Extended metabolic biosensor design for dynamic pathway regulation of cell factories. Boada et al.

Published: 28-06-2020| Version 2 | DOI: 10.17632/hpxhkyvctb.2
Contributors:
Yadira Boada,
Alejandro Vignoni,
Jesús Picó,
Pablo Carbonell

Description

This dataset comprises all the data resulting from the model of our dynamic pathway regulation strategy for cell factories: The Extended metabolic TF-based biosensor antithetic controller (EMBA). Analysis of this dataset was performed and published in the article “Extended metabolic biosensor design for dynamic pathway regulation of cell factories” Yadira Boadaa, Alejandro Vignoni, Jesús Picó, Pablo Carbonell, 2020, iScience. DOI: https://doi.org/10.1016/j.isci.2020.101305 Different data in the dataset was obtained by changing some of the simulation parameters. Perturbation Data includes: -Time-courses of Naringenin and CHS for the open-loop and the closed-loop for varying available amounts of Malonyl-CoA (in number of molecules per cell) -Static (equilibrium) production level of Naringenin for the open-loop and the closed-loop for varying available amounts of Malonyl-CoA (in g/L). Robustness Data includes: -Static (equilibrium) production level of Naringenin (in g/L). for the direct controller and the antithetic controller for varying available amounts of Malonyl-CoA (100% and 60% of available malonyl-CoA) for each one of the parameter combinations. -Static levels of Naringenin vs CHS, Naringenin Vs Kaempferol vs anti-sigma and Anti-sigma vs CHS; for 15% CV random values of the pathway enzymes to obtain the plots of the different Transfer Function (dose-response curve) circuit parts (metabolic part of the biosensor, TF-based biosensor and controller, and overall sensor-controller transfer function).

Files

Steps to reproduce

All this data can be reproduced with the model coded in https://github.com/sb2cl/EMBA