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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    Organic matter reduces the amount of detectable environmental DNA in freshwater
    Bochove, Kees van; Bakker, Freek T. ; Beentjes, Kevin K. ; Hemerik, Lia ; Vos, Rutger A. ; Gravendeel, Barbara - \ 2020
    Ecology and Evolution 10 (2020)8. - ISSN 2045-7758 - p. 3647 - 3654.
    degradation - detection - environmental DNA - Gammarus pulex - organic matter - pH

    Environmental DNA (eDNA) is used for monitoring the occurrence of freshwater organisms. Various studies show a relation between the amount of eDNA detected and target organism abundance, thus providing a potential proxy for reconstructing population densities. However, environmental factors such as water temperature and microbial activity are known to affect the amount of eDNA present as well. In this study, we use controlled aquarium experiments using Gammarus pulex L. (Amphipoda) to investigate the relationship between the amount of detectable eDNA through time, pH, and levels of organic material. We found eDNA to degrade faster when organic material was added to the aquarium water, but that pH had no significant effect. We infer that eDNA contained inside cells and mitochondria is extra resilient against degradation, though this may not reflect actual presence of target species. These results indicate that, although estimation of population density might be possible using eDNA, measured eDNA concentration could, in the future, be corrected for local environmental conditions in order to ensure accurate comparisons.

    Ecophysiology of sulfate-reducing bacteria and syntrophic communities in marine anoxic sediments
    Özüölmez, Deya - \ 2017
    Wageningen University. Promotor(en): A.J.M. Stams; Caroline M. Plugge. - Wageningen : Wageningen University - ISBN 9789463436540 - 225
    degradation - marine sediments - methanobacteria - microorganisms - organic matter - anoxia - sulfate reduction - degradatie - mariene sedimenten - methanobacteria - micro-organismen - organische stof - anoxie - sulfaatreductie

    Propionate, butyrate, acetate, hydrogen and formate are the major intermediates of organic matter degradation. Sulfate-reducing bacteria (SRB) contribute significantly to the consumption of these substrates in sulfate-rich marine sediments. In sulfate-depleted sediments, however, complete degradation of propionate or butyrate is only possible via syntrophic cooperation of acetogenic bacteria and methanogenic archaea. Despite that the predominance of SRB in sulfate-rich and methanogens in sulfate-depleted sediments was reported, recent studies showed that both types of microorganism could be present in upper and lower parts of marine sediments. In this thesis, propionate and butyrate conversions and the involved microbial community in sulfate, sulfate-methane transition and methane zone sediment of Aarhus Bay, Denmark were studied using sediment slurry incubations. Interspecies hydrogen transfer and coexistence during acetate degradation were investigated in mixed pure cultures.

    In Chapter 2, interspecies hydrogen transfer between aceticlastic Methanosaeta concilii and hydrogenotrophic microorganisms, Desulfovibrio vulgaris or Methanococcus maripaludis, was investigated. Additionally, coexistence of M. concilii and Desulfobacter latus growing on acetate under sulfidogenic conditions was studied. The results of Chapter 2 showed that D. vulgaris could reduce sulfate and grow on leaked hydrogen from M. concilii. Hydrogen leakage from M. concilii provides an explanation for biogeochemical zonation both for competitive (e.g. acetate) and non-competitive substrates (methyl compounds), and this indicates the possible coexistence of SRB and methanogens in sulfate-rich environments.

    In chapter 3 and 4, long term incubations were examined focusing on butyrate and propionate conversion and the microbial community dynamics in sediment slurry enrichments at different sulfate (o, 3 and 20 mM) concentrations and incubation temperatures (10°C and 25°C). Sulfate reduction is the dominant process for butyrate and propionate conversion in Aarhus Bay sediments. In the absence of sulfate, both substrates can be converted efficiently, indicating the presence of syntrophic communities throughout the sediment. The fluctuating methane concentrations and the enrichment of anaerobic methanotrophic archaea (ANME) during butyrate and propionate conversion at 10°C suggest the occurrence of anaerobic oxidation of methane (AOM) in sulfate-methane transition zone (SMTZ) of Aarhus Bay.

    The microbial community involved in butyrate and propionate conversions were investigated using next generation sequencing (NGS) of the 16S rRNA amplicon sequencing. The enriched sulfate-reducing bacteria at high sulfate concentration (20 mM) were different when butyrate and propionate were used as substrate. Desulfosarcina and Desulfobacterium dominate the butyrate-converting slurries (Chapter 3), whereas Desulfosarcina, Desulfobulbus and Desulforhopalus are the main SRB in propionate-converting slurries (Chapter 4). The increase in the relative abundance of Desulfobacteraceae and Desulfobulbaceae in SZ, SMTZ and MZ sediment slurries suggests the presence of sulfate reducers throughout the anoxic sediment column. In the absence of sulfate, Syntrophomonas and Cyrptanaerobacter become dominant which suggests their role in syntrophic butyrate and propionate conversion, respectively. These results were further supported in Chapter 6. The increase in the relative abundance of Syntrophomonas in the presence of sulfate (Chapter 3) and some members of Desulfobacteraceae (Chapter 4) in the absence of sulfate shows the metabolic flexibility of the microorganisms at different sulfate concentrations. Temperature has an impact on the microbial community (Chapter 4) and IPL composition (Chapter 5) in enrichment slurries. Cryptanaerobacter is dominant at 25°C, and, Desulfobacteraceae (Desulfofaba), especially Desulfobulbaceae members (Desulfobulbus, Desulforhopalus) become dominant at 10°C at 0 and 3 mM sulfate concentrations in propionate-amended enrichment slurries. In butyrate-amended slurries, Clostridiales have higher relative abundance at 10°C regardless of the sulfate concentration and the sediment depth which supports important role of Clostridiales in butyrate conversion in marine sediments. Archaeal community analyses revealed the dominance of hydrogenotrophic methanogens belonging to Methanomicrobiales in both butyrate- and propionate-converting slurries (Chapter 3 and 4) and enrichment cultures (Chapter 6) regardless of the sediment depth, the incubation temperature and the presence of sulfate, which indicate that they are the main syntrophic partners of butyrate and propionate degraders. The other syntrophic partner organisms are the aceticlastic methanogenic families: Methanosarcinaceae and Methanosaetaeceae. The presence of methane-oxidizing archaea (ANME-1b) in low temperature SMTZ slurries together with Desulfobacteraceae (Chapter 3 and 4) suggests the occurrence of anaerobic oxidation of methane (AOM) in SMTZ of Aarhus Bay.

    In conclusion, this thesis confirms the presence and activity of methanogens in sulfate-rich, and SRB in sulfate-depleted marine sediments; and their involvement in butyrate, propionate and acetate conversion. Novel bacterial and archaeal members enriched in the sediment slurries are likely involved in propionate, butyrate and acetate conversions at different depths of marine sediments in addition to known the cultured species.

    Degradation and excretion of the Fusarium toxin deoxynivalenol by an edible insect, the Yellow mealworm (Tenebrio molitor L.)
    Broekhoven, S. van; Mota Gutierrez, J. ; Rijk, T.C. de; Nijs, W.C.M. de; Loon, J.J.A. van - \ 2017
    World Mycotoxin Journal 10 (2017)2. - ISSN 1875-0710 - p. 163 - 169.
    degradation - deoxynivalenol - edible insect - excretion

    Insects could provide an alternative and more sustainable source of animal protein compared to conventional livestock. Yellow mealworms (Tenebrio molitor L.) can be grown on diets composed of organic by-products. However, these diets could be contaminated with mycotoxins. Thus far, little is known about possible retention, sequestration, excretion or detoxification of mycotoxins by edible insects. T. molitor larvae were grown on wheat flour naturally contaminated with mycotoxins among which deoxynivalenol (DON) was predominant (4.9 mg/kg), wheat flour spiked with 8 mg/kg pure DON, and uncontaminated wheat flour. Larval survival and weight gain on the three diets were compared. Survival was high for larvae on all dietary treatments (>98%) and no difference in weight gain was observed when comparing larvae grown on uncontaminated control diet with larvae grown on contaminated diets (P=0.091). Presence of mycotoxins in larvae and larval faeces was analysed using LC-MS/MS. No DON or DON-derivatives were detected in T. molitor after harvest of the larvae, pointing to degradation by the larvae. Excretion of DON in larval faeces was ca. 14% of the amount of DON ingested for larvae grown on naturally contaminated diet and ca. 41% for larvae grown on DON-spiked diet. These are promising results with respect to food safety of mealworms or derived products grown on mycotoxin-contaminated feed. However, enzymatic degradation of DON in T. molitor, as well as possible toxicity of the resulting metabolites, remain to be further investigated.

    Statistical Paradigm for Organic Optoelectronic Devices : Normal Force Testing for Adhesion of Organic Photovoltaics and Organic Light-Emitting Diodes
    Vasilak, Lindsay ; Tanu Halim, Silvie M. ; Gupta, Hrishikesh Das; Yang, Juan ; Kamperman, Marleen ; Turak, Ayse - \ 2017
    ACS Applied Materials and Interfaces 9 (2017)15. - ISSN 1944-8244 - p. 13347 - 13356.
    adhesion testing - degradation - interfaces - metal contact delamination - organic electronics - Weibull statistics

    In this study, we assess the utility of a normal force (pull-test) approach to measuring adhesion in organic solar cells and organic light-emitting diodes. This approach is a simple and practical method of monitoring the impact of systematic changes in materials, processing conditions, or environmental exposure on interfacial strength and electrode delamination. The ease of measurement enables a statistical description with numerous samples, variant geometry, and minimal preparation. After examining over 70 samples, using the Weibull modulus and the characteristic breaking strength as metrics, we were able to successfully differentiate the adhesion values between 8-tris(hydroxyquinoline aluminum) (Alq3) and poly(3-hexyl-thiophene) and [6,6]-phenyl C61-butyric acid methyl ester (P3HT:PCBM) interfaces with Al and between two annealing times for the bulk heterojunction polymer blends. Additionally, the Weibull modulus, a relative measure of the range of flaw sizes at the fracture plane, can be correlated with the roughness of the organic surface. Finite element modeling of the delamination process suggests that the out-of-plane elastic modulus for Alq3 is lower than the reported in-plane elastic values. We suggest a statistical treatment of a large volume of tests be part of the standard protocol for investigating adhesion to accommodate the unavoidable variability in morphology and interfacial structure found in most organic devices.

    In vitro fermentation and immunomodulating characteristics of dietary fibres
    Rösch, C. - \ 2016
    Wageningen University. Promotor(en): Harry Gruppen; Henk Schols. - Wageningen : Wageningen University - ISBN 9789462577954 - 130
    dietary fibres - degradation - enzymes - immunomodulatory properties - cytokines - glycosides - fermentation - voedingsvezels - degradatie - enzymen - immunomodulerende eigenschappen - cytokinen - glycosiden - fermentatie


    Dietary fibres are a diverse group of substances, indigestible by human digestive enzymes, but (partially) fermentable in the human large intestine by the resident microbiota. Many health beneficial effects of fibres such as lowering blood cholesterol levels or increasing stool bulk have been reported. For some fibres, immunomodulating properties have been shown. Other studies investigate the degradation fate of fibres by the bacteria. In this PhD thesis BMDCs from TLR2/4 knock out mice were validated to be unresponsive to naturally present contaminants like LPS and proved to be a good tool to analyse the immune response of dietary fibres. A variety of 44 fibres, was tested on these immune cells and all fibres were found to modulated the immune system differently. Also, different immunomodulating properties of an oat and barley β-glucan having rather similar chemical structures, were found. The insoluble fraction of the β-glucans induced highest amounts of cytokines. As a consequence, sample preparation such as drying, dispersing and heating were shown to affect the immunomodulatory properties. The in vitro fermentation characteristics of barley β-glucan and sugar beet pectin and the immunomodulatory properties of their degradation products on BMDCs were compared and shown to be substrate and degradation product specific. This study showed, that glycosidic degradation products of both fibres induced higher amounts of cytokines than their intact polysaccharide. An in vitro batch fermentation of soluble, indigestible maltodextrins by human faecal inocula was monitored and the activity of carbohydrate degrading enzymes, produced by the microbiota, was analysed. Results revealed that the maltodextrin was only slowly and incompletely fermented, despite the high potential of microbial enzymes present to degrade typical starch linkages.

    Overall, this thesis showed that dietary fibres interact and influence the immune system dependent on their individual chemical fine structure. Additionally, an evaluation of the health impact of dietary fibres can only be complete when also glycosidic fermentation products are considered.

    Alkaline pretreatments of lignin-rich by-products and their implications for enzymatic degradation
    Murciano-Martinez, P. - \ 2016
    Wageningen University. Promotor(en): Harry Gruppen, co-promotor(en): Mirjam Kabel. - Wageningen : Wageningen University - ISBN 9789462576629 - 156
    degradation - enzymes - pretreatment - byproducts - lignin - food chemistry - delignification - sugarcane bagasse - degradatie - enzymen - voorbehandeling - bijproducten - lignine - voedselchemie - delignificatie - suikerrietbagasse

    The increasing interest in plant biomass based biofuels and chemicals arouses mainly from the increased awareness of a possible finiteness of fuels. The current main challenge to produce such biofuels and biochemicals is economic efficiency, but also knowledge concerning type and effectiveness of both thermally assisted chemical and enzymatic treatments, needed to generate fermentable sugars, is lacking. The subject of this thesis is to gain understanding of the effect of both sulphuric acid and NaOH catalysed pretreatments of sugar cane bagasse and oil palm empty fruit bunches on subsequent enzymatic saccharification, with a focus on the NaOH catalysed pretreatments. The fate of the main polymers present, lignin, cellulose and xylan, was studied and also single-activity xylan degrading enzymes, all from Rasamsonia emersonii, were studied for their mode-of-action.

    Composting trial with BioFoam® products in a full scale commercial composting facility : final report, April 2015
    Zee, M. van der - \ 2015
    Wageningen : Wageningen UR - Food & Biobased Research (Wageningen UR Food & Biobased Research report 1561) - ISBN 9789462575141 - 31
    biobased economy - biobased materials - biomass - organic wastes - degradation - composts - composting - biotechnology - technology - plastic foam - biobased economy - materialen uit biologische grondstoffen - biomassa - organisch afval - degradatie - compost - compostering - biotechnologie - technologie - schuimplastic
    The main objective of the trial was to be able to judge whether BioFoam® material degrades at sufficient rate to be composted together with regular source separated municipal solid biowaste in a full scale industrial composting facility.
    Evaluation of the Dutch leaching decision tree with the substances bentazone, MCPA and mecoprop
    Linden, A.M.A. van der; Beltman, W.H.J. ; Boesten, J.J.T.I. ; Pol, J.W. - \ 2015
    Bilthoven : RIVM (RIVM report 2015-0095) - 78
    pesticides - groundwater - drinking water - water quality - water pollution - degradation - risk assessment - sorption - decision models - leaching - bentazone - mcpa - pesticiden - grondwater - drinkwater - waterkwaliteit - waterverontreiniging - degradatie - risicoschatting - sorptie - beslissingsmodellen - uitspoelen - bentazon - mcpa
    Sinds 2004 wordt een beslismodel (beslisboom) gebruikt om te beoordelen in welke mate een gewasbeschermingsmiddel uitspoelt naar het grondwater. Uit een evaluatie van het RIVM, het College voor de toelating van gewasbeschermingsmiddelen en biociden (Ctgb) en onderzoekinstituut Alterra blijkt dat de beslisboom goed werkt en state of the art is. Wel laten de stofgegevens waarmee wordt gerekend te wensen over. Om de kwaliteit van het grondwater te waarborgen moeten deze gegevens zorgvuldiger worden afgeleid.
    Estimation of degradation rates in cosm water : Guidance for inverse modelling using TOXSWA
    Deneer, J.W. ; Adriaanse, P.I. ; Griethuysen, C. van; Boesten, J.J.T.I. - \ 2015
    Wageningen : Alterra, Wageningen-UR (Alterra-rapport 2679) - 151
    pesticides - degradation - water - models - aquatic toxicology - toxicology - testing - pesticiden - degradatie - water - modellen - aquatische toxicologie - toxicologie - testen
    Characterisation of cell-wall polysaccharides from mandarin segment membranes
    Coll-Almela, L. ; Saura-Lopez, D. ; Laencina-Sanchez, J. ; Schols, H.A. ; Voragen, A.G.J. ; Ros-García, J.M. - \ 2015
    Food Chemistry 175 (2015). - ISSN 0308-8146 - p. 36 - 42.
    hairy ramified regions - cross-flow filtration - pectolytic enzyme - citrus-fruit - pectins - degradation - extraction - skin - rhamnogalacturonase - populations
    In an attempt to develop a process of enzymatic peeling of mandarin segments suitable for use on an industrial scale, the cell wall fraction of the segment membrane of Satsuma mandarin fruits was extracted to obtain a chelating agent-soluble pectin fraction (ChSS), a dilute sodium hydroxide-soluble pectin fraction (DASS), a 1 M sodium hydroxide-soluble hemicellulose fraction (1MASS), a 4 M sodium hydroxide-soluble hemicellulose fraction (4MASS) and a cellulose-rich residue (3.1, 0.9, 0.4, 0.7 and 1.6% w/w of fresh membrane, respectively). The ChSS pectin consisted mainly of galacturonic acid followed by arabinose and galactose. The DASS fraction contained less galacturonic acid and more neutral sugars than ChSS. Eighty-nine percent of the galacturonic acid present in the segment membranes was recovered in the above two pectin fractions. The two hemicellulosic fractions consisted of two different molecular weight populations, which also differed in their sugar composition. Arabinose, xylose, mannose, galactose and glucose were the main sugar constituents of these hemicellulose fractions. In addition to an (arabino)xylan and a xyloglucan, the presence of an arabinogalactan is suggested by the sugar composition of both hemicelluloses. The pectin fractions were also characterised by their degradability by the pectic enzymes polygalacturonase, pectinmethylesterase and rhamnogalacturonan hydrolase. However the degree of degradation of the pectin fractions by enzymes differed, and the amount of the polymeric materials resistant to further degradation and the oligomeric products also differed. Using pectic enzymes it is possible to obtain peeled mandarin segments ready to eat or for canning.
    Positional preferences of acetyl esterases from different CE families towards acetylated 4-O-methyl glucuronic acid-substituted xylo-oligosaccharides
    Neumüller, K.G. ; Carvalho de Souza, A. ; Rijn, J.H.J. van; Streekstra, H. ; Gruppen, H. ; Schols, H.A. - \ 2015
    Biotechnology for Biofuels 8 (2015). - ISSN 1754-6834 - 11 p.
    corn-silage polysaccharides - carbohydrate esterase - trichoderma-reesei - degradation - mode
    Background Acetylation of the xylan backbone restricts the hydrolysis of plant poly- and oligosaccharides by hemicellulolytic enzyme preparations to constituent monosaccharides. The positional preferences and deacetylation efficiencies of acetyl esterases from seven different carbohydrate esterase (CE) families towards different acetylated xylopyranosyl units (Xylp) - as present in 4-O-methyl-glucuronic acid (MeGlcA)-substituted xylo-oligosaccharides (AcUXOS) derived from Eucalyptus globulus - were monitored by 1H NMR, using common conditions for biofuel production (pH 5.0, 50°C). Results Differences were observed regarding the hydrolysis of 2-O, 3-O, and 2,3-di-O acetylated Xylp and 3-O acetylated Xylp 2-O substituted with MeGlcA. The acetyl esterases tested could be categorized in three groups having activities towards (i) 2-O and 3-O acetylated Xylp, (ii) 2-O, 3-O, and 2,3-di-O acetylated Xylp, and (iii) 2-O, 3-O, and 2,3-di-O acetylated Xylp, as well as 3-O acetylated Xylp 2-O substituted with MeGlcA at the non-reducing end. A high deacetylation efficiency of up to 83% was observed for CE5 and CE1 acetyl esterases. Positional preferences were observed towards 2,3-di-O acetylated Xylp (TeCE1, AnCE5, and OsCE6) or 3-O acetylated Xylp (CtCE4). Conclusions Different positional preferences, deacetylation efficiencies, and initial deacetylation rates towards 2-O, 3-O, and 2,3-di-O acetylated Xylp and 3-O acetylated Xylp 2-O substituted with MeGlcA were demonstrated for acetyl esterases from different CE families at pH 5.0 and 50°C. The data allow the design of optimal, deacetylating hemicellulolytic enzyme mixtures for the hydrolysis of non-alkaline-pretreated bioenergy feedstocks.
    Effect of species and harvest maturity on the fatty acids profile of tropical forages
    Khan, N.A. ; Farooq, M.W. ; Ali, M. ; Suleman, M. ; Ahmad, N. ; Sulaiman, S.M. ; Cone, J.W. ; Hendriks, W.H. - \ 2015
    The JAPS 25 (2015)3. - ISSN 1018-7081 - p. 739 - 746.
    neutral detergent fiber - dairy-cows - perennial ryegrass - maize silages - degradation - stability - grass
    The aim of this study was to quantify the fatty acid (FA) content and composition of forages commonly fed to dairy animals in the tropics. Twelve forage species, namely, Trifolium alexandrinum, Cichorium intybus, Hordeum vulgare L., Medicago sativa, Avena sativa, Pennisetum purpureum Setaria anceps, Sorghum almum, Panicum maximum, Rumex nepalensis, Panicum coloratum and Panicum antidotale were evaluated. Each forage species was grown in four replicate plots under standard agronomic conditions, and sampled at early, normal and late stages of maturity. The result of the present study showed that the chemical composition, dry matter digestibility and FA contents varied (P <0.001) among forage species and harvest maturity. Linolenic acid (C18:3n-3), palmitic acid (C16:0) and linoleic acid (C18:2n-6) were the predominant FAs with an average content of 8.65, 3.61 and 2.38 g/kg dry matter (DM), contributing on average to 53%, 22% and 14% of the total measured FAs, respectively. Among the individual FAs, C18:3n-3 had the largest variation ranging from 4.26 to 17.43 g/kg DM at first harvest. The content of C16:0, C18:2n-6 and C18:3n-3 decreased (P <0.001) with maturity, with the largest decrease being observed in C18:3n-3. This study highlights that harvest management is an important tool to manipulate the FA contents and composition within a forage species
    Catalytic and hydrodynamic properties of styrene monooxygenases from Rhocodoccus opacus 1CP are modulated by cofactor binding.
    Riedel, A. ; Heine, T. ; Westphal, A.H. ; Conrad, C. ; Rathsack, P. ; Berkel, W.J.H. van; Tischler, D. - \ 2015
    AMB Express 5 (2015). - ISSN 2191-0855 - 11 p.
    recombinant escherichia-coli - pseudomonas-fluorescens st - functional-analysis - crystal-structure - catabolism genes - strain vlb120 - putida ca-3 - degradation - mechanism - oxide
    Styrene monooxygenases (SMOs) are flavoenzymes catalyzing the epoxidation of styrene into styrene oxide. SMOs are composed of a monooxygenase (StyA) and a reductase (StyB). The latter delivers reduced FAD to StyA on the expense of NADH. We identified Rhodococcus opacus 1CP as the first microorganism to possess three different StyA isoforms occurring in two systems StyA1/StyA2B and StyA/StyB, respectively. The hydrodynamic properties of StyA isozymes were found to be modulated by the binding of the (reduced) FAD cofactor. StyA1 and SyA2B mainly occur as dimers in their active forms while StyA is a monomer. StyA1 showed the highest epoxidation activity and excellent enantioselectivity in aromatic sulfoxidation. The hydrodynamic and biocatalytic properties of SMOs from strain 1CP are of relevance for investigation of possible industrial applications.
    How Does Alkali Aid Protein Extraction in Green Tea Leaf Residue: A Basis for Integrated Biorefinery of Leaves
    Zhang, C. ; Sanders, J.P.M. ; Xiao, T.T. ; Bruins, M.E. - \ 2015
    PLoS ONE 10 (2015)7. - ISSN 1932-6203
    functional-properties - antioxidant activity - sugar-beet - cell-walls - cellulose - pectins - biomass - acid - degradation - hydrolysis
    Leaf protein can be obtained cost-efficiently by alkaline extraction, but overuse of chemicals and low quality of (denatured) protein limits its application. The research objective was to investigate how alkali aids protein extraction of green tea leaf residue, and use these results for further improvements in alkaline protein biorefinery. Protein extraction yield was studied for correlation to morphology of leaf tissue structure, protein solubility and hydrolysis degree, and yields of non-protein components obtained at various conditions. Alkaline protein extraction was not facilitated by increased solubility or hydrolysis of protein, but positively correlated to leaf tissue disruption. HG pectin, RGII pectin, and organic acids were extracted before protein extraction, which was followed by the extraction of cellulose and hemi-cellulose. RGI pectin and lignin were both linear to protein yield. The yields of these two components were 80% and 25% respectively when 95% protein was extracted, which indicated that RGI pectin is more likely to be the key limitation to leaf protein extraction. An integrated biorefinery was designed based on these results. Introduction
    How mushrooms feed on compost: conversion of carbohydrates and linin in industrial wheat straw based compost enabling the growth of Agaricus bisporus
    Jurak, E. - \ 2015
    Wageningen University. Promotor(en): Harry Gruppen, co-promotor(en): Mirjam Kabel. - Wageningen : Wageningen University - ISBN 9789462573116 - 156
    paddestoelen - champignonmest - koolhydraten - degradatie - substraten - compostering - agaricus bisporus - mushrooms - mushroom compost - carbohydrates - degradation - substrates - composting - agaricus bisporus


    In this thesis, the fate of carbohydrates and lignin was studied in industrial wheat straw based compost during composting and growth of Agaricus bisporus. The aim was to understand the availability and degradability of carbohydrates in order to help improve their utilization in the compost. The wheat straw based compost was characterized as being composed mainly of cellulose and lowly substituted xylan. During the first phase of composting, ester-bound substituents were removed from the xylan backbone and during the second phase of composting 50% of carbohydrates present in the original material where metabolized in a uniform manner. Lignin structure, however, remained unaltered during these composting stages. Over the period of A. bisporus mycelium growth, 20% of the original xylan became water soluble while xylan structures remained rather similar and the remaining water insoluble xylan was partially degraded. In addition, 40% of lignin was metabolized during mycelium growth with an increase in the ratio of syringyl to guaiacyl lignin units from 0.5 to 0.7 in mycelium grown compost compared to the basic compost mixture. During the fruiting body formation minor changes in lignin structure occurred, while accumulation of xylan substituents was observed for arabinosyl residues and glucuronic acid substituents. Finally, putative genes encoding carbohydrate degrading enzymes were identified in A. bisporus’ genome. Genes involved in the pentose and hexose catabolic pathway were found to be upregulated in A. bisporus mycelium. A. bisporus was found to produce both xylan and cellulose degrading enzymes and maximum activity was observed during the formation of the 1st flush of mushrooms. But, as observed from the remaining xylan structures analyzed, A. bisporus lacks the enzymatic activity to degrade xylan substituted with two arabinosyl- residues and glucuronic acid substituted xylan.

    Edita Jurak

    How Mushrooms feed on compost: Conversion of carbohydrates and linin in industrial wheat straw based compost enabling the growth of Agaricus bisporus

    Relationship between in vitro and in vivo methane production measured simultaneously with different dietary starch sources and starch levels in dairy cattle
    Hatew, B. ; Cone, J.W. ; Pellikaan, W.F. ; Podesta, S.C. ; Bannink, A. ; Hendriks, W.H. ; Dijkstra, J. - \ 2015
    Animal Feed Science and Technology 202 (2015). - ISSN 0377-8401 - p. 20 - 31.
    gas-production technique - rumen microbial-population - volatile fatty-acids - fermentation characteristics - ruminal fermentation - production profiles - degradation - emissions - kinetics - protein
    To investigate the relationship between in vitro and in vivo methane (CH4) production measured simultaneously using the same rumen-fistulated cows in both experiments, four dietary treatments based on concentrate that accounted for 400 g/kg of the mixed diet DM, were formulated to contain starch varying in rate of fermentation (slowly (S) vs. rapidly (R): native vs. gelatinized maize grain) and level of inclusion (low (L) vs. high (H): 270 vs. 530 g/kg of concentrate DM). Sixteen rumen-fistulated lactating dairy cows were used in a complete randomized block design with these treatments replicated in four periods of 17 d each. In experiment 1, after 12 d of adaptation, the cows were housed in respiration chambers for 5 d to measure CH4 production. In experiment 2, in each period in vitro gas and CH4 production were measured (in duplicate per period) for mixed diet samples from the same diet as fed to the donor cows using rumen inocula adapted to the respective diets for an average of 16 d. In addition, samples of two concentrate ingredients, viz. grass silage and beet pulp, were incubated with four different inocula obtained from individual donor cows. Gas production (GP) was measured using automated GP system with CH4 measured at distinct time points. In vitro (24-h) CH4 production of mixed diet was lower with R than S (42.9 vs. 49.5 ml/g of incubated organic matter (OM); P=0.004), and higher with L than H (49.8 vs. 42.6 ml/g of incubated OM; P=0.002). A significant interaction effect between source and level of starch (P=0.015) was also found, indicating the CH4 production of the RH diet decreased in particular. In vivo, an increased rate of starch fermentation resulted in a lower CH4 per unit of estimated rumen-fermentable OM (eRFOM; 55.6 vs. 61.2 ml/g of eRFOM; P=0.007), and higher level of starch tended (P=0.089) to reduce CH4 per unit of eRFOM, but dietary starch level and source did not affect CH4 per unit of OM consumed. Across the diets tested, 24-h in vitro CH4 (ml/g of incubated OM) correlated well with in vivo CH4 expressed per unit of eRFOM (R2 = 0.54; P=0.040), but not when expressed per unit of OM ingested (R2 = 0.04; P=0.878). For grass silage (the same trend for beet pulp), inocula adapted to R- and H-based diets compared with S- and L-based diets resulted in a lower CH4 production (36.1 vs. 44.8 ml/g of incubated OM, R vs. S; and 37.4 vs. 43.4 ml/g of incubated OM, H vs. L; P
    Short- to mid-term impact of conservation agriculture on yield variability of upland rice: evidence from farmer's fields in Madagascar
    Bruelle, G. ; Naudin, K. ; Scopel, E. ; Domas, R. ; Rabeharisoa, L. ; Tittonell, P.A. - \ 2015
    Experimental Agriculture 51 (2015)1. - ISSN 0014-4797 - p. 66 - 84.
    cropping systems - tillage systems - maize productivity - soil - erosion - africa - degradation - nigeria - surface - runoff
    Family farming in the tropics suffers from low crop productivity mainly due to a combination of poor soil fertility, low investment capacity, and a variable climate. The Lake Alaotra region of Madagascar is no exception and rainfed production is particularly hard hit. To evaluate the agronomic benefits of conservation agriculture (CA) in a region of erratic rainfall, we analysed four years of yield, management and climatic data from 3803 upland rice fields cultivated by farmers and monitored by researchers. Fields located on rainfed lowlands and hillsides were cultivated with sole rice using conventional tillage (Cv) or rice sown with no-tillage on dead organic mulch and rotated with other cereal/legume combinations (CA) from 2006 to 2011. A first global comparison across seasons, locations and years of adoption showed significantly higher average yields under CA, with no change in variance (on lowland: 2.6 ± 0.9 t ha–1 Cv, 2.8 ± 0.9 t ha–1 CA; on hillside: 2.1 ± 0.8 t ha–1 Cv, 2.4 ± 0.8 t ha–1 CA). Grouping fields according to the number of years under CA (first to fourth) revealed that CA gradually increased average yields and reduced the coefficient of variation in the short and mid-term (on lowland: +0.2 t ha–1 and –6% coefficient of variation; on hillside: +0.7 t ha–1 and –13% coefficient of variation, over four to six years of successive CA cropping). The average yield increase under CA was not associated with an increase in mineral fertiliser use, as farmers used the same amounts of fertilisers (or none) under Cv and CA. The comparison Cv versus CA also highlighted a major benefit of CA regarding climate: it widened the window of possible sowing dates. A classification and regression tree analysis of the entire dataset revealed that rice yield was more affected by agro-environmental factors than management factors (fertilisation, Cv or CA), and extreme climate variability such as the severe drought of 2007–2008 could not be offset by CA. The hypothesis of yield penalties during the first years of implementation of CA cannot be verified with the evidence presented in this study.
    Mode of action of Bacillus licheniformis pectin methylesterase on highly methylesterified and acetylated pectins
    Remoroza, C.A. ; Wagenknecht, M. ; Buchholt, H.C. ; Moerschbacher, B.M. ; Gruppen, H. ; Schols, H.A. - \ 2015
    Carbohydrate Polymers 115 (2015). - ISSN 0144-8617 - p. 540 - 550.
    sugar-beet pectins - aspergillus-niger - esterified oligogalacturonides - environmental-conditions - structural features - de-esterification - escherichia-coli - methyl esterase - degradation - calcium
    A gene encoding a putative pectinesterase from Bacillus licheniformis DSM13 was cloned and expressed in Escherichia coli. The resulting recombinant enzyme (BliPME) was purified and characterized as a pectin methylesterase. The enzyme showed maximum activity at pH 8.0 and 50 °C. BliPME is able to release up to 100% of the methylesters from lime pectin (DM 34–76 ¿ DM 0) and up to 73% of all methylesters from SBPs (DM 30–73 ¿ DM 14). BliPME efficiently de-methylesterifies lemon pectins and SBPs in a blockwise manner and is quite tolerant towards the acetyl groups present within the SBPs. Detailed analysis of the BliPME-modified pectins using HILIC–MSn and the classical calcium reactivity measurement showed that the enzyme generates pectins with low methylesterification (lime and SBP) and high acetyl content (SBP) while creating blocks of nonmethylesterified galacturonic acid residues. The high activity of BliPME towards highly methylesterified and acetylated pectins makes this novel esterase more efficient in removing methylesters from highly esterified beet pectin compared to other PMEs, e.g. Aspergillus niger PME.
    Shape Evolution Synthesis of Monodisperse Spherical, Ellipsoidal, and Elongated Hematite (alpha-Fe2O3) Nanoparticles Using Ascorbic Acid
    Tan, W.F. ; Yu, Y.T. ; Wang, M.X. ; Liu, F. ; Koopal, L.K. - \ 2014
    Crystal Growth and Design 14 (2014)1. - ISSN 1528-7483 - p. 157 - 164.
    iron-oxide nanoparticles - iron(iii) oxides - water-treatment - ferrihydrite - particles - transformation - size - degradation - dissolution - systems
    Spherical, ellipsoidal, and elongated hematite particles have been obtained via a simple chemical precipitation reaction of FeCl3 and NaOH in the presence of ascorbic acid,(AA). The effects of pH, molar ratio of AA/Fe(III), and time on the formation and shape of the hematite particles were investigated. The optimal conditions to well obtain crystalline hematite are 0.1 mol/L FeCl3, 6 mol/L NaOH, pH 7, and AA/Fe(III) ratios of 0.5-2.0%. The presence of AA catalyzed the formation of hematite by reductive dissolution of ferrihydrite and the molar ratio of AA/Fe(III) determined the crystal structure and morphology of hematite. As the ratio of AA increased from 0.5 to 2%, the morphology changed from spherical to ellipsoidal particles and then to elongated particles. The dissolution of Fe(II) from the ferrihydrite precursor is enhanced by AA, and this leads to the formation of hematite by precipitation and crystallization. The effect of AA on the particle shape can be explained by the difference in AA adsorption on the various crystal planes. The hematite samples with different morphologies enhanced the photodegradation of methylene blue in an acid solution with peroxide; the elongated particles that had the highest specific surface area were most effective with the methylene blue degradation.
    Farming systems in two less favoured areas in portugal: their development from 1989 to 2009 and the implications for sustainable land management
    Jones, N.M. ; Graaff, J. de; Duarte, F. ; Rodrigo, I. ; Poortinga, A. - \ 2014
    Land Degradation and Development 25 (2014)1. - ISSN 1085-3278 - p. 29 - 44.
    agricultural soil conservation - policy measures - european-union - consequences - degradation - typology - spain - ndvi
    Since the late 1980s, sustainable land management is one of the objectives of the European Commission in Less Favoured Areas. In this paper, we investigate the economic and environmental sustainability of farming systems in two less favoured areas in Centro and Alentejo areas of Portugal. The specific objectives were the following: (i) to characterise the farming systems; (ii) to analyse their development over a 20-year period (1989-2009); and (iii) to investigate to what extent these farming systems contribute to sustainable land management. The diversity of the farming systems was identified through a survey and cluster analysis and compared with the Farm Accountancy Data Network classification on types of farming. Indicators on the economic and environmental sustainability were estimated, namely, farm net income, return to labour and rotation management, on the basis of a survey, Farm Accountancy Data Network database and Landsat imagery, respectively. Results indicate an increased focus on livestock in the past 20years (1989-2009). In Centro, rotation management was not affected. The small ruminant farms have been able to retain a positive farm net income but that was only possible with a below average return to labour. In Alentejo, the increased focus on livestock, cattle in particular, led to an intensification of fodder production on certain plots. Mixed crop-livestock farms show a negative farm net income since 1995 and depend heavily on subsidies to remain viable. As other studies in southern Europe have shown, farm strategies have often been directed towards lowering labour inputs, lowering forage deficits through on-farm produced resources and acquiring subsidies. Copyright (c) 2013 John Wiley & Sons, Ltd.
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