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Blog post by Jacqueline Fukumoto



As a first year Neurobiology, Physiology, and Behavior major at UC Davis, I had calculus, biology, and an Asian American cultural studies class on my schedule for the fall quarter. However, I wanted to also try a seminar, to get some credits but also learn something new for fun in addition to the classes I had. Honestly, I chose this microbiome lab seminar at random. When learning what research we were going do for the quarter, my interest was piqued because this seminar was a research course, meaning it wasn’t something canned and done before where the results were predetermined, but something new to be discovered and observed. This research-based course explored the effects of various flowers and its nectar, how that might affect the microbiomes in the nectar, therefore possibly influencing different pollinators.

I think that the most interesting part of this lab experiment for me was the gel electrophoresis lab day. I had done this before during my senior year in high school, but didn’t really understand the science behind it. I had learned about how the DNA samples were negatively charged, and with electricity running through it, the DNA traveled towards the positive end of the electrode. Shorter strands of DNA would travel faster through the gel, while longer strands traveled at a slower rate. This process distinguishes DNA length. This was really fascinating to learn and witness. Additionally, for this class and as a contribution to this ongoing research project, I was paired with another student and we prepared the step-by-step instructions for the class for Sanger sequencing data analysis. This part of the experimental workflow is needed to edit and make sense of the gene sequence files we got back from the campus sequencing facility. After modifying the files, we were able to visualize and BLAST them to find out what kind of bacteria we isolated. The protocol we created for this step will be used in future classes! While this was just computer work, I had learned something new and it was really cool to finally see what kind of bugs we were working with this entire quarter. The sample I processed through SeqTrace turned out to be the Erwinia aphidicola partial 16S rRNA gene.

From this seminar, I learned in real time about science. We didn’t have perfect results. Some results were inconclusive, some samples couldn’t be used, all from mistakes. We went back for other samples and did the gel electrophoresis for those. It was all a process of learning from mistakes. Even though I chose this seminar randomly, it turned out to be a surprisingly educational and fun course from the different parts of experimenting to be doing actual research and exploring the work of a real scientist.

David Coil

David Coil is a Project Scientist in the lab of Jonathan Eisen at UC Davis. David works at the intersection between research, education, and outreach in the areas of the microbiology of the built environment, microbial ecology, and bacterial genomics. Twitter

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