20.109(F11):Module 2

Module 2
Instructors: Natalie Kuldell, Agi Stachowiak TA:

Getting systems that work right out of the box is something that we’ve come to expect from electrical and mechanical engineers. New car? Get some gas, turn the key and off you go! New digital camera? Charge the battery and then start taking pictures! Biological engineers—though notable in their achievements---have lagged behind in the design and construction of novel systems that work in reliable, scalable, intuitive ways. Biology simply does not always perform as intended. Moreover, tools for the design and testing stages of engineered living systems are not yet robust or standard. In this experimental module we’ll learn to design and tune a biological system—namely the bacterial photography system in which bacteria serve as pixels in a picture. The picture, though remarkable, is slow to develop, limited to two colors, and low in contrast. To improve the system, we’ll combine some powerful tools from biological science, namely genetics and evolution, with some of the fledgling tools in synthetic biology such as abstraction and standardization of biological parts, to improve and extend the performance of the bacterial photography system. In the process we may also learn something new about the natural systems upon which the engineered one is built. 

Lablinks: day by day
Day 1: Testing an engineered biological system Day 2: Measuring system performance Day 3: Tools for system engineering Day 4: Journal Club I Day 5: Assessing re-tuned system Day 6: Readout DNA Day 7: Readout Protein Day 8: Journal Club II

System engineering research article guidelines

Useful sequence files
[[Media:PCph8 DNA sequence from Jeff Tabor.docx| pCph8 plasmid sequence]] [[Media:Cph1-EnvZ DNAseq.docx| Cph8 ORF: DNA sequence]] [[Media:Cph8 Translated.txt| Cph8 ORF: translated]] [[Media:BuildingK+Library.xls| K+ mutant library]]

Notes for Teaching Faculty
TA notes, mod 2