20.20(S15):Advanced topics

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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 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
Ptashne M PMID: 15055587 pdf
Build Artificial
Brent R PMID: 15055588 pdf

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