Team:Stanford/NotebookPage/25 May 2010

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May 25 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: [http://www.springerlink.com/content/x6p4lqn1608267r1/fulltext.pdf Engineering RNA-based circuits]

• engineered riboregulators (possible mechanism for us): [http://www.nature.com/nbt/journal/v22/n7/pdf/nbt986.pdf 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 <biblio>

1. abnormalflora pmid=19538417

</biblio>