20.20(S12):Advanced topics

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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

16-220

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
    doi:10.1016/j.copbio.2011.12.026
  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
doi:10.1038/nrmicro2717
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
Modularity
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
doi:10.1038/nchembio.369
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
doi:10.1038/nbt.2018
Chassis
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
doi:10.1186/1475-2859-11-11
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
doi:10.1038/nature10722
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
doi:10.1038/nature10403
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
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