Tuesday, November 09, 2004

Rotation over. Your score: 3 to 1.

I'm done with my rotation in Drew Endy's lab. So, what did I get done in my rotation ? I built three new Biobricks, namely:

- Part I6401: Yellow Fluorescent Protein (YFP) with an AAV degradation tag transcribed from the pTet promoter
- Part I6402: YFP with an AAV degradation tag transcribed from the Luxpl promoter.
- Part I13976: (Actually a duplicate of an existing part, but I didn't know that) YFP with an AAV degradation tag transcribed from the Lac promoter.

[Actually, I was supposed to build four Biobricks, but I fried the pieces for one of them ...]

What does all this gobbledygook mean ? It's actually quite simple once you hack your way through the random jargon forest that seems to be a core attribute of biology: YFP is a protein that basically glows yellow when you shine light on it; it's a pretty useful experimental thing to have because it means you can "paint" things that you're interested in with YFP and watch what they're doing by following the yellow dot, so to speak. Now, in a cell, proteins aren't only manufactured, they're also broken down, and the breakdown process is so important that the folks who discovered how it works won this year's Nobel Prize in Chemistry. The way the breakdown works is that each protein is basically tagged with an "expiration date" ie something that tells the cell how quickly to break it down; these labels are called "degradation tags". Different degradation tags lead to different rates of breakdown. The "AAV degradation tag" that is on my protein is a medium-strength tag meaning that the protein is broken down at an intermediate rate. And, finally, "promoters" are essentially on/off switches that determine whether a protein gets made or not; different promoters respond to different chemicals to turn them on or off.

So, in summary, I built three proteins that glow yellow, have a medium lifetime, and can be turned on and off by 3 different switches. Pretty simple, isn't it =) ? Currently, the folks in the lab are using a version of the protein that hangs around for a really long time, which makes some of their measurements problematic, so my medium-lifetime protein should come in handy. And even if nobody ends up using it, hey, I still had fun doing the work.

My main intentions during this rotation were to get some experience with lab work, do something that would be useful to the other folks in the lab, learn more about synthetic biology and get a feel for the lab's culture and the way they approach problems. I think I achieved all of those goals and have a strong suspicion that it's the lab I'll want to end up in long-term.
My next rotation is in Doug Lauffenburger's lab; I have no idea what I'm going to work on there but he has a pretty big lab with people working on a host of different things so I'm sure I'll be able to find something interesting.

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