Blogs

 On Monday, Greta and I cleaned SATURN 03. The fishing company there is currently dumping fish waste in to the water. The waste often finds its way into our pumps and clogs them. Fortunately, that didn't happen on Monday and all Greta and I had to do was clean the bottom pump and the valves.
  On Tuesday and Wednesday, Greta and I helped with the Oceanography Camp. Some campers and high school interns came to Ilwaco, Washington where we boarded the Sea Breeze and departed for the Columbia. It was a lot of fun, and I'll talk more about next Friday.

This week mostly consisted of figuring out how to write the most difficult part of the code.  The problem sounds relatively straightforward.  Find the flat areas of each time series plot to get base, sample and calibration measurements.  Use MATLAB algorithms to find these more consistently and faster than a human. 

 In the fourth week I could make some plots of different flow meter currently under investigation. I also run an interpolation to see the changes that are in between the two flow meters and then create a histogram to make me see things more simple and reaching my conclusions. Enjoying and learning this weak, reading a lot to illustrate my mind. Waiting for the fifth week, I want get to keep learning new things and reach more interesting conclusions of this research.

On the other hand, I passed today a great experience at Bonneville Dan Tour. Amazing experience! 

This week I tried cloning from purified samples to search for cryptophytes. I am still currently learning the porcess and hoping to obtain results next from my plated samples by growing them in broth in order to later sequence them. I also did more extractions looked at more microscope slides of settled water samples of which no M. rubra was found. Friday we took a trip to the hatchery and saw big Sturgeon, and I attempted to hike a mile up mountain to see the waterfall. I am tired.

 This week started off with multiple DNA extractions from various locations off the north channel cruise. I ran PCR with those samples along with positive control samples that definitely contained Katablepharis sp. I used the 28s primers Pete Kahn and I designed the previous week. Following the PCR a run on the gel showed that the positive control samples showed 28s amplification. Next week we will continue to perform a cloning and transformation process so that we ultimately can begin to get some sequences for the 28s region!

     On Monday, I had my first experience with the method I'll be working with this summer aimed at capturing manganese oxidizers from ETM samples with specific peptide binding. One sample uses a specific peptide that someone else found to bind to manganese oxides, another sample is a random mix of peptides as a control for nonspecific binding, and a third sample is just water as further control. This time, peptide capture 6 (PC6), we experimented with the synthetic manganese oxides that we made last week.

This week I started what will be a long, and hopefully prosperous, relationship with the solar simulator. It’s the power of the sun, at the flip of a switch. It also risks a sunburn, so I wear glasses, a face shield, gloves, and long sleeves whenever I use it. Because titanium dioxide is a photocatalyst, I will be using the simulator a lot this summer to test out my surface modifications.

This week I have been working on getting the samples from the LP-6, the NH-10 and the CR-20 to amplifiy using a general bacterial primer. Suzanne and I got the cleaned SIP samples to amplify and then went on to PCR cleaning.  We introduced the vector into our samples and cloned them so we could send them over to the primate center for sequencing.

This week I have continued to translate the classroom activities that Grant gave me.I have completed the two about hypoxia and density. Now I am almost done with the activity about adequate marine habitats for organisms.