APPLICATION OF A GENERALIZED MWC MODEL FOR THE MATHEMATICAL SIMULATION OF METABOLIC PATHWAYS REGULATED BY ALLOSTERIC ENZYMES

In our effort to elucidate the systems biology of the model organism, Escherichia coli, we have developed a mathematical model that simulates the allosteric regulation for threonine biosynthesis pathway starting from aspartate. To achieve this goal, we used kMech, a Cellerator language extension that describes enzyme mechanisms for the mathematical modeling of metabolic pathways. These mechanisms are converted by Cellerator into ordinary differential equations (ODEs) solvable by Mathematica *These authors contributed equally to this work Biology correspondence should be addressed to G.W.H

Unraveling the inhibitory effects of acetate on ethanol production in CEN.PK

In this study, we used the ORACLE (Optimization and Risk Analysis of Complex Living Entities)[1] framework to study the impact of extracellular acetic acid on the S. cerevisiae metabolism with the aim to improve ethanol production in the presence of this inhibitor found in significant concentrations in lignocellulosic hydrolysates. First, we derived a consistently reduced core model (279 metabolites and 382 reactions) of S. cerevisiae from the iMM904 genome scale reconstruction. We integrated thermodynamic and experimentally measured information about the metabolite concentrations and reaction fluxes, to identify thermodynamically feasible operational configurations of the network under different experimental conditions using the novel Flux Directionality Profile Analysis (FDPA) technique[2,3]. We then computed a population of stoichiometrically, thermodynamically, kinetically and physiologically consistent log-linear kinetics models. These models were used to (i) explore the flexibility and robustness of the operational states; (ii) identify the differences of the flux profiles for different doses of acetate during ethanol production; and (iii) derive optimal strategies for improvement of the ethanol production under these physiological conditions

Human T-cell lymphotropic virus type I-transformed T-cells have a partial defect in ceramide synthesis in response to N-(4-hydroxyphenyl)retinamide

Treatment with the synthetic retinoid HPR [N-(4-hydroxyphenyl)-retinamide] causes growth arrest and apoptosis in HTLV-I (human T-cell lymphotropic virus type-I)-positive and HTLV-I-negative malignant T-cells [8]. It was observed that HPR-mediated growth inhibition was associated with ceramide accumulation only in HTLV-I-negative cells. The aim of the present study was to investigate the mechanism by which HPR differentially regulates ceramide metabolism in HTLV-I-negative and HTLV-I-positive malignant T-cells. Clinically achievable concentrations of HPR caused early dose-dependent increases in ceramide levels only in HTLV-I-negative cells and preceded HPR-induced growth suppression. HPR induced de novo synthesis of ceramide in HTLV-I-negative, but not in HTLV-I-positive, cells. Blocking ceramide glucosylation in HTLV-I-positive cells, which leads to accumulation of endogenous ceramide, rendered these cells more sensitive to HPR. Exogenous cell-permeant ceramides that function partially by generating endogenous ceramide induced growth suppression in all tested malignant lymphocytes, were consistently found to be less effective in HTLV-I-positive cells confirming their defect in de novo ceramide synthesis. Owing to its multipotent activities, the HTLV-I-encoded Tax protein was suspected to inhibit ceramide synthesis. Tax-transfected Molt-4 and HELA cells were less sensitive to HPR and C(6)-ceramide mediated growth inhibition respectively and produced lower levels of endogenous ceramide. Together, these results indicate that HTLV-I-positive cells are defective in de novo synthesis of ceramide and that therapeutic modalities that bypass this defect are more likely to be successful