Category: Uncategorized

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.

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.

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.

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.

Today we began with some plans for aesthetic work to be done to masters hall. This involves a lot of poster renovation and updating. I then got out some leftover DNA samples from my work last summer for Ben and Fash to analyze. They used diluted versions of their calibration standards from yesterday to calibrate the spectrometer, and then attempted to determine the DNA and ion concentrations. We found that there was actually a few errors in their calibration series, but they were still able to obtain decent results. I also spent some time today educating myself on osmotic pressure, because many of the series I will be soon looking at deal with PEG and osmotic pressure. I found one article that suggested that divalent cations could cause attractive forces between DNA molecules under proper solution conditions. No such attractive forces were found with +1 ions.

Today I prepared mystery solutions for Ben and Fash to identify using the spectrometer. These solutions had random amounts of Mg, Co and P that I had predetermined. I gave them some rough guidelines on what range my concentrations were in, which is around what we have when testing actual DNA samples. They made an accurate calibration series, and were able to identify the mystery solutions with very high accuracy. I also spent some time today looking over a lot of my results from last year, getting ready to start running actual DNA samples again.