Keys to the Lab!

So I'm finished with trees for the time being. Aside from my PI sending me one every few days as he finishes up his grant stuff and pushes towards publishing, I've been working on a new project.

Unfortunately, it's going to drive me mad.

All those genes I had to annotate on trees? Well, now I'm doing intron analysis. If I hadn't been required to take Intro Genetics, I would have completely forgotten what those were. You see, prokaryotes DON'T have introns, and that's what I've been studying for nearly two years now. In prokaryotes, you find an open reading frame (ORF) and you keep going until you find a stop codon. Nice and neat, no splicing, no guesswork.

Introns are a pain. They can wedge themselves between two amino acids or even within one and you'll be none the wiser until you start translating and realizing that your code is a lot larger than the protein. Hrm. Also, it's impossible to tell an intron from an exon by simply looking at the chromosome or the mRNA.

Cue an awesome little program called DS Gene. I love it already. It gives me potential ORFs; all I have to do is translate them and see if they match the recorded protein structure wherever the genome for these organisms are being held. Most of them are on NCBI, which is just dandy, but there are a few lurking elsewhere in cyberspace, though I think I've tracked most of them down by now.

One little hitch/piece of awesomeness (depending on how you look at it): DS Gene only runs on Windows. I have a Mac, a Mac that stubbornly resists Bootcamp for some reason. So last week I received keys to the lab so I can get in on days that the building is closed (if I need to do so) and run my analysis on the lab computer. Woo!

Continuing Education

So lately I've been considering, a lot, what I'm going to do after graduation. (How I realized I could have graduated this semester if I had been so inclined is another story)

I know I want to go to graduate school, that much is certain. However, I don't know if I want to do a masters or a PhD program. I know I can put in two more years, but I'm balking at the thought of four or more. Especially when my future plans aren't set in academia.

I want to work for the government, ideally as a weapons analyst. In the defense capacity, not offensively. I am so ethically opposed to the idea of engineering organisms for strategic purposes (translation: biological weapons) that it is slightly painful. But at the same time, I know there are people and groups out there researching and doing just that. And we need to be prepared.

This desire probably stems from my literary love for spy and crime novels, as well as the books by Richard Preston. In fact, his books are primarily what I want to do with my life--be on the defensive for whatever is out there waiting to infect and attack the human race.

In principle, these things aren't difficult, just time-consuming. But there are people who have nothing but time to tinker in a lab with the same skills I'm learning in classes (transformation, mutagenesis, etc), with potentially crippling results.

It doesn't even have to be something engineered. During irradication, it was determined that smallpox only needs 20,000 people within a two-week radius of each other to survive. Heck, there's more than that in a 15 minute radius on my college campus on any given weekday. Other diseases, like polio or measles, can have vast damaging effects, especially in an age where more and more people are refusing to vaccinate their kids. One day at the swimming pool and you can have at outbreak. In the 1980s, the Rajneeshees reminded us of our weakness to plain old Salmonella typhimurium by spreading it on the salad bar.

I want to do work with things like this, in a microbiologist's capacity. However, I'm not sure if I really have it in me to get a PhD, or if I even need a PhD to do these things. I don't want to run the show, I just want to get in the game.

On Sleep Deprivation

Strange things happen when I don't sleep. In my mind, at least.

I woke up this morning at about 500 EDT. I gave up on sleep around 730. In between, I fretted about everything from my weight to my being silly about my weight to what is going to happen when the sun dies and whether or not humanity will even make it to that point and how it's not really going to matter to me because I'll be long dead and then my brain tried to wrap itself around the possibility of my ending and what if I just rolled over and fell asleep and never woke up again...and then I'm afraid to fall asleep. Because we all count on waking up the next morning and living on.

Yeah. This is what happens when I can't sleep. It's a vicious cycle.

In other news, I am DONE annotating trees, with two days to spare before my PI's presentation. Provided he doesn't send me any new ones between now and then. Who knows what will happen after that.

Just a Quickie

Because I've got a report to edit and studying for my Microbial Physiology test to do.

Anywhoo, I've been busy, editing trees and all that. I'm finding that this one gene, A622 (with a supposedly unknown purpose in tobacco plants) has a lot of roots in...wait for it...diatoms and algae. Hrm...

Granted, I haven't spent that much time doing undergrad research in the past 2 weeks or so due to midterms and writing reports and pretending I want to have a life.

The snow is all right, I guess. We've got a lot, and of course VT didn't close. I'm kind of over it at this point, mostly because I know it's supposed to be in the 50s and 60s Thursday and Friday and that means it's going to melt and be a huge disgusting mess here. I'm just ready for Spring Break.

We're doing stuff with bioluminescence in the class lab. Hooray mutating E.coli to glow in the dark. I just wish I didn't have to write a report on how I did it. I hate writing lab reports. Especially when the prof rips them to bits every time.

I didn't even know they made them that large

...That's what she said. OK, seriously.

So I have a neuronoma in my foot. Which, according to the Mayo Clinic's website, is a swelling of a nerve. Due to injury, wearing tight shoes, or repetitive sports that put strain on the balls of the feet (i.e. running or tennis). In my case, injury. Maybe running from class to lab to class to lab to home to lab to Boyfriend's to class to lab to...you get the idea.

I thought it was a stress fracture or a pretty serious contusion, but nope. Apparently it's a neuronoma. Guess what the best treatment for those are? A shot.

A huge-ass cortisone-anesthetic shot. Oh and the standard RICE-ing. But the shot. I kid you not, the needle was as long as my pinky. And it wasn't one of those quick in-and-out shots like HPV or Tetanus--no, the doctor kept it in and had to inject slowly. And kept pushing the needle deeper. I swear, at one point, I could feel the it poking at the bottom of my foot.

On the bright side, I felt grrrrrr-EAT for the next 3 or so hours. Driving home was hilarious, too, as my foot fell asleep (of course it was my driving foot).

So that's my story for today.

Holy Nitrogen Fixation, Batman! Real Results!

So I was puttering around with my research today (Linux is all fixed, btw--Dr.J never changed the privacy settings in my files, so while I could see them, I couldn't access them), and found something exciting. AKA really nerdy and boring if you're not into microbio.

One of the proteins for which I was annotating a phylogeny, I noticed a huge group of the phyla Alphaproteobacteria were all of the same two genera: Rhodobacter and Rhodopseudomonas.While their proteins weren't directly related to the one I was working on--as noted by how the structure of my tree was shaping up to be--it was interesting that they were all of these two genera. You see, these two, as well as other Alphaproteobacteria whose genus name starts with Rhodo, are bacteria that reduce Hydrogen Sulfide to elemental Sulfur in metabolism. So I started going through my notes from when I took Microbial Diversity (so glad I ended up saving those) and found out some more information, though not enough. I'm going to have to search through the Journal of Bacteriology's archives or something.

I'm excited to present these results on Friday. I don't know what it means yet, but it's exciting.

Linux-ing, Part 2

I hate Linux and it hates me. Seriously.

Either that or Dr. J's main computer is out to get me. For real. It isn't letting me access any files, now including the ones I made myself. I was able to access one file for about an hour or so last Tuesday (basically, long enough for me to finish working with the data in that file) and then it decided I couldn't use it anymore.

And I'm the only undergrad having this problem. I think Dr. J might think I'm a moron.

In other news, I've been looking at Microbiology Master's programs (I don't think I've got it in me to get a Ph.D.), mostly in the Richmond to DC corridor. So that would be VCU, George Mason, and Georgetown. And I found two MS programs in Biohazard Defense that look pretty cool in addition to normal Master's programs.

Hopefully I can rock the GRE in May.