Blogs

On Monday Lydie and I went to Astoria in order to run maintenance on the ESP.  The amount of water being flushed through the syringe during the last deployment of the ESP did not match the volume that Lydie had expected to be flushed. This suggested that there could be a problem with the syringe but upon examining the ESP we found that the real problem was that the bag filled the flush solution had a kink in the line that prevent the liquid from flowing to the syringe. By simply moving the bag to a higher point on the ESP we were able to rectify the problem. 

Rather than running the soil samples in the HPLC, I had to start by making stock solutions of 2-CAP, acetophenone (AP), and 2-CPE. This took a bit of time and Dimin was still making sure that the HPLC was working correctly. After I made the stock solutions I made standards of each that were 0, 25, 50, 75, 100, and 150 micromolar concentrations. I ran those through the HPLC to make a standard curve for each compound. Dimin and I started out gathering data with the HPLC set to a wavelenth of 247 nanometers.

Monday: Finalizing with Charles that we will use Pyevolve for our Python environment. I’m looking forward to using and learning Python because it’s a very powerful language. It’s nice to know that it’s object oriented like Java and C++, since those are my first two languages I’ve been learning.

I have been practicing on building calibrations curves. This is important because the curve is used to calculate the concentration of tested samples. I have no problem with the leucoberbelin blue calibration curve which is used to calculate the concentration of KMnO4. So far the results were all very similar. On the other hand, the hydrogen peroxide (H₂O₂) calibration curve varied in every trial. A lot of noise came out while reading from the spectrophotometer with H₂O₂.

This week was very exciting, because I started studying the Antartica bacteria. I also learned a lot more about the context for my project and projects that other people in Tebo's lab are working on. It was interesting to learn about the diverse work that everyone in the lab is doing and yet it all ties together.

Wow, I can't believe another week has already gone by! On Monday I checked up on the bacteria I was growing on plates and in liquid, with various mutations, to observe the role of certain genes in manganese oxidation. The plates provided me with a much clearer conclusion than the liquid, because hardly any of the tubes showed Mn oxidation in liquid. We also continued with the conjugation experiment. Unfortunately it did not go exactly how we had planned.

This summer I am joining Tawnya Peterson’s lab where I will be mentored by Michelle Maier.  We will be culturing rotifers in the lab and observing how well they do when consuming phytoplankton, which are infected by chytrid fungus.  Rotifers live in the estuary of the Columbia River and where they are an available food source for juvenile salmon.  The chytrids attach to the phytoplankton and deplete nutrients from the phytoplankton cell.  When the rotifers can eat the phytoplankton, they eat the chytrids as well as the zoospores they produce.    We s

Like most lab work done in the Zuber lab, PCR (polymerase chain reaction, a way to amplify a select segment of DNA) was front and center, meaning so was headaches.  While PCR is a wonderful tool and has certainly come a long way from water baths upon water baths, it's still very finicky.

I started setting up experiments this week and it was quite the experience. The background on this project that Dimin (my Ph.D student mentor) and I are working on is that an air base nearby is looking for the best method of remediation for the contaminated soil at the base. They sent several bags of samples of different kinds of contaminated soil. For this experiment I had to fill 16 glass bottles with 200 grams of one soil sample each and another 16 bottles with 200 grams of a different soil sample.

Completion of week two has been even more extensive lit review in preparation for the weeks ahead. I am learning lots of stuff here. I have been exploring the SATURN observation network and virtual Columbia River to gain knowledge about computer modeling development and calibration. I have learned that there is alot of work in examination and comparison of both observational data and the simulation data to improve and ensure the accurasy and usability of computer modeling in science.