Blogs

Half way through a 10 week internship, it’s easy to get stuck in the rut of data collection. With the allure of producing data and tangible results, it’s no surprise that everything else is forgotten. My presentation Thursday went well. It served as an excuse to get out of that data rut. For example, I created my first presentation-quality graph. I re-read some background papers, and reminded myself of the objectives of my project. Far less is learned by collecting the data than is learned by explaining it to others, so I'm glad I had the opportunity to present my research.

This week was by far the busiest week of my internship thus far.  Monday and Tuesday I ran full plates of qPCR with variable results.  The first run displayed an efficiency of 107%, which was within the accepted range.  In effect, this data was viable, and displayed some interesting results.

Week 6 of my internship was a busy and productive, but relatively uneventful one. My frontline mentor, Kiley, was out for the week as she had returned home for a visit after the 4th of July weekend. This lack of direct supervision worked out just fine, as I have now been in the lab for a decent amount of time and am comfortable maneuvering around and completing my tasks on my own. I really just had one big task for the week- processing (seemingly endless) sediment cores that we had taken from our sample sites in both May and June.

This week was one of my busiest weeks at IEH. Now that I have collected all my chironomids from our various sampling sites, we need to begin our analysis projects. The first of these projects is the nitric acid digestion. However, before I can do any experiments, I need to clean the chironomids to make sure they don't have anything stuck to the outside of their bodies. Because we are doing a food web study, we only care about what is in the guts of the chironomids, so the cleaning step is critical.

This week, I spent most of my time working on improving and revising my code that I had written over the last two weeks. Although my code was fully functional, there were many revisions to make, style wise and readability-wise. Currently, my code was composed of an assortment of top-level functions. To increase usability, code maintenance, and take advantage of all the Python features, I used object-oriented programming - the concept of having objects with attributes and methods.

This week was a little bit slower for the others while we waited to hear back about the sequencing results concerning the DNA fragments we constructed in the previous few weeks. Monday morning we sent out all of the samples from last week to be sequenced. Afterward I prepared an LB/agar solution and put it in the autoclave. Then I spent some time finishing my blog for last week and working on my PowerPoint slide for the midterm presentations this Thursday. After lunch, I took the LB/agar mixture out of the autoclave and put it in the 55^oC water bath.

On Monday, I ran experiments with varying concentrations of MnO₂ and 4-chloroaniline. We hope to narrow down the reaction setup to concentrations of MnO₂ and 4-chloroaniline that give consistent results. Once we know our experiment is reproducible, we will be able to determine the kinetics of 4-chloroaniline. 4-chloroaniline is the compound we wish to compare all of our other tests to, so this will be a big step.

     This week was a very eventful one. Other than reading from documentation or literature regarding CompuCell3D or ovarian development, I had two workshops, successful simulation runs, and a mid-term presentation. The first workshop was about our mid-internship PowerPoint presentation. Sheree Watson led the talk, and she spoke about what topics we can discuss. She presented to us a worksheet that had five areas of focus: title, background, objectives/goals, methods/data, and preliminary results/next steps.

This week I tried more reactions for making some manganese ligands, most of which did not work. Last week I was able to make manganese oxalate by combining ammonium bicarbonate and oxalic acid and then adding manganese acetate. This procedure did not work for the other ligands I tested, although I am hoping to try it next week with formic acid and pyruvic acid. I also added potassium permanganate to benzoic, citric, and ascorbic acids, but this method was not productive either, although I tried several variations of the procedure.

       After completing the Diagram my next step was to add time handling to the Y and Z axis. Currently only the X axis of the data explorer can handle time.

"Current Data Explorer Interface"