Monday, May 11, 2009

Rotation #3 Diary: Week 8

I'm now in the last week of my third rotation. Soon I will be choosing the lab where I'll spend the rest of my graduate school career. Thankfully, I'm in the happy position of choosing between several good labs. I haven't completely made up my mind, but I am leaning in one direction. I hope to sort everything out and join a lab by the beginning of June. If any former or current grad students would care to offer me some advice on making this decision, I'd be happy to get your input!

Last week I presented my rotation work at lab meeting. I made a little PowerPoint presentation that went over my progress on a couple of projects, complete with cute cartoon mice and screenshots from the gene sequencing software I've been using. Then, much to my horror, I deleted the entire thing 30 minutes before the meeting. I know I should have backed it up, and I had intended to. My original plan was to fine-tune the presentation the night before, which would have involved transferring it from my laptop to my desktop either by email or by flash drive. Unfortunately, I spent the night before the meeting at the emergency room, being treated for a bad allergic reaction to a bee sting. (It really wasn't my week...) So, I got no work done, and never transferred the file between computers, and thus had only one copy. Which I deleted. As Charlie Brown would say, "AAUGH!"

Fortunately, my PI and labmates were understanding of the mishap, although they did scold me for not making a backup copy. (I know. I know!) I gave lab meeting as a "chalk talk" instead, drawing diagrams on the board when I needed to, but mostly just talking and glancing at some hastily-scribbled notes to remind me of the details. Despite the awkwardness, this forced me to really explain the reasoning behind what I did and summarize the relevant results, rather than being like, "Look! I ran a gel! And here it is!" Hopefully the lab doesn't think I'm too much of an airhead, despite my technical difficulties.

More lab foibles: We transformed some bacteria last week. After spending a while cloning and sub-cloning, we finally had some DNA plasmids that we wanted to make in large quantities. This is done by tricking bacteria into taking up the DNA, i.e. transforming them, and then growing cultures of the bacteria so we can extract plasmid DNA from them once they've been fruitful and multiplied. I'd done transformations before using heat shock (putting the bacteria into a hot water bath for a minute or two), but this protocol called for electroporation (zapping the bacteria with electricity). No one in the lab had used the electroporation machine before, and our first run did not go too well. In fact, a very impressive spark was produced, along with a crackling sound and a strong aroma of barbecued competent cells. After daring everyone in the lab to smell the tube, we adjusted the settings on the machine and it seemed to be okay after that. No more fireworks occurred, and my transformed bacteria grew on some ampicillin plates, so it worked for at least some of them. (The plasmid we put into the bacteria contains an ampicillin resistance gene, so we know that successfully transformed bacteria will grow even when treated with that antibiotic. The untransformed bacteria die when you put them in ampicillin.) Now I've selected transformed bacterial colonies and grown enough of them to make DNA preps. We'll have to do some more analysis to see which colonies have the plasmids we want -- some of them might have recombined in weird ways, which isn't desirable. Progress marches on, with tiny little steps. Someday we'll make these into a lentivirus, honest.

I also had my last class of the semester last week. (We had our final session of my graduate seminar at a pub. It was quite grueling.) This August, I'll be taking my written qualifying exam. Until I pass that, I don't want to jinx myself by updating my Blogger profile from "first-year" to "second-year." But, I am very happy to be one year closer to a PhD. Next year I'll be working on dissertation research, TA assignments, grant-writing, and serving as a student committee representative for the Graduates in Neuroscience organization. I'm excited!

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