Week 8: FISH and PCR

I can't believe there are only two weeks left in this internship! It seems like summer weather just got here. And there is quite a bit of work left to be done.

This week started out with subculturing about a dozen primary plates that had individual colonies. I also extracted DNA from the clumps that are growing in our nitrogen-fixing culture. This DNA was then amplified with PCR, which will eventually be used to sequence the bacteria.

A fifth round of FISH was completed this week. We have been getting high background (soils fluorescing when they should not) probably due to nonspecific binding, which has made identifying bacteria difficult. In order to try and reduce this background, we tried blocking the samples by applying nonfat milk onto the samples. This is very similar to what I have done with Western blots at a past research position. Blocking the samples was successful in one sense: the soils did not fluoresce, but neither did the bacteria that we want to visualize. So we will be proceeding with FISH without the blocking step, as it will not help us achieve the goal of observing bacteria.