Week 6: Continuing to optimize FISH

My lab work was focused around FISH again this week. Our first test run showed soils that were fluorescing, when only bacteria is (theoretically) supposed to fluoresce. This probably means that our probes are non-specifically binding to everything in the sample, which makes it hard to see bacteria potentially on the soil. My mentor and I decided that we would change a few things about the procedure this week. The literature about FISH indicated that we were using a too-low concentration of DAPI, so for this run, the concentration was increased. We decided to try FISH using 3 concentrations of SDS, which permeabilizes bacteria, allowing probes to stain the cells.

Unfortunately, it is hard to say what the best concentration of SDS to use is, because a lot of little things went wrong during the procedure, resulting in wells that were almost certainly cross-contaminated. So on Monday I will be re-doing the procedure, in order to verify what concentration to use. My mentor assures me that repeating an experiment with the exact same conditions is very common in science.

Vanessa asked the CMOP interns to think about how our research this summer matters (i.e. “why bother?”). I am excited to be a part of this project; very little is known about microbial life in this location. I think it is always beneficial to know about biodiversity in any environment. The ice caves around Mt. Erebus are particularly interesting, because of how extreme this environment is. This project offers a great opportunity to observe how biological systems adapt to hostile conditions.