Week 1: Testing the waters

I was really excited to start my internship at CMOP, and the first week was very busy. It started on Monday with introductions, pictures, safety training and learning a little bit more about the CMOP internship and my project. I met with my mentor Pete and he explained how this summer I will be focusing on the identification and quantification of protists in the Columbia River estuary.

Tuesday we drove to the Columbia River to get samples from five different sites. We took water sample from each of the site and measured their temperature, pH and salinity. When we arrived back at CMOP we processed the samples for nutrient, particle, and dissolved carbon analysis.

Wednesday we filtered the water so that we could later isolate the DNA present in the water samples. By looking at the DNA we will be able to identify the type of protists in the water, we are really interested in the presence of Katablepharis as well as analyzing the different types of ciliates present in the estuary. After filtering the water we then began extracting DNA from the filters. It was a long process but it was successful.

Thrusday we amplified the DNA of Katablepharis, using specific primers, through PCR (polymerase chain reaction). We also amplified general eukaryotic DNA using more general primers. To look at the DNA we ran our PCR products in a gel, unfortunately our Katablepharis PCR did not work well but we did get amplification from our general eukaryotic PCR.

Friday we tried to amplify Katablepharis DNA again using a different set of Primers, the forward primer was still specific to Katablepharis. We also amplified ciliate DNA using general ciliate primers. After running it on a gel we were glad to discover that we amplified PCR in both of our primers. We will be looking more closely at this DNA to confirm that it’s Katablepharis in the weeks to come. We also looked at some of the water samples under a microscope and were able to see many different microscopic organism swimming or floating around in the water, hopefully we will be able to culture some Katablepharis from the water samples. I am really excited to be working on this project and can’t wait to find out what I discover.