Re:Cello – a Verilog compiler for transcriptional logic in b...
by jhallenworld on Tuesday April 05, 2016 @09:12AM
(#11430048)
This is so cool... they have blinking LED debugging of genetic circuits:
"Debugging genetic circuits
We developed a strategy for “debugging” a malfunctioning circuit to determine which gate is causing the failure. This was done by creating a series of plasmids that transcriptionally fuse the output promoter of each gate to yfp."
Basically if the liquid fluoresces the gate you're debugging is outputting a 1.
If you have access, Figure S5 was helpful for understanding.
As an example, they created a plasmid (circular piece of DNA that's easy to engineer) to be an AND circuit. They added two genes (A and B) with promoters that are activated by two different signals (https://en.wikipedia.org/wiki/Promoter_(genetics)). The also added another gene, C, with two promoters that bind proteins A and B.
When genes A and B are activated, they create proteins that block the production of protein C. But this inhibition only happens if both A and B are present. Thus, you get an "AND".
You can then use the inhibition or production of C to do something else. In this case they used it to block the production of a protein that fluoresces, but you can do whatever you want with that logic. Like targeted treatment of IBD: only produce drug C when gut signals A and B are present, but not before.
Or make more complicated circuits.