20.20(S15):Advanced topics: Difference between revisions
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|'''DATE''' | |'''DATE''' | ||
|'''Discussion leader(s)''' | |'''Discussion leader(s)''' | ||
|'''Discussion paper | |'''Discussion paper I''' | ||
|'''Related paper | |'''Discussion or Related paper II''' | ||
|-- | |-- | ||
| <b>Preview of 20.385</b> | | <b>Preview of 20.385</b> | ||
| Line 50: | Line 50: | ||
| [[Natalie Kuldell]]<br>[[Media:20.385(S15) Cro2activator.pdf| ppt is here]] | | [[Natalie Kuldell]]<br>[[Media:20.385(S15) Cro2activator.pdf| ppt is here]] | ||
| '''Turning lambda Cro into a transcriptional activator'''<br>Bushman FD, Ptashne M.''Cell.'' (1988) Jul 15;54(2):191-7.<br>[[PMID: 2968842]]<br> | | '''Turning lambda Cro into a transcriptional activator'''<br>Bushman FD, Ptashne M.''Cell.'' (1988) Jul 15;54(2):191-7.<br>[[PMID: 2968842]]<br> | ||
| ''' | |'''Advances and current limitations in transcript-level control of gene expression'''<br> Leavitt JM, Alper HS. ''Curr Opin Biotechnol.'' (2015) Jan 2;34C:98-104. [[doi: 10.1016/j.copbio.2014.12.015.]] Review [[Media:Leavitt-Advances and Limitations Gene Expression-Current Opinion-2015.pdf| pdf]] | ||
|-- | |-- | ||
|'''Transcription-based Logic Devices'''<br> | |'''Transcription-based Logic Devices'''<br> | ||
| Week 3: <br>Wed Feb 18 | | Week 3: <br>Wed Feb 18 | ||
| <br> | | Heejo and Tushar<br> [[Media:20.385 Week 3.pdf| ppt is here]] | ||
|'''Rapid engineering of versatile molecular logic gates using heterologous genetic transcriptional modules'''<br>Baojun Wang and Martin Buck. ''Chem. Commun.'' (2014) 50: 11642-11644 [[DOI: 10.1039/C4CC05264A ]] | |||
|'''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]] | |'''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]] | ||
|-- | |-- | ||
| ''' DNA fine-tuning + evolution '''<br> | | ''' DNA fine-tuning + evolution '''<br> | ||
| Week 4:<br> Wed Feb 25 | | Week 4:<br> Wed Feb 25 | ||
| <br> | | Gabi and Ellie<br>[[Media:20.385 Week 4.pdf| ppt is here]] | ||
|''' | |'''Evolution-guided optimization of biosynthetic pathways'''<br>Raman S, Rogers JK, Taylor ND, Church GM.''Proc Natl Acad Sci U S A.'' (2014) Dec 16;111(50):17803-8. [[doi: 10.1073/pnas.1409523111]] | ||
|'''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> | ||
|- | |- | ||
|''' | |'''Top down vs. Bottom up'''<br> | ||
| Week 5: <br>Wed Mar 4 | | Week 5: <br>Wed Mar 4 | ||
| | |No presentations this week (response record for one or the other paper due) | ||
| ''' | |'''Five hard truths for synthetic biology'''<br> Kwok R. ''Nature''(2010) 463(7279):288-90.<br>[[doi: 10.1038/463288a]] | ||
|'''Bottom-up engineering of biological systems through standard bricks: a modularity study on basic parts and devices''' <br>Pasotti L, Politi N, Zucca S, Cusella De Angelis MG, Magni P. ''PLoS One'' (2012) 7(7):e39407. [[doi: 10.1371/journal.pone.0039407]] | |||
|-- | |||
| '''RNA Engineering'''<br> | |||
| Week 6:<br> <font color = blue> Wed Mar 11</font color> <br>day of 3 ideas presentations | |||
| Marianne and Jenn <br> [[Media: Week6 20.385.pdf| ppt is here]] | |||
|'''Protein-responsive ribozyme switches in eukaryotic cells.''' Kennedy AB, Vowles JV, d'Espaux L, Smolke CD.''Nucleic Acids Res.'' (2014) Oct 29;42(19):12306-21. [[doi: 10.1093/nar/gku875]] | |||
| '''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]] | ||
|-- | |-- | ||
| '''Engineering Biology | | '''Engineering Materials with Biology''' <br> | ||
| Week 7:<br> Wed Mar 18 | | Week 7:<br> Wed Mar 18 | ||
| <br> | | Paper #1: Gabi<br> [[Media:Week 7 Presentation (Garcia).pptx |ppt is here]] | ||
| ''' | |'''Engineering living functional materials'''<br>Chen AY1, Zhong C, Lu TK.''ACS Synth Biol.'' (2015) Jan 16;4(1):8-11. [[doi: 10.1021/sb500113b]]*AND '''Synthesis and patterning of tunable multiscale materials with engineered cells''' Chen AY, Deng Z, Billings AN, Seker UO, Lu MY, Citorik RJ, Zakeri B, Lu TK.(2014) Nat Mater. 13(5):515-23. [[doi: 10.1038/nmat3912]] | ||
|''' | |'''Programmable biofilm-based materials from engineered curli nanofibres.'''<br> Nguyen PQ, Botyanszki Z, Tay PK, Joshi NS.''Nat Commun.'' (2014) Sep 17;5:4945. [[doi: 10.1038/ncomms5945.]] | ||
|-- | |-- | ||
! colspan="3" | Spring Break Mar 23-27 | ! colspan="3" | Spring Break Mar 23-27 | ||
| Line 86: | Line 86: | ||
| | | | ||
|-- | |-- | ||
| ''' | | '''Genome editing technologies'''<br> | ||
| Week 8:<br> Wed Apr 1 | | Week 8:<br> Wed Apr 1 | ||
| <br> | | Paper #2: Jenn<br> [[Media:20.385CRISPRPresentation.pptx| ppt is here]]<br>[[Media:BaconCrispr 2015.pdf| also...bacon anyone?]] | ||
| ''' | | '''Circular permutation of a synthetic eukaryotic chromosome with the telomerator.'''<br>Mitchell LA, Boeke JD.''Proc Natl Acad Sci U S A.'' (2014) Dec 2;111(48):17003-10. [[doi: 10.1073/pnas.1414399111]] | ||
| '''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> | ||
|-- | |-- | ||
| ''' | | '''Recoded Organisms''' <br> | ||
| Week 9:<br> <font color = blue> Wed Apr 8 </font color><br> | | Week 9:<br> <font color = blue> Wed Apr 8 </font color><br> day of tech spec review | ||
| No presentations this week (response record for one or the other paper due) | | No presentations this week (response record for one or the other paper due) | ||
| ''' | | '''Recoded organisms engineered to depend on synthetic amino acids.''' Rovner AJ, et. al...Isaacs FJ. ''Nature'' (2015) Jan 21. [[doi: 10.1038/nature14095]] | ||
|'''A | |'''A bacterial strain with a unique quadruplet codon specifying non-native amino acids'''<br> Chatterjee A, Lajoie MJ, Xiao H, Church GM, Schultz PG. ''Chembiochem'' (2014) Aug 18;15(12):1782-6 [[doi: 10.1002/cbic.201402104]] | ||
|- | |- | ||
| ''' | | '''Cell-free Synthetic Biology''' <br> | ||
| Week 10: <br> Wed Apr 15 | | Week 10: <br> Wed Apr 15 | ||
| <br> | | Paper #1: Tushar<br> [[Media:20.385 Secondpresentation 041515.pptx| ppt is here]] | ||
|''' | |'''Paper-based synthetic gene networks''' <br> Pardee K, Green AA, Ferrante T, Cameron DE, DaleyKeyser A, Yin P, Collins JJ. ''Cell'' (2014) Nov 6;159(4):940-54. [[doi: 10.1016/j.cell.2014.10.004]] | ||
| ''' | | '''Linear DNA for rapid prototyping of synthetic biological circuits in an Escherichia coli based TX-TL cell-free system'''<br> Sun ZZ1, Yeung E, Hayes CA, Noireaux V, Murray RM. ''ACS Synth Biol.'' (2014) Jun 20;3(6):387-97. [[doi: 10.1021/sb400131a]] | ||
|-- | |-- | ||
| ''' | | '''Setting Standards'''<br> | ||
| Week 11:<br> Wed Apr 22 | | Week 11:<br> Wed Apr 22 | ||
|<br> | |Paper #1: Ellie<br> [[Media: SynbioLGDB pres.pptx| ppt is here]] | ||
|''' | |'''SynBioLGDB: a resource for experimentally validated logic gates in synthetic biology.'''<br> Wang L, et.al. Wang D.''Sci Rep.'' (2015) Jan 28;5:8090. [[doi: 10.1038/srep08090]] | ||
|''' | |'''Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca.'''<br> Temme K1, Zhao D, Voigt CA.''Proc Natl Acad Sci U S A.'' (2012) May 1;109(18):7085-90. [[doi: 10.1073/pnas.1120788109]] (moved from week 12) | ||
|-- | |-- | ||
| ''' | | '''Methods for Metabolic Engineering''' | ||
| Week 12:<br> Wed Apr 29 | | Week 12:<br> Wed Apr 29 | ||
| <br> | | Paper #1: Heejo<br> [[Media:Week 12 Presentation Heejo Choi.pdf| ppt is here]] | ||
|''' | |'''The case for decoupling assembly and submission standards to maintain a more flexible registry of biological parts'''<br>Alnahhas RN, Slater B, Huang Y, Mortensen C, Monk JW, Okasheh Y, Howard MD, Gottel NR, Hammerling MJ, Barrick JE.''J Biol Eng.'' (2014) Dec 1;8(1):28. [[doi: 10.1186/1754-1611-8-28]] (moved from week 11) | ||
|''' | |'''CONSTRICTOR: constraint modification provides insight into design of biochemical networks'''<br> | ||
Erickson KE, Gill RT, Chatterjee A. ''PLoS One'' (2014) Nov 25;9(11):e113820.[[doi: 10.1371/journal.pone.0113820]] | |||
|-- | |-- | ||
|'''Systems | |'''Synthetic Systems at Play''' | ||
| Week 13:<br> Wed May 6 | | Week 13:<br> Wed May 6 | ||
| <br> | | Paper #1: Marianne<br> [[Media:20.385SpacePresentation.pptx| ppt is here]] | ||
|''' | |'''Towards synthetic biological approaches to resource utilization on space missions'''<br> | ||
| ''' | Menezes AA, Cumbers J, Hogan JA, Arkin AP.''J R Soc Interface'' (2015) Jan 6;12(102):20140715. [[doi: 10.1098/rsif.2014.0715]] | ||
| '''Programmable bacteria detect and record an environmental signal in the mammalian gut'''<br> | |||
Kotula JW, Kerns SJ, Shaket LA, Siraj L, Collins JJ, Way JC, Silver PA. ''Proc Natl Acad Sci U S A.'' (2014) Apr 1;111(13):4838-43. [[doi: 10.1073/pnas.1321321111]] | |||
|-- | |-- | ||
| ''' | | '''Property rights in synthetic biology''' | ||
| Week 14: <br><font color = blue> Wed May 13 </font color><br> | | Week 14: <br><font color = blue> Wed May 13 </font color><br> last day of class | ||
| no presentations this week (response record only if you've missed a different discussion this term) | | no presentations this week (response record only if you've missed a different discussion this term) | ||
| ''' | |'''Bringing Standards to Life: Synthetic Biology Standards and Intellectual Property'''<br>AW Torrance and LJ Kahl ''Santa Clara High Technology Law Journal''(2014) 30(2) [http://ssrn.com/abstract=2426235 link]] | ||
| '''Synthetic | |''' 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> | ||
|} | |} | ||
Latest revision as of 14:11, 6 May 2015
20.385: Advanced Topics in Synthetic Biology
Assignments
Homework dropbox is here
|
Part 1: Readings
Instructions for these assignment are here |
Part 2: Team Mentoring
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 I | Discussion or Related paper II |
| Preview of 20.385 | Week 1: Wed Feb 4 |
Natalie Kuldell | preview of 20.385 | Factory of Life Witze A Science News pdf Two ‘What if' experiments |
| Parts™ | Week 2: Wed Feb 11 |
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 |
Advances and current limitations in transcript-level control of gene expression Leavitt JM, Alper HS. Curr Opin Biotechnol. (2015) Jan 2;34C:98-104. doi: 10.1016/j.copbio.2014.12.015. Review pdf |
| Transcription-based Logic Devices |
Week 3: Wed Feb 18 |
Heejo and Tushar ppt is here |
Rapid engineering of versatile molecular logic gates using heterologous genetic transcriptional modules Baojun Wang and Martin Buck. Chem. Commun. (2014) 50: 11642-11644 DOI: 10.1039/C4CC05264A |
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 |
| DNA fine-tuning + evolution |
Week 4: Wed Feb 25 |
Gabi and Ellie ppt is here |
Evolution-guided optimization of biosynthetic pathways Raman S, Rogers JK, Taylor ND, Church GM.Proc Natl Acad Sci U S A. (2014) Dec 16;111(50):17803-8. doi: 10.1073/pnas.1409523111 |
Directed evolution as a powerful synthetic biology tool Cobb RE, Sun N, Zhao H. Methods (2012) Mar 23. PMID: 22465795 |
| Top down vs. Bottom up |
Week 5: Wed Mar 4 |
No presentations this week (response record for one or the other paper due) | Five hard truths for synthetic biology Kwok R. Nature(2010) 463(7279):288-90. doi: 10.1038/463288a |
Bottom-up engineering of biological systems through standard bricks: a modularity study on basic parts and devices Pasotti L, Politi N, Zucca S, Cusella De Angelis MG, Magni P. PLoS One (2012) 7(7):e39407. doi: 10.1371/journal.pone.0039407 |
| RNA Engineering |
Week 6: Wed Mar 11 day of 3 ideas presentations |
Marianne and Jenn ppt is here |
Protein-responsive ribozyme switches in eukaryotic cells. Kennedy AB, Vowles JV, d'Espaux L, Smolke CD.Nucleic Acids Res. (2014) Oct 29;42(19):12306-21. doi: 10.1093/nar/gku875 | RNA synthetic biology Isaacs FJ, Dwyer DJ, Collins JJ. Nat Biotechnol. (2006) 24(5):545-54. PMID: 16680139 |
| Engineering Materials with Biology |
Week 7: Wed Mar 18 |
Paper #1: Gabi ppt is here |
Engineering living functional materials Chen AY1, Zhong C, Lu TK.ACS Synth Biol. (2015) Jan 16;4(1):8-11. doi: 10.1021/sb500113b*AND Synthesis and patterning of tunable multiscale materials with engineered cells Chen AY, Deng Z, Billings AN, Seker UO, Lu MY, Citorik RJ, Zakeri B, Lu TK.(2014) Nat Mater. 13(5):515-23. doi: 10.1038/nmat3912 |
Programmable biofilm-based materials from engineered curli nanofibres. Nguyen PQ, Botyanszki Z, Tay PK, Joshi NS.Nat Commun. (2014) Sep 17;5:4945. doi: 10.1038/ncomms5945. |
| Spring Break Mar 23-27 | No class all week | |||
|---|---|---|---|---|
| Genome editing technologies |
Week 8: Wed Apr 1 |
Paper #2: Jenn ppt is here also...bacon anyone? |
Circular permutation of a synthetic eukaryotic chromosome with the telomerator. Mitchell LA, Boeke JD.Proc Natl Acad Sci U S A. (2014) Dec 2;111(48):17003-10. doi: 10.1073/pnas.1414399111 |
Multiplex Genome Engineering Using CRISPR/Cas Systems Cong L et al. Science (2013) Jan 3. PMID: 23287718 |
| Recoded Organisms |
Week 9: Wed Apr 8 day of tech spec review |
No presentations this week (response record for one or the other paper due) | Recoded organisms engineered to depend on synthetic amino acids. Rovner AJ, et. al...Isaacs FJ. Nature (2015) Jan 21. doi: 10.1038/nature14095 | A bacterial strain with a unique quadruplet codon specifying non-native amino acids Chatterjee A, Lajoie MJ, Xiao H, Church GM, Schultz PG. Chembiochem (2014) Aug 18;15(12):1782-6 doi: 10.1002/cbic.201402104 |
| Cell-free Synthetic Biology |
Week 10: Wed Apr 15 |
Paper #1: Tushar ppt is here |
Paper-based synthetic gene networks Pardee K, Green AA, Ferrante T, Cameron DE, DaleyKeyser A, Yin P, Collins JJ. Cell (2014) Nov 6;159(4):940-54. doi: 10.1016/j.cell.2014.10.004 |
Linear DNA for rapid prototyping of synthetic biological circuits in an Escherichia coli based TX-TL cell-free system Sun ZZ1, Yeung E, Hayes CA, Noireaux V, Murray RM. ACS Synth Biol. (2014) Jun 20;3(6):387-97. doi: 10.1021/sb400131a |
| Setting Standards |
Week 11: Wed Apr 22 |
Paper #1: Ellie ppt is here |
SynBioLGDB: a resource for experimentally validated logic gates in synthetic biology. Wang L, et.al. Wang D.Sci Rep. (2015) Jan 28;5:8090. doi: 10.1038/srep08090 |
Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca. Temme K1, Zhao D, Voigt CA.Proc Natl Acad Sci U S A. (2012) May 1;109(18):7085-90. doi: 10.1073/pnas.1120788109 (moved from week 12) |
| Methods for Metabolic Engineering | Week 12: Wed Apr 29 |
Paper #1: Heejo ppt is here |
The case for decoupling assembly and submission standards to maintain a more flexible registry of biological parts Alnahhas RN, Slater B, Huang Y, Mortensen C, Monk JW, Okasheh Y, Howard MD, Gottel NR, Hammerling MJ, Barrick JE.J Biol Eng. (2014) Dec 1;8(1):28. doi: 10.1186/1754-1611-8-28 (moved from week 11) |
CONSTRICTOR: constraint modification provides insight into design of biochemical networks Erickson KE, Gill RT, Chatterjee A. PLoS One (2014) Nov 25;9(11):e113820.doi: 10.1371/journal.pone.0113820 |
| Synthetic Systems at Play | Week 13: Wed May 6 |
Paper #1: Marianne ppt is here |
Towards synthetic biological approaches to resource utilization on space missions Menezes AA, Cumbers J, Hogan JA, Arkin AP.J R Soc Interface (2015) Jan 6;12(102):20140715. doi: 10.1098/rsif.2014.0715 |
Programmable bacteria detect and record an environmental signal in the mammalian gut Kotula JW, Kerns SJ, Shaket LA, Siraj L, Collins JJ, Way JC, Silver PA. Proc Natl Acad Sci U S A. (2014) Apr 1;111(13):4838-43. doi: 10.1073/pnas.1321321111 |
| Property rights in synthetic biology | Week 14: Wed May 13 last day of class |
no presentations this week (response record only if you've missed a different discussion this term) | Bringing Standards to Life: Synthetic Biology Standards and Intellectual Property AW Torrance and LJ Kahl Santa Clara High Technology Law Journal(2014) 30(2) link] |
Synthetic biology: caught between property rights, the public domain, and the commons Rai A, Boyle J. PLoS Biol. (2007)5(3):e58 PMID: 17355173 |
