Week Seven: Sampling again

This week we went back to Astoria to collect more samples. This time we got them from ten of our sampling sights and for two of the sites we took a sample from the top layer and the bottom layer from two sites.  We also prepared the ESP for deployment on Wednesday and took it out to Sat 3 to set it up.

On Wednesday while the ESP was running I extracted DNA from my samples and worked with the BIORAD people to learn how to do a touchdown qPCR. It turned out the only problem was that the protocol had one to many steps so after deleting the 4C hold at the end the protocol worked.

On Thursday I ran the touchdown qPCR on the bacterial sediment samples and while the peak was still early it showed great application for all the 20x samples so we believe we may just need to clone the samples and see. Next week I will run the touchdown qPCR on the bacterial water samples to see if we get a similar result. We will also run a touchdown qPCR on the archaeal sediment samples to see if the numbers are comparable to those we previously had in order to see if the touchdown protocol is giving accurate results.

On Thursday I also ran the new archaeal sediment samples with a qPCR and while good application was seen I haven’t had a chance to analyze the data yet.

Friday we went to the Bonneville dam, which was a lot of fun and very educational, but because of this trip and my sampling on Monday I was unable to get a lot of data this week.