Biological Composition, Leaklessness, and Otter Deaths

Today I Learned:
1) A couple of tricks for composing biological parts (genetically encoded logic gates, switches, sensors, and the like). First, use really strong terminators! Transcriptional leakage is common, and using better terminators can help quite a bit. Second, put a ribozyme motif between your promoter and your ribosomal binding sites (RBSs). It will cleave off the promoter after transcription, which prevents different promoters from interacting differently with the RBS. 

Also, Chris Voigt’s lab is working on a piece of software called Cello, which should be available on the web soon, which can design complex genetic circuits based on a logical specification. It uses the tricks mentioned above, and has pretty detailed empirical characterization of performance and error for its parts, which it propagates through the circuits it designs to determine their expected performance. Also Voigt lab’s web page has a nice compendium of (mostly external) tools for synthetic biologists (and other biologists!): http://web.mit.edu/voigtlab/webtools.html

2) A motif for leafless strand displacement reactions! See http://solo.ucsf.edu/papers/dsd-leakless.pdf for details. Basically, there’s a whole bunch of nano tech things you can build from DNA that use a technique called DNA strand displacement, or DSD — it’s a really simple and elegant way of making DNA strands in a test tube dynamically interact with each other. The trouble is, DSD almost always features “leak”, which is unwanted reactions between certain kinds of strands that end up killing the whole thing over the long term. Today I heard a proposal for essentially eliminating leak reactions, which is a big deal in the field.

3) Most sea otters die from infectious diseases. Most of the infectious diseases are protists. Remember all the nasty little choanoflagellates and flagellate parasites from AP/Intro Bio? Yeah, sea otters get those a lot. There’s also a fair amount of death to injuries and predation (about 2.5% of otter deaths are from gunshot wounds).