Hello? Do you have any DNA?

Finally! A day where I felt my time spent in the lab was actually productive! My goal for the day was to extract DNA from one of my random fungi samples (I ended up using a fairly recent one out of the fridge, since I forgot my larger stash on the stairs at home), run PCR, then run the sample on a gel to see if I had intact DNA that could be sequenced.

I got a pretty good start to the day, doing most of the DNA extraction before lunch. After lunch (yes, I actually ate lunch in the dinning hall for the first time in quite awhile), I tested the DNA in the spectrophotometer and- for once- I actually had quite a bit! I quickly mixed it up with the needed reagents for PCR and put it in the thermocycler to run for about an hour and a half.

When the PCR was done, I made up an agarose gel and ran my samples. To do this, you mix your sample with a dye, then put it on a gel (with a standard), which is then attached to an electrical current. The current causes the DNA to separate in the gel based on size, and then you can determine the size of your DNA strand based on how far into the gel it has run and the size of the standard you've put in.

Anyway, after running a gel, we usually take pictures of them. But today, the camera didn't feel like turning on, so we just peered into the light box at it. I probably should have run the gel longer, but it did look like I had some intact DNA, which is pretty encouraging, considering how much trouble I was having with it last semester.

Finally, while the PCR was running, I got to have a bit of fun. First, Thursday afternoon is chemistry lab, so while my samples thermocycled, I watched the chemistry students use Thin Layer Chromatography (TLC) to separate some of the components of leafy greens. Thin Layer Chromatography is a technique used to separate components of a mixture by placing a small sample of the mixture at the bottom of a TLC plate (the stationary phase, usually made of silica, alumina, etc. with a plastic or metal back), then placing the plate in a mobile phase (often some kind of solvent), which moves up the plate via capillary action, taking the mixture with it and separating it into components along the way. This was particularly cool looking with the leafy greens because the solvent left bands components in fun shades of green.

ANYWAY, the second fun thing I got to do, was set up and test (a.k.a. play with) the new mini gas chromatograph! Gas chromatography is similar to TLC in that it separates a mixture into it's components. Except, gas chromatography uses a gas as the mobile phase and has a specially coated column that the gas (and sample) move through that acts as the stationary phase. As the sample moves out of the stationary phase, it is recorded, resulting in a graph with a bunch of peaks, each representing one of the components of the mixture. As always, I'm sure googling "gas chromatograph" will lead you to an article with more detail. Or, there's always Wikipedia.

Our new gas chromatograph is pretty awesome since it's very easy to use (you just inject a tiny, tiny, drop of your sample using a syringe), and it's hooked up to a computer that records the data! I realize that for many people, this would not be all that exciting, but for our lab, it's a pretty big deal. Our old gas chromatograph printed directly to a printer, making it difficult to transfer the graphs produced to a digital format. Mostly, I'm just excited to use a machine that works pretty much as soon as you take it out of the box, after spending last spring trying to get the HPLC to work (HPLC- high pressure (or performance) liquid chromatograph- yup, quite a bit like the gas chromatograph, but uses liquid as the mobile phase).

Whew! That was a lot of chatter that was not related to Plan. Sorry.

One final though for the day- I was encouraged this evening to get an email from my Plan Sponsor (like... a thesis advisor or some such, the professor I'm working with most at Marlboro) asking a few more questions about the work I'd done in the lab today since he'd been thinking about ways to check and see if the gel was running correctly. One of the things I love about Marlboro is having professors who put so much time and energy into their students projects! It's nice to know that I'm not the only one who think about my Plan after leaving the college in the evening. Thank you T! (I figured I'd just go with initials if I'm not talking about myself- for the sake of privacy and such)

That was far too much typing. Sorry about that, I'll have to learn to make shorter posts...