Synthetic Biology:Polka Dots

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As there still seems to be web hits on this page, the important contents of this page have been reformatted a bit and put up here for historical reference. In 2004, this Synthetic Biology class was taught at MIT during the month of January.

Synthetic Biology Lab: Engineered Genetic Polka Dots

The course web site is at https://stellar.mit.edu/S/project/iap/ia04/synthetic-biology-lab/index.html.

How to Apply

Please send an email to (no longer functional email address) that includes the following information:

  1. Name
  2. School
  3. Expected year of graduation (if appropriate)
  4. Major (if decided)
  5. The lab will run from Monday January 5 to Thursday January 29. Are you able to spend 2 hours per day in class/discussion and 1 to 6 hours per day working on your project? Yes/no?

Instructors & Contact Information

  • Drew Endy, Fellow, MIT Biology & Biological Engineering
  • Tom Knight, Senior Research Scientist, MIT AI Lab & EECS
  • Randy Rettberg, Distinguished Engineer, Sun, Apple & BBN (retired)
  • Gerald J. Sussman, Matsushita Professor of Electrical Engineering (on leave IAP 2004)
  • Very Special Guests, TBA

Information for Prospective Students

We appreciate your interest in MIT's 2004 IAP Synthetic Biology Lab. The theme this year is to design genetically encoded systems that make use of cell-cell signaling and cell-based logic to create polka-dot (or other) patterns in bacterial lawns. The course has no pre-requisites but requires "heavy-lifting" from all participants. Work includes, but is not limited to, literature scouring, database querying, DNA editing, and genetic device and system design, modeling, and simulation. The work is performed in groups; last-year's groups contained a good-mix of expertise (i.e., no one person had to learn/do everything). Enrollment is limited as it is the second time the course has been taught and we have finite resources for system fabrication and assembly. To apply please send a brief email to the instructors. There are no prerequisites or requirements; last year's participants ranged from first-year undergraduates to postdoctoral researchers. We expect to notify participants by December 8, 2003.

Frequently Asked Questions

  1. I won't be here <any random day/week> in January, can I still take the class? It depends. A random day here/there shouldn't be a problem (but you will need to coordinate with your group once the course starts).
  2. Can I sit in on the lectures? No, we do not allow for listeners (space, et cetera).
  3. How much time will the course require? ~2 hours per weekday for lecture and group discussions (lunch is provided). You should plan to spend an additional 1-6 hours per day to work on your project.
  4. Will I be doing experiments? Will I gain "wet-lab" experience? What will I be doing? The course is purposefully designed to avoid requiring any wet-lab experiments. Instead students (and instructors) first work to specify DNA encoding genetic devices. Once the newly specified DNA has been ordered the class shifts gears to work on the conception, design and specification of integrated biological systems. By analogy, the designer of a complex integrated electronic circuit does not typically also build the silicon chip. However, if you are a class participant and have extra time each morning, we may be able to arrange an experience "bashing" DNA (please indicate such an interest in your application).
  5. You made "blinkers" last IAP, did anything blink? Short answer: we are still building the systems but are closing in on completion. Long answer (copied from a report): During January, 2003 we conducted a four-week long experimental course in which 16 students were asked to design genetically-encoded oscillators using protein-DNA logic (PDL); students were given a 20,000 base pair DNA synthesis budget. In addition, students were asked to design their systems using standard biological parts such that the resulting parts could be used in more than one system (i.e, parts were shared across the class). The course workflow was: (i) model-based system design, (ii) model-driven simulation, (iii) layout, documentation, and plan of characterization, (iv) parts ordering via commercial suppliers, and (v) parts return and system assembly. Design, simulation, layout and documentation took one month. Editing the student-specified parts and placing the parts synthesis order took two months. Parts synthesis required another one to five months. System assembly from standard parts is taking an additional four months, for a total elapsed time of one year. Current estimates are that the 2004 course will run to completion in five months and that, given current technology, three months start-finish will be realized.

Expected Schedule

(DRAFT v0.1, 11/15/03. Content & structure subject to radical change until further notice.)

Scheduled class time: Noon-2p, M-F (lunch provided or BYO) Additional unstructured time to work on projects: whenever, ~1-6hr/day


Monday 1/5/04 Introduction, biological engineering theory, pattern formation intro.
Tuesday 1/6/04 Cell-cell signaling in bacteria
Wednesday 1/7/04 Standard biological parts
Thursday 1/8/04 Channels and gates -- device design and specification
Friday 1/9/04 Channels and gates -- device design and specification

Monday 1/12/04 Channels and gates -- device design and specification
Tuesday 1/13/04 Channels and gates -- device design and specification
Wednesday 1/14/04 Channels and gates -- device model and parameterization
Thursday 1/15/04 Channels and gates -- device model and parameterization
Friday 1/16/04 Channels and gates -- handoff of final device specifications

Monday 1/19/04 Amorphous computing -- languages and patterns; engineering biology and society
Tuesday 1/20/04 System design -- brainstorm I
Wednesday 1/21/04 System design -- brainstorm II
Thursday 1/22/04 System design -- system specification I
Friday 1/23/04 System design -- system specification II

Monday 1/26/04 System design -- reduce to practice I
Tuesday 1/27/04 System design -- reduce to practice II
Wednesday 1/28/04 System design -- reduce to practice III
Thursday 1/29/04 System design -- group presentations and wrap
Friday 1/30/04 NO CLASS -- ski, snowboard, make snowfolks, sleep


Sponsors (i.e., much thanks to)


Reading

Articles

  1. Taga ME and Bassler BL. Chemical communication among bacteria. Proc Natl Acad Sci U S A. 2003 Nov 25;100 Suppl 2(Suppl 2):14549-54. DOI:10.1073/pnas.1934514100 | PubMed ID:12949263 | HubMed [1]
  2. Dwyer MA, Looger LL, and Hellinga HW. Computational design of a Zn2+ receptor that controls bacterial gene expression. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11255-60. DOI:10.1073/pnas.2032284100 | PubMed ID:14500902 | HubMed [2]
  3. Looger LL, Dwyer MA, Smith JJ, and Hellinga HW. Computational design of receptor and sensor proteins with novel functions. Nature. 2003 May 8;423(6936):185-90. DOI:10.1038/nature01556 | PubMed ID:12736688 | HubMed [3]
  4. Yokobayashi Y, Weiss R, and Arnold FH. Directed evolution of a genetic circuit. Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16587-91. DOI:10.1073/pnas.252535999 | PubMed ID:12451174 | HubMed [4]
  5. Elowitz MB and Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature. 2000 Jan 20;403(6767):335-8. DOI:10.1038/35002125 | PubMed ID:10659856 | HubMed [5]

All Medline abstracts: PubMed | HubMed

Misc

"Amorphous computing"

Books (in you want to learn some basic biology re: gene expression regulation)

A Genetic Switch by Mark Ptashne (introductory)
The lac Operon by Benno Muller-Hill (more advanced/subtle)

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