Week Three: (July 6 - July 8, 2010): Extraction-o-rama!

This week was very short, only three days, because of the holiday on Monday and the ASE Midsummer Conference on Friday.

7/6/10:  I extracted DNA/RNA from two more samples, then ran an electrophoresis gel of the four samples I had previously extracted.  The gel results showed that somehow the gel (which I used from the freezer) had been contaminated, so Dr. Herfort had me re-run it.  The re-run showed the same signs of contamination, even though I prepared it correctly.  Dr. Herfort theorized that our buffer which was used to move the electrical currents through the gel was contaminated, so I went and made a a new liter of 1x tris-acetate ethylenediaminetetracetic acid (TAE) buffer.  I also made 2x tryptone and yeast extract (2xTY), a liquid solution that is used in growing cells and cloning.

7/7/10:  I got to the lab early today, so I started to clean sampling bottles and buckets that Dr. Herfort would need tomorrow for sampling.  Once I finished that I extracted two more samples, giving me a total of six extracted.  I also ran a NITS PCR on the six extracted samples to identify any M. rubra in the samples.  The extractions and PCR took the longest, so that was all I did today.

7/8/10:   When I first got in this morning I started to gel right away for the extractions and NITS PCR.  Four samples had M. rubra present, but the two deepest locations (130 M below sea level and 75 M) had no M. rubra.  The extractions showed good DNA and RNA, so anyone will be able to use them for their experiments.  After showing my results to Dr. Zuber, my senior mentor, he wanted me to run an 18S PCR which would show if the cryptophyte algae prey of M. rubra was in the samples.  When the results came back positive, he then asked me to run a duplex PCR of 18S and NITS to see the results of each sample side by side and I will get the results on Monday.  I also did two more extractions today, something that I am becoming very good at!

Cheers,

Deirdre