Berkeley Engineering Blogs

This year’s dual-sided iGEM project at UC Berkeley is headed by Chris Anderson, Terry Johnson, Megan Dueck, and Doug Densmore.  Whereas last year’s two Berkeley teams addressed specific problems in the medical world—one of which was the lack of low-cost and wide access to plasma for blood transfusions, whose project was affectionately called Bactoblood, the two teams under Berkeley’s header this year are attempting to ameliorate the actual processes used to do synthetic biology.

Lysophonix, the project belonging to the “wet team,” is looking at ways to make bacteria burst open in response to sound—not just specifically to ultrasound but to the sound of any full-length album that the lab researcher may want to blast that day—so that the process of part assembly may be more cleanly streamlined and efficient.  The idea would be that the correct amount of reagents needed to cut a plasmid at certain locations (here:  enzyme restriction sites) would be found within a bacteria, along with the part in a plasmid-to be mixed with a different bacteria that has reagents and the plasmid where the part is meant to be put.  This sound induced lysis would allow the assembly of parts to be less abrasive to the proteins involved and the process would allow for more efficient assembly.

Likewise, Berkeley’s “computational team” is working on a better version of ApE (A Plasmid Editor)-the DNA sequencing program that most manipulators of DNA are dependent upon-called Clotho, cleverly named after the youngest of the fates of Greek mythology.  Their goal is to make a more user-friendly and comprehensive software program that would interface with BioBricks or a similar parts registry, making the research done in the lab and access to standardized parts more streamlined.

The lab team leaders are branding this kind of research the inquiry into “foundational technologies”-it is meant to help define the protocols of doing synthetic biology (which is still an emerging science and engineering discipline) and at the same time provide a more fleshed-out definition of what synthetic biology is.

So, what does this mean to make a process more streamlined and more standard?  These projects at UC Berkeley, as well as many others involved in the iGEM competition (one of the “special prizes” portion of the judging process at the Jamboree includes the “Best New Standard”-perfecting the craft of doing synthetic biology is extremely important to the actual doing of the science), are working at how to work on the efficiency of synthetic biology, as if—as the name “Genetically Engineered Machines” implies—the entire research process were a sort of assembly line at a factory.  How do you confront questions of trouble-shooting this kind of “trial and error” science, as it has been coined, when so much biological life (though the E. coli or yeast organisms are argued to have been greatly mapped out and understood by biologists) is still uncharted and beyond our scientific knowledge?