SURF 2018: Resource Usage in TX-TL

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2018 SURF: project description

  • Mentor: Richard M. Murray
  • Co-mentor: William Poole


The goal of this project is to quantify how resources (NTPs, and Amino acids) are depleted during transcription and translation in cell free extract. First some background; we work with cell free extracts which is a purified lysate made from E. coli which we refer to as TX-TL. These extracts are very useful for prototyping and characterizing synthetic biological circuits. When genes are added to this extract they are transcribed to mRNA which are translated into proteins, giving rise to life-like biocircuit functionality. However, TX-TL has a limited lifetime determined in part by the depletion of energetic molecules (namely nucleic acids, amino acids, and ATP) and build up of waste products. The goal of this project is to mathematically model and experimentally characterize resource utilization in TX-TL. Specifically, we would like to build an experimental system to connect a TX-TL reaction to a reservoir of energetic molecules. By varying the size of this reservoir, the depletion rate of fuel molecules will be experimentally controllable allowing for different models of this process to be experimentally tested.


Background / Skills:

Potential SURFs should have taken courses in basic chemistry and biology, including at least one class with a laboratory component. Additionally the ability to simulate ordinary differential equations or models in Python/MATLAB will be necessary. Finally, a large component of this project will be hands-on work to design and construct the reservoir system, so experience building things will be helpful.


Relevant References:

The All E. coli TX-TL Toolbox 2.0: A Platform for Cell-Free Synthetic Biology: https://www.ncbi.nlm.nih.gov/pubmed/26818434

Linear DNA for Rapid Prototyping of Synthetic Biological Circuits in an Escherichia coli Based TX-TL Cell-Free System: http://pubs.acs.org/doi/abs/10.1021/sb400131a

Gene Circuit Performance Characterization and Resource Usage in a Cell-Free “Breadboard”: http://pubs.acs.org/doi/10.1021/sb400203p

Effect of the ATP level on the overall protein biosynthesis rate in a wheat germ cell-free system: https://www.ncbi.nlm.nih.gov/pubmed/8620031