Jadin Scott, Rohwer Lab, Week 3

The beginning of my third week studying microbiology and coral reefs in the Rohwer lab at SDSU was very similar to the past weeks.
On Monday, I again took photos of the CCA slides for the DOC experiment and then began reading Biology of Microorganism, a book referred to as “The Bible of Microbiology”. I also continued my education in coding, learning to create and run a script with Unix. On Tuesday, I completed a DNA extraction, but this time we used commercial kits rather than the lab’s “homemade” protocol that I learned before.

In my spare time during the extraction process, I learned how to pour agar plates for culturing bacteria. Wednesday was the last sampling day for the DOC experiments, so I collected and photographed the slides one last time. I then moved to the lab across the hall, which is focused on studying how microbial and viral communities persist in the lungs of people with cystic fibrosis, in order to design new treatment strategies. Here, I worked with Marisa Rojas and Greg Burkeen. Marisa taught me how to pour PHAGES as well as how to use the Typhoon imaging system to take pictures based on radioactivity. With Greg, I learned yet another method of DNA extraction called the CTAB protocol. It is called this because CTAB (cetyl trimethylammonium bromide) is used to disrupt the cell membranes. I continued working under Greg on Thursday, when he taught me about PCR DNA replication and walked me through running the protocol. This included learning to create a program on the PCR machine. On Friday, I attended another aquarium meeting with the lab members and then returned to the PCR work with Greg. I learned how to make a TAE buffer solution and an agarose gel for measuring the replicated DNA based on size-dependent displacement. Unfortunately, something must have gone wrong in our protocol, as when we used the typhoon to take an image of the gel, only the control “ladder” appeared. Greg explained that things mysteriously didn’t work quite often, and that we could try again next week. (Welcome to the world of science!)
This week I spent most of my evenings after work reading on the patio at my host-house. However, on Wednesday and Friday I opted for a change of scenery and spent more time in La Jolla Village and on the beach. This weekend my friend Presley came down from San Francisco for the 4th! We spent the weekend in Coronado where we went shopping, went boating, explored the neighborhoods, and watched a parade.