Week 9 - Denaturing Gradient Gel Electrophoresis (DGGE)

At the beginning of this week I finished up amplifying my samples and started the DGGE process. Suzanne and I had kind of learned how to set up the DGGE but had never actually set it up on our own with one of our samples.  On Monday, we cast the gel and loaded our amplified DNA and ran it over night.  When we came back on Tuesday, we realized that the current that helps denature the DNA had shut off at 10 pm the night before.  This is because there was a timer for the voltage that was not a part of the protocol and so we didn't know to set it.  It was a little frustrating and although we wouldn't be able to trust the results we saw from this particular DGGE gel, we decided to run the gel for 5 more hours and see if any bands formed.  This gel will also tell us if our DNA concentration is too small or too large.  

When we looked at the gel we saw definate bands which was exciting but even more interesting was that the bands formed from the 13C DNA seemed to remain constant during the ebb-flood transition but the 12C inactive organisms appeared to have changed during the tidal cycle.  We are going to run the DGGE again on Monday of next week when Lydie can help me set it up. 

For the rest of the week I worked on my paper and creating my presentation that I will give on next Thursday.  I am excited to share what I have done this whole summer with the rest of the interns and other mentors who attend my presentation.  For a while I thought that I was really behind everyone else on getting my project finished but now I have caught up and am really eager to see whether the microbial population changes with the tides and changing chemical parameters.  

On Friday, I we talked to Dr.  Bayta Maring about what we liked about the internship and what we thought needed improvement.  I  liked talking to her. She was very friendly and was interested in everyones opinions.  I have really enjoyed the CMOP program  here at OHSU.