Blogs

This week I was at SHARP and helped in the optimization of the impedance sensors.  Due to inconsistent data, different measures are being taken to figure out the problem.  We first began running the sensors at different frequency settings, and are now changing the concentrations of buffer and DNA targets, as well as different temperature controls.  This optimization usually is done using short oligonucleotide strands, but some of the chips were run with ds DNA targets I created here at CMOP. 

This week was mostly tying up loose ends of the code.  I wrote the measurement placement subroutine and added it to the main program, and tested it using full runs of data.  Those runs are about 200 files each, so they took a while to process. 

I just got back from China this week and have started working on the changes I need to make to my webpages for the Astoria field team scientists. This week I made another Image Entry Page which displays only stack plots and allows the user to view graphs of any stations' data in a 2, 7, or 15 day period, a very useful feature that was requested.

These last two weeks have been incredibly busy. Last Tuesday a group of interns and myself went on a one day reasearch cruise with the oceanography camp to learn how to take water samples. Not only did we learn that, we also learned why bananas are not allowed on a boat (they attract monkeys). Thursday we continued with this project by extracting DNA and putting in a gel to set. We were supposed to see the results on Friday, but that never happened. The rest of the week I worked on a summary of everything we had done so far for Antonio, as well as researching tides.

A lot has happened since I last blogged. First off, last week I was able to go with the oceanography camp on a one-day research cruise in the estuary. The cruise was a lot of fun. I learned a lot about lab work aboard a boat and some basic boat terminology. On Thursday after the boat cruise, I was able to extract the DNA from my water sample. After working in the lab for three hours, I was able to insert the DNA into the gel where it would set. I never did see the result of the DNA but it was a great experience to work in the lab.

This week I continued to research my topic, in order to have a strong background. I want to be able to make a real difference for the Quinault Indian Nation, so I need to know the topic extremely well. I have learned what criteria is used by the Department of Health (DOH) to determine whether a commercial shellfish growing area is approved, conditionally approved, restricted, or prohibited.  DOH has taken samples, and they know that there is contamination present.

Now that the sun has come out it tends to be a little more difficult to stay in the lab for 8 hours a day, but I've been persevering and making the most of it! I have plenty of data to show for it too.

This past week I spent two days at SLA doing quality control of the biosensors by either running oligonucleotides or double-stranded DNA targets and testing variable frequency settings.

At CMOP I made more double-stranded DNA targets and purified the PCR products.  I purified my RNA extractions, and I started the process of making single-stranded DNA targets...but have yet to purify them.

The week ended with a great trip to Bonneville Dam and a hike up Multnomah Falls which was awesome. :)

-Vena

Hello again!  I have learned a lot this week and I feel like my research is really getting underway here at CMOP.

6/28/10: I ran a PCR and gel by myself for the first time and obtained accurate results.  Afterwards, Dr. Herfort told me I will be learning how to clone samples sometime next week.  In light of this, she had me label petri dishes and pour agar into them with Sheedra.  Once we finished we went over what I would be doing the next day and starting packing supplies for the Oceanography Camp boating trip.