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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    De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology
    Nijkamp, J.F. ; Broek, M. van den; Datema, E. ; Kok, S. de; Bosman, L. ; Luttik, M.A. ; Daran-Lapujade, P. ; Vongsangnak, W. ; Nielsen, J. ; Heijne, W.H.M. ; Klaassen, P. ; Paddon, C.J. ; Platt, D. ; Kotter, P. ; Ham, R.C.H.J. van; Reinders, M.J.T. ; Pronk, J.T. ; Ridder, D. de; Daran, J.M. - \ 2012
    Microbial Cell Factories 11 (2012). - ISSN 1475-2859
    l-arabinose - alcoholic fermentation - biotin-prototrophy - chemostat cultures - gene prediction - yeast genome - glucose - evolutionary - protein - xylose
    Saccharomyces cerevisiae CEN.PK 113-7D is widely used for metabolic engineering and systems biology research in industry and academia. We sequenced, assembled, annotated and analyzed its genome. Single-nucleotide variations (SNV), insertions/deletions (indels) and differences in genome organization compared to the reference strain S. cerevisiae S288C were analyzed. In addition to a few large deletions and duplications, nearly 3000 indels were identified in the CEN.PK113-7D genome relative to S288C. These differences were overrepresented in genes whose functions are related to transcriptional regulation and chromatin remodelling. Some of these variations were caused by unstable tandem repeats, suggesting an innate evolvability of the corresponding genes. Besides a previously characterized mutation in adenylate cyclase, the CEN. PK113-7D genome sequence revealed a significant enrichment of non-synonymous mutations in genes encoding for components of the cAMP signalling pathway. Some phenotypic characteristics of the CEN. PK113-7D strains were explained by the presence of additional specific metabolic genes relative to S288C. In particular, the presence of the BIO1 and BIO6 genes correlated with a biotin prototrophy of CEN. PK113-7D. Furthermore, the copy number, chromosomal location and sequences of the MAL loci were resolved. The assembled sequence reveals that CEN. PK113-7D has a mosaic genome that combines characteristics of laboratory strains and wild-industrial strains.
    Influence of Roasting on the Antioxidant Activity and HMF Formation of a Cocoa Bean Model Systems
    Oliviero, T. ; Capuano, E. ; Cämmerer, B. ; Fogliano, V. - \ 2009
    Journal of Agricultural and Food Chemistry 57 (2009)1. - ISSN 0021-8561 - p. 147 - 152.
    maillard reaction-products - coffee - glycosylation - melanoidins - components - capacity - glycine - lactose - xylose - color
    During the roasting of cocoa beans chemical reactions lead to the formation of Maillard reaction (MR) products and to the degradation of catechin-containing compounds, which are very abundant in these seeds. To study the modifications occurring during thermal treatment of fat and antioxidant rich foods, such as cocoa, a dry model system was set up and roasted at 180 °C for different times. The role played in the formation of MR products and in the antioxidant activity of the system by proteins, catechin, and cocoa butter was investigated by varying the model system formulation. Results showed that the antioxidant activity decreased during roasting, paralleling catechin concentration, thus suggesting that this compound is mainly responsible for the antioxidant activity of roasted cocoa beans. Model system browning was significantly higher in the presence of catechin, which contributed to the formation of water-insoluble melanoidins, which are mainly responsible for browning. HMF concentration was higher in casein-containing systems, and its formation was strongly inhibited in the presence of catechin. No effects related to the degree of lipid oxidation could be observed. Data from model systems obtained by replacing fat with water showed a much lower rate of MR development and catechin degradation but the same inhibitory effect of catechin on HMF formation.
    Hemicellulase production in Chrysosporium lucknowense C1
    Hinz, S.W.A. ; Pouvreau, L.A.M. ; Joosten, R. ; Bartels, J. ; Jonathan, M.C. ; Wery, J. ; Schols, H.A. - \ 2009
    Journal of Cereal Science 50 (2009). - ISSN 0733-5210 - p. 318 - 323.
    recombinant saccharomyces-cerevisiae - fungus trichoderma-reesei - alpha-glucuronidase - aspergillus-niger - wheat arabinoxylan - ferulic acid - feruloylated oligosaccharides - degrading enzymes - maize bran - xylose
    Filamentous fungi are widely used for enzyme production for the biofuel industry. The ascomycetous fungus Chrysosporium lucknowense C1 was isolated as a natural producer of neutral cellulases. It is at present an attractive alternative to well known fungi like Aspergillus sp. and Trichoderma reesei for protein production on a commercial scale. Besides many cellulases, a large number of hemicellulases (particularly xylanases and arabinofuranosidases) and esterases (acetyl xylan esterases and ferulic acid esterases) encoding genes have also been identified in the C1 genome. Many of these extracellular enzymes have been selectively expressed in C1 and then purified and characterized. Four arabinofuranosidases, two acetyl xylan esterases, two ferulic acid esterases, an a-glucuronidase and four xylanases have been purified and characterized. All these enzymes were found to be active towards arabinoxylans, demonstrating the high potential of C1 as a producer of hemicellulolytic enzymes.
    Efficient hydrogen production from the lignocellulosic energy crop Miscanthus by the extreme thermophilic bacteria Caldicellulosiruptor saccharolyticus and Thermotoga neapolitana
    Vrije, G.J. de; Bakker, R.R. ; Budde, M.A.W. ; Lai, M.H. ; Mars, A.E. ; Claassen, P.A.M. - \ 2009
    Biotechnology for Biofuels 2 (2009). - ISSN 1754-6834 - 15 p.
    biohydrogen production - dark fermentation - corn stover - sp-nov - biomass - pretreatment - degradation - wastes - xylose - microorganisms
    The production of hydrogen from biomass by fermentation is one of the routes that can contribute to a future sustainable hydrogen economy. Lignocellulosic biomass is an attractive feedstock because of its abundance, low production costs and high polysaccharide content. Batch cultures of Caldicellulosiruptor saccharolyticus and Thermotoga neapolitana produced hydrogen, carbon dioxide and acetic acid as the main products from soluble saccharides in Miscanthus hydrolysate. The presence of fermentation inhibitors, such as furfural and 5-hydroxylmethyl furfural, in this lignocellulosic hydrolysate was avoided by the mild alkaline-pretreatment conditions at a low temperature of 75°C. Both microorganisms simultaneously and completely utilized all pentoses, hexoses and oligomeric saccharides up to a total concentration of 17 g l-1 in pH-controlled batch cultures. T. neapolitana showed a preference for glucose over xylose, which are the main sugars in the hydrolysate. Hydrogen yields of 2.9 to 3.4 mol H2 per mol of hexose, corresponding to 74 to 85% of the theoretical yield, were obtained in these batch fermentations. The yields were higher with cultures of C. saccharolyticus compared to T. neapolitana. In contrast, the rate of substrate consumption and hydrogen production was higher with T. neapolitana. At substrate concentrations exceeding 30 g l-1, sugar consumption was incomplete, and lower hydrogen yields of 2.0 to 2.4 mol per mol of consumed hexose were obtained. Efficient hydrogen production in combination with simultaneous and complete utilization of all saccharides has been obtained during the growth of thermophilic bacteria on hydrolysate of the lignocellulosic feedstock Miscanthus. The use of thermophilic bacteria will therefore significantly contribute to the energy efficiency of a bioprocess for hydrogen production from biomass
    Low Molecular Weight Melanoidins in Coffee Brew
    Bekedam, E.K. ; Roos, E. ; Schols, H.A. ; Boekel, M.A.J.S. van; Smit, G. - \ 2008
    Journal of Agricultural and Food Chemistry 56 (2008)11. - ISSN 0021-8561 - p. 4060 - 4067.
    maillard reaction-products - chemical-characterization - antioxidant activity - colored compounds - roasted coffee - arabica beans - model systems - polysaccharides - xylose - lysine
    Analysis of low molecular weight (LMw) coffee brew melanoidins is challenging due to the presence of many non-melanoidin components that complicate analysis. This study focused on the isolation of LMw coffee brew melanoidins by separation of melanoidins from non-melanoidin components that are present in LMw coffee brew material. LMw coffee fractions differing in polarity were obtained by reversed-phase solid phase extraction and their melanoidin, sugar, nitrogen, caffeine, trigonelline, 5-caffeoylquinic acid, quinic acid, caffeic acid, and phenolic groups contents were determined. The sugar composition, the charge properties, and the absorbance at various wavelengths were investigated as well. The majority of the LMw melanoidins were found to have an apolar character, whereas most non-melanoidins have a polar character. The three isolated melanoidin-rich fractions represented 56% of the LMw coffee melanoidins and were free from non-melanoidin components. Spectroscopic analysis revealed that the melanoidins isolated showed similar features as high molecular weight coffee melanoidins. All three melanoidin fractions contained ~3% nitrogen, indicating the presence of incorporated amino acids or proteins. Surprisingly, glucose was the main sugar present in these melanoidins, and it was reasoned that sucrose is the most likely source for this glucose within the melanoidin structure. It was also found that LMw melanoidins exposed a negative charge, and this negative charge was inversely proportional to the apolar character of the melanoidins. Phenolic group levels as high as 47% were found, which could be explained by the incorporation of chlorogenic acids in these melanoidins
    Production of lactic acid from xylose by Rhizopus oryzae
    Maas, R.H.W. ; Bakker, R.R. ; Eggink, G. ; Weusthuis, R.A. - \ 2005
    rhizopus - xylose - melkzuur - biobased economy - biopolymeren - rhizopus - xylose - lactic acid - biobased economy - biopolymers
    Poster met onderzoeksinformatie over de de omzetting van xylose in melkzuur door de schimmel Rhizopus oryzae. Deze omzetting kan nuttig zijn voor de productie van het afbreekbare polymeer PLA (Poly Lactic Acid).
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