Cas9 Specificity, Armadillo Polyembryony, and Relaxation Oscillators

Today I Learned:
1) ... a bit more about the specificity of Cas9. Turns out that cas9 can cut targets that differ from the guide by one or two nucleotides, though at reduced efficiency. More than that makes it completely non-functional. This is really important for genome editing, because you really don't want it cutting in places you don't expect. Cas9 used for regulation may be another story entirely. According to some iGEM data I found, cas9 may still be able to *bind* (but not necessarily cut) at an appreciable rate (5% of the maximum-efficiency rate) with a dozen nucleotide differences. These particular numbers seem a bit absurd to me, but I also recall seeing one paper in which the authors made tunable cas9 repressors by mutating the guide RNA a little bit off of the target. Unfortunately, I can't find that paper right now, so I'm not going to link it. This needs corroboration.

2) Armadillos use a rare form of reproduction called “polyembryony”, in which a mother has a single fertilized egg during pregnancy, but that egg splits into multiple embryos which develop into multiple genetically identical siblings. This is how you get identical twins in humans and other animals, but a few species of armadillos are the only vertebrate species known to exclusively reproduce through polyembryony.

Polyembryony is a particularly weird form of reproduction because it seems to combine the biggest disadvantages of both sexual and asexual reproduction. Unlike asexually-reproducing species, armadillos have to find mates to reproduce, and only pass half of their genes to their offspring. But unlike sexually-reproducing species, an armadillo’s offspring are not particularly diverse, and so are vulnerable to parasites, diseases, and environmental conditions that disproportionately affect certain genotypes.

Why polyembryony, then? The best proposed reason I’ve found is that it’s an adaptation to a sort of pre-existing evolutionary condition in the armadillo — the structure of the armadillo’s uterus is such that only one egg can be fertilized at a time. Why? We don’t know. Presumably it happened for some other reason, or perhaps entirely by accident, but whatever the reason, *if* you take it as a given that only one egg can be fertilized, yet the mother can provide for more than one offspring in a litter (armadillo mothers don’t care for the young particularly much or long), then polyembryony makes some sense.

Thanks to Heather Leigh for pointing me to this fascinating armadillo information!

3) A relaxation oscillator is a system that behaves periodically but not sinusoidally. Simple examples include square wave oscillators and sawtooth oscillators. A more complicated example would be a ring tone.

A typical way to think about relaxation oscillators is that there’s some timer that counts down, and when that timer hits zero, the system produces some distinct output, like a square wave or a spike or a measure from some musical piece. Then the timer resets and starts counting again. Relaxation oscillators are a common motif in electrical circuits, where the “timer” is often a capacitor. The capacitor’s charge spikes out, triggering the output signal, then slowly decays (relaxes) back to its charge value. Hence “relaxation oscillator”.