Biophysics 242r/2009:Syllabus

Note: This syllabus will be updated over the next few weeks as guest lecturer schedules are finalized.

Date	Lecturer	Topic	Papers / Assignments (due date indicated with an asterisk in the 'Date' column)
Jan. 29	Pam Silver / Jack Szostak	COURSE INTRO – required work; paper reading and project design and presentation Jack and Pam will present perspectives on interesting things that Nature does that can serve as basis for Synthetic Biology and examples of synthetic biology	SUGGESTED READING: A general overview of synthetic biology 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 | Drubin DA, Way JC, and Silver PA. Designing biological systems. Genes Dev. 2007 Feb 1;21(3):242-54. DOI:10.1101/gad.1507207 | Serrano L. Synthetic biology: promises and challenges. Mol Syst Biol. 2007;3:158. DOI:10.1038/msb4100202 | 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
Feb. 5	Pam Silver	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
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 | 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 | (OffEd)-1990 pmid=1693367 MOROWITZ HJ and TOURTELLOTTE ME. The smallest living cells. Sci Am. 1962 Mar;206:117-26. DOI:10.1038/scientificamerican0362-117 | Peterson SN and Fraser CM. The complexity of simplicity. Genome Biol. 2001;2(2):COMMENT2002. DOI:10.1186/gb-2001-2-2-comment2002 |
Feb. 17	Jeremy Gunawardena	COMBINED LECTURE/DISCUSSION: Quantitative considerations in complex system design	SUGGESTED READING:
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 | pmid=in press
Feb. 24	Pam Silver	LECTURE: Designing more complex systems
Feb. 26	Pam Silver	DISCUSSION: Designing more complex systems	Required reading: T.B.A.
Mar. 3	Joseph (Jay) Vacanti	LECTURE: Using principles derived from evolutionary biology for regenerative medicine
Mar. 5	Joseph (Jay) Vacanti	DISCUSSION: Using principles derived from evolutionary biology for regenerative medicine	REQUIRED 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 |
Mar. 10	George Church	LECTURE: Building artificial organisms, reprogramming cellular genomes, and in vitro genomes
Mar. 12	George Church	DISCUSSION: Building artificial organisms, reprogramming cellular genomes, and in vitro genomes	REQUIRED READING: Forster AC and Church GM. Synthetic biology projects in vitro. Genome Res. 2007 Jan;17(1):1-6. DOI:10.1101/gr.5776007 |
Mar. 17	William Shih	LECTURE: DNA nanostructures
Mar. 19	William Shih	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	n/a	n/a
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 | Winkler W, Nahvi A, and Breaker RR. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature. 2002 Oct 31;419(6910):952-6. DOI:10.1038/nature01145 | Savran CA, Knudsen SM, Ellington AD, and Manalis SR. Micromechanical detection of proteins using aptamer-based receptor molecules. Anal Chem. 2004 Jun 1;76(11):3194-8. DOI:10.1021/ac049859f | Winkler WC, Nahvi A, Roth A, Collins JA, and Breaker RR. Control of gene expression by a natural metabolite-responsive ribozyme. Nature. 2004 Mar 18;428(6980):281-6. DOI:10.1038/nature02362 |
Apr. 2	Jack Szostak	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!!!
Apr. 7	Jack Szostak	LECTURE: Evolution vs Design of Molecular Components (Folded Proteins, Enzymes)
Apr. 9	Jack Szostak	DISCUSSION: Evolution vs Design of Molecular Components (Folded Proteins, Enzymes)	REQUIRED 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 | 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
Apr. 16	Jack Szostak & TFs	DISCUSSION: Protocell Design: Self-Replicating Materials	REQUIRED READING: T.B.A.
Apr. 21	Irene Chen	COMBINED LECTURE/DISCUSSION: Re-design of phages as therapeutics for bacterial infections, or for non-medical biofilm problems	SUGGESTED READING: T.B.A.
Apr. 23	Open for project discussions
Apr. 28	n/a	Project discussions	Project due!
Apr. 30	n/a	Project discussions
May 6, 7, & 8	Craig Venter	Non-mandatory Prather lectures, not actually affiliated with this class, but attendance is recommended	n/a