Biophysics 242r/2009:Syllabus

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Biophysics 242r/2009:

Special Topics in Biophysics (Synthetic Biology)

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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:
  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 | PubMed ID:17289915 | 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 | PubMed ID:11201752 | HubMed [Szostak-Nature-2001]
All Medline abstracts: PubMed | HubMed
Feb. 3 Pam Silver LECTURE:

Designing simple biological systems

SUGGESTED READING:
  1. 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 | PubMed ID:16738572 | HubMed [Andrianantoandro-MolSystBiol-2006]
  2. Serrano L. Synthetic biology: promises and challenges. Mol Syst Biol. 2007;3:158. DOI:10.1038/msb4100202 | PubMed ID:18091727 | HubMed [Serrano-MolSystBiol-2007]
All Medline abstracts: PubMed | HubMed
Feb. 5 Pam Silver & TFs DISCUSSION:

Designing simple biological systems

REQUIRED READING:
  1. 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 | PubMed ID:15096621 | HubMed [Basu-ProcNatlAcadSci-2004]
Feb. 10 Tom Knight LECTURE:

Logic and engineering applied to biology

SUGGESTED READING:
  1. Peterson SN and Fraser CM. The complexity of simplicity. Genome Biol. 2001;2(2):COMMENT2002. PubMed ID:11182883 | HubMed [Peterson-GenomeBiology-2001]
  2. 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. PubMed ID:8816789 | HubMed [Mushegian-ProcNatlAcadSci-1996]
All Medline abstracts: PubMed | HubMed
Feb. 12 Tom Knight & TFs DISCUSSION:

Logic and engineering applied to biology

REQUIRED READING:
  1. 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 | PubMed ID:16407165 | HubMed [Glass-ProcNatlAcadSci-2006]
Feb. 17 Jeremy Gunawardena COMBINED LECTURE/DISCUSSION:

Watchmaking for the partially-sighted

SUGGESTED READING:
  1. Elowitz MB and Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature. 2000 Jan 20;403(6767):335-8. DOI:10.1038/35002125 | PubMed ID:10659856 | HubMed [Elowitz-Nature-2000]
  2. Lewis J. Autoinhibition with transcriptional delay: a simple mechanism for the zebrafish somitogenesis oscillator. Curr Biol. 2003 Aug 19;13(16):1398-408. PubMed ID:12932323 | HubMed [Lewis-CurrBiol-2003]
  3. 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 | PubMed ID:19148099 | HubMed [Tigges-Nature-2009]
All Medline abstracts: PubMed | HubMed
Feb. 19 Kristala Jones Prather COMBINED LECTURE/DISCUSSION:

Metabolic engineering or synthetic biology? Yes!

SUGGESTED READING:
  1. 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 | PubMed ID:18725289 | HubMed [Prather-CurrOpinBiotech-2008]
  2. 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 | PubMed ID:19064911 | HubMed [Zhang-ProcNatlAcadSci-2008]
All Medline abstracts: PubMed | HubMed
Feb. 24 Pam Silver LECTURE:

Designing more complex systems

SUGGESTED READING:
  1. 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 | PubMed ID:16330045 | HubMed [Anderson-JMolBiol-2006]
  2. 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 | PubMed ID:11152493 | HubMed [Jackson-JVirol-2001]
All Medline abstracts: PubMed | HubMed

REQUIRED READING:

  1. 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 | PubMed ID:19148099 | HubMed [Tigges-Nature-2009]
Feb. 26 Pam Silver & TFs DISCUSSION:

Designing more complex systems

REQUIRED READING:
  1. 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. PubMed ID:10741964 | HubMed [Thomas-Science-2000]
  2. 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 | PubMed ID:12803906 | HubMed [Burt-ProcBiolSci-2003]
All Medline abstracts: PubMed | HubMed
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:
  1. Langer R and Vacanti JP. Tissue engineering. Science. 1993 May 14;260(5110):920-6. PubMed ID:8493529 | HubMed [Langer-Science-1993]
  2. 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. PubMed ID:10437854 | HubMed [Vacanti-Lancet-1999]
All Medline abstracts: PubMed | HubMed

REQUIRED READING:

  1. 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 | PubMed ID:19199577 | HubMed [Weinand-TEA-2009]
Mar. 10 George Church LECTURE:

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

SUGGESTED READING:
  1. Forster AC and Church GM. Synthetic biology projects in vitro. Genome Res. 2007 Jan;17(1):1-6. DOI:10.1101/gr.5776007 | PubMed ID:17151344 | HubMed [Forster-GenomeRes-2007]
  2. 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 | PubMed ID:15591347 | HubMed [Noireaux-PNAS-2004]
  3. 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 | PubMed ID:19073939 | HubMed [Gibson-PNAS-2008]
All Medline abstracts: PubMed | HubMed
Mar. 12 George Church & TFs DISCUSSION:

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

REQUIRED READING:
  1. 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 | PubMed ID:18548004 | HubMed [Xiao-Nature-2008]
Mar. 17 William Shih LECTURE:

DNA nanostructures and DNA computing

Mar. 19 William Shih & TFs DISCUSSION:

DNA nanostructures

REQUIRED READING:
  1. Rothemund PW. Folding DNA to create nanoscale shapes and patterns. Nature. 2006 Mar 16;440(7082):297-302. DOI:10.1038/nature04586 | PubMed ID:16541064 | HubMed [Rothemund-Nature-2006]
  2. 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 | PubMed ID:18202654 | HubMed [Yin-Nature-2008]
All Medline abstracts: PubMed | HubMed
Mar. 24 & 26 Spring break, no class --- ---
Mar. 31 Jack Szostak LECTURE:

RNA control devices

SUGGESTED READING:
  1. Sassanfar M and Szostak JW. An RNA motif that binds ATP. Nature. 1993 Aug 5;364(6437):550-3. DOI:10.1038/364550a0 | PubMed ID:7687750 | HubMed [Sassanfar-Nature-1993]
  2. 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. PubMed ID:7690155 | HubMed [Bartel-Science-1993]
All Medline abstracts: PubMed | HubMed
Apr. 2 Jack Szostak & TFs DISCUSSION:

RNA control devices

REQUIRED READING:

Be sure to read supplemental material for this paper!

  1. 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 | PubMed ID:18927397 | HubMed [Win-Science-2008]
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:
  1. 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 | PubMed ID:17700701 | HubMed [Seelig-Nature-2007]
Apr. 9 Jack Szostak & TFs DISCUSSION:

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

REQUIRED READING:
  1. 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 | PubMed ID:18354394 | HubMed [Rothlisberger-Nature-2008]
Apr. 14 Jack Szostak LECTURE:

Protocell Design: Self-Replicating Materials

SUGGESTED READING:
  1. 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 | PubMed ID:18528332 | HubMed [Mansy-Nature-2008]
Apr. 16 Jack Szostak & TFs DISCUSSION:

Protocell Design: Self-Replicating Materials

REQUIRED READING:
  1. 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 | PubMed ID:18785673 | HubMed [Kita-Chembiochem-2008]
  2. 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 | PubMed ID:19021140 | HubMed [Ichihashi-Chembiochem-2008]
All Medline abstracts: PubMed | HubMed
Apr. 21 Irene Chen COMBINED LECTURE/DISCUSSION:

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

SUGGESTED READING:
  1. 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 | PubMed ID:17592147 | HubMed [Lu-ProcNatlAcadSci-2007]
  2. 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 | PubMed ID:11739958 | HubMed [Loeffler-Science-2001]
All Medline abstracts: PubMed | HubMed
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.

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