Blogs

This week Lydie was absent, so I performed DNA extractions tediously on soil samples collected by Kiley Seitz for the majority of the time.  However, Wednesday our normal routine was upturned as we took a trip to the coast to various sites in order to collect new soil and water samples for analysis.  As much as I was excited to get out of the lab for a bit and get some field experience, waking up at 2:45 in the morning was not ideal.  However, at 3:30 Wednesday morning, Lydie, Kylie, Kylie's intern Isla, and I were off to the coast.

After copious amounts of DNA extractions the first week of work I was ready to start some new projects.  This week I spent a few days running gels, which ended up not yielding the best images; the resulting bands were extremely faint if apparent at all in many of the runs due to the extremely low concentrations of DNA in the collected water samples.  However, we were able to identify a correlation between the quality of the images (whether there were bands present) and the quality of the filter from which the sample was collected.

Hi, my name is Paul Pan, and I am an undergraduate intern at CMOP for this summer. I will be working with Jesse Lopez in Dr. António Baptista’s group to develop a new web interface to create model products usable by non-specialists. Specifically, I will be creating the backend and frontend of an interface where users can upload their own data and generate different types of plots. Currently, this functionality is not possible with the data explorer on the CMOP web page.

My name is Maddie Hibshman, and I am working in the Simon lab under the mentorship of Lydie Herfort.  This summer I will be examining the microbial dynamics in the Columbia River Estuary by an autonomous adaptive sampling approach.  Lydie quickly got me acclimated to the work place and gave me an abundance of literature to read up on to obtain a more detailed understanding of my project for the summer.

With Dimin and almost everybody else in my lab group gone at a conference, I envied the neighboring lab group, who seemed to be busily experimenting away. Usually interns come in, spend most of the first week reading journal articles and background research, and then excitingly get to carry out their first experiments the second week. Counterintuitively, I worked on experiments the first week, and now got to read for much of the second. Furthermore, I waited for new filters to come in, so couldn’t even carry out basic tests that I planned on executing.

My first day here at CMOP was Monday, June 16^th. After a whirlwind tour of OHSU campus and a quick introduction to the other summer interns, I met my lab group. Our PI, Paul Tratnyek, explained the project to me; then my mentor, Dimin, showed me around the lab. Before I knew it, I was preparing a solution of Indigo Disulfonate to start testing! For my project, Redox Probes to Characterize Environmental Processes, I will work alongside Dimin to test probes that mimic real-life redox reactions.

This Monday we started two more PCR reactions.  Hiroaki did one of them to remind me of the steps, and I did the other.  The new primer that we needed came in over the weekend, so the first step was to prepare the primer with autoclaved water.  Then we diluted a portion of the primer to a walking solution and used that to prepare the PCR solution.  PCR takes around two and a half hours, so after we started the reaction we took a lunch break.  In the afternoon, we started the second PCR reaction which will run overnight.  Then Hiroaki showed me how to inoculate

This week, my mentor, primary investigator, and just about every other researcher in my lab was gone at a conference. This means that I have been mostly unable to perform any experiments, as nobody is around to help with troubleshooting the HPLC or to ensure we interns do not blow anything up. Instead of running additional experiments to attempt to explain our results from last week, I have been reading up on the literature and ensuring that I have a firm grasp of the theory behind our project.

I am an undergraduate intern at OHSU’s Institute of Environmental Health (IEH).  This summer I will be working with Hiroaki Naka in Margo Haygood’s lab.

I am John Koberstein, an undergraduate intern with CMOP, and will be studying the distribution and abundance of Cercozoan species in the Columbia River Estuary. This being the first week of the internship I have had to do a bit of learning. I am working under Dr. Peter Zuber and a research technician Ian Vorhees. To get acquainted with theories regarding microbial biogeography and dispersal Dr. Zuber has given me some reading to do from the current scientific literature.