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Northwestern University Feinberg School of Medicine

Student Q&A: John Brooks, Driskill Graduate Program in the Life Sciences

John Brooks

Where is your hometown?
Grand Blanc, Michigan, a suburb of Flint.

What is your educational background?
I obtained my bachelor of science degree in microbiology from the University of Michigan, Ann Arbor. During my undergraduate career, I performed research in the laboratory of Janine Maddock, PhD.  In those years I aimed to understand how the spatial organization of proteins was conferred in a prokaryotic cell. It was previously thought that the lack of organelles in the prokaryotic cell correlated to a lack of sub-cellular complexity. However, it has since been discovered that the prokaryotic cell possesses a high degree of sub-cellular organization in the sense of protein localization. 

The goal of my project was to identify proteins that localized specifically to the middle (septum) or end (polar) of the cell by performing a large screen. Graduate students in the lab are currently pursuing the mechanism by which some of those candidates find their cellular addresses.

What research are you involved with today?
My graduate training is taking place in the laboratory of Mark Mandel, PhD, assistant professor of microbiology and immunology, Feinberg. My fundamental research objective is to understand how specific symbiotic relationships between microbes and their animal hosts are established.

It is known that animals form functional beneficial relationships with bacteria, and we have come to understand that these relationships are vital, yet to date little is known about how animals acquire beneficial bacteria from the environment. To study this phenomenon, I utilize a model system in which Euprymna scolopes (squid) is colonized specifically by its beneficial microbial partner, the luminescent bacterium Vibrio fischeri.

My thesis project is to identify novel genetic factors required for the establishment of the symbiotic relationship between V. fischeri and the squid. To accomplish this goal, I am conducting a high-throughput negative selection screen that combines high-density transposing mutagenesis with Illumina deep sequencing technology. To date I have identified a number of  genes required for survival in oxidative and nitrosative stress conditions, envelope integrity, DNA mismatch repair, and protein stability. The squid environment is known to be replete with toxic compounds, and these mutants provide tools to understand how the bacterial symbionts signal and survive during symbiotic development. It is worth noting that pathogenic bacteria also utilize similar stress-responsive genes in order to cause disease, and these data suggests that many of the genes required for microbe-animal associations are conserved between beneficial and pathogenic bacteria.

What is the goal of your research?
Many people would be shocked to find that we as humans form life-long, beneficial relationships with more than 1,000 different bacterial species. This diverse collection of bacteria aid not only in the development of both our immune and digestive systems, but also act to protect against the invasion of pathogenic bacteria. Although we ultimately get colonized by trillions of bacteria, we are born germ-free, and it is through interactions with our environment that we become host to the specific lineages of bacteria that make up our microbial consortia. My plan of research seeks to clarify how beneficial bacteria are reliably acquired from the environment by their animal hosts to the exclusion of pathogenic bacteria.

What attracted you to the Driskill Graduate Program?
When I was looking at schools, the determining factor for me was interaction with the faculty members. The faculty at Feinberg seemed very excited when I discussed my previous research and seemed enthusiastic about the research they presented to me. That kind of passion only breeds good science, and that was one of the keynotes that brought me to Feinberg.

What do you hope to do in the future?
After graduate school I aim to obtain an academic post-doctoral fellowship, as my goal is to ultimately become a professor.

Connect with John Brooks on LinkedIn.