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iGEM 2005 - The summer 2005 intercollegiate Genetically Engineered Machine competition.

iGEM 2005 Jamboree, November 5 & 6

During the first weekend of November, students and instructors from all of the schools in this year's competition will meet at MIT to present their projects and celebrate their accomplishments. Please join us and learn how Synthetic Biology is changing the teaching and engineering of biology.

Participating Schools

Events

IBE Annual Meeting, March 10-12, 2006, Tucson, Arizona: Special Sessions on Synthetic Biology

Share your latest research! Make new friends! Bask in the Arizona sun!

Jay Keasling (an instructor for the Berkeley iGEM team) will be the keynote speaker at the Institute of Biological Engineering annual conference in Tucson.

Drew Endy and Tom Richard are organizing a technical session on synthetic biology. We would love to have some iGEM teams represented, and welcome presentations about other current research from your labs. In addition to this oral session focused on synthetic biology, there is an open poster session (with awards for student posters in both graduate and undergraduate divisions) and a student essay competition on bioethics.

Details are available at http://www.ibeweb.org/. If you have questions about the conference or IBE, please contact Tom Richard <trichard@psu.edu>

Teacher's Workshop - May 15-15, 2005

• • Parts, Devices, Systems & Engineering Theory
  • Risks and Rewards
  • Notes on Tom Knight's talk
  • Pam Silver's yeast powerpoint
• Jamboree, November 5-6, 2005

Papers for Students to Read

General Review Papers

• A. Malcolm Campbell. 2005. Meeting Report: Synthetic Biology Jamboree for Undergraduates. Cell Biology Education. 4: 19 - 23. (Meeting Report for 2004 Jamboree) URL
• Dan Ferber. 2004. Microbes Made to Order. Science. Vol. 303: 158 - 161. (Good general overview), URL

• Jeff Hasty, David McMillen, and J. J. Collins. 2002. Engineered Gene Circuits. Nature. Vol. 420: 224 - 230. (Scholarly Review Paper), URL

• Philip Ball. 2004. Starting from Scratch. Nature. Vol. 431: 624 - 626. (OK general overview), URL

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

Research Papers in Synthetic Biology

• Timothy S. Gardner, Charles R. Cantor, and James J. Collins. 2000. Construction of a genetic toggle switch in Escherichia coli. Nature. Vol. 403. 339 - 342. (Bistable gene regulatory network, toggled by transient chemical or thermal induction, to serve as cellular memory)

• Robert T. Batey, Sunny D. Gilbert, and Rebecca K. Montange. 2004. Structure of a Natural Guanine-responsive Riboswitch Complexed with a Metabolite Hypoxanthine. Nature. Vol. 432. 411 - 415. (Distinguishes Riboswitches from Aptamers and Antiswitches; also shows 3D structure of aptamer and ligand)

• News Summary of Batey et al. 2004. (Batey et al., paper above)

• Laising Yen et al. 2004. Exogenous Controlof Mammalian Gene Expression through Modulation of RNA Self-cleavage. Nature. Vol. 431: 471 - 476. (mRNA-mediated regulation of translation)

• Yina Kuang, Israel Biran, and David R. Walt. 2004. Simultaneously Monitoring Gene Expression Kinetics and Genetic Noise in Single Cells by Optical Well Arrays. Analytical Chemistry. Vol. 76: 6282 - 6286. (Analysis of two promoters)

• Thomas Bulter, Sun-Gu Lee, Wilson WaiChun Wong, Eileen Fung, Michael R. Conner, and James C. Liao. 2004. Design of artificial cell-cell communication using gene and metabolic networks. PNAS. 101(8): 2299-2304. (Quorum sensor using acetate signal)

• Hideki Kobayashi, Mads Kaern, Michihiro Araki, Kristy Chung, Timothy S. Gardner, Charles R. Cantor, and James J. Collins. Programmable cells: Interfacing natural and engineered gene networks. PNAS. 101(22): 8414-8419. (Toggle switch interfaced with 1) SOS signaling pathway for DNA damage response and 2) quorum sensing signalling pathway)

• Sara Hooshangi, Stephan Thiberge, and Ron Weiss. 2005. Ultrasensitivity and noise propagation in a synthetic transcriptional cascade. PNAS. 102(10): 3581–3586. (Basic Research Paper)

• Bayer, Travis S. and Christina D . Smolke. 2005. Programmable ligand-controlled riboregulators of eukaryotic gene expression. Nature Biotechnology. 23 (3): 337 - 343. (Antiswithces that turn off or on mRNA translation, regulated by amptamer binding ligands)

• Isaacs, Farren J. and James J. Collins. 2005. Plug-and-play with RNA. Nature Biotechnology. 23 (3): 306 -307. (Commentary on Bayer & Smolke, 2005.)

• Subhayu Basu, Yoram Gerchman, Cynthia H. Collins, Frances H. Arnold and Ron Weiss. 2005. A synthetic multicellular system for programmed pattern formation. Nature. Vol. 434:1130-1134 (Cool patterns, seeded with senders, with receivers responding to chemical gradients) URL

Mathematical Modeling in Synthetic Biology

• Hasty J, McMillen D, Isaacs F, Collins JJ. 2001. Computational studies of gene regulatory networks: in numero molecular biology. Nat Rev Genet. 2001 Apr;2(4):268-79.
• Guet, C&abreve;lin C., Elowitz, Michael B., Hsing, Weihong, Leibler, Stanislas Combinatorial Synthesis of Genetic Networks Science 2002 296: 1466-1470

• McAdams HH, Arkin A. Simulation of prokaryotic genetic circuits. Annu Rev Biophys Biomol Struct. 1998; 27:199-224. Link

Possible Fun Groups

1. Awards Panel
2. Jamboree Planning
3. Editorial Board
4. Standards of Practice
5. iGEM 2006 Planning
6. Others (Publicity?)

Resources

1. Blue Heron Point of Contact
2. Part Nicknames
3. Lab Protocols

Please see documentation on customizing the interface and the User's Guide for usage and configuration help.

Funding

iGEM is an initiative of the MIT iCampus program, which is funded by Microsoft Corp. iCampus sponsors faculty innovations in educational technology, helps incubate them through classroom use, and promotes their adoption, evaluation and continued evolution through worldwide multi-institutional cooperation.