20.109-Lecture-2011-03-08 - Amazon S3 comm. Pulse Gen Band detect ... communication signal •...
Transcript of 20.109-Lecture-2011-03-08 - Amazon S3 comm. Pulse Gen Band detect ... communication signal •...
![Page 1: 20.109-Lecture-2011-03-08 - Amazon S3 comm. Pulse Gen Band detect ... communication signal • Produce pigment ... Microsoft PowerPoint - 20.109-Lecture-2011-03-08](https://reader031.fdocuments.us/reader031/viewer/2022022515/5afbcee97f8b9aa34d8b4d3c/html5/thumbnails/1.jpg)
20.109Synthetic Biology Module
Lecture #1
Ron Weiss
Department of Biological Engineering
MIT
March 8, 2011Department of Biological Engineering
![Page 2: 20.109-Lecture-2011-03-08 - Amazon S3 comm. Pulse Gen Band detect ... communication signal • Produce pigment ... Microsoft PowerPoint - 20.109-Lecture-2011-03-08](https://reader031.fdocuments.us/reader031/viewer/2022022515/5afbcee97f8b9aa34d8b4d3c/html5/thumbnails/2.jpg)
Synthetic biology analogy: bio‐bots
![Page 3: 20.109-Lecture-2011-03-08 - Amazon S3 comm. Pulse Gen Band detect ... communication signal • Produce pigment ... Microsoft PowerPoint - 20.109-Lecture-2011-03-08](https://reader031.fdocuments.us/reader031/viewer/2022022515/5afbcee97f8b9aa34d8b4d3c/html5/thumbnails/3.jpg)
Synthetic biology analogy: bio‐bots
Robot
SENSORS PROCESSING ACTUATION
Environment
Electronic circuit & peripherals
![Page 4: 20.109-Lecture-2011-03-08 - Amazon S3 comm. Pulse Gen Band detect ... communication signal • Produce pigment ... Microsoft PowerPoint - 20.109-Lecture-2011-03-08](https://reader031.fdocuments.us/reader031/viewer/2022022515/5afbcee97f8b9aa34d8b4d3c/html5/thumbnails/4.jpg)
Synthetic biology analogy: bio‐bots
Biological cell
SENSORS PROCESSING ACTUATION
Environment
Synthetic gene circuit
![Page 5: 20.109-Lecture-2011-03-08 - Amazon S3 comm. Pulse Gen Band detect ... communication signal • Produce pigment ... Microsoft PowerPoint - 20.109-Lecture-2011-03-08](https://reader031.fdocuments.us/reader031/viewer/2022022515/5afbcee97f8b9aa34d8b4d3c/html5/thumbnails/5.jpg)
Synthetic biology applications
Microbial biochemicalsynthesis• artemisinin• other pharmaceuticals
Environmental applications• environmental remediation• toxin sensing• explosive sensing
Bioenergy production• biodiesel• hydrogen• methane• …
Biomedical applications• cancer therapeutic agents• artificial tissue homeostasis• programmed tissue regeneration• artificial immune system
![Page 6: 20.109-Lecture-2011-03-08 - Amazon S3 comm. Pulse Gen Band detect ... communication signal • Produce pigment ... Microsoft PowerPoint - 20.109-Lecture-2011-03-08](https://reader031.fdocuments.us/reader031/viewer/2022022515/5afbcee97f8b9aa34d8b4d3c/html5/thumbnails/6.jpg)
From idea to implementation
![Page 7: 20.109-Lecture-2011-03-08 - Amazon S3 comm. Pulse Gen Band detect ... communication signal • Produce pigment ... Microsoft PowerPoint - 20.109-Lecture-2011-03-08](https://reader031.fdocuments.us/reader031/viewer/2022022515/5afbcee97f8b9aa34d8b4d3c/html5/thumbnails/7.jpg)
System integration
Genetic parts
Modules
Applications
Hierarchical organization
![Page 8: 20.109-Lecture-2011-03-08 - Amazon S3 comm. Pulse Gen Band detect ... communication signal • Produce pigment ... Microsoft PowerPoint - 20.109-Lecture-2011-03-08](https://reader031.fdocuments.us/reader031/viewer/2022022515/5afbcee97f8b9aa34d8b4d3c/html5/thumbnails/8.jpg)
Genetic Building Block – Digital Inverter
0 1
CDS P
Transcription /Translation
output proteininput protein(repressor)
![Page 9: 20.109-Lecture-2011-03-08 - Amazon S3 comm. Pulse Gen Band detect ... communication signal • Produce pigment ... Microsoft PowerPoint - 20.109-Lecture-2011-03-08](https://reader031.fdocuments.us/reader031/viewer/2022022515/5afbcee97f8b9aa34d8b4d3c/html5/thumbnails/9.jpg)
Genetic Building Block – Digital Inverter
1 0
CDS P
Transcription /Translation
output proteininput protein(repressor)
![Page 10: 20.109-Lecture-2011-03-08 - Amazon S3 comm. Pulse Gen Band detect ... communication signal • Produce pigment ... Microsoft PowerPoint - 20.109-Lecture-2011-03-08](https://reader031.fdocuments.us/reader031/viewer/2022022515/5afbcee97f8b9aa34d8b4d3c/html5/thumbnails/10.jpg)
Amplifier
Inverter
Cascades
Toggle switch
1:2 MUX
digital
analog
comm.
Pulse Gen
Band detect
Send/Receive
Yeast QS
Consensus
Pop Ctrl
Modules implemented in Weiss lab
![Page 11: 20.109-Lecture-2011-03-08 - Amazon S3 comm. Pulse Gen Band detect ... communication signal • Produce pigment ... Microsoft PowerPoint - 20.109-Lecture-2011-03-08](https://reader031.fdocuments.us/reader031/viewer/2022022515/5afbcee97f8b9aa34d8b4d3c/html5/thumbnails/11.jpg)
Genetic Edge Detector
Goal: Implement a parallel edge detection algorithmwherein each bacterium within a population functionsas an independent signal processor, and the populationcooperates to find the edges.
A synthetic genetic edge detection program. Tabor JJ, Salis HM, Simpson ZB, Chevalier AA, Levskaya A, Marcotte EM, Voigt CA, Ellington AD. Cell. 2009 Jun 26;137(7):1273. Figure 1A
![Page 12: 20.109-Lecture-2011-03-08 - Amazon S3 comm. Pulse Gen Band detect ... communication signal • Produce pigment ... Microsoft PowerPoint - 20.109-Lecture-2011-03-08](https://reader031.fdocuments.us/reader031/viewer/2022022515/5afbcee97f8b9aa34d8b4d3c/html5/thumbnails/12.jpg)
Experimental Goals
Design: DNA modification
Sub-clone new DNA Express in bacteria Characterize new system
20.109 / System Engineering Module
Lab+Analytical Skills
Culture bacteria Make and analyze DNA Measure enzyme levels Model/make predictions Explore modular composition
Our goal: Understand, analyze, and improve edge detectorSpecifically: One technical aspect of the presentation today is incorrect (from paper). The goal of our 20.109 module is to fix this problem!
![Page 13: 20.109-Lecture-2011-03-08 - Amazon S3 comm. Pulse Gen Band detect ... communication signal • Produce pigment ... Microsoft PowerPoint - 20.109-Lecture-2011-03-08](https://reader031.fdocuments.us/reader031/viewer/2022022515/5afbcee97f8b9aa34d8b4d3c/html5/thumbnails/13.jpg)
A synthetic genetic edge detection program. Tabor JJ, Salis HM, Simpson ZB, Chevalier AA, Levskaya A, Marcotte EM, Voigt CA, Ellington AD. Cell. 2009 Jun 26;137(7):1273. Figure 1B, 1C
Genetic Edge Detection Algorithm
• Pseudocode:
IF NOT (light)produce signal
IF signal AND NOT (NOT light)produce pigment
• Produce signal –generate diffusible communication signal
• Produce pigment –produce black pigment
![Page 14: 20.109-Lecture-2011-03-08 - Amazon S3 comm. Pulse Gen Band detect ... communication signal • Produce pigment ... Microsoft PowerPoint - 20.109-Lecture-2011-03-08](https://reader031.fdocuments.us/reader031/viewer/2022022515/5afbcee97f8b9aa34d8b4d3c/html5/thumbnails/14.jpg)
Genetic Edge Detection Algorithm
I. Photographic Bacteria using Dark SensorII. Cell‐Cell CommunicationIII. InverterIV. Full Logic Function
![Page 15: 20.109-Lecture-2011-03-08 - Amazon S3 comm. Pulse Gen Band detect ... communication signal • Produce pigment ... Microsoft PowerPoint - 20.109-Lecture-2011-03-08](https://reader031.fdocuments.us/reader031/viewer/2022022515/5afbcee97f8b9aa34d8b4d3c/html5/thumbnails/15.jpg)
Dark Sensor
![Page 16: 20.109-Lecture-2011-03-08 - Amazon S3 comm. Pulse Gen Band detect ... communication signal • Produce pigment ... Microsoft PowerPoint - 20.109-Lecture-2011-03-08](https://reader031.fdocuments.us/reader031/viewer/2022022515/5afbcee97f8b9aa34d8b4d3c/html5/thumbnails/16.jpg)
II. Cell‐cell Communication
Communicate using V. fischeri quorum sensing system
Dark transcription of luxImembrane diffusible compound 3‐oxohexanoyl‐homoserine lactone (AHL)
AHL binds constitutively expressed LuxRβ‐galactosidase
Additional blurring component
A synthetic genetic edge detection program. Tabor JJ, Salis HM, Simpson ZB, Chevalier AA, Levskaya A, Marcotte EM, Voigt CA, Ellington AD. Cell. 2009 Jun 26;137(7):1275. Figure 3B
![Page 17: 20.109-Lecture-2011-03-08 - Amazon S3 comm. Pulse Gen Band detect ... communication signal • Produce pigment ... Microsoft PowerPoint - 20.109-Lecture-2011-03-08](https://reader031.fdocuments.us/reader031/viewer/2022022515/5afbcee97f8b9aa34d8b4d3c/html5/thumbnails/17.jpg)
II. Cell‐cell Communication
A synthetic genetic edge detection program. Tabor JJ, Salis HM, Simpson ZB, Chevalier AA, Levskaya A, Marcotte EM, Voigt CA, Ellington AD. Cell. 2009 Jun 26;137(7):1275. Figure 3B
![Page 18: 20.109-Lecture-2011-03-08 - Amazon S3 comm. Pulse Gen Band detect ... communication signal • Produce pigment ... Microsoft PowerPoint - 20.109-Lecture-2011-03-08](https://reader031.fdocuments.us/reader031/viewer/2022022515/5afbcee97f8b9aa34d8b4d3c/html5/thumbnails/18.jpg)
III. Inverter
B‐gal expressed only where AHL AND light
or more accuratelyAHL AND NOT (NOT light)
NOT function = genetic inverter
cI gene from phage λ dimeric transcriptional repressor turns OFF the output promoter when the input promoter is ON
Negative bacterial photograph
A synthetic genetic edge detection program. Tabor JJ, Salis HM, Simpson ZB, Chevalier AA, Levskaya A, Marcotte EM, Voigt CA, Ellington AD. Cell. 2009 Jun 26;137(7):1275. Figure 3C
![Page 19: 20.109-Lecture-2011-03-08 - Amazon S3 comm. Pulse Gen Band detect ... communication signal • Produce pigment ... Microsoft PowerPoint - 20.109-Lecture-2011-03-08](https://reader031.fdocuments.us/reader031/viewer/2022022515/5afbcee97f8b9aa34d8b4d3c/html5/thumbnails/19.jpg)
III. Inverter
A synthetic genetic edge detection program. Tabor JJ, Salis HM, Simpson ZB, Chevalier AA, Levskaya A, Marcotte EM, Voigt CA, Ellington AD. Cell. 2009 Jun 26;137(7):1275. Figure 3C
![Page 20: 20.109-Lecture-2011-03-08 - Amazon S3 comm. Pulse Gen Band detect ... communication signal • Produce pigment ... Microsoft PowerPoint - 20.109-Lecture-2011-03-08](https://reader031.fdocuments.us/reader031/viewer/2022022515/5afbcee97f8b9aa34d8b4d3c/html5/thumbnails/20.jpg)
A synthetic genetic edge detection program. Tabor JJ, Salis HM, Simpson ZB, Chevalier AA, Levskaya A, Marcotte EM, Voigt CA, Ellington AD. Cell. 2009 Jun 26;137(7):1275. Figure 3D
IV. Full Logic Function
• AHL AND NOT (NOT light) • Two‐input promoter Plux‐λ
– activated by AHL/LuxR– dominantly repressed by CI
![Page 21: 20.109-Lecture-2011-03-08 - Amazon S3 comm. Pulse Gen Band detect ... communication signal • Produce pigment ... Microsoft PowerPoint - 20.109-Lecture-2011-03-08](https://reader031.fdocuments.us/reader031/viewer/2022022515/5afbcee97f8b9aa34d8b4d3c/html5/thumbnails/21.jpg)
IV. Full Logic Function
A synthetic genetic edge detection program. Tabor JJ, Salis HM, Simpson ZB, Chevalier AA, Levskaya A, Marcotte EM, Voigt CA, Ellington AD. Cell. 2009 Jun 26;137(7):1275. Figure 3
![Page 22: 20.109-Lecture-2011-03-08 - Amazon S3 comm. Pulse Gen Band detect ... communication signal • Produce pigment ... Microsoft PowerPoint - 20.109-Lecture-2011-03-08](https://reader031.fdocuments.us/reader031/viewer/2022022515/5afbcee97f8b9aa34d8b4d3c/html5/thumbnails/22.jpg)
Logic Transfer Function X AND (NOT Y)
• Constitutively expressed luxR gene
• Exogenously vary AHL and light
•Measure β‐gal activitytwo‐dimensional transfer function of Plux‐λ
– as a function of [AHL] (u1) and [CI] (u2)
A synthetic genetic edge detection program. Tabor JJ, Salis HM, Simpson ZB, Chevalier AA, Levskaya A, Marcotte EM, Voigt CA, Ellington AD. Cell. 2009 Jun 26;137(7):1274 Figure 2B
![Page 23: 20.109-Lecture-2011-03-08 - Amazon S3 comm. Pulse Gen Band detect ... communication signal • Produce pigment ... Microsoft PowerPoint - 20.109-Lecture-2011-03-08](https://reader031.fdocuments.us/reader031/viewer/2022022515/5afbcee97f8b9aa34d8b4d3c/html5/thumbnails/23.jpg)
Edge Detection of Complex Patterns
![Page 24: 20.109-Lecture-2011-03-08 - Amazon S3 comm. Pulse Gen Band detect ... communication signal • Produce pigment ... Microsoft PowerPoint - 20.109-Lecture-2011-03-08](https://reader031.fdocuments.us/reader031/viewer/2022022515/5afbcee97f8b9aa34d8b4d3c/html5/thumbnails/24.jpg)
Next• Lab exercises
– Understand problem with edge detector– Design a fix by the second lab session