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Today the foreign factor was churning through papers again, this time looking at prior experimentation done with Nucleosome Core Particles (NCLs). These publications are along the lines of the work us internationals will be doing around the lab, so as we know what its like to be in a strange land, for those of you who are foreign to NCLs, we’ll turn this post into a lesson on NCLs and how they act in certain environments.

If you can imagine wrapping a thick string around a cylinder, that is a basic picture of an NCL, with DNA strands being the string and a histone octamer, or protein being the cylinder. As seen in the image to the right, the ‘nucleosome’ refers to this whole string and ball structure of a 146-147bp (base pair) DNA strand wrapped around the histone. This tiny structure (10nm) has a lesser negative charge than isolated DNA, due to the positive core, with an overall charge of -150. The nucleosomes can be thought of as the building blocks of chromosomes, as multiple nucleosomes can be wound together to form chromatin fibers, which be further arranged to form chromosomes. The reason we are interested in these nucleosomes is that due to the small, dense and complex structures, not much is known about the processes that compacts nucleosomes into chromatin fibers.

We’ll let that information be absorbed and talk about experimentation tomorrow. Foreign factor gone.

We moved on to different article that also tries to explain why the liked charged macroions/polyelectrolytes (DNA in particular) will want to stay attached together,in a condensed form ,when counterions are added to a solution in which they are in. We also learned ,from kurt, about the role that enthalpy and entropy play in this procedure. We learned about why the system as a whole chooses to preserve its entropy at the expense of its enthalpy by using its highest mutli-valent ion in the bonding process. I have learned a lot in just two days. It is going to be a great summer!!

Today, we basically had to catch up with the readings for research. We have a lot of fun stuff to read and get acquainted with, because the research involves a decent measure of biology. So I decided to get going with it right away and discover why two molecules(DNA) of the same charge will want to sit beside one another holding hands(be attracted to one another). They should be enemies according to the physics we all know. So to get to the bottom of this, Ben and I read our first article and then bombarded Kurt with all our uncertainties(there most always be uncertainties in labs right?)and he made them all clear. Tomorrow,we will be on to the next one.

p.s make sure you laugh at the uncertainty joke. Thanks

With a summer theme of Bio-Physics, it would seem important for Fash and Benjamin (the Foreign factor of the lab), the young Nigerian and New Zealand aspiring physicist to brush up on the prefix (Bio). Currently, although we are well versed in physical ideas, such as electrostatic repulsion, Fash’s and my biological knowledge doesn’t extend further then a semester of bio 112; leaving us about as lost as we felt line dancing at the local rodeo last weekend (although Fash did suit his pink rodeo hat).

Today — and most likely the remainder of the week — will be dedicated to becoming acclimated with the biological and chemical content of the Andressen lab, and also getting a good grasp on prior work that has been conducted on the unusual properties of DNA.

From the literature we covered today (DNA-Inspired Electrostatics – W. Gilbert, Electrostatics of Strongly Charged Biological Polymers: Ion-Mediated Interactions and Self-Organization in Nucleic Acids and Proteins – G. Wong, L. Pollack) the interesting behavior of DNA came to the forefront of Fash and my bilingual discussions. Switching effortlessly between New Zealandish, English and American, we conversed about the theme of electrostatics. We agreed that one of the most striking aspects of DNA was its charge to length ratio. The long thin DNA coil contians one unit of negative fundamental charge every 0.17nm of length. Even more remarkable than this fact, are the experimental observations that despite the repulsive effects one might expect from such dense, like charge, the DNA attracts itself under a range of solution conditions. This was a recurring theme in the literature studied, with numerous theories including Poisson-Boltzmann Mean-Field Theory, presented in an attempt to explain this unintuitive phenomena.

Also applicable to the work we will be doing was the descriptions of how DNA acts in varying ionic solutions. When placed in “physiological conditions,” (1MolL-1 NaCl) the DNA follows the shape of a coil, however, when placed in a highly dilute solution, the DNA forms into a torus (donut) shape with an average radius of 50nm. This resembles the experiments the foreign factor will most likely be looking into. However, instead of dealing with isolated DNA, we will be looking at how DNA, with nucleosomes still present within the structure, will act in varying solutions.

That seems like enough of an introduction, apologies for the accents, and until tomorrow, the Foreign half of team Andressen is out.

What an exciting time! This summer we have one returning researcher, John Giannini, and two new researchers, Olayinka O. Fasawe (Fash) (below) and Ben Constable (right). These two will be taking the reins on the nucleosome work that I just got funding for through the Research Corporation Cottrell College Science awards. They will be looking at all of the interesting ways that ions interact with nucleosomes and how these ions sometimes manage to make the nucleosomes behave in peculiar ways. John will be continuing his research on DNA condensation.

In addition to helping them all with this work, I’ll be working on a project that uses x-ray scattering to study these same nucleosomes. It should be a busy summer!

But with this talent and the wonderful resources available to us, we’re ready for it!

Today I put the finishing touches on my presentation. I added a few graphs from the first series, and changed around a bunch of the slides. Other than that I just worked on an outline for my own benefit. After listening to Alex’s presentation, I gave mine and received criticism on it. I still have some work to do on it, but it should be ready for my presentation in the spring.

Wednesday, I spent pretty much the entire day working on my presentation. I have made a series of animated pictures that will help explain overcharging and the counter ion density wave theories. I also recruited the aid of Atwater Animations Inc. to help with some of the method slides. I think that over all, my presentation is really coming together.

On Tuesday, I finished up with my final analysis of the data for the second series. I calculated all of the averages a different way, one which I found to be a much better representation of the data. I got the concentrated series to agree very closely with the diluted trials, which is very promising. I also began updating my presentation for Thursday.

I spent most of Monday organizing and analyzing the data from the second series. This included looking through all of the raw data from all of the trials, and making sure there were no large problems with it. I also updated it to take into account the standard deviation of the mean.

This is the website John and I created
http://gburgsummerphysics.webs.com/