Week Three: More reading and Education on Tribal Relations

Another week gone.  I have no idea where this summer has gone!  This week I learned about my specific project and its place within the overarching CMOP research. 

My project is called "Nitrification Potential and Niche Diversification of Ammonia Oxidizing Archaea in Columbia River sediment."  In a nutshell, I will be quantifying levels of ammonia, nitrite, and nitrate as well as levels of archaea and look for a relationship between the two.  It is my understanding that we will be setting up microcosms and measuring the values at set time intervals over the course of the rest of the summer.  Obviously, CMOP is focused on the Columbia River/Pacific Ocean interface and there is a lot of research involving nutrient cycling.  This project ties directly in that line of research because ammonia oxidation is the first and rate limiting step of nitrification.  Until recently, ammonia oxidation was only thought to be done by beta and gamma proteobacteria, but archaea has been shown to contaim the amoA gene that codes for ammonia oxidation.  Because archaea are so ubiquitious in the environment, the extent of their contribution to the global nitrogen cycle is important and a thriving area of research.

This week has been fairly uneventful.  On Monday, the rest of the interns arrived and we set up our blogs and got to know each other a little bit.  On Tuesday, I wrote my blogs for the past two weeks and read more primarly literature articles on my topic, particularly looking at papers involving freshwater sediment.  Little research has been done on freshwater sediment so it was somewhat of a challenge finding relevant articles.

On Wednesday, all of the interns took a group photo (which I fogot we were taking that day.  Shoot), and then we went to the OHSU Primate Center for lab safety training.  Three of the other interns and myself then went out for Chipotle :)  Yum.  After that, I learned how to quantify DNA using flourescent dye and a different NANO-DROP instrument.  This type of quantification of DNA concentration is generally more accurate because it detects the DNA in question (double strand, single strand, etc) preferentially based on the specifications you set.  This is unlike the other NANO-DROP instrument we used which detects all DNA, RNA, and proteins in the sample.

Thursday I read more articles and learned about qPCR.  Quantitative PCR is really cool.  Basically, you start out with a teeny tiny bit of DNA in flourescent dye with primers, and amplify it.  Quantitative PCR is often called Real-timePCR because as the DNA is amplified, the flourescense is measured after each cycle, showing an exponential increase of DNA.  From here, you can calculate the amplification efficiency and the threshold cycle (the number of cycles it takes that particular DNA to reach the number of amplicons at the threshold).  Sorry if that was confusing...

And here we are: Friday. I've been reading more articles and we're getting ready to run another qPCR; this time with bacteria (yesterday we amplified archaeal DNA).  This morning, Elizabeth Furse came to talk to us about her work and experiences involving Native American Tribes.  It was very interesting and I realized how little I knew about Tribal relations with the different levels of government (state, federal, etc).  A part of her talk that really stuck with me was when she said how little Congress knew about bills that came to them.  This is surprising to me because I guess I just had never really thought about it.  You can't possibly know everything about every topic, and they look at thousands of bills each year.  It's just kind of a difficult situtation. 

Anyways, off to do PCR.  Happy Friday!