biology

After a long stretch of doing basically nothing, today I set up my first “bio experiment”. I call it a bio experiment because it involves protein and water and plastic things instead of organic solvents and glass things. It really is more of a biochemical experiment, or, if we’re doing the in vogue things here, chemical biology. So don’t get too excited. I am just trying to reproduce some (awesome) results that Jake had a number of months ago. I am taking his fragments and some of the protein that was stored at -80*C upstairs and incubating them together to see if the protein will make itself a sticky little ligand.

It was really easy to set up. I guess I didn’t realize, but nothing was particularly difficult. I used pipetters to get exact volumes and sat around doing serial dilutions so that I was only working with a tiny, tiny portion of what we had.

I spent a lot of time with those pipetters, and in a way it’s sort of nice, a repetitive task that’s fairly satisfying at its core, but the arm does tire after a while. After what seemed like an endless series of tasks – check the fragments to be sure they haven’t decomposed, dilute all solutions, let the protein thaw on ice, dilute the protein, plus a little bit of math and establishing a key so that I know what I put in which wells on the 96 well plate.

Eventually I had the plate – I was only using 24 of the 96 wells – all finished, and I capped it off with the very satisfying task of sealing it with an adhesive foil, pressing it down so that I could see each little well as an imprint in the silvery seal. Then Jake and I took the plate upstairs and put it in an incubator at 37*C – or roughly body temperature. It will stay there until Thursday, when we have time on one of the mass spectrometers, and Jake is going to show me how to use it.

It is kind of exciting, and it is definitely nice to feel legitimately productive, even if I’m just currently working on reproducing results.

Then I set up those same reactions in my hood without any protein, dissolving them up in toluene and putting them into little glass vials (the organic chemist in me sings!), rigging up a clamp to hold four little vials stirring merrily away, and I lowered them into an oil bath set to 110*C (the boiling point of toluene). I wrapped the tops with Teflon tape, because the solvent will want to boil but the container is closed.

Usually we don’t do that, heating a sealed container, but these reactions are so tiny that we don’t have a reflux condenser small enough to attach (and I have four reactions, so the logistics would be difficult). I am hoping that they do not explode. It would be especially nice if they didn’t explode and also worked, but you can’t have it all. So I guess we’ll see.

I am almost certainly getting sick and it is manifesting itself in a weird sore throat (much lower than usual, almost feels like a catch in my chest) and fairly severe muscle aches. I have done a decent amount of work today, so I think I might head home and crawl into bed with a cup of tea. Sometimes, life is hard.