In science there are experiments that try to construct simple, tractable models of complex phenomena, with the goal of developing insights that will be relevant to the more complicated systems. Alternatively, there are experiments that try to infer insights amid a flurry of coexisting factors. Each of these approaches has its merits and flaws. I … Continue reading How to build a gut microbiome in 119 easy steps
About a recent paper from my lab: Deepika Sundarraman, T. Jarrod Smith, Jade V. Z. Kast, Karen Guillemin, and Raghuveer Parthasarathy, “Disaggregation as an interaction mechanism among intestinal bacteria,” Biophysical Journal (2022). Some bacteria stick together; others do not. We have seen these variations among bacteria inside the zebrafish gut, and it’s probably the case … Continue reading Things Fall Apart; The Bacterial Cluster Cannot Hold
The third in a series of biophysical questions (one, two). Finding food is an essential activity for any organism. We and many other animals interpret sights, sounds, and smells to make decisions about where to go or what to do to get things to eat. But what about a bacterium, a single-celled organism just a … Continue reading Can a brainless bacterium navigate? (What is biophysics? #3)
About a recent paper from my lab: B. H. Schlomann and R. Parthasarathy, “Gut bacterial aggregates as living gels,” eLife, 10: e71105 (2021). DOI: 10.7554/eLife.71105. What do gut bacterial colonies look like? My group has been exploring this question for years, and ever since our first forays peering inside larval zebrafish it has been evident … Continue reading Living Gels
About a paper from my lab [1] on competition and cooperation among gut microbes. Is the whole more than the sum of its parts? This question arises throughout the sciences, as one wonders whether understanding the constituents of some system suffices to understand the system as a whole. Sometimes the answer is “yes.” Electromagnetic fields, … Continue reading Tossing Starfish from the Tidepools — Gut Microbiome Edition
About a new paper from my lab [1] on why gut bacteria swim, and whether their host cares. Many bacteria swim. It’s a great way to explore one’s surroundings, run away from toxins, or move toward regions with more food. Over the past several years, as we’ve used 3D microscopy to peer inside zebrafish to … Continue reading Putting the brakes on gut bacteria
Synopsis: In a recent paper from my lab [1], we report on watching gut bacteria get pummeled by low doses of antibiotics. The antibiotics induce changes in the spatial organization of the microbes, with major consequences for their ability to persist in the gut. Motivations At high enough doses, antibiotic drugs will kill bacteria, or at … Continue reading An intestinal amplifier for antibiotics
A few evenings ago I gave a “science pub” talk — part of a long-running series of public presentations that the Oregon Museum of Science and Industry runs at several sites in the state. (This was at a local pizza place, so thankfully I could just bike to it.) I called the talk “Glimpses of … Continue reading Science Pub 2016
(A more technical post than most, in which we look at bacterial population densities, and watch a movie.) This term I taught a graduate biophysics course, about which I’ll write a recap later. Bacteria came up a lot in the course, both because they’re important but also because they offer many nice illustrations of how … Continue reading Bacteria and Boltzmann
I was a participant (contestant?) in our local “Physics Slam” two weeks ago, in which half a dozen physics faculty gave 10 minute talks to the general public, with a “winner” chosen by about five judges selected from the audience. About 500 people came, filling an auditorium: My talk, Why do bacteria care about physics?, … Continue reading Slammed! (Why do bacteria care about physics?)
The Eighteenth Elephant 