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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    Deceleration-Stats Save Much Time During Phototrophic Culture Optimization
    Hoekema, S. ; Rinzema, A. ; Tramper, J. ; Wijffels, R.H. ; Janssen, M. - \ 2014
    Biotechnology and Bioengineering 111 (2014)4. - ISSN 0006-3592 - p. 792 - 802.
    rate a-stat - photosynthetic efficiency - panel photobioreactor - escherichia-coli - smooth change - steady-state - growth - microalgae - light - model
    In case of phototrophic cultures, photobioreactor costs contribute significantly to the total operating costs. Therefore one of the most important parameters to be determined is the maximum biomass production rate, if biomass or a biomass associated product is the desired product. This is traditionally determined in time consuming series of chemostat cultivations. The goal of this work is to assess the experimental time that can be saved by applying the deceleration stat (D-stat) technique to assess the maximum biomass production rate of a phototrophic cultivation system, instead of a series of chemostat cultures. A mathematical model developed by Geider and co-workers was adapted in order to describe the rate of photosynthesis as a function of the local light intensity. This is essential for the accurate description of biomass productivity in phototrophic cultures. The presented simulations demonstrate that D-stat experiments executed in the absence of pseudo steady-state (i.e., the arbitrary situation that the observed specific growth rate deviates
    Combining in vitro embryotoxicity data with physiologically based kinetic (PBK) modelling to define in vivo dose-response curves for developmental toxicity of phenol in rat and human
    Strikwold, M. ; Spenkelink, A. ; Woutersen, R.A. ; Rietjens, I. ; Punt, A. - \ 2013
    Archives of Toxicology 87 (2013)9. - ISSN 0340-5761 - p. 1709 - 1723.
    stem-cell test - substituted phenols - 2-generation reproduction - pharmacokinetic models - protein-binding - risk-assessment - drug clearance - steady-state - human liver - metabolism
    In vitro assays are often used for the hazard characterisation of compounds, but their application for quantitative risk assessment purposes is limited. This is because in vitro assays cannot provide a complete in vivo dose-response curve from which a point of departure (PoD) for risk assessment can be derived, like the no observed adverse effect level (NOAEL) or the 95 % lower confidence limit of the benchmark dose (BMDL). To overcome this constraint, the present study combined in vitro data with a physiologically based kinetic (PBK) model applying reverse dosimetry. To this end, embryotoxicity of phenol was evaluated in vitro using the embryonic stem cell test (EST), revealing a concentration-dependent inhibition of differentiation into beating cardiomyocytes. In addition, a PBK model was developed on the basis of in vitro and in silico data and data available from the literature only. After evaluating the PBK model performance, effective concentrations (ECx) obtained with the EST served as an input for in vivo plasma concentrations in the PBK model. Applying PBK-based reverse dosimetry provided in vivo external effective dose levels (EDx) from which an in vivo dose-response curve and a PoD for risk assessment were derived. The predicted PoD lies within the variation of the NOAELs obtained from in vivo developmental toxicity data from the literature. In conclusion, the present study showed that it was possible to accurately predict a PoD for the risk assessment of phenol using in vitro toxicity data combined with reverse PBK modelling.
    The Reaction Kinetics of 3-Hydroxybenzoate 6-Hydroxylase from Rhodococcus jostii RHA1 Provide an Understanding of the para-Hydroxylation Enzyme Catalytic Cycle
    Sucharitakul, J. ; Tongsook, C. ; Pakotiprapha, D. ; Berkel, W.J.H. van; Chaiyen, P. - \ 2013
    Journal of Biological Chemistry 288 (2013)49. - ISSN 0021-9258 - p. 35210 - 35221.
    para-hydroxybenzoate hydroxylase - p-hydroxyphenylacetate 3-hydroxylase - 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase - steady-state - ornithine hydroxylase - vibrio-campbellii - crystal-structure - gentisic acid - in-vitro - mechanism
    3-Hydroxybenzoate 6-hydroxylase (3HB6H) from Rhodococcus jostii RHA1 is an NADH-specific flavoprotein monooxygenase that catalyzes the para-hydroxylation of 3-hydroxybenzoate (3HB) to form 2,5-dihydroxybenzoate (2,5-DHB). Based on results from stopped-flow spectrophotometry, the reduced enzyme-3HB complex reacts with oxygen to form a C4a-peroxy flavin with a rate constant of 1.13 ± 0.01 × 10(6) m(-1) s(-1) (pH 8.0, 4 °C). This intermediate is subsequently protonated to form a C4a-hydroperoxyflavin with a rate constant of 96 ± 3 s(-1). This step shows a solvent kinetic isotope effect of 1.7. Based on rapid-quench measurements, the hydroxylation occurs with a rate constant of 36 ± 2 s(-1). 3HB6H does not exhibit substrate inhibition on the flavin oxidation step, a common characteristic found in most ortho-hydroxylation enzymes. The apparent kcat at saturating concentrations of 3HB, NADH, and oxygen is 6.49 ± 0.02 s(-1). Pre-steady state and steady-state kinetic data were used to construct the catalytic cycle of the reaction. The data indicate that the steps of product release (11.7 s(-1)) and hydroxylation (36 ± 2 s(-1)) partially control the overall turnover
    Genome-scale metabolic model for Lactococcus lactis MG1363 and its application to the analysis of flavor formation
    Flahaut, N.A.L. ; Wiersma, A. ; Bunt, B. van der; Martens, D.E. ; Schaap, P.J. ; Sijtsma, L. ; Martins Dos Santos, V.A.P. ; Vos, W.M. de - \ 2013
    Applied Microbiology and Biotechnology 97 (2013)19. - ISSN 0175-7598 - p. 8729 - 8739.
    amino-acid catabolism - streptococcus-lactis - cremoris mg1363 - steady-state - bacteria - growth - reconstruction - networks - systems - cheese
    Lactococcus lactis subsp. cremoris MG1363 is a paradigm strain for lactococci used in industrial dairy fermentations. However, despite of its importance for process development, no genome-scale metabolic model has been reported thus far. Moreover, current models for other lactococci only focus on growth and sugar degradation. A metabolic model that includes nitrogen metabolism and flavor-forming pathways is instrumental for the understanding and designing new industrial applications of these lactic acid bacteria. A genome-scale, constraint-based model of the metabolism and transport in L. lactis MG1363, accounting for 518 genes, 754 reactions, and 650 metabolites, was developed and experimentally validated. Fifty-nine reactions are directly or indirectly involved in flavor formation. Flux Balance Analysis and Flux Variability Analysis were used to investigate flux distributions within the whole metabolic network. Anaerobic carbon-limited continuous cultures were used for estimating the energetic parameters. A thorough model-driven analysis showing a highly flexible nitrogen metabolism, e.g., branched-chain amino acid catabolism which coupled with the redox balance, is pivotal for the prediction of the formation of different flavor compounds. Furthermore, the model predicted the formation of volatile sulfur compounds as a result of the fermentation. These products were subsequently identified in the experimental fermentations carried out. Thus, the genome-scale metabolic model couples the carbon and nitrogen metabolism in L. lactis MG1363 with complete known catabolic pathways leading to flavor formation. The model provided valuable insights into the metabolic networks underlying flavor formation and has the potential to contribute to new developments in dairy industries and cheese-flavor research.
    Quantifying heterogeneous transport of a tracer and a degradable contaminant in the field, with snowmelt and irrigation
    Schotanus, D. ; Ploeg, M.J. van der; Zee, S.E.A.T.M. van der - \ 2012
    Hydrology and Earth System Sciences 16 (2012). - ISSN 1027-5606 - p. 2871 - 2882.
    well-structured soil - solute transport - water-flow - preferential flow - spatial variability - propylene-glycol - unsaturated zone - saturated soil - steady-state - nonequilibrium
    To examine the persistence of preferential flow paths in a field soil, and to compare the leaching of a degradable contaminant with the leaching of a tracer, two field experiments were performed using a multi-compartment sampler (MCS). The first experiment was carried out during the snowmelt period in early spring, characterized by high infiltration fluxes from snowmelt. The second experiment was carried out in early summer with irrigation to mimic homogeneous rainfall. During the second experiment, the soil was warmer and degradation of the degradable contaminant was observed. For both experiments, the highest tracer concentrations were found in the same area of the sampler, but the leached tracer masses of the individual locations were not highly correlated. Thus, the preferential flow paths were stable between the two experiments. With a lower infiltration rate, in the second experiment, more isolated peaks in the drainage and the leached masses were found than in the first experiment. Therefore, it is concluded that the soil heterogeneity is mainly caused by local differences in the soil hydraulic properties, and not by macropores. With higher infiltration rates, the high and low leaching cells were more clustered. The leached masses of the degradable contaminant were lower than the leached masses of the tracer, but the masses were highly correlated. The first-order degradation rate and the dispersivity were fitted with CXTFIT; the first-order degradation rate was 0.02 d-1, and the dispersivity varied between 1.9 and 7.1 cm. The persistence of the flow paths during the experiments suggests soil heterogeneity as the driver for heterogeneous flow and solute transport in this soil. At the MCS scale, heterogeneous snowmelt did not seem to have much influence on the flow and solute paths
    Quantifying catchment-scale mixing and its effect on time-varying travel time distributions
    Velde, Y. van der; Torfs, P.J.J.F. ; Zee, S.E.A.T.M. van der; Uijlenhoet, R. - \ 2012
    Water Resources Research 48 (2012)6. - ISSN 0043-1397 - 13 p.
    flow route contributions - solute transport - transit-time - lowland catchment - residence time - steady-state - hydrology - model - soil - discharge
    Travel time distributions are often used to characterize catchment discharge behavior, catchment vulnerability to pollution and pollutant loads from catchments to downstream waters. However, these distributions vary with time because they are a function of rainfall and evapotranspiration. It is important to account for these variations when the time scale of interest is smaller than the typical time-scale over which average travel time distributions can be derived. Recent studies have suggested that subsurface mixing controls how rainfall and evapotranspiration affect the variability in travel time distributions of discharge. To quantify this relation between subsurface mixing and dynamics of travel time distributions, we propose a new transformation of travel time that yields transformed travel time distributions, which we call Storage Outflow Probability (STOP) functions. STOP functions quantify the probability for water parcels in storage to leave a catchment via discharge or evapotranspiration. We show that this is equal to quantifying mixing within a catchment. Compared to the similar Age function introduced by Botter et al. (2011), we show that STOP functions are more constant in time, have a clearer physical meaning and are easier to parameterize. Catchment-scale STOP functions can be approximated by a two-parameter beta distribution. One parameter quantifies the catchment preference for discharging young water; the other parameter quantifies the preference for discharging old water from storage. Because of this simple parameterization, the STOP function is an innovative tool to explore the effects of catchment mixing behavior, seasonality and climate change on travel time distributions and the related catchment vulnerability to pollution spreading.
    Evaluating variations of physiology-based hyperspectral features along a soil water gradient in a Eucalyptus grandis plantation
    Cho, M.A. ; Aardt, J. van; Main, R. ; Majeke, B. - \ 2010
    International Journal of Remote Sensing 31 (2010)12. - ISSN 0143-1161 - p. 3143 - 3159.
    multiple linear-regression - red edge position - chlorophyll content - vegetation indexes - reflectance indexes - steady-state - precision agriculture - spectral reflectance - absorption features - leaf reflectance
    Remote sensing is viewed as a cost-effective alternative to intensive field surveys in assessing site factors that affect growth of Eucalyptus grandis over broad areas. The objective of this study was to assess the utility of hyperspectral remote sensing to discriminate between site qualities in E. grandis plantation in KwaZulu-Natal, South Africa. The relationships between physiology-based hyperspectral indicators and site quality, as defined by total available water (TAW), were assessed for E. grandis plantations through one-way analysis of variance (ANOVA). Canopy reflectance spectra for 68 trees (25 good, 25 medium and 18 poor sites) were collected on clear-sky days using an Analytical Spectral Device (ASD) spectroradiometer (350-2500 nm) from a raised platform. Foliar macronutrient concentrations for N, P, K, S, Ca, Mg and Na and their corresponding spectral features were also evaluated. The spectral signals for leaf water - normalized difference water index (NDWI), water band index (WBI) and moisture stress index (MSI) - exhibited significant differences (p 0.05) between sites. The magnitudes of these indices showed distinct gradients from the poor to the good sites. Similar results were observed for chlorophyll indices. These results show that differences in site quality based on TAW could be detected via imaging spectroscopy of canopy water or chlorophyll content. Among the macronutrients, only K and Ca exhibited significant differences between sites. However, a Tukey post-hoc test showed differences between the good and medium or medium and poor sites, a trend not consistent with the TAW gradient. The study also revealed the capability of continuum-removed spectral features to provide information on the physiological state of vegetation. The normalized band depth index (NBDI), derived from continuum-removed spectra in the region of the red-edge, showed the highest potential to differentiate between sites in this study. The study thus demonstrated the capability of hyperspectral remote sensing of vegetation canopies in identifying the site factors that affect growth of E. grandis in KwaZulu Natal, South Africa.
    Metabolic Networks: How to Identify Key Components in the Regulation of Metabolism and Growth
    Stitt, M. ; Sulpice, R. ; Keurentjes, J.J.B. - \ 2010
    Plant Physiology 152 (2010). - ISSN 0032-0889 - p. 428 - 444.
    quantitative trait loci - adp-glucose pyrophosphorylase - recombinant inbred lines - organic-acid metabolism - growing potato-tubers - arabidopsis-thaliana - steady-state - mass-spectrometry - genetic-variation - natural variation
    Plants display enormous diversity in their metabolism. Although the biosynthesis and function of the myriads of plant metabolites has been studied for decades, we have little understanding of the interactions between metabolites, metabolite signaling, interactions with development and the role of metabolism in genotype-to-phenotype relationships. Technologies for the analysis of metabolites have made tremendous progress in recent years, both in terms of the number of metabolites that are identified and of throughput. Recent developments allow the construction of metabolic networks, and study of the role of these networks in plant growth and development. In this review, we discuss what types of information can be obtained from measurements of metabolites and what requirements they have with respect comprehensiveness of coverage and precision of identification and quantification, and outline procedures that can be implemented to validate the measurements. We then discuss what sorts of perturbations can be used to disturb metabolic networks, including environmental and physiological treatments, chemicals, reverse genetics and the use of natural genetic diversity.
    A model for chlorophyll fluorescence and photosynthesis at leaf scale
    Tol, C. van der; Verhoef, W. ; Rosema, A. - \ 2009
    Agricultural and Forest Meteorology 149 (2009)1. - ISSN 0168-1923 - p. 96 - 105.
    stomatal conductance model - electron flow - water-stress - c-3 plants - co2 assimilation - steady-state - leaves - energy - simulation - zeaxanthin
    This paper presents a leaf biochemical model for steady-state chlorophyll fluorescence and photosynthesis of C3 and C4 vegetation. The model is a tool to study the relationship between passively measured steady-state chlorophyll fluorescence and actual photosynthesis, and its evolution during the day. Existing models for chlorophyll fluorescence and photosynthesis are integrated into a relatively simple deterministic model to quantify chlorophyll fluorescence, electron transport, carboxylation and deactivation of antennae in case of light and moisture stress. The model explains the behaviour of the relationship between fluorescence and photosynthesis that has been reported in the literature. Simulations, a sensitivity analysis, and measurements show that variations in total chlorophyll fluorescence correlate well with variations in actual photosynthesis in the late morning and afternoon. Then, photosynthesis is light saturated and limited by stomatal regulation. To calculate the actual photosynthesis rate, an estimate of the maximum carboxylation capacity is needed beside chlorophyll fluorescence.
    Inherited complex I deficiency is associated with faster protein diffusion in the matrix of moving mitochondria
    Koopman, W.J.H. ; Distelmaier, F. ; Hink, M.A. ; Verkaart, S. ; Wijers, M. ; Fransen, J. ; Smeitink, J.A.M. ; Willems, P.H.G.M. - \ 2008
    American Journal of Physiology: Cell Physiology 294 (2008)5. - ISSN 0363-6143 - p. C1124 - C1132.
    fluorescence correlation spectroscopy - ubiquinone oxidoreductase deficiency - leigh-syndrome - human nadh - oxidative-phosphorylation - correlation microscopy - skin fibroblasts - steady-state - mutations - motility
    Mitochondria continuously change shape, position, and matrix configuration for optimal metabolite exchange. It is well established that changes in mitochondrial metabolism influence mitochondrial shape and matrix configuration. We demonstrated previously that inhibition of mitochondrial complex I (CI or NADH: ubiquinone oxidoreductase) by rotenone accelerated matrix protein diffusion and decreased the fraction and velocity of moving mitochondria. In the present study, we investigated the relationship between inherited CI deficiency, mitochondrial shape, mobility, and matrix protein diffusion. To this end, we analyzed fibroblasts of two children that represented opposite extremes in a cohort of 16 patients, with respect to their residual CI activity and mitochondrial shape. Fluorescence correlation spectroscopy (FCS) revealed no relationship between residual CI activity, mitochondrial shape, the fraction of moving mitochondria, their velocity, and the rate of matrix-targeted enhanced yellow fluorescent protein (mitoEYFP) diffusion. However, mitochondrial velocity and matrix protein diffusion in moving mitochondria were two to three times higher in patient cells than in control cells. Nocodazole inhibited mitochondrial movement without altering matrix EYFP diffusion, suggesting that both activities are mutually independent. Unexpectedly, electron microscopy analysis revealed no differences in mitochondrial ultrastructure between control and patient cells. It is discussed that the matrix of a moving mitochondrion in the CI-deficient state becomes less dense, allowing faster metabolite diffusion, and that fibroblasts of CI-deficient patients become more glycolytic, allowing a higher mitochondrial velocity.
    Least-inference methods for constructing networks of trophic flows
    Ulanowicz, R.E. ; Scharler, U.M. - \ 2008
    Ecological Modelling 210 (2008)3. - ISSN 0304-3800 - p. 278 - 286.
    ecosystem attributes - environ analysis - bay ecosystem - steady-state - dynamics - estuaries
    The construction of material and energy budgets within ecosystems has long been accomplished via manual calculation. Recently, optimization techniques have been adapted to automate the procedure, but these methods require assumptions that may not square with biological reality. Two algorithms are developed to construct ecosystem budgets under minimal inference. Although the methods do not recapitulate the model used to generate the input data, analysis reveals that the results do not differ statistically from networks that were constructed manually.
    Ecological network analysis: network construction
    Fath, B.D. ; Scharler, U.M. ; Ulanowicz, R.E. ; Hannon, B. - \ 2007
    Ecological Modelling 208 (2007)1. - ISSN 0304-3800 - p. 49 - 55.
    food-web dynamics - environ analysis - inverse methods - flow networks - steady-state - ecosystem - models - community - ecopath - systems
    Ecological network analysis (ENA) is a systems-oriented methodology to analyze within system interactions used to identify holistic properties that are otherwise not evident from the direct observations. Like any analysis technique, the accuracy of the results is as good as the data available, but the additional challenge is that the data need to characterize an entire ecosystem's flows and storages. Thus, data requirements are substantial. As a result, there have, in fact, not been a significant number of network models constructed and development of the network analysis methodology has progressed largely within the purview of a few established models. In this paper, we outline the steps for one approach to construct network models. Lastly, we also provide a brief overview of the algorithmic methods used to construct food web typologies when empirical data are not available. It is our aim that such an effort aids other researchers to consider the construction of such models as well as encourages further refinement of this procedure.
    Metal speciation dynamics in colloidal ligand dispersions. Part 2: Electrochemical lability
    Pinheiro, J.P. ; Minor, M. ; Leeuwen, H.P. van - \ 2006
    Journal of Electroanalytical Chemistry 587 (2006)2. - ISSN 1572-6657 - p. 284 - 292.
    association dissociation kinetics - different diffusion-coefficients - stripping chronopotentiometry - limiting current - complex systems - steady-state - trace-metals - voltammetry - microelectrodes
    We investigate the dynamic nature of metal speciation in colloidal dispersions using a recently proposed theory [J.P. Pinheiro, M. Minor, H.P. Van Leeuwen, Langmuir, 21 (2005) 8635] for complexing ligands that are situated on the surface of the particles. The new approach effectively modifies the finite rates of association/dissociation of the colloidal metal complexes, thus invoking consideration of the two basic dynamic criteria: the association/dissociation kinetics of the volume complexation reaction (the "dynamic" criterion), and the interfacial flux of free metal to a macroscopic surface due to dissociation of complex species (the "lability" criterion). We demonstrate that the conventional approach for homogeneous systems that assume a smeared-out ligand distribution, overestimates both the dynamics and the lability of metal complexes when applied to colloidal ligands. It is also shown that the increase of lability with increasing particle radius, as expected for a homogeneous solution, is moderated for spherical microelectrodes and practically eliminated for planar electrodes.
    The effects of operational and environmental variations on anaerobic wastewater treatment systems: A review
    Leitao, R. ; Haandel, A.C. van; Zeeman, G. ; Lettinga, G. - \ 2006
    Bioresource Technology 97 (2006)9. - ISSN 0960-8524 - p. 1105 - 1118.
    fluidized-bed reactor - treatment-plant - uasb reactors - shock loads - sewer systems - 1st flush - microbial methanification - transient-behavior - mass-transfer - steady-state
    With the aim of improving knowledge about the stability and reliability of anaerobic wastewater treatment systems, several researchers have studied the effects of operational or environmental variations on the performance of such reactors. In general, anaerobic reactors are affected by changes in external factors, but the severity of the effect is dependent upon the type, magnitude, duration and frequency of the imposed changes. The typical responses include a decrease in performance, accumulation of volatile fatty acids, drop in pH and alkalinity, change in biogas production and composition, and sludge washout. This review summarises the causes, types and effects of operational and environmental variation on anaerobic wastewater treatment systems. However, there still remain some unclear technical and scientific aspects that are necessary for the improvement of the stability and reliability of anaerobic processes
    Photosynthetic induction responses of two rainforest tree species in relation to light environment
    Poorter, L. ; Oberbauer, S.F. - \ 1993
    Oecologia 96 (1993)2. - ISSN 0029-8549 - p. 193 - 199.
    neotropical rain-forest - ribulose-1,5-bisphosphate carboxylase - alocasia-macrorrhiza - emergent trees - steady-state - plants - sunflecks - c-3
    Photosynthetic induction of in situ saplings of two Costa Rican rainforest tree species wre compared in relation to their light environment, using infrared gas analysis and hemispherical photography. The species studied were Dipteryx panamensis, a climax species found in bright microsites, and Cecropia obtusifolia, a pioneer species. In the morning, when leaves were most responsive, induction time necessary to reach 90% of the lightsaturated rate of photosynthesis was on average 16 min for Dipteryx and 10 min for Cecropia. However, induction times for both species increased in the afternoon resulting in shorter daily average induction times for Dipteryx than for Cecropia. Dipteryx also maintained higher levels of induction for a longer period under low light conditions than did Cecropia. The two species differed in the way they adjusted to light availability. Dipteryx saplings growing in shady sites had faster rates of induction than saplings growing in bright sites, with no difference in light-saturated photosynthetic rate. In contrast, Cecropia saplings growing in bright sites had higher light-saturated photosynthetic rates than saplings growing in shady sites, with no difference in rates of induction. Dipteryx appears to exploit temporal variation in light availability by refining the quickness of the induction response to the light environment, while Cecropia adjusts its scale of exploitation by realizing a higher lightsaturated photosynthetic rate in sites of higher light
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