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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Reductive dechlorination of 1,2-dichloroethane in the presence of chloroethenes and 1,2-dichloropropane as co-contaminants
Peng, Peng ; Schneidewind, Uwe ; Haest, Pieter Jan ; Bosma, Tom N.P. ; Danko, Anthony S. ; Smidt, Hauke ; Atashgahi, Siavash - \ 2019
Applied Microbiology and Biotechnology 103 (2019)16. - ISSN 0175-7598 - p. 6837 - 6849.
1,2-Dichloroethane - Co-contaminants - Dechlorination kinetics - Dehalococcoides - Dehalogenimonas

1,2-Dichloroethane (1,2-DCA) is one of the most abundant manmade chlorinated organic contaminants in the world. Reductive dechlorination of 1,2-DCA by organohalide-respiring bacteria (OHRB) can be impacted by other chlorinated contaminants such as chloroethenes and chloropropanes that can co-exist with 1,2-DCA at contaminated sites. The aim of this study was to evaluate the effect of chloroethenes and 1,2-dichloropropane (1,2-DCP) on 1,2-DCA dechlorination using sediment cultures enriched with 1,2-DCA as the sole chlorinated compound (EA culture) or with 1,2-DCA and tetrachloroethene (PCE) (EB culture), and to model dechlorination kinetics. Both cultures contained Dehalococcoides as most predominated OHRB, and Dehalogenimonas and Geobacter as other known OHRB. In sediment-free enrichments obtained from the EA and EB cultures, dechlorination of 1,2-DCA was inhibited in the presence of the same concentrations of either PCE, vinyl chloride (VC), or 1,2-DCP; however, concurrent dechlorination of dual chlorinated compounds was achieved. In contrast, 1,2-DCA dechlorination completely ceased in the presence of cis-dichloroethene (cDCE) and only occurred after cDCE was fully dechlorinated. In turn, 1,2-DCA did not affect dechlorination of PCE, cDCE, VC, and 1,2-DCP. In sediment-free enrichments obtained from the EA culture, Dehalogenimonas 16S rRNA gene copy numbers decreased 1–3 orders of magnitude likely due to an inhibitory effect of chloroethenes. Dechlorination with and without competitive inhibition fit Michaelis-Menten kinetics and confirmed the inhibitory effect of chloroethenes and 1,2-DCP on 1,2-DCA dechlorination. This study reinforces that the type of chlorinated substrate drives the selection of specific OHRB, and indicates that removal of chloroethenes and in particular cDCE might be necessary before effective removal of 1,2-DCA at sites contaminated with mixed chlorinated solvents.

A specific synbiotic-containing amino acid-based formula restores gut microbiota in non-IgE mediated cow's milk allergic infants: A randomized controlled trial
Wopereis, Harm ; Ampting, Marleen T.J. Van; Cetinyurek-Yavuz, Aysun ; Slump, Rob ; Candy, David C.A. ; Butt, Assad M. ; Peroni, Diego G. ; Vandenplas, Yvan ; Fox, Adam T. ; Shah, Neil ; Roeselers, Guus ; Harthoorn, Lucien F. ; Michaelis, Louise J. ; Knol, Jan ; West, Christina E. - \ 2019
Clinical and Translational Allergy 9 (2019)1. - ISSN 2045-7022
Cow's milk allergy - Gut microbiota - Pediatrics - Prebiotics - Probiotics

Background: Altered gut microbiota is implicated in cow's milk allergy (CMA) and differs markedly from healthy, breastfed infants. Infants who suffer from severe CMA often rely on cow's milk protein avoidance and, when breastfeeding is not possible, on specialised infant formulas such as amino-acid based formulas (AAF). Herein, we report the effects of an AAF including specific synbiotics on oral and gastrointestinal microbiota of infants with non-IgE mediated CMA with reference to healthy, breastfed infants. Methods: In this prospective, randomized, double-blind controlled study, infants with suspected non-IgE mediated CMA received test or control formula. Test formula was AAF with synbiotics (prebiotic fructo-oligosaccharides and probiotic Bifidobacterium breve M-16V). Control formula was AAF without synbiotics. Healthy, breastfed infants were used as a separate reference group (HBR). Bacterial compositions of faecal and salivary samples were analysed by 16S rRNA-gene sequencing. Faecal analysis was complemented with the analysis of pH, short-chain fatty acids (SCFAs) and lactic acids. Results: The trial included 35 test subjects, 36 controls, and 51 HBR. The 16S rRNA-gene sequencing revealed moderate effects of test formula on oral microbiota. In contrast, the gut microbiota was substantially affected across time comparing test with control. In both groups bacterial diversity increased over time but was characterised by a more gradual increment in test compared to control. Compositionally this reflected an enhancement of Bifidobacterium spp. and Veillonella sp. in the test group. In contrast, the control-fed infants showed increased abundance of adult-like species, mainly within the Lachnospiraceae family, as well as within the Ruminococcus and Alistipes genus. The effects on Bifidobacterium spp. and Lachnospiraceae spp. were previously confirmed through enumeration by fluorescent in situ hybridization and were shown for test to approximate the proportions observed in the HBR. Additionally, microbial activity was affected as evidenced by an increase of l-lactate, a decrease of valerate, and reduced concentrations of branched-chain SCFAs in test versus control. Conclusions: The AAF including specific synbiotics effectively modulates the gut microbiota and its metabolic activity in non-IgE mediated CMA infants bringing it close to a healthy breastfed profile. Trial registration Registered on 1 May 2013 with Netherlands Trial Register Number NTR3979.

Modelling Potato Protein Content for Large-Scale Bulk Storage Facilities
Grubben, Nik L.M. ; Heeringen, Luc van; Keesman, Karel J. - \ 2019
Potato Research 62 (2019)3. - ISSN 0014-3065 - p. 333 - 344.
Post-harvest protein development - Potato storage - Protein degradation modelling - Protein synthesis modelling

The potato (Solanum tuberosum) is one of the main sources of natural starch. In recent decades, the valorisation of potato protein that results as a by-product in the starch industry has been gaining interest as well. As potato supply is seasonal and the protein content of potatoes during long-term storage is temperature-dependent, optimal storage of potatoes is of great importance. This paper explores a model describing potato protein content during a full storage season for the Miss Malina and Agria cultivars. The model combines Michaelis-Menten protein kinetics with the Arrhenius equation. Laboratory analyses were performed to monitor the protein components in both potato cultivars and to use for estimation of the kinetic parameters. The results indicate that the two cultivars have different synthesis and degradation kinetics.

A specific synbiotic-containing amino acid-based formula in dietary management of cow's milk allergy : A randomized controlled trial
Fox, Adam T. ; Wopereis, Harm ; Ampting, Marleen T.J. van; Oude Nijhuis, Manon M. ; Butt, Assad M. ; Peroni, Diego G. ; Vandenplas, Yvan ; Candy, David C.A. ; Shah, Neil ; West, Christina E. ; Garssen, Johan ; Harthoorn, Lucien F. ; Knol, Jan ; Michaelis, Louise J. - \ 2019
Clinical and Translational Allergy 9 (2019)1. - ISSN 2045-7022
Bifidobacterium breve M-16V - Cow's milk allergy - Gut microbiota - Prebiotic - Probiotic - Symptoms

Background: Here we report follow-up data from a double-blind, randomized, controlled multicenter trial, which investigated fecal microbiota changes with a new amino acid-based formula (AAF) including synbiotics in infants with non-immunoglobulin E (IgE)-mediated cow's milk allergy (CMA). Methods: Subjects were randomized to receive test product (AAF including fructo-oligosaccharides and Bifidobacterium breve M-16V) or control product (AAF) for 8 weeks, after which infants could continue study product until 26 weeks. Fecal percentages of bifidobacteria and Eubacterium rectale/Clostridium coccoides group (ER/CC) were assessed at 0, 8, 12, and 26 weeks. Additional endpoints included stool markers of gut immune status, clinical symptoms, and safety assessments including adverse events and medication use. Results: The trial included 35 test subjects, 36 controls, and 51 in the healthy reference group. Study product was continued by 86% and 92% of test and control subjects between week 8-12, and by 71% and 80%, respectively until week 26. At week 26 median percentages of bifidobacteria were significantly higher in test than control [47.0% vs. 11.8% (p < 0.001)], whereas percentages of ER/CC were significantly lower [(13.7% vs. 23.6% (p = 0.003)]. Safety parameters were similar between groups. Interestingly use of dermatological medication and reported ear infections were lower in test versus control, p = 0.019 and 0.011, respectively. Baseline clinical symptoms and stool markers were mild (but persistent) and low, respectively. Symptoms reduced towards lowest score in both groups. Conclusion: Beneficial effects of this AAF including specific synbiotics on microbiota composition were observed over 26 weeks, and shown suitable for dietary management of infants with non-IgE-mediated CMA.

Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study
Hellenkamp, Björn ; Schmid, Sonja ; Doroshenko, Olga ; Opanasyuk, Oleg ; Kühnemuth, Ralf ; Rezaei Adariani, Soheila ; Ambrose, Benjamin ; Aznauryan, Mikayel ; Barth, Anders ; Birkedal, Victoria ; Bowen, Mark E. ; Chen, Hongtao ; Cordes, Thorben ; Eilert, Tobias ; Fijen, Carel ; Gebhardt, Christian ; Götz, Markus ; Gouridis, Giorgos ; Gratton, Enrico ; Ha, Taekjip ; Hao, Pengyu ; Hanke, Christian A. ; Hartmann, Andreas ; Hendrix, Jelle ; Hildebrandt, Lasse L. ; Hirschfeld, Verena ; Hohlbein, Johannes ; Hua, Boyang ; Hübner, Christian G. ; Kallis, Eleni ; Kapanidis, Achillefs N. ; Kim, Jae Yeol ; Krainer, Georg ; Lamb, Don C. ; Lee, Nam Ki ; Lemke, Edward A. ; Levesque, Brié ; Levitus, Marcia ; McCann, James J. ; Naredi-Rainer, Nikolaus ; Nettels, Daniel ; Ngo, Thuy ; Qiu, Ruoyi ; Robb, Nicole C. ; Röcker, Carlheinz ; Sanabria, Hugo ; Schlierf, Michael ; Schröder, Tim ; Schuler, Benjamin ; Seidel, Henning ; Streit, Lisa ; Thurn, Johann ; Tinnefeld, Philip ; Tyagi, Swati ; Vandenberk, Niels ; Vera, Andrés Manuel ; Weninger, Keith R. ; Wünsch, Bettina ; Yanez-Orozco, Inna S. ; Michaelis, Jens ; Seidel, Claus A.M. ; Craggs, Timothy D. ; Hugel, Thorsten - \ 2018
Nature Methods : techniques for life scientists and chemists 15 (2018)9. - ISSN 1548-7091 - p. 669 - 676.

Single-molecule Förster resonance energy transfer (smFRET) is increasingly being used to determine distances, structures, and dynamics of biomolecules in vitro and in vivo. However, generalized protocols and FRET standards to ensure the reproducibility and accuracy of measurements of FRET efficiencies are currently lacking. Here we report the results of a comparative blind study in which 20 labs determined the FRET efficiencies (E) of several dye-labeled DNA duplexes. Using a unified, straightforward method, we obtained FRET efficiencies with s.d. between ±0.02 and ±0.05. We suggest experimental and computational procedures for converting FRET efficiencies into accurate distances, and discuss potential uncertainties in the experiment and the modeling. Our quantitative assessment of the reproducibility of intensity-based smFRET measurements and a unified correction procedure represents an important step toward the validation of distance networks, with the ultimate aim of achieving reliable structural models of biomolecular systems by smFRET-based hybrid methods.

Stability estimation of autoregulated genes under Michaelis-Menten-type kinetics
Arani, Babak M.S. ; Mahmoudi, Mahdi ; Lahti, Leo ; González, Javier ; Wit, Ernst C. - \ 2018
Physical Review. E, Statistical nonlinear, and soft matter physics 97 (2018)6. - ISSN 2470-0045

Feedback loops are typical motifs appearing in gene regulatory networks. In some well-studied model organisms, including Escherichia coli, autoregulated genes, i.e., genes that activate or repress themselves through their protein products, are the only feedback interactions. For these types of interactions, the Michaelis-Menten (MM) formulation is a suitable and widely used approach, which always leads to stable steady-state solutions representative of homeostatic regulation. However, in many other biological phenomena, such as cell differentiation, cancer progression, and catastrophes in ecosystems, one might expect to observe bistable switchlike dynamics in the case of strong positive autoregulation. To capture this complex behavior we use the generalized family of MM kinetic models. We give a full analysis regarding the stability of autoregulated genes. We show that the autoregulation mechanism has the capability to exhibit diverse cellular dynamics including hysteresis, a typical characteristic of bistable systems, as well as irreversible transitions between bistable states. We also introduce a statistical framework to estimate the kinetics parameters and probability of different stability regimes given observational data. Empirical data for the autoregulated gene SCO3217 in the SOS system in Streptomyces coelicolor are analyzed. The coupling of a statistical framework and the mathematical model can give further insight into understanding the evolutionary mechanisms toward different cell fates in various systems.

A synbiotic-containing amino-acid-based formula improves gut microbiota in non-IgE-mediated allergic infants
Candy, David C.A. ; Ampting, Marleen T.J. Van; Oude Nijhuis, Manon M. ; Wopereis, Harm ; Butt, Assad M. ; Peroni, Diego G. ; Vandenplas, Yvan ; Fox, Adam T. ; Shah, Neil ; West, Christina E. ; Garssen, Johan ; Harthoorn, Lucien F. ; Knol, Jan ; Michaelis, Louise J. - \ 2018
Pediatric Research 83 (2018)3. - ISSN 0031-3998 - p. 677 - 686.
BackgroundPrebiotics and probiotics (synbiotics) can modify gut microbiota and have potential in allergy management when combined with amino-acid-based formula (AAF) for infants with cow's milk allergy (CMA).MethodsThis multicenter, double-blind, randomized controlled trial investigated the effects of an AAF-including synbiotic blend on percentages of bifidobacteria and Eubacterium rectale/Clostridium coccoides group (ER/CC) in feces from infants with suspected non-IgE-mediated CMA. Feces from age-matched healthy breastfed infants were used as reference (healthy breastfed reference (HBR)) for primary outcomes. The CMA subjects were randomized and received test or control formula for 8 weeks. Test formula was a hypoallergenic, nutritionally complete AAF including a prebiotic blend of fructo-oligosaccharides and the probiotic strain Bifidobacterium breve M-16V. Control formula was AAF without synbiotics.ResultsA total of 35 (test) and 36 (control) subjects were randomized; HBR included 51 infants. At week 8, the median percentage of bifidobacteria was higher in the test group than in the control group (35.4% vs. 9.7%, respectively; P<0.001), whereas ER/CC was lower (9.5% vs. 24.2%, respectively; P<0.001). HBR levels of bifidobacteria and ER/CC were 55% and 6.5%, respectively.ConclusionAAF including specific synbiotics, which results in levels of bifidobacteria and ER/CC approximating levels in the HBR group, improves the fecal microbiota of infants with suspected non-IgE-mediated CMA.
Browse species from Ethiopia: role in methane reduction and nematode control in goats
Mengistu, Genet F. - \ 2017
Wageningen University. Promotor(en): Wouter Hendriks, co-promotor(en): Wilbert Pellikaan. - Wageningen : Wageningen University - ISBN 9789462579767 - 130
goats - browsing - nematode control - methane - anthelmintic properties - browse plants - ethiopia - geiten - afgrazen - nematodenbestrijding - methaan - wormdrijvende eigenschappen - graasplanten - ethiopië

The aim of the research reported in this thesis was to evaluate browse species collected from Ethiopia for preference by goats, and for their in vitro anthelmintic and methane (CH4) reduction properties. During the conduct of the studies observations were made warranting a further aim, to compare in vitro fermentation patterns of browse species using inocula from goats and cows kept on identical dietary regime.

The preference of browse species using dry matter intake (DMI) as a proxy and in combination with polyethylene glycol (PEG), relationships between browse species intake and chemical composition were determined in Chapter 2. Air-dried leaves of Acacia etbaica, Cadaba farinosa, Capparis tomentosa, Dichrostachys cinerea, Dodonaea angustifolia, Euclea racemosa, Maerua angolensis, Maytenus senegalensis, Rhus natalensis and Senna singueana were used. Two cafeteria trials, each lasting 10 days were conducted using goats receiving a daily ration of grass hay and wheat bran, without (trial 1) or with (trial 2) the inclusion of PEG. Preference measured as the first 10 min browse DMI differed significantly among browse species and with PEG (P<0.0001). Browse with higher tannin content, D. cinerea, R. natalensis and A. etbaica were the most preferred species regardless of PEG presence. Preference appeared to be based on digestible fibre fraction, hemicellulose rather than tannin levels in the browse species.

Extracts of the 10 browse species were evaluated for their anthelmintic activity against Haemonchus contortus (Chapter 3). The larval exsheathment inhibition assay (LEIA) was applied using H. contortus third stage larvae (L3) in a dose dependent manner with extract concentrations of 0, 150, 300, 600, 1200 µg/ml phosphate buffered saline (PBS). The role of polyphenols in the inhibition against L3 was evaluated using polyvinylpolypyrrolidone (PVPP). All browse extracts significantly (P<0.0001) inhibited larval exsheathment in a dose dependent manner with the dose required to inhibit 50% of the L3 (EC50) being highest in C. farinosa and lowest in E. racemosa and M. senegalensis. Polyvinylpolypyrrolidone treated A. etbaica, C. tomentosa, M. angolensis, R. natalensis and D. cinerea were different (P<0.001) from the control (only PBS), indicating that larval inhibition was largely due to non-phenolic compounds. Absence of significant differences between PVPP treated E. racemosa, M. senegalensis, D. angustifolia and S. singueana, and control suggest that inhibition was mostly attributable to tannins and other polyphenols. Browse species anthelmintic property against H. contortus L3 was due to the presence of phenolic and non-phenolic compounds.

In vitro gas production (GP), CH4, volatile fatty acids (VFA) and in vitro organic matter digestibility (IVOMD) of the 10 browse species were determined using PEG 6000 in Chapter 4. Proanthocyanidins (PA) were quantified using a modified HCl-butanol method and PA composition was determined by UPLC-DAD, with detection of other polyphenols by UPLC-ESI-MS/MS. Substrates were inoculated in buffered goat rumen fluid with or without PEG 6000 for 72 h to measure GP with head space gas sample measurements taken at 0, 3, 6, 9, 12, 24, 30, 48, 54, and 72 h for CH4. At the end of incubation, VFA, ammonia (NH3) and IVOMD were determined. Increased (P<0.0001) GP, CH4 and total VFA were observed after PEG addition indicating PA were mainly involved in reducing methanogenesis and to a lower extent also overall fermentability. Prodelphinidins were the major explaining factors for this reduction but other polyphenols like quercetin, myricetin and kaempferol were also involved in CH4 reduction. The effect of PEG addition on IVOMD was variable among browse and could be due to artefacts from the tannin-PEG complexes in the incubation residue. Proanthocyanidins were mainly responsible for the reduced in vitro fermentative activities with possible minor effects of other phenolic and non-phenolic components.

Due to unusual fermentation patterns observed in Chapter 4, a comparison was made between goat and cow inocula on in vitro gas and CH4 production and kinetics parameters as well as VFA production in Chapter 5. Leaves of A. etbaica, C. tomentosa, D. cinerea, R. natalensis, freeze-dried maize and grass silage, and a concentrate were inoculated for 72 h to measure GP, in buffered inocula from goats and cows kept on an identical feeding regime. During incubation, headspace gas samples were obtained at 0, 3, 6, 9, 24, 30, 48, 54, and 72 h, and analysed for CH4 with VFA determined at the end of incubation. A triphasic and monophasic modified Michaelis-Menten equation was fitted to the cumulative GP and CH4 curves, respectively. Total GP and CH4 (P<0.0001), half-time for asymptotic (P<0.012) and rate (P<0.0001) of GP were higher for goat inoculum. The total VFA were higher (P<0.0001) in goats and the proportion of individual VFA differed significantly (P<0.002) between animal species. Differences between goat and cow inocula were attributable to variation in the activity and composition of the microbial population, and differences were more pronounced for fermentation of browse species than grass and maize silages.

A synthesis of the results from the four research chapters is provided in the general discussion (Chapter 6). The present work highlights the browse species characteristics which can be strategically exploited in goat production systems to improve health and feed utilization efficiency.

Parameter estimation in tree graph metabolic networks
Astola, Laura ; Stigter, Hans ; Gomez Roldan, Maria Victoria ; Eeuwijk, Fred van; Hall, Robert D. ; Groenenboom, Marian ; Molenaar, Jaap J. - \ 2016
PeerJ 2016 (2016)9. - ISSN 2167-8359
Glycosylation - Kinetic models - Metabolic networks - Network inference - Solanum lycopersicum - Systems biology

We study the glycosylation processes that convert initially toxic substrates to nu- tritionally valuable metabolites in the flavonoid biosynthesis pathway of tomato (Solanum lycopersicum) seedlings. To estimate the reaction rates we use ordinary differential equations (ODEs) to model the enzyme kinetics. A popular choice is to use a system of linear ODEs with constant kinetic rates or to use Michaelis-Menten kinetics. In reality, the catalytic rates, which are affected among other factors by kinetic constants and enzyme concentrations, are changing in time and with the approaches just mentioned, this phenomenon cannot be described. Another problem is that, in general these kinetic coefficients are not always identifiable. A third problem is that, it is not precisely known which enzymes are catalyzing the observed glycosylation processes. With several hundred potential gene candidates, experimental validation using purified target proteins is expensive and time consuming. We aim at reducing this task via mathematical modeling to allow for the pre-selection of most potential gene candidates. In this article we discuss a fast and relatively simple approach to estimate time varying kinetic rates, with three favorable properties: firstly, it allows for identifiable estimation of time dependent parameters in networks with a tree- like structure. Secondly, it is relatively fast compared to usually applied methods that estimate the model derivatives together with the network parameters. Thirdly, by combining the metabolite concentration data with a corresponding microarray data, it can help in detecting the genes related to the enzymatic processes. By comparing the estimated time dynamics of the catalytic rates with time series gene expression data we may assess potential candidate genes behind enzymatic reactions. As an example, we show how to apply this method to select prominent glycosyltransferase genes in tomato seedlings.

Structural features of condensed tannins affect in vitro ruminal methane production and fermentation characteristics
Huyen, N.T. ; Fryganas, C. ; Uittenbogaard, G. ; Mueller-Harvey, I. ; Verstegen, M.W.A. ; Hendriks, W.H. ; Pellikaan, W.F. - \ 2016
The Journal of Agricultural Science 154 (2016)8. - ISSN 0021-8596 - p. 1474 - 1487.

An in vitro study was conducted to investigate the effects of condensed tannin (CT) structural properties, i.e. average polymer size (or mean degree of polymerization), percentage of cis flavan-3-ols and percentage of prodelphinidins in CT extracts on methane (CH4) production and fermentation characteristics. Condensed tannins were extracted from eight plants in order to obtain different CT types: blackcurrant leaves, goat willow leaves, goat willow twigs, pine bark, redcurrant leaves, sainfoin plants, weeping willow catkins and white clover flowers. They were analysed for CT content and CT composition by thiolytic degradation, followed by high performance liquid chromatography (HPLC) analysis. Grass silage was used as a control substrate. Condensed tannins were added to the substrate at a concentration of 40 g/kg, with or without polyethylene glycol (+ or −PEG 6000 treatment) to inactivate tannins, then incubated for 72 h in mixed buffered rumen fluid from three different lactating dairy cows per run. Total cumulative gas production (GP) was measured by an automated GP system. During the incubation, 12 gas samples (10 µl) were collected from each bottle headspace at 0, 2, 4, 6, 8, 12, 24, 30, 36, 48, 56 and 72 h of incubation and analysed for CH4. A modified Michaelis-Menten model was fitted to the CH4 concentration patterns and model estimates were used to calculate total cumulative CH4 production (GPCH4). Total cumulative GP and GPCH4 curves were fitted using biphasic and monophasic modified Michaelis-Menten models, respectively. Addition of PEG increased GP, GPCH4, and CH4 concentration compared with the −PEG treatment. All CT types reduced GPCH4 and CH4 concentration. All CT increased the half time of GP and GPCH4. Moreover, all CT decreased the maximum rate of fermentation for GPCH4 and rate of substrate degradation. The correlation between CT structure and GPCH4 and fermentation characteristics showed that the proportion of prodelphinidins within CT had the largest effect on fermentation characteristics, followed by average polymer size and percentage of cis flavan-3-ols.

Modeling of slurry staged bubble column for biomimetic CO2 capture
Russo, Maria Elena ; Bareschino, Piero ; Olivieri, Giuseppe ; Chirone, Riccardo ; Salatino, Piero ; Marzocchella, Antonio - \ 2016
International Journal of Greenhouse Gas Control 47 (2016). - ISSN 1750-5836 - p. 200 - 209.
Carbonic anhydrase - CO capture - Immobilized enzyme - Slurry - Staged bubble column

The biomimetic CCS strategy is based on the enhancement of CO2 absorption rate into aqueous solutions by the enzyme carbonic anhydrase (CA). Immobilized CA on fine dispersed solids promotes the heterogeneous biocatalysis close to the gas-liquid interface and the enhancement of CO2 absorption rate. In this work a theoretical model of a slurry absorption unit for the biomimetic CO2 capture in K2CO3 solutions was developed and solved using the commercial software package Comsol Multiphysics®. The staged bubble column (SBC) configuration was selected to capture CO2 in aqueous slurry containing immobilized CA under counter-current gas-liquid flow. The theoretical framework included: the 'tanks-in-series' model to describe the unit; the two films theory to describe the absorption rate at the gas-liquid interface; the pseudo-homogeneous approach and a reversible Michaelis and Menten kinetics to model CO2 conversion by the slurry biocatalyst. The simulations provided the CO2 capture rate and the CO2 concentration profiles in the liquid boundary layer. Simulation results showed that the CO2 capture rate poorly increased when dissolved CA was used within the solubility limit (≈100 mg/L). Remarkably, about three fold enhancement of the CO2 absorption rate with respect to pure alkaline solvent when absorption in the presence of CA immobilized on fine particles was simulated.

Chrysanthemyl diphosphate synthase operates in planta as a bifunctional enzyme with chrysanthemolsynthase activity
Yang, T. ; Gao, L. ; Hu, H. ; Stoopen, G.M. ; Wang, C. ; Jongsma, M.A. - \ 2014
Journal of Biological Chemistry 289 (2014). - ISSN 0021-9258 - p. 36325 - 36335.
dimethylallyl diphosphate - squalene synthase - monoterpene synthase - terpene synthases - biosynthesis - expression - arabidopsis - metabolism - cloning - leaves
Chrysanthemyl diphosphate synthase (CDS) is the first pathway-specific enzyme inthe biosynthesis of pyrethrins, the most widely used plant-derivedpesticide.CDScatalyzes c1’-2-3 cyclopropanation reactions of two molecules of dimethylallyl diphosphate (DMAPP) to yield chrysanthemyl diphosphate (CPP). Three proteinsare known to catalyzethis cyclopropanation reactionof terpene precursors.Two of them, phytoene and squalenesynthase, arebifunctional enzymes with both prenyltransferase and terpenesynthase activity. CDS, the other member,was reported to perform only the prenyltransferase step.Here, we show thatthe NDXXD catalytic motif of CDS,under lowersubstrate conditions prevalent inplants,also catalyzesthe next step converting CPP into chrysanthemolby hydrolyzing the diphosphatemoiety.The enzymatic hydrolysis reactionfollowed conventional Michaelis-Menten kinetics, withaKM value for CPP of 196 µM.For the chrysanthemol synthase activity, DMAPP competed with CPP as substrate. The DMAPP concentration required for half-maximal activity to produce chrysanthemolwas ~100 µM, and significant substrate inhibition was observed at elevated DMAPP concentrations. The N-terminal peptide of CDS was identified as a plastid targeting peptide. Transgenic tobacco plants overexpressing CDS emitted chrysanthemolat arate of 0.12 –0.16 µg•h-1•g-1FW. We propose that CDS should be renamed a chrysanthemol synthase(CHS)utilizingDMAPP as substrate.
Kinetics of dechlorination by Dehalococcoides mccartyi using different carbon sources
Schneidewind, U. ; Haest, P.J. ; Atashgahi, S. ; Maphosa, F. ; Hamonts, K. ; Maesen, M. ; Calderer, M. ; Seuntjens, P. ; Smidt, H. ; Springael, D. ; Dejonghe, W. - \ 2014
Journal of Contaminant Hydrology 157 (2014). - ISSN 0169-7722 - p. 25 - 36.
chlorinated aliphatic-hydrocarbons - reductive dechlorination - electron-donors - hydrogen - ethenes - tce - culture - tetrachloroethene - groundwater - growth
Stimulated anaerobic dechlorination is generally considered a valuable step for the remediation of aquifers polluted with chlorinated ethenes (CEs). Correct simulation and prediction of this process in situ, however, require good knowledge of the associated biological reactions. The aim of this study was to evaluate the dechlorination reaction in an aquifer contaminated with trichloroethene (TCE) and its daughter products, discharging into the Zenne River. Different carbon sources were used in batch cultures and these were related to the dechlorination reaction, together with the monitored biomarkers. Appropriate kinetic formulations were assessed. Reductive dechlorination of TCE took place only when external carbon sources were added to microcosms, and occurred concomitant with a pronounced increase in the Dehalococcoides mccartyi cell count as determined by 16S rRNA gene-targeted qPCR. This indicates that native dechlorinating bacteria are present in the aquifer of the Zenne site and that the oligotrophic nature of the aquifer prevents a complete degradation to ethene. The type of carbon source, the cell number of D. mccartyi or the reductive dehalogenase genes, however, did not unequivocally explain the observed differences in degradation rates or the extent of dechlorination. Neither first-order, Michaelis–Menten nor Monod kinetics could perfectly simulate the dechlorination reactions in TCE spiked microcosms. A sensitivity analysis indicated that the inclusion of donor limitation would not significantly enhance the simulations without a clear process understanding. Results point to the role of the supporting microbial community but it remains to be verified how the complexity of the microbial (inter)actions should be represented in a model framework
Chain length distribution and kinetic characteristics of an enzymatically produced polymer
Mulders, K.J.M. ; Beeftink, H.H. - \ 2013
e-Polymers 13 (2013)1. - ISSN 1618-7229 - p. 261 - 272.
monte-carlo-simulation - multiple attack mechanism - sequential reactions - actin-filaments - enzyme - model - transglycosylation - fragmentation - competition - reactors
Non-processive enzymatic polymerization leads to a distribution of polymer chain lengths. A polymerization model was developed to investigate the relation between the extent of this distribution on one hand, and the polymerization start conditions and reaction kinetics on the other hand. The model describes changes in concentration of chains of length n as the result of two elongation reactions: elongation by monomer addition to length n-1 and elongation by monomer addition to length n. Polymerization reactions were assumed to be zero order in monomer concentration and to obey Michaelis-Menten kinetics with respect to polymer concentrations. In addition, the amount of enzyme available for each individual reaction (n n+1) is assumed to be Non-processive enzymatic polymerization leads to a distribution of polymer chain lengths. A polymerization model was developed to investigate the relation between the extent of this distribution on one hand, and the polymerization start conditions and reaction kinetics on the other hand. The model describes changes in concentration of chains of length n as the result of two elongation reactions: elongation by monomer addition to length n-1 and elongation by monomer addition to length n. Polymerization reactions were assumed to be zero order in monomer concentration and to obey Michaelis-Menten kinetics with respect to polymer concentrations. In addition, the amount of enzyme available for each individual reaction (n n+1) is assumed to be proportional to the concentration of polymer substrate of length n. The development of the shape of the chain length distribution was found to be independent of the value of the overall reaction rate constant; only the rate at which these shapes developed was influenced by the 1st-order rate constant. The value of the Michaelis parameter did affect the form of the chain length distribution curve since it affects the reaction order. An increase in reaction order was found to promote widening of the chain length distribution. Differences in kinetic parameters between the subsequent polymerization reactions, if any, were also found to have a large effect on the development of the chain length distribution. An increase in rate constants with chain length entailed a wider distribution; a more narrow distribution would require a decrease in rate constants with chain length.proportional to the concentration of polymer substrate of length n. The development of the shape of the chain length distribution was found to be independent of the value of the overall reaction rate constant; only the rate at which these shapes developed was influenced by the 1st-order rate constant. The value of the Michaelis parameter did affect the form of the chain length distribution curve since it affects the reaction order. An increase in reaction order was found to promote widening of the chain length distribution. Differences in kinetic parameters between the subsequent polymerization reactions, if any, were also found to have a large effect on the development of the chain length distribution. An increase in rate constants with chain length entailed a wider distribution; a more narrow distribution would require a decrease in rate constants with chain length.
Interpreting experimental data on egg production - applications of dynamic differential equations
France, J. ; Lopez, S. ; Kebreab, E. ; Dijkstra, J. - \ 2013
Poultry Science 92 (2013)9. - ISSN 0032-5791 - p. 2498 - 2508.
drosophila-melanogaster - gastrointestinal-tract - quantitative genetics - mathematical-models - phosphorus - calcium - absorption - fertility - algorithm
This contribution focuses on applying mathematical models based on systems of ordinary first-order differential equations to synthesize and interpret data from egg production experiments. Models based on linear systems of differential equations are contrasted with those based on nonlinear systems. Regression equations arising from analytical solutions to linear compartmental schemes are considered as candidate functions for describing egg production curves, together with aspects of parameter estimation. Extant candidate functions are reviewed, a role for growth functions such as the Gompertz equation suggested, and a function based on a simple new model outlined. Structurally, the new model comprises a single pool with an inflow and an outflow. Compartmental simulation models based on nonlinear systems of differential equations, and thus requiring numerical solution, are next discussed, and aspects of parameter estimation considered. This type of model is illustrated in relation to development and evaluation of a dynamic model of calcium and phosphorus flows in layers. The model consists of 8 state variables representing calcium and phosphorus pools in the crop, stomachs, plasma, and bone. The flow equations are described by Michaelis-Menten or mass action forms. Experiments that measure Ca and P uptake in layers fed different calcium concentrations during shell-forming days are used to evaluate the model. In addition to providing a useful management tool, such a simulation model also provides a means to evaluate feeding strategies aimed at reducing excretion of potential pollutants in poultry manure to the environment.
A physiologically based kinetic model for bacterial sulfide oxidation
Klok, J.B.M. ; Graaff, C.M. de; Bosch, P.L.F. van den; Boelee, N.C. ; Keesman, K.J. ; Janssen, A.J.H. - \ 2013
Water Research 47 (2013)2. - ISSN 0043-1354 - p. 483 - 492.
afvalwaterbehandeling - biotechnologie - zwavelwaterstof - oxidatie - ontzwaveling - alkalibacillus haloalkaliphilus - microbiële fysiologie - afvalwaterbehandelingsinstallaties - waste water treatment - biotechnology - hydrogen sulfide - oxidation - desulfurization - alkalibacillus haloalkaliphilus - microbial physiology - waste water treatment plants - sulfur-oxidizing bacteria - biologically produced sulfur - dissolved sodium sulfide - parameter-estimation - hydrogen-sulfide - soda lakes - bioreactors - thiosulfate - mechanisms - pathways
In the biotechnological process for hydrogen sulfide removal from gas streams, a variety of oxidation products can be formed. Under natron-alkaline conditions, sulfide is oxidized by haloalkaliphilic sulfide oxidizing bacteria via flavocytochrome c oxidoreductase. From previous studies, it was concluded that the oxidation-reduction state of cytochrome c is a direct measure for the bacterial end-product formation. Given this physiological feature, incorporation of the oxidation state of cytochrome c in a mathematical model for the bacterial oxidation kinetics will yield a physiologically based model structure. This paper presents a physiologically based model, describing the dynamic formation of the various end-products in the biodesulfurization process. It consists of three elements: 1) Michaelis–Menten kinetics combined with 2) a cytochrome c driven mechanism describing 3) the rate determining enzymes of the respiratory system of haloalkaliphilic sulfide oxidizing bacteria. The proposed model is successfully validated against independent data obtained from biological respiration tests and bench scale gas-lift reactor experiments. The results demonstrate that the model is a powerful tool to describe product formation for haloalkaliphilic biomass under dynamic conditions. The model predicts a maximum S0 formation of about 98 mol%. A future challenge is the optimization of this bioprocess by improving the dissolved oxygen control strategy and reactor design.
Interpreting experimental data on egg production - Modeling considerations
France, J. ; Lopez, S. ; Dijkstra, J. - \ 2012
In: Poultry Science Association Annual Meeting abstracts, Athens, Georgia July 9-12, 2012. - - p. 81 - 82.
This contribution focuses on applying mathematical models based on systems of ordinary first-order differential equations to synthesize and interpret data from egg production experiments. Models based on linear systems of differential equations are contrasted with those based on nonlinear systems. Regression equations arising from analytical solutions to linear compartmental schemes are considered as candidate functions for describing egg production curves, together with aspects of parameter estimation. Extant candidate functions are reviewed, a role for growth functions such as the Gompertz equation suggested, and a function based on a simple new model outlined. Structurally, the new model comprises a single pool with an inflow and an outflow. Compartmental simulation models based on non-linear systems of differential equations, and thus requiring numerical solution, are next discussed and aspects of parameter estimation considered. This type of model is illustrated in relation to development and evaluation of a dynamic model of calcium and phosphorus flows in layers. The model consists of 8 state variables representing calcium and phosphorus pools in the crop, stomachs, plasma, and bone. The flow equations are described by Michaelis-Menten or mass action forms. Experiments that measures Ca and P uptake in layers fed different calcium concentrations during shell-forming days are used to evaluate the model. In addition to providing a useful management tool, such a simulation model also provides a means to evaluate feeding strategies aimed at reducing excretion of potential pollutants in poultry manure to the environment.
Crystal Structure of Agaricus bisporus Mushroom Tyrosinase: Identity of the Tetramer Subunits and Interaction with Tropolone
Ismaya, W.T. ; Rozeboom, H.J. ; Weijn, A. ; Mes, J.J. ; Fusetti, F. ; Wichers, H.J. ; Dijkstra, B.W. - \ 2011
Biochemistry 50 (2011)24. - ISSN 0006-2960 - p. 5477 - 5486.
polyphenol oxidase - diffraction data - multiple forms - protein - mechanism - sequence - inhibition - refinement - plant - activation
Tyrosinase catalyzes the conversion of phenolic compounds into their quinone derivatives, which are precursors for the formation of melanin, a ubiquitous pigment in living organisms. Because of its importance for browning reactions in the food industry, the tyrosinase from the mushroom Agaricus bisporus has been investigated in depth. In previous studies the tyrosinase enzyme complex was shown to be a H(2)L(2) tetramer, but no clues were obtained of the identities of the subunits, their mode of association, and the 3D structure of the complex. Here we unravel this tetramer at the molecular level. Its 2.3 Å resolution crystal structure is the first structure of the full fungal tyrosinase complex. The complex comprises two H subunits of ~392 residues and two L subunits of ~150 residues. The H subunit originates from the ppo3 gene and has a fold similar to other tyrosinases, but it is ~100 residues larger. The L subunit appeared to be the product of orf239342 and has a lectin-like fold. The H subunit contains a binuclear copper-binding site in the deoxy-state, in which three histidine residues coordinate each copper ion. The side chains of these histidines have their orientation fixed by hydrogen bonds or, in the case of His85, by a thioether bridge with the side chain of Cys83. The specific tyrosinase inhibitor tropolone forms a pre-Michaelis complex with the enzyme. It binds near the binuclear copper site without directly coordinating the copper ions. The function of the ORF239342 subunits is not known. Carbohydrate binding sites identified in other lectins are not conserved in ORF239342, and the subunits are over 25 Å away from the active site, making a role in activity unlikely. The structures explain how calcium ions stabilize the tetrameric state of the enzyme
Evaluating effects of tannins on extent and rate of in vitro gas and CH4, production using an automated pressure evaluation system (APES)
Pellikaan, W.F. ; Stringano, E. ; Leenaars, J. ; Bongers, L.J.G.M. ; Laar-van Schuppen, S. van; Plant, J. ; Mueller-Harvey, I. - \ 2011
Animal Feed Science and Technology 166-167 (2011). - ISSN 0377-8401 - p. 377 - 390.
performance liquid-chromatography - ionization mass-spectrometry - hydrolyzable tannins - methane production - medicinal-plants - rumen fluid - polymeric procyanidins - condensed tannins - ruminal methane - fermentation
An in vitro study was conducted to investigate effects of tannins on extent and rate of gas and CH4 production using an automated pressure evaluation system (APES). In this study three condensed tannins (CT; quebracho, grape seed, green tea tannins) and four hydrolysable tannins (HT; tara, valonea, myrabolan, chestnut tannins) were evaluated with lucerne as a control substrate. CT and HT were characterised by matrix assisted laser desorption ionisation–time of flight mass spectrometry (MALDI–TOF MS). Tannins were added to the substrate at an effective concentration of 100 g/kg, either with or without polyethylene glycol (PEG 6000), and incubated for 72 h in pooled buffered rumen liquid from four lactating dairy cows. After inoculation, fermentation bottles were immediately connected to the APES to measure total cumulative gas production (GP). During the incubation, 11 gas samples were collected from each bottle at 0, 1, 4, 7, 11, 15, 23, 30, 46, 52 and 72 h of incubation and analysed for CH4. A modified Michaelis–Menten model was fitted to the CH4 concentration patterns, and model estimates were used to calculate total cumulative CH4 production (GPCH4). GP and GPCH4 curves were fitted using a modified monophasic Michaelis–Menten model. Addition of quebracho reduced (P=0.002) GP, whilst the other tannins did not affect GP. Addition of PEG increased GP for quebracho (P=0.003), valonea (P=0.058) and grape seed tannins (P=0.071), suggesting that these tannins either inhibited, or tended to inhibit, fermentation. Addition of quebracho and grape seed tannins reduced (P=0.012) the maximum rate of gas production, indicating that microbial activity was affected. Quebracho, valonea, myrabolan and grape seed decreased (P=0.003) GPCH4 and the maximum rate (0.001=P=0.102) of CH4 production. Addition of chestnut, green tea and tara tannins did not affect total gas nor CH4 production. Vvalonea and myrabolan tannins have the most promise at reducing CH4 production as they had only a minor impact on gas production.
Modeling the efficiency of phosphorus utilization in growing pigs
Kebreab, E. ; Strathe, A.B. ; Yitbarek, A. ; Nyachoti, C.M. ; Dijkstra, J. ; Lopez, S. ; France, J. - \ 2011
Journal of Animal Science 89 (2011)9. - ISSN 0021-8812 - p. 2774 - 2781.
soybean meal diets - growth - phytase - nutrition - efficacy
Microbial phytase has been used to reduce P excretion from swine to mitigate environmental pollution. The objective of the study was to quantify the effect of feeding a low-P phytase-supplemented diet on growth and P utilization in growing pigs using mathematical models. A total of 20 weaned piglets (BW = 6.5 kg) housed in metabolism cages were randomly assigned to a standard diet (STD) or P-amended diet containing reduced P content and supplemented with phytase (AMN) with 10 pigs/diet. Body weight and feed consumption were recorded weekly so complete growth and cumulative P intake (cPI) curves could be modeled. A function with fixed point of inflexion (Gompertz) and a variable point of inflexion (generalized Michaelis-Menten) were considered in determining bioequivalence by analyzing BW vs. age relationships, whereas the monomolecular function was used to describe BW vs. cPI. All functions were incorporated into a nonlinear mixed effects model, and a first-order autoregressive correlation structure was implemented to take into account repeated measures. There was no difference between the 2 groups in final BW when the Gompertz equation was fitted (176 vs. 178 kg with SE of 7 kg for the STD and AMN, respectively) or the rate parameter (0.0140 vs. 0.0139 with SE of 0.0004 for the STD and AMN, respectively). The generalized Michaelis-Menten equation also showed a similar trend. When BW was expressed as a function of cPI the derivative with respect to cPI represented P efficiency, so it was possible to analyze the expected difference of the 2 diets in using P for BW gain and express it as a continuous function of cPI. The analysis showed through the entire growth period the difference in P efficiency was different from zero. On average, 56 g of supplemented inorganic P was consumed by a pig fed the AMN to reach market weight. In contrast, 309 g of supplemented inorganic P was consumed by the group fed the STD to reach similar BW. It would depend on other factors, but feeding pigs the AMN can result in economic benefit. Pigs fed the AMN excreted 19% less P compared with those fed the STD. In conclusion, nonlinear mixed model analysis (with repeated measures) was suitable for growth and efficiency analysis and showed that pigs fed the AMN consumed less than 20% of the inorganic P and performed as well as those fed the traditional inorganic P supplemented diet. The implications for mitigating P pollution, especially in areas where P loading is already problematic, are substantial.
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