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:
Error fetching PMID 17289915:
Error fetching PMID 11201752:
  1. Error fetching PMID 17289915: [Drubin-GenesDev-2007]
  2. Error fetching PMID 11201752: [Szostak-Nature-2001]
All Medline abstracts: PubMed HubMed
Feb. 3 Pam Silver LECTURE:

Designing simple biological systems

SUGGESTED READING:
Error fetching PMID 16738572:
Error fetching PMID 18091727:
  1. Error fetching PMID 16738572: [Andrianantoandro-MolSystBiol-2006]
  2. Error fetching PMID 18091727: [Serrano-MolSystBiol-2007]
All Medline abstracts: PubMed HubMed
Feb. 5 Pam Silver & TFs DISCUSSION:

Designing simple biological systems

REQUIRED READING:
Error fetching PMID 15096621:
  1. Error fetching PMID 15096621: [Basu-ProcNatlAcadSci-2004]
Feb. 10 Tom Knight LECTURE:

Logic and engineering applied to biology

SUGGESTED READING:
Error fetching PMID 11182883:
Error fetching PMID 8816789:
  1. Error fetching PMID 11182883: [Peterson-GenomeBiology-2001]
  2. Error fetching PMID 8816789: [Mushegian-ProcNatlAcadSci-1996]
All Medline abstracts: PubMed HubMed
Feb. 12 Tom Knight & TFs DISCUSSION:

Logic and engineering applied to biology

REQUIRED READING:
Error fetching PMID 16407165:
  1. Error fetching PMID 16407165: [Glass-ProcNatlAcadSci-2006]
Feb. 17 Jeremy Gunawardena COMBINED LECTURE/DISCUSSION:

Watchmaking for the partially-sighted

SUGGESTED READING:
Error fetching PMID 10659856:
Error fetching PMID 12932323:
Error fetching PMID 19148099:
  1. Error fetching PMID 10659856: [Elowitz-Nature-2000]
  2. Error fetching PMID 12932323: [Lewis-CurrBiol-2003]
  3. Error fetching PMID 19148099: [Tigges-Nature-2009]
All Medline abstracts: PubMed HubMed
Feb. 19 Kristala Jones Prather COMBINED LECTURE/DISCUSSION:

Metabolic engineering or synthetic biology? Yes!

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

Designing more complex systems

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

REQUIRED READING:

Error fetching PMID 19148099:
  1. Error fetching PMID 19148099: [Tigges-Nature-2009]
Feb. 26 Pam Silver & TFs DISCUSSION:

Designing more complex systems

REQUIRED READING:
Error fetching PMID 10741964:
Error fetching PMID 12803906:
  1. Error fetching PMID 10741964: [Thomas-Science-2000]
  2. Error fetching PMID 12803906: [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:
Error fetching PMID 8493529:
Error fetching PMID 10437854:
  1. Error fetching PMID 8493529: [Langer-Science-1993]
  2. Error fetching PMID 10437854: [Vacanti-Lancet-1999]
All Medline abstracts: PubMed HubMed

REQUIRED READING:

Error fetching PMID 19199577:
  1. Error fetching PMID 19199577: [Weinand-TEA-2009]
Mar. 10 George Church LECTURE:

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

SUGGESTED READING:
Error fetching PMID 17151344:
Error fetching PMID 15591347:
Error fetching PMID 19073939:
  1. Error fetching PMID 17151344: [Forster-GenomeRes-2007]
  2. Error fetching PMID 15591347: [Noireaux-PNAS-2004]
  3. Error fetching PMID 19073939: [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:
Error fetching PMID 18548004:
  1. Error fetching PMID 18548004: [Xiao-Nature-2008]
Mar. 17 William Shih LECTURE:

DNA nanostructures and DNA computing

Mar. 19 William Shih & TFs DISCUSSION:

DNA nanostructures

REQUIRED READING:
Error fetching PMID 16541064:
Error fetching PMID 18202654:
  1. Error fetching PMID 16541064: [Rothemund-Nature-2006]
  2. Error fetching PMID 18202654: [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:
Error fetching PMID 7687750:
Error fetching PMID 7690155:
  1. Error fetching PMID 7687750: [Sassanfar-Nature-1993]
  2. Error fetching PMID 7690155: [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!

Error fetching PMID 18927397:
  1. Error fetching PMID 18927397: [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:
Error fetching PMID 17700701:
  1. Error fetching PMID 17700701: [Seelig-Nature-2007]
Apr. 9 Jack Szostak & TFs DISCUSSION:

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

REQUIRED READING:
Error fetching PMID 18354394:
  1. Error fetching PMID 18354394: [Rothlisberger-Nature-2008]
Apr. 14 Jack Szostak LECTURE:

Protocell Design: Self-Replicating Materials

SUGGESTED READING:
Error fetching PMID 18528332:
  1. Error fetching PMID 18528332: [Mansy-Nature-2008]
Apr. 16 Jack Szostak & TFs DISCUSSION:

Protocell Design: Self-Replicating Materials

REQUIRED READING:
Error fetching PMID 18785673:
Error fetching PMID 19021140:
  1. Error fetching PMID 18785673: [Kita-Chembiochem-2008]
  2. Error fetching PMID 19021140: [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:
Error fetching PMID 17592147:
Error fetching PMID 11739958:
  1. Error fetching PMID 17592147: [Lu-ProcNatlAcadSci-2007]
  2. Error fetching PMID 11739958: [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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