August 08, 2016 at 03:29AM

Today I Learned: 1) The bacteria Bacillus Subtilis (B. sub) can differentiate into at least 8 cell types. The "default" cell type (the one it defaults to if no other genetic differentiation programs are activated) a highly motile, flagellar type, good for moving around and finding fresh sites to colonize. Once a B. sub colony takes hold and starts to grow, the colony will differentiate into a few different cell types. "Miner" cells specialize in excreting hydrolytic enzymes into the environment, which is good for digesting random proteins into amino acids that the colony can eat. Others specialize in excreting the extracellular matrix proteins that make up the bulk of the colony's mass and protect it from small-scale intrusion and viral infiltration... but those cells won't actually excrete matrix protein without signals from B. sub specialized for surfactin production. Surfactin also acts as a broad-spectrum antibiotic, further protecting the colony. When exposed to stress, B. sub can and does differentiate into all of the above, plus a few emergency-response phenotypes. Some go motile again, fleeing for more fertile ground. Others enter a cannibalistic state, in which they specialize in eating up dead B. sub, therefore taking maximal advantage of all the dead material around. A few enter a state called competency, which means they open up their membranes a bit and start sucking down any DNA floating around in the hopes that something will carry a gene that will let them survive.* Most competent cells will fail and die, so it's not worth having much of the population attempt competency, but occasionally it works. The last-resort phenotype, and the one that all B. sub will flip to if stressed hard enough, is sporulation. A sporulating B. sub gives up any hope of surviving in the present environment and forms a kind of extremely tough lifeboat for its DNA and just enough machinery to boot up a new cell. Committing to sporulation is not a decision to make lightly -- the spore is built *inside* the mother cell**, and is dehydrated and released forcibly, killing the mother cell. It's a measure of last resort, but it *does* let cells survive ridiculously hostile conditions, like being boiled or actively attacked with lytic toxins. This is just a reminder that bacteria, though technically single-celled, can really be thought of as a kind of colonial organism. For more details on B. sub population differentiation, see http://ift.tt/2aTBCfO (not sure if it's open access, sadly). It one of the cuter and more helpful first figures I've seen in a paper, so at least check it out for that. * That competency works at all should tell you something about how different the microbial world is from our macro-scale world -- bacteria live in an environment where eating and incorporating random genes is a matter of choice, and is occasionally useful. That's a bit like a poisoned person eating every random plant in sight in the hopes of finding an antidote, or a computer under attack grabbing random download links for binary files and trying to execute them in case it helps. I'd say the other emergency-response phenotypes are totally familiar to anyone who's read any apocalyptic space opera, but competency is a stress response more or less alien to human experience. ** The spores are impressively complex. Check out the "Structure" subsection on the Wiki page for "Endospore". In case you don't, here's a summary: the cell's DNA is packaged tightly inside UV-protective, chromatin-like proteins. The DNA/protein mix is further packed with calcium dipicolinate, a small acid that essentially acts as packing foam by protecting and stabilizing the core contents, along with a bunch of ribosomes and critical enzymes. The core is packaged inside a peptidoglycan membrane called the "cortex" that I asssume forms the outer cell wall of a hatched spore. The cortex is further wrapped in a molecular seive that protects the spore against most toxins, especially lytic enzymes. This package is released 2) One of the weird quirks of studying bacteria is that the bacteria we study in the lab aren't really what's in the wild. After all, lab conditions are only vaguely similar to real environmental conditions, and bacteria start evolving to adapt to lab environments *very quickly*. After a couple of days-to-weeks of growth in a lab, bacterial populations become "domesticated" -- they lose a lot of their wild adaptations and become heavily optimized for lab conditions, which are extremely nutrient-rich and well-mixed (not spatially-structured). In some ways, this makes them more convenient for lab work, since domesticated bacteria grow more quickly and more robustly (in a lab) than their wild counterparts. If you just want to use bacteria to grow plasmids, it's great, but if you want to *actually study* bacteria, domestication can be a real annoyance. Today I learned that one of the hallmarks of domestication is that bacteria lose a lot of their phenotypes related to colonial life. The colonies formed by domesticated bacteria are weirdly smooth and unstructured, and in many cases are smaller than wild-type colonies. This makes sense -- bacteria in a lab are usually grown in shaken liquid media, where they have no opportunity to form colonies. In those conditions, evolution favors bacteria that can eat and divide quickly, not bacteria that can form stable, thriving colonies. See http://ift.tt/2aZXjw3 for details, especially figure 2 (probably paywalled, sorry!). Incidentally (or maybe not incidentally), similar changes happens in mammalian cell culture all the time, too. That's doubly true for cancer lines, since cancers tend to mutate early and often. That's *extra* annoying because cancer cells are used disproportionately for cell culture studies due to their unlimited replicative potential. 3) Cleaned a keyboard for the first time today. Not really a fact to put here, but I now have a very good idea what's under the keys in a ten-year-old keyboard. (...actually, there *is* a bit of a fact to this one -- today I learned that keyboards are a really efficient sink for, of all things, cat hair. This keyboard hasn't cohabitated with a cat for somewhere between 4 and 6 years, yet it had a nice thick layer of redish cat hair under the keys)