FBA shows mainly uptake and secretion of demand/sink reactions after applying medium constraints

[Nicole van der Zanden]

Hello everyone, 

I'm currently trying to model cell cultures using Recon3D and DMEM high-glucose medium. To do this, I converted the concentrations of medium compounds to fluxes using the approach described in Chapter 10 of the COBRApy documentation:

"For instance, by assuming that 1 gDW of your organism cannot consume the entire concentration of a metabolite in 24 hours, you can estimate the upper exchange flux as concentration / (1 gDW * 24h). This results in relatively low flux boundaries."

Moreover, all other exchange reactions were set to 0, except for water, oxygen, carbon dioxide, hydrogen, and bicarbonate. When running FBA using the standard biomass objective, I noticed that the model primarily uses sink reactions for various compounds, whereas I expected it to rely mainly on glucose from a biological perspective. Consequently, I decided to set all sink/demand reactions to 0. However, this resulted in no growth.

Does anyone have tips for what to do in this situation?

  

Thanks in advance!