Question about best practices for uptake constraint estimation

[YN F]

Hello everyone, 

I am working with the B. subtilis 168 model from BiGG, and have a question on how exactly to estimate uptake constraints on a relativley uncharacterized medium. 

I am trying to represent 168's metabolism being grown on Belitzky minimal medium, and wanted to ask what the best practices are in setting an uptake constraint in the absence of experimental data. I do have gene expression data, including the glucose transporter, however I am not sure how to convert this into a constraint. Is it considered "ok" to estimate the uptake rate from other studies where another medium is being used? 

Any input would be much appreciated. 

Best regards.

[Bruno Batista]

Hello,

To estimate the uptake rate (qs) in mmol/gDWC*h, I usually use kinetic graphs from literature, as well as experimental biomass and sugar consumption data over time. The uptake rate can be approximated using the following formula:

qs = d(sugar) / [ d(Biomass) * d(time)]

Where:

d(sugar) is the variation in sugar concentration (e.g., in mmol),

d(Biomass) is the variation in biomass (e.g., in gDWC),

d(time) is the time interval over which the changes occur (e.g., in hours).

I dont know if this approach is consensus, but it provides a reasonable approximation for the specific substrate uptake rate based on measured data.