Friday, November 16, 2007

Is this Biochemistry?

I have reached the unfortunate conclusion that I am a molecular biologist pretending to be a biochemist. Most of the time I do not even pretend. After all, I chose to be a molecular biologist and not a biochemist for a reason: Namely that I am more interested in genetics than in protein science, and not particularly interesting in reaction kinetics (whether that be for a folding reaction, a binding reaction, or an enzymatic reaction). Also I, in general, appreciate working with more natural systems rather than more artificial ones (namely, if studying biological systems, we should perhaps use biological systems, like cells and animals, rather than non-biological systems, like test-tubes and monolayers). (I also note that there is a time and a place where the non-biological systems are incredibly useful and that my own systems are, in many ways, very artificial themselves). In any case, none of this would be an issue if I didn't want to write an honors thesis. Which I do, and since I am majoring in biochemistry (primarily), I feel like that should be in biochemistry. So my question: does this sound like biochemistry?

Gene regulation in eukaryotes is an incredibly complex process which is not completely understood. Until recently, the model for transcriptional control has been based on a view of DNA as linear, neutral, and controlled by the function of transcriptional activators and repressors – proteins designed to interact both with DNA and with the transcription complex. However, DNA is, in reality, in a dynamic nuclear environment not solely determined by the various transcription factors present. Long-distance DNA-DNA interactions such as chromosomal kissing disprove the linearity of DNA, and the effect of nuclear localization on gene expression disproves the transcription-neutrality of its position in the nucleus. My project attempts to determine the significance of this localization effect in gene expression. To do this, I have created a system called TCIS (Tagged Chromosomal Insertion Site) with which I can repeatedly insert pieces of DNA into the same, easily visible, genomic location. This site is usually found in the center of the nucleus but can be tethered to the edge of the nucleus as well. I will insert various promoter regions into this TCIS, tether them to the edge of the nucleus, and measure the difference in expression levels between tethered and untethered samples.

I know it's rough, I'll work on that once I get something that actually might convince someone I'm almost a biochemist (if they're being really generous).


Duff said...

I am not really competent to say whether it is biochemistry or not, but insofar as you are analyzing a system with signal/response modality, then it is arguable biophysics/electrical engineering related. Whatever it is, mappping out the nonlinearity of signal transduction in DNA sounds very interesting.

John said...

Yes; I would say this could qualify as biochemistry. (Though it does border on romance novel in the "chromosomal kissing" part.) As blunt as it may be, I've always found a sure-fire way to convince somebody that something is in a field is to include a field in the description. Instead of "in a complex nuclear environment," what about "in the complex biochemical environment of the nucleus" ? (I'm sure there's a much more smooth way to do that, but unfortunately the screen where I get to type comments is not the same as the one where I get to read your project description.