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Today we ran a second test.  This morning we ran the spectrometer and the samples.  Brian and I set up the machine and computer by ourselves, getting used to the program.  This afternoon we looked at our data.  My data came out much better than yesterday.  The control seems to still have a little magnesium, but barely as much as yesterday.  Also we ran all of our samples on axial, so my sodium came out very correlated this time.  Unlike yesterday we got some really bad data for it.  Then we spent the rest of the afternoon continuing to play with the program and figuring out how to export data.  It’s really not a program that is intuitive at all.  Brian and I spent minutes staring at the screen going “wait…what just happened?”  The prime of this computer programming comes with me saving my re-calibrated data and WinLab deleting Brian’s simultaneously.  Thankfully he only had to make up 2 minutes worth of work.  Finally got my data into excel with everything I could want.  Will continue to clean it up and organize to my liking.

This morning Lauren and I ran the samples we made yesterday as well as the samples from last week. This took us the entire morning. After lunch we started to analyze this data. We saw that I accidentally made 2 samples of the same thing. The sample which was supposed to contain only water and cobalt also had P, Mg, and Mn in it as well. We were able to get around this by using one of Lauren’s data points. We tried to learn how to export our data to excel and it gave us a lot of trouble. Eventually we got Professor Andresen to help us. Overall, Lauren and I learned a lot about using the spectrometer and the computer program without Professor Andresen guiding us through step by step. Tomorrow we will be further introduced to our individual projects and will being to work on them. We hope to have data by the end of next week.

Today, Professor Andresen showed us how to use the spectrometer. We put in our samples in the morning and ran the machine until lunch. After lunch, we analyzed the data we got. At around 4, we realized the machine used a lot of some of our samples so we had to make new ones. I had to make 3 new samples.

Today we learned how to use the spectrometer and ran the samples we made last week.  My control sample came up with some magnesium that should not have been there and all of the sodium gave weird data.  However it was a good trial run, learning how to use the machine, and analyze it.  We will run it again tomorrow, so in the late afternoon we made up more samples of 1, 5 and 10 to replace the lack of sample left over after today’s run.  Also, we will see if my control sample was just contaminated by running the new control (sample 1) tomorrow.  If thats not the issue then maybe it’s the distilled water?  I’m thinking it’s not because the rest of the samples did not come up with a really high magnesium count.

Until tomorrow team America.

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.