That zebrafish movie annotated and explained, a little

By popular request, here’s a roughly annotated version of that zebrafish development movie.

Stuff to watch for:

  • This movie starts at the 8-16 cell stage. The cells of the embryo proper (blastomeres) are at the top, sitting on a large yolk cell.

  • The pulsing is caused by the synchronous early divisions of all the cells. They lose synchrony at the mid-blastula transition.

  • Epiboly is the process by which the cells migrate downward over the yolk. An arrow will briefly flash, pointing to about 11:00, in the direction of the animal pole (where the future nose will form, sorta). That happens just before the whole animal begins to rotate within the chorion, just to make following everything more difficult.

  • After the animal rolls over, the animal pole is pointing straight up at you, and the migrating cells will form the germ ring, a thickening around the equator of the embryo. Cells will also migrate towards one point along the ring, forming a thickening called the keel. This is where the embryonic axis is forming; cells are migrating into the interior at this point in the process called gastrulation, and this region is roughly equivalent to the dorsal lip of a frog.

  • The whole animal is going to roll over again, this time to its side. The keel is thickening and lengthening towards the animal pole. The body of the fish is going to form along the right side of spherical embryo in this view.

  • While the keel is extending anteriorly, cells are still also migrating to surround the yolk—epiboly continues, with the yolk bulging out a bit until it is finally surrounded and closed off at the blastopore.

  • The head and tail extend. You’ll see the eye forming, so you’ll be able to tell which end is the head end.

  • Along the right side, you’ll also see the tissue form regular little blocks: these are the somites, or body segments.

  • The tail continues to extend and lifts off the surface of the yolk. When there are about 18 somites (the resolution is too low, so don’t try to count them), the animal will begin to twitch.

I’ll load up another one in a bit that will show a hint of the horrible stuff we do to them in the lab: we get the babies drunk and watch deformities develop.

A zebrafish timelapse recording

At my talk on Tuesday, the centerpiece was a short movie of zebrafish development—I was trying to show just how amazingly cool the process was. People seemed to like that part of the show, at least, so I thought I’d try to figure out this YouTube doohickey and upload it for general viewing. So here it is, a timelapse recording of about 18 hours of zebrafish embryology compressed into 48 seconds:

I’ve got more, and my students will be making videos of their own soon enough, so maybe I’ll try uploading some other stuff soon. I’m discovering that YouTube is a little tricky about the aspect ratio, and the conversions do add some distracting compression artifacts to the movie…I may have to tinker quite a bit to get a more satisfactory image.

Squid Hox genes

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It’s April (not anymore—it’s September as I repost this), it’s Minnesota, and it’s snowing here (not yet, but soon enough). On days like this (who am I fooling? Every day!), my thoughts turn to spicy, garlicky delicacies and warm, sunny days on a lovely tropical reef—it’s a squiddy day, in other words, and I’ve got a double-dose of squidblogging on this Friday afternoon, with one article on the vampire squid, Vampyroteuthis infernalis, and this one, on squid evolution and cephalopod Hox genes.

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Evolution of alcohol synthesis

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We need to appreciate beer more. Alcohol has a long history in human affairs, and has been important in purifying and preserving food and drink, and in making our parties livelier. We owe it all to a tiny little microorganism, Saccharomyces cerevisiae, which converts complex plant sugars into smaller, simpler, more socially potent molecules of ethanol. This is a remarkable process that seems to be entirely to our benefit (it has even been argued that beer is proof of the existence of God*), but recent research has shown that the little buggers do it all entirely for their own selfish reasons, and they’ve been busily making alcohol that has gone undrunk by humankind for tens of millions of years.

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How to dismantle a body

Don’t be too grossed out, but the University of Wisconsin Madison has put a whole series of high-quality videos of human dissection online. It’s extremely cool, but not for the squeamish—there’s more than just the sight of a cadaver getting hacked up, and the sound of a saw on bone or a chisel being used to peel up the cranium are, ummm, memorable. At least you’re spared the odor and the textures.

I’d almost forgotten how muscular gross anatomy is—it takes some heft and brute force to take apart a body.

(via Mind Hacks)

Palaeos reborn!

First I reported that Palaeos was lost, and then that it might be found, but now it looks like we can safely say it is being reborn. The old version of Palaeos has been at least partially restored, but the really important news is that a Palaeos wiki has been set up and people are working on reassembling old content and creating new information in a much more flexible format. If you’ve got some phylogenetic or palaeontological expertise, you might want to consider joining the Palaeos team and helping out with this big project.