Tag: grad school

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Of exams and triumph…

So, I took my first exam today…and it wasn’t terribly difficult, but the section I was most worried about was Dr. Shilati’s… It was a 10 point question (out of 80…so relatively hefty…) asking you to describe the process whereby you would assay a protein for a given function, how you would purify it, and how you would observe if it works in vivo (i.e. in a living organism). So I wrote out my answer (took 1.5 pages…) and wasn’t terribly confident, mainly on the last part of that question… After talking to other students in the class, all of us were worried about that whole question…which means that, theoretically, the curve will work out fine with all of us in the same spot… The rest of the test was generally alright…I dropped the ball on one 4 pt question, but was confident on the remainder of the exam…

…well…then I was walking back to the lab from getting a soda and Dr. Shilati stops me in the hall…and says “good job on my section of the test”…

…score one for Dr. Andy Linsenbardt, Ph.D… 😀

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How chemists do it…

Per my grand-little’s away message (Sarah Hobbs…in AXE @ Truman…):

How chemists do it…

Chemists do it reactively.

Chemists do it in test tubes.

Chemists do it in equilibrium.

Chemists do it in the fume hood.

Chemsits do it in an excited state.

Chemists do in periodically on the table.

Chemists do in organically and inorganically.

Electrochemists do it with greater potential.

Polymer chemists do it in chains.

Pharmaceutical chemists do it with drugs.

Analytical chemists to it with precision and accuracy.

…so true on so many levels…

…stoopid grad skool and studying for tests…grrrrrrrrrrrr…

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…mmmm…fly paper…

So, Nathan said he wanted to know what I’m up to in my research rotation for the next few weeks… I’m working for Dr. Joel Eissenberg (who reminds me quite a bit of Dr. Buckner at Truman…) in the Department of Biochemistry. He works primarily with fruit flies, but most specifically, a protein known as dELL. This protein is known as an “RNA elongation factor.” For those who know anything about genetics, DNA is coded into mRNA by RNA Polymerase II; Pol II will sometimes pause along the transcription process, thereby causing the DNA to be transcribed more slowly. dELL prevents this “transient pausing,” allowing transcription to be carried out more efficiently. dELL has also been linked to leukemia (which is how it was discovered in the first place).

Anyway, Dr. Eissenberg is trying to get various characteristics of dELL from his research. I’m taking part in the work by using a technique known as gel electrophoresis (SDS-PAGE, to be more specific…) to isolate the protein from extracts obtained from fly cells. I then take the gel and apply it to a Western Blot analysis. The protein extracts (nuclear extracts, technically…meaning that they came from the cell’s nucleus…) are obtained by either Size-Exclusion Chromatography or Ion Exchange Chromatography, neither of which I’ll explain, but they’re both pretty cool… On the Western Blots, we use selective antibodies to detect and expose the proteins we’re interested in…one antibody binds to dELL and then a second antibody binds to the first one…but that second antibody has a luminescent “probe” (i.e. chemical) attached that allows us to see it… By carrying out this whole process, we are able to see in which cells/extracts/etc. that dELL is present and/or active.

There’s a lot more to it, honestly…most of which I don’t know. Regardless, I’m just running a bunch of SDS-PAGEs and Westerns right now…both of which are relatively time consuming…so it takes me a good two afternoons to take care of each of them… It’s relatively interesting, but not really what I want to do with the rest of my life. If anything, it’s interesting to see how proteins are isolated and such…seeing how all of this has been done in the past…

…and why everyone hates Western Blots… 😛

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…so it begins…

“Why do we need explosive detection methods? Terrorists. Because they all want to increase your entropy?”
– Joel Brockmeyer

So classes have officially started. All I had today was BBS 501: the “BBS” stands for “Basic Biomedical Sciences” and, essentially, this class is Graduate School Biochemistry (officially titled “Beginning Basic Biomedical Sciences I”, I think). Today we began a few lectures on thermodynamics, hence the aforementioned quote regarding entropy…spoken by Joel during my Junior Chemistry Seminar class Junior year at Truman…

If today’s class is any indication of the future, then it shouldn’t be too terribly hard for the first few weeks. We had a review on thermodynamics, and by “review,” I mean back to Freshman year of college. I’m sure it’ll get more difficult, but flipping through the first few weeks of the syllabus, all I can see is stuff I’ve, at the very least, heard of if not studied on multiple occasions in various classes throughout undergrad. I think the primary difficulty will be in the sheer amount of material, however. As in, I’ve got this class weekday mornings at 9:00 am…so when I have my first test in just over 2 weeks, I’ll have had about 11 lectures…which is the equivalent of almost a month of lectures (MWF) at Truman. So yeah, I dunno…it could be easy…could get a lot harder really quickly…

The exams will be completely in essay form and we are assured 3 hours to take the exam and each lecture will be covered by only one question on the test…therefore, we are relatively aware of what’s going to be on the test already…that, and we are being told to a). get the previous tests from upperclassmen and b). that the questions are very similar from year to year.

Graduate school?! So far, it sounds a lot easier than I would have thought in many of my undergrad classes…on the other hand, I’ve only had one day to deal with…but, then again, I only have two real classes to worry about: this one and a class twice a week that deals with reading “classic” papers (i.e. the original Watson and Crick DNA structure paper, etc.).

Only time will tell, I guess…

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I'm poor now…

…or something like it… As some have heard, Brooke and I got a car…a 2003 Hyundai Elantra GT…had 30,000 mi on it, so it’s somewhat used (more of a “program car,” technically), but in great condition and we got an incredible deal on it, so it was hard to pass it up. But yeah, we’re hoping this car will last us a good 5 years until I’m in the workforce (…assuming that ever happens…).

Otherwise, 3 weeks are done in my first of four lab rotations…things are going quite well, actually… As of last Thursday, we finally got the camera system to work properly such that it can record a signal sent on axons in the turtle cerebellum…which rocks tremendously, considering that I’ve spent 3 weeks on it… 😛 Anyway, I think this grad school thing will work out alright as long as I stick with it…I guess that means I’ll have to study, too…grrrrr…

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I’m poor now…

…or something like it… As some have heard, Brooke and I got a car…a 2003 Hyundai Elantra GT…had 30,000 mi on it, so it’s somewhat used (more of a “program car,” technically), but in great condition and we got an incredible deal on it, so it was hard to pass it up. But yeah, we’re hoping this car will last us a good 5 years until I’m in the workforce (…assuming that ever happens…).

Otherwise, 3 weeks are done in my first of four lab rotations…things are going quite well, actually… As of last Thursday, we finally got the camera system to work properly such that it can record a signal sent on axons in the turtle cerebellum…which rocks tremendously, considering that I’ve spent 3 weeks on it… 😛 Anyway, I think this grad school thing will work out alright as long as I stick with it…I guess that means I’ll have to study, too…grrrrr…

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New Section, etc.

So yeah, today was pretty good… I went by the Employee Health center and they said I officially don’t have tuberculosis…woo hoo… For some odd reason, SLU makes all its employees take a TB test every year…I guess if I don’t have to pay for it, I don’t really care… Anyway, after that I went to work and saw a Master’s thesis defense, which was relatively interesting…I guess it’s good to see what research counts as Master’s degree material…didn’t seem too hard…hehehe… 😛 After that, Dr. Ariel ended up leaving early, which meant I got to leave early too… I went by EB Games and got a used copy of “X-Men: Legends” for Gamecube, which I’m quite pleased with so far. Should keep me entertained for the rest of the summer, certainly…

Other than that, I have started a new section of the website titled “Articles” (link’s up at the top, yo…). I’m intending this as a place to post things like…well…like the editorial I posted there by Paul Krugman, who writes for the New York Times, among other periodicals/books. This editorial is essentially about why politics shouldn’t dictate what is taught in our schools…and I agree with it wholeheartedly…which is why I posted it… 😛

Anyway, check that page from time to time…I’ll post other stuff there, too…eventually…

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…fun with turtles…

So yeah, I’m working for Dr. Michael Ariel here at Saint Louis University in the Pharmacology and Physiology department for the next six weeks. This is the first of three lab rotations that I need to carry out for the Ph.D. before I can start my actual research work. Dr. Ariel’s focus is the brain, specifically, the reflex action that causes muscles to move your eyes when you turn your head. As he explains it, when you turn your head, your eyes want to stay focused on a given location, so the muscles cause your eyes to stay on that position while your head moves from side to side. He does this work in turtles, which is somewhat rare in a world where mice and rats tend to dominate research. He uses turtles because, this specific box turtle, can live underwater in the winters of Wisconsin for up to 5 months without having to come up for oxygen (crazy, eh?!). Well, when you remove the brain tissues from the turtle’s body, the tissues will actually stay alive for a few days without being attached to the rest of the body…something that mice/rats/us can’t do…

Currently, I’m helping Dr. Ariel set up his new $70,000 camera device that will record brain stimulation. We will put a voltage-sensitive dye into turtle brain tissue and then shock it with an electric pulse; the neurons are then excited the response travels throughout the neurons along certain pathways. The camera reads the changes in the dye so that we can trace where the signal starts and stops. Neat, eh? 😉

Thus far, the work has been interesting, but it’s difficult getting used to 8 hour workdays again… Now that the camera is mostly set up, I’m sure I’ll be working on other projects by mid- to late-next week… Fascinating times, I tell you…

…and on a side-note, I get to play with my new praise band tonight at Webster Hills UMC…those drums won’t know what hit ’em…

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Time for a BBQ

Well, Brooke and I went to Hannibal yesterday for Tom Sawyer Days…yes, they have a festival about Tom Sawyer… They had some interesting stuff going on and it was gorgeous outside, so it was a good day overall…just really long… Regardless, we made it back here late last night and we’re checking out a new church this morning…hopefully I can play some drums sometime in the near future, eh? This afternoon, we’re gonna BBQ a bit and go down to Fair St. Louis…Switchfoot is performing tonight and then, of course, fireworks…

On a side-note, Friday went pretty well when I went to SLU to investigate professors to work for. Dr. Ariel does some fascinating stuff with turtles, so I will probably work for him, but I’m still meeting with another guy Tuesday morning. Now, the catch is that I can’t start work for another week (July 11th), which leaves me quite open for this week…therefore, I think Brooke and I are going down to New Orleans as a semi-honeymoon-type deal… We’ll probably leave Tuesday late-morning and come back on Saturday. We found a couple hotels within a block of the French Quarter, so this should be really cool (actually, quite warm, sadly…).

Oh yeah, apparently, some Japanese guy set a new record and memorized and recited 83,431digits of Pi…seriously, some people have way too much time on their hands for their own good…

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…and then…there were two…

Yup, I’m married…crazy, eh? Brooke and I have moved into our new place in St. Louis and are almost done putting everything where it needs to go…by the end of tomorrow, we should be mostly done…until the next volley of wedding presents arrives this weekend… That, and I start at SLU for graduate school on Friday. I’m glad that things are starting to settle down a bit, since these last few weeks have been absolutely insane…but a good “insane,” I guess… 😛

Brooke and I went to Hermann, MO for Saturday night and Sunday night to stay at a B&B (…we hope to take a “real” honeymoon in mid-August, of course…suggestions as to where?), which was pretty cool…they upgraded our room to a suite for the two nights at no charge, so we actually had a living room, bedroom, bathroom and kitchen to ourselves; we’ll have pictures up eventually… We also toured the Stone Hill Winery and the Adam Puchta Winery (after sampling their excellent wines, we both had to take a nap…heh…). Overall, great wine, great food and a great time…nice and relaxing!

We just got DSL hooked up today after SBC got their act together… This $15/mo DSL service is great, though…moves a bit quicker than I expected, honestly…hopefully it keeps up… Therefore, we’ll hopefully both be online a bit more often now, although I’ll likely be somewhat busy at school…

Keep in touch, everyone!