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Today, we went to check on the nucleosome solutions we left to filter in the cold room and found out that they were in good condition. We then sorted out the collected samples by figuring out which test tubes had the single and double nucleosomes in them. We then tested the samples containing the single nucleosomes to find out the concentration. We did this using a UV based spectrometer which I will show in my next post. After this, we concentrated the sample by using a centrifuge running at 5000g to collect only the nucleosomes from the solution. We tested the concentration of nucleosomes in the concentrated sample and found out that we lost roughly about 7% of the nucleosomes in the solution probably due to the filter in the centrifuge. But over all it was a good result.

Today I spent the entire day looking at the results that I measured yesterday. There was a lot of information there, and it took some time to modify my spreadsheets from last summer. Two of the series displayed clear patterns, and one of them seems somewhat random. The series with a large concentration of Tris has a clear spike at higher concentrations of Tris. The series with a large concentration of Mg has a clear spike of Mg at lower concentrations of Tris. These patterns should be interesting to investigate with future trials. Tomorrow I will be making what will hopefully be a very accurate calibration series to run some concentrated trials.

Today I spent the morning reading several articles on osmotic pressure. I am trying to get a better idea of the results I should expect from the new PEG series I am running. In these tests, the main variable that we will be testing is osmotic pressure. The best idea that I can build as of now is that osmotic pressure has to do with the concentrations of solutes in a solvent. It has several different definitions, depending on the context in which it is being used. The one that seems most relevant to our work is the energy density of solvent molecules. The idea that I am getting is that PEG takes up space in solution that used to be available to water.
I spent the afternoon running my three dilute series after the nitrogen arrived. I will be able to analyze these tomorrow.

Today we revisited last years NCP samples, from Xiangyun Qiu. The day began with a nervous visit to the cold room where we found a good set of UV data from a sample of NCP solution that was left to separate the night before. The picture to the right shows this sample, where particles in a solution were separated through a beaded solution by size. The high spike corresponds to the solution that contained the NCP. Using this graph we were able to pull about 50ml of NCP from the sample, a tone for the experiments we will be running in the future.

From here we centrifuged the NCP solution to create a highly concentrated solution of NCP. Tomorrow we will be using the sample to recreate Aurelie Bertin’s experiments of observing the changing concentration of NCPs in varrying cation (Mg) solutions.

This morning, we had a meeting to discuss both our goals for the next week, and a series of papers that we read. I presented the paper on osmotic pressure and viruses. For the rest of the day, I prepared myself to run the three new series next week when the gas tanks get here. I prepared dilute samples of all three series and a calibration series to go with them. On Monday, assuming the gas gets here on time, I will be able to get preliminary results for all of the new series.

Today, we were involved in various activities in the lab. First we kicked of the day with presentations on pre-chosen articles. I talked about the electrostatics that has to do with the nucleosomes in general from the article ” DNA inspired electrostatics”.

Next, we continued trying to figure out how the optimum level at which the water we feed into the “chromatography” test tube comes out at the other end at the same rate in order to prevent the “beads” from drying up.

Next, we prepared the stock solutions of the NaCl and Triz solutions. Professsor andresen showed us,using the NaCl, how to go about measuring the right mass of the solutes and also the correct way to dilute them with the solvent( water) and then finally how to filter any dirt from the solution. Ben and I then proceeded to do thesame for the Triz solute .

Lastly, we had to dilute the stock solutions we made to a 1 litre solution. We did our calcutations and verified with Professor Andresen before proceeding with the dilution. We are looking forward to next week when we get deeper in the research!!

Today we spent the morning preparing a talk to give the department describing the basic theory and motivation behind our work. We described how our work applies to the protein-DNA interactions that occur naturally in the body many times per second. Our work also can be used to package DNA in useful ways and facilitate its uptake into cells for gene therapy. I also spent a good deal of time reading over the paper I will present tomorrow on osmotic pressure’s effect on virus DNA ejection. The virus system does not exactly apply to our work, but a lot of the concepts, including osmotic pressure and DNA-DNA interactions are very similar.

Today I spent most of the day reading through the first half of Prof. Andresen’s PhD thesis. His work uses anomalous small-angle x-ray scattering (ASAXS) to describe competition between different valence ions in the ion atmosphere surrounding DNA. I found his background of the basic biological theory behind the work especially useful, because it was laid out in a very clear manner. He also described the motivation behind the work we are doing, which was also very interesting.

Today, We had a presentation where Ben,John and I explained what our research was about to all other students involved in research with other professors. We talked about the motivation of our respective researches.

I also had to prepare for our article presentation tommorow. The Andresen team all have to pick an article each and explain to the other members of the team. I picked the article ” DNA inspired electrostatics”

Lastly, we finished working on the “packing” of the beads I talked about yesterday by making sure they did not dry up in the tube. I will post the picture of the apparatus used for better understanding .