Science in the City

Today was the first ‘official’ day back in my microbiology lab, even though I’ve been back with increasing frequency as the school year gradually wound down and the Summer plans geared up.

There was the trip to say ‘hey’,

then the one to show my Summer student intern around,

then another to plan out what projects he and I will be doing this year,

and another after my orientation meeting at the program office….you know….just to get some cells started to work with.

I don’t know if I could have walked in ‘cold’ and felt good about it.

It’s funny how familiar and strange it all feels at once. Given the usual turnover in an academic lab setting (post-docs leaving, people having kids, new grad students coming in) I had to re-introduce myself, say goodbye to a familiar face, and saw for only the third time since the beginning of LAST Summer the scientist who was back with her baby…all in the first few hours back. I had to explain to two people what the whole point of a science teacher in an active research lab was for….all before I could even really burrow into what I’m ostensibly there to pursue – scientific understandings.

After all that dithering, the whole first day was spent digging around what, with a good modem and access to the online database licenses of my august hosting university, I may have been able to do from anywhere. In a nutshell: I’m cross-referencing a published pathway for vitamin B6 metabolism in budding yeast with the imputed and known homologs from our model organism, the fission yeast. Strangely, each species has it’s own little academic fiefdom which assigns their own nomenclature and has their own standards for classifying them. So a gene given a functional name for what it does in E. coli, has a different name in budding yeast, and yet another completely different name in fission yeast. For example:

PdxK (pyridoxine kinase) in E coli

is BUD16 in S. Cerevisciae,

coded YELO029C for that organism,

but SPAC6F6.11c in S. pombe, and unnamed as such.

I finally decided that the best way to straighten it all out was to create a cross-reference table, which seemed like a good idea until some of the edges failed to line up. Something that is listed as four genes in budding yeast all point back to a single gene in fission yeast. There’s a functional homolog in E. coli and my organism that line up, but I’m worried that there isn’t a connecting intermediate step in the budding yeast to give me confidence that I haven’t missed something….I go through crests and furrows of confidence and dejection as I work through this, ebbing between feeling like I have true command of the concepts before wondering if I’m not really more confused than I was before. After all, I only got 2 of 12 that I tried to map from organism to organism cleanly. Either I’m at the cutting edge of human understanding, or I screwed up. I’ll let you guess which I suspect is more likely.

After I get the table done, I will create the (first ever?) map of the reactions/products of these enzymes using the labels for our organism. This will probably be a slide in my presentation due for the project, and help crystallize my own grasp of what my future test series will be. Already, what I got from this review explains an unexplained result I got last Fall….so it’s all worth the effort, even though it’s a challenging re-introduction to the work.

On top of which – it HAS been fun, I learned, and realized that the longer I spent with it, the more conversant I was about it. And besides….where else BUT the lab would I be able to complain about this arcane problem, and have an intelligent person shake their head in regrettable been-there-done-that commiseration? By itself, that made me feel less lonely today!

Oh – and remember to take your Vitamin B. All the literature makes this look like it’s next big antioxidant. Who knew?