Author: Prof. Andresen

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.

Today, we ran solutions similar to the ones we did yesterday. The only was change was that we diluted the 1,2,4,6,8,10(ppm) solutions to 1,20,40,60,80,100(parts per billion(ppb)) respectively and then calibrated the spectrometer with them. Also , the samples we used this time were some of the DNA samples John used last year.

We also learned more about analyzing the results from the spectrometer. We noticed one point( the 80ppb) on the graphs were out of place. We probably added a little too much of Cobalt in the original 8ppm solutions we made yesterday. Otherwise, every other thing seemed pretty okay.

Today the veteran put the foreign powers to the test by pulling out an old batch of DNA and left us alone to test the ions present in the solution. The foregin fact passed fairly sucessfully with most of the data corresponding to Johns previous tests. One of the calibrating solutions (80ppb) had a out lying concentration of Cobalt, which threw the calibration and results off a little. But all and all a good day, and feeling more comfortable using the equipment.

Today,John “the veteran” made solutions of magnesium, cobalt and phosphorus of unknown concentrations and our task was to use results from the spectrometer to make good estimates of their concentrations. We started off by making calibrations of the same solution varying from 1ppm(parts per million) to 9ppm.

We then ran these calibrations in the machine along sides johns samples so we could use our calibrations to deduct the concentrations of his solutions. This was another opportunity for us to improve our pipetting skills. Ben taught me how to pipette properly after he noticed that I was unknowingly drawing out to much solution each time.

We ended up getting the right answers to the concentrations of johns mysterious solutions.We are looking forward to the next task.

Today we began with a lesson on chemical safety. After that, I gave a crash course of the basic chemistry that is required for our lab work. We then each prepared a set of samples, spanning from 1 to 10 ppm of Mg, Co and P. Using my set as the calibration, we tested the other sets for accuracy, and they were both very close, especially for first tries.