Coding: The First Attempt

While meeting with the only other member of the team besides Professor Aday with any DTRA experience, Diya Uthappa, it became clear that the biggest obstacle we need to overcome in order to be able to code a large amount of DTRA is standardizing our practices. The goal of this summer has just become figuring out how to code so that no matter who is doing it, the results are pretty similar, or at the very least between Diya and I if one of us is coding it will likely be similar to the other.

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The summer of ChIP

Hi,

I’ve had a busy summer. All summer I have been working on my Chromatin Immunoprecipitation (ChIP) assay with the hope of showing that the Huntington protein can bind to DNA. After my second try I think I got it to work. However, the results were inconclusive since the no antibody smaple had the same fragment amplification as the sample with htt. Therefore, I think the antibody I used was not working, so I ordered a new anti-htt antibody which will hopefully allow me to successfully complete the assay. If I’m lucky by next week I should have results!

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Artist’s Dye Fading Part 2: Jun 16th – Jun 30th

The new thing that I learned since the last post is that science is frustrating. As I continued with the solvatochromism studies it occured to me that I needed to carry out control experiments on the solvents that I was using. This led me to realize that some of the data that I was seeing was actually an artifact of the fluorimeter that I was using. Apparently there is a small amount of light that scatters off the solvent and gives rise to an emission peak which I had previously assumed was a result of Alizarin fluorescing. Fortunately by this point we had only made preliminary hypotheses based on the false data and any major disaster was avoided. This doesn’t change the fact that it is a pain in my butt. Although I think that the fluorimeter is stupid and that I shouldnt have to deal with this, I have learned a valuable lesson to always do control experiments.

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American Chestnut project update

The last month has gone by incredibly fast! At the beginning of the summer, we set out all of the American Chestnut and Red Oak seedlings at Sullivan Greenhouse, near the law school. So far, all are growing well and look extremely healthy.  Olivia and I have been out every week or so to either apply fungicide or take measurements on plant growth. It’s really just a big waiting game at the moment, as the mycorrhizae in the plant soil will not be ready for analysis until the end of the summer. In the mean time, my biggest project-related job will be to learn how to perform the experimental procedures (both PCR and root staining) that we will be doing later on to identify the quantity and type of mycorrhizae living on these tree roots. Hopefully all of our materials will come in within the next week so that I can start practicing on tree roots that we’ve collected from the college woods.milkweed2

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Cloning Fun

Hello! It has taken me a while to get underway with results from what I’ve been working on because so far I’ve just been doing a lot of cloning (which has been giving me some trouble).  I began by designing and ordering SUMO-deficient mutants of TR using GeneArt.  Then, I worked on cloning these mutants into m-Cherry so that I would be able to visualize the mutant once transfected.  Unfortunately, I have been having some trouble sub-cloning successfully and had to try multiple times to clone the mutants into m-Cherry.  I am 90% sure I have successfully cloned my mutants into m-Cherry as of now (from checking on a gel), this confirmation has just been put on pause for a while because of issues with sequencing.  However, I believe that the sequencer will be working again soon and I will be able to 100% confirm my clone.

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