User:Jason R. Kelly

Bio

Jason Kelly

Endy:Lab Fire Marshall

2nd Year Biological Engineering Graduate Student @ MIT

S.B. in Biology and Chemical Engineering @ MIT, 2003

Thesis Project

To date, engineered biological systems have been constructed via a variety of ad hoc approaches. The resulting systems should be thought of as pieces of art. Here, I propose to explore how existing forward engineering approaches might be combined with evolution to make routine the construction of engineered biological systems. I will specify a procedure for construction of biological systems via screening of subcomponent libraries and rational re-assembly. I will develop tools to enable this approach including a high-throughput screening system to measure the input/output function of an arbitrary genetic device. I will apply this approach to construct a collection of ring oscillators and bi-stable switches. Furthermore, I anticipate that performance of these devices will decay over time due to spontaneous errors in replication of the genetic information encoding the systems. As an engineer, I would like to be able to design systems with behavior that is predictable in the face of mutation and selection. I will explore mechanisms for increasing or decreasing the susceptibility of engineered biological systems to loss of function as a result of mutation.

Specific Aims

1. PoPS Device Screening Plasmid
2. Library-based Construction
3. Evolutionary Stability
   • Genetic Stability
   • Performance Stability

Thesis Proposal PDF

Experimental Plan

Library-based Construction Lab Notebook

OWW Pages in Progess

BioBricks construction tutorial - a step-by-step tutorial for a single Biobrick assembly.

Microfluidics - a page describing the endy lab microfluidics setup and linking to relevant protocols, etc.

Papers of Interest

Evolutionary Stability

Inhibition of Mutation and Combating of the Evolution of Antibiotic Resistance (Cirz et al)

Strains

Library Construction Strain Box 1

Synchronized Oscillator Strain Box 1