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Week Ten: The end of one chapter, the beginning of another

Like all good things, this too must end.  Today is my final day here at CMOP, and I'm grateful for the knowledge I've gained here, the experiences I will leave with, and the connections I've made.  There is T-minus 80 minutes until my final presentation, maybe one final qPCR to run, and goodbyes to be had.  My experience here was filled with self exploration, and I'm leaving with a stronger sense of self and more confidence in my interests and desires for my future.  Anyways, enough personal reflection; here's what I did this week.

Week Nine: Wrapping up experiments and prepping for final week

This week was super busy!  We've been trying to wrap up the experiment from a couple weeks ago and I've been working on my final presentation for next Friday.  Although I am sad that this adventure is almost over, I can't wait to see what doors it has helped me open for the future!

Monday:  I purified the RNA from last week.  Because we had 20 samples, it took quite some time.

Week Eight: The Calm Before the Storm

This week was, for the most part, pretty uneventful.  We started a new experiment last week, so most of the beginning of this week just involved testing nitrate/nitrite concentrations each day.

On Thursday, we collected our day 7 sediment and extracted DNA.  We also tested the day 7 nitrate/nitrite levels.

Week Seven Already??

Alrighty, this was yet another busy week with lots of traveling.  We were able to go up to Astoria to gain a better understanding of SATURN and the instruments involved in monitoring the estuary.  I also went back out into the field to collect more sediment samples to run some more tests on our archaea and bacteria.

Week Six: Midterms, hiking, and extractions, oh my!

What a busy week.  We're almost done working directly with our samples, and will be doing lots of data analysis in the upcoming weeks.

On Monday, we worked on purifying our day 0 RNA.  The RNA extraction procedure doesn't distinguish between RNA and DNA and so we need to remove the DNA contamination from our RNA samples. 

Week Five: Take 2.

Something weird happened just now.  I had almost completely finished my blog entry for this week and it was suddenly gone!  So that's frustrating, but I'll try again.  This week was one of the busiest for me thus far.  Lots of driving and lots of pipetting.

On Monday we prepared the freshwater medium that we will be using for some of our samples and autoclaved the glassware we will use to house our samples and the plastic collections flasks we will use in the field tomorrow.

Week Four: NSF visit and technique improvement

What a busy week!  I spent most of my time this week working on my PCR and nitrate quantification technique but this week was also the NSF visit.  What a wonderful group of scientists to have around to pick their brains!

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.

More reading and the start of lab independence (Week 2)

This week started out a little slow.  My mentor is off to present at a conference Monday and Tuesday, so she's been pretty busy preparing for that, not to mention the entire CMOP facility preparing for the arrival of NSF at the end of this month.

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. 

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