Reengineering Life: Synthetic Biology Seminar

Fall, 2007 (Tuesdays: 1 - 4 pm, Dana 153)

A. Malcolm Campbell

Reengineering Life: Synthetic Biology Seminar
(jump to weekly schedule)

Course Wiki


Must have taken at least one of the following courses at Davidson: Genetics, Microbiology, Immunology, Genomics, Development, Biochemistry, or Bioinformatics. If you have not taken these biology courses (e.g., your are a younger Biology major, Chemistry, Math, or Physics majors, etc.) and are still interested, you can seek permission from the instructor.

Overview articles to see if you might like this course:

Dan Ferber. 2004. Microbes Made to Order. Science. Vol. 303: 158 - 161. (Good general overview)

Philip Ball. 2004. Starting from Scratch. Nature. Vol. 431: 624 - 626. (Good general overview)

Editors of Nature. 2004. Futures of Artificial Life. Nature. Vol. 431: 613. (Editorial that addresses ethical considerations)

A. Malcolm Campbell. 2005. Meeting Report: Synthetic Biology Jamboree for Undergraduates. Cell Biology Education. Vol. 4: 19 - 23. (Explanation of friendly competition for students who design and build synthetic biological devices)

Baker, et al. Engineering Life: Building a FAB for Biology. Scientific American. June 2006. 44-51.

2006 Scientist of the Year. Jay Keasling - synthetic biologist. Discover. December, 2006.


Course Goals

1) Learn the various areas within the new and rapidly evloving field of synthetic biology.

2) Produce an integrated understanding of life blending math, computer science, biology, and engineering.

3) Discover biological principles and characteristics revealed through experimentation.


Course Design

1) Read research papers and reviews that cover diverse areas within synthetic biology.

2) Students will lead 2 discussions based on papers they have chosen.

3) Other students will be assigned as support personnel to a primary presenter.

4) Other students will be designated as "official skeptics" for each paper.

5) Each student will pick an area of enquiry and write a paper describing the state of the field. This paper will be posted on the course wiki (see #7).

6) Entire class will invite to campus a guest speaker in the area of synthetic biology.

7) Entire class will produce a Synthetic Biology web site (using wiki) that summarizes the field and links to each of their papers.


Required Reading

Many papers from recent literature.

Tipping Point by Malcolm Gladwell.

Grades will be based on lead presentations (30%), supporting roles (15%), skeptic roles (15%), wiki site (10% - group grade), term paper (20%), and speaker visit (10%). Assignments turned in late will be docked 1 letter grade for each 24 hour period.

Logistical Details
Ceiling will be capped at 12 students. Order of student presentations will be organized the first day of class, as will assignments for inviting a speaker and producing a Synthetic Biology web site. Instructor will lead the first session with students serving in other roles.

Honor Code
Work presented by you (in oral or written format) is to be original work produced by you. It is considered an Honor Code violation if someone takes credit for work he or she does not deserve. Clearly, you will rely heavily on the written work of others, but you need to balance the number and amount of direct quotes with a synthesis of their work written in your own words. You should consult the Biology Department's plagiarism web site for additional help.

Schedule (tentative)

Week 1 (August 28)

1) Define synthetic biology *

2) Read one review paper for lay audiences (during class for 20 minutes and report back)

3) Discuss iGEM Jamboree 2007share some past projects from 2006

4) Find some newspaper stories (search for 15 minutes and report back)

5) Each person report on one lab doing synthetic biology – possible speakers

6) Discuss wiki project

* Good starting places: SyntheticBiology.Org , Implications and Applications of Synthetic Biology , iGEM Educational Resources.


Week 2 (September 4)

Campbell leads discussion of

1) A synthetic oscillatory network of transcriptional regulators
Michael B. Elowitz & Stanislas Leibler

2) Production of the antimalarial drug precursor artemisinic acid in engineered yeast
Ro et al.

3) Discuss semester assignments and possible speaker

4) How to play each of the roles assigned

5) Assign roles and weeks. Discuss appropriate papers.


Week 3 (September 11)

Presentation by Erin Zwack

Enginnered riboregulators enable post-transcriptional control of gene regulation
Farren Isaacs, et al. 2004.

Official Supporter
Designated Skeptic

2) Status of letter

3) questions about roles and papers; project clarification


Week 4 (September 18)

Presentation by Hunter Stone

PPT file for assistance

Official Supporter
Designated Skeptic

1) Engineering Yeast Transcription Machinery for Improved Ethanol Tolerance and Production
Hal Alper et al., 2006

2) Construction of lycopene-overproducing E. coli strains by combining systematic and combinatorial gene knockout targets.
Hal Alper et al., 2005.


Week 5 (September 25)

Presentation by Mike Waters

Official Supporter
Designated Skeptic

Wiki Links to Supplement Readings

1) Tuning genetic control through promoter engineering
Hal Alper et al., 2005


2) Combinatorial promoter design for engineering noisy gene expression
Kevin Murphy et al., 2007


Week 6 (October 2)

Presentation by Samantha Simpson

Official Supporter
Designated Skeptic

1) Conversion of the Vibrio fischeri Transcriptional Activator, LuxR, to a Repressor
Krisit A. Egland and E. P. Greenberg, 2000.

2) Environmentally Controlled Invasion of Cancer Cells by Engineered Bacteria
J. Christopher Anderson, et al., 2006

Week 7 (October 9)

(all wiki project selections submitted)

Presentation by Will DeLoache

Official Supporter
Designated Skeptic

1) Construction of a genetic toggle switch in Escherichia coli
Timothy S. Gardner, et al. 2000.

2) Rational design of memory in eukaryotic cells
Caroline M. Ajo-Franklin, et al. 2007.



Week 8 (October 16) - no class: Fall Break

no class: Fall Break


Week 9 (October 23)

Presentation by Laura Voss

Wiki Links

Official Supporter
Designated Skeptic

1) Predictive and Interpretive Simulation of Green Fluorescent Protein Expression in Reporter Bacteria
by Johan H. J. Leveau et al. 2001.

2) Biological Sensor for Sucrose Availability: Relative Sensitivities of Various Reporter Genes
William G. Miller et al. 2001

Week 10 (October 30)

Presentation by Emma Garren

Official Supporter
Designated Skeptic

1) BioLogic Gates Enable Logical Transcription Control in Mammalian Cells
by Beat P. Kramer, et al., 2004

2) Environmental signal integration by a modular AND gate
by J Christopher Anderson et al., 2007

Link to wiki for additional information

Week 11 (November 6)

Presentation by Danielle Jordan

Official Supporter
Designated Skeptic

1) Efficient Bacterial Transcription of DNA Nanocircle Vectors with Optimized Single-Stranded Promoters
by Tatsuo Ohmichi, et al. 2002.

2) A modular and extensible RNA-based gene-regulatory platform for engineering cellular function.
Maung Nyan Win and Christina D. Smolke, 2007.

Link to wiki for additional information

PPT File for Background and Clarity

Week 12 (November 13)

Student Papers (first draft of wiki due)

Present Wikis (part 1)



Week 13 (November 20)

Present Wikis (part 2)



Week 14 (November 27)

Campbell leads discussion of:

1) Dispersing biofilms with engineered enzymatic bacteriophage
Lu and Collins, 2007

2) Protein synthesis in liposomes with a minimal set of enzymes
Murtas et al., 2007

3) Nano-enabled synthetic biology
Doktycz, 2007

4) The economics of synthetic biology
Henkel and Maurer, 2007

Official Supporter
Designated Skeptic


Week 15 (December 4) - no class: ASCB Meeting

Final wiki page due at 5 pm, eastern time zone :-)


Week 16 (December 11)

Final Meeting


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