IGEM:Stanford/2010/Notebook/25 May 2010: Difference between revisions
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'''Tinkering With the araBAD Promoter''' | '''Tinkering With the araBAD Promoter''' | ||
<biblio> | <biblio> | ||
pmid=12080425 | #araBAD pmid=12080425 | ||
</biblio> | </biblio> | ||
*Figure 2 shows output as a response to arabinose concentration. The squares (filled and open) and the open diamonds seem to show a linear response curve over ~4 orders of magnitude. | *Figure 2 shows output as a response to arabinose concentration. The squares (filled and open) and the open diamonds seem to show a linear response curve over ~4 orders of magnitude. | ||
Revision as of 16:46, 13 June 2010
Meeting Notes
We discussed our two models for our ratiometric sensor:
- mRNA dimerized by miRNA/sRNA, lysed
- Equilibrium Position of a reaction (methylation? phosphorylation? something else?) influenced by inputs
For Next Time
The idea for this coming week is to start from the general models that we have created and fill in the missing parts. We should look to find specific examples of promoters, model ligands, output proteins, etc.
Specific starting points:
- small RNA's in bacteria: what's been done, what are some particulars about using them?
- here's a good reference: Engineering RNA-based circuits
- engineered riboregulators (possible mechanism for us): Engineered riboregulators enable post-transcriptional control of gene expression
- enzyme pairs we could use in the equilibrium position model (kinase/phosphorylase, methylation, etc.)
- promoters we could use (note: we want a promoter that experiences minimal cooperative binding. That is, we want a change in concentration of our input substance to correspond linearly to a change in expression of the promoter, preferably across a wide range of concentrations.)
Also, to better nail down exactly what we want our system to do, we should look more into the application. We should either help Isis and Karina develop the preterm labor idea or come up with a different one.
Preterm Labor References
Abnormal vaginal flora as a predictor of preterm labor
- Donders GG, Van Calsteren K, Bellen G, Reybrouck R, Van den Bosch T, Riphagen I, and Van Lierde S. Predictive value for preterm birth of abnormal vaginal flora, bacterial vaginosis and aerobic vaginitis during the first trimester of pregnancy. BJOG. 2009 Sep;116(10):1315-24. DOI:10.1111/j.1471-0528.2009.02237.x |
Promoters
Tinkering With the araBAD Promoter
- Khlebnikov A, Skaug T, and Keasling JD. Modulation of gene expression from the arabinose-inducible araBAD promoter. J Ind Microbiol Biotechnol. 2002 Jul;29(1):34-7. DOI:10.1038/sj.jim.7000259 |
- Figure 2 shows output as a response to arabinose concentration. The squares (filled and open) and the open diamonds seem to show a linear response curve over ~4 orders of magnitude.
