Blogs

Ok so I am a little behind as I spent ten days on a research cruise in th CRE. Gathering data can be exciting and time consuming work. when the data was good there were a few sleepless nights for some people. I was amazed to learn how everyones intrests in the data evolved. Methods were discussed on the spot, if something wasnt working the way it was intended then great minds came together and tried to figure out why, perhaps it was test protocol that needed changeing , or air bubbles contaminating the expected results.

On Monday I ran the 98 hour samples from the leap tank sediments on the HPLC and prepped the TNT samples for Hayley to analyze. I also made a new 2-CAP stock solution since I was running out of the one I made earlier. This new stock is much more concentrated, about 5 times more, so it should last a bit longer. Dr. Tratnyek received some graphene samples from a professor at PSU that are supposed to be excellent catalysts, so I prepped for the 2-CAP and TNT tests we would run on them.

I started this week by running my last time-point from last week’s experiment which was growing P. putida with and without light in minimal medium A with 100uM manganese and 0.37 uM  iron. Then Matt and I wanted to look at the differences on filtered and unfiltered medium with P. putida. We believe that if the P. putida produced catalase in the medium, we would see the concentration of hydrogen peroxide decrease over time on the time scale we set up: 14, 8, 4, 2, 1, 0 minutes. However, it did not came out as we expected.

This blog entry is late again because I came down with a stomach flu on Friday. Unfortunately I was bedridden all weekend and forgot to update my blog.

I can't believe that we have already passed week seven! Just a few more weeks and I will be back at Lewis & Clark starting my junior year. This week I started running experiments with 2,4-dinitroanisole, or DNAN for short. DNAN is currently being used as an explosive compound in ammunitions production, and so it is of high interest in this project. We expected DNAN to have a slightly faster half life than that of DNT, but slower than TNT, and that turned out to be true, so it was easy to get 3-4 different reaction vials going in one day.

Week7 (Jul 22 – July 26, 2013):

This week we went back to Astoria to collect more samples. This time we got them from ten of our sampling sights and for two of the sites we took a sample from the top layer and the bottom layer from two sites.  We also prepared the ESP for deployment on Wednesday and took it out to Sat 3 to set it up.

Here is a map showing hypoxia on the Washington coast during July 2013. Data is based on the minimum oxygen value seen by the glider over a 4 hour period.

The Carbon Source Experiment I started last week (many identical cultures growing and plating dilutions every couple of days) involves a lot of repetition repetition repetition. I start the day with counting colonies on the dilution plates from the other day and calculate colony forming units (CFU) per mL. Then I make all of the same dilutions as I did before, but with a different set of cultures (that have had more time to grow), and I plate two dilutions for each.

Most of this week was spent working with primers. Firstly, I had to optimize the new primer sets. I used the qPCR machine, so that I could do the samples at different temperatures all at one time. This was the biggest PCR I'd ever done: 44 tubes. I can't imagine filling up an entire 96-well plate. After that, I ran all of the PCR results on gels. The results weren't as clear as I had hoped.