Kevin Duffy's blog

Today marks the final day and final blog of my summer internship here at CMOP. My time here has been wonderful. I have learned a variety of new techniques, built amazing relationships, and gained vast amount of  knowledge in a field of science I know little about. I know that I am taking away valuable lessons and skills that will assist me in my future as a college student and as a scientist. CMOP has opened doors to new possibilities and has given me new perspectives on career options.

This week has been one of intense trial and error. The first PCR I ran on the archaeal Fosmids resulted in a band in the negative control, therefore causing the results to be unreliable (Pictured in the below attachment as the circle). Basically throughout all of Monday, Tuesday, and Wednesday, my mentor and I tried to locate where the contamination was coming from. We finally had to replace our primers with new ones because our stocks appeared to be the source of the contamination.

What a packed, yet fun week!

This week has been full of new and exciting events. From mid-term presentations to lots of DNA analysis to an NSF site visit, this week has been packed.

This week involved a whole lot of looking for Archael DNA in the E.coli clone colonies. Based off a previous experiment that used chemiluminescence to detect for the Archael 16S rRNA, we found colonies that were positive for the gene (the black spots pictured below).

From the previous week, I extracted DNA from cultures grown in anaerobic conditions. These cultures were originally started from what we call a recyclostat that contains soil samples with archaea, bacteria, and fungi. On Monday of this week, I quantified the amount of DNA I extracted using a fluorospectrometer. The results were fairly low, showing that there was very little growth in the anaerobic conditions.

This week I learned more about my project and I carried out several procedures, allowing me to understand and become quite comfortable with the lab work I will be conducting as my internship continues this summer. This week consisted of various lab work: from inoculating liquid culture, to making more agar media for Petri dishes. Each day I either ran some lab work I have never done before, or become more comfortable with experiments I have only a little experience with.

This week I have been focusing mostly on the extraction of DNA from collected samples of the Columbia River soil. The bioreactor, or recyclostat, is where bacteria, archaea, fungi, and other microbes have successfully been cultured from the river samples. The goal of my project is to learn more about the archaea that live in the Columbia River ecosystem. The archaea we are interested in and are targeting are those that oxidize ammonia and possibly use it for their energy source.

This internship is going to be different than any job I have ever worked before and so arriving on the first day was a mix of emotions. The feelings of excitement and intimidation both played large roles. However, as I began to meet the other interns and the staff of CMOP, I felt more welcome and relaxed than intimidated. The first day mostly consisted of a large amount of information being laid out at once. It was sort of overwhelming, but that is how most orientations are.