Six Months Later...

And so it continues...
It's been quite a while since I last had a blog post, despite the occasional words of encouragement from Claire. Things in graduate school are pretty much always busy. It's hard to justify wasting time writing a blog. It's far easier to waste time on Reddit or elsewhere in the cesspool of the internet where no remnant of the lost moment will remain.
Alas, things are pretty good here. I have a deeper understanding of my expectations now and have learned to grow as a scientist and be sane simultaneously. Our year lost a couple more students, I can't help but wonder if they're better off. It seems like every week I read another article about how the university system is the next unsustaniable bubble that's going to burst, or how the Ph.D. is useless these days. There's lots of Ph.D.s and simply not enough jobs I fear. Academics don't retire and open up the gates for new academics. I guess that's an artifact of not actually enjoying your life until you're 40 when things settle down and you're actually running a lab. I've said time and again that I wouldn't be doing this if I felt like there was something else better to do. I guess I have this pipe dream of being a bona fide scientist with his own lab doing what he wants and letting his interests guide his work. It seems like quite the journey from here.

So what have I been doing in the last six months? The short story is, well, a lot. I rotated through Josep Comeron's lab early this year and sequenced 24 complete genomes to address the question of how recombination varies within a species at different conditions. It was a really great rotation project, and added to the labs over 4000 genomes they've compiled in the last year. It was a lot of work but I really enjoyed the people, pace, questions, and approach.
The rotation ended and then I got to go to Sarit Smolikove's lab. Sarit is perhaps the best adviser that one could wish for. She's dedicated, interested, and very involved. I have to reject the null hypothesis that Ph.D.s don't actually do benchwork when I'm around her (P<.01). She teaches and spends at least 10 hours a day actively doing research, and that gives me a lot of hope for my future career. My project in her lab was to determine what proteins interacted with one that they had implicated in synaptonemal complex dissassembly (the protein scaffolding that holds together homologous chromosomes during meiosis)--the first protein discovered to be involved in this process. I produced a lot of hits, and knocked a few of them out in vivo to see how they affected meiosis. A really cool project. I feel like I'd be in her lab right now if she had a grant. It's sad, but she already has two graduate students and no grants to keep them going. I think she'll eventually pick up a solid grant, but I just can't risk having to teach every semester and watch my productivity take a nose dive.
So, that left me to join Josep's lab. I started last week and will be there for the next four to five years working on recombination variation. Our first task is to get a review paper out the door. As such, I've been reading articles pretty much every day. Basically this way I can get my first paper in the lab, the first quarter of my comprehensive exam written, part of a grant application, and a piece of my thesis written within the first semester of my work in the lab. I think Josep is really thinking ahead on this one, which is a very good thing if I'm to get out of here in a reasonable amount of time.
I suppose the next obstacle in my way is our Qualifying Exam. We've been given the topics for the exam and are expected to know them well enough to answer specific questions within the topics on July 10th. I've started the studying process and should be ready by that time. Some topics are specific and doable, like "The biology of small interfering RNAs", while others are extremely broad, "The origins and maintenance of diversity in natural populations." Oh well, just another hoop to jump through.

I suppose that's all I've got. Haley will be passing through Iowa City in early June and staying the night at my place with Ari--I still haven't told her that I don't actually have a couch for her to sleep on, but I'll drag out the small mattress for her. It should be a fun time.

Cheers,
Andrew

Microscopy

So I just wanted to do a quick update with an image that Dr. Dailey and I captured last week.
It's a shot of cilliated epithelium from a live (or rather, dying) snail foot. I've labeled all of the interesting tidbits.

This is from about 100x using DIC microscopy. I'll be utilizing one of our confocal microscopes in the coming week after I get trained on Monday. With any luck, I can get to play around on the Multiphoton Confocal to peer deep into tissue.

Awesome flourescently labeled nuclei picture to come!

Graduate School

Wow... It's been a while since I've posted. I can assure you there's been good reason for that.
Well, here I am in the great state of Iowa. I'll be here for the next 5 or so years so I suppose I'll have to rename the blog to something else with a fun alliterative phrase. (Though I can't really think of anything that rhymes well with Iowa.) I suppose I could just leave it as a indicator of my past and progress towards my goals. I'm not sure what I'll end up doing with the title. Suggestions?

Let me begin by saying that I am fairly comfortable here. If I had my cat the place would be nearly perfect. The city, aside from being quite rowdy on game days, is a fun and interesting place. I never knew how much I would enjoy walking everywhere I needed to go. I haven't driven in my car for more than 15 miles or so since I got here in late July. The people are fairly nice and there's even a vast assortment of delicious beers. I enjoy being able to drop by the local grocery co-op to pick up fresh bread and walk back to my place (utilizing those fabric grocery bags that I would always forget back in Alabama). Downtown always has something going on, too.

Last weekend a few of the second years and I went to the Amana colonies for a beer festival. I got to eat hearty, authentic German food and wash it down with genuinely delicious, local beer. I think there's another beer festival downtown sometime soon as the pumpkin beers and winter spiced ales start to roll in. Gives me something to look forward to.

Graduate school has been great so far. I've started my first rotation through the Neiman lab working on a cell size project. Essentially I'm trying to prove that the flow cytometer is crazy (which I have), and look at the relationship between cell size and genome size. Since many of her snail populations are known polyploids (For my liberal arts readers: that is, has multiple chromosome copies which increases the DNA content per cell by a factor of 2,3, or even 4), we're trying to determine if the polyploid populations hava larger cells or not. This, as you can imagine, could have profound effects on the biology of the organism. Typically larger cells means less of them, which would have interesting consequences throughout the organism.
So far it's been fun. I've essentially developed the methods and started going. It's real research!

Anyhow,...I just wanted to tell everyone that everything is going great and give an update of what's going on.
Cheers!