Author: Prof. Andresen

Team America here.  Brian named us this after reading some of Fasch and Ben’s posts from last summer, who called themselves the Internationals.  This morning we started out coming up with questions to guide our continued reading about our projects.

Clarification/ Reading Questions:
1.  Explain Poisson-Boltzmann Mean Field Theory
2.  Explain Figure 4 in the Bai article.  What is the upside down triangle symbol?
3.  What do the different histones do?  H1?
4.  What exactly is “nucleic acid thermodynamics”?
5.  Gelbart pg 39.  Help visualize attraction of macro ions.

Big Picture Questions:
1.  What work has been done on this project before me?
2.  Why do we use Na+ and Mg2+ ions in the experiment?
3.  Why are our ions all cations?
4.  What are the histone tails?
5.  Do the tails only come out when the chromatin is unwrapped, do we have to unwrap them first?

We also talked about what we learned so far and Brian and I explained to each other what each of our projects would be.  Then this afternoon we held a Team meeting.  Discussed the questions, got answers, and talked about what we learned and what else we could read articles about.  Goal for the end of the week: read 5 more articles.

Team America out.

This morning, after a brief meeting with Professor Andresen, Lauren and I compiled a list of the things we learned from the readings last week. We also made two lists of questions we wanted to get answered. The first list was made up of specific terms and graphs from the readings we were confused about and the second list contained bigger picture questions. When we had compiled all our questions we read for the rest of the morning. After lunch, we met with Professor Andresen to discuss our questions. Our meeting lasted approximately two hours. After the meeting we read more articles to finish out the day. Tomorrow we will start working in the lab.

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.

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.

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.

 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.

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.

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!

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.