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 LilliputHow 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
———. "How Gene Activators Work." Scientific American 260, no. 1 (January 1989): 40-47. |
Slide rule optionalComputational 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 VegasDNA 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 wellDirected 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 silenceNature'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 DesignFunctional 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 codeDNA 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 enjoyStemmer, 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 humanWhat 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 CorvetteOnce 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 enjoyPósfai, 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-legGetting 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, goSystem 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 codeBuilding 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 mineProperty 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 enjoyKaye, 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 hotSafety! | 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.
- Background information: to set the stage for your talk. Includes the nouns and verbs of your topic, the knowns and unknowns
- High level summary: one slide only
- Primary evidence: the key data and any explanation needed to understand the experimental method used
- Secondary/supportive evidence: other experiments or techniques that bolster primary data
- Key assumptions: can be in method, in conclusion or in experimental design
- 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?
- Significance: then and now; follow-up work since publication if relevant