Model overview

Introduction:

In the overall project, we, the modeling team, acted as a sort of "guide". Because getting significant biological result is always slower through experiments than through computer simulations, we were the first to get clues about the project's success.
In the begining, the team's goal was to chelate iron in the duodenum, using bacteria that would flush through the duodenum. We made a qualitative model showing promising conclusions, but when we ran a metabolic model, we realised that the siderophore production is a very slow phenomenon. It is thus impossible to chelate the iron using a flush-strategy.
Then came the idea of a gel containing our bacteria, that would stick to the very begining of the Jejunum's wall. Among all the safety issues this strategy creates, the most important question that raised at this point was : "can our bacteria produce siderophores like crazy and still survive long enough to chelate a significant quantity of iron?". A Flux Balance Analysis helped solving this question.

Introduction:

The modeling part heavily influenced the early stages of the project. In fact, before any biological result our simulations, gave the preliminar hints to the team in the strategy to adopt for the iron-sensing inverter and the strategy to opt in the design of the capsule.
In the begining, the team's goal was to chelate iron in the duodenum, using bacteria that would flush through the duodenum. We made a qualitative model showing promising conclusions, but when we ran a metabolic model, we realised that the siderophore production is a very slow phenomenon. It is thus impossible to chelate the iron using a flush-strategy.
Then came the idea of a gel containing our bacteria, that would stick to the very begining of the Jejunum's wall. Among all the safety issues this strategy creates, the most important question that raised at this point was : "can our bacteria produce siderophores like crazy and still survive long enough to chelate a significant quantity of iron?". A Flux Balance Analysis helped solving this question.

Modeling Parts:

(schémas avec des liens vers les parties modeling)
duodénum                      zoom sur les parois                      bactérie                      FBA