Looking towards the end of the calendar year

The final stretch of the semester is finally here.

While talk of the end has been buzzing around campus for a while, the feeling does not come until the final week before finals. On Tuesday, the Williams lab presented our progress reports wrapping up four months of hard work.

Alex gave an amazing talk on her grueling process towards perfecting the ChIP protocol. She performed her experiment multiple times under different protocol permutations in order to identify the factor that generates the problem. She figured out that the main cause of variability was due to non-specific bindings either from the type of beads that she was using or from the addition of pre-clearing and pre-blocking. With changing the bead type and removing those steps, Alex’s controls worked and she’s excited to continue her project with the newly minted Ahr1B antibody.

Maddie’s project were going great as well. She has collected multiple confocal and SEM pictures of the otoliths between the AB strain and the Nfe2-KO strain in the presence of tBOOH, an oxidative stress inducer. She described the trend of differences between the treatment groups where specifically, at the 48 hour mark, the neuromast score of the WT strain is significantly less when treated with tBOOH. She plans to collect more SEM images in the future, as well as continuing with her observations of the KO strain.

Jacob’s diligence pays off greatly as we get to see some of the data he collected. Unfortunately since the treatment was not standardized with previous research done at the University of Massachusetts Amherst, Jacob has to replicate that work as well. Even though this seems like a setback, he is confident that this will not only enhance his lab skills, but also give a more comprehensive look. Jacob is looking forward to further continuing his project and starting qPCR

With regards to my work, I am in the process of interpreting the transcriptome dynamics comparison between the WT and KO strain in terms of the expression patterns and functional analysis. I compared different gene lists generated in order to determine whether genes changes expressed only at one point in time or at multiple time points, the direction of expression changes as well as which stages experienced the most stages. Subsequently, I also compared my lists with a previous research on transcriptome dynamics of the AB strain across developmental time points, and identify specific genes that show up on both lists and determine which ways they are disregulated by the absence of Nfe2. I am also excited to start the wet-lab part of my project with molecular cloning and capped mRNA injections.
The semester has been fun, however we all are excited of the coming challenges.