Understanding glucose uptake rate

[soma ghosh]

Dear all,

I am a beginner in COBRA and trying to understand the parameters in the model. I am not able to understand the relation between glucose uptake rate ( eg: 8mmol gDW-1 hr-1) and glucose concentration in an experimental media. Could some one please explain me how to convert the uptake rates of glucose defined in the model to concentration values of glucose given in the experimental media. For eg: If i keep 8mmolgDW-1hr-1 as the uptake rate then what should be the corresponding glucose concentration in the media.

Thanks
Soma

[Nathan Lewis]

There really isn't a relationship between concentration and uptake rate that one could compute. As long as there is some glucose in the media, the uptake rate will depend on numerous factors (e.g., amount of time the cells have been growing in that medium, temperature, aeration, strain, other substances in the media, how the glassware was washed, the phase of the moon, etc., etc., etc.). When all variables are controlled, there is a correlation between uptake rate and concentration, but this is more qualitative (i.e., if you suddenly dump in a lot of glucose, the cells may show an increase in uptake rate)

[Payam Setoodeh]

Dear Soma,

A number of researchers have tried to use correlations to relate key
components uptake rates to their concentration in the medium and
consequently simulate the dynamic behaviour of the microorganism
during batch or fed-batch fermentations using genome-scale metabolic
reconstructions. For this aim, some dynamic flux balance modeling
frameworks (combination of steady-state intracellular model of carbon
metabolism with key-components mass-balance-corresponding ODEs via
Michaelis-Menten uptake kinetics) have been developed. For more
information might take a look at the following articles:

Hjersted, J.L., Henson M.A., 2006. Optimization of fed-batch
Saccharomyces cerevisiae fermentation using dynamic flux balance
models. Biotechnol. Progr. 22, 1239–1248.
Hjersted, J.L., Henson, M.A., 2009. Steady-state and dynamic flux
balance analysis of ethanol production by Saccharomyces cerevisiae.
IET Syst. Biol. 3,167-179.
Hjersted, J.L., Henson, M.A., Mahadevan, R., 2007. Genome-scale
analysis of Saccharomyces cerevisiae metabolism and ethanol production
in fed-batch culture. Biotech. Bioeng. 97, 1190-1204.

Eslamloueyan, R., Setoodeh, P., 2011. Optimization of fed-batch
recombinant yeast fermentation for ethanol production using a reduced
dynamic flux balance model based on artificial neural networks. Chem.
Eng. Comm. 198, 1309–1338.

and

Vargas, F.A., Pizarro, F., Pérez-Correa, J.R., Agosin, E., 2011.
Expanding a dynamic flux balance model of yeast fermentation to
genome-scale. BMC Syst. Biol. 5, 75.

[soma ghosh]

Dear Nathan and Payam,

Thank you for the quick response. I would read the papers you suggested. I want to calculate the experimental growth rate of ecoli at different carbon concentrations and calculate the same using the model at different glucose uptake rate.

Is there some way of mapping the model and experiment on the basis of concentration of carbon source in the experimental media.

Thanks,
Soma

[Payam Setoodeh]

Dear Soma,

It is somehow difficult and not quantitatively accurate. But, you
might use Michaelis-Menten kinetics to correlate carbon-source uptakes
to its concentrations in the medium. Afterwards, you might change the
lower bond value for carbon source uptake (set the lower bond to the
correlated values step-wisely) and determine the corresponding
specific growth rates. Through this way you might do mapping.
Please do not forget that high carbon source concentrations
practically may contribute to inhibition effects on cell growth while
this fact is not considered in steady-state FBA. You might handle the
problem by consideration of the inhibition constants (the optimal
values should be determined) in Michaelis-Menten kinetics.

Good Luck

Payam