Tuesday, August 04, 2009

Another Lab Cameo

I spent a chunk of a day early last month dusting off my old lab skills. The rationale was that we were losing the senior lab tech who was supporting a lot of the projects I'm involved in. She's actually an old friend from Millennium (we started & left in near synchrony there) who has been lured back to that fold and will be greatly missed (until we steal her back!).

Anyway, it looked like we'd have a gap in lab support for some PCR projects. A back-fill position was open, but hiring is never instantaneous. Perhaps some resources could be shifted, perhaps not. So I imposed a bit on my friendship to get a quick refresher in PCR.

One interesting factoid is that I have now run PCR in every decade it has existed. In the 80's, when it was still new, some of my undergraduate classes used it. I didn't really appreciate then how cutting edge we were being. Another class had us running PCR in the 90's. I never quite got my hands wet at Millennium (despite several invitations or schemes to, the last coming just before I was shown the door), but I did once supervise PCR runs in a hotel ballroom as part of an Invitrogen-sponsored high school program. At Codon I did spend a morning in the sequencing lab and set up cycle sequencing, which isn't quite PCR but is very similar.

Of course this also means my time in molecular biology labs spans 20 years. Some things haven't changed at all. Pipetmen remain a masterpiece of industrial design, completely functional yet sleekly styled. Lots of other paraphenalia have hardly changed -- microfuge tubes, desktop centrifuges, etc.

However, there are some new items -- leading to new puzzles. I've heard of strip tubes, but this was my first time using them. Nice and simple & organizes the samples. But, after pipetting my aliquots onto the side as I was taught, how do you spin the things down? The e-gels sure beat pouring your own, though it does take away the possibility for excitement. I only ever coated the microwave ceiling with overboiled agar, but one junior faculty member was forever remembered for blowing the door off a microwave.

My guide was also trying to train someone else & so was dashing from lab to lab. Some problems could be solved by asking (where do I get more tips?) but some required waiting. The answer to the strip tubes was a different 'fuge, but one that was being very heavily used that day by multiple scientists.

There is also a lot of lore that either I had forgotten -- or needed some more practice. You should always use the smallest pipettor which will accommodate your load, but with 5 pipettors (I'd never had more than 3 before) to choose from I sometimes used a size larger than desirable. I had forgotten that you should always dial down to the correct amount, never up. Both of these improve precision.

In the end, my experiment wasn't a stunning success. Out of my two sets of samples, only 1 had a working positive control and none of the experiments came out positive (some should have based on prior experiments). However, while that is disappointing it is great how fast the experiment could go from start to finish, yielding immediate feedback. Also, I now know where all the samples and reagents and tools are, so I could dive in.

Reaction to this ranged from amusement to mild alarm (most memorably on one colleagues face simultaneously!). Actually, one informatics person expressed jealousy, stating that he had been thwarted in similar attempts. But, as one other scientist put it, perhaps this isn't the best use of my time. If I really wanted to get good, I'd need to spend a lot of time practicing. Then maybe I'd be okay at PCR, but at the cost that we'd have to train someone else to do the bioinformatics stuff! So I didn't put "Become PCR whiz" in my career development plan. And, despite (or perhaps in reaction to) my efforts, resources were shifted about and we stole a skilled experimentalist from another group within the company.

However, I would regard this as more than a stunt. It is useful to find out what lab work is really like. Partly it helps with one's humility (I really expected both controls to work!) but also with considering the actual work involved in an experiment. That in turns helps with proposing experiment designs; more than once I've suggested designs that are scientifically sound but operationally unrealistic.

One final note: I did feel some pangs of nostalgia for Codon. The business didn't work, but boy did we have some slick automation. For an extended period I could get complex PCR experiments run by simply injecting some rows in an Oracle database -- and by run, I mean oligos ordered, PCRs run, clones picked and sequence verified (not all of these steps were roboticized, but those that weren't would be executed by the staff without any intervention by me -- a veritable assembly line). For a computer jockey, that's a really slick setup - and one I wished I still had.

I doubt I'll be making more trips in the lab soon, though I would like to keep PCRing once a decade for the rest of my days. But who knows? I might again go from riding the bench to working on it!

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