Introduction to Biological Engineering Design

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 Ptashne, Mark. Genetic Switch: Phage Lambda and Higher Organisms. Malden, MA: Blackwell, 1992. ISBN: 9780865422094. ———. “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 Pósfai, 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