Constraint-based metabolic control analysis for rational strain engineering.

The advancements in genome editing techniques over the past years have rekindled interest in rational metabolic engineering strategies. While Metabolic Control Analysis (MCA) is a well-established method for quantifying the effects of metabolic engineering interventions on flows in metabolic networks and metabolite concentrations, it does not consider the physiological limitations of the cellular environment and metabolic engineering design constraints. We report here a constraint-based framework, Network Response Analysis (NRA), for rational genetic strain design. NRA is cast as a Mixed-Integer Linear Programming problem that integrates MCA, Thermodynamically-based Flux Analysis (TFA), biologically relevant constraints, as well as genome editing restrictions into a comprehensive platform for identifying metabolic engineering targets. We show that the NRA formulation and its core constraints are equivalent to the ones of Flux Balance Analysis (FBA) and TFA, which allows it to be used for a wide range of optimization criteria and with various physiological constraints. We also show how the parametrization and introduction of biological constraints enhance the NRA formulation compared to the classical MCA approach, and we demonstrate its features and its ability to generate multiple alternative optimal strategies given several user-defined boundaries and objectives. In summary, NRA is a sophisticated alternative to classical MCA for rational metabolic engineering that accommodates the incorporation of physiological data at metabolic flux, metabolite concentration, and enzyme expression levels.

Hemodynamics in stenotic vessels of small diameter under steady state conditions: Effect of viscoelasticity and migration of red blood cells.

BACKGROUND: In microcirculation, the non-Newtonian behavior of blood and the complexity of the microvessel network are responsible for the high flow resistance and the large reduction of the blood pressure. Red blood cell aggregation along with inward radial migration are two significant mechanisms determining the former. Yet, their impact on hemodynamics in non-straight vessels is not well understood. OBJECTIVE: In this study, the steady state blood flow in stenotic rigid vessels is examined, employing a sophisticated non-homogeneous constitutive law. The effect of red blood cells migration on the hydrodynamics is quantified and the constitutive model's accuracy is evaluated. METHODS: A numerical algorithm based on the two-dimensional mixed finite element method and the EVSS/SUPG technique for a stable discretization of the mass and momentum conservation equations in addition to the constitutive model is employed. RESULTS: The numerical simulations show that a cell-depleted layer develops along the vessel wall with an almost constant thickness for slow flow conditions. This causes the reduction of the drag force and the increase of the pressure gradient as the constriction ratio decreases. CONCLUSIONS: Viscoelastic effects in blood flow were found to be responsible for steeper decreases of tube and discharge hematocrits as decreasing function of constriction ratio.