Lab Notes from a Pathology Intern

Week 1:      Today I got to perform a PCR all by myself. Okay, not all by myself-- under relatively intense supervision. But still, I got to awkwardly pipette micrometer amounts of primers and DNA templates.  That’s neat, right?

My first week at Pawlowska lab in Bradfield Hall (that tall, castle-like building behind the ag quad) allowed me to join the multitude of other students, trying their hands at research.

Professor Teresa Pawlowska, plant pathology, studies the evolution of arbuscular mycorrhizal fungi. Mycorrhizal fungi share symbiotic relationships with the majority of plants — potentially an evolutionary key in their ability to flourish on land. Shadowing this week has been an expansion of what is otherwise a roughly four-page explanation of basic microbiology in my giant biology text.  I learned about everything from Polymerase Chain Reactions to Gel Electropheresis. (It has been awesome.)

While the textbook description of Polymerase Chain Reaction is equal parts straightforward and vague, the actual process is expectedly more complicated and delicate.  The Reactions allow for DNA samples to be amplified, which is useful if there is not too much of a particular sample. The PCR kit has primers for the particular sample binding sites that allow DNA fragments to attach and create chains. After mixed, the products enter heating and cooling cycles that changes to optimal temperatures for an unzipping stage during which denaturing occurs, an annealing stage which is the time for primer bonding, and an extension stage for the polymerase to extend chain.

If you’re super obsessive compulsive, a lab might be a good place for you. (Then again, if you’re super obsessive, it could be a nightmare.)

I think I understand why science majors are so strongly encouraged to work in a lab. It feels less about mastering a project and more about learning the intricacies of solving big problems. It is the scientific process, and it can be a beautiful thing.

However, in times like these, it can be utterly devastating. I get to paste the empty band sheet on the second page of my lab notebook. My gel electrophoresis on yesterday’s PCR sample turned out to be blank. Apparently this happens often enough, but I was convinced that my sample would work. I’m not completely sure what my sample was, but I felt very attached to it..

My gel electrophoresis was supposed to check if the PCR worked out properly. Since DNA is negative, it runs in the wells from the negative to positive electrical current. The buffered agarose gel has ethidium bromide, which allows DNA to be seen under UV light.  The DNA appears like florescent blue bands.  Unfortunately however, I had no bands. 

Week 2:         My PCR worked! I think I will brag about this all day. This is quite the achievement! The gel left these perfect strands. It was probably the most beautiful thing I’ve ever seen. It’s in the top three at least. However, I don’t really have photographic evidence for this. This is the same PCR that I genomophied earlier, but it worked!

Week 3:         I heard a rumor that shiny vampire Edward Cullen would be filming on campus this summer. Now, while I am not at all a Twihard, would it not have been cool to have seen Cedric Diggory? And to tell a bunch of crazed fan girls about their beloved RPatz?  However, despite keeping a close eye out, he seems AWOL. I guess I’m doomed for disappointment.

Likewise, there are way too many sources of error when it comes to microscopic things. I’m not sure I have the right temperament for it. I’m fidgety and I get nervous.

I’ve come to gather that pipetting is an art form.  It’s important to be able to pipette the right amount of anything, but when the largest amount of fluid I’ve worked with was 250 microliters, every drop seems to matter. 

I think I am figuring it out though. Maybe I don’t have to succumb to the premed temptation just yet.

I guess the samples I used had to come from somewhere. Today, I got some hands-on field experience, planting seeds of a rare Native American corn species whose roots will be studied. I did in fact plant flowers with my mom once in first grade, so I have experience. 

Week 4:       Did you know there’s an indoor passage from Bradfield to the Biotech building? I didn’t. It’s pretty neat.

DNA and enzymes used in all these reactions are sensitive and can breakdown under strained conditions. However, pure DNA is able to last for years. PCR samples that work properly can be purified—a pretty nifty process. A process with generous use of the cylinder allows for DNA to elute through a filter separating it from other PCR materials. These pure DNA samples can then get sequenced which determines the order of the nucleotide bases. That’s pretty neat. 

I think this is a good sign. While I’m still indecisive about what I plan to do, as long as I find the longevity of pure DNA samples neat, I might be okay.