20.20(S15):Advanced topics: Difference between revisions
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|'''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]] | |'''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]] | ||
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| '''Metabolic Engineering | | '''Metabolic Engineering''' | ||
| Week 12:<br> Wed Apr 29 | | Week 12:<br> Wed Apr 29 | ||
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| | |'''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]] | ||
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Revision as of 17:59, 28 January 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(s) | Related paper(s) to enjoy |
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 |
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 |
An Autonomous In Vivo Dual Selection Protocol for Boolean Genetic Circuits. Beneš D1, Sosík P, Rodríguez-Patón A. Artif Life. (2015) Jan 26:1-14. doi:10.1162/ARTL_a_00160 |
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 4 |
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 | |
SynBio for Science |
Week 6: Wed Mar 11 day of 3 ideas presentations |
No presentations this week (response record for one or the other paper due) | 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 |
Engineering Materials with Biology |
Week 7: Wed Mar 18 |
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. |
Engineering living functional materials Chen AY1, Zhong C, Lu TK.ACS Synth Biol. (2015) Jan 16;4(1):8-11. doi: 10.1021/sb500113b | |
Spring Break Mar 23-27 | No class all week | |||
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Genome editing technologies |
Week 8: Wed Apr 1 |
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-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 | |
Standardization and Measurement |
Week 11: Wed Apr 22 |
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 |
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 | |
Metabolic Engineering | Week 12: Wed Apr 29 |
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 |
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Synthetic Systems at Play | Week 13: Wed May 6 |
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 day of final presentations |
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 |