CGXII simulation shows additional metabolites necessary for growth

[famosab]

In issue #5 of C_striatum_GEMs I discussed that some metabolites are present in the medium but cannot be consumed by the model. The models on the other hand say that cobalt2, nmn, ala_B, pnto__R and cgly are missing to enable growth on the CGXII medium. Since CGXII is chemically defined, adding and removing metabolites should be rather straight forward. We only need to research concentrations used in other media.

Open:

• [x] 16: log-phase transfer with higher-conc of additives (?)
• [x] 16: log-phase transfer with Tween80

Later:

• [x] test growth rates in plate reader with additives

Done:

• [x] all strains: simple transfer with higher starting ODs
• [x] check for appropriate concentrations for the addition of the metabolites mentioned above
• [x] test growth on CGXII with strain specific additions according to the model predictions
• [x] test growth in the lab on CGXII without ni2, 34dhbz and btn but with the other metabolites shown to be needed by simulation (cobalt2, cgly and pnto__R)
• [x] research L-Arginine and N-Acetyl-D-glucosamine concentrations
• [x] strain 15, 16: test binary growth with L-Arginine and N-Acetyl-D-glucosamine
• [x] manual growth curve in TSB to check when the log-phase is

[famosab]

All of the growth tests will be done in flasks to ensure proper oxygenation. All tests will be started roughly at OD 0.1 using the log-phase transfer method.

[famosab]

I am measuring a manual growth curve of all strains in TSB today (grown in flasks) to make sure that the time point I picked for the log-phase transfer is correct.

I will also measure the final OD twice: once after around 20h and once after around 40h.

[famosab]

Finished laboratory experiments, closing this.