Biophysics 242r/2009:Syllabus

Note: This syllabus is now finalized, and should stay as it is now for the remainder of the semester.

Date	Lecturer	Topic	Papers	Assignments
Jan. 29	Pam Silver / Jack Szostak	1. Brief presentations from Jack and Pam about their views on Synthetic Biology and what will be covered in the course. Total time - about one hour (or less) 2. Presentation from faculty and TFs about requirements for the course (about 30 min including time for questions).	SUGGESTED READING: Drubin DA, Way JC, and Silver PA. Designing biological systems. Genes Dev. 2007 Feb 1;21(3):242-54. DOI:10.1101/gad.1507207 | Szostak JW, Bartel DP, and Luisi PL. Synthesizing life. Nature. 2001 Jan 18;409(6818):387-90. DOI:10.1038/35053176 |
Feb. 3	Pam Silver	LECTURE: Designing simple biological systems	SUGGESTED READING: 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 | Serrano L. Synthetic biology: promises and challenges. Mol Syst Biol. 2007;3:158. DOI:10.1038/msb4100202 |
Feb. 5	Pam Silver & TFs	DISCUSSION: Designing simple biological systems	REQUIRED READING: 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 |
Feb. 10	Tom Knight	LECTURE: Logic and engineering applied to biology	SUGGESTED READING: Peterson SN and Fraser CM. The complexity of simplicity. Genome Biol. 2001;2(2):COMMENT2002. DOI:10.1186/gb-2001-2-2-comment2002 | 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. DOI:10.1073/pnas.93.19.10268 |
Feb. 12	Tom Knight & TFs	DISCUSSION: Logic and engineering applied to biology	REQUIRED READING: 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 |
Feb. 17	Jeremy Gunawardena	COMBINED LECTURE/DISCUSSION: Watchmaking for the partially-sighted	SUGGESTED READING: Elowitz MB and Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature. 2000 Jan 20;403(6767):335-8. DOI:10.1038/35002125 | Lewis J. Autoinhibition with transcriptional delay: a simple mechanism for the zebrafish somitogenesis oscillator. Curr Biol. 2003 Aug 19;13(16):1398-408. DOI:10.1016/s0960-9822(03)00534-7 | 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 |
Feb. 19	Kristala Jones Prather	COMBINED LECTURE/DISCUSSION: Metabolic engineering or synthetic biology? Yes!	SUGGESTED READING: 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 | 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 |
Feb. 24	Pam Silver	LECTURE: Designing more complex systems	SUGGESTED READING: 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 | 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 | REQUIRED READING: 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 |
Feb. 26	Pam Silver & TFs	DISCUSSION: Designing more complex systems	REQUIRED READING: 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. DOI:10.1126/science.287.5462.2474 | 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 |
Mar. 3	Joseph (Jay) Vacanti	LECTURE: Using principles derived from evolutionary biology for regenerative medicine
Mar. 5	Joseph (Jay) Vacanti & TFs	DISCUSSION: Using principles derived from evolutionary biology for regenerative medicine	SUGGESTED READING: Langer R and Vacanti JP. Tissue engineering. Science. 1993 May 14;260(5110):920-6. DOI:10.1126/science.8493529 | 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. DOI:10.1016/s0140-6736(99)90247-7 | REQUIRED READING: 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 |
Mar. 10	George Church	LECTURE: Building artificial organisms, reprogramming cellular genomes, and in vitro genomes	SUGGESTED READING: Forster AC and Church GM. Synthetic biology projects in vitro. Genome Res. 2007 Jan;17(1):1-6. DOI:10.1101/gr.5776007 | 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 | 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 |
Mar. 12	George Church & TFs	DISCUSSION: Building artificial organisms, reprogramming cellular genomes, and in vitro genomes	REQUIRED READING: 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 |
Mar. 17	William Shih	LECTURE: DNA nanostructures and DNA computing
Mar. 19	William Shih & TFs	DISCUSSION: DNA nanostructures	REQUIRED READING: Rothemund PW. Folding DNA to create nanoscale shapes and patterns. Nature. 2006 Mar 16;440(7082):297-302. DOI:10.1038/nature04586 | 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 |
Mar. 24 & 26	Spring break, no class	---	---
Mar. 31	Jack Szostak	LECTURE: RNA control devices	SUGGESTED READING: Sassanfar M and Szostak JW. An RNA motif that binds ATP. Nature. 1993 Aug 5;364(6437):550-3. DOI:10.1038/364550a0 | 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. DOI:10.1126/science.7690155 |
Apr. 2	Jack Szostak & TFs	DISCUSSION: RNA control devices	REQUIRED READING: Be sure to read supplemental material for this paper! 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 |	ASSIGNMENTS: 1 page blurb about project due!!! Submit via email to Paul and/or Devin before class starts today.
Apr. 7	Jack Szostak	LECTURE: Evolution vs Design of Molecular Components (Folded Proteins, Enzymes)	SUGGESTED READING: 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 |
Apr. 9	Jack Szostak & TFs	DISCUSSION: Evolution vs Design of Molecular Components (Folded Proteins, Enzymes)	REQUIRED READING: 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 |
Apr. 14	Jack Szostak	LECTURE: Protocell Design: Self-Replicating Materials	SUGGESTED READING: 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 |
Apr. 16	Jack Szostak & TFs	DISCUSSION: Protocell Design: Self-Replicating Materials	REQUIRED READING: 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 | 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 |
Apr. 21	Irene Chen	COMBINED LECTURE/DISCUSSION: Re-design of phages as therapeutics for bacterial infections, or for non-medical biofilm problems	SUGGESTED READING: 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 | 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 |
Apr. 22		No class		Powerpoint slides due by 5pm for those presenting on the 23rd. (send to paul.cowgill@gmail.com)
Apr. 23	Jack, Pam, and TFs	First 7 project presentations
Apr. 27		No class		Powerpoint slides due by 5pm for those presenting on the 28th. (send to paul.cowgill@gmail.com)
Apr. 28	Jack, Pam, and TFs	Next set of 8 project presentations
Apr. 29		No class		Powerpoint slides due by 5pm for those presenting on the 30th. (send to paul.cowgill@gmail.com)
Apr. 30	Jack, Pam, and TFs	Remaining 7 project presentations
May 8	Craig Venter	Non-mandatory Prather lectures, not actually affiliated with this class, but attendance is recommended. "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.	---