Interesting question when you are more a biologist than a mathematician (too many complicated equations!!!) And as most of your team members were biologists/biochemists, we tried to explain the model easily for everyone.

Definitions:

A model is a symbolic representation of an object’s or phenomenon’s aspects in the real world.

“All models are false. Some are useful.” Georges Box

Modeling is the process that allows the development of a model. It’s taking into account:

• The phenomenon to represent
• A specific formal system (equation, diagram..)
• Objectives (what we want to do with the model)
• Data (for variables) and knowledge (relation between variables) available or accessible by experimentation or observation

The tasks to obtain the model depend on the biological situation and the formal system chosen. Nevertheless, it must:

• have a formalization work, which is the model writing
• Manipulate the model in the formal system to make it "usable" and to study its properties
• Objectives (what we want to do with the model)
• Establish relationships with other representations (computer program, graph function)
• Interpret and compare different representations obtained in the formal world with the biological reality (often that reality is seen through experimental data)

Situation

After the destruction of the biofilm by “Biofilm Killer” bacteria, we want to have the choice to create either a surfactant to prevent the recolonization of the surface, or a protector biofilm. The switch is done by environmental condition: two inducers can be added to select one behaviour or another.

Biological system to model:

For this, we have created the following construction, with a double regulation:


figure 1: the construction of the biological model, The elements of this model are: 2 promoters (Pxyl and Plac), 2 repressors (LacI and XylR proteins) and 2 inducers (IPTG and Xylose), and also sfp and abrB genes for Sfp and AbrB proteins.

This system is a gene-regulatory network, where two different states are possible:

• formation of a naturally toxic bio-surfactant through sfp gene, which has antimicrobial properties that prevents the recolonization of the surface. The surfactant used is surfactine, which is regulated by sfp gene.
• creation of a protector biofilm by the inhibition of the main biofilm repressor abrB gene.

Figure 2: The two possible states: surfactant formation for the green construction or biofilm formation for the red construction

encore blablabla

BEn on en a pas !