After starting the ICP- OES, I created 5 mL samples including 50 uL of the samples provided that consist of DNA with 1 mM Cobalt2+ and varied amounts of Sodium+ ions dissolved in a solution of KCl and Tris. The samples had sodium amounts from 0 to 80 mM. The samples were run with the calibration of cobalt, sodium and phosphorus that were created previously. I had the chance to modify the method for this run from the method used yesterday. The ICP was then put on standby for Monday and I have several graphs to make on Monday based on the data from today’s run. Hopefully I can put a few of them in on Monday once they are completed.
P.S.
I almost forgot to mention a revelation I had while Prof. Andresen was explaining the physics (mostly thermo) behind what we are attempting to do. For over ten years, studies have been undertaken to determine why, under certain conditions that I don’t remember exactly, DNA will attract another DNA even though they are both negatively charged. The Poisson- Boltzmann equation fits what is observed except for the attraction part. In lab, we are trying to evaluate what is causing this attraction. This leads to my revelation, Prof. Andresen explained this to me today and all I thought about was a scene in Chasing Liberty (a movie about the president’s daughter on an adventure in Europe) and the part where the president’s daughter was a “Chickie buffer (that) negates the potential for man-touching-man discomfort” so that the two guys in the movie could hug with her between them. So this summer, I am trying to find the chickie buffer!
Author: Prof. Andresen
Week 1 Day 4
Today I delved into some LabVIEW code that we will be using for our magnetic tweezers setup. We identified the sub VIs pertaining to motor control and basically figured out how they work. We also identified possibilities for future motor control.
Week 1 Days 1/2/3
Day 1
Day 3
Week One: Day Three
I started up the ICP with help from Prof. Andresen, including putting new tubing on the Peristaltic pump. I ran a calibration set for 50mL solutions comprising of 0-500ppb of Na, Co, and P for a total of six calibrations. These were also used as the samples. In the afternoon, I read through the software manual and then Prof. Andresen and I reprocessed the samples from the morning and reviewed the data.
Week 9
Last week and probably final post for the summer. Finished that last trial and ran the samples 4 times, averaging. Then ran the buffer and spin 8 again another 4 times and averaged them in. Took standard deviation of the data points for my error. Unfortunately the phosphorus count was very low, and the trend was not defined in the sodium. But error bars were a little smaller and we were on the right track.
Next, I only had enough nucleosomes for 3 more samples. So I made the second, third, and fifth sample a last time, spun in the cold room, ran the NCP, buffer, spin 8 and spin 7 many times and averaged them together. This time the phosphorus count came out well, the trend was defined, and the error bars much MUCH smaller. Certainly a good place to end for the summer. Hopefully after Andresen makes more nucleosomes, I can run again in the fall and perfect the experiment, getting reproducible data again and again. For now I can work on a poster for Celebration next spring, and in the future (maybe?) help get the data published?
Week 8 day 3
Today, I finished analyzing my data from the last two experiments I ran. My second experiment came out very weird, but the data from my first appeared good except for the sodium. Now I am going to run the experiment again to drive down my error bars. Today I made my NCP samples and spun them. I also made a new calibration set because I discovered that my previous data was not covered completely by the previous calibration. Tomorrow I will run the spectrometer and analyze this new data.
Week 8 Day 1-2
In the last couple days I have gone through the steps of another trial. Spun friday, made samples and ran monday/ tuesday. This time per Andresen request I ran the samples out, 4 times. I will average the data and take the standard deviation from those 4 trials. The I will go through the same steps of analysis to come up with my graphs. Looks good in the preliminary raw data. Will see how I feel later on tomorrow.
On another note I ran the chlorine and bromine calibrations I made. Lets just say the spectrometer didn’t detect any difference in the 0 ppm Br and the 1000 ppm Br samples. The chlorine detected something, but the correlation is really bad. For both of these elements when you go to look at the spectra in the offline Winlab mode, there really is no peak to see. Perhaps the spectrometer isn’t looking at the right wavelength? More thought will be put into this.
Lab Instructions
Finished the lab instructions for my experiment with the help of Brian.
Week 7 Day 4
Today, I decided to try to redo my experiment but with different concentrations of MgCl. After making the samples, the concetrations are 0, 1, 10, 12, and 50 mM. I ran out of nucleosomes while making the last sample so sample 3 has only 15 microliters of NCP rather than 41. After making the samples, I spun them and pipetted out the top and bottom into separate tubes. I am ready to run the samples again when we have gas.
Week 7 Day 4
As with all science, you can’t just do an experiment once to prove a hypothesis. So today I made another set of samples just like the last set, to repeat the experiment and see if I can get the same results. Of course I don’t anticipate having the same problems with the scale again, so I think this next run will go smoother and I can get results quicker!