Load the Model Ecoli Core Model.Mat from the Directory Cobra/Testing/Testgrowthexpmatch

Browsing the model

Load the model ecoli_core_model.mat from the directory cobra/testing/testGrowthExpMatch .

You can now browse the value of the variable model to see what is stored there.

1. What are the internal names (i.e. abbreviations) for cytosolic acetate and external acetate? What are their position numbers in the vector of metabolites?

1. What is the internal name for the acetate exchange reaction, and what is its position in the vector of reactions?

Browsing the FBA solution

Make sure you’ve completed Supplementary Example 1 from the tutorial before attempting these questions.

1. What command would you use to model a situation in which a cell was unable to export ethanol (abbreviated “etoh”)?

1. What is the predicted maximum growth rate for a cell growing on glucose in the absence of oxygen when it is unable to export ethanol?

1. The predicted fluxes for many of the exchange reactions change when the cell is unable to export ethanol. What are the two exported products whose fluxes increase the most when ethanol can’t be exported? Comment on why these might or might not make sense.

Growth on various carbon sources

1. What are the aerobic growth rates on succinate (lower bound -20), ac (lower bound -20), and both? Is the predicted growth rate on succinate plus acetate the same as the sum of the predicted growth rate on succinate and the predicted growth rate on acetate? If not, what is the difference and to what do you attribute it?

Calculating input-output ratios

Carbon consumed as, e.g., glucose, can have one of three basic fates: Incorporation into biomass, excretion as C02, or excretion as small metabolites, primarily ethanol. The ratios of these three fates can be determined from several different combinations of measurements. For example, if you know the amount incorporated as biomass, the amount of glucose consumed, and the amount of CO2 produced, you can calculate the oxygen consumed.

1. Reload the e. coli core model to reset all the parameters. Suppose you grow an e. coli culture with ample dissolved oxygen and measure that it is consuming glucose at a rate of 18.5mmol gDW-1 hr-1. What is the maximum amount of ethanol it can produce? How much CO2 is produced when ethanol production is maximized? What is the maximum rate of CO2, when that is the objective function? How much ethanol is produced when CO2 is maximized?

1. Now do the same for aneorobic conditions (no oxygen import). What are the max ethanol and CO2 production rates?

1. Now suppose you’ve grown a culture in ample oxygen and measured the glucose consumption rate as 18.5 mmol gDW-1 hr-1 and the CO2 production rate as 10. Write a “soluble carbon excretion” reaction that considers the number of carbon molecules excreted in soluble metabolites in all the exchange reactions. Rather than treating these all as exchange reactions on the boundary of the model, take the external molecules of the excreted carbon and treat them as inputs to a single carbon sink.