Siliceous and Delicious

First order of the day is to order the one batch-cultured diatom species for my extant diatom FIB and diatom sonication projects, since Andy authorized my suggestion to do that over the weekend. Which one should I order first? Thalassiosira pseudonana has the advantage of being the first diatom for which there’s a whole genome (I’m not sure if there are others). I’m a little concerned that it might be hard to work with due to its small size (4-6 µm diameter) for FIBbing, given my past experience. But I suppose I will have to face that regardless, if I ever get to that point. But maybe I can make my life a little easier by starting with a slightly bigger species—that way it’ll also be easier to get good SEM images of cleaved surfaces for the sonication project. Thalassiosira weissflogii is larger, but then if I want a sequenced diatom amongst my line-up, I’ll need two from the same genus, adding T. pseudonana later. Coscinodiscus wailesii is big, but maybe too big—I’m not convinced I’ll get enough cells out of a 20L culture to do all the trial runs I’ll need in order to get it right. Fuck. Maybe Lithodesmium undulatum is the best compromise. It’s intermediate in size and phylogeny, and although it’s not a model organism, it might just do fine. Let’s see. At some point you have to stop agonizing and just go ahead. Here we go. Phew! First thing checked of the list for today!

Sent an email to Lars in Germany, replying to his suggestion that Andy and I should come and visit in September. In all honesty, I’m not too excited at the thought of another trip, but then again, I’ll be traveling to Germany in October anyway for Peter’s wedding—so perhaps I can arrange a combination trip?

Next, I really have to face the music and try to start picking samples for the radiolarian lineage project. As much as I hate it. Again, I’m not sure where to start. Where are the slides used in defining the Didymocyrtis-Diartus lineages, for example? The Riedel and Sanfilippo (1980) paper, for instance, cites a bunch of papers for the bottom of the Didymocyrtis-Diartus lineage, but only one for the rest, and says nothing about where the samples might be found. The latter reference, Kling (1978) in the Haq & Boersma book, actually lists a lot of lineages (like the chapter in the Bolli volume), but does not provide any supporting references or citations about what samples might be consulted to see these transitions.

I’m not particularly satisfied with my progress today. Yes, it was a stiflingly hot day, yes, I was tired from staying up late last night. But I am really quite stuck on this question of sample selection, and I’m not sure how to go ahead from here. The frustrating thing is that it’s going to be a whole week until I get another chance at this—but that’s just my lot with having six parallel projects to work on. I’ve put in my hours today, and tomorrow I’ll turn my attention to the next project.