Becoming more comfortable with my project (Week 3)

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.

            On Monday I took the streak plates I made on Friday, and inoculated a liquid media with single colonies of the E.coli clones that are positive for the Archaeal DNA. This skill I learned in my last term at Pacific University while taking a Microbiology class. I was quite excited that I was able to use a technique that I actually learned from a college course and apply it into a summer job. Not exactly something I could do with my previous summer job working at a nickel arcade. On Monday I also extracted more fosmid DNA from E.coli clones, a procedure I have done now two times successfully, and a procedure that I will continue to do throughout the summer.

            For Tuesday, I ran PCR to amplify the fosmid DNA I had extracted the day before. This time I ran PCR, I did it with very little oversight from my mentor in order to become more used to doing it by myself. However, the gel electrophoreses did not turn out as we expected and did not show signs of the gene we were looking for. This could have been due to contamination.

            To try to figure out why the gel on Tuesday did not work right, I ran PCR and a gel on Wednesday that contained samples known to have the gene we are looking for and mixed them with two random extraction samples. From this we saw better results, telling us that there was just something wrong with the first PCR procedure. That day I also used dry ice to freeze the E.coli cultures I had made on Monday. They are being frozen and stored in order to preserve them for later trials.

            Thursday was quite an interesting day because undergraduate research students from Pacific University came to learn about CMOP. Since Pacific University is a small school and I attend there, I knew just about everyone in the tour group. It was very fun to show some of my friends and classmates where I worked and what kind of research goes on here! Thursday was also a day where I had to stretch my few chemistry skills by making media for more Petri dishes.

            On Friday I learned how to extract microbial samples from anaerobic (no oxygen) cultures. From these extractions I carried out more DNA extraction in order to test for the amoA gene, or the ammonia-oxidizing gene. These anaerobic cultures were set up to test different growing conditions for the archaea. Friday also contained a Brown Bag seminar about the treaty laws between the U.S. and the Native Americans.

            This week overall has been exciting and full of learning. I am becoming quite comfortable with my internship and I look forward to it as the summer goes on.