Doctoral Thesis: Design of a robust ratiometric sensor and a long-term memory genetic toggle switch

Ukjin Kwon

Abstract:
We design two biological sensors – a robust ratiometric sensor and a long-term memory genetic toggle switch by using mathematical analyses. A ratiometric response gives an output that is proportional to the ratio between the magnitudes of two inputs. Ratio computation has been observed in nature and is also needed in the development of smart probiotics and organoids. We achieve ratiometric gene expression response in bacteria E. coli with the incoherent merger network. In this network, one input molecule activates expression of the output protein while the other molecule activates an intermediate protein that enhances the output’s degradation. When degradation rate is first order and faster than dilution, the output responds linearly to the ratio between the input molecules’ levels over a wide range with R^2 close to 1. Response sensitivity can be quantitatively tuned by varying the output’s translation rate. Furthermore, ratiometric responses are robust to global perturbations in cellular components that influence gene expression because such perturbations affect the output through an incoherent feedforward loop. A genetic toggle switch requires to maintain either of its states for a sufficiently long time. We propose a bacterial toggle switch design that is inspired by a chromatin modification circuit ubiquitous in mammalian systems. We specifically propose a bacterial implementation based on two DNA invertases, in which each invertase is auto-catalyzing its own expression while also catalyzing the other invertase’s repression. We perform a mathematical analysis of the time to memory loss of the circuit’s stable states in a simplified stochastic model of the system. The analysis shows that we can increase the time to memory loss by increasing the expression rates of the invertases, allowing to design the circuit for long-term memory. We validate the theoretical findings by stochastic simulations of the full set of reactions describing the circuits. We believe these biological sensors can be widely used from environmental sensing to therapeutics.

Details

• Date: Tuesday, January 10
• Time: 12:30 pm - 2:00 pm
• Category: Thesis Defense

Additional Location Details:

Thesis Supervisor: Prof. Domitilla Del Vecchio

Thesis Committee members – Profs. Bruce Tidor, Collin Stultz

 

This defense will be virtual.  Please contact the doctoral candidate for details, ujkwon@mit.edu