20.20(S13):Advanced topics

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| preview of 20.385
| preview of 20.385
|before next week read
|before next week read
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#''Factory of Life ''<br>A. Witze<br>Science News (2013) 183:1 [[http://www.sciencenews.org/view/feature/id/347263/description/Factory_of_Life]]
+
#''Factory of Life ''<br>A. Witze<br>Science News (2013) 183:1 [http://www.sciencenews.org/view/feature/id/347263/description/Factory_of_Life]
#''Two ‘What if' experiments''<br>Ptashne, M. <br>[[PMID: 15055587]]
#''Two ‘What if' experiments''<br>Ptashne, M. <br>[[PMID: 15055587]]
#''Build Artificial''<br> Brent, R. <br> [[PMID: 15055588]]   
#''Build Artificial''<br> Brent, R. <br> [[PMID: 15055588]]   
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| Week 3: <br>Wed Feb 20   
| Week 3: <br>Wed Feb 20   
|  
|  
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|'''Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology '''<br> Wang B, et al. ''Nat. Commun.'' (2011) 2 : 508 <br>[[doi: 10.1038/ncomms1516]]  
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|'''Rational Diversification of a Promoter Providing Fine-Tuned Expression and Orthogonal Regulation for Synthetic Biology'''<br> Blount BA, Weenink T, Vasylechko S, Ellis T.<br>PLoS ONE (2012) 7(3): e33279.<br> [[doi:10.1371/journal.pone.0033279]]
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|'''A synthetic oscillatory network of transcriptional regulators'''<br>Elowitz, MB, and Leibler, S. ''Nature'' (2000) 403:335–338 <br>[[PMID: 10659856]] <br>'''Construction of a genetic toggle switch in Escherichia coli'''<br> Gardner TS, et al.''Nature''(2000) 403:339–342 <br>[[PMID: 10659857]]<br>
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|'''Directed evolution as a powerful synthetic biology tool'''<br>Cobb RE, Sun N, Zhao H. ''Methods'' (2012) Mar 23. <br>[[PMID: 22465795]] <br>
|--  
|--  
|'''Transcription-based Logic Devices'''<br>  
|'''Transcription-based Logic Devices'''<br>  
| Week 4:<br> Wed Feb 27
| Week 4:<br> Wed Feb 27
|  
|  
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|'''Direct and specific chemical control of eukaryotic translation with a synthetic RNA–protein interaction'''<br> Goldfless SJ, et al. ''NAR'' (2012) 1-12<br>[[DOI: 10.1093/nar/gks028]]
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|'''Genetic programs constructed from layered logic gates in single cells'''<br> Moon TS, Lou C, Tamsir A, Stanton BC, Voigt CA ''Nature'' (2012) 491: 249–253 <br>[[doi:10.1038/nature11516]]
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|'''Versatile RNA-sensing transcriptional regulators for engineering genetic networks''' <br>Lucks JB, et al. ''PNAS'' (2011) 108(21): 8617-8622 <br> [[DOI: 10.1073/pnas.1015741108]]
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|'''Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology '''<br> Wang B, et al. ''Nat. Commun.'' (2011) 2 : 508 <br>[[doi: 10.1038/ncomms1516]]  
|-
|-
|'''RNA Engineering'''<br>  
|'''RNA Engineering'''<br>  

Revision as of 20:39, 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 before next week read
  1. Factory of Life
    A. Witze
    Science News (2013) 183:1 [1]
  2. Two ‘What if' experiments
    Ptashne, M.
    PMID: 15055587
  3. 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 Designed Proteins from a Library of Artificial Sequences Function in Esherichia Coli and Enable Cell Growth
Fisher MA, et al. PLoS One (2011)6(1):e15364
DOI: 10.1371/journal.pone.0015364
Directed evolution of recombinase specificity by split gene reassembly
Gersbach, CA, et al. NAR (2010) 38(12): 4198-4206-1543
DOI: 10.1093/nar/gkq125
Modularity
Week 6:
Wed Mar 13
before 3 ideas presentations
Modularity of a carbon-fixing protein organelle
Bonacci W et al. PNAS (2012)109(2):478-483
DOI: 10.1073/pnas.1108557109
A modular positive feedback-based gene amplifier
Nistala GJ et al. JBE (2010) 4:4
DOI: 10.1186/1754-1611-4-4]
(re)Programming Systems
Week 7:
Wed Mar 20
Reprogramming bacteria to seek and destroy an herbicide
Sinha, J. et al. Nature Chemical Biology (2010)6: 464–470
doi:10.1038/nchembio.369
Scaling up synthetic biology: Do not forget the chassis
A Danchin FEBS letters (2012)
pdf here
Spring Break Mar 26-30 No class all week
DNA construction and editing technologies
Week 8:
Wed Apr 3
Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement
Isaacs FJ et al. Science (2011) 333(6040):348-353
DOI: 10.1126/science.1205822
Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting.
Cermak T et al. NAR (2011) 39(12):7879
PMID: 21493687
Feedback and Insulation
Week 9:
Wed Apr 10
before tech spec review
A yeast synthetic network for in vivo assessment of reverse-engineering and modeling approaches
Cantone I et alCell (2009)137(1):172-181
PMID: 19327819
In silico feedback for in vivo regulation of a gene expression circuit
Milias-Argeitis A et al.Nature BioTech (2011) 29(12):1114–1116
doi:10.1038/nbt.2018
Chassis
Week 10:
Wed Apr 17
An E. coli Cell-Free Expression Toolbox: Application to Synthetic Gene Circuits and Artificial Cells
Shin J, and Noireaux, V. ACS Synthetic Biology (2012) 1(1):29–41
DOI: 10.1021/sb200016s
Low-mutation-rate, reduced-genome Escherichia coli: An improved host for faithful maintenance of engineered genetic constructs
Csorgo B et al. Microbial Cell Factories (2012)11:11
doi:10.1186/1475-2859-11-11
Programming with Models & Noise
Week 11:
Wed Apr 24
Model-Driven Engineering of RNA Devices to Quantitatively Program Gene Expression
Carothers JM et al. Science (2011)334(6063):1716-1719
DOI: 10.1126/science.1212209
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
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
Organization of Intracellular Reactions with Rationally Designed RNA Assemblies
Delebecqu CJ et al. Science (2011) 333:470
DOI: 10.1126/science.1206938
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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