I Don’t Give a Rat’s…. (About Anything but Phage Lab)

by Norah Oles

…Not even my birthday. I could care less about the whole turning-another-year-older thing, about the presents, or about the birthday wishes. What I would really like are good lab results.

All I want for my birthday is a nice gel electrophoresis. To anyone who doesn’t frequent a lab, this may sound like some kind of frilly spa treatment, but anyone who knows anything about biology knows that I just want some clear banding patterns to analyze my phage (Sherlock’s) DNA.

On Monday, I set up reactions with several different restriction enzymes (BamHI, ClaI, EcoRI, HaeIII, and HindIII), which I let incubate at 37 degrees C for a few hours. Since then, they’ve been stored at 4 degrees C, waiting for me to come back to the lab.

Hopefully, everything will go well, and my analysis of the DNA will indicate that it is a good candidate for the genomics portion of the program. I’m sure Sherlock will pass the test (or else…).

So, how did I get here? It’s not like I just scooped up some soil (infused with a nice dose of rat poop, might I add), and filtered DNA out of it. It has been a long, long, long process, rife with contamination, lack of incubation, and more curse words upon seeing bad results than I can count.

Sherlock’s story: (the semi-abbreviated version) My soil sample came from a rat’s nest by the side of the MSE library. Why a rat’s nest? A few days before I got my sample, I witnessed a giant rat trundling across the cobblestones, headed for a small patch of bushes. I, being deprived of animals here at college (I have a veritable zoo back home), followed the little bugger to the bushes. Under the bush, I saw a writhing mass of rodent bodies, and knew that this was the perfect place from which to gather a soil sample. Rat crap had to equal fertile, bacteria-ridden soil—the perfect environment for phages.

My instincts proved correct, and after an enrichment, three streaks, and a few spot tests, I had a confirmed phage.

Next came time to do the titer-assay. After several rounds filled with pain and agony (first, the plates did not get incubated, next, the top agar didn’t solidify), I finally got a usable titer-assay sequence of plates. I calculated my titer, and was ready to move onto the ten-plate infection. Luckily, I had a plate that was a nearly perfect web from my titer-assay dilutions, so I just upped the concentration of my dilutions from 10-4 to 10-3.8. These yielded ten perfect web plates, which I flooded and harvested to get my high-titer lysate, the titer of which was of the magnitude of 1011 — meaning I had A LOT of phage.

Finally, it was time to see them.

I could hardly wait to cross the courtyard from Macaulay to Dunning and take electron micrographs of my phages. Three of us had phage samples ready that day, and we were all balls of barely contained excitement.

Dr. Schildbach led us to a lab, where we met Michael, owner of two adorable dogs and the keeper of the electron microscope. After he prepared our samples, we all took a break to meet his dogs—something that was entirely necessary at that point in the day.

My sample was last to go into the electron microscope, and I was about to explode with anticipation. Finally, my sample went in. Michael zoomed in, focused.

My titer didn’t lie.

A veritable field of phages spread before my eyes, all their tails overlapping and intertwining, capsids crowded together. I broke into a huge grin, and, if memory serves, let out a very un-scientific squeal about how “cute” they looked. I finally had a visual of my phages. Sure, I’d seen the plaques they made time and time again, but that could only tell me so much. For the rest of the day, I was like annoying new parent, showing off my pictures to everyone and anyone who cared or didn’t care to see them.

Previously, I had planned on naming my phage Scabbers, since it originated in a rat’s nest. Once I saw all of them, though, I couldn’t bring myself to name it after one of the most cowardly and hated characters in the Harry Potter series. It just wouldn’t be fair. Instead, I settled on Sherlock (as in Holmes, of course), which I found to be much more respectable.

This brings us more or less up to the present (there was the leaking nuclease mix fiasco, but that’s another story). With only a few weeks left in the semester, I can’t believe phage lab is nearly over. I can’t believe I have a phage, let alone have a chance at sending it to the HHMI for genome sequencing. And, most of all, I can’t believe what a great experience this has been.


About noraholeole

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