Team:ETH Zurich/Modeling

"What I cannot create I do not understand."
- Richard Feynmann

Modeling

Overview

Our system consists of a signalling chain, with a lactate sensor triggering the amplification of AHL production which is sensed my neighboring cells. When AHL becomes sufficiently concentrated, it triggers the production of a fluorescent signal. Our model was divided into the modules pictured below.

Figure 1. The genetic design of the MicroBeacon system.

These were modeled and tested independently before being merged into a single model of the whole system. Each module was first evaluated and characterized at the single cell level in MATLAB in order to evaluate their initial states, steady states, and to study their dynamics. Then, each module was implemented in COMSOL Multiphysics to characterize their spatial and temporal behavior, and to implement additional biological properties of our system.

The final result is a model providing a reasonable approximation of the behavior of our system under our test conditions. In addition, our characterization of the lactate module is a significant contribution to the understanding of this system.

Goals

  • Studying the fold-change sensor.
  • Check different approaches for the control of the quorum sensing module.
  • Determine conditions in which our system works as an AND-gate
  • Implementing a reaction-diffusion model to feature biological properties of our system
  • Characterization of the biological part, to be included in the simulations

    • Lactate module

    AHL module

    Combined model

    GFP concentration over time in four cases: A) Cancer cell, bound E. coli B)Cancer cell, unbound E. coli C) Normal cell, bound E. coli D) Normal cell, unbound E. coli

    Conclusions

    We characterized our system by simulating its modules separately and together through a series of increasingly-complex models. We show that under certain parameters, our lactate module is able to produce LuxR such that the lactate production input signal is amplified. Simulation of the AHL module with a simplified compartment model and with a more accurate reaction-diffusion model show that degradation of AHL by the E. coli does not significantly delay the self-activation of our LuxI and AHL production feedback loop. Instead, riboregulation of the LuxR promoter to prevent leaky expression of LuxI is sufficient to prevent this self-activation within the timescale of our experiment. This demonstrates the viability of our system as a specific CTC detection system utilizing these two general cancer markers.

    We would like to thank our sponsors