Working side-by-side with our Brad Chaires and his team at University of Louisville was awesome. We completed almost everything we planned and learned much more than we anticipated.Barrett and I left Louisville feeling accomplished, heavy from all the amazing food, and ready to explore the new ideas we have from this experience. The accessibility, generosity, and patience that we were shown has left an impression on our development as aspiring scientists and, more importantly, our hearts.
- Deondre and Barrett
Bill Dean showing us how to use a viscometer to determine the exact viscosity of our buffer, which is an important parameter in fitting AUC data
Excitement filled our first day of work! Barrett started his AUC experiments and spent quality time with the, AUC guru, Bill Dean running samples for 2CoreL# (for the elongated vs beads models). He also spent some time with Bill learning how buffer density and viscosity measurements are made, and we retested and confirmed the earlier values for 100K2Mg (which we need for the Sedfit AUC analysis). With Bob Gray and Brad, I learned how to run the global fitting program and completed analysis for all the 3D full wavelength experiments for 1Core and 2Core. To end a day full of good work, Brad, Debbie (Brad's wife), Barrett, and I stuffed ourselves at a Thai restaurant followed by a trip through the street with the most spooky Halloween decorations. Tomorrow, Barrett plans to work with more AUC samples (1CoreL# and 1Core inosine mutants), AUC data analysis, and preliminary molecular dynamics. I will be investigating the intermediates of the melting transition for 1Core and 2Core and begin work with our library of CD spectra for our various repeats.
Hard at work
Day two proved just as engaging as day one. I spent today collecting and processing the AUC runs from yesterday (2CoreL# samples) with Bill, as well as starting a new round of samples (1CoreG#I mutants). I have a decent sense of how Sedfit works and I'm currently trying to try to download it on my own computer. I also worked with John on understanding how Hydropro works and how to run it. Deondre spent a large time today talking with Brad about improving full wavelength data using SVD and approaches towards identifying intermediate species. He also discussed classification of our CD spectra library via PCA and HCA (hierarchical clustering analysis) and the point mutants and 2AP mutants with Brad.
We made our own dinner tonight, and are doing some additional work this evening before heading back for Day 3 tomorrow!
Another day full of great adventures in the Louisville lab has passed us. I am coming very close to identifying the intermediate species in the melting transitions for both 1Core and 2Core--which may have some interesting results. I also spent some quality time with Brad and Barrett learning how to use PCA and HCA in Origin. The coolest part of the day was easily running our library of CD spectra through Rafa's program for GQ, which I have all the materials for (thanks to Brad and John!) so we can have bring it to lab! Meanwhile, Barrett successfully installed and used Hydropro on Tel22, ran the last round of AUC, and discussed all of our current AUC data with Bill. He also reviewed paper 2 in the context of AUC and came up with a few potential new conclusions to write about.
Of course the day would not be complete without Mexican food with Brad for dinner so we went out and enjoyed ourselves once again.
Tomorrow Barrett plans to run Sedfit himself on the latest AUC data and organize the return of the samples to Swarthmore. I plan to look over the intermediates once more with Brad and leave knowing their CD spectra. Finally, Barrett and I will discuss some of our lingering questions about paper 2 with Brad.
We have made it back to Swarthmore safe and sound! Our last day in Louisville was filled with much discussion about our project with Brad and some good Vietnamese food with Bill, John, and Brad of course. Barrett and I were able to ask more questions to the whole team including Bob who has been great assistance to me in understanding global fits. Overall, we completed everything on our list besides ITC which will be completed once Lin has returned. We feel very accomplished with what we have achieved through this trip. Thank you once again for supporting us to have this memorable experience.