Readings (20.902)

This page lists the papers assigned to and presented by 20.902 students in the 20.020 class. Each week during the 20.020 three-hour studio session, a 20.902 student leads a presentation and discussion on a relevant paper.

Some additional readings for the 20.020 students are woven into their homework, as described on the assignments page.

Schedule

Discussions will be 1 hour long during each week's studio session.

TOPICS PAPERS FOR PRESENTATION & DISCUSSION

A Voyage To Lilliput

How a small number of AA substitutions change activity of a protein

Bushman, F. D., and M. Ptashne. "'Turning Lambda Cro Into a Transcriptional Activator." Cell 15, no. 2 (July 15, 1988): 191-7. PMID: 2968842

Example review presentation (PDF)

Related readings to enjoy

Amazon logo Ptashne, Mark. Genetic Switch: Phage Lambda and Higher Organisms. Malden, MA: Blackwell, 1992. ISBN: 9780865422094. [Preview in Google Books]

———. "How Gene Activators Work." Scientific American 260, no. 1 (January 1989): 40-47.

Slide rule optional

Computational design of novel protein activities

Humphris, E. L., and T. Kortemme. "Design of Multi-Specificity in Protein Interfaces." PLoS Computational Biology 3, no. 8 (2007): e164. DOI: 10.1371/journal.pcbi.0030164

Nature heart Legos™

Proteins are modular too

Jin. T., and M. Inouye. "Ligand Binding to the Receptor Domain Regulates the Ratio of Kinase to Phosphatase Activities of the Signaling Domain of the Hybrid Escherichia Coli Transmembrane Receptor, Taz1." J Mol Biol 232, no. 2 (1993): 484-92. PMID: 8393937

Better odds in Vegas

DNA elements are modular too, allowing for circuits, but circuits don't always work

Anderson, J. C., C. Voigt, and A. P. Arkin. "Environmental Signal Integration by a Modular AND Gate." Molecular Systems Biology 3, no. 133 (2007). DOI: 10.1038/msb4100173

Darwin is alive and well

Directed evolution at the parts and device level

Saito, H., and T. Inoue. "RNA and RNP as New Molecular Parts in Synthetic Biology." Journal of Biotechnology 132, no. 1 (2007): 1-7. DOI: 10.1016/j.jbiotec.2007.07.952

I demand the cone of silence

Nature's constraints on genetic circuit design

Blake, W. J., et al. "Phenotypic Consequences of Promoter-mediated Transcriptional Noise." Molecular Cell 24, no. 6 (2006): 853-65. DOI: 10.1016/j.molcel.2006.11.003

Intelligent Design

Functional composition at the device level

Maeder, M. L., et. al. "Rapid "open-source" Engineering of Customized Zinc-finger Nucleases for Highly Efficient Gene Modification." Molecular Cell 31, no. 2 (2008): 294-301. DOI: 10.1016/j.molcel.2008.06.016

Writing in genetic code

DNA construction and editing technologies

Shao, Z., and H. Zhao. "DNA Assembler, An in vivo Genetic Method for Rapid Construction of Biochemical Pathways." Nucleic Acids Res 37, no. 2 (December 12, 2008): e16. DOI: 10.1093/nar/gkn991

Related reading to enjoy

Stemmer, W. P., et al. "Single-step Assembly of a Gene and Entire Plasmid from Large Numbers of Oligodeoxyribonucleotides." Gene 164, no. 1 (October 16, 1995): 49-53. DOI: 10.1016/0378-1119(95)00511-4

We're only human

What is the state of the art?

Skerker, J. M., et al. "Rewiring the Specificity of Two-component Signal Transduction Systems." Cell 133, no. 6 (2008): 1043-54. DOI: 10.1016/j.cell.2008.04.040

Little Red Corvette

Once you've got the DNA, where do you put it? Introducing... THE CHASSIS

Osawa, M., D. E. Anderson, and H. P. Erickson. "Reconstitution of Contractile FtsZ Rings in Liposomes." Science 320, no. 5877 (2008): 792-4. DOI: 10.1126/science.1154520

Related reading to enjoy

PĆ³sfai, G., et al. "Emergent Properties of Reduced-genome Escherichia Coli." Science 312, no. 5776 (2006): 1044-6. DOI: 10.1126/science.1126439

Secret map hidden in the peg-leg

Getting DNA to speak in binary

Portney, N. G., et al. "Length-based Encoding of Binary Data in DNA." Langmuir 24, no. 5 (2008): 1613-6. DOI: 10.1021/la703235y

On your mark, get set, go

System dynamics

Bashor, C. J., et al. "Using Engineered Scaffold Interactions to Reshape MAP Kinase Pathway Signaling Dynamics." Science 319, no. 5869 (2008): 1539-1543. DOI: 10.1126/science.1151153

Rough consensus and running code

Building patterns and memories

Ajo-Franklin, C. M., et al. "Rational Design of Memory in Eukaryotic Cells." Genes Dev 21, no. 18 (2007): 2271-6. DOI: 10.1101/gad.1586107

Mine mine mine

Property rights in synthetic biology

Rai A., Boyle. "Synthetic Biology: Caught Between Property Rights, The Public Domain, and The Commons." J PLoS Biol 5, no. 3 (2007): e58. DOI:10.1371/journal.pbio.0050058

Related reading to enjoy

Kaye, J., N. Hawkins, and J. Taylor. "Patents and Translational Research in Genomics." Nature Biotech 25, no. 7 (2007): 739-741. DOI: 10.1038/nbt0707-739

Drop it like it's hot

Safety!

Samuel, G. N., M. J. Selgelid, and I. Kerridge. "Managing the Unimaginable. Regulatory Responses to the Challenges Posed by Synthetic Biology and Synthetic Genomics." EMBO Reports 10, no. 1 (2009): 7-11. DOI: 10.1038/embor.2008.232

 

Readings Presentation Guidelines

Presentations on the readings should cover the following points.

  1. Background information: to set the stage for your talk. Includes the nouns and verbs of your topic, the knowns and unknowns
  2. High level summary: one slide only
  3. Primary evidence: the key data and any explanation needed to understand the experimental method used
  4. Secondary/supportive evidence: other experiments or techniques that bolster primary data
  5. Key assumptions: can be in method, in conclusion or in experimental design
  6. Uh oh!?: if you had been reviewing this paper for publication, what questions or concerns would you have? Would you recommend that the paper be published? Or, not?
  7. Significance: then and now; follow-up work since publication if relevant