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.

Wells: “Darwinism is Doomed” because we keep making progress

There are days when I simply cannot believe how dishonest the scoundrels at the Discovery Institute can be. This is one of them. I just read an essay by Jonathan Wells that is an appalling piece of anti-scientific propaganda, an extremely squirrely twisting of some science news. It’s called “Why Darwinism is doomed”, and trust me, if you read it, your opinion of Wells will drop another notch. And here you thought it was already in the gutter!

[Read more…]

Squid Hox genes

i-ccbc028bf567ec6e49f3b515a2c4c149-old_pharyngula.gif

i-cba1474d669ccfffe2c2d613f0545014-euprymna_icon.jpg

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.

[Read more…]

Hox cluster disintegration

i-ccbc028bf567ec6e49f3b515a2c4c149-old_pharyngula.gif

Hox genes are metazoan pattern forming genes—genes that are universally associated with defining the identities of regions of the body. There are multiple Hox genes present, and one of their unusual properties is that they are clustered and expressed colinearly. That is, they are found in ordered groups on the chromosome, and that the gene on one end is typically turned on first and expressed at the head end of the embryo, the next gene in order is turned on slightly later and expressed further back, and so on in sequence. That the tidy sequential order on the chromosome is associated with an equally tidy spatial and temporal pattern of expression in the body has always been one of the more fascinating aspects of these genes, and they are one of the few cases where we see an echo of phenotypic form comprehensibly laid out in the DNA.

[Read more…]

Rhabdomeric and ciliary eyes

i-ccbc028bf567ec6e49f3b515a2c4c149-old_pharyngula.gif

We are all familiar with the idea that there are strikingly different kinds of eyes in animals: insects have compound eyes with multiple facets, while we vertebrates have simple lens eyes. It seems like a simple evolutionary distinction, with arthropods exhibiting one pattern and vertebrates another, but the story isn’t as clean and simple as all that. Protostomes exhibit a variety of different kinds of eyes, leading to the suggestion that eyes have evolved independently many times; in addition, eyes differ in more than just their apparent organization, and there are some significant differences at the molecular level between our photoreceptors and arthropod photoreceptors. It’s all very confusing.

There has been some recent press (see also this press release from the EMBL) about research on a particular animal model, the polychaete marine worm, Platynereis dumerilii, that is resolving the confusion. The short answer is that there are fundamentally two different kinds of eyes based on the biology of the cell types, and our common bilaterian ancestor had both—and the diversity arose in elaborations on those two types.

[Read more…]

Developmental Biology 4181: Week 2

This week, my students are thinking about SIDS,
aging,
Christiane Nusslein-Volhard,
oncogenes,
hunger,
individuality,
worm movies,
obesity,
sunscreen, and whether to
divide or die. A fairly typical set of undergraduate concerns, right?

They’ve all also been reading chapters 3 and 4 of Carroll’s Endless Forms Most Beautiful, and their summaries are here: α,
β,
γ,
δ,
ε, and
ζ.

If you missed it, here’s Last week’s digest and a brief explanation of what it’s all about.

Patterning the nervous system with Bmp

I’m a little surprised at the convergence of interest in this news report of a conserved mechanism of organizing the nervous system—I’ve gotten a half-dozen requests to explain what it all means. Is there a rising consciousness about evo-devo issues? What’s caused the sudden focus on this one paper?

It doesn’t really matter, I suppose. It’s an interesting observation about how both arthropods and vertebrates seem to partition regions along the dorso-ventral axis of the nervous system using exactly the same set of molecules, a remarkable degree of similarity that supports the idea of a common origin. Gradients of a molecule called Bmp may be the primitive mechanism for establishing dorso-ventral polarity in animals.

[Read more…]

How to make a tadpole

i-0971a73433e3e9f1ec34d16d40e543e1-tadpole.jpg

I’ve been tinkering with a lovely software tool, the 3D Virtual Embryo, which you can down download from ANISEED (Ascidian Network of In Situ Expression and Embryological Data). Yes, you: it’s free, it runs under Java, and you can get the source and versions compiled for Windows, Linux, and Mac OS X. It contains a set of data on ascidian development—cell shapes, gene expression, proteins, etc., all rendered in 3 dimensions and color, and with the user able to interact with the data, spinning it around and highlighting and annotating. It’s beautiful!

Unfortunately, as I was experimenting with it, it locked up on me several times, so be prepared for some rough edges. I’m putting it on my list of optional labs for developmental biology—3-D visualization of morphological and molecular data is one of those tools that are going to be part of the future of embryology, after all—but it isn’t quite reliable enough for general student work. At least not in my hands, anyway. If one of my students were to work through the glitches and figure out how to avoid them, though, it could be a useful adjunct to instruction in chordate development.

If you want to play with it, I’ll give you a quick overview of what’s going on in the dataset. A paper by Munro et al. has used these kinds of data to summarize key events in the transformation of a spherical ball of cells into an elongate, swimming tadpole larva.

[Read more…]