Author: Prof. Andresen

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 .

Today, we had to improvise for a cord needed to run the UV monitor and the fraction collector. So we got our hands dirty with connecting wires and I also got to solder for the first time! The connection using the improvised cord worked as planned with some help form Prof Andresen. We also used a form of chromatograhpy to separate some mini beads from solution. We will use these beads later on to separate the single, double..etc chromosomes from one another and then analyze them using the fraction collector and the UV monitor.We also got familiar with the new labbelling device which we will use to label our test tubes from now on.

Today I prepared a new calibration series, and some more DNA samples to run. We ran these samples under the supervision of a PerkinElmer tech, and took away some important lessons. We learned that altering the current through the plasma coil can give us higher counts for elements that require ionization. We also learned that slowing the flow of sample through the nebulizer will increase this effect. I prepared a new calibration series to run new PEG samples tomorrow.

After a memorial weekend of reading up on the theoretical models of the binding of cations to DNA, the lab took a day to tidy and read more on what the future holds. A lab tech came in to assess the OES and answer any questions we had. Hopefully getting our hands dirty in the lab tomorrow.

We had a technician show us better ways of using the spectrometer today. I also started reading another article named Electrostatic mechanism of chromatin folding which was written by David J. Clark and Takeshi Kimura.The article talked about the behavior of the nucleosomes in a salt solution of NaCl with the cations also present in the solution. It investigated the behavior with low and high concentrations of the salt solution and the DNA. With kurt back, we will soon kick into a higher gear in the research.