Week 1 Jumping right into my project!

My first week here at CMOP was very exciting and extremely productive. On Monday, I met all of the 2012 CMOP interns except for Julia. Vanessa gaves us an orientation and after we each got to meet our mentors. I'm working in the Zuber lab with Ben Li, and my project title is: Understanding Dinoflagellate population and diversity in the Columbia River Estuary.

I was not quite sure what to expect when I met Ben. I thought he was going to throw me a bunch of scientific papers to read at home. Instead, we started on my project right away. We started with transformation of E.Coli cells with ligated plasmid DNA with the PCR product insert; plated the transformed cells on the LB/Amp plates and prepared more agar plates for the lab. It was a long day...... but super productive.

The next few days Ben and I were like a super team (my opinion anyways). Ben and I were so productive, we did all sorts of experiments: DNA extraction from field samples, PCR amplification, gel electrophoresis, DNA gel extraction, ligation of plasmid with insert, transformation of E.coli cells with plasmid and plasmid isolation from E.coli cells.I work in a chemistry lab back at U of O and I also have taken biochemistry lab classes, so I'm very familiar working in a lab environment and have some level of biochemistry lab techniques. Not only did I improve my lab techniques for certain experiments, I also learnt so much new techniques. We basically covered all kinds of experiments and techniques I will be performing for my project, so I will be ready to work on my project independently. I will also be meeting with my principal investigator Dr. Peter Zuber soon, so I'm excited to find out what samples he has in mind for me to analyze.

The Zuber lab's goal is to characterize the infleunce of M.Rubra blooms on the higer trophic level of the Columbia river ecosystem. My specific project is to charaterize dinoflagellate population and diveristy associated with the M.Rubra blooms. I found out that M.Rubra is a cilliate when they bloom in the late summer, they perform high rates of photosynthesis, changing the community structure from hetetrophic to autotrophic (COOL). However, M.Rubra is prey to toxic dinoflagellates called dinophysis. If M.Rubra blooms to create large amounts of red waters every summer, wouldn't these toxic dinophysis bloom too since they will be provided with large amounts of "food"? How would these dinoflagellates community structure change with M.Rubra blooms this summer? Will I be able to find a difference in dinoflagellates species and population before M.Rubra bloom, during bloom and after bloom? During the next 10 weeks, I will be trying to figure this out. In order to do this, I will need to analyze all sorts of water samples, extract specifically dinoflagellate 18s rDNA and sequence these DNAs. Different types of dinoflagellates have slightly  different types of 18s rDNA. By doing this, I will be able to obtain a library of different 18s rDNA that belongs to different types of dinoflagellate, to analyze the community structure and diversity.