P.C. Shannon

For my third rotation, I am in Alan Lambowitz’s lab working on the group II intron stuff. It’s nice to be finally doing, you know, actual molecular biology after more than six months in grad school. I’d kinda forgotten how much I enjoy pipetting DNA and setting up reactions. Maybe the novelty will wear off before too long. The biggest complication at this point is that the post-doc with whom I was assigned to work went home to the Czech Republic for two weeks. That was four weeks ago. When he tried to come back, his papers weren’t in order or something and they sent him back to Prague. I’ve heard horror stories about Chinese students being stuck out of the country for four months. Welcome to Bush’s America. So it goes. In the meantime, I’ll do my best to get by without the post-doc and vote Democrat.

I’ve started work on my second rotation in Andy Ellington’s lab. It’s a bioinformatics problem, so I’ve had a crash course in Perl before I started writing any programs. But so far it’s progressing very nicely, and Andy is excited about it. I hope that before too long, I’ll be able to put the keyboard down and start doing some bench work to verify the computational work.

Previous people in the lab — mainly an undergrad who is now at Cambridge on a Marshall Scholarship — developed a database of amino acid-nucleotide interactions called “AANT”. I’ll spare you the details on how this was done, but there is a Nucleic Acids Research paper on it. Now I’m going back through the data looking for nucleotide-amino acid interactions that are at approximately the same distance and orientation as other interactions. I think ultimately Andy would like to be able to intelligently design aptamers (RNA molecules that bind other molecules) to bind proteins rather than having to screen for them, which can take months.