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February 15, 2005

Rotation Progression

I just realized I don't talk much about what's been going on in my rotations - although folks ask me about it all the time and it really is the most interesting part of the semester...

I'm having a lot of fun in the Keating lab. For this rotation, my time is split between doing wet lab and dry lab work. The wet lab stuff is amazing, mostly because I've never really had this kind of experience before. Every other biology student I talk to is surprised that I've never spent much time in the wet lab... but the truth is that all the research work I've done has been computer work. It's not even like we're doing anything super exciting - working with DNA and plasmids, transforming strains of E. coli, expressing and purifying protein, and running gels. Standard biochemistry techniques - but nothing that I've really had hands-on experience doing, other than biology teaching lab which only encourages you to follow the recipe, not really remember why you're doing what you're doing. And so far, everything that I've done in the wet lab has worked, thank goodness, despite my nervousness at screwing things up. I'm working with the technician in the lab - he essentially just does basic things that need to get done in the lab, he doesn't have his own research project - and so far he's screwed up more than me ;) of course, when you do things a million times you get less careful so I understand completely. I appreciate how he lets me work alongside him... with me asking all the time how to do things.

With the dry lab stuff, I've got a fairly independent project on the computer. This stuff I understand a bit more, mostly because I'm already familiar with it. One of the questions the lab wants to address is protein interactions. A very important part of biology is how proteins interact, and many times they do so by sticking together. Also, an important part of many proteins is what's called a coiled coil - if you've ever seen a telephone cord get all twisted up, that's a coiled coil. What happens many times is that one half of the coiled coil will be one protein and the other half will be another. If you've ever tried to untwist a phone cord you know how tough it can be - imagine if the phone cord was cut in half but each half stuck to each other, how hard that would be to separate. But predicting these interactions isn't always easy, because not all coiled coil halves (we call them domains) stick to every other one. Furthermore, they could coil in either a parallel or antiparallel fashion, but they usually prefer one over the other. My project is to evaluate a particular method called "statistical potentials" to see whether we can predict which interactions are good (i.e. they happen in nature) and which aren't. Also, I'd like to see if I can predict whether a particular pair prefers parallel or antiparallel orientation. It isn't working well yet, so I've got to dig in a bit more, but it's been lots of fun :)

Well, gotta run and get my laundry, then more paper reading for another class... the work never stops.

Posted by kgutwin at February 15, 2005 08:00 PM

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Posted by: prematureejaculation at July 3, 2005 07:01 PM