Blogs

Like the last one, this posting is delayed because maintenance to the CMOP servers kept the website down the past week. Week eight was exciting because a lot of results were produced, but it was a lot of work. I worked entirely on the neighboring lab’s UV vis, since ours is broken and won’t be fixed before I leave. This has turned out to be a blessing in disguise, as this alternate UV vis is faster and easier to use.

I started out the week running some sediment DNA samples through the fluorospectrometer to try to accurately quantify the DNA.  The fluorospectrometer has proved a lot easier to handle ever since we got new chemicals, and all of the samples but two showed readings in the range of the standards.  I also ran a PCR of some samples of different dilutions to see which dilutions we would use for sequencing; after PCR, I ran the samples in a gel, but we could not verify which bands were indicative of the correct base pair when using the 1 kb ladder as a reference.

     At the beginning of the week, Karen helped me to prioritize my work. She stated that I should focus more on the simulation, which helps. I was also able to find an article that helped me with my size scaling for my simulations. For the rest of week, I had a couple more meetings with Karen, and I attended a presentation by Elizabeth Furse. In the meetings with Karen, she continued to help me focus for my paper and poster. She suggested that I should steer toward the poster since it’s due sooner.

Even if you know close to nothing about my project, knowing that I’m using spectrometry (rather than the more conventional electrode technique) for characterizing ORP is enough to realize that a broken spectrometer poses a large problem. Fortunately we have other labs next door whose equipment I can borrow. However, that has been accompanied by a headache of new calibrations and blanks that I’ve had to run, ensuring that the data from our spectrometer will line up with theirs.

This week I continued to measure the stability and reactivity of the manganese pyrophosphate, citrate, DFOb, and malate solutions I made last week. I also started a new experiment to study the interaction of manganese oxides (MnO_x) with sodium ligands. This involved making up solutions of sodium oxalate, pyruvate, formate, citrate, pyrophosphate, and acetate, and then adding manganese oxides. Fine suspensions of manganese oxide minerals in solution look a lot like muddy water, but the oxides can be easily removed by filtration.

       This week I restored a feature which was disabled in an earlier version of the program. This feature would gather data from the Fixed Station User Interface and send it to data explorer to generate a plot. This feature was proven to be very useful before so I implemented it back into the Data Explorer so it may generate desired plots.

On Monday, I created fits for my various plots of 4-chloroaniline experiments, and compared them to the literature values we have been studying. While there is a bit of variation in the reaction constants between our replicates, overall the data fits well with what is represented in the literature. This is exciting news, and means we can move forward in our project.

On Monday, I had a fortunate and embarrassing realization. Late last week, we seemed to have finally got our method down to a replicable state, but the concentration still seemed to be dropping from the initial spiked amount down to around 3 or 4 μM too quickly. This bothered me, so I rechecked my math, and realized I had completely miscalculated how much aniline I needed to inject into the reaction vial, and was starting the reaction off at 4 μM of aniline rather than 20 μM. This reality meant that our results made much more sense, and that I had an embarrassing talk with Ali.

Monday, 07/28/14:

Week 8 of my internship was really exciting as I reached a day I never thought would come- the end of sediment core dissections! As I've mentioned before in my blogs, core dissections involve sawing at frozen mud in the CMOP cold room- so while it yields some really interesting and valuable results, it can be a bit of a tiring (and messy!) process. It felt good to be free of the cold room, and it felt even better to have a complete picture of the snail abundance in our various sites throughout the summer months.