Blogs

Because of the Finals schedule at Oregon State University, two weeks worth of work was rolled into one.

On Monday, I started off the day with getting my OHSU ID as an intern for CMOP and meeting the new interns that just arrived. After getting my ID I went back to the lab and looked at slides of samples from Soda Bay on the microscope. As i was doing that i characterized each sample and noted it in my lab book. At three o' clock I attended a safety training along with all the ohter interns.
On Tuesday, I looked at more slides of samples from Soda Bay and characterizing them in my lab book.

This week I continued to do PCR of our target dsDNA.  Two of our genes had clear enough bands and were the right length to continue on with purification, and so I purified our PCR samples and determined the DNA concentration.

Because we are waiting on an order of new primers, I began RNA extraction of ocean water samples.  The first time I assisted in the extraction, and the next two times I performed the extraction on my own.  The next step with our RNA pellet is to completely purify by removing any DNA present with DNase.

This first week I had to juggle finals and working with the people here in Astoria. Fortunately I was able to work Tuesday, Thursday, and Friday.

 In this second week was an adaptation to the MATLAB Program to keep working and understanding the salinity and temperature changes in the estuary. I've also started reading some papers that will be helpful to my research. I will continue working hard to propose my goals in this project.

Thanks!

These week I learned how to do
16S and 18S PCR, as well as other kinds of PCR. I have done alot of Total Extractions and I am learning how to balance my time so that I can do the PCR, extracts and look at my water samples, which are preserved in Lugol, under a microscope within the same day.

 My first week in the CMOP program is off and running! Following Monday's orientation, Pete Kahn (my frontline mentor) and I immediately got to work on designing primers for targeting the 28s and non-transcribable region of rDNA of Katablepharis.

For past few days, I have gathered more data than this blog can hold.

Here are some interesting data that make this project of detecting nanoscale Zero Valent Iron seem promising.

1. Using Induced Polarization system, I introduced different amounts of nZVI (Fe cmc-BH) to aerobic and anaerobic system. Here are the resulting Phase Difference. (Phase Difference is defined as the phase difference between applied sinusoidal AC voltage and detected voltage.)

6-14-10
Using a 1% gel run for ~45mins at 110V, only the ladder was visible in imaging afterward. We speculate that this is because the nanodrop concentrations were so low that they cannot be visualized by this method. Therefore, we are using DNA purifcation followed by PCR to amplify the number of DNA products and thus allow them to be visualized to confirm their existence in these samples.
DNA purification: