Development of a superpathway model for primary leaf metabolism.

<p>The model structure was derived from stoichiometric and biochemical information provided by genome-scale metabolic networks and databases. The model is provided in SBML format in the supplements (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0092299#pone.0092299.s003" target="_blank">Model S1</a>).</p

Contribution of metabolite interconversion functions to the best numerical solution of the simplified metabolic network model.

<p>Numbers of metabolite interconversion functions are indicated on x- and y-axis. The colour bar indicates the relative decrease of the cost function value, i.e. improvement of solution, when a function or a combination of functions was varied during the optimization process. All cost function values were normalised to the best of all optimization runs (100%). Functions were optimized for the simulation of the metabolic homeostasis of Col-0 under extended darkness.</p

Simplified model structure of the primary metabolism according to metabolic clusters.

<p>The model was derived by interconnecting the metabolic clusters by functions of interconversion (<i>f_i</i>). Clusters are named according to the description in the main text (<i>Results)</i> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0092299#pone.0092299.s002" target="_blank">Table S1</a>.</p

Relative changes of metabolic clusters under light and extended night conditions.

<p>Bars indicate the ratios of metabolic clusters from Col-0 under extended night and light conditions. Clusters are named according to the description in the main text (<i>Results)</i> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0092299#pone.0092299.s002" target="_blank">Table S1</a>.</p

Relative activity of the pyruvate dehydrogenase complex in Col-0 under conditions of light and extended night.

<p>Enzyme activity is given in arbitrary units which are normalised to gram fresh weight. The blue bar shows relative activity under normal light condition, the red bar shows activity under condition of extended darkness. The difference of relative activity is significant (p<0.05) and bars represent means ± SD (n  = 5).</p

Differential Jacobian of Col-0 under conditions of light and extended night.

<p>Bars represent the log₂-ratio of the entries in the Jacobian matrices of Col-0 under conditions of light (L) and extended night (EN), which were derived from covariance data of metabolomics data sets. Blue colour indicates a ratio >1, i.e. the Jacobian entry of the samples of extended night was higher than under normal light. White colour indicates a ratio <1, i.e. the Jacobian entry of the samples of extended night was lower than under normal light. All entries represent median values of 10³ calculations normalised to the square of interquartile distance. (<b>A</b>) and characterize the entries of the Jacobian matrix and refer to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0092299#pone.0092299.e001" target="_blank">equation 1</a>. (<b>B</b>) shows the diagonal entries of the Jacobian matrix belonging to the metabolites described on the horizontal axis.</p