Tuesday, February 22, 2005

So I've just finished a take home quiz...

and boy, I'm glad to be in graduate school. This isn't a mockery of some kind - I really am *ecstatic* to be at a level where every question is in an essay form, the only things they make you memorize can be drawn out on a sheet of paper as a graphic, and most of the tests/quizzes are take-home. No more are the annoying multiple-choice questions that could go either way and I think are actually conceived with annoying the smarter-than-average undergraduates in mind just because the professor gets off on putting them 'back in their place'...

Here's an excerpt of the quiz I finished - one of the questions:

3. How would you localize a promoter using a lacZ fusion? How would you use such a fusion to clone a repressor gene?

As lacZ is a gene which codes for β-galactosidase, by measuring the amount of β-galactosidase present in a system one can deduce that the lacZ gene has been transcribed and translated. To use the lacZ gene to localize a promoter, you could do one of two main things. Firstly, you could take the part of the DNA you think may be a promoter, insert (fuse) the lacZ gene directly downstream, then measure the amount of β-galactosidase produced in the bacteria. If that amount has increased, you have localized a promoter. It is important to note that the lacZ gene does not initiate transcription itself, it requires a promoter for the RNA polymerase to bind to begin transcribing, therefore the presence of β-galactosidase implies the presence of a promoter directly upstream. Secondly, you could fuse lacZ downstream of the proposed promoter, make sure you have increased amounts of β-galactosidase, and then induce mutations/knockouts in the sequence you think is a promoter. If the amount of β-galactosidase is down-regulated, then the sequence is a promoter in that region. If you wanted to use a lacZ fusion to clone or identify a repressor gene, you would fuse the lacZ to directly downstream of the promoter, introduce one possible repressor at a time, then measure the amount of β-galactosidase present. If the amount is unchanged from the control condition (no repressor) then the substance is not a repressor for that promoter. If β-galactosidase is down-regulated, however, then you have most likely isolated the repressor sequence for that promoter. Additionally, if you induce a mutation in or knock out the gene for the previously identified repressor and the amount of β-galactosidase is up-regulated again, you have further evidence that you have isolated a repressor for the promoter in question.

*whew* I really did like answering this question, though. I get to present the original paper that discovered this mechanism back in the 1960's on friday, so I'd better know what I'm talking about... that and I was smart and copied and pasted B-galactosidase every time so that I didn't have to go up to symbol and pick it in Word each time. I know, I'm sooo Hermione. But I like it and I think it suits me well... :)

Like Ed says, I've really found my thing, and bless me for being as interested in it as I am. :)

My thesis quest has also started making more sense. Just earlier today I was wondering how I'd ever figure out how to do an experiment based on the 50-some-odd studies I'd found and had to go through. Once I eliminated all but about 8 as being impertinent in one way or another, it got kind of easy. I get to go back to the biomed library at vanderbilt thursday and hang out in the stacks for a while again... I think I might just study there from now on, when I can - it reminds me of how much I'd like to go to vanderbilt for a Ph.D. and therefore I study harder and try to find everything I can to make my thesis publishable. That's what will get me into a Ph.D. program, not my endearing personality and awesome teaching ideas (unfortunately)...

Erin, you kept bugging me to post again, so here it is... *post*... I think that you & Ed are the only two people who read this (and maybe Melissa Sandefur+child on occasion) - so if there's anyone out there who wants to admit to reading my weirdness-on-parade, just leave me a comment. If not, no harm done. I'm not here for anyone's entertainment or even feedback, really. Those who know me best know that I'm *way* too amused with myself - which is exactly how I feel about this blog... :)

Time to go try and read Scientific American before I fall asleep... we'll see how that goes.

Oh, and also, the seminar last friday wasn't as easy-to-describe as the previous two. A professor from Meharry came over and was talking about the relationship between heart disease and insulin resistance (diabetes) on the endocrine level, with all the names of the hormones invloved & stuff. The most interesting part was when she talked about the body's way of regulating blood pressure - the pathway by which it does that is complicated but intriguing. For an example of how the hour went, the title of her presentation is, 'Angiotensin II inhibits insulin signaling in vascular smooth muscle cells' - which is a fancy way of saying that high blood pressure contributes to diabetes. :)

We'll see what transpires this friday... Until then... *sigh*


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