Blogs

As the last intern to arrive, I managed to get here when Portland had decided to finally allow summer weather to appear. It seems a shame to have to spend the time indoors, but my project and the lab more than make up for the inconvenience. I'm helping with a project entitled "Assessment and Prediction of the Transformatoin Kinetics Determining the Environmental Fate of Contaminants of Concern." I'm looking at how long it takes for munition compounds to hydrolyze in an alkaline solution. I learned the process using TNT, but we're going to move onto DNAN now.

I have to admit right from the start that this was an eventful week. Monday through Wednesday consisted of the usual process of analyzing observation data from Cunningham Slough and comparing it to model data generated from Forecast-26. This week, however, the analysis process took a new turn. This week I used a script provided by Grant to generate virtual .mov files of temperature and elevation data. Could this be the production break I have always wanted? Just Kidding!!! They turned out really cool.

This past week was very busy.  I learned how to use a new piece of equipment called a FlowCAM.  It analyzes particles in water, such as algae, bacteria, and organic matter, and provides various metrics on each particle.  It can process tens of thousands of particles within a half an hour.  The part that excites me most about this equipment is that it takes a picture of each particle that it takes measurements on.  While the system is running you can see the particles in real time.  It was very interesting to watch the particles and try to identify some of them

So far during my internship all I have done is: read 10 articles discussing NZVI technology, attend a day full of lectures about recent CMOP projects, brave the scrutinous review of the NSF site vist team, stumble my way through using labview to autonomously collect data, conduct rheology experiments for 7 different fluids, redo rheology experiments, and redo rheology experiments. And I thought my summer would be full of excitement...

 This week has been mostly bug fixes. Charles attempted to use my annotation interface and would a few problems that I have been remedying. It appears that the test data that I was working with had different properties than some of the other data. This resulted in the interface sometimes failing to grab the deployment id. Without the deployment id the interface had no way to get previous comments on the data or make new comments.

What a busy week!  I spent most of my time this week working on my PCR and nitrate quantification technique but this week was also the NSF visit.  What a wonderful group of scientists to have around to pick their brains!

Monday: Finished up the background readings and feel like I have a good understanding of the study area and what we’re trying to accomplish. Discussed the project in more detail with Logan and Grant- what we hope to gain from each step, the planned scope of the project, and specifics about the dynamics of the model and study area we’re working with. I then took the plunge and began working with UNIX commands and Matlab- software in which I’m not quite familiar.

My second week at CMOP has largely been an interest-driven, rather than project-focused week. Because I am still patiently awaiting the Mt. Erebus metagenomic sequences to arrive, I have continued work on the hydrothermal vent data trying to learn more about the metabolic potential of microbes in deep-sea hydrothermal environments. I began my week searching through the literature to learn about the metabolic pathways involved in methane oxidation as well as the principal genes involved.