Select dual carbon source for Azo-Rhodo consortia

[djinnome]

Rather than forcing Azo to eat what Rhodo is willing to part with, or vice versa, we can select two carbon sources, one of which only Rhodo can eat, and possibly one that only Azo can eat.

I say possibly, because when Rhodo grows, it produces Bisabolene, which may very well kill Azoto, so as long as Azoto can outcompete Rhodo for carbon source 2 early on, then the carbon will be available to Rhodo after Azoto dies.

[djinnome]

This also has the benefit that during growth phase, Rhodo needs a nitrogen source, but during production phase, it is fine to produce bisabolene in a nitrogen starved state. Thus, by killing off azoto when a high enough Bisabolene titer has been reached, we automatically switch to nitrogen starved mode without any genetic modifications.

[JamesPino]

How can we model a "no growth/poison" signal in the models? Also, do we have the bisabolene reaction added to Rhodo?

[JamesPino]

EX_lyx__L_e
EX_hom__L_e
EX_glu__L_e
EX_tre_e
EX_arab__L_e
EX_leu__L_e
EX_man_e
EX_4abut_e
EX_galt_e
EX_dha_e

as carbon sources for RT all result in EX_glyclt_e, which AZ can use.

[JamesPino]

@djinnome
Carbon sources for RT are above

Notebook is https://github.com/PNNL-CompBio/ConsortiumModels/blob/ternary_growth_on_gly/Notebooks/rt_av_find_biolog_compatible_growth.ipynb

[djinnome]

@PBohutskyi Can you please check whether the binary culture grows in any of these carbon sources:

Carbon source to Rhodo	Rhodo byproduct to Azo
L-Homoserine	Glycolate
L-Lyxose	Glycolate
L-Glutamate	Glycolate
L-Leucine	Glycolate
Dihydroxyacetone	Glycolate
D-Mannose	Glycolate
Galactitol	Glycolate
4-Aminobutanoate	Glycolate
Trehalose	Glycolate
L-Arabinose	Glycolate