20.109(F07): Module 1 oral presentations

The list of papers below is provided as a guideline for the types of papers that might be relevant for your presentation. You will notice that the papers fall roughly into four categories- parts, devices, systems and artificial life.

You are not limited to the following list of primary research articles. The list is provided simply to give you an idea of the kinds of subjects that could make suitable presentations for the class. Search pubmed yourself to find articles of interest to you. Once you have decided on a paper for your presentation, please email it to nkuldell AT mit DOT edu, and also "reserve" it by putting your (initials/lab section/team color) next to the listing here. As you prepare your talk be sure to follow the specific guidelines for oral presentations in this class.

For visibility, please use the following format to sign up if possible, substituting in your own initials and team colour: [ANS/WF/Yellow]. Thanks!

Parts

 * 1) Dwyer, M.A., Looger, L.L., and Hellinga, H.W. 2004. Computational design of a biologically active enzyme. Science 304: 1967–1971
 * 2) Knight, T. 2003. Idempotent vector design for standard assembly of biobricks. http://hdl.handle.net/1721.1/21168. In DSpace Massachussetts Institute of Technology Artificial Intelligence Laboratory, MIT Synthetic Biology Working Group
 * 3) Phillips, I. and Silver, P.A. 2006. A new biobrick assembly strategy designed for facile protein engineering. http://hdl.handle.net/1721.1/32535. In DSpace Massachussetts Institute of Technology Artificial Intelligence Laboratory, MIT Synthetic Biology Working Group.

Devices

 * 1) Fields S, Song OK. 1989. A novel genetic system to detect protein-protein interactions. Nature 340: 245-246.
 * 2) Hasty, J., McMillen, D., and Collins, J.J. 2002. Engineered gene circuits. Nature 420: 224–230.
 * 3) Elowitz, M.B. and Leibler, S. 2000. A synthetic oscillatory network of transcriptional regulators. Nature 403: 335–338.
 * 4) Bayer, T.S. and Smolke, C.D. 2005. Programmable ligand-controlled riboregulators of eukaryotic gene expression. Nat. Biotechnol. 23: 337–343.
 * 5) Atsumi, S. and Little, J.W. 2004. Regulatory circuit design and evolution using phage {lambda}. Genes & Dev. 18: 2086–2094.
 * 6) Gardner, T.S., Cantor, C.R., and Collins, J.J. 2000. Construction of a genetic toggle switch in Escherichia coli. Nature 403: 339–342. [RSZ/TR/Pink]
 * 1)  Anderson, J.C., Voigt, C., and Arkin A.P.  2007. Environmental signal integration by a modular AND gate. Molecular Systems Biology  3.
 * 2) Win MN, Smolke CD. 2007. A modular and extensible RNA-based gene-regulatory platform for engineering cellular function. Proc Natl Acad Sci U S A. 2007 Aug 20; Epub ahead of print

Systems

 * 1) Basu, S., Gerchman, Y., Collins, C.H., Arnold, F.H., and Weiss, R. 2005. A synthetic multicellular system for programmed pattern formation. Nature 434: 1130–1134.  [Spenser/WF/Red]
 * 2) Anderson, J.C., Clarke, E.J., Arkin, A.P., and Voigt, C.A. 2006. Environmentally controlled invasion of cancer cells by engineered bacteria. J. Mol. Biol. 355: 619–627.
 * 3) Dejong, J.M., Liu, Y., Bollon, A.P., Long, R.M., Jennewein, S., Williams, D., and Croteau, R.B. 2006. Genetic engineering of taxol biosynthetic genes in Saccharomyces cerevisiae. Biotechnol. Bioeng. 93: 212–224.
 * 4) Levskaya, A., Chevalier, A.A., Tabor, J.J., Simpson, Z.B., Lavery, L.A., Levy, M., Davidson, E.A., Scouras, A., Ellington, A.D., and Marcotte, E.M., et al. 2005. Synthetic biology: Engineering Escherichia coli to see light. Nature 438: 441–442.
 * 5) Martin, V.J., Pitera, D.J., Withers, S.T., Newman, J.D., and Keasling, J.D. 2003. Engineering a mevalonate pathway in Escherichia coli for production of terpenoids. Nat. Biotechnol. 21: 796–802.
 * 6) Noireaux, V. and Libchaber, A. 2004. A vesicle bioreactor as a step toward an artificial cell assembly. Proc. Natl. Acad. Sci. 101: 17669–17674.
 * 7) Wang, L., Xie, J., and Schultz, P.G. 2006. Expanding the genetic code. Annu. Rev. Biophys. Biomol. Struct. 35: 225–249.
 * 8) Yeh BJ, Rutigliano RJ, Deb A, Bar-Sagi D, Lim WA. 2007. Rewiring cellular morphology pathways with synthetic guanine nucleotide exchange factors.Nature 447(7144):596-600.
 * 9) Dueber JE, Mirsky EA, Lim WA. 2007. Engineering synthetic signaling proteins with ultrasensitive input/output control.Nat Biotechnol 25(6):660-662.

Artificial Life

 * 1) Glass, J.I., Assad-Garcia, N., Alperovich, N., Yooseph, S., Lewis, M.R., Maruf, M., Hutchison III, C.A., Smith, H.O., and Venter, J.C. 2006. Essential genes of a minimal bacterium. Proc. Natl. Acad. Sci. 103: 425–430.
 * 2) Ishikawa, K., Sato, K., Shima, Y., Urabe, I., and Yomo, T. 2004. Expression of a cascading genetic network within liposomes. FEBS Lett. 576: 387–390.
 * 3) Smith, H.O., Hutchison III, C.A., Pfannkoch, C., and Venter, J.C. 2003. Generating a synthetic genome by whole genome assembly: {phi}X174 bacteriophage from synthetic oligonucleotides. Proc. Natl. Acad. Sci. 100: 15440–15445.
 * 4) Tumpey, T.M., Basler, C.F., Aguilar, P.V., Zeng, H., Solorzano, A., Swayne, D.E., Cox, N.J., Katz, J.M., Taubenberger, J.K., and Palese, P., et al. 2005. Characterization of the reconstructed 1918 Spanish influenza pandemic virus. Science 310: 77–80.
 * 5) Itaya M, Tsuge K, Koizumi M, Fujita K. 2005 Combining two genomes in one cell: stable cloning of the Synechocystis PCC6803 genome in the Bacillus subtilis 168 genome. Proc Natl Acad Sci U S A. Nov 1;102(44):15971-6.
 * 6) Lartigue C, Glass JI, Alperovich N, Pieper R, Parmar PP, Hutchison CA 3rd, Smith HO, Venter JC. 2007. Genome transplantation in bacteria: changing one species to another. Science. 317(5838):632-8.  -Matt

Other

 * 1) Haywood, Annika FM, Staveley, Brian E. 2004. parkin counteracts symptoms in a Drosophila model of Parkinson's disease. BMC Neuroscience. 5:14. http://www.biomedcentral.com/1471-2202/5/14. Juliana Rotter (TR)