BE.109:Systems engineering

Module 3

Instructors: Drew Endy and Natalie Kuldell

TA: Reshma Shetty

Nucleotides have been called the building blocks of life, but as you’ve seen it’s not trivial to build something with them. Recall you spent nearly three weeks truncating the gene for GFP, and your efforts to rationally modify an enzyme yielded a complex mixture of proteins and results. If one reasonable definition of a biological engineer is someone who builds things from biological materials, then let’s get building. We’ll start with an existing and clever design that uses bacteria as the pixels in a photograph. The bacterial cells have been engineered to respond to light, churning out a familiar enzyme (beta-gal) to turn the media black in the dark. You’ll be using this system to take black and white pictures, identifying experimental changes that can affect the operation of system. You will also invert the logic in the existing design and add a red-fluorescent protein in the readout to generate two-color pictures. Finally you’ll use quantitative PCR to characterize the simple or complex circuit, cataloging your findings at the Registry of Standard Biological Parts for future biological engineers to “build” on.

Bacterial self-portrait.
Photo credit: Marsha Miller, University of Texas at Austin

Lab handouts

Day 1: Tools for systems engineering

Day 2: Basic bacterial photography: black and white

Day 3: Advanced bacterial photography: 2 color

Day 4: Device characterization

Day 5: Measuring DNA, RNA, protein

Day 6: RT-PCR data analysis

References

Note: PDF reprints are provided below within the context of fair use. Please obtain copies from the publisher if appropriate.

1. Foundations for engineering biology
   Nature 24 November 2005 DOI:10.1038/nature04342
   Drew Endy
   URL PDF reprint
2. Adventures in synthetic biology (comic)
   Nature 24 November 2005 Cover & Online
   Drew Endy, Isadora Deese and Chuck Wadey
   Reprint & background
   
3. Engineering Escherichia coli to see light
   Nature 24 November 2005 DOI:10.1038/nature04405
   A. Levskaya et al.
   URL
4. The engineer's approach to biology
   H. Breithaupt
   EMBO Reports Jan 2006 DOI:10.1038/sj.embor.7400607
   URL