August 23, 2017 at 06:57PM

Today's TIL is actually facts from yesterday, but I didn't get a chance to compile them yesterday. So here they are, today: 1) ...about Rho-factor termination in prokaryotes. Rho-factor termination is one of the two main mechanisms that prokaryotic genes use to stop transcription (termination). The *other* termination mechanism is called "Rho-independent termination", and is what I usually think of when I think of a terminator. Rho-independent terminators are (usually GC-rich) regions of DNA at the end of a gene that, when transcribed, form a long hairpin. The hairpin is shaped just right so that when RNA polymerase produces the terminator, it gumms up the polymerase and makes it get stuck, so it sits there until it eventually falls off on its own. Roughly. Rho-dependent termination is a little more convoluted. Rho-dependent termination is dependent on a protein called, uh, Rho factor. Thus "Rho-dependent". Anyway, Rho factor bind to a specific sequence of *RNA* just upstream of a more standard terminator hairpin. When the Rho binding site is transcribed, Rho factor binds to it and starts moving down the still-growing transcript, towards the transcription fork (how it does this isn't entirely know, but it' suspected that Rho factor forms a barrel-like structure and pulls the RNA transcript through the center, spooling it onto the other end of the Rho factor as it goes. In any case, the process is ATP-dependent). Meanwhile, a more normal terminator makes RNA polymerase pause long enough for Rho factor to catch up; when it does, it unwinds the transcription bubble somehow, popping off RNA polymerase, halting transcription, and releasing the new RNA. 2) So-called "cold" plasmas don't have a well-defined temperature. It turns out that, at a stat mech level, the charged ions in a cold plasma act as though they're at a different temperature than neutrally-charged particles. So the whole thing, taken as a whole, doesn't really have a single temperature. 3) You can use MCMC to sample phylogenetic trees. It's basically the same process as usual MCMC, but there are two particular challenges for phylogenetic trees. One problem is mixing, which can be particularly bad in tree-space -- but that's always solvable with more computing power. Another is visualization -- it's not obvious how you plot, say, a collection of 25,000 likely tree reconstructions in a way that's useful. There are some algorithms for calculating distance metrics between trees, which can then be plotted in whatever-D you can visualize (so, 2D or 3D). For more general information about MCMC on phylogenetic trees, see http://ift.tt/2xtANmR. For more information on *visualizing* MCMC results on phylogenetic trees, see http://ift.tt/2wzJQpE.