te laten invullen door een paar respondenten en hier feedback over te vragen. Het is aanbevolen om de resultaten van de enquête ook dit jaar in een focusgroep discussie te bespreken.
Vloeistof spat op als een eiffeltoren
Rijn, Cees van - \ 2018
Nieuwe inzichten in de waarde van Nederlandse genenbank voor runderrassen
Doekes, Harmen - \ 2018

De Nederlandse genenbankcollectie voor runderrassen bestaat sinds 1993 en wordt beheerd door het Centrum voor Genetische Bronnen, Nederland (CGN) van Wageningen University & Research. De collectie bevat genetisch materiaal (sperma) van zeldzame Nederlandse rassen, alsmede een dwarsdoorsnede van de Nederlandse fokpopulaties voor Holstein Friesian (HF) en Maas-Rijn-IJssel (MRIJ) van de afgelopen decennia. Onderzoekers van Wageningen University & Research lieten zien dat het opgeslagen materiaal voor HF en MRIJ waardevol is voor behoud van genetische diversiteit en bij eventuele sterke veranderingen van het fokdoel.

Emanating Jets As Shaped by Surface Tension Forces
Rijn, Cees J.M. van - \ 2018
Langmuir 34 (2018)46. - ISSN 0743-7463 - p. 13837 - 13844.

We show that emanating jets can be regarded as growing liquid towers, which are shaped by the twofold action of surface tension: first the emanated fluid is being accelerated back by surface tension force, herewith creating the boundary conditions to solve the shape of the liquid tower as a solution of an equation mathematically related to the hydrostatic Young-Laplace equation, known to give solutions for the shape of pending and sessile droplets, and wherein the only relevant forces are gravity g and surface tension γ. We explain that for an emanating jet under specific constraints all mass parts with density ρ will experience a uniform time dependent acceleration a(t). An asymptotic solution is subsequently numerically derived by making the corresponding Young-Laplace type equation dimensionless and by dividing all lengths by a generalized time dependent capillary length λc(t) = γ(t)/ρ(a(t)-g). The time dependent surface tension γ(t) can be derived by measuring both time dependent acceleration a(t) and time dependent capillary length λc(t). Jetting experiments with water and coffee show that the dynamic surface tension behavior according to the emanating jet method and with the well-known maximum bubble pressure method are the same, herewith verifying the proposed model.

The Impacts of Cocoa Sustainability Initiatives in West Africa
Ingram, V.J. ; Rijn, F.C. van; Waarts, Y.R. ; Gilhuis, Henk - \ 2018
Sustainability 10 (2018)11. - ISSN 2071-1050
To tackle the multiple challenges facing the cocoa sector, voluntary sustainability standards and corporate initiatives, largely focusing on farm and farmer group scale, are often implemented by public–private–civil society partnerships of stakeholders further in the value chain. This paper looks at the social, economic, and environmental effects of such initiatives, based on empirical evidence from large-scale, mixed-method studies using a suite of socioeconomic, agronomic, and environmental indicators to compare the situation of UTZ certified with non-certified farmers in 2012 and 2015 in Ghana, and 2013 and 2017 in Ivory Coast. The results show that, on average, outcomes are mixed and generally modest. However, significant cocoa productivity and income increases were experienced by certified farmers receiving a full package of services. However, the type and intensity of services has changed over time, decreasing for half of the farmers, and productivity and income increases are levelling off. These findings suggest that whilst partnerships have created new governance arrangements with an increased focus on sustainable value chains, initiatives which result in a living income and optimise productivity, whilst limiting environmental impacts, require sectoral transformation, continued partnerships, plus a range of other policy instruments to address the persistent, wicked problems in cocoa production.
Negative hydrostatic pressure is an unnoticed but significant source of contamination in tissue culture
Askari, N. ; Klerk, G.J. de - \ 2018
In: Proceedings of the 2017 Annual Meeting of the International Plant Propagators' Society. - International Society for Horticultural Science (Acta Horticulturae ) - ISBN 9789462612099 - p. 85 - 87.
Plants are characterized by a negative hydrostatic pressure, brought about by transpiration and by capillary activity of xylem vessels (Taiz and Zeiger, 2010). Because of this, a stem that is being cut sucks up what is nearby. Often this is air but it may also be liquid. The diameter of the xylem vessels is 50-100 μm, so when the liquid contains bacteria (that are typically 0.5-5.0 μm), they will enter deeply into the tissue (Askari et al., 2014; De Klerk et al., 2014). To our knowledge, this alleged source of contamination has never been examined.
De kinkenwegen: landschappelijk erfgoed in de Euregio Maas-Rijn
Paulissen, Maurice - \ 2018
Invited talk during the Open Monument Day in Klimmen, The Netherlands
ITC’s contribution to export competitiveness : verification of intervention logic in the Information Technology & Services Sector in Bangladesh: final report July 2018
Pamuk, Haki ; Rijn, Fedes van - \ 2018
Wageningen : Wageningen Economic Research (Wageningen Economic Research report 2018-048) - ISBN 9789463434782 - 47
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