20.20(S11):Advanced topics

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| '''Transcription-based Logic Devices'''<br>  
| '''Transcription-based Logic Devices'''<br>  
| Wed Feb 16  
| Wed Feb 16  
-
| Pei-Ann, Jessica
+
| Pei-Ann, Jessica<br>[[Media:2 16 Jessica and Pei.ppt| ppt is here]]
|'''Environmental signal integration by a modular AND gate'''<br> Anderson JC, Voigt C, Arkin, AP ''Molecular systems biology'' (2007) 3:133 <br>[[PMID: 17700541]]
|'''Environmental signal integration by a modular AND gate'''<br> Anderson JC, Voigt C, Arkin, AP ''Molecular systems biology'' (2007) 3:133 <br>[[PMID: 17700541]]
|'''A synthetic oscillatory network of transcriptional regulators'''<br>Elowitz, MB, and Leibler, S. ''Nature'' (2000) 403,
|'''A synthetic oscillatory network of transcriptional regulators'''<br>Elowitz, MB, and Leibler, S. ''Nature'' (2000) 403,
Line 62: Line 62:
|'''Protein Design: directed evolution'''<br>  
|'''Protein Design: directed evolution'''<br>  
| Wed Feb 23
| Wed Feb 23
-
| Yuan, Amber
+
| Yuan, Amber<br>[[Media:Amber yuan.ppt| ppt is here]]
|'''De Novo Designed Proteins from a Library of Artificial Sequences Function in Esherichia Coli and Enable Cell Growth''' <br>Fisher MA, et al. ''PLoS One'' (2011)6(1):e15364<br>[[DOI: 10.1371/journal.pone.0015364]]
|'''De Novo Designed Proteins from a Library of Artificial Sequences Function in Esherichia Coli and Enable Cell Growth''' <br>Fisher MA, et al. ''PLoS One'' (2011)6(1):e15364<br>[[DOI: 10.1371/journal.pone.0015364]]
|'''Directed evolution of recombinase specificity by split gene reassembly''' <br>Gersbach, CA, et al. ''NAR'' (2010) 38(12): 4198-4206-1543 <br> [[DOI: 10.1093/nar/gkq125]]
|'''Directed evolution of recombinase specificity by split gene reassembly''' <br>Gersbach, CA, et al. ''NAR'' (2010) 38(12): 4198-4206-1543 <br> [[DOI: 10.1093/nar/gkq125]]
Line 68: Line 68:
|'''RNA Engineering'''<br>
|'''RNA Engineering'''<br>
| Wed Mar 2
| Wed Mar 2
-
| Andrew, Tina
+
| Andrew, Tina<br> [[Media:Tinaandrew20.385.ppt| ppt is here]]
| '''Reprogramming Cellular Behavior with RNA Controllers Responsive to Endogenous Proteins'''<br>Culler, SJ, Hoff, KG, Smolke, CD. ''Science'' (2010) 330:1251-1255 <br>[[DOI: 10.1126/science.1192128]]
| '''Reprogramming Cellular Behavior with RNA Controllers Responsive to Endogenous Proteins'''<br>Culler, SJ, Hoff, KG, Smolke, CD. ''Science'' (2010) 330:1251-1255 <br>[[DOI: 10.1126/science.1192128]]
| '''The Case for RNA''' <br>Chang, CL, Arkin AP.  ''Science'' (2010) 330:1185-1186<br>[[DOI: 10.1126/science.1199495]]  
| '''The Case for RNA''' <br>Chang, CL, Arkin AP.  ''Science'' (2010) 330:1185-1186<br>[[DOI: 10.1126/science.1199495]]  
|--
|--
| '''Tuning the system: Network Composition''' <br>  
| '''Tuning the system: Network Composition''' <br>  
-
| <font color = blue> Wed Mar 10</font color> <br>after 3 ideas presentations
+
| <font color = blue> Wed Mar 10</font color> <br>before 3 ideas presentations, meet in 4-163
-
| Colin, Raven
+
| Colin, Raven<br> [[Media:Raven 20110309Presentation.pptx| ppt is here]]
| '''A modular positive feedback-based gene amplifier''' Nistala GJ et al. ''JBE'' (2010) 4:4<br>[[DOI: 10.1186/1754-1611-4-4]]
| '''A modular positive feedback-based gene amplifier''' Nistala GJ et al. ''JBE'' (2010) 4:4<br>[[DOI: 10.1186/1754-1611-4-4]]
|'''A fast, robust and tunable synthetic gene oscillator''' <br>Stricker, J. et al. ''Nature'' (2008) 456, 516–519<br>[[PMID: 18971928]]
|'''A fast, robust and tunable synthetic gene oscillator''' <br>Stricker, J. et al. ''Nature'' (2008) 456, 516–519<br>[[PMID: 18971928]]
Line 80: Line 80:
| '''(re)Programming Systems''' <br>  
| '''(re)Programming Systems''' <br>  
| Wed Mar 16  
| Wed Mar 16  
-
| Patrick
+
| Patrick, Nick<br>[[Media:Presentation 3.16.2011.pptx| ppt is here]]
| '''Highly Efficient Reprogramming to Pluripotency and Directed Differentiation of Human Cells with Synthetic Modified mRNA''' Warren L, et al. ''Cell Stem Cell'' (2010) 7:618-630<br>[[DOI:10.1016/j.stem.2010.08.012]]
| '''Highly Efficient Reprogramming to Pluripotency and Directed Differentiation of Human Cells with Synthetic Modified mRNA''' Warren L, et al. ''Cell Stem Cell'' (2010) 7:618-630<br>[[DOI:10.1016/j.stem.2010.08.012]]
| '''Reprogramming bacteria to seek and destroy an herbicide''' <br>Sinha, J. et al. ''Nature Chemical Biology'' (2010)6: 464–470<br>[[doi:10.1038/nchembio.369]]
| '''Reprogramming bacteria to seek and destroy an herbicide''' <br>Sinha, J. et al. ''Nature Chemical Biology'' (2010)6: 464–470<br>[[doi:10.1038/nchembio.369]]
Line 90: Line 90:
| '''DNA construction and editing technologies'''<br>  
| '''DNA construction and editing technologies'''<br>  
| Wed Mar 30
| Wed Mar 30
-
|  
+
| Raven, Andrew<br> [[Media:Yang20.385SingleStepAssembly.pptx| Andrew's ppt is here]]<br> [[Media:Raven 20110330Presentation.pptx| Raven's ppt is here]]
| '''Programming cells by multiplex genome engineering and accelerated evolution'''<br>Wang HH, et al. ''Nature'' (2009) Aug 13;460(7257):894-8. <br>[[PMID: 19633652 ]]
| '''Programming cells by multiplex genome engineering and accelerated evolution'''<br>Wang HH, et al. ''Nature'' (2009) Aug 13;460(7257):894-8. <br>[[PMID: 19633652 ]]
| '''Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides'''<br>Stemmer WP, et al. ''Gene'' (1995) 164(1):49-53 <br>[[PMID: 7590320]] <br>
| '''Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides'''<br>Stemmer WP, et al. ''Gene'' (1995) 164(1):49-53 <br>[[PMID: 7590320]] <br>
|--
|--
| '''Measurement technologies''' <br>
| '''Measurement technologies''' <br>
-
| <font color = blue> Thursday Apr 7 </font color>
+
| <font color = blue> Wed Apr 6 </font color><br> before tech spec review, meet in 56-114
-
|
+
| Nick<br> [[Media:Nick paper 2.pptx| ppt is here]]
| '''Nascent transcript sequencing visualizes transcription at nucleotide resolution'''Churchman LS and Weissman JS.''Nature'' (2011)469:368-373 [[DOI: 10.1038/nature09652]]  
| '''Nascent transcript sequencing visualizes transcription at nucleotide resolution'''Churchman LS and Weissman JS.''Nature'' (2011)469:368-373 [[DOI: 10.1038/nature09652]]  
|'''Measuring the activity of BioBrick promoters using an in vivo reference standard''' <br> Kelly J, et al. ''Journal of Biological Engineering'' (2009) 3:4<br> [[doi:10.1186/1754-1611-3-4]]
|'''Measuring the activity of BioBrick promoters using an in vivo reference standard''' <br> Kelly J, et al. ''Journal of Biological Engineering'' (2009) 3:4<br> [[doi:10.1186/1754-1611-3-4]]
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| '''Chassis''' <br>  
| '''Chassis''' <br>  
| Wed Apr 13  
| Wed Apr 13  
-
|  
+
| Jessica, Tina<br> [[Media:Tina Presentation 20.385 4.13.2011-1.pptx| Tina's ppt is here]]<br> Jessica will present next week
|'''Study of messenger RNA inactivation and protein degradation in an Escherichia coli cell-free expression system'''<br> Shin J, and Noireaux, V. ''JBE'' (2010) 4:9<br> [[DOI: 10.1186/1754-1611-4-9]]
|'''Study of messenger RNA inactivation and protein degradation in an Escherichia coli cell-free expression system'''<br> Shin J, and Noireaux, V. ''JBE'' (2010) 4:9<br> [[DOI: 10.1186/1754-1611-4-9]]
| '''Emergent properties of reduced-genome Escherichia coli.''' <br> Pósfai G, et al. ''Science.''(2006)312(5776):1044-6.<br> [[PMID: 16645050]]
| '''Emergent properties of reduced-genome Escherichia coli.''' <br> Pósfai G, et al. ''Science.''(2006)312(5776):1044-6.<br> [[PMID: 16645050]]
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| '''Signal Connectivity'''<br>
| '''Signal Connectivity'''<br>
| Wed Apr 20
| Wed Apr 20
-
|  
+
| Amber (will present Skerker paper next week)<br> [[Media:4 20 Journal Club Presentation.pptx| Jessica's ppt is here]]
|'''Rewiring the specificity of two-component signal transduction systems'''<br>Skerker JM, et al. ''Cell'' (2008)133(6):1043-54.<br>[[PMID: 18555780]]
|'''Rewiring the specificity of two-component signal transduction systems'''<br>Skerker JM, et al. ''Cell'' (2008)133(6):1043-54.<br>[[PMID: 18555780]]
|'''Tunable Signal Processing in Synthetic MAP Kinase Cascades''' <br>O'Shaughnessy, EC, et al. ''Cell''(2011) 144:119-131<br>[[DOI: 10.1016/j.cell.2010.12.014]]
|'''Tunable Signal Processing in Synthetic MAP Kinase Cascades''' <br>O'Shaughnessy, EC, et al. ''Cell''(2011) 144:119-131<br>[[DOI: 10.1016/j.cell.2010.12.014]]
Line 114: Line 114:
| '''Metabolic Engineering'''  
| '''Metabolic Engineering'''  
| Wed Apr 27
| Wed Apr 27
-
|
+
| Yuan<br> [[Media:Amber 20385 presentation2 signal specificity.ppt| Amber's ppt is here]]<br>[[Media:Yuan 385 talk.ppt| Yuan's ppt is here]]
| '''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 (2010) [[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 (2010) [[PMID: 20117231]]
|'''Production of the antimalarial drug precursor artemisinic acid in engineered yeast'''<br>Ro DK, et al. ''Nature'' (2006) 440, 940–943 <br>[[PMID: 16612385]]
|'''Production of the antimalarial drug precursor artemisinic acid in engineered yeast'''<br>Ro DK, et al. ''Nature'' (2006) 440, 940–943 <br>[[PMID: 16612385]]
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|'''Cell Cell Communication/System Ecology'''  
|'''Cell Cell Communication/System Ecology'''  
| Wed May 4  
| Wed May 4  
-
|  
+
| Colin <br> [[Media:Multicellular computing CMR.pptx| ppt is here]]
-
|'''Robust multicellular computing using genetically encoded NOT gates and chemical 'wires''''<br>Tamsir, a., Tabor, J.J., Voigt, C.A. ''Nature'' 2011 Jan 13;469:212-215.<br>[[DOI: 10.1038/nature09565]]
+
|'''Robust multicellular computing using genetically encoded NOT gates and chemical 'wires''''<br>Tamsir, a., Tabor, J.J., Voigt, C.A. ''Nature'' 2011 Jan 13;469:212-215.<br>[[DOI: 10.1038/nature09565]]<br>[[Media:NORgate+ChemWires SuppInfo nature09565-s1.pdf| + supplementary info]]
| ''' Division of logic labour''' <br> Li B and You L.''Nature'' (2011) 469:171-172<br>[[DOI:10.1038/469171a]]
| ''' Division of logic labour''' <br> Li B and You L.''Nature'' (2011) 469:171-172<br>[[DOI:10.1038/469171a]]
|--
|--
| '''Property rights in synthetic biology'''  
| '''Property rights in synthetic biology'''  
-
|  <font color = blue> Tue May 10? </font color>  
+
|  <font color = blue> Wed May 11 </font color><br> before final presentations, meet in 56-114
-
|
+
| Pei <br> [[Media:PeiPresentationBoyle.pptx| ppt is here]]
|''' 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>
|'''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.]]
|'''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.]]
|--
|--
|'''Safety!'''  
|'''Safety!'''  
-
| <font color = blue> Tue May 10? </font color>  
+
| <font color = blue> Wed May 11 </font color> <br> before final presentations, meet in 56-114
-
|  
+
| Patrick <br> [[Media:Darwin’s Surprise.pptx| ppt is here]]
| '''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>
| '''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>
|'''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]
|'''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]
|}
|}

Current revision

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

26-152

TOPIC DATE Discussion leader(s) Discussion paper(s) Related paper(s) to enjoy
Preview of 20.385 Wed Feb 2 Natalie Kuldell preview of 20.385 before next week read
  1. The promise of synthetic biology
    Pleiss,J.
    DOI:10.1007/s00253-006-0664-3
  2. Two ‘What if' experiments
    Ptashne, M.
    PMID: 15055587
  3. Build Artificial
    Brent, R.
    PMID: 15055588
Parts™ Wed Feb 9 Natalie Kuldell
ppt is here
Turning lambda Cro into a transcriptional activatorBushman FD, Ptashne M.Cell. (1988) Jul 15;54(2):191-7.
PMID: 2968842
Improving the Lac System for Synthetic Biology
Penumetcha, P., et al. Bios (2011) 81(1):7-15.
pdf
Transcription-based Logic Devices
Wed Feb 16 Pei-Ann, Jessica
ppt is here
Environmental signal integration by a modular AND gate
Anderson JC, Voigt C, Arkin, AP Molecular systems biology (2007) 3:133
PMID: 17700541
A synthetic oscillatory network of transcriptional regulators
Elowitz, MB, and Leibler, S. Nature (2000) 403,

335–338
PMID: 10659856
Construction of a genetic toggle switch in Escherichia coli
Gardner TS, et al.Nature(2000) 403, 339–342
PMID: 10659857

Protein Design: directed evolution
Wed Feb 23 Yuan, Amber
ppt is here
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
RNA Engineering
Wed Mar 2 Andrew, Tina
ppt is here
Reprogramming Cellular Behavior with RNA Controllers Responsive to Endogenous Proteins
Culler, SJ, Hoff, KG, Smolke, CD. Science (2010) 330:1251-1255
DOI: 10.1126/science.1192128
The Case for RNA
Chang, CL, Arkin AP. Science (2010) 330:1185-1186
DOI: 10.1126/science.1199495
Tuning the system: Network Composition
Wed Mar 10
before 3 ideas presentations, meet in 4-163
Colin, Raven
ppt is here
A modular positive feedback-based gene amplifier Nistala GJ et al. JBE (2010) 4:4
DOI: 10.1186/1754-1611-4-4
A fast, robust and tunable synthetic gene oscillator
Stricker, J. et al. Nature (2008) 456, 516–519
PMID: 18971928
(re)Programming Systems
Wed Mar 16 Patrick, Nick
ppt is here
Highly Efficient Reprogramming to Pluripotency and Directed Differentiation of Human Cells with Synthetic Modified mRNA Warren L, et al. Cell Stem Cell (2010) 7:618-630
DOI:10.1016/j.stem.2010.08.012
Reprogramming bacteria to seek and destroy an herbicide
Sinha, J. et al. Nature Chemical Biology (2010)6: 464–470
doi:10.1038/nchembio.369
Spring Break Mar 21-25 No class all week
DNA construction and editing technologies
Wed Mar 30 Raven, Andrew
Andrew's ppt is here
Raven's ppt is here
Programming cells by multiplex genome engineering and accelerated evolution
Wang HH, et al. Nature (2009) Aug 13;460(7257):894-8.
PMID: 19633652
Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides
Stemmer WP, et al. Gene (1995) 164(1):49-53
PMID: 7590320
Measurement technologies
Wed Apr 6
before tech spec review, meet in 56-114
Nick
ppt is here
Nascent transcript sequencing visualizes transcription at nucleotide resolutionChurchman LS and Weissman JS.Nature (2011)469:368-373 DOI: 10.1038/nature09652 Measuring the activity of BioBrick promoters using an in vivo reference standard
Kelly J, et al. Journal of Biological Engineering (2009) 3:4
doi:10.1186/1754-1611-3-4
Chassis
Wed Apr 13 Jessica, Tina
Tina's ppt is here
Jessica will present next week
Study of messenger RNA inactivation and protein degradation in an Escherichia coli cell-free expression system
Shin J, and Noireaux, V. JBE (2010) 4:9
DOI: 10.1186/1754-1611-4-9
Emergent properties of reduced-genome Escherichia coli.
Pósfai G, et al. Science.(2006)312(5776):1044-6.
PMID: 16645050
Signal Connectivity
Wed Apr 20 Amber (will present Skerker paper next week)
Jessica's ppt is here
Rewiring the specificity of two-component signal transduction systems
Skerker JM, et al. Cell (2008)133(6):1043-54.
PMID: 18555780
Tunable Signal Processing in Synthetic MAP Kinase Cascades
O'Shaughnessy, EC, et al. Cell(2011) 144:119-131
DOI: 10.1016/j.cell.2010.12.014
Metabolic Engineering Wed Apr 27 Yuan
Amber's ppt is here
Yuan's ppt is here
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 (2010) PMID: 20117231 Production of the antimalarial drug precursor artemisinic acid in engineered yeast
Ro DK, et al. Nature (2006) 440, 940–943
PMID: 16612385
Cell Cell Communication/System Ecology Wed May 4 Colin
ppt is here
Robust multicellular computing using genetically encoded NOT gates and chemical 'wires'
Tamsir, a., Tabor, J.J., Voigt, C.A. Nature 2011 Jan 13;469:212-215.
DOI: 10.1038/nature09565
+ supplementary info
Division of logic labour
Li B and You L.Nature (2011) 469:171-172
DOI:10.1038/469171a
Property rights in synthetic biology Wed May 11
before final presentations, meet in 56-114
Pei
ppt is here
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! Wed May 11
before final presentations, meet in 56-114
Patrick
ppt is here
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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