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So today we made it to the labs! I met Dr. Cedric Bouzigues and a graduate student, Rachid, with whom I'll be working all summer. My project is basically the current stage of his Thesis. Dr. Bouzigues took me on a quick tour of the facility, focusing on the room my desk is in and the lab the TIRF microscope is in. I worked with Rachid in the lab and already got to work with the microscope . I was trying to focus it on a line drawn on a cover slip first with 20X which was easy and then 100X which was trickier. Rachid says it will take some practice to get a feel for when to move closer or further away from the slide with the scope. Then as we discussed what was actually going to be done, I discovered that my project was quite a bit different from what I originally imagined which was probably part of the point of our whole presentations. However all the background research that I did was definitely helpful! I was able to answer a lot of questions correctly such as why we needed a liquid on the slides (so the refractive index is the same as the cover slip, the refractive index of the air is too different), knew that the slide was lighted from below by a laser, understood the overall objective of the project (to study how proteins repair broken dna), what gain is, and a couple other things I do not remember right now.

I will be spending my time this summer split between two general activities, taking data and analyzing it, for each stage. For taking data I will be preparing slides and then using the camera to take pictures and videos of the interactions between dna and proteins. I can not actually see the dna or the proteins but rather if either one is interacting they light up the entire pixel they are in. One of the sources of error in this project is the fact that both of these molecules are significantly smaller than the pixel itself so its not very well localized. Then when I analyze, I will be using matlab programs that Rachid has written to watch the pixels that seem to be dna and determine how many possible interactions each has per trial and how long these interactions last. When you first select the dna spot to study you determine its precise location with a matlab program. This is also within a margin of error because of the fact that the dna is smaller than a pixel but you obviously cant see smaller than a pixel and another error arises for this calculation because the slide is always moving a little bit from natural oscillations. One of the possible solutions to this problem would be to use quantum dots as markers for the slide and then measuring the relative positions of the dna and proteins to those quantum dots. Quantum dots are like the other molecules that have been dyed fluorescent but unlike those, their fluorescence doesn't ever die (the fluorescence of the dna and proteins disappears after an average of two seconds because of interactions with air molecules) because they are composed of inorganic materials.

To begin this summer my project is too optimize the surfaces to produce the most dna and protein interactions. To achieve this we are going to try covering the surface with a thin layer of proteins. The other proteins will not be able to interact with these proteins and so will hopefully be attracted more often to the broken dna "flaps". I am not yet sure how we cover a slide with proteins but I did get to watch Rachid prepare a slide today and place it on the microscope.

After we achieve this, I will be working with Rachid on studying the length of time interactions take to occur. The resulting average could help distinguish the strength of the current contradictory theories for the proteins behavior.