Help for no biomass growth

[na lv]

Dear everyone,

I am having trouble with getting biomass growth with seed draft model by cobra toolbox(matlab).

How can I check all the biomass precursors in the biomass reaction that can be really produced?

Should I just check whether there is a reaction that could produce every  biomass precursor? I have checked  in my reaction list that there indeed have reactions (or transport reactions) that could produce every biomass precursor.

But at last my biomass growth is zero.

Or must I visualize the model to see whether there are feasible pathways that produce the every biomass precursor? But until now I don’t know how to visualize the pathway.

Hope someone could help me. Thanks!

Na Lv
The Ohio State University
Chemical and Biomolecular Engineering

[Vijesh Bhute]

Hi everyone,

 

Even I am getting a similar problem while solving FBA for the Recon_1 and several other tissue specific models. I found out that there were several metabolites which are not being consumed at all in the biomass reaction although the biomassPrecursorcheck does not show any metabolite. Mainly, glycogen and lpchol-hs are the ones that when included in the biomass reaction make the FBAsolution.f = 0. I am not sure how to get around this and I am still looking for a bug or some conceptual error that I am making. I have checked all the reactions in which glycogen is used and found they do carry flux but when I have my biomass reaction as "glygn1[c] -->" the FBA solution becomes 0. I would highly appreciate if someone could guide me.

 

Thank you.

 

Regards,

Vijesh Bhute

Department of Chemical & Biological Engineering

University of Wisconsin-Madison

[Samara Silva de Souza]

Hello everyone,

I'm having the same problems with my biomass reaction.

I read this protocol, Thiele, I. and Palsson, B. O.*,"A protocol for generating a high-quality genome-scale metabolic reconstruction."

And there is one command: Step 60 -> PrintBiomass, but I didn't find. This command will be used to test if biomass precursors can be produced in standard medium.

Someone asked the same question and the answer was to use printRxnFormula, but this command just print the reactions in the command window. Someone knows how to do???

Another question, I check a lot of reconstructions metabolics, and sometimes the biomass reaction has the metabolite biomass, like this:

0.205 G6P + 0.052 F6P + 0.87 R5P + 0.233 E4P ....... ---> ..... ADP + 41.3 PI +.....NADH + 41.3 H +.... + BIOMASS

Is it right??? I'm using the core of E.coli to start my model, and I checked the biomass reaction and doesn't have it.

Another question, how I optimize the production of each one of the components of the biomass reaction individually???

Thanks for your help

Samara Silva de Souza

Chemical Engineer

Federal University of Santa Catarina-BRAZIL

Integrated Technologies Laboratory - InteLAB

Bioinformatics and Systems Biology

Skype: samara.souza88