20.20(S13):Advanced topics

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| [[Natalie Kuldell]]
| [[Natalie Kuldell]]
| preview of 20.385
| preview of 20.385
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|''Factory of Life ''<br> Witze A [http://www.sciencenews.org/view/feature/id/347263/description/Factory_of_Life]<br>
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|'''Factory of Life '''<br> Witze A [http://www.sciencenews.org/view/feature/id/347263/description/Factory_of_Life| Science News]<br>
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''Two ‘What if' experiments''<br> Ptashne M [[PMID: 15055587]]<br>
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'''Two ‘What if' experiments'''<br> Ptashne M [[PMID: 15055587]]<br>
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''Build Artificial'' <br> Brent R  [[PMID: 15055588]]   
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'''Build Artificial''' <br> Brent R  [[PMID: 15055588]]   
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| <b>Parts™</b>
| <b>Parts™</b>
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|''' Synthetic biology: caught between property rights, the public domain, and the commons''' <br>Rai A, Boyle ''J. PLoS Biol.'' (2007)5(3):e58<br>[[PMID: 17355173]] <br>
|''' Synthetic biology: caught between property rights, the public domain, and the commons''' <br>Rai A, Boyle ''J. PLoS Biol.'' (2007)5(3):e58<br>[[PMID: 17355173]] <br>
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|'''Patents and Translational Research in Genomics'''<br>Kaye J, Hawkins N, and Taylor J. ''Nature Biotech'' (2007) 25(7): 739–741.[[doi: 10.1038/nbt0707-739.]]
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|'''Preparing synthetic biology for the world'''<br>Moe-Behrens GH, Davis R, Haynes KA. ''Front Microbiol'' (2013) 4:5 <br> [[doi: 10.3389/fmicb.2013.00005]]
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|'''Safety!'''
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| Week 14: <br><font color = blue> Wed May 16 </font color> <br> before final presentations
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| '''Managing the unimaginable. Regulatory responses to the challenges posed by synthetic biology and synthetic genomics.''' <br>Samuel GN, Selgelid MJ, Kerridge I. ''EMBO reports'' (2009) 10(1):7-11.<br>[[DOI: 10.1038/embor.2008.232]]<br>
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|'''Darwin’s Surprise: Why are evolutionary biologists bringing back extinct deadly viruses?''' <br>Michael Specter [http://www.newyorker.com/reporting/2007/12/03/071203fa_fact_specter New Yorker article]
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Revision as of 22:17, 29 January 2013

Contents

20.385: Advanced Topics in Synthetic Biology

Assignments

Homework dropbox is here

Part 1: Readings

  • Paper 1 (10%)
  • Paper 2 (15%)
  • Response record (20%): your thoughts about the papers you don't present.
  • Participation in class discussions (5%): your thoughtful questions and ideas during the presentations of others

Instructions for these assignment are here

Part 2: Team Mentoring

  • Progress and Mentoring Reports (30%): one page summaries of your freshman team's work and dynamics
  • Team's project average (15%): based on the grade for the 3 major assignments submitted by your freshman team
  • Instructor Leverage (5%): discretionary adjustment by NK

Instructions for these assignments are here

Reading Schedule

Discussions will be 1 hour long during Wednesday 2-5 studio block

16-220

TOPIC DATE Discussion leader(s) Discussion paper(s) Related paper(s) to enjoy
Preview of 20.385 Week 1:
Wed Feb 6
Natalie Kuldell preview of 20.385 Science News]

Two ‘What if' experiments
Ptashne M PMID: 15055587
Build Artificial
Brent R PMID: 15055588

Parts™ Week 2:
Wed Feb 13
Natalie Kuldell
ppt is here
Turning lambda Cro into a transcriptional activator
Bushman FD, Ptashne M.Cell. (1988) Jul 15;54(2):191-7.
PMID: 2968842
Synthetic biology devices as tools for metabolic engineering
Shiue E, Prather K. Biochemical Engineering Journal (2012) 65:82–89
doi:10.1016/j.bej.2012.04.006
DNA fine-tuning + evolution
Week 3:
Wed Feb 20
Rational Diversification of a Promoter Providing Fine-Tuned Expression and Orthogonal Regulation for Synthetic Biology
Blount BA, Weenink T, Vasylechko S, Ellis T.
PLoS ONE (2012) 7(3): e33279.
doi:10.1371/journal.pone.0033279
Directed evolution as a powerful synthetic biology tool
Cobb RE, Sun N, Zhao H. Methods (2012) Mar 23.
PMID: 22465795
Transcription-based Logic Devices
Week 4:
Wed Feb 27
Genetic programs constructed from layered logic gates in single cells
Moon TS, Lou C, Tamsir A, Stanton BC, Voigt CA Nature (2012) 491: 249–253
doi:10.1038/nature11516
Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology
Wang B, et al. Nat. Commun. (2011) 2 : 508
doi: 10.1038/ncomms1516
RNA Engineering
Week 5:
Wed Mar 6
De novo automated design of small RNA circuits for engineering synthetic riboregulation in living cells.
Rodrigo G, Landrain TE, Jaramillo A. PNAS(2012) 109(38):15271-6.
PMID: 22949707
RNA synthetic biology
Isaacs FJ, Dwyer DJ, Collins JJ. Nat Biotechnol. (2006) 24(5):545-54.
PMID: 16680139
Engineering Biology
Week 6:
Wed Mar 13
before 3 ideas presentations
Towards practical, high-capacity, low-maintenance information storage in synthesized DNA
Goldman N et al. Nature (2013)
doi:10.1038/nature11875
A fully decompressed synthetic bacteriophage øX174 genome assembled and archived in yeast
Jaschke PR et al. Virology(2012)434(2):278-84.
doi: 10.1016/j.virol.2012.09.020
SynBio for Science
Week 7:
Wed Mar 20
Synthetic biology challenges long-held hypotheses in translation, codon bias and transcription
Forster AC. Biotechnol J. (2012) 7(7):835-45.
doi: 10.1002/biot.201200002
Five hard truths for synthetic biology
Kwok R. Nature(2010) 463(7279):288-90.
doi: 10.1038/463288a
Spring Break Mar 26-30 No class all week
DNA construction and editing technologies
Week 8:
Wed Apr 3
Knockout mice created by TALEN-mediated gene targeting.
Sung YH et al. Nat Biotechnol (2013) 31(1):23-4.
doi: 10.1038/nbt.2477
Multiplex Genome Engineering Using CRISPR/Cas Systems
Cong L et al. Science (2013) Jan 3.
PMID: 23287718
Cell Physiology
Week 9:
Wed Apr 10
before tech spec review
Shared control of gene expression in bacteria by transcription factors and global physiology of the cell
Berthoumieux S et alMol Syst Biol (2013) 9:634
doi: 10.1038/msb.2012.70
A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis
Picotti P et al.Nature (2013) Jan 20.
doi: 10.1038/nature11835
Chassis
Week 10:
Wed Apr 17
Towards a metabolic engineering strain "commons": An Escherichia coli platform strain for ethanol production
Woodruff LB, May BL, Warner JR, Gill RT. Biotechnol Bioeng (2013) Jan 15.
doi: 10.1002/bit.24840
Contextualizing context for synthetic biology--identifying causes of failure of synthetic biological systems
Cardinale S, Arkin AP.Biotechnol J(2012) 7(7):856-66.
doi: 10.1002/biot.201200085
Programming in the Noise
Week 11:
Wed Apr 24
Iterative plug-and-play methodology for constructing and modifying synthetic gene networks
Litcofsky KD et al. Nat Methods(2012) 9(11):1077-80.
doi: 10.1038/nmeth.2205
A sensing array of radically coupled genetic ‘biopixels’
Prindle A et al. Nature(2012)481:39–44
doi:10.1038/nature10722
Metabolic Engineering Week 12:
Wed May 1
Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs Na D et al. Nat Biotechnol (2013) Jan 20.
doi: 10.1038/nbt.2461
Synthetic protein scaffolds provide modular control over metabolic fluxDueber JE et al. Nat Biotechnol (2009) 27(8):753-9.
doi: 10.1038/nbt.1557
Systems & Communities Week 13:
Wed May 8
Engineered cell-cell communication via DNA messaging
Ortiz ME, Endy D. JBE (2012) 6(1):16.
doi: 10.1186/1754-1611-6-16
Autonomous bacterial localization and gene expression based on nearby cell receptor density
Wu HC et al. Mol Syst Biol (2013) 9:636.
doi: 10.1038/msb.2012.71
Property rights in synthetic biology Week 14:
Wed May 15
before final presentations
Synthetic biology: caught between property rights, the public domain, and the commons
Rai A, Boyle J. PLoS Biol. (2007)5(3):e58
PMID: 17355173
Preparing synthetic biology for the world
Moe-Behrens GH, Davis R, Haynes KA. Front Microbiol (2013) 4:5
doi: 10.3389/fmicb.2013.00005
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