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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.

On Tuesday, we went up to Cathlamet on the Washington side of the Columbia River.  We collected about 2 liters of sitewater, surface sediment, and subsurface sediment.  When we returned to lab, we homogenized the surface and subsurface sediment and put about 200g of sediment into each flask in 5 different conditions in duplicate:  freshwater medium, sitewater, sitewater + antibiotics, sitewater + ammonia oxidizing inhibitor low concentration, sitewater + ammonia oxidizing inhibitor high concentration.  We tested the pH of the sitewater, and adjusted the pH of the freshwater medium so that they were equal.  We then collected two sediment samples from each flask to use for DNA and RNA extraction.  DNA and RNA will be extracted from day 0 (today), and the last day of the experiment so we can compare the levels of active archaea.  We also will collect about 0.7 ml of water at the same time each day to test for the the levels of nitrogenous species.  On Tuesday night I drove to my hometown, about 40 min south of Eugene, OR to spend time with my family on the Fourth of July.

On Thursday morning I drove back up to work and we did the DNA extraction for Tuesday's soil, and also ran the colorimetic nitrate/nitrite analysis for the water samples from Day 0 and Day 1.  It doesn't sound like much, but it took a long, long time to pipette all those samples into the wells.  We then extracted water for day 2.

On Friday Veronika Megler led a brown bag seminar discussing her unique career trajectory.  It was interesting to think about the places you'll end up several years down the road, and even more interesting to think that you can plan out all you want, but life never quite goes as planned.  It's definitely a good thing to keep in the back of your mind.  Today we ran some more nitrate/nitrite analysis and began RNA extraction for our day 0 samples.