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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    Boron Adsorption to Ferrihydrite with Implications for Surface Speciation in Soils : Experiments and Modeling
    Eynde, Elise Van; Mendez, Juan C. ; Hiemstra, Tjisse ; Comans, Rob N.J. - \ 2020
    ACS Earth and Space Chemistry 4 (2020)8. - ISSN 2472-3452 - p. 1269 - 1280.
    boron - CD-MUSIC modeling - ferrihydrite - goethite - humic acid

    The adsorption and desorption of boric acid onto reactive materials such as metal (hydr)oxides and natural organic matter are generally considered to be controlling processes for the leaching and bioavailability of boron (B). We studied the interaction of B with ferrihydrite (Fh), a nanosized iron (hydr)oxide omnipresent in soil systems, using batch adsorption experiments at different pH values and in the presence of phosphate as a competing anion. Surface speciation of B was described with a recently developed multisite ion complexation (MUSIC) and charge distribution (CD) approach. To gain insight into the B adsorption behavior in whole-soil systems, and in the relative contribution of Fh in particular, the pH-dependent B speciation was evaluated for soils with representative amounts of ferrihydrite, goethite, and organic matter. The pH-dependent B adsorption envelope of ferrihydrite is bell-shaped with a maximum around pH 8-9. In agreement with spectroscopy, modeling suggests formation of a trigonal bidentate complex and an additional outer-sphere complex at low to neutral pH values. At high pH, a tetrahedral bidentate surface species becomes important. In the presence of phosphate, B adsorption decreases strongly and only formation of the outer-sphere surface complex is relevant. The pH-dependent B adsorption to Fh is rather similar to that of goethite. Multisurface modeling predicts that ferrihydrite may dominate the B binding in soils at low to neutral pH and that the relative contribution of humic material increases significantly at neutral and alkaline pH conditions. This study identifies ferrihydrite and natural organic matter (i.e., humic substances) as the major constituents that control the B adsorption in topsoils.

    Structure and Colloidal Stability of Adsorption Layers of Macrocycle, Linear, Comb, Star, and Dendritic Macromolecules
    Leermakers, Frans A.M. ; Léonforte, Fabien ; Luengo, Gustavo S. - \ 2020
    Macromolecules 53 (2020)17. - ISSN 0024-9297 - p. 7322 - 7334.

    The equilibrium theory of polymer adsorption on a solid/liquid interface is well established. De Gennes explained that linear homopolymers adsorbing on a surface develop a proximal, central, and distal region in their adsorption profile, wherein the central region has a universal scaling self-similar structure with power-law coefficient -4/3. More pictorially, the layer is composed of trains, loops, and tails. Linear chains have just two tails, and therefore it is often assumed that the adsorption layer consists of loops only. Branched macromolecules have multiple tails, and the loops-only approach is argued to become progressively less accurate. Using self-consistent field theory of Scheutjens and Fleer (SF-SCF), we consider the macrocycle (chain without ends), linear, star-like, dendritic, and comb-like (homo)polymers and focus on the effects of tails. We show that the adsorption profile changes systematically with the degree of branching. Typically, for significantly branched chains the polymer density in the outer part of the central region has an effective scaling coefficient that may exceed the -4/3 value. Comb polymers adsorb with their backbone preferentially and generate a "brush"-like layer through adsorption, which we refer to as a hedge layer as the backbone and branches are hidden behind the free ends. By way of an array of "out-going"side chains, such a layer acts as a superb colloid stabilizer and as a lubricant, outperforming star-like polymers or dendritic polymers which qualitatively behave similar to linear chains.

    Performance evaluation of the Hydroluis drainpipe-envelope system in a saline-sodic soil
    Alavi, Seyed Abdollah ; Naseri, Abd Ali ; Bazaz, Azam ; Ritzema, Henk ; Hellegers, Petra - \ 2020
    Agricultural Water Management 243 (2020). - ISSN 0378-3774
    Clogging - Filter function - New drainpipe - PP450 envelope - Soil tank test - Subsurface drainage

    Subsurface drains, when installed in non-cohesive soil, are typically covered with an envelope to tackle problems of clogging and siltation. Selecting a suitable envelope material, however, is complicated and depends primarily on soil characteristics in the area where the drains are to be installed. A new promising drainpipe-envelope concept, Hydroluis, has been developed which the designers claim works in a wide range of soils. The Hydroluis drainpipe consists of a corrugated inner pipe with three rows of perforations at the top and an unperforated outer pipe that covers the top two thirds of the inner pipe. We analysed the hydraulic and filter functions of this new drainpipe in a soil tank laboratory model with a saline-sodic problem soil from south-western Iran and compared Hydroluis performance with that of a locally-manufactured synthetic envelope material (PP450). The silty clay soil used in this study was 40 % clay, with a plasticity index (IP) of 16.9 and an exchangeable sodium percentage (ESP) of 60.4 %. The Hydroluis drainpipe clogged during the first two weeks of the test due to invasion of the test soil into the space between the inner and outer pipes. Of the substantial volume of sediment that entered the Hydroluis inner pipe, 38 % removed from the pipe in the first day. In contrast, the PP450 drainpipe showed good hydraulic and filter functions, entering very little sediment to drainpipe during the entire test period and stabilizing at drainage rate of 28 mm/day and entrance resistance of 55 days/m, at around day 50. Our analyses suggest that the clogging and poor drainage function of the Hydroluis drainpipe was caused by the higher flow velocity (21.5 times higher) at the soil-envelope interface of the drainpipe, in addition to the lower Hydroluis drainpipe's soil retention capacity (18 times lower) compared to the PP450 drainpipe. Assuming Stokes’ Law governs filter function, the results of Hydroluis design evaluation also suggest that in stable soils, very fine sand or coarser soil particles (D > 0.05 mm) place no serious limitations for Hydroluis drainpipe application, whereas the current design is unsuitable for filtering fine silt particles (0.002 < D < 0.02 mm). In conclusion, we suppose the Hydroluis drainpipe does not perform well in silty saline-sodic soils, such as those found in south-western Khuzestan Province, Iran.

    Long Tails with Flower-like Conformations Undergo an Escape Transition in Homopolymer Adsorption Layers
    Leermakers, Frans A.M. - \ 2020
    Macromolecules 53 (2020)10. - ISSN 0024-9297 - p. 3900 - 3906.

    De Gennes predicted that homopolymer adsorption on a solid-liquid interface results in an adsorption profile with a proximal, a central, and a distal region, wherein, for a good solvent, the central region has a self-similar structure with a density profile that decays as a power law with a coefficient of -4/3. Recent numerical self-consistent field (SCF) predictions for the long-chain length (N) limit revealed a more complex central region with an inner part, where the loops dominate the layer, with a (mean-field) power-law coefficient of -2 and an outer part, where tails dominate, with a "de Gennes" scaling of -4/3. The tails with length t < t∗ contribute to the inner part of the central region, and these have similar conformations as the loops. The outer part is populated by tails with a length t > t*, and these behave differently. With the increasing length of the tails, there exists a weak escape transition at t = tescape ≈ N/10. Long tails in the adsorption profile (t ≳ t∗ ∝ N0.733) show enhanced fluctuations due to this nearby escape transition, and this explains the excluded volume scaling for the outer part of the central region in SCF. With this interpretation, the -2 scaling found by SCF for the inner part should be classified as a mean-field result.

    Border-row proportion determines strength of interspecific interactions and crop yields in maize/peanut strip intercropping
    Wang, Ruonan ; Sun, Zhanxiang ; Zhang, Lizhen ; Yang, Ning ; Feng, Liangshan ; Bai, Wei ; Zhang, Dongsheng ; Wang, Qi ; Evers, Jochem B. ; Liu, Yang ; Ren, Jianhong ; Zhang, Yue ; Werf, Wopke van der - \ 2020
    Field Crops Research 253 (2020). - ISSN 0378-4290
    border-row effect - relative yield total - row configuration - strip cropping - yield components

    Strip intercropping enables increases in yields and ecological services in agriculture. Crop yields of species grown in strip intercropping are often related to the yield responses (increases or decreases) in the outer rows of the strips: the border rows. This suggests that the yield response can be modulated by changing the proportion of border rows in the field. Here we studied the relationship between component species yields and proportion of border rows in strip intercrops of maize (Zea mays L.) and peanut (Arachis hypogaea Linn.). We tested four different intercrops with equal proportions of maize and peanut but a different number of rows per strip: M2P2 (2 rows maize intercropped with 2 rows peanut), M4P4, M6P6, M8P8, and sole maize (SM) and sole peanut (SP). The border-row proportions were 1, 0.5, 0.33 and 0.25 for the intercropping M2P2 to M8P8, respectively, and 0 for the pure stands. Yield responded positively to the proportion of border rows for maize, but negatively for peanut, confirming the dominance of maize in this system. Kernel number per ear of maize and pod number per plant of peanut were the main yield components that responded to the border-row proportion. Across three years, relative maize yield (yield in intercropping divided by yield in monoculture), varied from 0.76 in M2P2 to 0.56 in M8P8, while relative peanut yield varied from 0.19 in M2P2 to 0.39 in M8P8. Relative yield total was not significantly different from one in any of the mixtures. Yield of intercropped maize in border rows was 48% higher than in inner rows and the sole crop, in part due to a significantly higher kernel number per ear (13%). Yield of intercropped peanut in border rows was on average 29% lower than in inner rows and 48% lower than in sole peanut. Yield responses in border rows were independent from the border-row proportion. The results show that relative crop yields responded strongly to variation in border-row proportion resulting from variation in strip width from 1 to 4 m. Strip width thus provides a mechanism to control the strength of interspecific plant interactions and relative yields in strip intercropping.

    What happens under the reef? A study towards the identity and functioning of the cryptobenthic community in two contrasting coral reef habitats
    Streekstra, M.A. ; Folkers, M. ; Schoon, Bart ; Jorissen, Hendrikje ; Nugues, Maggy M. ; Goeij, Jasper M. De; Murk, A.J. ; Osinga, R. - \ 2020
    In: WIAS Annual Conference 2020. - WIAS - p. 28 - 28.
    Hidden in the gaps, cracks and crevices of the coral reef three-dimensional framework,complex benthic communities reside. These communities are largely composed of filter feeders such as sponges and ascidians and it becomes increasingly clear that this community plays a vital role in retaining nutrients on the reef. Little is known on how the species composition of the crypto benthic community relates to its ecological functioning (e.g.biochemical cycling), despite the cryptic habitat being the largest surface area on coral reefs. Here we show -for the first time- how the composition of the crypto benthic community influences it’s biochemical cycling (oxygen and organic carbon) in two distinct reef habitats.These habitats are the hard coral dominated outer reef of Mo’orea (French Polynesia)and the ‘shifted’ reef of Curacao (Dutch Caribbean), where algae and cyanobacteriahave become the dominant benthos. In both locations, we deployed 36 experimental structures using the established ARMS (Autonomous Reef Monitoring Structures) methodology.We adapted the methodology by 1) adjusting the size of the standard ARMS (to eachmini ARMS totaling a 0.14m2 surface area) and 2) equipping part of the structures with nutrient dispensers to test for the effect of environmental perturbation on community composition and functioning. After 15 months of colonization, we quantified metabolic fluxes(respiration of oxygen in the light and dark, uptake of dissolved and total carbon, bacteria and nutrients) of the mini ARMS communities using in situ respiration chambers. We subsequently determined the composition of the sessile and mobile communities using pictures(Photoquad) and meta barcoding. Preliminary data from Mo’orea show a clear distinction between the upper surface and cryptic spaces, with 83% of the miniARMS being net phototrophicin the light (mean Pn 38.04 mmol O2 m-2 day-1) and heterotrophic during dark incubations (mean Rd -36.89 mmol O2 m-2 day-1). The upper surface of the ARMS were largely dominated by CCA, whereas ascidians were most abundant in the cryptic spaces. From the large mobile fraction (>2mm), we retrieved on average 5.6 phyla per ARMS and 213animals m-2, with gastropods (24%), bivalves (24%), crabs (21%) and hermit crabs (19%) being the most dominant groups. Future analyses will integrate carbon flux data with community composition to improve our understanding of the ecological role of the cryptobenthosin different reef systems.
    Automated spider mite damage detection on tomato leaves in greenhouses
    Nieuwenhuizen, A.T. ; Kool, J. ; Suh, H.K. ; Hemming, J. - \ 2020
    Acta Horticulturae 1268 (2020). - ISSN 0567-7572 - p. 165 - 172.
    Deep learning - Greenhouse - Machine vision - Pest detection - Spider mite

    Spider mites are one of the most challenging pests in the greenhouse, and their management is more and more challenging due to resistance to pesticides. Spider mites prefer young leaves at the outer canopy, stay at the bottom of leaves, and can crawl to nearby plants. Typical symptoms are small yellow and white spots on the upper side of the leaf due to chlorophyll depletion, leading to bronzing of the leaves. The challenge is to detect the spider mite damage in an early stage, as it is hardly possible to detect the actual spider mites underneath the leaves. Based on a structured requirement list, the following camera systems were identified as detection system candidates. Three multispectral cameras and one RGB camera were further investigated in the research. A lab study with hyperspectral imaging was performed that identified discriminating wavebands between healthy and diseased leaves. The wavebands 700, 716 and 747 nm were selected and used in the multispectral systems. Using Fisher LDA, accuracies up to 0.88 could be reached at pixel level with these multispectral cameras. However, none of the setups could meet the spatial resolution to detect spider mite damage at early stage on the leaves. Second step was to perform color image analysis. An identical accuracy of 0.88 with sufficient spatial resolution was reached. Based on these results, a high resolution RGB camera was mounted on a measurement cart. Experiments were performed in a greenhouse compartment with an ongoing spider mite damage infestation in a tomato crop. The results show the automated pipeline for spider mite damage detection in a time series of four recordings over three months, having an accuracy of 0.90. Heat maps of the infestation rate are presented to the grower and are used for input in models for integrated pest management and to support the decision on the release of beneficial insects.

    Effect of oil droplet inhomogeneity at different length scales on mechanical and sensory properties of emulsion-filled gels: Length scale matters
    Fuhrmann, P.L. ; Sala, G. ; Stieger, M. ; Scholten, E. - \ 2020
    Food Hydrocolloids 101 (2020). - ISSN 0268-005X
    Emulsion-filled gels - Fat-related perception - Oil distribution - Oil droplet clustering

    We studied the effect of inhomogeneity in oil droplet distribution at different length scales on the mechanical and sensory properties of emulsion-filled food gels. Two approaches were followed to obtain an inhomogeneous distributions at different length scales: (1) clustering of o/w-emulsions by hetero-aggregation and subsequent gelation to obtain inhomogeneity at μm-scale, and (2) incorporating particles of emulsion-filled gels into emulsion-filled gel matrices with a different volume fraction of oil droplets to obtain gel-in-gels with inhomogeneity at mm-scale. Upon clustering of oil droplets at μm-scale, the Young's modulus of the gels increased by up to 60%, whereas fracture stress and strain depended on emulsifier-matrix interactions. Clustering of oil droplets affected mainly the perception of texture-related sensory attributes, such as hardness, but did not significantly affect the perception of fat-related sensory attributes. Fat-related sensory attributes, such as creaminess and melting, were dominated by emulsifier matrix interactions. For gel-in-gels, the inhomogeneous distribution of oil droplets at mm-scale did not affect Young's modulus or fracture strain. The incorporation of particles decreased the fracture stress of the gels, independently of the droplet distribution. The perception of fat-related sensory attributes changed significantly. Oiliness was lower in samples with lower oil content in the outer phase of the gel than in the inner dispersed particles, whereas coating perception increased in samples in which the oil droplet distribution was inhomogeneous, independently on whether the outer phase or the inner gel particles contained a higher oil volume fraction. Creaminess was only slightly affected. We conclude that oil droplet clustering at μm-scale can be used to modify mechanical properties and texture-related perception of emulsion-filled gels, whereas inhomogeneity at mm-scale allows altering fat-related sensations. Sensory perception can be controlled by modifying the interactions between dispersed oil droplets and matrix using different emulsifiers and by incorporating inhomogeneity in the oil droplet distribution of emulsion-filled gels at different length scales.

    Isolation of Starch from Oil Palm Trunks
    Claassen, P.A.M. ; Hamid, Fazliana Abd. ; Mokhtar, Anis ; Aziz, Astimar Abdul ; Elbersen, H.W. ; Visser, Jochem ; Haaksman, I.K. ; Slaghek, T.M. - \ 2019
    Oil palm trunks were harvested and divided in three sections to represent top, middle and bottom part of the trunk. The trunks were processed in a plywood factory within 24 hours of felling. The inner cores, which remained after removal of the outer layer for veneer production, were chipped and immediately frozen. Fresh samples showed starch granules with sizes between 5 and 15 μm, which is in agreement with earlier reports on palm starch from different palm tree species. The presence of native starch in the samples prepared by cryogenic milling was confirmed by the Maltese crosses after examination with polarized light. The concentration of starch showed a gradient over the oil palm trunk with 42-59% at the top decreasing to less than 10% at the bottom. The concentration of (hemi)cellulose was the reverse. As free sugars were virtually absent, starch hydrolysis seemed to be successfully prevented by this method.
    Optimal strategies for ecosystem services provision in Amazonian production forests
    Piponiot, Camille ; Rutishauser, Ervan ; Derroire, Géraldine ; Putz, Francis E. ; Sist, Plinio ; West, Thales A.P. ; Descroix, Laurent ; Guedes, Marcelino Carneiro ; Honorio Coronado, Eurídice N. ; Kanashiro, Milton ; Mazzei, Lucas ; Oliveira, Marcus Vinicio Neves D'; Pena Claros, Marielos ; Rodney, Ken ; Ruschel, Ademir R. ; Souza, Cintia Rodrigues De; Vidal, Edson ; Wortel, Verginia ; Hérault, Bruno - \ 2019
    Environmental Research Letters 14 (2019)12. - ISSN 1748-9318
    Amazonia - Biodiversity - Carbon - Ecosystem services - Multi-criteria optimisation - Selective logging - Timber production

    Although tropical forests harbour most of the terrestrial carbon and biological diversity on Earth they continue to be deforested or degraded at high rates. In Amazonia, the largest tropical forest on Earth, a sixth of the remaining natural forests is formally dedicated to timber extraction through selective logging. Reconciling timber extraction with the provision of other ecosystem services (ES) remains a major challenge for forest managers and policy-makers. This study applies a spatial optimisation of logging in Amazonian production forests to analyse potential trade-offs between timber extraction and recovery, carbon storage, and biodiversity conservation. Current logging regulations with unique cutting cycles result in sub-optimal ES-use efficiency. Long-term timber provision would require the adoption of a land-sharing strategy that involves extensive low-intensity logging, although high transport and road-building costs might make this approach economically unattractive. By contrast, retention of carbon and biodiversity would be enhanced by a land-sparing strategy restricting high-intensive logging to designated areas such as the outer fringes of the region. Depending on management goals and societal demands, either choice will substantially influence the future of Amazonian forests. Overall, our results highlight the need for revaluation of current logging regulations and regional cooperation among Amazonian countries to enhance coherent and trans-boundary forest management.

    Multi-Tree Decomposition Methods for Large-Scale Mixed Integer Nonlinear Optimization
    Nowak, I. ; Muts, P. ; Hendrix, E.M.T. - \ 2019
    In: Large Scale Optimization in Supply Chains and Smart Manufacturing / Velásquez-Bermúdez, J.M., Khakifirooz, M., Fathi, M., Springer (Springer Optimization and Its Application ) - ISBN 9783030227876 - p. 27 - 58.
    Most industrial optimization problems are sparse and can be formulated as block-separable mixed-integer nonlinear programming (MINLP) problems, defined by linking low-dimensional sub-problems by (linear) coupling constraints. Decomposition methods solve a block-separable MINLP by alternately solving master problems and sub-problems. In practice, decomposition methods are sometimes the only possibility to compute high-quality solutions of large-scale optimization problems. However, efficient implementations may require expert knowledge and problem-specific features. Recently, there is renewed interest in making these methods accessible to general users by developing generic decomposition frameworks and modelling support. The focus of this chapter is on so-called multi-tree decomposition methods, which iteratively approximate the feasible area without using a single (global) branch-and-bound tree, i.e. branch-and-bound is only used for solving sub-problems. After an introduction, we describe first outer approximation (OA) decomposition methods, including the adaptive, multivariate partitioning (AMP) and the novel decomposition-based outer approximation (DECOA) algorithm . This is followed by a description of multi-tree methods using a reduced master problem for solving large-scale industrial optimization problems. The first method to be described applies parallel column generation (CG) and iterative fixing for solving nonconvex transport optimization problems with several hundred millions of variables and constraints. The second method is based on a novel approach combining CG and compact outer approximation. The last methodology to be discussed is the general Benders decomposition method for globally solving large nonconvex stochastic programs using a reduced mixed-integer programming (MIP) master problem.
    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.
    Continuous production of Neisseria meningitidis outer membrane vesicles
    Gerritzen, Matthias J.H. ; Stangowez, Lilli ; Waterbeemd, Bas van de; Martens, Dirk E. ; Wijffels, René H. ; Stork, Michiel - \ 2019
    Applied Microbiology and Biotechnology 103 (2019)23-24. - ISSN 0175-7598
    Chemostat - Continuous processing - Neisseria meningitidis - OMV - Outer membrane vesicles

    Outer membrane vesicles (OMVs) are nanoparticles secreted by Gram-negative bacteria that can be used for diverse biotechnological applications. Interesting applications have been developed, where OMVs are the basis of drug delivery, enzyme carriers, adjuvants, and vaccines. Historically, OMV research has mainly focused on vaccines. Therefore, current OMV production processes have been based on batch processes. The production of OMVs in batch mode is characterized by relatively low yields and high costs. Transition of OMV production processes from batch to continuous processes could increase the volumetric productivity, reduce the production and capital costs, and result in a higher quality product. Here, we study the continuous production of Neisseria meningitidis OMVs to improve volumetric productivity. Continuous cultivation of N. meningitidis resulted in a steady state with similar high OMV concentrations as are reached in current batch processes. The steady state was reproducible and could be maintained for at least 600 h. The volumetric productivity of a continuous culture reached 4.0 × 1014 OMVs per liter culture per day, based on a dilution rate of 1/day. The tested characteristics of the OMVs did not change during the experiments showing feasibility of a continuous production process for the production of OMVs for any application.

    Mito-docking: A Novel In Vivo Method to Detect Protein–Protein Interactions
    Shao, Wei ; He, Lihong ; Deng, Fei ; Wang, Hualin ; Vlak, Just M. ; Hu, Zhihong ; Wang, Manli - \ 2019
    Small Methods 3 (2019)10. - ISSN 2366-9608
    in vivo - method - Mito-docking - nuclear import - protein–protein interactions

    Many methods have been developed to detect protein–protein interactions (PPIs) and explore cellular processes. However, effective methods for detecting complicated PPIs under physical conditions are still in demand. Here, a simple and efficient mitochondria-docking (Mito-docking) method for PPI detection in vivo is developed. The strategy is to anchor a “bait” protein to mitochondrial outer membrane (MOM), and then trap the “prey” protein onto MOM. In this way, interacting signals are enriched to allow easy detection. This method efficiently detects the well-known interaction between two G protein subunits (Gγ2 with Gβ1) and is successfully applied to investigate the recognition of importin α superfamily members for the classical nuclear localization signal (NLS) of simian virus 40 (SV40) large T antigen, which are highly dynamic and not easily visualized by conventional methods. As far as is known, this is the first time that the interaction between human importin α receptors with NLSs has been visualized. The results prove that Mito-docking can be used as a simple, straightforward, and intuitive method to study PPIs qualitatively and quantitatively in vivo.

    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.

    Activity and phylogenetics of the broadly occurring family of microbial nep1-like proteins
    Seidl, Michael F. ; Ackerveken, Guido Van Den - \ 2019
    Annual Review of Phytopathology 57 (2019). - ISSN 0066-4286 - p. 367 - 386.
    Cytolytic activity - GIPC binding - NEP1-like proteins - Pattern-Triggered immunity - Phylogeny - Phytotoxins

    Necrosis-and ethylene-inducing peptide 1 (Nep1)-like proteins (NLP) have an extremely broad taxonomic distribution; they occur in bacteria, fungi, and oomycetes. NLPs come in two forms, those that are cytotoxic to eudicot plants and those that are noncytotoxic. Cytotoxic NLPs bind to glycosyl inositol phosphoryl ceramide (GIPC) sphingolipids that are abundant in the outer leaflet of plant plasma membranes. Binding allows the NLP to become cytolytic in eudicots but not monocots. The function of noncytotoxic NLPs remains enigmatic, but the expansion of NLP genes in oomycete genomes suggests they are important. Several plant species have evolved the capacity to recognize NLPs as molecular patterns and trigger plant immunity, e.g., Arabidopsis thaliana detects nlp peptides via the receptor-like protein RLP23. In this review, we provide a historical perspective from discovery to understanding of molecular mechanisms and describe the latest developments in the NLP field to shed light on these fascinating microbial proteins.

    Redox-flow battery design for a methane-producing bioelectrochemical system
    Geppert, Florian ; Liu, Dandan ; Weidner, Eckhard ; Heijne, Annemiek ter - \ 2019
    International Journal of Hydrogen Energy 44 (2019)39. - ISSN 0360-3199 - p. 21464 - 21469.
    Biocathode - Bioelectrochemical power-to-gas - Methane - Methanogenic archaea - Reactor design

    Methane production at biocathodes is an innovative approach of storing renewable electrical energy in chemical energy via the biological conversion of carbon dioxide. Methane-producing microorganisms use electricity to catalyze the conversion of carbon dioxide into methane; a form of carbon-neutral natural gas. However, the rates of methane production remain too low for practical application. To improve performance, high area-to-volume ratio with good mass transfer is required. In this study, we used the design of redox flow-batteries with a high area-to-volume ratio of 2.0 cm2/cm3 and an external capillary manifold for flow distribution. Current densities up to 35 A/m2 were applied, resulting in volumetric methane production rates of up to 12.5 L CH4/L/d, three times higher than rates reported so far. The highest energy efficiency of 30% was obtained at 25 A/m2. Even with a low relative abundance of methanogens in the microbial community (20%), dense biofilm growth was observed on the outer surface of the biocathode. Flow-battery cell design shows promising performance for application of methane-producing biocathodes.

    Spontaneously released Neisseria meningitidis outer membrane vesicles as vaccine platform: production and purification
    Gerritzen, Matthias J.H. ; Salverda, Merijn L.M. ; Martens, Dirk E. ; Wijffels, René H. ; Stork, Michiel - \ 2019
    Vaccine 37 (2019)47. - ISSN 0264-410X - p. 6978 - 6986.
    Lyme disease - Neisseria meningitidis - Outer membrane vesicles - Tangential flow filtration - Vaccine - Vaccine platform

    Outer membrane vesicles (OMVs) are nanoparticles produced by Gram-negative bacteria that can be used as vaccines. The application of OMVs as vaccine component can be expanded by expressing heterologous antigens on OMVs, creating an OMV-based antigen presenting platform. This study aims to develop a production process for such OMV-based vaccines and studies a production method based on meningococcal OMVs that express heterologous antigens on their surface. As a proof of concept, the Borrelia burgdorferi antigens OspA and OspC were expressed on Neisseria meningitidis OMVs to create a concept anti-Lyme disease vaccine. Production of OMVs released in the culture supernatant was induced by high dissolved oxygen concentrations and purification was based on scalable unit operations. A crude recovery of 90 mg OMV protein could be obtained per liter culture. Expressing heterologous antigens on the OMVs did result in minor reduction of bacterial growth, while OMV production remained constant. The antigen expression did not alter the OMV characteristics. This study shows that production of well characterized OMVs containing heterologous antigens is possible with high yields by combining high oxygen concentrations with an optimized purification process. It is concluded that heterologous OMVs show potential as a vaccine platform.

    Unraveling the regulation of plant vascular identity
    Smit, Margot Evelien - \ 2019
    Wageningen University. Promotor(en): D. Weijers. - Wageningen : Wageningen University - ISBN 9789463439572 - 206

    During plant embryogenesis, the future body plan of the plant is laid down. Part of this development is the specification of cell identities: the outer epidermis, the middle ground tissue and the inner vascular cells. In this thesis we have looked at the genetic components that control plant vascular identity. We have traced back the first vascular cells to the 16-cell embryo and discovered that the development of vascular identity is not a single step but rather a multi-step process. Upstream of this multi-step process we discovered a large set of candidate regulators that control vascular identity. After focusing one of these candidates we now hypothesize that the protein GBF2 can regulate vascular gene expression. Together with proteins that act downstream of the plant hormone auxin, GBF2 interacts with specific DNA sequences to regulate the initiation of vascular development.

    Electrochemical and microbiological characterization of single carbon granules in a multi-anode microbial fuel cell
    Caizán-Juanarena, Leire ; Servin-Balderas, Ivonne ; Chen, Xuan ; Buisman, Cees J.N. ; Heijne, Annemiek ter - \ 2019
    Journal of Power Sources 435 (2019). - ISSN 0378-7753
    Capacitive bioanode - Charge storage - Charge/discharge cycles - Granular activated carbon - Microbial community - Total nitrogen

    Capacitive microbial fuel cells (MFCs) use bacteria on a capacitive anode to oxidize organics in wastewater and simultaneously charge the electrode. This study aims to gain knowledge on the performance of single activated carbon (AC) granules, which are used as capacitive bioanodes. To this end, a multi-anode MFC that allows the testing of up to 29 granules under the same experimental conditions is used. 2 types of AC granules (PK and GAC) and 3 different size-ranges (n = 8 each) are studied in terms of current production, biomass quantification, microbial community and charge storage. Additionally, charge storage of PK granules (n = 24) is determined for different charging/discharging times. Results show that total produced charge directly relates to biomass amount, which has a linear relation towards granule outer surface area. Small AC granules have higher volumetric current densities, which could be of interest for their application in up-scaled reactors. PK granules show slightly higher biomass and current production than GAC granules, while these latter ones show larger volumetric charge storage capacity. Similarly, it is shown that short charging/discharging times are needed to obtain maximum charge storage and current output. These findings are of importance to design and operate MFCs with capacitive properties.

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