Thursday, June 28, 2012

Week 5 Day 4

This morning Brian and I made the diluted samples of the spin 7, spin 8, NCP, and Buffer.  Then we ran them in the spectrometer.  After lunch I analyzed the data.  Not really sure what I should conclude from it, but Andresen can help with that tomorrow morning.  Here are the graph's I got, though.  Error bars are shown, but many of them are small enough that you can't see them.  I do think it is a problem that we have such small counts in the magnesium, but the sodium seems fine.

Week five day four

This morning, Lauren and I finished diluting our samples from the spinning yesterday and ran them in the spectrometer. After lunch, she analyzed the data while I started on a new calibration set. We still have enough of the previous set for a few more runs. The percent errors on the new set are very low so hopefully it will be as good as the previous set.

Wednesday, June 27, 2012

Week 5 Day 3

This morning I looked a the data from the last test run.  It came out really well, all the concentrations were consistent with each other, percent errors were low.  So we decided to do the real run aka same experiment just adding nucleosomes.  So Brian and I made up new samples and spent the afternoon spinning them.  We decided to keep the calibration set from last time, because there is enough for a few more runs and as you could see from the picture, very correlated!  Not enough time to run the spectrometer today, but we'll do that tomorrow and see how everything went.

Week 5 Day 3

This morning I read an article about DNA condensation while Lauren analyzed the data from yesterday. After discussing her findings with Prof. Andresen, we started making samples to run an actual experiment with. After lunch we went to the cold room to spin these samples. We spun 8 times, collecting the sample after spin 7, spin 8, and after we flipped the filter.

Tuesday, June 26, 2012

Semajno kvin tagon du

This morning I went to the cold room in the science center to spin samples. This took me up until lunch. After lunch, I finished making these samples to be run in the spectrometer. I collected the spin through liquid from spins 7 and 8. I also collected what was left in the tubes after all the spins. We will see the results of the samples tomorrow.

This correlation made me cry tears of joy

This picture deserves a post of it's own.  Except for that one point, this is the most beautiful correlation I have ever made with the spectrometer.

Monday, June 25, 2012

Week 5 Day 1

Fairly calm day.  Went over the data this morning.  The Spin 7 and Buffer samples came back consistent with each other.  However the left over samples were incredibly high, way too high.  I'm pretty sure it's because I messed up that part, when I flipped the filter for the spin I accidentally put it in the same tube, not a new one.  Also I forgot to do a spin 8....incidentally Brian and I spent the afternoon making new samples and calibrations.  We ran the calibrations to make sure there were ok, but it looks like we'll have to re-do them tomorrow morning, since the magnesium and phosphorus correlation weren't very good.  And tomorrow we are going to go to the cold room again and do the experiment right this time.  (And also bring a sweater ^_^)

Week 4 Day 5

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.

Friday, June 22, 2012

septimana quattuor die quinque

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.

Thursday, June 21, 2012

Week 4 Days 3 and 4

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!

Sample ID  
Calc Conc    Actual Conc SD               % Error

Sam 1 NaCo 0.5811 0.598 0.005   2.812361468
Sam 2 NaCo 0.8173 0.799 0.00636 -2.29319108

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!

ceithre seachtaine ceithre lá

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.

Tuesday, June 19, 2012

וואָך פיר טאָג צוויי

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.

Week 4 Day 2

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.

Monday, June 18, 2012

Week 4 Day 1

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.

Четири недеље један дан

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.

Friday, June 15, 2012

ہفتے میں تین دن پانچ

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.

Week 3 Day 5

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!

Thursday, June 14, 2012

Týden tři dny čtyři

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.

Week 3 Day 4; Sodium has it in for me

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.....

Wednesday, June 13, 2012

Color Coding FTW

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 :D how's that for organization?

Uke tre Dag tre

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.

Tuesday, June 12, 2012


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.

Monday, June 11, 2012


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.

Week 3 Day 1

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.

Friday, June 8, 2012

Week 2 Day 5

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.

Thursday, June 7, 2012

Week 2 Day 4

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.

Wednesday, June 6, 2012

Week 2 Day 3

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.

Week 2 Day 3

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.

Tuesday, June 5, 2012

Week 2 Day 2

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.

Week 2 Day 2

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.

Monday, June 4, 2012

Week 2 Day 1

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.

Week 2 Day 1

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.