Never be afraid to get dirty, but be sufficiently sure-footed to avoid the abyss of contamination.

Variations on a Theme

Information theory, statistical decision theory, and game theory have developed methods to analyze what some may consider adversarial situations. Lessons in these fields have certainly influenced how I model problems involving adversaries. Perhaps it should come as no surprise then that such models were in my thoughts as I attempted to read about host-pathogen interactions. The work in question was a review paper from Hidde Ploegh’s lab. Ploegh’s lab studies mechanisms by which seemingly simple bacteria have been able to infiltrate our complex immune systems.

How does the lab conduct this research? Renuka Sastry, a researcher at the Whitehead Institute and one of Ploegh’s graduate students, gave me a tour of the lab. Our first stop was at what appeared to be a cylindrical dark room.

“It’s used for western blots,” Renuka said. As she explained, a western blot is a technique to test for a specific protein in a tissue sample. The results are represented as lines on a plastic page, where a line indicates the presence of said protein.

Surprisingly, it takes some effort to extract this bit of information. Part of the process was unfolding on Renuka’s workbench. A gel electrophoresis was running, but there were a couple differences from ones I had seen for DNA. First, the gel was positioned vertically instead of horizontally. Second, the gel looked significantly thinner than an agarose gel. Renuka’s electrophoresis was one stage in an experiment to test for a particular protein. She was hoping the result would validate an observation she had made earlier.

Noticeably absent from the workbench was a computer. While there was a computer in that room, our next destination was filled with them. The mass spectrometry room is used to identify proteins, and computers are used to crunch numbers and consult databases for protein matches. Of course, the proteins come from living cultures, and in the final part of our tour, I saw one under a microscope.

What struck me during the visit was that these methods and techniques could also be applied to problems that did not involve hosts and pathogens. What drew Renuka to the work?

“I wanted to do biochemistry research,” she responded. I left with a better appreciation for this research. Whether this appreciation might inspire new ways to model aspects of these host-pathogen interactions is an open question.

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