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.
Today I spent more time looking into papers on osmotic pressure. The first one I read was by Hansen et al, and it described a new way of looking at ions around DNA called the cell model formulation. This model is more accurate for determining osmotic pressure at low salt concentrations. It says that this “cell” acts as a neutralization volume for the counterions, and the electric field vanishes at the cell wall. Within the cell, the ions follow the PB equation. I also read another paper by Evilevitch (EVIL!) about DNA ejection from viruses. This paper suggested that PEG can be used to prevent the ejection of DNA from viruses. The use of smaller osmotic pressure changing molecules such as Glycol does not prevent the ejection of the DNA.
Today I ran another competition between Ben and Fash, aiming to hone their pipette and calibrating skills. I also read a paper on DNA counterions. This paper suggested that counterions can contribute to the macroscopic properties of DNA solutions, such as osmotic pressure. It said that at High DNA concentrations, the counterion contribution to osmotic pressure prevails. Also, this paper suggested that there was a certain DNA/SAlt concentration range where osmotic pressure was proportional to the DNA concentrations, and independent of the salts.
Today, with Ben away in Phili,I went over the articles we read last week to further strengthen my knowledge in the biology of the research.
Today, Ben and I wanted to become more familiar with pipetting,calibrating and operating the spectrometer in general. So we decided to compete in making solutions of Mg,Co and P of 0.05,2,4,6,and 8ppms.
We then ran random samples which John provided with our respective calibrations to see which ones matched better. Well, to cut the story short, I won!! Although I have to admit that my Mg calibrations were a bit off. We will be working more on our pipetting skills over the next few days.
