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 ''Witze A''Science News (2013) 183:1 [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]<br>
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''Two ‘What if' experiments''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''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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| '''Metabolic Engineering'''  
| '''Metabolic Engineering'''  
| Week 12:<br> Wed May 1
| Week 12:<br> Wed May 1
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| '''Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs'''  Na D et al. ''Nat Biotechnol'' (2013) Jan 20. <br> [[doi: 10.1038/nbt.2461]]
| '''Use of modular, synthetic scaffolds for improved production of glucaric acid in engineered E. coli.'''Moon TS et al. ''Metabolic Engineering'' (2010) 12: 298-305 <br>[[PMID: 20117231]]
| '''Use of modular, synthetic scaffolds for improved production of glucaric acid in engineered E. coli.'''Moon TS et al. ''Metabolic Engineering'' (2010) 12: 298-305 <br>[[PMID: 20117231]]
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|'''Organization of Intracellular Reactions with Rationally Designed RNA Assemblies'''<br>Delebecqu CJ et al. ''Science'' (2011) 333:470 <br>[[DOI: 10.1126/science.1206938 ]]
 
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|'''Systems & System Ecology'''  
|'''Systems & System Ecology'''  

Revision as of 22:05, 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 Factory of Life
Witze A [1]

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
Use of modular, synthetic scaffolds for improved production of glucaric acid in engineered E. coli.Moon TS et al. Metabolic Engineering (2010) 12: 298-305
PMID: 20117231
Systems & System Ecology Week 13:
Wed May 8
Synthetic chromosome arms function in yeast and generate phenotypic diversity by design
Dymond JS et al. Nature (2011) 477: 471–476
doi:10.1038/nature10403
Engineered bidirectional communication mediates a consensus in a microbial biofilm consortium
Brenner K PNAS (2007) 104(44):17300-17304
DOI: 10.1073/pnas.0704256104
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
Patents and Translational Research in Genomics
Kaye J, Hawkins N, and Taylor J. Nature Biotech (2007) 25(7): 739–741.doi: 10.1038/nbt0707-739.
Safety! Week 14:
Wed May 16
before final presentations
Managing the unimaginable. Regulatory responses to the challenges posed by synthetic biology and synthetic genomics.
Samuel GN, Selgelid MJ, Kerridge I. EMBO reports (2009) 10(1):7-11.
DOI: 10.1038/embor.2008.232
Darwin’s Surprise: Why are evolutionary biologists bringing back extinct deadly viruses?
Michael Specter New Yorker article
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