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: Error fetching PMID 11201752 Drubin DA, Way JC, and Silver PA. Designing biological systems. Genes Dev. 2007 Feb 1;21(3):242-54. DOI:10.1101/gad.1507207 |
Feb. 3	Pam Silver	LECTURE: Designing simple biological systems	SUGGESTED READING: Error fetching PMID 18091727 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 |
Feb. 5	Pam Silver & TFs	DISCUSSION: Designing simple biological systems	REQUIRED READING: Error fetching PMID 15096621
Feb. 10	Tom Knight	LECTURE: Logic and engineering applied to biology	SUGGESTED READING: Error fetching PMID 11182883 Error fetching PMID 8816789
Feb. 12	Tom Knight & TFs	DISCUSSION: Logic and engineering applied to biology	REQUIRED READING: Error fetching PMID 16407165
Feb. 17	Jeremy Gunawardena	COMBINED LECTURE/DISCUSSION: Watchmaking for the partially-sighted	SUGGESTED READING: Error fetching PMID 12932323 Error fetching PMID 19148099 Elowitz MB and Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature. 2000 Jan 20;403(6767):335-8. DOI:10.1038/35002125 |
Feb. 19	Kristala Jones Prather	COMBINED LECTURE/DISCUSSION: Metabolic engineering or synthetic biology? Yes!	SUGGESTED READING: Error fetching PMID 18725289 Error fetching PMID 19064911
Feb. 24	Pam Silver	LECTURE: Designing more complex systems	SUGGESTED READING: Error fetching PMID 11152493 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 | REQUIRED READING: Error fetching PMID 19148099
Feb. 26	Pam Silver & TFs	DISCUSSION: Designing more complex systems	REQUIRED READING: Error fetching PMID 10741964 Error fetching PMID 12803906
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: Error fetching PMID 8493529 Error fetching PMID 10437854 REQUIRED READING: Error fetching PMID 19199577
Mar. 10	George Church	LECTURE: Building artificial organisms, reprogramming cellular genomes, and in vitro genomes	SUGGESTED READING: Error fetching PMID 17151344 Error fetching PMID 19073939 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 |
Mar. 12	George Church & TFs	DISCUSSION: Building artificial organisms, reprogramming cellular genomes, and in vitro genomes	REQUIRED READING: Error fetching PMID 18548004
Mar. 17	William Shih	LECTURE: DNA nanostructures and DNA computing
Mar. 19	William Shih & TFs	DISCUSSION: DNA nanostructures	REQUIRED READING: Error fetching PMID 18202654 Rothemund PW. Folding DNA to create nanoscale shapes and patterns. Nature. 2006 Mar 16;440(7082):297-302. DOI:10.1038/nature04586 |
Mar. 24 & 26	Spring break, no class	---	---
Mar. 31	Jack Szostak	LECTURE: RNA control devices	SUGGESTED READING: Error fetching PMID 7687750 Error fetching PMID 7690155
Apr. 2	Jack Szostak & TFs	DISCUSSION: RNA control devices	REQUIRED READING: Be sure to read supplemental material for this paper! Error fetching PMID 18927397	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: Error fetching PMID 17700701
Apr. 9	Jack Szostak & TFs	DISCUSSION: Evolution vs Design of Molecular Components (Folded Proteins, Enzymes)	REQUIRED READING: Error fetching PMID 18354394
Apr. 14	Jack Szostak	LECTURE: Protocell Design: Self-Replicating Materials	SUGGESTED READING: Error fetching PMID 18528332
Apr. 16	Jack Szostak & TFs	DISCUSSION: Protocell Design: Self-Replicating Materials	REQUIRED READING: Error fetching PMID 18785673 Error fetching PMID 19021140
Apr. 21	Irene Chen	COMBINED LECTURE/DISCUSSION: Re-design of phages as therapeutics for bacterial infections, or for non-medical biofilm problems	SUGGESTED READING: Error fetching PMID 11739958 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 |
Apr. 22		No class		Powerpoint slides due by 5pm for those presenting on the 23rd. (send to [email protected])
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 [email protected])
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 [email protected])
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.	---