Author: Prof. Andresen

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!

This morning I ran the spectrometer. When I got the results they were all over the place. However I forgot to account for the fact that there was no Cobalt as an internal standard for my nucleosome solutions. After I did this, the data did not look good so we are going to run the experiment again. This time I will keep the liquid that comes out during spinning. We will look at this to see if the nucleosomes come out of the solution. In the afternoon I remade the buffer solutions and started remaking the calibration samples. Tomorrow I will finish the samples and spin them.

So today I ran three of those tests I was working on with the sodium.  Didn’t even bother running the 4th because we were getting consistent data….that didn’t match our actual concentration.  We tried analyzing it the normal way, and by taking away the calibration.  That didn’t help.  So possibly it is because I calculated the concentrations in my sample wrong, since the spectrometer DID give us consistent calculated concentrations across trials.  So now I’m going to do a weighted average of each wavelength and sample to get one graph with error bars.  Then I am going to try remaking my samples to see if that was an issue.  I’m also thinking in spare time to do a little internet research…there must be some other frustrated scientist out there working with this piece of equipment who had the same issue and found a solution…..

sorry about not posting yesterday.  Basically what I did for the past two days was make up one large set of samples and 4 sets of calibrations.  Took a long time.  What we want to know is exactly how well our spectrometer measures sodium, since so far it doesn’t seem very good.  I made up large samples with NaCl concentrations and cobalt and then calibrations with Na and Co.  I then ran the first of the four sets we will run.  Haven’t looked at the data yet, but seeing as Brian and I are sharing the spectrometer tomorrow, I’ll have time to review it then.

A note about my awesome color coding skills.  All the stands that the sample and calibration tubes are set in match the color strip in its corresponding excel document 😀 how’s that for organization?

Today I spun my samples in the centrifuge for the first time. I spun the nucleosomes 4 times with the samples I made a few days ago. Then I spun the nuclesomes with water 12 times. This took me until past lunchtime. After a spun the samples I put them into tubes and put in about 6 ml of water. Tomorrow I will run the samples in the spectrometer. I would’ve done that today but Lauren was using it.