Blogs

       This week I wrote out an email to users of the data explorer requesting for volunteer beta testers. I received many emails from people wanting to beta test as well as many bugs reported.

                Last week I added individual time modification handling to the Z axis. This week I focused on adding individual time modification to the Y Axis. Currently if you apply a time modification the modification is applied to X and Y Axes. With this this update users will be able to generate plots such as, Time vs. Salinity plot colored by Temperature. After completing this update all the axes can have individual time modifiers.

This week I once again started out with a qPCR of the same plate I ran last week because the efficiency had been too low.  I made new standards and ran a full plate, yet unfortunately, when I analyzed the results the efficiency was still too low to my frustration.  The next day I used Kiley's standards for the same plate of qPCR because her standards had yielded good efficiency in her last run.  The data looked good upon analysis although some of the lower standards had to be thrown out.

Week six of my internship was an exciting if rater uneventful week.  Monday was not too busy.  I transformed the Δ1990 DNA fragment into the E. coli competent cells that we made last week.  These then got plated onto an LB/agar plate containing Kanamycin.  We also sent in to be sequenced ten DNA fragment samples for the ΔtnbA gene, and I re-streaked ten new ΔtnbA colonies to use in case the sequencing results come back with mutations in all of the fragments.  Because we did not have a lot of work, I had some time to myself to work and read journal articles.

Tuesday, 07/22/14:

                Last week I added time handling to the Y and Z axis. This week I focused on adding individual time modification to the z Axis. Currently if you apply a time modification the modification is applied to all axes(X Axis, Y Axis, and Z Axis). With this this update users will be able to plot graphs such as, Temperature vs. Salinity plot colored by Day of Year.

"Colored by: Time example"

This week was a great week as I had my first really great result from the nitric acid digestions I have been working on. The nitic acid digestion is a procedure that allows us to digest the soft tissue of chironomids and other plant species leaving only diatom frustules. The end result provides clear and easily-identifiable diatoms from the chironomid guts. Our first nitric acid digestion trial with the May samples using a single chironomid did not provide good results. There were likely two problems with the first run.

This week I tried another method of making manganese ligands. It involves combining manganous sulfate (MnSO₄) with the sodium version of a ligand, such as sodium pyrophosphate or sodium citrate, and then adding potassium permanganate (KMnO₄). I was able to make manganese citrate and pyrophosphate this way, but the reaction did not work for EDTA.  After six weeks of making and testing manganese ligands, I have several different methods that work for making manganese citrate and manganese pyrophosphate.

As some of the other blogs have mentioned, this past week was one of my busiest weeks here as an IEH intern! The week began quickly as Kiley returned from her trip and we all got to work. On Monday, we had a busy day of continuing sediment core dissections and extracting DNA from previously processed cores. In the mid-afternoon, we had a lab meeting. These meetings are a good time in the week for all of us- myself and my mentor, as well as my fellow intern Maddie and her mentor- to get together with our Principal Investigator, Dr. Holly Simon, to talk about our progress in the lab.

This past week was the sixth week of the program and we have reached past the halfway point. During this week I collected most of the data for my side project. First, I needed to finish gathering all of the perturbation data from the concentration that I used in the previous week. This concentration with a ratio of 1:11 took two days to collect and assess all of the data. Each day after I finished my perturbation data collection, my mentor and I tested the liquid manifold for overnight data collection.