Testing New (Old) Machines
Once again, I find myself apologizing to the hordes of Solar Slug fans for the long period of silence. After the frenzy and freedom of summer, it has been hard to find time to experiment, or even mess with the site, but I am hopeful that things will change now that the semester is tapering off. There has been a little news along the way.
A few weeks ago, the students participating in the Biology Honors Research Program at UM College Park invited me to give a seminar. Since my fly work is old and stale, it seemed like a good chance to talk about the beginnings of the Solar Slug project. As far as I could tell, the students found the ideas intriguing (golly, who wouldn’t?), and it was a great chance for me to assemble a seminar and impose some order on my thoughts.
Last month, we submitted a report to CONANP, who oversees the Biosphere Reserve in Bahia de los Angeles, about the past summer’s activities. A good chance to think hard about what we did, why it matters, and where it will lead. In related news, because of overwhelming time demands from the opening of their new Living Lab, Ocean Discovery Institute will not be working in Bahia in 2017. It is disappointing, but, at least in principle, will give me some time to put together more substantial funding for future years.
But let’s talk science. Several months ago, I acquired two old PCR machines from the surplus equipment program at the National Institutes of Health. It’s a great program, in which equipment that is no longer wanted by researchers at NIH can be acquired by educational institutions. The major caveat is that one can never be sure that the equipment is functional until it gets back to the lab and is tested. My students in the Cell Biology and Physiology lab course were running some PCR samples, so I thought it would be a good time to test out the new (old) machines in parallel with the very fancy PCR machine we use for student labs.
The thermocyclers are Applied BioSystems GeneAmp 9700s. In principle, they should do everything we need, plus they have a nice post-cycling chill cycle, so I can set them up and go home without worrying about the DNA sitting in the machine and degrading at room temperature. But do they work?
The choice of what to amplify was easy. Another Elysia fanatic, Susanne, had sent me a piece of parapodium from an E. diomedea that had an unfortunate encounter with a filter. Don’t fret, the slug survived, but she was nice enough to carefully preserve the tissue in ethanol, pack it, and ship it to USG.
The fragment sat forlorn for about a month. It was very exciting to be able to finally extract the DNA and see if we could amplify the rbcL region. I set about mashing and processing a small piece, and all looked well.
At the end, I had produced a tube of clear liquid. Was there DNA?
I amplified DNA from E. diomedea, a control sample from BioRad (to make sure the machines functioned at all), and some DNA I had extracted from an Avrainvillea plant in the slug system. During the thermal cycling, I used a thermocouple probe to check the temperatures of the machines. Machine 1 was just about perfect, whereas Machine 2 was way too warm during the cooler parts of the cycle, and I expected poor results.
The control samples worked in both machines, which was somewhat surprising based on the temperature measurements. I guess you can get away with a lot if you start with really clean DNA and well-established primers. The only sample from the new extracts that worked was the E. diomedea DNA in machine 2. I expect we can get things to work better if I reduce the DNA concentration, but it is puzzling that a sample in the less reliable machine worked better. Nonetheless, I now have some DNA I can send off for sequencing when there’s a little time.