20.20(S13):Advanced topics

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| '''Synthetic biology devices as tools for metabolic engineering''' <br>Shiue E, Prather K. ''Biochemical Engineering Journal'' (2012) 65:82–89<br>[[doi:10.1016/j.bej.2012.04.006]]
| '''Synthetic biology devices as tools for metabolic engineering''' <br>Shiue E, Prather K. ''Biochemical Engineering Journal'' (2012) 65:82–89<br>[[doi:10.1016/j.bej.2012.04.006]]
|--
|--
-
| ''' DNA fine-tuning + evolution '''<br>  
+
|'''Transcription-based Logic Devices'''<br>
| Week 3: <br>Wed Feb 20   
| Week 3: <br>Wed Feb 20   
-
|  
+
| Paula + NK
 +
|'''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]]
 +
|'''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]]
 +
|--
 +
| ''' DNA fine-tuning + evolution '''<br>
 +
| Week 4:<br> Wed Feb 27
 +
| Jessica + NK
|'''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]]
|'''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]]
|'''Directed evolution as a powerful synthetic biology tool'''<br>Cobb RE, Sun N, Zhao H. ''Methods'' (2012) Mar 23. <br>[[PMID: 22465795]] <br>
|'''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>
 
-
| Week 4:<br> Wed Feb 27
 
-
|
 
-
|'''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]]
 
-
|'''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>  
| Week 5: <br>Wed Mar 6
| Week 5: <br>Wed Mar 6
-
|  
+
| Kristine + Ryan
| '''De novo automated design of small RNA circuits for engineering synthetic riboregulation in living cells.''' <br>Rodrigo G, Landrain TE, Jaramillo A. ''PNAS''(2012) 109(38):15271-6.<br> [[PMID: 22949707]]
| '''De novo automated design of small RNA circuits for engineering synthetic riboregulation in living cells.''' <br>Rodrigo G, Landrain TE, Jaramillo A. ''PNAS''(2012) 109(38):15271-6.<br> [[PMID: 22949707]]
| '''RNA synthetic biology''' <br>Isaacs FJ, Dwyer DJ, Collins JJ. ''Nat Biotechnol.'' (2006) 24(5):545-54. <br> [[PMID: 16680139]]
| '''RNA synthetic biology''' <br>Isaacs FJ, Dwyer DJ, Collins JJ. ''Nat Biotechnol.'' (2006) 24(5):545-54. <br> [[PMID: 16680139]]
Line 72: Line 72:
| '''Engineering Biology''' <br>  
| '''Engineering Biology''' <br>  
| Week 6:<br> <font color = blue> Wed Mar 13</font color> <br>before 3 ideas presentations
| Week 6:<br> <font color = blue> Wed Mar 13</font color> <br>before 3 ideas presentations
-
|  
+
| Divya + NK
|'''Towards practical, high-capacity, low-maintenance information storage in synthesized DNA'''<br> Goldman N et al.    ''Nature'' (2013)<br> [[doi:10.1038/nature11875]]  
|'''Towards practical, high-capacity, low-maintenance information storage in synthesized DNA'''<br> Goldman N et al.    ''Nature'' (2013)<br> [[doi:10.1038/nature11875]]  
| '''A fully decompressed synthetic bacteriophage øX174 genome assembled and archived in yeast''' <br>Jaschke PR et al. ''Virology''(2012)434(2):278-84. <br> [[doi: 10.1016/j.virol.2012.09.020]]  
| '''A fully decompressed synthetic bacteriophage øX174 genome assembled and archived in yeast''' <br>Jaschke PR et al. ''Virology''(2012)434(2):278-84. <br> [[doi: 10.1016/j.virol.2012.09.020]]  
Line 78: Line 78:
| '''SynBio for Science''' <br>  
| '''SynBio for Science''' <br>  
| Week 7:<br> Wed Mar 20  
| Week 7:<br> Wed Mar 20  
-
|
+
| Holly + NK
| '''Synthetic biology challenges long-held hypotheses in translation, codon bias and transcription''' <br>Forster AC. ''Biotechnol J.'' (2012) 7(7):835-45.<br> [[doi: 10.1002/biot.201200002]]
| '''Synthetic biology challenges long-held hypotheses in translation, codon bias and transcription''' <br>Forster AC. ''Biotechnol J.'' (2012) 7(7):835-45.<br> [[doi: 10.1002/biot.201200002]]
|'''Five hard truths for synthetic biology'''<br> Kwok R. ''Nature''(2010) 463(7279):288-90.<br>[[doi: 10.1038/463288a]]
|'''Five hard truths for synthetic biology'''<br> Kwok R. ''Nature''(2010) 463(7279):288-90.<br>[[doi: 10.1038/463288a]]
Line 88: Line 88:
| '''DNA construction and editing technologies'''<br>  
| '''DNA construction and editing technologies'''<br>  
| Week 8:<br> Wed Apr 3
| Week 8:<br> Wed Apr 3
-
|  
+
| Jess (Sung et al paper)
| '''Knockout mice created by TALEN-mediated gene targeting.'''<br>Sung YH et al. ''Nat Biotechnol'' (2013) 31(1):23-4. <br> [[doi: 10.1038/nbt.2477]]
| '''Knockout mice created by TALEN-mediated gene targeting.'''<br>Sung YH et al. ''Nat Biotechnol'' (2013) 31(1):23-4. <br> [[doi: 10.1038/nbt.2477]]
| '''Multiplex Genome Engineering Using CRISPR/Cas Systems'''<br>Cong L et al. ''Science'' (2013) Jan 3. <br>[[PMID: 23287718]] <br>
| '''Multiplex Genome Engineering Using CRISPR/Cas Systems'''<br>Cong L et al. ''Science'' (2013) Jan 3. <br>[[PMID: 23287718]] <br>
Line 94: Line 94:
| '''Cell Physiology''' <br>
| '''Cell Physiology''' <br>
| Week 9:<br> <font color = blue> Wed Apr 10 </font color><br> before tech spec review  
| Week 9:<br> <font color = blue> Wed Apr 10 </font color><br> before tech spec review  
-
|  
+
| No presentations this week (response record for one or the other paper due)
| '''Shared control of gene expression in bacteria by transcription factors and global physiology of the cell'''<br>Berthoumieux S et al''Mol Syst Biol'' (2013) 9:634 <br> [[doi: 10.1038/msb.2012.70]]
| '''Shared control of gene expression in bacteria by transcription factors and global physiology of the cell'''<br>Berthoumieux S et al''Mol Syst Biol'' (2013) 9:634 <br> [[doi: 10.1038/msb.2012.70]]
|'''A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis''' <br> Picotti P et al.''Nature'' (2013) Jan 20. <br> [[doi: 10.1038/nature11835]]
|'''A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis''' <br> Picotti P et al.''Nature'' (2013) Jan 20. <br> [[doi: 10.1038/nature11835]]
Line 100: Line 100:
| '''Chassis''' <br>  
| '''Chassis''' <br>  
| Week 10: <br> Wed Apr 17  
| Week 10: <br> Wed Apr 17  
-
|
+
| Kristine (Woodruff paper)<br> Ryan (Cardinale paper)
|'''Towards a metabolic engineering strain "commons": An Escherichia coli platform strain for ethanol production'''<br> Woodruff LB, May BL, Warner JR, Gill RT. ''Biotechnol Bioeng'' (2013) Jan 15.<br> [[doi: 10.1002/bit.24840]]
|'''Towards a metabolic engineering strain "commons": An Escherichia coli platform strain for ethanol production'''<br> Woodruff LB, May BL, Warner JR, Gill RT. ''Biotechnol Bioeng'' (2013) Jan 15.<br> [[doi: 10.1002/bit.24840]]
| '''Contextualizing context for synthetic biology--identifying causes of failure of synthetic biological systems''' <br> Cardinale S, Arkin AP.''Biotechnol J''(2012) 7(7):856-66. <br> [[doi: 10.1002/biot.201200085]]  
| '''Contextualizing context for synthetic biology--identifying causes of failure of synthetic biological systems''' <br> Cardinale S, Arkin AP.''Biotechnol J''(2012) 7(7):856-66. <br> [[doi: 10.1002/biot.201200085]]  
Line 106: Line 106:
| '''Programming in the Noise'''<br>
| '''Programming in the Noise'''<br>
| Week 11:<br> Wed Apr 24
| Week 11:<br> Wed Apr 24
-
|  
+
| Divya (Litcofsky paper)
|'''Iterative plug-and-play methodology for constructing and modifying synthetic gene networks'''<br>Litcofsky KD et al. ''Nat Methods''(2012) 9(11):1077-80.<br> [[doi: 10.1038/nmeth.2205]]
|'''Iterative plug-and-play methodology for constructing and modifying synthetic gene networks'''<br>Litcofsky KD et al. ''Nat Methods''(2012) 9(11):1077-80.<br> [[doi: 10.1038/nmeth.2205]]
|'''A sensing array of radically coupled genetic ‘biopixels’''' <br>Prindle A et al. ''Nature''(2012)481:39–44<br>[[doi:10.1038/nature10722]]
|'''A sensing array of radically coupled genetic ‘biopixels’''' <br>Prindle A et al. ''Nature''(2012)481:39–44<br>[[doi:10.1038/nature10722]]
|--
|--
-
| '''Metabolic Engineering'''  
+
| '''Property rights in synthetic biology'''  
| Week 12:<br> Wed May 1
| Week 12:<br> Wed May 1
-
|
+
| Holly (Rai paper)
-
| '''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]]
+
|''' 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 protein scaffolds provide modular control over metabolic flux'''Dueber JE et al. ''Nat Biotechnol'' (2009) 27(8):753-9. <br> [[doi: 10.1038/nbt.1557]]
+
|'''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]]
|--
|--
|'''Systems & Communities'''  
|'''Systems & Communities'''  
| Week 13:<br> Wed May 8  
| Week 13:<br> Wed May 8  
-
|  
+
| Paula (Oritz paper)
|'''Engineered cell-cell communication via DNA messaging'''<br>Ortiz ME, Endy D. ''JBE'' (2012) 6(1):16. <br> [[doi: 10.1186/1754-1611-6-16]]
|'''Engineered cell-cell communication via DNA messaging'''<br>Ortiz ME, Endy D. ''JBE'' (2012) 6(1):16. <br> [[doi: 10.1186/1754-1611-6-16]]
| ''' Autonomous bacterial localization and gene expression based on nearby cell receptor density''' <br> Wu HC et al. ''Mol Syst Biol'' (2013) 9:636.<br> [[doi: 10.1038/msb.2012.71]]
| ''' Autonomous bacterial localization and gene expression based on nearby cell receptor density''' <br> Wu HC et al. ''Mol Syst Biol'' (2013) 9:636.<br> [[doi: 10.1038/msb.2012.71]]
|--
|--
-
| '''Property rights in synthetic biology'''  
+
| '''Metabolic Engineering'''  
| Week 14: <br><font color = blue> Wed May 15 </font color><br> before final presentations  
| Week 14: <br><font color = blue> Wed May 15 </font color><br> before final presentations  
-
|  
+
| no presentations this week (response record only if you've missed a different discussion this term)
-
|''' 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>
+
| '''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]]
-
|'''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]]
+
| '''Synthetic protein scaffolds provide modular control over metabolic flux'''Dueber JE et al. ''Nat Biotechnol'' (2009) 27(8):753-9. <br> [[doi: 10.1038/nbt.1557]]
|}
|}

Revision as of 08:42, 15 February 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 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
Transcription-based Logic Devices
Week 3:
Wed Feb 20
Paula + NK 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
DNA fine-tuning + evolution
Week 4:
Wed Feb 27
Jessica + NK 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
RNA Engineering
Week 5:
Wed Mar 6
Kristine + Ryan 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
Divya + NK 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
Holly + NK 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
Jess (Sung et al paper) 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
No presentations this week (response record for one or the other paper due) 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
Kristine (Woodruff paper)
Ryan (Cardinale paper)
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
Divya (Litcofsky paper) 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
Property rights in synthetic biology Week 12:
Wed May 1
Holly (Rai paper) 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
Systems & Communities Week 13:
Wed May 8
Paula (Oritz paper) 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
Metabolic Engineering Week 14:
Wed May 15
before final presentations
no presentations this week (response record only if you've missed a different discussion this term) 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
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