20.20(S12):Advanced topics

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20.385: Advanced Topics in Synthetic Biology


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


TOPIC DATE Discussion leader(s) Discussion paper(s) Related paper(s) to enjoy
Preview of 20.385 Wed Feb 8 Natalie Kuldell preview of 20.385 before next week read
  1. Innovation at the intersection of synthetic and systems biology
    Lanza AM, Crook NC, and HS Alper
  2. Two ‘What if' experiments
    Ptashne, M.
    PMID: 15055587
  3. Build Artificial
    Brent, R.
    PMID: 15055588
Parts™ Wed Feb 15 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
Computational tools for the synthetic design of biochemical pathways
Medema, M, et al. Nature Rev Micro (2012) January 23
Transcription-based Logic Devices
Wed Feb 22 article 1 = Jamal and Queenie, ppt is here 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
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
RNA Engineering
Wed Feb 29 article 1 = Lauren and Alfred, ppt is here Direct and specific chemical control of eukaryotic translation with a synthetic RNA–protein interaction
Goldfless SJ, et al. NAR (2012) 1-12
DOI: 10.1093/nar/gks028
Versatile RNA-sensing transcriptional regulators for engineering genetic networks
Lucks JB, et al. PNAS (2011) 108(21): 8617-8622
DOI: 10.1073/pnas.1015741108
Protein Design: directed evolution
Wed Mar 7 article 1 = Hannah and Sabina
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
Wed Mar 14
before 3 ideas presentations
article 1 = Shelley and Donnie
ppt is here and pdf is here
Modularity of a carbon-fixing protein organelle
Bonacci W et al. PNAS (2012)109(2):478-483
DOI: 10.1073/pnas.1108557109
A modular positive feedback-based gene amplifier
Nistala GJ et al. JBE (2010) 4:4
DOI: 10.1186/1754-1611-4-4]
(re)Programming Systems
Wed Mar 21 article 1 (+2 as needed) = PJ, Nahum and Shlomiya
ppt is here and pdf is here
Reprogramming bacteria to seek and destroy an herbicide
Sinha, J. et al. Nature Chemical Biology (2010)6: 464–470
Scaling up synthetic biology: Do not forget the chassis
A Danchin FEBS letters (2012)
pdf here
Spring Break Mar 26-30 No class all week
DNA construction and editing technologies
Wed Apr 4 article 1 = PJ ppt pdf
article 2 = Shelley ppt pdf
Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement
Isaacs FJ et al. Science (2011) 333(6040):348-353
DOI: 10.1126/science.1205822
Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting.
Cermak T et al. NAR (2011) 39(12):7879
PMID: 21493687
Feedback and Insulation
Wed Apr 11
before tech spec review,
article 1 = Alfred, pptx pdf
article 2 = Jamal pptx pdf
A yeast synthetic network for in vivo assessment of reverse-engineering and modeling approaches
Cantone I et alCell (2009)137(1):172-181
PMID: 19327819
In silico feedback for in vivo regulation of a gene expression circuit
Milias-Argeitis A et al.Nature BioTech (2011) 29(12):1114–1116
Wed Apr 18 article 1 = Hannah
article 2= Queenie ppt pdf
An E. coli Cell-Free Expression Toolbox: Application to Synthetic Gene Circuits and Artificial Cells
Shin J, and Noireaux, V. ACS Synthetic Biology (2012) 1(1):29–41
DOI: 10.1021/sb200016s
Low-mutation-rate, reduced-genome Escherichia coli: An improved host for faithful maintenance of engineered genetic constructs
Csorgo B et al. Microbial Cell Factories (2012)11:11
Programming with Models & Noise
Wed Apr 25 article 1 = Lauren pptx pdf
article 2 = Sabina pptx pdf
Model-Driven Engineering of RNA Devices to Quantitatively Program Gene Expression
Carothers JM et al. Science (2011)334(6063):1716-1719
DOI: 10.1126/science.1212209
A sensing array of radically coupled genetic ‘biopixels’
Prindle A et al. Nature(2012)481:39–44
Metabolic Engineering Wed May 2 Guest discussion leader for paper 1 = Tae Seok Moon
discussion to start @4:15
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
PMID: 20117231
Organization of Intracellular Reactions with Rationally Designed RNA Assemblies
Delebecqu CJ et al. Science (2011) 333:470
DOI: 10.1126/science.1206938
Systems & System Ecology Wed May 9 article 1 from April 18th
= Hannah ppt and pdf
article 2 (here)
= Shlomiya ppt and pdf
Synthetic chromosome arms function in yeast and generate phenotypic diversity by design
Dymond JS et al. Nature (2011) 477: 471–476
Engineered bidirectional communication mediates a consensus in a microbial biofilm consortium
Brenner K PNAS (2007) 104(44):17300-17304
DOI: 10.1073/pnas.0704256104
Property rights in synthetic biology Wed May 16
before final presentations,
article 1 = Nahum ppt 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 16
before final presentations,
article 2 = Donnie ppt 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