Talk:Silver: Synthetic Biology Review Article

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Comments on the working outline

  • RS 13:33, 7 July 2006 (EDT):

Another (related) option for how to classify synthetic biology endeavors is to do so in two dimensions:

One dimension is based on the key event which is being engineered:

  1. Transcription (protein-DNA binding)
  2. Translation (riboswitches)
  3. Post-translation (phosphorylation, methylation)
  4. Enzymatic conversion of substrates (metabolic engineering of pathways)
  5. Genome design

The other is the purpose for which the device is being built:

  1. Sensors (Hellinga's ligand binding proteins, Levskaya et al.'s light sensor)
  2. Information processing (logic)
  3. Actuators (reporters)
  4. Chemical synthesis or production (metabolic engineering)

Just wanted to throw this out there as another possible organization for section II.

Also, I am not clear on what you mean by Biological Modularity in section I.

By Biological Modularity, we just meant a discussion of how modularity can occur in biology at several levels, ie. RNA (UTR-based regulatory elements for example), protein (activation and DNA binding domains for example), etc.

These are comments that have been received thus far.

artificial vesicle based biology

  1. Noireaux V, Bar-Ziv R, Godefroy J, Salman H, and Libchaber A. Toward an artificial cell based on gene expression in vesicles. Phys Biol. 2005 Sep 15;2(3):P1-8. DOI:10.1088/1478-3975/2/3/P01 | PubMed ID:16224117 | HubMed [lib1]
  2. Noireaux V and Libchaber A. A vesicle bioreactor as a step toward an artificial cell assembly. Proc Natl Acad Sci U S A. 2004 Dec 21;101(51):17669-74. DOI:10.1073/pnas.0408236101 | PubMed ID:15591347 | HubMed [lib2]
  3. Chen IA, Roberts RW, and Szostak JW. The emergence of competition between model protocells. Science. 2004 Sep 3;305(5689):1474-6. DOI:10.1126/science.1100757 | PubMed ID:15353806 | HubMed [szostak]

All Medline abstracts: PubMed | HubMed

Mathematical or Quantitative (Predictive) Models of Gene Networks

  1. Tuttle LM, Salis H, Tomshine J, and Kaznessis YN. Model-driven designs of an oscillating gene network. Biophys J. 2005 Dec;89(6):3873-83. DOI:10.1529/biophysj.105.064204 | PubMed ID:16183880 | HubMed [lib]

materials for teaching undergrads

Beyond iGEM, there are some initial teaching efforts from courses taught at
UC Berkeley [[1]]
and at MIT [[2]] and [[3]]. Some of the MIT material was adapted as iGEM 06 teaching material at BU [[4]] so it didn't take long for the use of even a fledgling curriculum effort to spread.

Hopefully, as Synthetic Biology advances, the research will provide examples and technologies that capture the distinguishing aspects of the field. It would be great if teaching materials could be developed in parallel to rigorously educate a larger number students who might later do this work. Perhaps somewhere in your review there could be an explicit call for curriculum development as well. - Natalie

other ideas

  • I think it would be nice to see where Systems Biology meets Synthetic Biology, e.g the use of modeling tools in synthetic biology.