Week 2

Week 2 started off great with a visit from the NSF site visit team Monday.  There they gave some background on the aspects of their funding and also assessed each individual project within CMOP to see how they were going.  Each intern had the opportunity to speak with an NSF representative during lunch.  I spoke with an engineer from the University of Florida who had some insightful things to say about his studies with ocean currents and turbulence.

The rest of the week proved to be very exciting as well- I got to perform a variety of protocols dealing with

• DNA isolation of 12 samples from 2007 cruise(s)
• PCR amplification of 4 of these samples
• Gel Electrophoresis
• DNA purification (Error Analysis)

Unfortunately the PCR amplification was unsuccessful for the 4 samples we ran so my mentor Dr. Smit is currently trouble shooting the machine and redoing the primers.  Hopefully next week when we run more tests we will be more successful.

Error Analysis:

With four of the samples there were experimental errors in the last steps of the isolation/extraction process involving buffer solution present in the final solution.  Thus we used a quick and easy purification proccess to clean the solution and then test to see if DNA was still present.  After centrifugation there were visible pellets of DNA in the sample tubes  and after electrophoresis the purification process proved successful.

This week we also visited the main campus of OHSU.   I had a great time especially seeing some of the research projects they are involved with there.  The campus is huge compared to what I had previously thought.

I am very excited to get back to the rest of the samples from 2008 and 2009 next week.  Hopefully the PCR process will prove more successful and we can move onto microarray analysis.