Blogs

I started doing lab work on Wednesday. I am surprised by the amount of independent work I am doing already! My PI has the following policy: if there is a simple document explaining the step-by-step process, she will show me the document and I should do the work on my own. If the work is more complicated, she or her research assistant Wren will show me once and then watch me as I do it to make sure I’m alright. Afterwards, I am on my own. Thanks to this policy, I have done approximately 2/3 of the week’s lab work independently (with minimal to no supervision).

This week has been intense! Since I was introduced to many new things, I have a lot to write about. I promise not all of my blogs will be this long.

In my third week, I continued developing my proficiency in the lab. This week I focused less on the sediment coring and more on molecular techniques that will allow me to quantitatively analyze our sediment samples. I got very comfortable with extracting DNA from sediment samples, as well as analyzing its concentration using the NanoDrop, making series dilutions and updating the Simon lab Excel sample sheet we use to keep everyone up to date on our sample processing.

During this second week I got the opportunity to run the tests on my own that I learned how to do last week with my mentor. It was a good reminder of the importance of keeping a detailed lab notebook, as I had to refer back to it a lot to get all the details of how to make the solutions correctly. That took two days, and after that I started making solutions of manganese ligands. I did this by first making solutions of sodium ligands, such as sodium oxalate, and then adding a solution of manganese pyrophosphate, which would then bind to the oxalate ligand.

In my second week in lab, I began to perform some of the procedures by myself, rather than shadowing Kiley or doing htem with her assistance, as I did in my first week. My first challenge was gaining confidence with sediment coring, which is crucial to my project. Sediment coring isn't a formal lab procedure, but is rather a method Kiley has developed during her time at CMOP to help with her project. Sediment samples are taken in 50ml tubes from strategic sites out on the coast, near Astoria, where the P. antipodarum are known to exist.

My name is Isla McKerrow and I am an undergraduate intern with the Institute of Environmental Health at OHSU. This summer, I am working in Dr. Holly Simon's lab, under the mentorship of graduate student Kiley Seitz. My project is entitled "The Potential Effects of the Invasive Gastropod Potamopyrgus antipodarum on the Columbia River Estuary." The invasive New Zealand mud snail, P. antipodarum, has been an invasive species in the waterways of the western United States for years.

My name is Cruz Orozco an undergraduate summer intern at CMOP. Together, with my mentor Charles Seaton, I will be working with the data explorer, which is used to plot data such as: salinity, temperature, oxygen, etc. from the Columbia River. There are many stations across the Columbia River along with instruments, which are collecting data on a daily basis at different depths.

For the third week we begin testing for the base data of the gas manifold system. I learned that using the chemostat can work in two different ways when regulating the pH of the system. One way is using a specified CO₂ gas mixture through a gas manifold. This specified gas mixture creates turbulence in the culture and would be harmful to the dinoflagellate culture. That is the main reason why a liquid manifold of acid and base mixtures will be used. However, the project has once again come across problems.

This week I continued to photograph chironomids to prove that they were diatom free on the outside. Claudia, my frontline mentor, was out of town, so I was working indenpendently to get the pictures done, sort through more samples, and also prepare for a DNA extraction. Once again, because Chironomids are a new area of study for this lab, I needed to look through the literature to determine the best way to get DNA from a whole chironomid and how to ensure that diatoms in their guts would also have their DNA extracted.

            This week, I jumped into the project by beginning to sort through samples from the Columbia River for Chironomids. It took a day to get comfortable with sorting through all the detritus and other zooplankton to find the Chironomids, but I am now pretty good at finding Chironomids. The number of Chironomids found at each site varied a great deal. In the May Welch Island sample, I found 11 Chironomids. In the May Campbell Slough sample, I found about 30.