So, I’m going to be 100% completely honest with you right here, right now, but I’m going to be writing this blog post instead of studying for my chemistry exam because who really cares about crystal field splitting anyways? Or who really wants to think that they’re sitting in Brody Reading Room at 12:21am on a Tuesday night with a few more hours to go?—yeah, not me.
Because that is actually the case, Hunter keeping me company and you know how they say misery loves company, I’m going to just talk about my experiment. But I would like to preface that if you read Marissa’s blog post earlier, all those things are true about our annotation process; $2800 errors, and corrupted files, and forgetting to hit post, but I guess the process wasn’t so bad in and of itself. I think of course there must’ve been better ways of going about annotating this genome, since we were plugging in information we obtained from other sources, but the issue is more of the comparison with other annotations of the same genome, which we quickly saw when we were all one or two genes off since something got added or deleted midway, somewhere? And I think I got a few massages out of working with Hunter and Marissa so it was well worth it.
But, as much as we all loved so much annotation, I think I can speak for the most of us at least, if not only myself—I missed the lab; not the smell of the incubator, though — that I forgot about. More or less, my wet lab experiment consists of using Taylor’s mycobacteriophage Phatniss and testing its fecundity in environments of different pH. There was, and here’s some more honesty, a lot of hiccups—luckily Taylor was running a similar experiment so we teamed up, but let me just say one thing: Most wasteful experiment ever. I think we went through at least 30+ 50ml conical tubes, countless pipettes and pipette tips, and almost 100 microcentrifuge tubes. I think that’s a little ironic since today’s Earth Day, but it is what it is, for science right?
I guess we just did not understand the scope of our experiment as we proposed it, and the most difficult part was determining a way to control the most variables in changing the pH. We had thought of everything from resuspending a pellet of Phatniss into a pH-controlled solution to simply adding enough acid or base to each dilution to change the pH, which we would just measure and watch using a pH meter. We more or less settled upon diluting the PB to create a weaker buffer as to be able to change the pH more easily, which was a struggle in and of itself to create all the solutions ranging from 1-14pH, which was finished today! Hurrah! I think we were about to actually lose our minds because dang that pH meter is so slow or because we’re mathematically challenged and literally kept adding in the same amounts of acid or base.
Hopefully everything will be done in one or two more labs, the plan is for each of us to do serial dilutions using each of the different pH diluted PB. And from that, plate the max web plate of 50ul of 10^-6 and compare the results and photograph the range, which we are expecting to drop off under a pH of 4 and above 9—though maybe we’ll be surprised, we’ll just have to see.