Wednesday, March 30, 2016

Congratulations to Swati Banerjee Carr!

On Monday at Boston University, I attended the successful Ph.D. thesis defense of Swati Banerjee Carr, who I have been co-advising with Doug Densmore for the past couple of years.

Swati's work is, to my thinking, a classic case of how a lot of science doesn't start with "Eureka!" but with "That's funny..." or, as in Swati's thesis: "Why doesn't any of this work?!?!"  Originally, she was building a simple test system to characterize various different pairs of repressors and promoters in E. coli.  These are some of the most basic and common building blocks in synthetic biology: a repressor acts on a promoter to suppress the gene controlled by that promoter, which means that controlling repressors can switch things on and off in a cell, including other repressors, making it one of the foundational tools for controlling the behavior of cells.  Practically everybody uses them, and in her system she was using some of the most well-known and best understood biological parts around, and yet when she put them together nothing worked.  When she put the parts together in different orders, however, sometimes it worked and sometimes it didn't.  "That's funny..."

With a bit of study, including results of some of my other recent work, the key problem was identified as being the bits of DNA just before the promoters, which changes depending on what else is in the system and how the parts are arranged. And so, Swati's project ended up shifting away from the original plan and focusing instead on solving that problem of context dependence. Now, at the end of her doctoral work, our work together has resulted in a lovely protocol for creating "upstream insulators" that make a promoter behave pretty much the same no matter where you put it.  The data is really beautiful, but I can't share it quite yet: not until Swati has officially deposited the thesis.  What it shows, however, is a remarkably stark contrast:

  • Without insulators: a genetic circuit in which every permutation is different, pretty much none of them are "working" by even the most generous definition, and there's not even any real pattern to the chaos
  • With insulators: every permutation does almost exactly the same thing, with quite strong and consistent signals for all of them.  
I think this has the potential to be quite a big deal, and don't know why anybody would ever use an uninsulated promoter again once this gets released.

Swati gave a good talk to a packed room, standing room only.  She's got some homework from me and the others on the committee, to improve her actual thesis document some more before it can be considered quite complete, but she's on the home stretch, having done some damned good work, of which I think she can rightly be quite proud.
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