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Orientation to CMOP and PCR (Week One)

I started at CMOP on the 4th of June with Logan, Marc, and Connor.  We met with Vanessa Green and learned the ins and outs of the CMOP facility, current research at the center, and got to meet our mentors.  I'm working with Mouzhong Xu, a 5th year Ph.D. student here at CMOP working with Holly Simon. 

For the rest of Monday and Tuesday, I read research articles and worked on understanding my project.  My favorite article to date is Bacteria rather than Archaea dominate microbial ammonia oxidation in agricultural soil by Zhongjun Jia and Ralf Conrad.  In this paper, the authors concisely show that even though archaea is more abundant in agricultural soil, bacteria does the majority of ammonia oxidation.  For my project, I will be looking at Nitrification Potential and Niche Diversification of Ammonia Oxidizing Archaea in Columbia River sediments.  This is an area of interest because few studies to date have been done involving freshwater sediments.  Ammonia oxidation is the first, and rate limiting step in nitrification and is the conversion (oxidation) of ammonia to nitrite.  Nitrite is then oxidized to nitrate in the second step of nitrification.  Ammonia oxidation is a very important process because of the high anthropogenic input of ammonia into the environment.  Previously, ammonia was only thought to be oxidized by beta and gamma proteobacteria.  These proteobacteria also participate in the denitrification process, resulting in the production of nitrous oxide, a potent greenhouse gas.  Studies to date suggest that archaea don't follow this same pathway, and thus do not produce nitrous oxide.  Due to the ubiquity of archaea in the environment, the effectiveness and level of ammonia oxidation is highly studied.

On Wednesday, Thursday, and Friday, I learned the basics of PCR, the general PCR procedure, DNA purification procedure, and the procedure for gel electrophoresis.  PCR allows us to amplify DNA extracted from our sediment samples, which can then be sequenced and characterized.  DNA purification allows us to ensure that only the DNA we're looking for is present in our samples.  After we purify the DNA, we can quantify the levels using the Nano-Drop 2000.  This measures the absorbance of the sample (and we are able to determine whether the sample is DNA, RNA, or protein based on the absorbance) and the concentration of the sample.  Pretty cool stuff.  Finally, electrophoresis allows us to check the purity of our DNA by looking for any smearing of the bands. 

As an environmental chemistry major, most of these procedures are out of my area of expertise.  But I am excited to be working in this type of lab where I am able to build a strong foundation of applicable skills and participate in something I may not have otherwise had the opportunity to be involved with.