In vitro evolution system (Oli)

Meet Oli.

Oli is a DNA hairpin of about 120 base pairs, and is intended to be used for experimental evolution. Oli is more complex than most in-silico organisms, yet much simpler than a virus. You can get the sequence from the manuscript, and synthesize Oli yourself, and then do all sorts of cool experimental evolution, providing you have access to a RT PCR machine and have or are willing to develop awesome pipetting skillz.  By manipulating the chemistry of the PCR reaction, Oli can be used for experiments that examine adaptive dynamics and outcomes at the genetic, phenotypic and fitness levels. Oli’s fitness can be calculated as the rate of population increase during PCR. Primer recruitment success can be used as a phenotype, and Oli’s secondary structure also acts as a phenotype, and can be predicted using the freely-available UNAfold software. Finally, entire Oli populations can be sequenced using 454 sequencing (or something better, if you have it).

I’ve made Oli freely available through arXiv. (http://arxiv.org/abs/1211.4223). I developed the system and confirmed that it works, but there was one of those moments of Bad Science where I learned by experience how not to make DNA libraries for sequencing, and I couldn’t get the data I wanted from my first Oli experiment. At the moment, I have neither the money nor the hands to redo the experiment. It seems silly to hold up others just because I can’t do this right now. Plus, I want to see what you’ll do with Oli.

In the interest of giving you full information: This manuscript was rejected from Evolution, based on two positive reviews and one negative review. While I cannot make these reviews publicly available, it boils down to this: two of the reviewers thought Oli was a good system, and pretty cool, though they also pointed out that had I not had a bit of a “learn by doing it wrong” moment pre-sequencing, the data would have been a lot better. The third reviewer felt that they system was neither novel nor useful, and not substantially different from aptamer systems used for in-vitro evolution studies in organic chemistry labs. They also had some concern about evolved Oli populations escaping the restriction digestion step during selection.

I cannot address the reviewer or editor comments on novelty. On this point I respectfully disagree. As to whether or not Oli will be useful, I say “wait and see”. I can demonstrate that the evolved Oli populations did not escape restriction digestion, which shows that the steps I took were sufficient for the experiment I did, which involved a dozen rounds of selection, and over 400 rounds of reproduction with mutation, at varying intensities of selection.

If you want to collaborate on an Oli project, or are a student/postdoc who would like to work with me on the Oli system (and you have mad lab skills),  or if you just need more information on using the Oli system, email me.