Madeline Dyke ’21

El-Samad Systems Biology Lab, UC San Francisco, San Francisco, CA

Me, fetching plates with bacteria that my mentor and I genetically engineered to express genes that we made.
Me, fetching plates with bacteria that my mentor and I genetically engineered to express genes that we made.

This summer, I joined the El-Samad Lab at UCSF. The lab, as part of the Biophysics and Bioengineering departments, uses genetic engineering to better understand chemical signaling pathways on a single cell level. I worked closely with Alain Bonny, a graduate student studying the stress response in Human Embryonic Kidney cells. With Alain, I researched the signaling pathway(s) that allow the cell division cycle, central metabolism (glycolysis), and the stress response to communicate. This work would shed better light on how cancer works on a cellular level, since cancerous cells are known to have aberrant metabolisms and overactive division cycles. If the scientific community can better understand how normal cell metabolism, division, and stress response works, then it will be easier to understand how cancer hijacks these processes. So of course, after finishing lunch or coming back from a lab meeting, Alain and I liked to joke, “Are you ready to go cure cancer?” Our experiment also fills a niche in the extant literature on the cell stress response, since no one has studied how these three processes (cell division, metabolism, and stress response) interact. Alain was the first to study these interactions in yeast, and Alain and I are the first to study them in human cells. Although Alain was the architect of the experiment, he entrusted me with its execution and gave me complete autonomy to modify it as I saw fit.

Our experiment is what is known as a “screen,” meaning we test many different genes to see which ones are important for signaling. To test those genes, we first genetically engineered the cells to express CRISPR, then programmed that CRISPR to target a certain gene or pair of genes, and finally observed the effects in the cell. Specifically, we used deactivated CRIPSR bound to a repressor to inactivate target genes. If we had used regular CRISPR, it would have targeted the gene and cut it out of the genome. Our deactivated CRISPR was still able to locate the correct gene, but it could no longer cut DNA. Instead, we were able to induce its expression with a drug called doxycycline, which means that we can toggle CRISPR’s activity. If regular CRIPSR is like a light switch with two options, on and off, then our inducible deactivated CRISPR bound to a repressor is like a dimmer, with a continuum of options between on and off.

This perturb and observe style of experiment is quite common in areas with little extant research. It is typically one of the first experiments to be done, since it generates a fairly broad data set for future researchers to build on and draw inspiration from. To observe the effects of gene inactivation on the cells, we genetically engineered all our cell lines to express florescent proteins. We read the literature to identify a protein that is canonically important for each of our three silos—cell stress response, cell division, and cell metabolism—and attached a different colored florescent protein to each one so we could visualize which processes were active. After we inactivated a pair of genes with CRISPR and put the cell under stress, we could use these key proteins as proxies for cellular activity. If we saw that with any two given genes missing that there was more or less metabolism happening, we knew that those genes were implicated in metabolism. If we see altered florescent activity for all three of our reporters, then we know the deactivated genes are implicated in all three processes, thereby answering our guiding question of how the processes “speak” to each other.

Although the experimental design was clever, and the underlying biology was intricate, I was particularly struck by the lab’s collaborative culture. This may have just been specific to the El-Samad lab, but it seemed like every member of the lab had a project in the works in collaboration with someone else in the lab, regardless of academic rank. Perhaps this was a product of the lab’s small size of 13, or perhaps it can be attributed to the philosophies and leadership style of the Principle Investigator (PI). The intimate and collaborative environment was reinforced by biweekly group meetings. Every Monday, we gathered for journal club, where rotating members of the lab presented on a new academic journal article that inspired them in some way. These journal clubs serve to keep the lab up to date on the latest important literature in their field. On Fridays, we met for lab meeting, where rotating members of the lab presented on their own research as it developed. Lab meeting was a time to crowd source feedback, no matter the stage of the experiment. These meetings were quite long, as the PI encouraged debate and deep engagement with the presentation, not too unlike our seminars at Williams.

I was also struck by the informality of the work calendar. My mentor, Alain, put it to me best: “In grad school, every day is Saturday! Except we work on Saturdays.” This quip came to encompass much of my summer experience, literally, since I did go into the lab on Saturdays. It also speaks more broadly to my experience in that it reflects the freedom I had. Especially in contrast to my hyper-scheduled life on campus, the freedom to make my own schedule was refreshing. It allowed me to waitress a few nights a week at a restaurant in my neighborhood and still keep up with my training schedule for the Williams crew team.

I also learned many lab techniques that I hope will open doors to future lab research or opportunities in the biotechnology industry. For example, I worked extensively with bacteria, so I am well-practiced at bacterial transformation, plating, inoculation, DNA purification, gel electrophoresis, and DNA sequencing. I also worked with online tools to engineer plasmids in silico and then build them using the lab’s innovative Mammalian Toolkit (a spin-off of a Berkeley lab’s Yeast Toolkit) and Golden Gate Assembly. I also learned tissue culture methods for epithelial human cells and lentiviruses (deactivated HIV virus). These skills position me well for future research, which I hope to pursue at Williams, outside of Williams during summers, and perhaps even after Williams in a Ph.D. program. Although I would not say that this internship has helped cement my major and career path, it has certainly affected and guided my thinking. I feel confident that biology is a path I am truly interested in, and accordingly, I plan to take more biology classes at Williams, at the very minimum. It also taught me that I am not interested in a career in academia.

I would like to thank the Williams Class of 1972 for sponsoring my experience at UCSF this summer. Without their generosity, I would not have been exposed to the wonderfully collaborative environment of the El-Samad lab and would not be so excited about studying Genetics and Neurobiology this coming semester.