Reconstruction of dynamic network models from metabolite measurements

Impact of Thermodynamic Principles in Systems Biology

“…In the last two studies it was shown that lin-log kinetics should not be applied to datasets where metabolite concentrations become zero (which is obvious). Even more impressive was a recent study [42] in which a lin-log model was parameterised on a rapid pulse experiment. The model represents E. coli central metabolism and anabolism to all cell compounds, comprising 126 reactions and 130 metabolites (7 conserved moieties).…”

Simplified absolute metabolite quantification by gas chromatography–isotope dilution mass spectrometry on the basis of commercially available source material

“…Quantitative measurements of intra-and extracellular metabolites rose to prominence in the early nineties as a highly directed and targeted analysis of selected compounds during so-called "stimulus-response" experiments designed for the identification of enzyme kinetics under in vivo conditions [1][2][3][4][5][6][7]. The analytical tools utilized in these earlier targeted, model driven metabolite measurements were either enzymatic assays or HPLC.…”

“…The computer-aided robotic sampler [6,57] consists of: (i) a gate-valve and (ii) a Cartesian position system (X/Y-robot) with a mounted thermo-insulated tray accommodating a rack for 60 tubes of 15 mL each (Fig. 1).…”

Quantitative Metabolomics and Its Application in Metabolic Engineering of Microbial Cell Factories Exemplified by the Baker’s Yeast

“…Ingenious devices have been developed in the last years that enable rapid sampling and quenching simultaneously at the millisecond scale. The various manual, semiautomatic and fully automatic rapid sampling techniques and their pros and cons have been comprehensively discussed and the reader is referred to (Reuss et al 2007;van Gulik 2010;Villas-Bôas 2007a). A disadvantage in this context is that most of these devices are not available on the market and therefore not accessible to the scientific community.…”

“…Rate equations based on the steady-state or rapid equilibrium assumption for enzyme catalyzed reactions are comprehensively summarized in (Segel 1993). However kinetic parameters typically used in this approach are determined by in vitro assays and it has been shown that in vitro generated data can significantly differ from those observed in vivo (Aragón and Sánchez 1985;Mauch et al 2000;Reuss et al 2007). This discrepancy is most likely due to the incomplete knowledge of the cellular composition and associated enzyme metabolite interactions as well as the difficulty to analyze enzymes under in vivo-like conditions at the lab bench.…”