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

Participating Schools

Events

• [http://parts2.mit.edu/r/parts/htdocs/iGEM2005/ttt.cgi Teacher's Workshop] - May 15-15, 2005
  • Parts, Devices, Systems & Engineering Theory
  • Risks and Rewards
  • Notes on Tom Knight's talk
  • [http://web.mit.edu/endy/www/scraps/talks/iGEM/Silver.yeast.ppt Pam Silver's yeast powerpoint]
• Jamboree, November 5-6, 2005 (to change the name of the Jamboree, please send Drew Endy a check for $30,000,000)

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) [http://www.cellbioed.org/pdf/04-11-0047.pdf URL]
• Dan Ferber. 2004. Microbes Made to Order. Science. Vol. 303: 158 - 161. (Good general overview), [http://www.sciencemag.org/cgi/content/full/303/5655/158 URL]

• Jeff Hasty, David McMillen, and J. J. Collins. 2002. Engineered Gene Circuits. Nature. Vol. 420: 224 - 230. (Scholarly Review Paper), [http://www.nature.com/nature/journal/v420/n6912/abs/nature01257_fs.html URL]

• Philip Ball. 2004. Starting from Scratch. Nature. Vol. 431: 624 - 626. (OK general overview), [http://www.nature.com/news/2004/041004/pf/431624a_pf.html URL]

• Editors of Nature. 2004. Futures of Artificial Life. Nature. Vol. 431: 613. (Editorial that addresses ethical considerations), [http://www.bio.davidson.edu/courses/synthetic/papers/Synthetic_Editorial.pdf 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) [http://www.nature.com/nature/journal/v434/n7037/abs/nature03461.html 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, Călin 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. [http://dx.doi.org/10.1146/annurev.biophys.27.1.199 Link]

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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

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Funding

iGEM is an initiative of the MIT [http://icampus.mit.edu/ 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.