This tool version is unpublished and cannot be run. If you would like to have this version staged, you can put a request through HUB Support.
Certain strains of bacteria produce an antimicrobial peptide known as nisin. The production of nisin is regulated by a set of genes, as shown in supporting documents, which involves a positive feedback loop. Thus, active nisin serves to activate its own production. When nisin concentrations reach a certain threshold, it induces cell death, thereby regulating the density of the bacterial population. By introducing a fluorescent protein which is under the control of a nisin-inducible promoter, we can visualize nisin concentrations in a bacterial population. High levels of nisin will induce cell death, medium levels will induce fluorescence, and low levels will yield negligible changes.
To visualize this phenomenon, we have constructed a tool on nanohub to simulate nisin diffusion and interaction with a bacterial population. The user selects from a list of predefined initial distributions of nisin in the chemical mask above the agar layer. The nisin then diffuses across the agar layer to the cell layer according to a three dimensional diffusion equation with degradation.