Week 2 - PCR and Cloning

This week I have been working on getting the samples from the LP-6, the NH-10 and the CR-20 to amplifiy using a general bacterial primer. Suzanne and I got the cleaned SIP samples to amplify and then went on to PCR cleaning.  We introduced the vector into our samples and cloned them so we could send them over to the primate center for sequencing. When we got the sequences back we blasted them to find what organisms were in our samples.  We found that there was a large amount of pseudomonous in our CR-20 samples which means they likely were contaminated along the way at some point either in the PCR or cloning steps. We started mass cloning so that we could send the cloning plates off to recieve data in order to construct a philogenetic tree.  We didn't do this we the CR-20 samples because we are going to try the SIP process again.  This will tell us the organisms and their trends that occur in the sites in the light and dark and in the presence of carbon.
  I have also been working on my growth curve plates butone of the reagents for the media most likely the SWCm was contaminated which we found out because our blank that we didn't put cells in, was increasing in optical density.  Next week we will have alot to do because we have to start the SIP process, PCR, vector introduction, and cloning on the CR-20 samples and we have to auto clave the SWCm, yeast extract, and marine broth that comprise the media we use for the growth curve plates.  I will remake these on Monday.