February 3, 2005

And the Fun Begins

I apologize for the long delay in posting. Right now, I'm finishing up a manuscript on the design of biological AND gates that activate gene expression if and only if two or more transcription factors are present. I won't mention any details until the paper is accepted, but these facts should pique your interest:
-- They're made of readily available molecular parts
-- They require no special cooperativity or allosteric changes (ie. no intensive engineering)
-- They can be made for two or three inputs (and probably more, but I didn't want to push it)

After the paper's out the door, it's time for the real fun: experiments!

So far, most of the work has been computational: developing new algorithms and software to quickly design and analyze synthetic biological systems. The methods have been shown to be accurate, but there's always a lingering doubt that the in silico results won't match the in vivo results. Now, it's time to go back to the (wet) lab and really see if it all works. The Fun Begins.

To test out our methodoloy, we thawed out some strains of E. coli producing GFP under control of the lac operon and sent it through a flow cytometer (courtesy of Dr. Friedrich Srienc, thank you very much). The pictures it produces are simply fantastic.

It's amazing how stochastic simulations and flow cytometry complement one another. A stochastic simulation will produce the probability distribution of the solution at whatever time points you want, but requires numerous independent trials (usually 10,000, each representing a single cell). A flow cytometer, on the other hand, can count hundreds of thousands of cells and measure the fluorescence in each individual cell, producing a very smooth distribution, but only for a relatively few number of time points. Using the simulations, you can gain a high-resolution (in time) picture of the dynamics. Using the flow cytometer, you can validate the results at specific time points and easily produce very smooth distributions. Very nice.

If you're interested in computational design of biological systems, check out http://hysss.sourceforge.net. HySSS, or Hybrid Stochastic Simulation for Supercomputers, is a software package that creates, simulates, and analyzes biological or chemical systems. It uses the hybrid homogeneous stochastic simulation previously mentioned. That paper actually was published on February 1st (not Jan 15th, woops) in J Chem Phys.

Posted by sali0090 at 9:58 PM