BE.109:Systems engineering: Difference between revisions
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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 [http://parts.mit.edu Registry of Standard Biological Parts] for future biological engineers to “build” on. | 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 [http://parts.mit.edu Registry of Standard Biological Parts] for future biological engineers to “build” on. | ||
[[Image:Macintosh HD-Users-nkuldell-Desktop-bacterialselfportrait.jpg|thumb|center|400px|'''Bacterial self-portrait.<br> Photo credit: Marsha Miller, University of Texas at Austin''']] | |||
==Lab handouts== | |||
'''[[BE.109:Systems engineering/Tools for systems engineering | Day 1: Tools for systems engineering]]''' | |||
'''[[BE.109:Systems engineering/Basic bacterial photography: black and white | Day 2: Basic bacterial photography: black and white]]''' | |||
'''[[BE.109:Systems engineering/Advanced bacterial photography: 2 color | Day 3: Advanced bacterial photography: 2 color]]''' | |||
'''[[BE.109:Systems engineering/Device characterization | Day 4: Device characterization]]''' | |||
'''[[BE.109:Systems engineering/Measuring DNA, RNA, protein | Day 5: Measuring DNA, RNA, protein]]''' | |||
'''[[BE.109:Systems engineering/RT-PCR data analysis | Day 6: RT-PCR data analysis]]''' | |||
==References== | ==References== | ||
'''Note:''' PDF reprints are provided below within the context of [http://www.copyright.gov/fls/fl102.html fair use]. Please obtain copies from the publisher if appropriate. | |||
#'''Foundations for engineering biology'''<br>''Nature'' 24 November 2005 DOI:10.1038/nature04342<br> [[Drew Endy]]<br> [http://www.nature.com/nature/journal/v438/n7067/abs/nature04342.html URL] [http://openwetware.org/images/0/0d/Nature04342.pdf PDF reprint] | |||
#'''Adventures in synthetic biology''' (comic)<br> ''Nature'' 24 November 2005 Cover & Online<br> [[Drew Endy]], Isadora Deese and [http://www.chuckwadey.com Chuck Wadey]<br> [[Adventures | Reprint & background]]<br> | |||
#'''Engineering Escherichia coli to see light'''<br> ''Nature'' 24 November 2005 DOI:10.1038/nature04405<br> A. Levskaya ''et al.''<br> [http://www.nature.com/nature/journal/v438/n7067/full/nature04405.html URL] | |||
#'''The engineer's approach to biology'''<br>H. Breithaupt<br> ''EMBO Reports'' Jan 2006 DOI:10.1038/sj.embor.7400607<br> [http://www.nature.com/embor/journal/v7/n1/full/7400607.html URL] | |||
</div> | </div> | ||
Latest revision as of 12:46, 10 August 2006
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.
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
References
Note: PDF reprints are provided below within the context of fair use. Please obtain copies from the publisher if appropriate.
- Foundations for engineering biology
Nature 24 November 2005 DOI:10.1038/nature04342
Drew Endy
URL PDF reprint - Adventures in synthetic biology (comic)
Nature 24 November 2005 Cover & Online
Drew Endy, Isadora Deese and Chuck Wadey
Reprint & background - Engineering Escherichia coli to see light
Nature 24 November 2005 DOI:10.1038/nature04405
A. Levskaya et al.
URL - The engineer's approach to biology
H. Breithaupt
EMBO Reports Jan 2006 DOI:10.1038/sj.embor.7400607
URL
