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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.

So lets get started.  On Monday, I prepped for qPCR of our archaeal amoA genes.  This is one of my favorite things to do in lab, but it can be a little stressful because you really can't mess up.  The instrument is so sensitive, that any mismeasurement is obvious.  I'm also having some trouble with getting air bubbles in my master mixes, so I have to centrifuge quite a bit to bring all the liquid back together.  Learning curve.  ;)  Mouzhong and I met with Dr. Simon this afternoon to discuss our preliminary results and we observed that in the inhibited conditions, we say reduced inhibition to our archaea than to our bacteria.  We would like to run another experiment using more conditions with varying levels of inhibitors to see if we can completely inhibit bacteria but not our archaea.  Then we can see if ammonia oxidation is happening.  If we see ammonia oxidation occuring when only archaea is active, we can see how active a player our archaea is in ammonia oxidation.  Pretty exciting stuff.

On Tuesday, I went up to Astoria with the other interns as well as a group of interns from Pacific University (yay!) and we were able to go to MERTS (Marine and Environmental Research and Training Station) where a team of four scientists monitor and maintain the instruments used in the Columbia River and off the coast.  They use a glider named Phoebe to measure data vertically.  It's pretty cool stuff.  Type Phoebe in the search bar above to check it out :)  After MERTS, we went to the Astoria Column and the Maritime Museum.  How cool was that?  We got a guided tour and a lot of the interns participated in hands on stuff like making rope.

Anyways, it was back to work on Wednesday where I did qPCR for our bacterial amoA. I did better today than Monday bubble wise at least.  We also autoclaved everything we'll need to take into the field tomorrow, and I prepped lysing tubes for RNA extraction.

Thursday we went back up to Cathlamet to collect our water and sediment.  Here's a picture of our sampling location:  As you can see, it's a little muddy.  When we got back to lab, we prepped a 10:1 innoculation of five conditions in duplicate looking at 3 different concentrations of inhibitor, a sitewater control, and a condition with added pyruvate as a source of carbon.  We collected our water and sediment samples for day 0.

On Friday, we extracted DNA and RNA from our day 0 sediment and check the nitrate/nitrite levels for days 0 and 1 water samples.