Gas station without pumps

2013 May 1

Senior thesis reading leads to learning

Filed under: Uncategorized — gasstationwithoutpumps @ 17:00
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Reading senior theses has lead me to learning a bunch of new things—not so much from the theses themselves, which are often rather light on background information, but in trying to help students debug their problems and fill in their missing background.

For example, today I found out a little about how nitrogenases (which usually fix nitrogen N2 to make ammonia NH3) produce H2—I did a search with the student to try to find the stochiometry of the reaction, and we found a paper that explained not just the reactions but what mutations had been needed to turn off the normal control of the nitrogenase, so that it would continue to be active (and producing lots of hydrogen) even when there was no nitrogen to fix.  I couldn’t see any reason for the nitrogenase to be active when it wasn’t producing ammonia, and indeed it isn’t in the wild-type bacterium.

I also helped another student look at pitch detection algorithms (for finding pulse rate from video feeds), using cepstral analysis. He’d been using FFTs, which are not bad, but which can be confusing to interpret when there are higher harmonics present.  The cepstrum is often easier to find the fundamental from, and I’m curious whether it will help with the rather noisy data he has to work from.

A third student was having trouble with non-expression of a viral protein in an archaeal host system, and I suggested looking for the viral sequence in the CRISPR repeats of the archaeal genome, to see if the strain had been previously infected by this virus and so was chopping up the DNA or mRNA they were trying to express. I didn’t know before looking whether CRISPR systems would attack RNA or just viral DNA—the article I looked at suggested that it would attack RNA as well as DNA.  I also suggested that they look to see whether the desired mRNA was actually being expressed (using cDNA and PCR), to see whether the problem was a translation problem or a transcription/RNA-processing problem.

A fourth student had questions about whether he should include an electron micrograph from the literature to show the structure of the virus he was trying to express a protein from, so we brought up the paper on my computer (with a bit of a detour, since he had mis-spelled one of the author names).  The picture was worth including for the purposes of his thesis.  We also talked about whether a particular part of his thesis writing should be given more prominence and more generally about his paragraph and section structure.


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