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Friday was fairly uneventful.  This morning I ran the samples in the centrifuge in the cold room.  I was very cold, but managed to get it done before lunch.  Realized I should have run the spin one more time to get the spin 8 samples, so I only have the leftover sample, spin 7, and buffer to run in the spectrometer.  Ran the spectrometer in the afternoon.  Will start analyzing data Monday.

This morning I ran calibrations in the spectrometer to make sure they were good enough to run samples. The results were good. So in the afternoon, I helped Lauren prepare samples. Then we ran the spectrometer. We will look at the results on Monday.

So yesterday I ran three more trials on the spectrometer to measure Sodium.  After running about half the trials, I realized I put 1/10 the amount of cobalt I should have.  No worries, I just took out the internal standard in the analysis part!  Got back 2.81% error of the 0.6 ppm sample and 2.29% error on the 0.8 ppm sample.   That was after averaging all the data together.  Not too shabby!

ps, can’t get the formatting on that right….

So today we moved on to doing a trial run with out the nucleosomes.  Basically making up the samples to be spun and then run in the spectrometer and the calibration set.  I struggled all day with the calibrations and the pipets… But it’s all ready to be run tomorrow!

This morning Professor Andresen and I put the samples into the gel. Then we plugged it into a power source and let it run for a few hours. After lunch, we went to the science center. We put the gel into ethidium bromide. After we rinsed off the excess, we put it into another machine to see what the samples did. It turned out that our nucleosome supply is still mostly good.
When we got back I helped Lauren on her project by making her buffers.

Professor Andresen was out of town today. I read about electrophoresis. It was confusing, but I think it will become much clearer when I am shown how to do it. I also helped empty out the cabinet on the first floor of Masters.

Today I ran two trials in the spectrometer.  After looking at the data, I realized I completely botched the calibrations for set 5, but set 6 was fine.  This completely threw off the data for set 5, but set 6 was consistent with the data I took on Friday.  After looking at the errors and correlations, I have determined that our machine is just bad at measuring very small concentrations.  What we can do is make sure our calibration sets are dead on, because that improves error significantly.  Also getting the internal standard in the sample right on seems to help.  But with the lowest concentration of sodium, I’m still getting a 20% error.  The other concentrations are almost all in the single digits for percent error.  I’m hoping that when we actually take data, we can run the calibration first, look at the correlation in sodium and decide of its going to be good enough to run with the samples.  We’ll just have to make enough to run the calibration set twice if need be.

After looking over the sodium trials data from Friday and knowing the fact that when we take away the calibration constant from analyzing the data, Andresen and I decided to run the Sodium trials again, this time still using the highly concentrated NaCl solution and diluting it down, but this time making a diluted sample of Co.  We are doing this because the analysis of the data seems to be very dependent on a very good calibration constant, the cobalt.  So if we dilute it, then take a lot of it to get the same concentration in our samples as we did before, then it will be easier to get the exact amount of cobalt.  So I made that dilution, then made two more sets of sample and two more sets of calibrations.  All ready to run and analyze tomorrow.

This morning I ran my samples in the Spectrometer. The pattern of my results looked good. The sample that contained Mg consistently had more Mg than the sample without Mg. The second sample contained less P which it was supposed to. However the data was consistently off by a factor of about 10. In the afternoon, I ran the excess liquid from the centrifuge in the second spectrometer to see where the nucleosomes went. Most fell out of the samples during the first spin.

This morning I finished my calibration samples. I also noticed a mistake in my buffers so I had to remake them too. After I did this we had our group meeting in the physics lounge. Dr. Good had some Good pizza. After lunch I put nucleosomes in new samples and spun them in the centrifuge with my buffers and then water. I did four spins with the buffers and 5 spins with the water. The water was supposed to only be 4 spins but I accidentally spun them a fifth time. When I retrieved my solutions after spinning, I weighed to find the amount of nucleosomes. My first sample had .0232g and my second sample had .0044g. This seems like a very large separation. I also added cobalt as an internal standard to the solution and filled up to 6 ml with water.

Today we decided to remake the sodium samples and run them again, since it seemed that there was such high correlation in my trial runs that did not match my expected values.  So thats what I did.  I re-made the samples this time by first making a concentrated solutions and then diluting it down to the concentrations I wanted.  At thank god it mostly worked.  My percent errors went down significantly.  A good way to end a Friday!  Of course, I’ll see if I can play around with this sodium data a little bit more to see if there is a trick with getting the error lower.  Till funday monday!