2007 Synthetic Biology Team Challenge

March 19-23, 26Instructors: Howard Salis, Jeff Tabor

Course Information

• Monday – Friday: 9AM-5PM

• Final Presentations: Monday 3/26 1:30-3PM GH 114

• Course wiki: http://openwetware.org/wiki/Jeff_Tabor/UCSF_Synthetic_Biology_Team_Challenge

Schedule

• Monday– Intro to Synthetic Biology– Lab: Registry of Standard Biological Parts

• Tuesday– Survey of useful parts– Journal Club– Lab: Engineer novel genetic logic

• Wednesday– Modeling gene networks in MATLAB (H. Salis)– Homework: Brainstorm synthetic system

• Thursday– Develop plan for system– Optimize system with model

• Friday– Specify system with appropriate parts from literature– Document parts and systems in the registry– Simulations of final systems

• Monday (1:30-3:00)– ~15 min Final presentations.– 5 Faculty judges decide winner– Winning group’s design is synthesized.

Outline - Monday

1. Brief History of Molecular Biology

2. Dawn of Synthetic Biology1. Concepts driving early designs2. Building genomes from scratch

3. Landmark efforts in system design

4. System talks1. Liz Clarke2. Dan Widmaier3. Matt Eames

5. Abstracting/formalizing the design process

6. Lunch

7. Afternoon Lab. MIT’s registry of Standard Biological Parts.

Chronology of Molecular Biology

• 1953. Structure of DNA. Watson and Crick

• 1961. Concept of mRNA, Regulator/operator pairs, Operons. Jacob and Monod.

-(Gene networks of any desired property can be assembled from combinations of simple regulatory elements)

• 1961+. Discovery of codons and the genetic code

• 1973. Recombinant DNA technology (Cohen and Boyer, UCSF)

• 1977. DNA Sequencing Technology.

• 1983. Invention of PCR. "Beginning with a single molecule of the genetic material DNA, the PCR can generate 100 billion similar molecules in an afternoon.“ –K. Mullis

• 1987. First Automated Sequencer (Applied Biosystems Prism 373)

• 1997. Sequence of E.coli genome published (Blattner, UW)

• 2001. Sequence of human genome published (HGP/Celera)

• 2002. CSI:Miami debuts on CBS

Synthetic Biology

Nature 403, January 2000

Cells are composed of complex networks

Adapted From: Lee et al., Science, 2004

Complex networks are composed of simpler modules

Modules can be reconfigured into synthetic networks

Elowitz and Leibler. Nature, 2000

Simulating a synthetic gene network

Continuous Model Discreet Model

Elowitz and Leibler. Nature, 2000

Genetic Toggle Switch

Gardner et al. Nature, 2000

Carlson, Pace & Proliferation of Biological Technologies, Biosec. & Bioterror. 1(3):1 (2003)

c/o Drew Endy

-DNA synthesis capacity has doubled each 1.5 years over the past 10 years

-System design and fabrication can routinely be decoupled

(Endy, Nature 2005)

Building genomes from scratch

• 2002. Assembly of functional poliovirus genome (~7.5kb; Cello et al., Science 2002).– Oligos designed computationally, ordered commercially

– [C332652 H492388 N98245 O131196 P7501 S2340]

• 2003. Assembly of a bacteriophage genome (~5kb; Smith et al., PNAS 2003).– 2 weeks assembly time

• 2005. Assembly of the 1918 flu virus (~13kb). (Tumpey et al., Science 2005).

• Craig Venter’s Mycoplasma genitalium genome = 580kb

Rewriting genomes (Chan et al., Molecular Systems Biology, 2005)

wt

refactored

Genetic pulse generator

http://www.pnas.org/content/vol0/issue2004/images/data/0307571101/DC1/07571Movie1.mov

Basu et al., PNAS 2005

Sender E.coli Receiver E.coli

Genetic pattern formation circuit

Basu et al., Nature 2005

2004 UT-Austin/UCSF Bugwarz Team

Not pictured: Andy Ellington, Chris Voigt

High-resolution spatial control of gene expression

Projector

Agar plate Agar plate

Engineering light-dependent gene expression in E. coli

Bacterial photography

Wild-typeEnvZ

Mask Bacterial lawn

“Light Cannon”

Mercury vapor lamp

Concave grating spectrometer

Actuator

Projected image

37 degree incubator

Double Guass focusing lens

35 mm slide

632nm bandpass filter

Improved black and white photography

Endyrichia coliEscherichia ellington

‘Biofilm’ capable of continuous expression response

Levskaya et al., Nature, 2005

Continuous response allows capture of high information images

Bacterial edge detector

Projector

Agar plate

Genetic logic for edge detection

Only occursat edge of light/dark

Gates mismatched: LOW output from gate 1 interpreted as HIGH input at gate 2

Light repression isincomplete

Matching gates through RBS redesign

Contributed Talks

• 10:00-10:30: L. Clarke ‘A Bacterial Thermometer’• 10:30-11:00: D. Widmaier ‘Secreting Spider Silk in

Salmonella’• 11:00-11:30: M. Eames ‘Remote Controlled Bacteria’

Genetic “Parts” for programming living cells

Voigt, Curr. Opin Biotechnol., 2006

Genetic “devices” integrate signal inputs

Voigt, Curr. Opin Biotechnol., 2006

Device outputs control “actuators” which determine cellular behaviors

Voigt, Curr. Opin Biotechnol., 2006

Making Biology a reliable engineering discipline

• Standardization– Composability

• Characterization – ‘off the shelf’ functionality

• Centralization– Well documented repositories

• Abstraction– Distribution of expertise/labor

Device characterization

http://parts.mit.edu/registry/index.php/Part:BBa_F2620

Abstraction hierarchy for the engineering of biology

Endy, Nature 2005

Lunch

• GH 114

sai