Week 5- Mystery Meat and Columbia River Samples

This week was a sucessful week for Suzanne and I. We started off the week by decideing to send out samples for the Columbia River site back tothe primate center to make sure that a mistake wasn't made since out first sequencing came back as P. Putida.  We knew that this just meant a mistake was made or somewhere along the line our sample was contaminated. Suzanne and I recloned the CR-20 samples and cloned the "Mystery Meat" samples for the first time and sent those over to the primate center for sequencing.  When we got the sequencing back it turned out that there was a mistake and our samples from CR-20 were not contaminated which allowed us to continue on to mass cloning.  We were now going to be able to send the CR-20 samples along with the NH-10 and the LP-6 samples, which were in the -80 freezer, for mass cloning. We were really excited for this. We will send these samples out on Monday of next week because the CR-20 samples have to freeze in the -80 degrees.  Because we don't have enough money  to send away all of our samples for cloning we are only sending these samples. 
With the rest of our samples we will be doing qPCR and amplifying them with TR-FLP.  We will use this method on the Strawberry Hill and Cape Mears samples.  We have been working on getting the TR-FLP to work  but it has been failing. Next week we have decided to do 5 tubes in the SIP for each sample ( SH-light, SH-dark, CM-light, and CM-dark).  This will allow us to get more DNA out of the SIP and in turn have more to amplify.  We are really hoping this works because we want to be able to analyze these extra samples we don't have the money to clone. 
We got back the sequencing for the "Mystery Meat" and it is not actinamyces and shows not even to be a flavobacteria.  We even thought that the sample of plated sea water which we call mystery meat was gram positive after gram staining it but the organism that the primate center sequenced it as was gram negative.We will be doing more research into these samples later on.
On Friday, we set up the 15 degrees Polaribacter irgensii growth plates and we saw some interesting growth patterns.  We we continue looking at the growth into next week and we will start new plates as a check at the end of next week. This week has been very productive!!