About a new paper from my lab  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 , 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
Synopsis: A blurb about a recent paper from my lab , on our discovery that the bacterium that causes cholera can manipulate the mechanical environment of an animal gut to expel resident bacteria. Introduction: cholera’s tools, and ours Cholera killed more people in the 19th century than any other epidemic disease, and it continues to … Continue reading New Tricks from an Old Bacterium
Review articles — papers that summarize a topic or a technique, assessing our present state of understanding and our hopes for the future — are useful and often enjoyable to read. In Physics, these are well respected but rather rare. In Biology, it sometimes seems like the ratio of primary articles to review articles isn’t … Continue reading The Once and Future Light Sheet
An extremely long post, mainly written to have something to point people to as a commentary on some recent work. A new paper from my lab came out recently in PLOS Biology, on watching and learning about the competition between gut microbes. I like the paper a lot, and, with one possible exception, it took more hard labor … Continue reading How are your intestines like a tide pool?
I was thrilled yesterday morning to learn that super-resolution microscopy is the subject of a Nobel Prize this year. (Or more accurately, that Eric Betzig, Stefan Hell, and William E. Moerner were awarded the Nobel Prize “for the development of super-resolved fluorescence microscopy.”) Super-resolution microscopy is wonderful, as I’ve written before. In all its various … Continue reading The 2014 Nobel Prizes: Switched at Birth?
Our Physics Department Colloquium this week is on a topic I’m fond of: the analysis of super-resolution microscopy images. This occurrence isn’t surprising, since I invited the speaker, Alex Small, with whom I co-wrote a recent review paper on the subject. The problem that superresolution microscopy confronts is that it’s hard to see tiny things. … Continue reading I should think of a title involving the words “Small” and “Microscopy”
I spent much of the morning being livid, after stumbling on a paper. First, some background: In 2012, I published a paper in Nature Methods that introduced and described a new algorithm for rapidly and accurately determining the location of particles in images — something that’s very important to super-resolution microscopy, measuring fluid properties using … Continue reading Stop, thieves!
A theme shared by all the experiments in my lab is that images contain information about the physical properties of materials. One of my students gave a talk on Monday about his work exploring the fluid environment experienced by swimming microbes (see my earlier post on the microbiome). Planning it beforehand, we were thinking of … Continue reading Orbitz!