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Seaton D.D.,University of Edinburgh | Smith R.W.,University of Edinburgh | Smith R.W.,Laboratory of Systems and Synthetic Biology | Song Y.H.,University of Washington | And 11 more authors.
Molecular Systems Biology | Year: 2015

Clock-regulated pathways coordinate the response of many developmental processes to changes in photoperiod and temperature. We model two of the best-understood clock output pathways in Arabidopsis, which control key regulators of flowering and elongation growth. In flowering, the model predicted regulatory links from the clock to CYCLING DOF FACTOR 1 (CDF1) and FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 (FKF1) transcription. Physical interaction data support these links, which create threefold feed-forward motifs from two clock components to the floral regulator FT. In hypocotyl growth, the model described clock-regulated transcription of PHYTOCHROME-INTERACTING FACTOR 4 and 5 (PIF4, PIF5), interacting with post-translational regulation of PIF proteins by phytochrome B (phyB) and other light-activated pathways. The model predicted bimodal and end-of-day PIF activity profiles that are observed across hundreds of PIF-regulated target genes. In the response to temperature, warmth-enhanced PIF4 activity explained the observed hypocotyl growth dynamics but additional, temperature-dependent regulators were implicated in the flowering response. Integrating these two pathways with the clock model highlights the molecular mechanisms that coordinate plant development across changing conditions. Synopsis Crosstalk between the circadian clock and light/temperature signals controls seasonal plant development. Integrated mathematical models of the clock, flowering and elongation pathways identify new behaviours in light and temperature signalling. CCA1 negatively regulates FKF1 and CDF1 transcription. GI has an FKF1-independent role in CDF1 protein stabilisation. PIF proteins function throughout light:dark cycles. Temperature regulates flowering time and hypocotyl elongation pathways at distinct times of day. Crosstalk between the circadian clock and light/temperature signals controls seasonal plant development. Integrated mathematical models of the clock, flowering and elongation pathways identify new behaviours in light and temperature signalling. © 2015 The Authors. Published under the terms of the CC BY 4.0 license. Source

Omony J.,Wageningen University | MacH-Aigner A.R.,Institute of Chemical Technology | De Graaff L.H.,Laboratory of Systems and Synthetic Biology | Van Straten G.,Wageningen University | Van Boxtel A.J.B.,Wageningen University
IEEE/ACM Transactions on Computational Biology and Bioinformatics | Year: 2012

One of the challenges in genetic network reconstruction is finding experimental designs that maximize the information content in a data set. In this paper, the information value of mRNA transcription time course experiments was used to compare experimental designs. The study concerns the dynamic response of genes in the XlnR regulon of Aspergillus niger, with the goal to find the best moment in time to administer an extra pulse of inducing D-xylose. Low and high D-xylose pulses were used to perturb the XlnR regulon. Evaluation of the experimental methods was based on simulation of the regulon. Models that govern the regulation of the target genes in this regulon were used for the simulations. Parameter sensitivity analysis, the Fisher Information Matrix (FIM) and the modified E-criterion were used to assess the design performances. The results show that the best time to give a second D-xylose pulse is when the D-xylose concentration from the first pulse has not yet completely faded away. Due to the presence of a repression effect the strength of the second pulse must be optimized, rather than maximized. The results suggest that the modified E-criterion is a better metric than the sum of integrals of absolute sensitivity for comparing alternative designs. © 2004-2012 IEEE. Source

Heshof R.,Laboratory of Systems and Synthetic Biology | van Schayck J.P.,Laboratory of Systems and Synthetic Biology | Tamayo-Ramos J.A.,Laboratory of Systems and Synthetic Biology | de Graaff L.H.,Laboratory of Systems and Synthetic Biology
AMB Express | Year: 2014

Aspergillus sp. contain ppo genes coding for Ppo enzymes that produce oxylipins from polyunsaturated fatty acids. These oxylipins function as signal molecules in sporulation and influence the asexual to sexual ratio of Aspergillus sp. Fungi like Aspergillus nidulans and Aspergillus niger contain just ppo genes where the human pathogenic Aspergillus flavus and Aspergillus fumigatus contain ppo genes as well as lipoxygenases. Lipoxygenases catalyze the synthesis of oxylipins and are hypothesized to be involved in quorum-sensing abilities and invading plant tissue. In this study we used A. nidulans WG505 as an expression host to heterologously express Gaeumannomyces graminis lipoxygenase. The presence of the recombinant LOX induced phenotypic changes in A. nidulans transformants. Also, a proteomic analysis of an A. nidulans LOX producing strain indicated that the heterologous protein was degraded before its glycosylation in the secretory pathway. We observed that the presence of LOX induced the specific production of aminopeptidase Y that possibly degrades the G. graminis lipoxygenase intercellularly. Also the presence of the protein thioredoxin reductase suggests that the G. graminis lipoxygenase is actively repressed in A. nidulans. © 2014, Heshof et al.; licensee Springer. Source

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