Jordan Nakayama's blog

 Accidentally forgetting to write my blog for last week here is my final blog entry...

Over the last two I had just been busy working on finishing up what I could for my project by tying up loose ends in regard to the PCR primers. Since most primers proved to be ineffective I had spent most of last week just trying to find an optimal temperature along with magnesium concentration. While the temperature experiment was successful the magnesium experiment continued to fail. After four tries I realized I needed to get rolling on the final presentation and paper. 

 The week started with me running the gel for the 24x PCR reaction that tested all of the available primers and the pooled DNA extract template. Unfortunately this was unsuccessful for almost all of my primer sets I ran several other experiments to make sure that nothing was wrong with my methods. Yet, while I was able to get amplification throughout the week I had still been unable to get the 16s primers to amplify so I will need to continue testing to see if I can get that to happen.

 The Amoa primer reaction was somewhat successful since the bands indicate a definite presence of the Amoa gene in 2/3 of the cDNA samples. However, the locations of the bands on the gels indicate strands are present that are longer than expected. I had been about to investigate this a little more but the primers I designed arrived and I had been excited to use those in an experiment. The initial reaction run showed a slight amplification in only one of the six new primers which is very frustrating.

 Week 6 was highlighted by the tuesday project presentations. I had been pretty nervous since I had only recently started my individual project but overall I feel that things went well. As for working on my project I had a busy week running various PCR reactions trying to get primers to work. Early on I had trouble doing so and had begun to worry that the primers were no good but from reactions run thursday at a lower temperature of 48 degrees I was successfully able to amplify. I also ran a reaction with Amoa primers and will run a gel for those products on monday.

After returning on tuesday from the holiday weekend I have been busy just trying to catch up with my work. Since Tyler and I have begun branching off to work on our own individual projects I have spent most of the week working independently diluting solutions and running PCR reactions on various cDNA cruise samples using different gene primers. 

My fourth week interning at CMOP has really gone by fast. So far my time has been spent working on extracting DNA samples which I can proudly say was completed on tuesday afternoon. It was also really good to see that there were concentrations of DNA present in each which appeared after running an electrophoresis gel.

 This has been a busy yet very productive week. Monday was spent amplifying the pseudo-nitzschia PCR samples from last week using. On tuesday Tyler and I ran the samples on a gel. I also attended a lab meeting with Holly, Jon, Mariya, and Tyler where the project goals were discussed. Many of my questions in regard to the project itself were answered and it was relieving to hear that the direction of the final paper is still undetermined. I was just glad to hear that since the overall direction of the project was what I had been previously most confused about.

Being friday I see it as a good time to sit down and type out my blog for week two. Looking back it was an extremely busy week but I have to say that it went by really fast. Most of my time was spent in the lab doing running DNA extractions and PCR amplifications. I think I am also finally starting to understand the relevance of identifying bacteria and archaea in waterways. While this is good I have also learned a lot by making mistakes in the lab in regards to the DNA extraction due to my misunderstanding instructions.

With my first week of work at CMOP coming to an end I can honestly say I have been enjoying myself. Working with my mentor Jon Schnorr I have been able to complete two Polymerase Chain Reaction (PCR) amplifications of Archaea DNA samples collected from the Columbia River plume by Dr. Mariya Smit. I believe the goal of this project is to study the microorganisms of the Columbia River, its estuary, and plume using the PCR method of DNA analysis.