Ribosome Exit Tunnels, Cas9 Tricks, and Theories of Others of Ducks

Today I Learned:
1) I quote: “…the exit tunnel of the ribosome admits ~28 amino acids of the extended polypeptide”. So while a protein is being translated into existence, *28* of its amino acids are ensconced inside the ribosome at any given time. That’s way more than I thought — I usually think of the ribosome as a little unit about the size of an amino acid, but that’s clearly very wrong — it’s made up of RNA, after all, and RNA is made of nucleic acids, and nucleic acids are bigger than amino acids. This seems like a fun number to know.

Quote quoted from http://ift.tt/1FbxJhA (free access).

2) A couple of new tricks with cas9. In particular, there’s a way to functionalize dCas9 (that’s the version of cas9 lacking DNA-cutting capability) without fusing stuff to your dCas9. It’s a bit technical and a drawing might help, so here’s a rough diagram of Cas9 and its associated RNAs: http://ift.tt/1LvoXYH

The trick is to use the sgRNA loop shown at the top of the diagram in the REC domain to recruit other proteins. You extend the loop out of the protein (it normally sticks out at least somewhat) and add a single-stranded loop with a known DNA binding site for some DNA binding protein. Then you can make a fusion of that DNA binding protein with whatever you want to functionalize your cas9 with, and it will bind to the sgRNA. This gives you an extra level of indirection between your target sequence and your cas9-mediated function, which as any computer scientist can tell you will can solve a lot of problems before they crop up.

3) Ducks, apparently, do not have much of a theory of others when it comes to turtles. That or they’re just jerks. Today I observed several incidents of ducks swimming, walking, and flapping on and around turtles with no apparent regard for said turtles’ existence. Poor things.

Not really related, but I also watched a turtle crawl around on land for a while before grabbing a rather large twig (several times longer than its body) and dragging it straight back to the water. It then dropped the twig, hung around for a minute, and left with no further ceremony. Did it think the twig was food, only to discover otherwise when it got to the water? I have a theory that turtles (unlike tortoises) can’t really eat or taste effectively unless they’re in water, which would support this interpretation. What do you think?