Week One: I have not missed you, PCR

Like most lab work done in the Zuber lab, PCR (polymerase chain reaction, a way to amplify a select segment of DNA) was front and center, meaning so was headaches.  While PCR is a wonderful tool and has certainly come a long way from water baths upon water baths, it's still very finicky.  I'm no stranger to contamination or PCRs not working (I'm pretty sure 90% of my time my first summer here was spent figuring out just what the heck was wrong), but it can be particularly frustrating when:  there is a limited amount of sample, we can't buy anymore reagents until July, and I have to wait over 3 hours to learn that my PCR didn't work.  Luckily for me the contamination was in the water used, meaning a very simple and quick fix (thank goodness).

After redoing my PCRs, that little 250 base pair segment that I was looking for showed up in three samples - strangely enough, they were all from Ilwaco Harbor.  What this means, at the moment, is that the Euduboscquella dinoflagellate I'm looking for might only be present in Ilwaco Harbor.  Of course one test can't prove this (especially since we're in the middle of cloning & sequencing), so I'm now looking at the bigger picture.  Ilwaco Harbor is a small harbor in Baker Bay and is across from Young's Bay, so next week (this week, technically) I'll be redoing my PCR with different samples to see if this was just an anomaly.

I've also been running some PCRs to identify some different variable regions; which organisms these belong to are unknown so, just like the DUB PCR I'm cloning and sequencing several of the samples to see what shows up.  This isn't directly related to my main project, but it'll definitely be interesting to see what comes back - fingers crossed it will help with my Euduboscquella project, that would be awesome.

Until next week, Deirdre