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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    The diurnal stratocumulus-to-cumulus transition over land in southern West Africa
    Pedruzo-bagazgoitia, Xabier ; Roode, Stephan R. De; Adler, Bianca ; Babić, Karmen ; Dione, Cheikh ; Kalthoff, Norbert ; Lohou, Fabienne ; Lothon, Marie ; Vilà-guerau De Arellano, Jordi - \ 2020
    Atmospheric Chemistry and Physics 20 (2020)5. - ISSN 1680-7316 - p. 2735 - 2754.
    The misrepresentation of the diurnal cycle of boundary layer clouds by large-scale models strongly impacts the modeled regional energy balance in southern West Africa. In particular, recognizing the processes involved in the maintenance and transition of the nighttime stratocumulus to diurnal shallow cumulus over land remains a challenge. This is due to the fact that over vegetation, surface fluxes exhibit a much larger magnitude and variability than on the more researched marine stratocumulus transitions. An improved understanding of the interactions between surface and atmosphere is thus necessary to improve its representation. To this end, the Dynamics-aerosol-chemistry-cloud interactions in West Africa (DACCIWA) measurement campaign gathered a unique dataset of observations of the frequent stratocumulus-to-cumulus transition in southern West Africa. Inspired and constrained by these observations, we perform a series of numerical experiments using large eddy simulation. The experiments include interactive radiation and surface schemes where we explicitly resolve, quantify and describe the physical processes driving such transition. Focusing on the local processes, we quantify the transition in terms of dynamics, radiation, cloud properties, surface processes and the evolution of dynamically relevant layers such as subcloud layer, cloud layer and inversion layer. We further quantify the processes driving the stratocumulus thinning and the subsequent transition initiation by using a liquid water path budget. Finally, we study the impact of mean wind and wind shear at the cloud top through two additional numerical experiments. We find that the sequence starts with a nighttime well-mixed layer from the surface to the cloud top, in terms of temperature and humidity, and transitions to a prototypical convective boundary layer by the afternoon. We identify radiative cooling as the largest factor for the maintenance leading to a net thickening of the cloud layer of about 18 g m−2 h−1 before sunrise. Four hours after sunrise, the cloud layer decouples from the surface through a growing negative buoyancy flux at the cloud base. After sunrise, the increasing impact of entrainment leads to a progressive thinning of the cloud layer. While the effect of wind on the stratocumulus layer during nighttime is limited, after sunrise we find shear at the cloud top to have the largest impact: the local turbulence generated by shear enhances the boundary layer growth and entrainment aided by the increased surface fluxes. As a consequence, wind shear at the cloud top accelerates the breakup and transition by about 2 h. The quantification of the transition and its driving factors presented here sets the path for an improved representation by larger-scale models
    Towards Adaptive Grids for Atmospheric Boundary-Layer Simulations
    Hooft, J.A. van; Popinet, Stéphane ; Heerwaarden, Chiel C. van; Linden, Steven J.A. van der; Roode, Stephan R. de; Wiel, Bas J.H. van de - \ 2018
    Boundary-Layer Meteorology 167 (2018)3. - ISSN 0006-8314 - p. 421 - 443.
    Adaptive mesh refinement - Atmospheric boundary layer - Direct numerical simulations - Large-eddy simulations - Turbulence
    We present a proof-of-concept for the adaptive mesh refinement method applied to atmospheric boundary-layer simulations. Such a method may form an attractive alternative to static grids for studies on atmospheric flows that have a high degree of scale separation in space and/or time. Examples include the diurnal cycle and a convective boundary layer capped by a strong inversion. For such cases, large-eddy simulations using regular grids often have to rely on a subgrid-scale closure for the most challenging regions in the spatial and/or temporal domain. Here we analyze a flow configuration that describes the growth and subsequent decay of a convective boundary layer using direct numerical simulation (DNS). We validate the obtained results and benchmark the performance of the adaptive solver against two runs using fixed regular grids. It appears that the adaptive-mesh algorithm is able to coarsen and refine the grid dynamically whilst maintaining an accurate solution. In particular, during the initial growth of the convective boundary layer a high resolution is required compared to the subsequent stage of decaying turbulence. More specifically, the number of grid cells varies by two orders of magnitude over the course of the simulation. For this specific DNS case, the adaptive solver was not yet more efficient than the more traditional solver that is dedicated to these types of flows. However, the overall analysis shows that the method has a clear potential for numerical investigations of the most challenging atmospheric cases.
    Regime transitions in near-surface temperature inversions : A conceptual model
    Wiel, Bas J.H. Van de; Vignon, Etienne ; Baas, Peter ; Hooijdonk, Ivo G.S. van; Linden, Steven J.A. van der; Hooft, J.A. van; Bosveld, Fred C. ; Roode, Stefan R. de; Moene, Arnold F. ; Genthon, Christophe - \ 2017
    Journal of the Atmospheric Sciences 74 (2017)4. - ISSN 0022-4928 - p. 1057 - 1073.
    Boundary layer - Inversions - Nonlinear models - Snow - Surface observations - Thermodynamics

    A conceptual model is used in combination with observational analysis to understand regime transitions of near-surface temperature inversions at night as well as in Arctic conditions. The model combines a surface energy budget with a bulk parameterization for turbulent heat transport. Energy fluxes or feedbacks due to soil and radiative heat transfer are accounted for by a "lumped parameter closure," which represents the "coupling strength" of the system. Observations from Cabauw, Netherlands, and Dome C, Antarctica, are analyzed. As expected, inversions are weak for strong winds, whereas large inversions are found under weak-wind conditions. However, a sharp transition is found between those regimes, as it occurs within a narrow wind range. This results in a typical S-shaped dependency. The conceptual model explains why this characteristic must be a robust feature. Differences between the Cabauw and Dome C cases are explained from differences in coupling strength (being weaker in the Antarctic). For comparison, a realistic column model is run. As findings are similar to the simple model and the observational analysis, it suggests generality of the results. Theoretical analysis reveals that, in the transition zone near the critical wind speed, the response time of the system to perturbations becomes large. As resilience to perturbations becomes weaker, it may explain why, within this wind regime, an increase of scatter is found. Finally, the so-called heat flux duality paradox is analyzed. It is explained why numerical simulations with prescribed surface fluxes show a dynamical response different from more realistic surface-coupled systems.

    Expression of the dyslexia candidate gene kiaa0319-like in insect cells
    Holster, Savanne ; Oers, Monique M. van; Roode, Els C. ; Tsang, Otto W.H. ; Yeung, Venus S.Y. ; Vlak, Just M. ; Waye, Mary M.Y. - \ 2015
    In: Biochemistry and Molecular Biology: The Complexity of Human Traits and Diseases Nova Science Publishers - ISBN 9781634823135 - p. 11 - 19.
    Baculovirus expression system - Dyslexia - kiaa0319 - kiaa0319-like

    The human kiaa0319-like gene is one of the candidate genes for developmental dyslexia, but the exact function of the encoded KIAA0319L (KL) protein is not known. To allow functional analysis a purified, biologically active KL protein is required. The kiaa0319-like gene was expressed in insect cells using the baculovirus expression system. To optimize the expression of the kiaa0319-like gene and to be able to purify the KL protein, several approaches were used. Two different recombinant baculoviruses were made, one with the full length coding sequence of KL and one that lacked the transmembrane domain to facilitate purification.. Versions in which the kiaa0319L sequences were cloned downstream of the honeybee melittin signal sequence were also made. All four constructs contained a C-terminal influenza hemagglutinin (HA)-tag. Sf9 insect cells infected with these recombinant baculoviruses produced the KL protein, as demonstrated by Western blot analysis using either the HA-antibody or KL-specific polyclonal serum.

    Salatin leert vleesboeren hoe je geld kunt verdienen
    Boer, Imke de - \ 2014
    Expression of the dyslexia candidate gene kiaa0319-like in insect cells
    Holster, S. ; Oers, M.M. van; Roode, E.C. ; Tsang, O.W.H. ; Yeung, V.S.Y. ; Vlak, J.M. ; Waye, M.M.Y. - \ 2013
    Journal of Biochemistry and Molecular Biology in The Post Genomic Era 2 (2013)1. - ISSN 2156-5732 - p. 45 - 52.
    The human kiaa0319-like gene is one of the candidate genes for developmental dyslexia, but the exact function of the encoded KIAA0319L (KL) protein is not known. To allow functional analysis a purified, biologically active KL protein is required. The kiaa0319-like gene was expressed in insect cells using the baculovirus expression system. To optimize the expression of the kiaa0319-like gene and to be able to purify the KL protein, several approaches were used. Two different recombinant baculoviruses were made, one with the full length coding sequence of KL and one that lacked the transmembrane domain to facilitate purification.. Versions in which the kiaa0319L sequences were cloned downstream of the honeybee melittin signal sequence were also made. All four constructs contained a C-terminal influenza hemagglutinin (HA)-tag. Sf9 insect cells infected with these recombinant baculoviruses produced the KL protein, as demonstrated by Western blot analysis using either the HA-antibody or KL-specific polyclonal serum.
    Multiple regression model for thermal inactivation of Listeria monocytogenes in liquid food products
    Lieverloo, J.H.M. ; Roode, M. de; Fox, M.B. ; Zwietering, M.H. ; Wells-Bennik, M.H.J. - \ 2013
    Food Control 29 (2013)2. - ISSN 0956-7135 - p. 394 - 400.
    sublethal heat-shock - escherichia-coli o157-h7 - growth temperature - scott-a - pseudomonas-aeruginosa - salmonella-typhimurium - resistance - milk - ph - thermotolerance
    A multiple regression model was constructed for thermal inactivation of Listeria monocytogenes in liquid food products, based on 802 sets of data with 51 different strains and 6 cocktails of strains published from 1984 to 2010. Significant variables, other than inactivation temperature, were pH, sodium chloride content, sugar content, the temperature of growth or storage before inactivation, in addition to a heat shock before inactivation. The constructed model for thermal inactivation of L. monocytogenes has a reduced variability as these variables are known to influence the thermal resistance (and these are known or controllable in practice). Mean simulation results of inactivation of L. monocytogenes during pasteurisation (20 s, 76 °C) of raw milk (calculated mean level after growth 14 cfu/l) were comparable with results of a single regression model constructed from inactivation data found in experiments in milk only (175 data sets, 18 strains/cocktails). Both models predicted a probability of survival of less than 1 in a billion litres. The study shows that multiple regression modelling can be used to obtain a model from all data available, with a limited and realistic uncertainty level, while retaining the variability of heat resistance due to the 51 strains and 6 cocktails of strains (unknown and not controllable in practice).
    The impact of climate change on the critical weather conditions at Schiphol airport (Impact)
    Jacobs, A.J.M. ; Barkmeijer, J. ; Siebesma, A.P. ; Plas, E.V. van der; Wichers Schreur, B.G.J. ; Roozekrans, J.N. ; Holtslag, A.A.M. ; Steeneveld, G.J. ; Ronda, R.J. ; Roode, S.R. de - \ 2012
    Utrecht/Wageningen : Knowledge for Climate Programme Office (Knowledge for Climate KfC 53/2012) - ISBN 9789490070571 - 76
    luchthavens - betrouwbaarheid - weersgegevens - klimaat - modellen - weersvoorspelling - haarlemmermeer - airports - reliability - weather data - climate - models - weather forecasting - haarlemmermeer
    Schiphol is van groot belang voor de economische positie van Nederland. De luchthaven is erg gevoelig voor kritieke weersomstandigheden zoals mist, intensieve neerslag en hevige wind. Als gevolg van klimaatverandering verwachten we dat ook de variabiliteit van het weer op de luchthaven en de frequentie en intensiteit van kritieke weersomstandigheden zullen veranderen, maar een precieze kwantificering daarvan ontbreekt. De belangrijkste doelstelling van dit project is daarom het verstrekken en demonstreren van het volgende generatie weer‐ en klimaatmodel HARMONIE. Dit is een nieuw model dat beter geschikt lijkt om het effect van klimaatverandering op lokale kritieke weersomstandigheden op de luchthaven te kwantificeren en te begrijpen. Bovendien zal kennis uit dit project worden gebruikt om de kwaliteit van onze huidige en toekomstige weersvoorspellingen te verbeteren. In dit project wordt het potentieel van het HARMONIE model, om meer gedetailleerdere en nauwkeurigere weersvoorspellingen voor luchthaven Schiphol te leveren dan ons huidige operationele weermodel HIRLAM, nagegaan in het huidige klimaat.
    Refinement and application of a regional atmospheric model for climate scenario calculations of Western Europe
    Meijgaard, E. van; Ulft, L.H. van; Lenderink, G. ; Roode, S.R. de; Wipfler, E.L. ; Boers, R. ; Timmermans, R.M.A. van - \ 2012
    Wageningen : KVR (KVR report KVR 054/12) - ISBN 9789088150463 - 44
    klimaatverandering - scenario-analyse - temperatuur - neerslag - aërosolen - grenslaagmeteorologie - modellen - noordzee - nederland - climatic change - scenario analysis - temperature - precipitation - aerosols - boundary-layer meteorology - models - north sea - netherlands
    Het KNMI regionaal klimaat model RACMO wordt in toenemende mate gebruikt bij de detaillering van Klimaatscenario’s. Voorbeelden zijn de frequentie en intensiteit van hittegolven en de veranderingen daarin. Of te verwachten wijzigingen in het optreden van lokale neerslagextremen. In dit project zijn een aantal componenten van RACMO verder ontwikkeld. De bodemhydrologie van het model is verder verfijnd door ruimtelijke heterogeniteit in te voeren voor een aantal bodemparameters, zoals bodemtype en worteldiepte. Deze aanpassing resulteert in meer uitgesproken ruimtelijke structuren op regionale schaal.
    Multivariate regression model of thermal inactivation of Listeria monocytogenes in liquid food products
    Lieverloo, J.H.M. ; Roode, M. de; Fox, M.B. ; Zwietering, M.H. ; Wells-Bennik, M.H.J. - \ 2011
    In: Conference Proceedings 7th International Conference on Predictive Modelling of Food Quality and Safety, Dublin, Ireland, 12 - 15 September, 2011. - Teagasc, Dublin, Ireland : UCD, DIT - ISBN 9781900454469 - p. 202 - 205.
    Vertical wind velocity observations at the Cabauw tower
    Ouwersloot, H.G. ; Roode, S.R. de; Bosveld, F.C. ; Kroon, P.S. - \ 2010
    In: 19th Symposium on Boundary Layers and Turbulence, American Meteorological Society, 2-6 August 2010, Keystone, Colorado, USA. - Boston : AMS - p. P1.2 - P1.2.
    If vertical turbulent fluxes are computed from time series collected at a fixed point, it is assumed that the temporal mean vertical velocity is zero. This paper discusses the validity of this assumption by analysis of time series of the vertical wind velocity collected with sonic anemometers at four different heights ranging from 3 to 180 m from the Cabauw tower. It is shown that even for averaging times of 1 hour, the mean vertical velocity can have values of the order of 10 cm/s.
    Establishment of a cell line from Chrysodeixis chalcites permissive for Chrysodeixis chalcites and Trichoplusia ni nucleopolyhedrovirus
    Xu, F. ; Lynn, D.E. ; Roode, E.C. ; Muñoz, D. ; Lent, J.W.M. van; Vlak, J.M. ; Oers, M.M. van - \ 2010
    Journal of Invertebrate Pathology 105 (2010)1. - ISSN 0022-2011 - p. 56 - 62.
    nuclear polyhedrosis-virus - single-nucleocapsid nucleopolyhedrovirus - dna photolyase genes - insect cells - baculovirus vectors - identification - infectivity - protein - genome - replication
    A new cell line was established from the embryos of the insect Chrysodeixis chalcites (Lepidoptera, Noctuidae, Plusiinae). The cell line contains several morphologically different cell types and was distinguished from three other lepidopteran cell lines propagated in the laboratory by DNA amplification fingerprinting. The cultured cells, which we officially named WU-CcE-1 cells, were permissive for infection by C. chalcites nucleopolyhedrovirus (ChchNPV) and large numbers of occlusion bodies were produced that retained their infectivity for C. chalcites larvae. The CcE-1 cells were also permissive for Trichoplusia ni single nucleopolyhedrovirus (TnSNPV). ChchNPV could be passaged in these cells for at least four passages indicating that budded virus production was supported. Autographa californica multiple nucleopolyhedrovirus (AcMNPV) and Helicoverpa armigera (Hear) NPV both induced apoptosis in these cells. The results obtained indicate that the CcE-1 cell line will be a useful tool in the study of both ChchNPV and TnSNPV
    Formulation of the Dutch Atmospheric Large-Eddy Simulation (DALES) and overview of its applications
    Heus, T. ; Heerwaarden, C.C. van; Jonker, H.J.J. ; Siebesma, A.P. ; Axelsen, S. ; Dries, C.L.A.M. van den; Geoffroy, O. ; Moene, A.F. ; Pino, D. ; Roode, S.R. de; Vilà-Guerau de Arellano, J. - \ 2010
    Geoscientific Model Development 3 (2010)2. - ISSN 1991-959X - p. 415 - 444.
    convective boundary-layer - shallow cumulus convection - characteristic length scales - topped mixed layers - liquid water path - aircraft observations - marine stratocumulus - radiative-transfer - simple parameterization - turbulent dispersion
    The current version of the Dutch Atmospheric Large-Eddy Simulation (DALES) is presented. DALES is a large-eddy simulation code designed for studies of the physics of the atmospheric boundary layer, including convective and stable boundary layers as well as cloudy boundary layers. In addition, DALES can be used for studies of more specific cases, such as flow over sloping or heterogeneous terrain, and dispersion of inert and chemically active species. This paper contains an extensive description of the physical and numerical formulation of the code, and gives an overview of its applications and accomplishments in recent years
    QSARs in ecotoxicological risk assessment
    Roode, D. De; Hoekzema, C.C. ; Vries-Buitenweg, S. de; Waart, B. van de; Hoeven, J. Van der - \ 2006
    Regulatory Toxicology and Pharmacology 45 (2006)1. - ISSN 0273-2300 - p. 24 - 35.
    aquatic toxicity - environmental-pollutants - applicability domain - existing chemicals - organic-compounds - fish - model - pharmaceuticals - descriptors - pesticides
    The need for more ecotoxicological data encourages the use of QSARs because of the reduction of (animal) testing, time and cost. QSARs may however only be used if they prove to be reliable and accurate. In this paper, four QSARs were attempted to predict toxicity for 170 compounds from a broad chemical class, using them as a black-box. Predictions were obtained for 122 compounds, indicating an important drawback of QSARs, i.e., for 28% of the compounds QSARs cannot be used at all. Ecosar, Topkat, and QSARs for non-polar and polar narcosis generated predictions for 120, 39, 24, and I I compounds, respectively. Correlations between experimental and predicted effect concentrations were significant for Topkat and the QSAR for polar narcosis, but generally poor for Ecosar and the QSAR for non-polar narcosis. When predicted effect concentrations for fish were allowed to deviate from experimental values by a factor of 5, correct predictions were generated for 77%, 54%, 68%, and 91% of the compounds using Ecosar, Topkat, and the QSARs for non-polar and polar narcosis, respectively. It was impossible to indicate specific chemical classes for which a QSAR should be used or not. The results show that currently available QSARs cannot be used as a black-box.
    Meerwaarde door gebiedsgerichte samenwerking in natuurbeheer?
    Vreke, J. ; Pleijte, M. ; Apeldoorn, R.C. van; Corporaal, A. ; Dam, R.I. van; Wijk, M.N. van - \ 2006
    Wageningen : Wettelijke Onderzoekstaken Natuur & Milieu (WOt-rapport 30) - 118
    natuurbescherming - ecologie - financiën - milieubeheer - nederland - agrarisch natuurbeheer - nature conservation - ecology - finance - environmental management - netherlands - agri-environment schemes
    Dit rapport is een verslag van de aanzetten tot en gerealiseerde gebiedsgerichte samenwerking tussen reguliere natuurterreinbeheerders en particuliere terreinbeheerders zoals agrarische natuurverenigingen en landgoedeigenaren. In het verslag wordt aangegeven of en hoe gebiedsgerichte samenwerking tot meerwaarde kan leiden in ecologische, financiele, bestuurlijke en maatschappelijke zin. Verder wordt aangegeven waarom gebiedsgerichte samenwerking al dan niet van de grond komt en wat overheden kunnen doen om gebiedsgerichte samenwerking te versterken. Trefwoorden: agrarisch natuurbeheer, beheersplan, bestuurlijk draagvlak, Drentsche Aa, ecologisch, financiën, maatschappelijk draagvlak, meerwaarde, natuurbeheer, gebiedsplan, particulier natuurbeheer, Roode beek, samenwerking, Soerel, westelijke Langstraat.
    The 5' nontranslated region of Varroa destructor virus 1 (Iflavirus): Structure prediction and IRES activity in insect cells
    Ongus, J.R. ; Roode, E.C. ; Pleij, C.W.A. ; Vlak, J.M. ; Oers, M.M. van - \ 2006
    In: Abstract Book of the 9th International Colloquium on Invertebrate Pathology and Microbial Control, Wuhan, China, 27-08 t/m 01-09-2006. - Wuhan : - p. 178 - 178.
    Development of chronic tests for endocrine active chemicals. Part 2. An extended fish earli-life stage test with an androgenic chemical in the fathead minnow (Pimephales promelas)
    Bogers, R. ; Vries-Buitenweg, S. de; Gils, H.A.M. van; Baltussen, E. ; Hargreaves, A. ; Waart, B. van de; Roode, D.F. de; Legler, J. ; Murk, A.J. - \ 2006
    Aquatic Toxicology 80 (2006)2. - ISSN 0166-445X - p. 119 - 130.
    medaka oryzias-latipes - zebrafish danio-rerio - secondary sex characteristics - mill effluent - in-vivo - nonaromatizable androgens - receptor agonist - methyltestosterone - disruption - growth
    The Endocrine Modulators Study Group (EMSG) of the European Chemical Industry has proposed an extended fish early-life stage (ELS) test based on OECD test guideline 210 in combination with a fish pair-breeding reproduction study as a possible alternative for fish full life cycle testing. In this paper the androgen methyldihydrotestosterone (MDHT) was tested in an extended ELS test with fathead minnow supplementary to such a test with the weak estrogen 4-tert-pentylphenol (4TPP). Main endpoints were secondary sexual characteristics (SSC), plasma vitellogenin (VTG) induction and gonadal development. Early blastula embryos were exposed to 0, 0.10, 0.32 and 1.0 ¿g MDHT l-1 for up to 114 days post-hatch (dph). A batch of fish exposed to 1.0 ¿g l-1 was transferred to clean water after 30 or 63 dph for the remainder of the study. Ethinylestradiol (EE2) was included as estrogenic reference substance at 0.01 ¿g l-1. Exposure to MDHT had no significant effect on hatching success or survival, but significantly increased the condition factor of fish exposed for 63 and 114 dph (up to 150% of the control). At 63 dph MDHT exposure induced appearance of tubercles on the snout (a male SSC) of more than 80% of fish. Compared to the controls, plasma VTG was not detectable or significantly lower in fish exposed to MDHT at 0.10 ¿g/l, but not significantly affected at higher MDHT concentrations. Both lower levels of MDHT significantly inhibited the development of female gonads as of 30 dph. Fish exposed to MDHT at 0.32 and 1.0 ¿g l-1 showed higher incidences of mixed sex gonads (10-25%) and smaller testes or dysplasia of gonadal tissue. Dysplasia was present in 80% of the fish continuously exposed to 1.0 ¿g l-1 up to 114 dph, but reversible when fish were transferred to dilution water. Results indicate that suppression of ovarian development was the most sensitive endpoint for MDHT exposure after 30 dph. Other endpoints (e.g., growth and SSC) required exposure during at least up to 63 dph to yield a significant effect. Androgenic effects on VTG production required even longer exposure, i.e., until sufficient number of females had matured
    Alternative approaches can greatly reduce the number of fish used for acute toxicity testing
    Hoekzema, C.C. ; Murk, A.J. ; Waart, B.J. van de; Hoeven, J.C.M. van der; Roode, D.F. de - \ 2006
    Environmental Toxicology and Chemistry 25 (2006)5. - ISSN 0730-7268 - p. 1322 - 1325.
    toxiciteit - chemicaliën - tests - toxicologie - testen - vissen - toxicity - chemicals - tests - toxicology - testing - fishes - european-union - ecotoxicity - strategy - daphnia - embryo - algae
    We first examined the uptake kinetics of Cd and Zn in the juvenile marine black sea bream (Acanthopagrus schlegeli) over a wide range of ambient Cd and Zn concentrations, and the relationships with metal accumulation (uptake rate and amount of nonexchangeable surface binding) were established for different fish tissues. Both Cd and Zn accumulation in the body increased linearly with exposure time after the initial metal surface binding. The dissolved Cd and Zn uptake rate constants were 2.64 and 6.50 L/kg/d, respectively, and the kinetics followed a first-order process. No evidence of biphasic transport was found, in contrast to the situation in freshwater fish. Viscera were the most important sites of metal uptake, and gills were the second most important sites. The black sea breams were then acclimated at different Cd or Zn concentrations from either waterborne or dietary source for one week, and the alteration of metal uptake kinetics or subcellular distribution and metallothionein (MT) induction were further quantified. The Cd body burden was enhanced up to 8.6- and 49-fold after waterborne and dietary Cd pre-exposure, respectively. Cadmium pre-exposure also altered the tissue-specific subcellular Cd distribution and significantly elevated tissue MT levels. In contrast, the black sea breams were able to regulate Zn accumulation, and waterborne or dietary Zn pre-exposure had only weak influences on Zn body burden and redistribution. Both Cd and Zn pre-exposures enhanced the metal uptake rate constants, whereas the nonexchangeable surface bindings were less impacted by these pre-exposures. We demonstrated a positive relationship between the Cd uptake rate and Cd or MT concentration in the fish. Pre-exposure to metals may substantially modify the kinetics of metal uptake.
    The 5' non-translated region of Varroa destructor virus 1 (genus Iflavirus): structure prediction and IRES activity in Lymantria dispar cells
    Ongus, J.R. ; Roode, E.C. ; Pleij, C.W.A. ; Vlak, J.M. ; Oers, M.M. van - \ 2006
    Journal of General Virology 87 (2006)11. - ISSN 0022-1317 - p. 3397 - 3407.
    internal ribosome entry - picorna-like-virus - rhopalosiphum-padi virus - cricket-paralysis-virus - nucleotide-sequence analysis - hepatitis-c virus - translation initiation - triatoma-virus - rna viruses - insect
    Structure prediction of the 5' non-translated region (NTR) of four iflavirus RNAs revealed two types of potential internal ribosome entry site (IRES), which are discriminated by size and level of complexity, in this group of viruses. In contrast to the intergenic IRES of dicistroviruses, the potential 5' IRES structures of iflaviruses do not have pseudoknots. To test the activity of one of these, a bicistronic construct was made in which the 5' NTR of Varroa destructor virus 1 (VDV-1) containing a putative IRES was cloned in between two reporter genes, enhanced green fluorescent protein and firefly luciferase (Fluc). The presence of the 5' NTR of VDV-1 greatly enhanced the expression levels of the second reporter gene (Fluc) in Lymantria dispar Ld652Y cells. The 5' NTR was active in a host-specific manner, as it showed lower activity in Spodoptera frugiperda Sf21 cells and no activity in Drosophila melanogaster S2 cells
    Stabilized baculovirus vector expressing a heterologous gene and GP64 from a single bicistronic transcript
    Pijlman, G.P. ; Roode, E.C. ; Fan, X.X. ; Roberts, L.O. ; Belsham, G.J. ; Vlak, J.M. ; Oers, M.M. van - \ 2006
    Journal of Biotechnology 123 (2006)1. - ISSN 0168-1656 - p. 13 - 21.
    nuclear polyhedrosis-virus - ribosome entry site - non-hr origin - autographa-californica - insect cells - spodoptera-frugiperda - dna-replication - recombinant baculovirus - trichoplusia-ni - foreign genes
    The efficient scale-up of recombinant protein production in insect-cell bioreactors using baculovirus expression vectors is hampered by reductions in yield with increasing viral passage, the so-called passage effect. This phenomenon is characterized by the generation and subsequent accumulation of defective interfering baculoviruses (DIs), which interfere with the replication of genomically intact virus. A novel baculovirus expression vector is presented equipped with a bicistronic expression cassette that allows the simultaneous expression of the recombinant gene (GFP, first cistron) and an essential baculovirus gene (GP64, second cistron) from a single messenger RNA (mRNA). The translation of GP64 is mediated by an internal ribosome entry site (IRES) element from Rhopalosiphum padi virus (RhPV) while the native GP64 gene is deleted. In this way, a dominant selection pressure is placed on the entire bicistronic mRNA and hence on the maintenance of the foreign gene. The bicistronic expression vector was superior to the control baculovirus vector in that GFP expression remained at much higher levels upon continued virus passage. The versatility of this stabilized vector was demonstrated by its ability to propagate in a number of cell lines including Sf21, Sf9 and High Five cells. This novel baculovirus vector is especially valuable for large-scale recombinant protein production in insect-cell bioreactors where the number of viral passages is high.
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