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Week 7 Last 5 years of M. rubrum samples & a boat trip on the CRE

This week started out pretty tough. L. I’ve done a lot of PCR reactions already but the past few reactions I’ve done don’t seem to work or make sense. My negative control reaction always seems like it is contaminated, and my results is not what I expected either. I still can’t make the conclusion if my reagents are contaminated or somehow every PCR reaction I will mess something up. This week, I started on amplifying post bloom water samples from 10/27/2011 from the main channel and the Iwaco Harbor. Even though I already amplified post bloom water samples from 9/21/2011, since these samples are collected 1 week after the M.Rubra bloom, there might be a high chance that this “post bloom” sample might still be “bloom”. In order to make sure that the water samples are strictly “post bloom”, we decided to amplify samples that are 1 month after the bloom formation. This PCR reaction took me 3 times to work along with Ben’s help.

I also dug out some samples from the -80 degree fridge and found 2009 red water Sterivex filters. Unfortunately, the lab was out of 2007, 2008 and 2010 red water Sterivex filters. It would be great if we could do DNA sequence analysis on these consecutive year’s water samples, but since we are missing all of these filters, it is very hard to make any conclusion with the current red water samples 2009 and 2011. I extracted the DNA from 2009 red water filters anyways. The DNA concentrations showed of the extracted DNA were acceptable, however since the original samples themselves were very dirty and contaminated, the extracted DNA also was not in good quality and not pure.

Michael helped me find some of the 2007, 2008, 2009 and 2010 extracted DNA samples, and we found some very ancient samples in our freezer. Now, I have 2007, 2008 and 2010 extracted DNA samples (not fresh extracted DNA), and 2009 and 2011 sterviex filters (that I can extract fresh DNA). Since I have collected 5 years of DNA samples, I can amplify the DNA samples by using dinoflagellate 18S primers to check if any dinoflagellate DNAs are present. The first PCR run was unsuccessful, the negative control showed a bright band indicating contamination from some unknown source. 2007 and 2008 and 2010 samples didn’t show any bands, which is also not supposed to happen because 2010 red water samples were proved earlier to contain dinoflagellate DNA. Due to the constant erroneous PCR results, Ben had to re-do my PCR reaction. XX

We were also able to visit the OHSU main campus near the water front and on top of the hill. It was a very great trip. Our first stop, we stopped at the water front OHSU at the department of biomedical engineering. There, a postdoc Kevin showed us his optics related research at the McCarthy lab. He has been a post doc for 5 years and planning to move on to a faculty position in Portland. We then got a chance to take the OHSU tram to the main campus, where we met Aaron (who was doing cancer biology research) and Alison (who was doing behavioral biology and neuroscience). We also met the graduate program director Rick, who was super helpful the entire tour. It was very interesting to learn more about different kinds of research that relate to the biomedical field, such as Kevin’s physics related optics research in a biology lab that study’s blood cells and platelets, Aaron’s biochemistry related research that study’s that formation and growth of tongue cancer, and Alison’s behavioral biology research that study’s alcoholism with a focus on addiction. We discussed the best ways to approach a principal investigator prior to applying to a graduate school, what criteria/aspects do graduate programs look in their applicants (GRE/GPA/Research experience), what are the graduate student’s goals after they graduate, how to look good at an interview (know about the graduate school’s research you wish to apply), and try to join a lab that publishes many papers etc. The information I got from the graduate students were priceless. You don’t get to talk to very experienced graduate students often and also it is extremely hard to ask for their advice when you actually need them (such as applying to graduate school). If I were to apply to graduate school without even knowing the advice they shared with us, I wouldn’t know where to start and I would be thinking to myself “it would be nice to be able to talk to a graduate student now”…..

On Friday, Ben and I went on a cruise to collect more water samples from the ocean, instead of water samples from the shore. We are “volunteering” and hopping on the NOAA (National Oceanographic Atmospheric Administration) research team for their crab research. Our Captain was Brian and Curtis was the federal NOAA scientist. I got to see how the CTD works on a sampling cruise, which is you put down the CTD machine into the water and lift it back up, apparently that is how it takes data, very simple. Ben and I successfully collected water samples from every station and were able to preserve the samples with paraformaldehyde and lugols solution right away. No one got sea sick and the best part was that I got to take a crab back home for dinner