PFA toolbox: a MATLAB tool for Metabolic Flux Analysis.

Background: Metabolic Flux Analysis (MFA) is a methodology that has been successfully applied to estimate metabolic fluxes in living cells. However, traditional frameworks based on this approach have some limitations, particularly when measurements are scarce and imprecise. This is very common in industrial environments.

Validation of an FBA model for Pichia pastoris in chemostat cultures.

Background: Constraint-based metabolic models and flux balance analysis (FBA) have been extensively used in the last years to investigate the behavior of cells and also as basis for different industrial applications. In this context, this work provides a validation of a small-sized FBA model of the yeast Pichia pastoris. Our main objective is testing how accurate is the hypothesis of maximum growth to predict the behavior of P.

Validation of a constraint-based model of Pichia pastoris metabolism under data scarcity.

Background: Constraint-based models enable structured cellular representations in which intracellular kinetics are circumvented. These models, combined with experimental data, are useful analytical tools to estimate the state exhibited (the phenotype) by the cells at given pseudo-steady conditions.

Results: In this contribution, a simplified constraint-based stoichiometric model of the metabolism of the yeast Pichia pastoris, a workhorse for heterologous protein expression, is validated against several experimental available datasets.

Which metabolic pathways generate and characterize the flux space? A comparison among elementary modes, extreme pathways and minimal generators.

Important efforts are being done to systematically identify the relevant pathways in a metabolic network. Unsurprisingly, there is not a unique set of network-based pathways to be tagged as relevant, and at least four related concepts have been proposed: extreme currents, elementary modes, extreme pathways, and minimal generators. Basically, there are two properties that these sets of pathways can hold: they can generate the flux space--if every feasible flux distribution can be represented as a nonnegative combination of flux through them--or they can comprise all the nondecomposable pathways in the network.

A possibilistic framework for constraint-based metabolic flux analysis.

Background: Constraint-based models allow the calculation of the metabolic flux states that can be exhibited by cells, standing out as a powerful analytical tool, but they do not determine which of these are likely to be existing under given circumstances. Typical methods to perform these predictions are (a) flux balance analysis, which is based on the assumption that cell behaviour is optimal, and (b) metabolic flux analysis, which combines the model with experimental measurements.

Results: Herein we discuss a possibilistic framework to perform metabolic flux estimations using a constraint-based model and a set of measurements.