Week 1 Day 3

This morning we continued to make our calibration samples.  I had a lot of trouble getting the correct amount of phosphorus, since it was such a tiny amount to measure.  I had to do one of the samples 4 times before I got the amount of phosphorus at a reasonable percent error.  Then I helped brian make one of his samples that he was having trouble with as well.  After lunch, we calculated the adjusted concentrations in our calibration samples.  Then we read about and learned about the computer program and the spectrometry machine we will be using to analyze samples throughout the summer.  Finished up with the day with a meeting with Prof. Andresen about the actual projects we will undertake this summer.  Mine is a continuation of his previous research.  Basically figuring out whether or not the tails that come off of nucleosomes are wrapped or not.  I will be working on getting those error bars down to reasonable sizes.

Week 1 Day 3

Today, Lauren and I finished our calibration samples in the morning. We tried to reduce our errors as much as possible. After lunch, we figured out the adjusted concentrations in our samples. When we both finished, we were introduced to the spectrometer. However we had trouble with the computer system. Lauren and I both met with Professor Andresen individually and he told us what experiments he has planned for us this summer. To finish the day, Lauren and I read more articles.

Week 1 Day 2

This morning we continued to read articles and catch up on latest research in the field.  Then in the afternoon we started making calibration samples.  I am making 10 samples, each 10 mL.  They each have 1 ppm of Co, 0-5 ppm of Mg and Na, and 0-1 ppm of P.  The rest of the sample is water.  I started out with the water.  Came out fine on the percent errors.  However I had to redo three of the samples next, when I added the Co.  Third, I added the Na.  Some of the percent errors were a little high, but not high enough to redo the samples.  Today I will finish adding the Mg and P.

Week 1 Day 2

 Yesterday, Lauren and I read again in the morning. In the afternoon, we went back into the lab. We started making samples to put in the spectrometer. I started 11 samples. They all contained 1 ppm of Co. The rest will range from 0-5 ppm of Mg and Mn. They will all contain 0-1 ppm of P. So far I have put in the water, the Co, and the P.

Week 1 Day 1

Today we started by reading a paper from Physics Today titled DNA-Inspired Electrostatics and by doing some textbook reading to catch up on basic biology and biochemistry.  In the afternoon Brian and I learned how to pipet properly.  We practiced getting the correct amount of water in 1.5 mL sample tubes with each of the six pipets.  After we were done, I had less than a 1% error in the majority of my measurements.  However I had significant errors in the 2 and 10  microliter pipets.  So I remeasured the water for those pipets.  After this second try I got much smaller errors in my measurements.  At 4 pm we went to the Lab Safety Training and then called it a day.

Week 1 Day 1

Lauren and I started our summer research yesterday. We were given an article about DNA-inspired electrostatics to read. Professor Andresen also gave us numerous textbooks to read so we could learn basic biology and chemistry. In the afternoon, we went to the lab and worked on basic pipetting techniques. We were given the task of transferring water from one vial to 1.5 ml sample tubes.  My first attempt was not very good. However I was able to reduce my error bars on my second attempt.

Week 10 - Day 3

Today, Ben and I finished working on our slides for our presentation to cap off the research. Based on suggestions from Prof Andresen and John, we made changes to our data arrangement and delivery. We did a practice session with John spotting out more ways to improve the presentation. We were finally ready but the end of the day and gave our presentation. I think it went pretty well and we are now assured that the rest of the Physics research have a good idea of what we did during the summer!

Week 10 - Day 2

We got the results today and it was another disappointment. The Na concentration was fluctuating while the Mg concentration seemed better but not still up to expectation. Professor Andresen decided to check the parts of the spectrometer again to see if there is any problem wrong with it and he also personally made some solutions to see what happens. Ben and I also started working on our slide show for the presentation we have tomorrow. We are gathering our data and doing some final analysis on them.

Week 10 - Day 1

Today, I made buffer solutions once again and tested them in the spectrometer. The results will be analyzed tomorrow as we are going to run it overnight.

Week 9 - Day 5

I remade the solutions using the right concentrations of Mg today. The results we great! What a sense of relief. All the prepared concentrations fell with 1% of their intended concentration. So we decided to step it up one notch. Professor Andresen suggested that I made more solutions in ppb But this time I should make two sets: One with only Mg diluted with water and then the other one with the complete components ( tris and Nacl). I made the solutions and stored them in the fridge so we could test them on Monday and analyze the results.

Week 9- Day 4

Today, we ran and analyzed the results of the solutions I made in ppb (parts per billion). There was another problem today as the results showed that there was no Mg in the solutions at all. I checked through my calculations and found out that my calculations were off by a decimal place which made my calculations for the Mg concentrations 1/10th of the actual values they should have been thereby making them undetectable by the spectrometer. I decided to repeat making the solutions tomorrow.

Week 9- Day 3

Today, we got the results for the solutions I made yesterday. We had both good and bad news. Good news first: The Na concentrations we almost on points as we had only two samples falling of the 10mM concentration it was supposed to be(7.9 & 7.7mM).The rest were about within 5% of the 10mM intended concentration. However, the bad news is that the Mg concentrations were all off by a factor of 7. This was surprising and confusing at the same time because I was pretty sure I did not multiply my calculations by any factor at all. So, the conclusion today was that I should make some solutions of just different Mg concentrations and water without the tris and NaCl. I made about 5 samples starting form an Mg concentration of 300ppb with an increase of 600ppb between solutions.

Week 9 - Day 2

Today, I took special care in making the solutions. I weighed them instead of the normal approach of just pippetting the needed volumes into test tubes. I also talked to Professor Andresen about possible problems with the whole experiment and we decided that we wait for the results of this run and then we can change our approach to making the buffer solutions.

Week 9- Day 1

After the little success we got, I decided to make more solutions today. However, the results are not looking good. The next step will have to be for me to weigh them instead of just relying on the pipette to measure the amount of solution that I put into the test tubes.

W9D1

Today I ran two large sets of samples, one for myself and one for Fash. Fash's samples were his latest set of buffers, for which we have high hopes. After fixing our problems last week, these results should be very consistent. We will look at the concentration data tomorrow. I finished running all of my Cohex 10mM series, and the preliminary results show a clear pattern. As expected, at high Mg concentrations, very little DNA precipitated, so the results are somewhat unreliable. Tomorrow I will double check the buffer solution, and begin to write up some summaries of our data.

Week 8

Last week was a busy week, which kept me from posting much. I'll try to give a somewhat decent account of what happened, and the status of our projects. Last week, we had some trouble getting consistent results from Fash's buffers. We investigated a variety of variables, from my calibration technique to pippetting errors. We also had a problem with counts from the spectrometer. We eventually discovered that part of our problem may have been coming from the plasma torch area being dirty. There was also a possible problem with consistent nitrogen flow. We now think we have most of the issues figured out, and should be able to proceed with collecting consistent results. Ben has been getting consistent buffer values, and is proceeding with his NCP experiments. For my project, last week I ran the second buffer solution, and began to test the actual samples. The second buffer solution had somewhat surprising concentrations, because they came out to consistently around 8 mM Cohex, when we thought they were 10. I am going to double check these results after I test the actual samples further.

Week 8- Day 5

I prepared more solutions today. But since John was leaving early today I kept them in the fridge so we could run them on Monday. Hopefully they turn out good!

Week 8 - Day 4

Today we tested johns results, and although they looked better than mine, they are not as close as we wanted them to be. So we were left wondering what was wrong with either the machine, the stocks or us! Well, we ruled the machine out because Ben's results were good. We were on the verge of ordering new stock solutions when professor Andresen decided to check the sprayer in the machine( spectrometer) and found out it was kind of clogged and worn out. He changed it with a new one and we hoped that as the problem with the machine. So I made some more solutions are we quickly tested them. Surprisingly we got really good results but there was a little problem because the measured concentrations of Mg we measured were in multiples of 10 of what I actually prepared. This might have been a mistake on my part so we decided to make more solutions tomorrow.

Week 8- Day 3

We tested and analyzed the samples I made yesterday. They still turned out random. So John and I decided that he made a few samples of his own so we could conclude if the problem was with my measurement or the stock solutions themselves. John made solutions with magnesium concentrations of 1mM and 2mM. We will test the results tomorrow.

Week 8 - Day 2

After the conference we each have some new assignments. Mine - to test the ionic attachment of Magnesium to NCP. It's simular to the last tasks, but a different method. Instead of adding Mg solutions of different concentrations to NCP, we are adding NCP to pre tested concentrations of Mg solutions, and testing the difference between the two. The goal is to get really careful and accurate data, so yesterday and today was spent working on the method. Yesterdays concentrations had a 6 sample standard divination of 1.4%, hopefully today's samples will be even less.