science diet!

so i had a pretty science-riffic day. this morning was lab meeting for the larger of the 2 labs i belong to, which was a presentation from (i think) the most senior grad student in the lab, who's been doing a ton of work on membrane biophysics in the nucleus magnacellularis (part of the cochlear nucleus) in chick. so evidently, neurons in this part of the brainstem fire with a stereotypical pattern that is different from many other types of neurons, and he's trying to figure out why. the short answer is that it has different potassium channels expressed, but the long answer sure was a lot more interesting than i'm going to be able to explain here. the data were pretty much a bunch of voltage traces, and associated graphs. interesting to me, not so interesting to other people... but very educational, and he presented it very clearly and succinctly.

after lab meeting, i had a meeting with the boss of that lab (the more senior of my two PIs) to "discuss my future." which was pretty cool... what i got from him was: 1 - yes, we'll pay you to stick around for a year before grad school, you're too valuable for us to let you go; 2 - a bunch of advice regarding which graduate schools to apply to and where he can get me in. so now i'm supposed to spend a day or so researching not just programs but also particular labs i'd be interested in doing my thesis work, which at this point i think will have something to do with determining the genetic mechanisms behind neuronal differentiation, development, circuit-formation, something like that. so his main point was that there are a lot of good neuroscience programs out there, but not a whole lot of people doing the kind of work that i'm interested in, so i should start narrowing it down. also, he said, fish for lab names not from nature, science, nature neuroscience, but go through issues of neuron, j neurosci, things like that, and try to find some names. so i'm supposed to meet with him again in a month to further discuss. hooray! someone on my side. oh, he also said he could get me into the sanger program "no sweat." so that's certainly something to think about! (sigh. just remembered that i have to take the GREs.)

so then after that, i went to a lecture by Gail Mandel, who did her doctoral and postdoc work on sodium channel expression, and in the process discovered a sort of "master switch" for neural cell fate. It's a transcription factor called REST - Repressor Element-binding Silencing Transcription Factor - and it's basically expressed everywhere but the nervous system. She had a ton of data and a really interesting model of how this particular switch is turned on and off and how that precisely determines whether a cell becomes neural or non-neural. Evidently there are binding sites for this protein beside nearly every gene involved in neural development - ion channels, synaptic proteins, and even other transcription factors known to direct neural cell fate, like NeuroD and neurogenin 1 (which a grad student in my (other, smaller) lab studies!)

After that seminar, I did some other stuff like work on homework, go to class, set up fish for next week, etc. And then at 5:30, when I was debating going home, I decided to go to the Neurology Grand Rounds (a seminar series I've never been to before) - Jeff Barker gave a talk summarizing 15+ years of work on neural stem cells. His group has pretty much amassed an ass-ton of gene expression data in different cell types, from flow cytometry/cell sorting to in situs with some really pretty fluorescent imaging data. I guess they have a 5-color confocal microscope up at the NIH (when you're government you get all the cool toys) - he had images showing expression of 5 different genes, all labeled with different colors, in different parts of the developing rat cortex. it was pretty amazing data, and i learned that what most people call "neural stem cells" are more accurately lineage-restricted progenitor cells which may or may not be multipotent. repeat after me: just because they're proliferating doesn't make them stem cells. There was also a lot of stuff about FGFs and FGF receptors... but I don't really have time to go into it all right now. (FGF stands for fibroblast growth factor, and it's pretty much one of many, many secreted peptides and molecules that guide development.)

so yeah, i'm completely geeked out right now. i felt super-special because Dr. Barker mentioned Elizabeth Grove in his talk, and I just heard her speak last month at the NW developmental biology meeting! they both work on FGFs. i had to flip through my talk notebook when he mentioned her name and try to remember her presentation... the key thing I remember is that she had showed that you can shift different brain structures forwards or backwards by increasing or decreasing FGF activity.

so anyway, now i have to write a program to mimic the way a BLAST search works, and then one to do a protein sequence alignment. why did i register for this genome informatics class again?

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