Week of June 6
McVey Lab
This week was my first McVey Lab meeting; I sat in on a practice talk about the roles of structure-specific endonucleases in DNA damage tolerance. Attending these meetings will reinforce the biological context for my project this summer and hopefully future projects as well.
Cowen Group
I spent the first part of my week preparing my first BCB group talk of the summer. Each week at BCB group meetings, a grad student gives a talk explaining the current state of their research. This week was my turn. I explained where I had wrapped up at the end of the spring semester and what I was currently working on. Feedback from the group helped direct my next steps.
Research Highlights
At a meeting at the end of the week, my advisors and I agreed to try realigning the repaired sequences to their references with a custom piece of software to see if we could produce more useful, accurate information about true mutations than the out-of-the-box alignment tool used previously. The use case for most aligners is a scenario in which researchers have a query sequence to compare to a massive database of potentially-homologous DNA, but our problem is simpler than that: we only need to align the repaired sequence to an exact copy of the repair substrate. I made plans to address this beginning in Week 3, which will begin in two weeks, after a trip to the west coast.
What I’m Reading
J. Brown, A.T. Al-Soodani, M. Saul, S. Her, J.C. Garcia, D.A. Ramsden, C. Her, and S.A. Roberts, “High-Throughput Analysis of DNA Break-Induced Chromosome Rearrangements by Amplicon Sequencing,” Methods in Enzymology, vol. 601, no. 0076-6879, pp.111-144, March 2018. doi: 10.1016/bs.mie.2017.11.028