Blogs

This week was my catchup week, as I have been in Honduras for the past 14 days. It was a great trip, but I am glad to come home to the nice wet Oregon weather. Down in Honduras I was doing mission work on a small island in the Caribbean. To my surprise I didn't miss my email or phone too much, but I really like being able to hear the news here and know what is going on in the world.

7-6
The idea is to purify the plasmid that was inserted into competent Ecoli cells. We know they took up the plasmid because WT ecoli are not kan resistant, but all of the harvested bacteria was grown on LBKan plates. Competent Ecoli was plated to verify the plasmid was taken up.
Protocol for Plasmid DNA Purification:
1. Resuspend pelleted bacteria cells in 250µl Buffer P1 and transfer to a microcentrifuge tube
2. Add 250µl Buffer P2 and mix thoroughly by inverting the tube 4-6 times

I completed the lacZ assay and was able to make a few graphs on excel.  The result is closer to what it is suppose to be.  This week into the next week i will be focusing on purifing my nasD fragment and ligate it into the pTK-lac vector.  I am hoping that this procedure works better than my experience with the other experiments. So far, i have been learning how to make PCR reactions, operate the PCR machine and running my product on agarose and low-melting gels. 

I can't believe this summer is going by so fast already.  4 weeks into it and we're almost half way done with the internship!

This week I was working by myself most of the time because Suzanne was out of town.  It was exciting that I had learned all these new skills and how to use the equipment and now I could go and use all I had learned by myself in the lab.  I extracted the DNA from the rest of the samples we took in Astoria but ran into some trouble and will have to redo one of the exptractions next week.  This week I also did alot of research on my project so that I will be prepared for my practice presentations on July 14th.  This will be a good way for me to practice presenting my projec

     This week has gone by surprisingly fast. We’ve been doing a whole bunch of dives at the stations. All of them this week were to retrieve the seabed CT from a station and replace it with one that was clean and in good working order. We didn’t dive on Monday, but we did go to Pt. Adams (SATURN 03) to clean the pump and thermistor and replace the antenna. On Tuesday we had an early dive at the Sand Island Light station.

     I have been familiarizing myself with the CMOP website, specifically the data observations section.  My goal this summer is create activities and curriculum which will use the CMOP knowledge and research as its learning target.  I will be the "vehicle" for transporting CMOP's research to students.  Initially when Antonio said he wanted me to be the "vehicle"  I nodded my head and thought to myself "ok, sounds good I can get started right away" and at the time didn't think very much of it.  As the week progressed

This week has been much more productive than the last few.  I've added a picture to help illustrate what I did to the plasmid that was giving me so much trouble (pDH32).  After that, I was able to successfully ligate all three of my fragments of interest into another plasmid, pDG793.  The three fragments I've been working with are all segments of the B. anthracis narG (narG is part of the narGHIJ operon, which encodes a nitrate reductase) promoter region. 

For my second week of work we have been working a lot with the CMOP website. I have been learning how to plot graphs and use the simulations. This stuff is really confusing but with a lot of help I am getting it. Monica and I have been teamed up to do research and create models of Flourecence and salinity. I hope I keep learning new things (:

After writing the essays about CMOP, gliders, wind-driven circulation, and hypoxia, we are now starting our real project. Since there are four of us, Antonio divided us into groups of two. I am working with Maria and our job is to see how salinity and fluorescence are distributed, their processes, how they change over time and other things like that, in the Columbia River estuary and the plume. Right now we are exploring the CMOP website and playing around with the model tools and generating cool-looking graphs that will later be helpful with our project.