Blogs

Hello there! My name is Logan Smesrud, and I am an environmental engineering student at Oregon State University. I am a summer intern at CMOP through the Johnson Fellowship program, organized through my university. The Johnsons are alums of my engineering department and started this program specifically for chemical, biological, and environmental engineering students who have just finished their first year. Their mission is to give young undergraduates a taste of research and real work experience at the beginning of our undergraduate career.

The first week was just full of so much information and I was fortunate enough to start from day one. My mentor showed me how things work in the lab and on the first day I learned how to do cell counts, and culture transfers as well as helping her record data for her current experiment. On tuesday I was taught how to make media and acid washes, the rest of the week I took time to read papers that would help me gain a better understanding of my project. The second week was prety much dedicated to cell counts.

This week, most of my time was spent on practicing with hydrogen peroxide – A-red assay, a couple of Leucoberbelin Blue (LBB) assay to build calibration curves I also worked with Kati Geszvain and Christine Romero. They let me work a little bit with bacteria, such as streaking plates, inoculating bacteria from plates to liquid media, sterilize media and pipette tips in the steam sterilizer and oven.  As I said last week there were some complications in this protocol procedure. My mentor, Matthew Jones, and I had been working on clarifying out the procedure.

This week I tackled qPCR, starting with the DNA that I extracted from the soil samples last week, as well as some that Lydie had already extracted, in order to get an idea of the amount of Ammonium Oxidizing Archaea. My first attempt at qPCR showed half of the samples with skewed results and, as it turned out, all of the samples that gave pour results were the ones I had extracted. Between that and messing up to the standards the run had to be completely disregarded.

This week I did a series of PCRs and gel electrophoresis experiments. Again and again and again. I learned that science is about repeating things again and again and again. I also learned that it's very frustrating when your experiment doesn't go as planned, which happens all the time, I'm told.

As I am continuing to talk to Ali and Paul, I am beginning to understand more about the significance of the research that I am doing. The reason I am doing these trials to figure out the reaction rates of nitro compounds is because of concern about environmental contamination by munitions compounds (especially near manufacturing facilities and military training sites). One way to help prevent some of this contamination is to use compounds that are more environmentally friendly—less toxic, less likely to accumulate, and they will persist in the environment for shorter periods of time.

I'm working more closer now with symbolic regression which is essentially genetic programming. It seems that the models we are making are based on using evolutionary algorithms. From these algorithms, there are a category of potential solutions to a problem. From these answers, they are possible answers mathematically that can be achieved in real world use. The chief directive of evolutionary algorithms is to locate the best solution throughout the evolutionary process. 

Havent gotten to any real science experiments yet, just getting reoriented to the lab so i can find everything i need for when the real fun begins. I havent loss my touch either, I can still meet my mentor Chelsey Kline's standards, her magical 6 0.9's.

Looking forward to getting some kind of results good or bad and making some mutants. Hopefully I can set another new standard with western blots again this year too.

As I head into the last day of week two, I can’t even believe how much I have done in just one week! This week I started three experiments with differing concentrations of iron porphyrin and I started tracking the reaction rate. The data that I was getting is close to what we expect it to be, but there was an anomaly on the curve that made us think about what might have caused it. From there we realized that our glove box (a box filled with nitrogen and helium instead of oxygen) actually had really high levels of oxygen in it.

What a crazy first week here at CMOP! I am working in Dr. Paul Tratnyek’s lab under the guidance of my mentor Ali Salter-Blanc. They are in the middle of a four-year project and I just got plopped right into the middle of it all. The phase of the project that we are currently working on, is determining reaction rates of nitro reduction reactions.