Summer Plans

Posted By on May 24, 2007

Or
“Wherein I Volunteer My Time Towards Wasting Other’s”

.: This past semester I took a course called Molecular Genetics along with its associated lab. The class was one of my favorites and the professor, Dr. Chris Kearney, one of the best I’ve ever had. I performed reasonably well in the lab and secured a B+ for my efforts (off by one question on the final — drats!). I thought I came away with a pretty darn good understanding of the techniques employed in the lab, but, as will be made excruciatingly clear during the remainder of this post, I was terribly, woefully, and not all together unhilariously, mistaken.

.: My sister, an interim student at University of Texas, San Antonio, has been working in a bio-lab for the past few months. She told the lab coordinator (or supervisor, or boss — I’ll have time to nail the precise terminology later) that I was interested in doing lab work, and through her I was allowed to volunteer my precious summer doing what are essentially the same procedures I ostensibly learned this past semester.

.: Right now, as near as I can tell, the lab’s current big project is investigating certain interactions between JIP [{Jun N-terminal Kinase (JNK)} Interacting Proteins] variants, ApoE (apolipoprotein E) variants, parkin, and ubiquitin — all with the notion that somehow a part of this interaction is involved in Alzheimer’s Disease. Curiously, certain mutations of parkin have already been linked with a type of Parkinson’s Disease, but that’s another story (I think… I can barely make out what JIP stands for; how the hell am I supposed to figure this out?).

.: My immediate task is to figure out what the hell is going on. That is, what we’re doing and why. Why do I need to know how ApoE Receptors react with differential exon splicing? How is that related to what we’re doing in the lab? What’s the significance of a recent finding that says exon 19 of ApoE Receptor 2 paradoxically prevents neuronal loss with aging while simultaneously promoting neuronal loss from trauma? Did I even get that question right from my reading of the paper, or is it the other way around? Those are the kind of questions I’ll be busying myself with.

Restriction Digest.: My official task, as far as I can make out, is to simply learn the basic techniques that the B+ on my transcript says I’ve already acquired. Eventually, I’m told, I’ll be given a small project to work on all summer, and this will somehow work itself into the big picture of what people are already doing in the lab. As of right now I’m doing three things: mini-preps, restriction digests, and restriction digests. Restriction digests help verify whether or not a certain gene is present on a piece of DNA by showing how long those pieces are. Restriction enzymes cut at specific places; it’s not a random affair. A strand of DNA with an inserted gene would be longer than the strand alone. If you know what to expect in terms of band length for a naked strand of DNA compared to a strand with an insertion, then a restriction digest can serve as a simple tool for verification. Or, if you’re more like me, a restriction digest can serve as a simple tool for filling a notebook with pages of failed experiments.

.: Mini-preps, on the other hand, are done before the restriction digests, so if you have a problem with the DNA in the digest, you run another one before you consider, Hmm, maybe it was something wrong with the mini-prep? This simple curiosity seems to explain the ratio of mini-preps to restriction digests in my notebook.

.: I know my sister showed this blog to the lab coordinator before I showed up, so there’s a nonzero possibility that she’s reading this (Hi there!). So far my experience in the lab has been positive, despite a few small failings and misunderstandings on my part. Hopefully those will disappear in due time and my presence will not ultimately waste everybody’s time. I guess I’ll find out soon enough.

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One Response to “Summer Plans”

  1. Gigi says:

    Ahhh, so that’s what you’ve been up to. How much of your summer is this going to take up?

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