April 4th, 2007


Thesis update

Bravery pays off, it seems.

So, based on my talks with Committee Member, things weren't going well. He wanted me to do analyses that my data didn't allow, and then do analyses with data from other studies that didn't even relate to my project. Specifically, to put my genus in the greater phylogenetic context, which I already knew had been well established.

After struggling with it for a while, I did what I should have done right off the bat...a literature review. Right away, I came up with two recent papers that did a phylogenetic analysis of the entire Alnus genus, and another for the entire Betulaceae family. So, here was proof. What he wanted me to do had already been done, far better than I could possibly do it.

And then I had an inspiration. I shared it with Jack the next day. Both of those studies were based on sequence data from the ITS 1 and ITS 2 regions, which are nuclear ribosomal. The sequences I'd been studying for my thesis are from chloroplast loci. How about I extract DNA from every alder species in this region (there's four, counting mine), sequence it at my chloroplast locus, analyze it, and see if I get the same trees as the nuclear data suggest.

And he paused, thought for a moment, and said okay.

So that's what I'm doing now...finishing the sequencing prep on Alnus incana, Alnus sinuata, and Alnus rhombifolia, and then I'll crunch the sequences with Alnus rubra, Alnus japonica, and Betula occidentalis and see how it measures up to nuclear findings. It'll be an interesting aside for my thesis, a good topic for my class project, and possibly an answer to whether nuclear and mitochondrial DNA tell the same story.

  • Current Mood
    crazy triumphant

(no subject)

I am feeling...

...efficient. I got a bunch of samples extracted, amplified, troubleshot, and sequenced (mostly) in less than a week.

...impatient. I want to be done.

...ouchy. We had a substitute teacher in Pilates yesterday, who somehow managed to lead us through a routine of exercises that not only didn't actually exercise or work out our muscles in a satisfying way, but actually strained them in a painfully bad way. We did one thing that seriously screwed up my right pectoralis. I refused to do the other side, and good thing, because that muscle's been killing me all day. Ow. Also, I have a canker sore.

...smug. My dentist appointment this morning was perfect.

...disappointed. I've been working out for 10 weeks and I haven't lost as much mass as I hoped. Still sticking with it.

...nightmarish. I dreamed about ethnic cleansing last night.

...loved. Things with Tyler are going great. :)

...excited. I have a lot to look forward to, what with apartment hunting, picking up Jason in San Diego with my Dad, the Ren Faire, the end of school (maybe forever), our wedding, and graduation. Good stuff a'comin.