Deep-Sea and Antartica Bacteria (Week 2)

This week was very exciting, because I started studying the Antartica bacteria. I also learned a lot more about the context for my project and projects that other people in Tebo's lab are working on. It was interesting to learn about the diverse work that everyone in the lab is doing and yet it all ties together.

On Monday, Rick and I took the DNA from one of his deep-sea bacteria down to the Primate Center to have it sequenced. The next day, we got the information on it and Rick showed me how to interpret the data. Apparently, it is very closely related to Photobacterium profundum. Since members of this genus can apparently glow in the dark, Rick thought we could try to culture the bacteria on a media that would encourage it to glow. So, I transfered it to a different media, but so far it hasn't started glowing. I also started the process of making new media to grow the deep-sea bacteria. The solution has to have lots of different salts in order to simulate sea-water. Hopefully, we can find a media that will get the bacteria to glow!

However, my work with Rick's deep-sea bacteria isn't actually part of my project. I just worked on that a little bit in my spare time while waiting for PCRs and gels to finish. Like I said earlier, this week I was able to start working with Antartica bacteria, since I am now familar with some of the basic techniques. On Monday, I extracted DNA from three Antartica soil samples. After that, I did a PCR to amplify the DNA and then I did a gel to see if we got DNA. Everything went well. Not only did the DNA from the cave samples show up clearly on the gel, but the negative control had no contamination. After having so much trouble last week with contamination from the BSA, I was very pleased to see that there was no apparent contamination in this PCR.

I spent most of Wednesday digging through frozen samples of Antartica soil and transferring it from bags into tubes. Apparently, when they collected the soil samples, they ran out of tubes, so they collected several samples in bags, instead. Since bags are liable to breaking and contaminating the soil, it's better to have the soil in tubes. So, I worked on transferring some of the soil to tubes. It was very interesting to notice how different the soil samples were. Some were soft and sandy, some were filled with hard, tiny rocks, and one sample was so hard and packed that I had to hack at it in order to break it up before I could transfer it.

On Thursday, I went on a field trip to Astoria with some of the other interns. There, we learned a lot about the instruments that CMOP uses to collect information about the river. We also went to the maritime museum and climbed up the Astoria column.