1. 1 SynBio & iGEM Stories Mon 8-May-2006 Your role(s) Parts Devices Systems Selections Technologies Tests & datasheets http://parts.mit.edu/r/parts/partsdb/view.cgi?part_id=5114 40 teams * 10 people = $2M / quarter yr

2. 2 The 2004 iGEM poster was synthetic, but not biological ( an artifact of light sensitive dyes) Privately rehabilitated in time for 2005 iGEM jamboree & then publication: Levskaya A, et al. Nature 2005 Nov 24 Synthetic biology: engineering E.coli to see light.

3. 3 iGEM Goals Past & Future Cool Photogenic Stunts Basic Enabling Technologies Save the World Projects Bull’s eye A-to-D & thresholds Biosensors & 3D fabrication BiofilmCell-CPU interfaces Smart materials A synthetic multicellular system for programmed pattern formation Basu, et al. Nature 434:1130

4. 4 iGEM Goals Past & Future Enabling TechnologiesUseful Applications SecretionBioenergy. Human compatible bacteriaTumor busting. Metabolic engineeringAntibiotic manufacture. Recombinases, telomeresGene therapy & counters New genetic codesProtein stability, viral resistance, safety

5. 5  trp/  tyrA pair of genomes shows the best co-growth Reppas, Lin & Church ; Shendure et al. Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome(2005) Science 309:1728 Second Passage First Passage Synthetic combinatorics & selection for secretion

6. 6 Environmentally controlled invasion of cancer cells by engineered bacteria. Anderson et al. J Mol Biol. 2006 Optical imaging: bacteria, viruses, and mammalian cells encoding light- emitting proteins reveal the locations of primary tumors & metastases in animals. Yu, et al. Anal. Bioanal. Chem. 2003. accumulate in tumors at ratios in excess of 1000:1 compared with normal tissues. http://www.vionpharm.com/tapet_virulence.htmlhttp://www.vionpharm.com/tapet_virulence.html

7. 7 LPS - Capsule + Dap - for safety 7

8. 8 Engineering a mevalonate pathway in Escherichia coli for production of terpenoids. Martin VJ, et al. Nat. Biotech 2003 Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Ro DK, et al. Nature. 2006 8

9. 9 Programmable ligand-controlled riboregulators of eukaryotic gene expression. Bayer & Smolke 2005 Nature Biotech. ON OFF

10. 10 Combinatorial characterization P1-GFP-RegP2-RiboRegCR-Output-AA-Stop-Term-P3-RiboRegTA. 50 900 50 25 900 30 3 25 50 90 bp 1 1 10 10 6 10 1 1 10 1E3 # combinations (= 6E8 total) This gives analog logic (P2, P3 & riboreg) which can be characterized in situ to quasi-automatically produce pages for a parts properties handbook. RegP2,P3: lac, tet, ara, heat, cold, cell-cycle, light(2), quorum, hypoxia(3) RiboRegCR: cis-regulator: non-cross-reacting 5 types * two strengths. RiboRegTA: Smolke, Isaacs -- Explore variations on the tiny ligand-specifying region. Output: Ds-Red, cat, kan, luciferase, tetR, RiboReg2, biosynthetic enzyme AA: nil, lite, Flag, his-tag, PKS-association, leu-zipper BBa_R0053 BBa_B0030 BBa_E0040 BBa_B0011 BBa_I0500 BBa_J01010

11. 11 Combinatorial Synthesis of Genetic Networks Guet et al. Science 2002

12. 12 Combinatorial Synthesis of Genetic Networks Guet et al. Science 2002 14

13. 13 Nutriceuticals & cosmetics The FDA does not require disclosure of color or flavor additives if GRAS ("generally recognized as safe"). A natural flavor is not necessarily more healthful or purer than an artificial one. When almond flavor -- benzaldehyde -- is derived from natural sources, such as peach and apricot pits, it contains traces of hydrogen cyanide, a deadly poison. Benzaldehyde derived by mixing oil of clove and amyl acetate does not contain any cyanide. Nevertheless, it is legally considered an artificial flavor and sells at a much lower price. Feb 2005 the FDA issued an unprecedented warning to the cosmetics industry stating that the Agency is serious about enforcing the law requiring companies to inform consumers that personal care products have not been safety tested. http://www.rense.com/general7/whyy.htm http://www.ewg.org/issues/cosmetics/FDA_Warning/

14. 14 NIH Guidelines: Recombinant DNA molecules that are constructed outside living cells by joining natural or synthetic DNA segments to DNA molecules that can replicate in a living cell. U.S. National Organic Standards Board definition of genetic engineering & GMOs: "Made with techniques that alter the molecular or cell biology of an organism by means that are not possible under natural conditions or processes… It shall not include traditional breeding, conjugation, fermentation, hybridization, in-vitro fertilization, or tissue culture." http://www4.od.nih.gov/oba/rac/guidelines_02/NIH_Guidelines_Apr_02.htm#_Toc7261549 http://www.omri.org/OMRI_GMO_policy.html

15. 15 Conjugation Conjugation between bacterial and mammalian cells. Waters VL. Nat Genet. 2001 Transformation of isolated mammalian mitochondria by bacterial conjugation. Yoon YG, Koob MD. Nucleic Acids Res. 2005 Rapid alternative to DNA transformation?

16. 16 Organism Menu SpeciesGeneration (hr) Genome size (Mbp) Homologous recombination Library size, comments In vitro.01 to 24.000211E15 phage.08.0081E-21E10 E.coli.351E-41E9, tame pathogen S. cerevisiae1.5121E-31E7, tasty Synechocystis33.51E-3?, green C.elegans48100RNAi1E6, can of worms Mouse stem cells 2430001E-6 & RNAi 1E6, cute

17. 17.