Week 7: Presenting and More Sampling

As some of the other blogs have mentioned, this past week was one of my busiest weeks here as an IEH intern! The week began quickly as Kiley returned from her trip and we all got to work. On Monday, we had a busy day of continuing sediment core dissections and extracting DNA from previously processed cores. In the mid-afternoon, we had a lab meeting. These meetings are a good time in the week for all of us- myself and my mentor, as well as my fellow intern Maddie and her mentor- to get together with our Principal Investigator, Dr. Holly Simon, to talk about our progress in the lab. Monday was Kiley's turn to present, and she showed Dr. Simon data and a graph that I had made earlier in the day. The data was all of the snails found thus far in May and June samples, as well as their precise locations. It was cool and a little intimidating to see my own work from start to finish- from taking the sediments out at the coast to processing and finally, to representing graphically. Dr. Simon had some interesting ideas for how to revise our lab methods to increase our productivity. Up to now, we have been dissecting an entire, several-centimeter-long core, and extracting DNA from all of these fractions. However, most of the snails have been found only in the uppermost fraction, where it seems like most of the exciting stuff is going on. Therefore, from here on out we will only be examining the surface levels of the cores. This makes my job easier and will allow us to do more comparative qPCR runs and hopefully start seeing some patterns between snail presence and archaeal abundance!

We decided to go sampling for July earlier to give us more processing time, so we headed back out to Astoria area on Wednesday! This meant that Tuesday was very busy with preparations for sampling and, as before, a scramble to find rain boots and clothes that I didn't mind getting dirty. Wednesday's sampling trip was a bit easier than our prior trip, because we left at 7AM from OHSU, instead of at 3:30. The extra couple hours sleep really made the whole experience a lot more pleasant! Furthermore, we added in three new sampling sites around Baker Bay- one of the Columbia River estuary lateral bays we study- to get a more complete idea of P. antipodarum presence, which means I got to see some new places. Unfortunately, I got stuck in the mud at our messiest site, and had to spend fifteen minutes with a lot of help to pull myself out. Needless to say, my pants and boots were messy after that, so I spent the rest of the trip barefoot in shorts. I'm sure I deeply confused the Dairy Queen workers who saw me wiping mud off my legs in their bathroom after the fall. However, all's well that ends well, and we made it back to OHSU in the mid-afternoon with many new samples. 

Thursday was a bit of a nerve-wracking day! We delivered our mid-term presentations in the afternoon, in a formal-seeming lecture hall. All of the other interns and their mentors were there, so I wanted to be sure I did a good job in explaining my project and making it seem important. We only had five minutes to present, so I was under a real time crunch, as my project has 3 major components. I had to explain the estuary bays, the snails themselves, and the ammonia-oxidizing archaea that consume the snails' waste product. I also had to relate them to each other, and explain that we were looking for a correlation between snail presence and archaeal abundance. Finally, I had to explain how we were doing this- by using qPCR to amplify the amoA gene in the sediment-extracted DNA, and quanitfy its abundance. amoA is the gene that codes for the active site (A) of ammonia-monooxygenase (amo), the enzyme that allows the archaea to oxidize and therefore metabolize the ammonia. Since all archaea must express this gene to survive, we use this gene as a biomarker. That is, the relative abundance of amoA in a fraction correlates directly with archaeal abundance there. I thought the presentation went well, and, perhaps more importantly, Kiley thought it went well. All in all a tiring but very rewarding week!