Browsing by Department "Wageningen University and Research Centre"

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  • The chaos in calibrating crop models
    (2021-11) Wallach, Daniel; Palosuo, Taru; Thorburn, Peter; Hochman, Zvi; Gourdain, Emmanuelle; Andrianasolo, Fety; Asseng, Senthold; Basso, Bruno; Buis, Samuel; Crout, Neil; Dibari, Camilla; Dumont, Benjamin; Ferrise, Roberto; Gaiser, Thomas; Garcia, Cecile; Gayler, Sebastian; Ghahramani, Afshin; Hiremath, Santosh; Hoek, Steven; Horan, Heidi; Hoogenboom, Gerrit; Huang, Mingxia; Jabloun, Mohamed; Jansson, Per Erik; Jing, Qi; Justes, Eric; Kersebaum, Kurt Christian; Klosterhalfen, Anne; Launay, Marie; Lewan, Elisabet; Luo, Qunying; Maestrini, Bernardo; Mielenz, Henrike; Moriondo, Marco; Nariman Zadeh, Hasti; Padovan, Gloria; Olesen, Jørgen Eivind; Poyda, Arne; Priesack, Eckart; Pullens, Johannes Wilhelmus Maria; Qian, Budong; Schütze, Niels; Shelia, Vakhtang; Souissi, Amir; Specka, Xenia; Srivastava, Amit Kumar; Stella, Tommaso; Streck, Thilo; Trombi, Giacomo; Wallor, Evelyn; Wang, Jing; Weber, Tobias K.D.; Weihermüller, Lutz; de Wit, Allard; Wöhling, Thomas; Xiao, Liujun; Zhao, Chuang; Zhu, Yan; Seidel, Sabine J.
     A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
    Calibration, the estimation of model parameters based on fitting the model to experimental data, is among the first steps in many applications of process-based models and has an important impact on simulated values. We propose a novel method of developing guidelines for calibration of process-based models, based on development of recommendations for calibration of the phenology component of crop models. The approach was based on a multi-model study, where all teams were provided with the same data and asked to return simulations for the same conditions. All teams were asked to document in detail their calibration approach, including choices with respect to criteria for best parameters, choice of parameters to estimate and software. Based on an analysis of the advantages and disadvantages of the various choices, we propose calibration recommendations that cover a comprehensive list of decisions and that are based on actual practices.
  • Occurrence and function of enzymes for lignocellulose degradation in commercial Agaricus bisporus cultivation
    (2017) Kabel, Mirjam A.; Jurak, Edita; Mäkelä, Miia R.; De Vries, Ronald P.
     A2 Katsausartikkeli tieteellisessä aikakauslehdessä
    The white button mushroom Agaricus bisporus is economically the most important commercially produced edible fungus. It is grown on carbon- and nitrogen-rich substrates, such as composted cereal straw and animal manure. The commercial mushroom production process is usually performed in buildings or tunnels under highly controlled environmental conditions. In nature, the basidiomycete A. bisporus has a significant impact on the carbon cycle in terrestrial ecosystems as a saprotrophic decayer of leaf litter. In this mini-review, the fate of the compost plant cell wall structures, xylan, cellulose and lignin, is discussed. A comparison is made from the structural changes observed to the occurrence and function of enzymes for lignocellulose degradation present, with a special focus on the extracellular enzymes produced by A. bisporus. In addition, recent advancements in whole genome level molecular studies in various growth stages of A. bisporus in compost are reviewed.
  • Production of α-1,3-L-arabinofuranosidase active on substituted xylan does not improve compost degradation by Agaricus bisporus
    (2018-07-01) Vos, Aurin M.; Jurak, Edita; de Gijsel, Peter; Ohm, Robin A.; Henrissat, Bernard; Lugones, Luis G.; Kabel, Mirjam A.; Wösten, Han A.B.
     A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
    Agaricus bisporus consumes carbohydrates contained in wheat straw based compost used for commercial mushroom production. Double substituted arabinoxylan is part of the ~40% of the compost polysaccharides that are not degraded by A. bisporus during its growth and development. Genes encoding α-1,3-L-arabinofuranosidase (AXHd3) enzymes that act on xylosyl residues doubly substituted with arabinosyl residues are absent in this mushroom forming fungus. Here, the AXHd3 encoding hgh43 gene of Humicola insolens was expressed in A. bisporus with the aim to improve its substrate utilization and mushroom yield. Transformants secreted active AXHd3 in compost as shown by the degradation of double substituted arabinoxylan oligomers in an in vitro assay. However, carbohydrate composition and degree of arabinosyl substitution of arabinoxylans were not affected in compost possibly due to inaccessibility of the doubly substituted xylosyl residues.
  • Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions
    (2021-05) Eldjarn, Grimur Hjorleifsson; Ramsay, Andrew; Van Der Hooft, Justin J.J.; Duncan, Katherine R.; Soldatou, Sylvia; Rousu, Juho; Daly, Ronan; Wandy, Joe; Rogers, Simon
     A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
    Specialised metabolites from microbial sources are well-known for their wide range of biomedical applications, particularly as antibiotics. When mining paired genomic and metabolomic data sets for novel specialised metabolites, establishing links between Biosynthetic Gene Clusters (BGCs) and metabolites represents a promising way of finding such novel chemistry. However, due to the lack of detailed biosynthetic knowledge for the majority of predicted BGCs, and the large number of possible combinations, this is not a simple task. This problem is becoming ever more pressing with the increased availability of paired omics data sets. Current tools are not effective at identifying valid links automatically, and manual verification is a considerable bottleneck in natural product research. We demonstrate that using multiple link-scoring functions together makes it easier to prioritise true links relative to others. Based on standardising a commonly used score, we introduce a new, more effective score, and introduce a novel score using an Input-Output Kernel Regression approach. Finally, we present NPLinker, a software framework to link genomic and metabolomic data. Results are verified using publicly available data sets that include validated links.