Biophysics 242r/2009:Syllabus

2. Presentation from faculty and TFs about requirements for the course (about 30 min including time for questions).

1. Drubin DA, Way JC, and Silver PA. Designing biological systems. Genes Dev 2007 Feb 1; 21(3) 242-54. doi:10.1101/gad.1507207 pmid:17289915. PubMed HubMed [Drubin-GenesDev-2007]
2. Szostak JW, Bartel DP, and Luisi PL. Synthesizing life. Nature 2001 Jan 18; 409(6818) 387-90. doi:10.1038/35053176 pmid:11201752. PubMed HubMed [Szostak-Nature-2001]

Designing simple biological systems

3. Andrianantoandro E, Basu S, Karig DK, and Weiss R. Synthetic biology: new engineering rules for an emerging discipline. Mol Syst Biol 2006; 2 2006.0028. doi:10.1038/msb4100073 pmid:16738572. PubMed HubMed [Andrianantoandro-MolSystBiol-2006]
4. Serrano L. Synthetic biology: promises and challenges. Mol Syst Biol 2007; 3 158. doi:10.1038/msb4100202 pmid:18091727. PubMed HubMed [Serrano-MolSystBiol-2007]

Designing simple biological systems

5. Basu S, Mehreja R, Thiberge S, Chen MT, and Weiss R. Spatiotemporal control of gene expression with pulse-generating networks. Proc Natl Acad Sci U S A 2004 Apr 27; 101(17) 6355-60. doi:10.1073/pnas.0307571101 pmid:15096621. PubMed HubMed [Basu-ProcNatlAcadSci-2004]

Logic and engineering applied to biology

6. Peterson SN and Fraser CM. The complexity of simplicity. Genome Biol 2001; 2(2) COMMENT2002. pmid:11182883. PubMed HubMed [Peterson-GenomeBiology-2001]
7. Mushegian AR and Koonin EV. A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc Natl Acad Sci U S A 1996 Sep 17; 93(19) 10268-73. pmid:8816789. PubMed HubMed [Mushegian-ProcNatlAcadSci-1996]

Logic and engineering applied to biology

8. Glass JI, Assad-Garcia N, Alperovich N, Yooseph S, Lewis MR, Maruf M, Hutchison CA 3rd, Smith HO, and Venter JC. Essential genes of a minimal bacterium. Proc Natl Acad Sci U S A 2006 Jan 10; 103(2) 425-30. doi:10.1073/pnas.0510013103 pmid:16407165. PubMed HubMed [Glass-ProcNatlAcadSci-2006]

Watchmaking for the partially-sighted

9. Elowitz MB and Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature 2000 Jan 20; 403(6767) 335-8. doi:10.1038/35002125 pmid:10659856. PubMed HubMed [Elowitz-Nature-2000]
10. Lewis J. Autoinhibition with transcriptional delay: a simple mechanism for the zebrafish somitogenesis oscillator. Curr Biol 2003 Aug 19; 13(16) 1398-408. pmid:12932323. PubMed HubMed [Lewis-CurrBiol-2003]
11. Tigges M, Marquez-Lago TT, Stelling J, and Fussenegger M. A tunable synthetic mammalian oscillator. Nature 2009 Jan 15; 457(7227) 309-12. doi:10.1038/nature07616 pmid:19148099. PubMed HubMed [Tigges-Nature-2009]

Metabolic engineering or synthetic biology? Yes!

12. Prather KL and Martin CH. De novo biosynthetic pathways: rational design of microbial chemical factories. Curr Opin Biotechnol 2008 Oct; 19(5) 468-74. doi:10.1016/j.copbio.2008.07.009 pmid:18725289. PubMed HubMed [Prather-CurrOpinBiotech-2008]
13. Zhang K, Sawaya MR, Eisenberg DS, and Liao JC. Expanding metabolism for biosynthesis of nonnatural alcohols. Proc Natl Acad Sci U S A 2008 Dec 30; 105(52) 20653-8. doi:10.1073/pnas.0807157106 pmid:19064911. PubMed HubMed [Zhang-ProcNatlAcadSci-2008]

Designing more complex systems

14. Anderson JC, Clarke EJ, Arkin AP, and Voigt CA. Environmentally controlled invasion of cancer cells by engineered bacteria. J Mol Biol 2006 Jan 27; 355(4) 619-27. doi:10.1016/j.jmb.2005.10.076 pmid:16330045. PubMed HubMed [Anderson-JMolBiol-2006]
15. Jackson RJ, Ramsay AJ, Christensen CD, Beaton S, Hall DF, and Ramshaw IA. Expression of mouse interleukin-4 by a recombinant ectromelia virus suppresses cytolytic lymphocyte responses and overcomes genetic resistance to mousepox. J Virol 2001 Feb; 75(3) 1205-10. doi:10.1128/JVI.75.3.1205-1210.2001 pmid:11152493. PubMed HubMed [Jackson-JVirol-2001]

REQUIRED READING:

11. Tigges M, Marquez-Lago TT, Stelling J, and Fussenegger M. A tunable synthetic mammalian oscillator. Nature 2009 Jan 15; 457(7227) 309-12. doi:10.1038/nature07616 pmid:19148099. PubMed HubMed [Tigges-Nature-2009]

Designing more complex systems

16. Thomas DD, Donnelly CA, Wood RJ, and Alphey LS. Insect population control using a dominant, repressible, lethal genetic system. Science 2000 Mar 31; 287(5462) 2474-6. pmid:10741964. PubMed HubMed [Thomas-Science-2000]
17. Burt A. Site-specific selfish genes as tools for the control and genetic engineering of natural populations. Proc Biol Sci 2003 May 7; 270(1518) 921-8. doi:10.1098/rspb.2002.2319 pmid:12803906. PubMed HubMed [Burt-ProcBiolSci-2003]

Using principles derived from evolutionary biology for regenerative medicine

Using principles derived from evolutionary biology for regenerative medicine

18. Langer R and Vacanti JP. Tissue engineering. Science 1993 May 14; 260(5110) 920-6. pmid:8493529. PubMed HubMed [Langer-Science-1993]
19. Vacanti JP and Langer R. Tissue engineering: the design and fabrication of living replacement devices for surgical reconstruction and transplantation. Lancet 1999 Jul; 354 Suppl 1 SI32-4. pmid:10437854. PubMed HubMed [Vacanti-Lancet-1999]

REQUIRED READING:

20. Weinand C, Gupta R, Weinberg E, Madisch I, Neville CM, Jupiter JB, and Vacanti JP. Toward regenerating a human thumb in situ. Tissue Eng Part A 2009 Sep; 15(9) 2605-15. doi:10.1089/ten.TEA.2008.0467 pmid:19199577. PubMed HubMed [Weinand-TEA-2009]

Building artificial organisms, reprogramming cellular genomes, and in vitro genomes

21. Forster AC and Church GM. Synthetic biology projects in vitro. Genome Res 2007 Jan; 17(1) 1-6. doi:10.1101/gr.5776007 pmid:17151344. PubMed HubMed [Forster-GenomeRes-2007]
22. Noireaux V and Libchaber A. A vesicle bioreactor as a step toward an artificial cell assembly. Proc Natl Acad Sci U S A 2004 Dec 21; 101(51) 17669-74. doi:10.1073/pnas.0408236101 pmid:15591347. PubMed HubMed [Noireaux-PNAS-2004]
23. Gibson DG, Benders GA, Axelrod KC, Zaveri J, Algire MA, Moodie M, Montague MG, Venter JC, Smith HO, and Hutchison CA 3rd. One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome. Proc Natl Acad Sci U S A 2008 Dec 23; 105(51) 20404-9. doi:10.1073/pnas.0811011106 pmid:19073939. PubMed HubMed [Gibson-PNAS-2008]

Building artificial organisms, reprogramming cellular genomes, and in vitro genomes

24. Xiao H, Murakami H, Suga H, and Ferré-D'Amaré AR. Structural basis of specific tRNA aminoacylation by a small in vitro selected ribozyme. Nature 2008 Jul 17; 454(7202) 358-61. doi:10.1038/nature07033 pmid:18548004. PubMed HubMed [Xiao-Nature-2008]

DNA nanostructures and DNA computing

DNA nanostructures

25. Rothemund PW. Folding DNA to create nanoscale shapes and patterns. Nature 2006 Mar 16; 440(7082) 297-302. doi:10.1038/nature04586 pmid:16541064. PubMed HubMed [Rothemund-Nature-2006]
26. Yin P, Choi HM, Calvert CR, and Pierce NA. Programming biomolecular self-assembly pathways. Nature 2008 Jan 17; 451(7176) 318-22. doi:10.1038/nature06451 pmid:18202654. PubMed HubMed [Yin-Nature-2008]

RNA control devices

27. Sassanfar M and Szostak JW. An RNA motif that binds ATP. Nature 1993 Aug 5; 364(6437) 550-3. doi:10.1038/364550a0 pmid:7687750. PubMed HubMed [Sassanfar-Nature-1993]
28. Bartel DP and Szostak JW. Isolation of new ribozymes from a large pool of random sequences [see comment]. Science 1993 Sep 10; 261(5127) 1411-8. pmid:7690155. PubMed HubMed [Bartel-Science-1993]

RNA control devices

Be sure to read supplemental material for this paper!

29. Win MN and Smolke CD. Higher-order cellular information processing with synthetic RNA devices. Science 2008 Oct 17; 322(5900) 456-60. doi:10.1126/science.1160311 pmid:18927397. PubMed HubMed [Win-Science-2008]

1 page blurb about project due!!! Submit via email to Paul and/or Devin before class starts today.

Evolution vs Design of Molecular Components (Folded Proteins, Enzymes)

30. Seelig B and Szostak JW. Selection and evolution of enzymes from a partially randomized non-catalytic scaffold. Nature 2007 Aug 16; 448(7155) 828-31. doi:10.1038/nature06032 pmid:17700701. PubMed HubMed [Seelig-Nature-2007]

Evolution vs Design of Molecular Components (Folded Proteins, Enzymes)

31. Röthlisberger D, Khersonsky O, Wollacott AM, Jiang L, DeChancie J, Betker J, Gallaher JL, Althoff EA, Zanghellini A, Dym O, Albeck S, Houk KN, Tawfik DS, and Baker D. Kemp elimination catalysts by computational enzyme design. Nature 2008 May 8; 453(7192) 190-5. doi:10.1038/nature06879 pmid:18354394. PubMed HubMed [Rothlisberger-Nature-2008]

Protocell Design: Self-Replicating Materials

32. Mansy SS, Schrum JP, Krishnamurthy M, Tobé S, Treco DA, and Szostak JW. Template-directed synthesis of a genetic polymer in a model protocell. Nature 2008 Jul 3; 454(7200) 122-5. doi:10.1038/nature07018 pmid:18528332. PubMed HubMed [Mansy-Nature-2008]

Protocell Design: Self-Replicating Materials

33. Kita H, Matsuura T, Sunami T, Hosoda K, Ichihashi N, Tsukada K, Urabe I, and Yomo T. Replication of genetic information with self-encoded replicase in liposomes. Chembiochem 2008 Oct 13; 9(15) 2403-10. doi:10.1002/cbic.200800360 pmid:18785673. PubMed HubMed [Kita-Chembiochem-2008]
34. Ichihashi N, Matsuura T, Kita H, Hosoda K, Sunami T, Tsukada K, and Yomo T. Importance of translation-replication balance for efficient replication by the self-encoded replicase. Chembiochem 2008 Dec 15; 9(18) 3023-8. doi:10.1002/cbic.200800518 pmid:19021140. PubMed HubMed [Ichihashi-Chembiochem-2008]

Re-design of phages as therapeutics for bacterial infections, or for non-medical biofilm problems

35. Lu TK and Collins JJ. Dispersing biofilms with engineered enzymatic bacteriophage. Proc Natl Acad Sci U S A 2007 Jul 3; 104(27) 11197-202. doi:10.1073/pnas.0704624104 pmid:17592147. PubMed HubMed [Lu-ProcNatlAcadSci-2007]
36. Loeffler JM, Nelson D, and Fischetti VA. Rapid killing of Streptococcus pneumoniae with a bacteriophage cell wall hydrolase. Science 2001 Dec 7; 294(5549) 2170-2. doi:10.1126/science.1066869 pmid:11739958. PubMed HubMed [Loeffler-Science-2001]

"A Genomic View of the World"

12:00pm - 1:00pm

Sherman Fairchild 177, 7 Divinity Ave

"Synthetic Life"

4:00pm - 5:00pm

Northwest B-103, 52 Oxford St.