Staff Publications

Staff Publications

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    We will mail you new results for this query: keywords==biochemistry
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Schimmel verbetert productie bioplastic
Weusthuis, Ruud ; Eggink, Gerrit - \ 2017
bioplastics - biochemistry - fungi - genetic engineering - biomass conversion - biobased chemistry - biobased economy

Onderzoekers van Wageningen Food & Biobased Research hebben samen met oliemaatschappij Total een genetisch gemodificeerde schimmel ontwikkeld waarmee bioplastics efficiënter kunnen worden geproduceerd

Biobased itaconzuur en methacrylzuur : Chemische bouwstenen van de toekomst
Es, D.S. van - \ 2016
Fluids Processing Benelux (2016)4. - ISSN 1874-7914 - p. 46 - 47.
biobased economy - chemie op basis van biologische grondstoffen - chemicaliën uit biologische grondstoffen - zuren - biomassa - glucose - biochemie - biobased chemistry - biobased chemicals - acids - biomass - biochemistry
Wageningen UR Food & Biobased Research is van plan een flinke stap te zetten in de productie van biobased itaconzuur en methacrylzuur. Deze zuren kunnen bouwstenen zijn voor hoogwaardige materialen, zoals biobased verf en drukinkt. De stoffen worden geproduceerd uit biomassa (glucose) en vormen alternatieven voor fossiele grondstoffen. Voor verdere ontwikkeling wordt samengewerkt met de Amerikaanse agrifoodproducent Archer Daniels Midland, leverancier voor de verfindustrie EOC Belgium en de Nederlandse verfproducent Van Wijhe Verf. Daan van Es, is senioronderzoeker bij Wageningen UR en treedt op als projectleider.
Energie en eiwitwaardeschatting gras-klaverkuilen
Schooten, H.A. van; Spek, J.W. - \ 2016
Wageningen : Wageningen Livestock Research (Wageningen Livestock Research rapport 994) - 33
grasklaver - eiwitten - energie - voedingswaarde - biochemie - diervoedering - grass-clover swards - proteins - energy - nutritive value - biochemistry - animal feeding
Plant growth promotion by Pseudomonas fluorescens : mechanisms, genes and regulation
Cheng, X. - \ 2016
Wageningen University. Promotor(en): Francine Govers; J.M. Raaijmakers, co-promotor(en): M. van der Voort. - Wageningen : Wageningen University - ISBN 9789462578753 - 192 p.
soil bacteria - pseudomonas fluorescens - plants - growth stimulators - soil suppressiveness - plant diseases - induced resistance - biochemistry - biosynthesis - plant-microbe interactions - transcriptomics - bodembacteriën - planten - groeistimulatoren - bodemweerbaarheid - plantenziekten - geïnduceerde resistentie - biochemie - biosynthese - plant-microbe interacties - transcriptomica

Pseudomonas fluorescens is a Gram-negative rod shaped bacterium that has a versatile metabolism and is widely spread in soil and water. P. fluorescens strain SBW25 (Pf.SBW25) is a well-known model strain to study bacterial evolution, plant colonization and biocontrol of plant diseases. It produces the biosurfactant viscosin, a lipopeptide that plays a key role in motility, biofilm formation and activity against zoospores of Phytophthora infestans and other oomycete pathogens. In addition to viscosin, Pf.SBW25 produces other metabolites with activity against plant pathogens. The production of these yet unknown metabolites appeared to be regulated by the GacS/GacA two-component regulatory system (the Gac-system). The second P. fluorescens strain SS101 (Pf.SS101) studied in this thesis is known for its plant growth-promoting activities but the underlying mechanisms and genes are largely unknown. Therefore, in this study, we aimed to identify novel metabolites and biosynthetic genes in Pf.SBW25 and Pf.SS101, and to investigate their role in plant growth promotion and biocontrol. To this end, a multidisciplinary approach involving bioinformatic analysis of the genome sequences of strains Pf.SBW25 and Pf.SS101, microarray-based expression profiling, screening of genomic libraries, bioactivity assays, mass spectrometric image analysis (MALDI-IMS) and GC/MSMS analysis was adopted. In conclusion, we showed that the GacS/GacA two-component system as a global regulator of the expression of genes play important roles in antagonism of Pseudomonas fluorescens toward plant pathogenic microbes as well as in plant growth promotion and ISR. Growth promotion by P. fluorescens is associated with alterations in auxin biosynthesis and transport, steroid biosynthesis, carbohydrate metabolism and sulfur assimilation. Moreover, advanced chemical profiling allowed us to compare the metabolite profiles of free-living P. fluorescens and P. fluorescens living in association with plant roots. A better understanding of yet unknown mechanisms exploited by the various Pseudomonas fluorescens strains will lead to new opportunities for the discovery and application of natural bioactive compounds for both industrial and agricultural purposes.

Chemie - Van suiker naar mobiel : Kennisclip Bogo-project e-learning
Baltissen, A.H.M.C. - \ 2016
Groen Kennisnet
biopolymeren - suiker - biobased economy - biochemie - chemische reacties - polymelkzuur - melkzuur - bioplastics - tuinbouw - lesmaterialen - biopolymers - sugar - biochemistry - chemical reactions - polylactic acid - lactic acid - horticulture - teaching materials
Deze kennisclip maakt onderdeel uit van de lesmodule Biobased Economy van het CIV T&U.
The first wolf found in the Netherlands in 150 years was the victim of a wildlife crime
Gravendeel, B. ; Groot, G.A. de; Kik, M. ; Beentjes, K. ; Bergman, H. ; Caniglia, R. ; Cremers, H. ; Fabbri, E. ; Groenenberg, D. ; Grone, A. ; Groot Bruinderink, G.W.T.A. ; Font, I. ; Hakhof, J. ; Harms, V. ; Jansman, H.A.H. ; Janssen, R. ; Lammertsma, D.R. ; Laros, I. ; Linnartz, L. ; Marel, D. van der; Mulder, J.L. ; Mije, S. van der; Nieman, A.M. ; Nowak, C. ; Randi, E. ; Rijks, M. ; Speksnijder, A. ; Vonhof, H.B. - \ 2013
Lutra 56 (2013)2. - ISSN 0024-7634 - p. 93 - 109.
wolven - fauna - migratie - diergedrag - dna - biochemie - menselijke invloed - centraal-europa - noordoostpolder - wolves - migration - animal behaviour - biochemistry - human impact - central europe
On July 4th 2013 a dead subadult female wolf-like canid was found by the roadside between Luttelgeest and Marknesse in the Noordoostpolder in the central part of the Netherlands. As the last observations of wild wolves in the Netherlands date back to 1869 the discovery of this animal generated a lot of media attention. European wolf populations have been expanding since the 1950s and the first packs recently established themselves in Germany in geographic proximity of the Dutch border, so natural re-appearance of the species in the Netherlands seemed likely. We investigated the taxonomy of the animal, its geographical origin, and its most recent history. Macroscopic and biochemical analyses of the dead animal convincingly showed that it was a purebred wolf, related to populations from eastern Europe. Bullet impacts and shattered fragments found in the chest and flank, and a discrepancy between the timing of the post mortem and rigor mortis intervals indicated that this wolf was shot prior to illegal transport to the Netherlands. The wolf fed on beaver in either the Carpathian mountains or the Eifel which is too far for the animal to have walked from by itself within the 24 hours needed to digest its last meal. These geographical areas are the only regions where haplotypes and 87Sr/86Sr isotopes retrieved from both the dead wolf and the beaver remains in its stomach co-occur. We therefore conclude that the first Dutch wolf found in the Netherlands in 150 years did not enter the Netherlands by itself but sadly proved to be the victim of wildlife crime. Keywords: Canis lupus, Europe, haplotypes, isotopes, microsatellites, wildlife forensics, wolf.
Physiology and biochemistry of aromatic hydrocarbon-degrading bacteria that use chlorate and/or nitrate as electron acceptor
Oosterkamp, M.J. - \ 2013
Wageningen University. Promotor(en): Fons Stams, co-promotor(en): Caroline Plugge; Peter Schaap. - Wageningen : Wageningen University - ISBN 9789461737779 - 191
bacteriën - aromatische koolwaterstoffen - fysiologie - biochemie - elektronen - genomen - nitraten - chloraten - microbiologie - bacteria - aromatic hydrocarbons - physiology - biochemistry - electrons - genomes - nitrates - chlorates - microbiology
The biochemical basis of plant development
Weijers, D. - \ 2013
Wageningen : Wageningen University - ISBN 9789461736215 - 23
fytochemie - plantenontwikkeling - planten - plantenweefsels - celbiologie - moleculaire biologie - biochemie - plantenembryo's - phytochemistry - plant development - plants - plant tissues - cellular biology - molecular biology - biochemistry - plant embryos
Plants develop highly elaborate structures, ranging from small mosses to large trees. All these structures are made by stem cells and consist of a few basic types of tissue. The field of Biochemistry of Plant Development studies the mechanisms by which regulatory proteins control the formation of stem cells and tissues. The young embryo, developing within the seed, is the simplest model to study these fundamental processes, and to gain understanding of the basis for plant development at cellular, molecular and atomic scale.
Measurement methods and variability assessment of the Norway spruce total leaf area: Implications for remote sensing
Homolova, L. ; Lukes, P. ; Malenovsky, Z. ; Lhotakova, Z. ; Kaplan, V. ; Hanus, J. - \ 2013
Trees-Structure and Function 27 (2013)1. - ISSN 0931-1890 - p. 111 - 121.
chlorophyll-a - light-interception - hyperspectral data - picea-abies - imaging spectroscopy - conifer needles - surface-area - gas-exchange - canopy - biochemistry
Estimation of total leaf area (LAT) is important to express biochemical properties in plant ecology and remote sensing studies. A measurement of LAT is easy in broadleaf species, but it remains challenging in coniferous canopies. We proposed a new geometrical model to estimate Norway spruce LAT and compared its accuracy with other five published methods. Further, we assessed variability of the total to projected leaf area conversion factor (CF) within a crown and examined its implications for remotely sensed estimates of leaf chlorophyll content (Cab). We measured morphological and biochemical properties of three most recent needle age classes in three vertical canopy layers of a 30 and 100-year-old spruce stands. Newly introduced geometrical model and the parallelepiped model predicted spruce LAT with an error >5 % of the average needle LAT, whereas two models based on an elliptic approximation of a needle shape underestimated LAT by up to 60 %. The total to projected leaf area conversion factor varied from 2. 5 for shaded to 3. 9 for sun exposed needles and remained invariant with needle age class and forest stand age. Erroneous estimation of an average crown CF by 0. 2 introduced an error of 2-3 µg cm-2 into the crown averaged Cab content. In our study, this error represents 10-15 % of observed crown averaged Cab range (33-53 µg cm-2). Our results demonstrate the importance of accurate LAT estimates for validation of remotely sensed estimates of Cab content in Norway spruce canopies.
Natuurkwaliteit Drentse vennen opnieuw gemeten : bijna een eeuw ecologische veranderingen
Dam, H. van; Arts, G.H.P. ; Bijkerk, R. ; Boonstra, H. ; Belgers, J.D.M. ; Mertens, A. - \ 2013
Amsterdam [etc.] : Herman van Dam Adviseur Water en Natuur [etc.] (Alterra-rapport 2351) - 286
stilstaand water - plassen - zoetwaterecologie - biochemie - macrofauna - aquatische ecologie - ecologisch herstel - zure regen - verdroging - drenthe - standing water - ponds - freshwater ecology - biochemistry - aquatic ecology - ecological restoration - acid rain - desiccation
In 2010-2011 zijn in 18 Drentse vennen inventarisaties uitgevoerd van beïnvloeding en beheer, waterstandsfluctuaties, waterchemie, vegetatie, kiezelwieren, sieralgen en macrofauna. De resultaten worden vergeleken met die van vergelijkbare inventarisaties in 1990 – 1994 en 2003. In de afgelopen dertig jaar is de kwaliteit van de onderzochte vennen aanzienlijk toegenomen, vooral door de afname van verzurende atmosferische depositie, maar ook door maatregelen tegen eutrofiëring zoals het uitbaggeren van vennen en het bestrijden van meeuwenkolonies. Ook anti-verdrogingsmaatregelen hebben rendement opgeleverd. Gemiddeld is de kwaliteit van de vegetatie, sieralgen en kiezelwieren nu even goed als of zelfs beter dan in de eerste helft van de twintigste eeuw. In de meeste vennen is de kwaliteit van de macrofauna sinds begin jaren negentig niet vooruitgegaan, mogelijk door het slechte koloniserende vermogen van veel macrofaunasoorten, de zuurstofarme waterbodem met toxische zwavelverbindingen en een eventuele ontoereikende omgevingskwaliteit van de vennen. In sommige vennen draagt externe belasting door overnachtende ganzen bij tot eutrofiëring. In vennen waar dat niet het geval is treedt soms interne eutrofiëring op. Door stijging van de pH door afname van verzuring wordt organische stof uit het sediment gemineraliseerd en komen voedingsstoffen vrij in de waterlaag. Vooral in de laatste vijf jaar heeft dat tot achteruitgang van de kwaliteit van algen en macrofauna geleid. Er worden aanbevelingen voor beheer en onderzoek gedaan, zoals het continueren van het huidige beheer, aangevuld met het opnieuw graven van veenputten in dichtgroeiende vennen, het beperken van de invloed van ganzen en grazende runderen en het voorkómen van invasies van exoten. Om de effecten van beleidsmaatregelen en beheer in de toekomst te blijven volgen wordt aanbevolen het onderzoek in alle vennen elke 10-12 jaar te herhalen, aangevuld met frequentere monitoring in een klein aantal vennen.
Triacylglycerol (TAG) accumulation in microalgae
Breuer, Guido - \ 2012
triacylglycerols - biochemistry - algae - biobased chemicals - biobased economy
Structural and biochemical characterization of 3-hydroxybenzoate 6-hydroxylase
Montersino, S. - \ 2012
Wageningen University. Promotor(en): Willem van Berkel, co-promotor(en): A. Mattevi. - [S.l.] : s.n. - ISBN 9789461732781 - 158
aspecifiek mono-oxygenase - moleculaire structuur - biochemie - unspecific monooxygenase - molecular conformation - biochemistry

The thesis deals with the characterization of a new flavoprotein hydroxylase 3 hydroxybenzoate 6-hydroxylase (3HB6H) from Rhodococcus jostii RHA1. 3HB6H is able to insert exclusively oxygen in para-position and the enzyme has been chosen to study the structural basis of such regioselectivity. As main result, functional mirror image active sites direct regioselective 3-hydroxybenzoate hydroxylation. Moreover, the nature and role of unprecedented phospholipid binding has been analyzed demonstrating a role in enzyme oligomerization and a possible protective role during catalysis. To conclude, the knowledge acquired improves our insight into the strategies of flavin-dependent regioselective hydroxylation and the results emerged in this thesis provide a foundation for further structural and kinetic studies on 3HB6H and related enzymes.

Quantification of net exudation for the plant-microbial fuel cell
Kuijken, R.C.P. ; Snel, J.F.H. ; Bouwmeester, H.J. ; Marcelis, L.F.M. - \ 2011
wortelexudaten - analyse - microbiële brandstofcellen - biobased economy - biochemie - root exudates - analysis - microbial fuel cells - biochemistry
The objective of this project is to develop a simple procedure to estimate net root exudation to study genetic and environmental effects on exudation.
Quantifying root exudate influx into the Plant microbial fuel cell
Kuijken, Rene - \ 2010
microbial fuel cells - bioenergy - electricity generation - root exudates - biochemistry - research projects - biobased economy
Use of homologous and heterologous gene expression profiling tools to characterize transcription dynamics during apple fruit maturation and ripening
Costa, F. ; Alba, R. ; Schouten, H.J. ; Soglio, V. ; Gianfranceschi, L. ; Serra, S. ; Musacchi, S. ; Sansavini, S. ; Costa, G. ; Fei, Z. ; Giovannoni, J. - \ 2010
BMC Plant Biology 10 (2010). - ISSN 1471-2229 - 36 p.
cdna microarrays - ethylene biosynthesis - climacteric fruit - sequence tags - melon fruit - tomato - genomics - identification - morphogenesis - biochemistry
Background - Fruit development, maturation and ripening consists of a complex series of biochemical and physiological changes that in climacteric fruits, including apple and tomato, are coordinated by the gaseous hormone ethylene. These changes lead to final fruit quality and understanding of the functional machinery underlying these processes is of both biological and practical importance. To date many reports have been made on the analysis of gene expression in apple. In this study we focused our investigation on the role of ethylene during apple maturation, specifically comparing transcriptomics of normal ripening with changes resulting from application of the hormone receptor competitor 1-Methylcyclopropene. Results - To gain insight into the molecular process regulating ripening in apple, and to compare to tomato (model species for ripening studies), we utilized both homologous and heterologous (tomato) microarray to profile transcriptome dynamics of genes involved in fruit development and ripening, emphasizing those which are ethylene regulated. The use of both types of microarrays facilitated transcriptome comparison between apple and tomato (for the later using data previously published and available at the TED: tomato expression database) and highlighted genes conserved during ripening of both species, which in turn represent a foundation for further comparative genomic studies. The cross-species analysis had the secondary aim of examining the efficiency of heterologous (specifically tomato) microarray hybridization for candidate gene identification as related to the ripening process. The resulting transcriptomics data revealed coordinated gene expression during fruit ripening of a subset of ripening-related and ethylene responsive genes, further facilitating the analysis of ethylene response during fruit maturation and ripening. Conclusion - Our combined strategy based on microarray hybridization enabled transcriptome characterization during normal climacteric apple ripening, as well as definition of ethylene-dependent transcriptome changes. Comparison with tomato fruit maturation and ethylene responsive transcriptome activity facilitated identification of putative conserved orthologous ripening-related genes, which serve as an initial set of candidates for assessing conservation of gene activity across genomes of fruit bearing plant species
Polymorphisms in glyoxalase 1 gene are not associated with vascular complications: the Hoorn and CoDAM studies
Engelen, L. ; Ferreira, I. ; Brouwers, O. ; Henry, R.M.A. ; Dekker, J.M. ; Nijpels, G. ; Heine, R.J. ; Greevenbroek, M.M.J. van; Kallen, C.J.H. van der; Blaak, E.E. ; Feskens, E.J.M. ; Cate, H. ten; Stehouwer, C.D.A. ; Schalkwijk, C.G. - \ 2009
Journal of Hypertension 27 (2009)7. - ISSN 0263-6352 - p. 1399 - 1403.
diabetic complications - methylglyoxal - glycation - biochemistry - hypertension - increases - cells
Objectives Methylglyoxal is a major precursor in the formation of advanced glycation endproducts (AGEs), which are known to contribute to vascular complications such as hypertension and arterial stiffness. Methylglyoxal can be detoxified by glyoxalase 1 (GLO1). Because genetic variation in the GLO1 gene may alter the expression and/or the activity of GLO1, we investigated whether single nucleotide polymorphisms ( SNPs) in the GLO1 gene are associated with vascular complications. Methods The study entailed cross-sectional data analyses of the Cohort study of Diabetes and Atherosclerosis Maastricht (CoDAM) study and the Hoorn study, comprising a total of 1289 participants, aged 64.5 +/- 8.58 years, of whom 43.5% had normal glucose metabolism, 23.2% had impaired glucose metabolism and 33.3% had type 2 diabetes mellitus. Nine tag SNPs that cover the common GLO1 gene variation were genotyped. Levels of blood pressure and markers of atherosclerosis, arterial stiffness, renal function and AGEs were compared across genotypes. Results All genotyped SNPs were in Hardy-Weinberg equilibrium. Prevalence of hypertension and markers of atherosclerosis, arterial stiffness, renal function and AGEs did not differ across genotypes of the nine SNPs. In additive models, SNP18 (rs2736654) was associated with pulse pressure [-1.20 mmHg (95% confidence interval: -2.26;-0.14)] and SNP40 (rs10484854) was associated with systolic blood pressure [-1.77 mmHg (-3.40;-0.14)]. Conclusion Polymorphisms in the GLO1 gene are not associated with the prevalence of hypertension, markers of atherosclerosis, renal function and AGEs and are weakly associated with pulse pressure and systolic blood pressure ( possibly due to chance) in two Dutch cohorts of patients with normal glucose metabolism, impaired glucose metabolism and type 2 diabetes mellitus
Pectins and pectinases
Schols, H.A. ; Visser, R.G.F. ; Voragen, A.G.J. - \ 2009
Wageningen : Wageningen Academic Publishers - ISBN 9789086861088 - 331
pectinen - biochemie - plantaardige producten - voedselsamenstelling - pectins - biochemistry - plant products - food composition
Effect of surface coating on ripening and early peel spotting in 'Sucrier' banana (Musa acuminata)
Promyou, S. ; Ketsa, S. ; Doorn, W.G. van - \ 2007
New Zealand Journal of Crop and Horticultural Science 35 (2007)2. - ISSN 0114-0671 - p. 259 - 265.
biochemistry - storage - fruit
Sucrier¿ bananas (Musa acuminata, AA Group) show peel spotting when the peel is just about as yellow as green, which coincides with optimum eating quality. As consumers might relate the spotting to overripe fruit, early spotting is considered undesirable, especially for export markets. Fruit were left uncoated (controls) or coated with polyethylene parafilm wax at concentrations of 20%, 25%, and 30% (v/v) and then held at 29¿30°C for 5 days. Compared with controls, each of the concentrations delayed early peel spotting. Eating quality was not affected by the 20% coating, but was negatively affected by the higher concentrations. Further tests, using 20% coating, showed that the delay of peel spotting was not associated with a change in peel total free phenolics or with polyphenol oxidase (PPO) activity, but it was accompanied by reduced in vitro phenylalanine ammonia lyase (PAL) activity. Results suggest that the delay in peel spotting, after surface coating, is a result, at least in part, of reduced PAL activity. Low rate of oxygen diffusion through the coating might be the factor that limits the last step to blackening.
High oxygen levels promote peel spotting in banana fruit
Maneenuam, T. ; Ketsa, S. ; Doorn, W.G. van - \ 2007
Postharvest Biology and Technology 43 (2007)1. - ISSN 0925-5214 - p. 128 - 132.
phenylalanine ammonia-lyase - biochemistry - physiology - quality
We studied the effect of high oxygen on early peel spotting in `Sucrier¿ bananas held at 25 °C and 90% RH. Fruit first ripened to colour index 3¿4 (about as yellow as green) and were then held in containers with a continuous gas flow of 18 ± 2 kPa (control) or 90 ± 2 kPa oxygen. High oxygen promoted peel spotting. The in vitro activities of phenylalanine ammonia lyase (PAL) and polyphenol oxidase (PPO), measured both in the whole peel and in peel spots, were lower in high oxygen than in the controls. The level of total free phenolics, both in the whole peel and in peel spots, was lower in the high oxygen treatment. Dopamine content in the peel spots decreased rapidly, earlier in the high oxygen treatments than in controls. It is concluded that peel spotting was not correlated with in vitro PAL and PPO activities. Decrease in dopamine levels correlated with peel spotting, indicating that it might be used as a substrate for the browning reaction.
Hyperspectral remote sensing of biochemical and biophysical parameters: the derivate red-edge "double-peak feature", a nuisance or an opportunity?
Cho, M.A. - \ 2007
Wageningen University. Promotor(en): Andrew Skidmore, co-promotor(en): Sip van Wieren. - [S.l.] : S.n. - ISBN 9789085046226 - 206
remote sensing - vegetatie - biochemie - biofysica - vegetation - biochemistry - biophysics
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