Author: Prof. Andresen

This morning I made the axial align solution for the spectrometer. In the afternoon I ran the spectrometer with the samples I made yesterday.

The data came out well except for the sodium. The correlation coefficient was around 0.916 after initial reprocessing. I tried to fix the data by deleting sample 2. This sample had 0.049 ppm of Na. The spectrometer read it as having negative sodium. However the data did not look any better after deleting the point. The correlation coefficient was 0.90. Na 589.592 gave the worst data. It gave a negative value for Na when there was 0.33 ppm in the sample.

The correlation coefficients of the Mg and P were better. The Mg was about 0.98 and the P was greater than 0.990.

This morning I made the buffer solutions. I made 4 of them. In the afternoon I had to make more calibration samples because I made a mistake in my previous ones. I also added Na to these samples.

Today I continued to analyze data.  Fixed problems andresen found within my excel spreadsheets, and then spent the afternoon on error propagation.  Long tedious work to say the least, and it is almost completely impossible to come up with a way of organizing the error propagation steps in an excel spreadsheet, but i’ll take another stab at that tomorrow when i’m fresh.

This morning I finished making the excel spreadsheets from yesterday pretty.  Also doubled the NCP dilutions for the mM concentrations because originally AP and KA diluted it to 200 ml instead of 100 ml accidentally.  Next I found the excess ions per nucleosome.  For this calculation the average P was the average of the two P data sets from the NCP data.  At the end of the morning we had a department meeting just to share with everyone what we are doing this summer.  In the afternoon I went over the data with Andresen.  It looks like it isn’t good.  As the Na decreases, the Mg should increase.  But according to the data the Na and Mg increase together.  So I moved on to the second set of data.  File labeled Nucleosome Trial 4-AP.  I followed the same steps as last time, except this time I already had the excel spread sheets, so I just copy pasted stuff in and then made it look pretty.  Will talk about the results with Andresen on monday.

This morning I ran my samples from yesterday in the spectrometer. My results showed that the Spectrometer will give good results at 0.1ppm Mg. In the afternoon I made more samples of the same elements. Next week I will make a buffer with 0, 1, 2 and 3 mM Mg and 1 mM Na-Trs.

First things first:  We have accepted a challenge to play laser tag.  Andresen’s Lab vs. Thompson’s Lab.

And the less (actually more) important aspects of the day…
Started out the first hour working on organizing the data from our samples run on tuesday while Brian talked to Andresen.  Then I had my hour with Andresen to talk about my project.  We looked over Alicia’s data and talked about how I should go about the analysis.  The from the end of the morning through till 5 I worked with the Method in Winlab called Nucleosome Trial-AP.  To make the data more correlated I weighted the lower points more and took out point 7.  Then I exported the data and spent the afternoon organizing it.  See notebook and document named NucleosomeTrial-APc for the extensive data.  The last thing I did was set up an excel document to convert the diluted sample concentration to the original concentration.  Will continue analysis tomorrow.

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.