Those under-appreciated carbohydrates

This is a promotional video for the University of Utrecht, but it doesn’t lie (although I’m beginning to detest the phrase “dark matter of the ______”). Glycans are essential components of the cell.

In our cell biology course — and probably in most cell bio courses — we start with an overview of those key macromolecules, carbohydrates, lipids, proteins, and nucleic acids, and then spend almost all of the semester focused on proteins and nucleic acids. I think in part it’s because we have a straightforward connection between them, and so much of the discipline of molecular biology is about just those two. It’s also the case that there is no such thing as a gene coding for a lipid or a glycan, which immediately removes them from consideration or interest to many biologists. Instead, glycans and lipids are produced indirectly by the cellular and extracellular environment, which makes them an order of magnitude more difficult to understand.

But that should make them even cooler!

It doesn’t make them “dark matter of the cell”, though.

This is why I’m not a nuclear physicist

It’s just too scary, and radioactive materials are just too weird.

The metal rods in the top photo are plutonium. Rods can roll. These rods could roll closer to each other and perhaps produce the kind of runaway neutron reaction that killed Slotin and Daghlian. Putting a hand in to separate them could make the reaction worse because the water in a human body reflects the neutrons.
I had formal safety training, informal discussions with more experienced people, and made it a point to internalize rules of thumb. Keep pieces of plutonium separate. Abide by glovebox limitations; every glovebox has a sign with the limits of plutonium allowed in it. For solutions, keep them dilute and in flat containers. Flat/thin is safer; the closer a shape is to spherical, the less material is needed to go critical. IIRC, there were racks to put rods in if you were working with that shape of metal, so that they didn’t accidentally roll together.

Daghlian and Slotin? I made the mistake of looking them up and finding out about the Demon Core.

My version of safety rules is don’t eat sandwiches in the lab, don’t drink the mystery fluid in that test tube, wear latex gloves when playing with the nasties, the lab alcohol is not for parties, and wash your hands every once in a while. “Don’t let these two tubes touch each other, or invisible rays will instantly flash out and kill everyone in the room in slow grisly painful ways” isn’t part of the set of instructions I have to give students.

Friday Cephalopod: The good news about global warming

We’re making the planet a better place for cephalopods. It also helps that humans are busily destroying teleost populations.

David Wiltshire

P.S. There’s a video at the link titled “8 reasons octopuses rule the oceans”. Don’t bother with it. It is 8 incredibly idiotic reasons that have nothing to do with their success. I felt stupider after watching it.

Mystery structure explained!

That strange tissue I showed in a previous post is…the chorion of the embryonic zebrafish. It’s homologous to a structure called the zona pellucida in mammals, and it’s also made of the same stuff: a collection of highly conserved glycoproteins called ZP (for zona pellucida proteins) that form a tight extracellular matrix around the egg. There are four groups of related proteins creatively called ZPA, ZPB, ZPC, and ZPX, and most are found in fish, frogs, birds, reptiles, mammals — so they really are universal.

One distinction is that only mammalian ZPs/chorions have the property of sperm recognition — in other groups the chorion acts explicitly as a barrier to sperm entry. Fish have a tiny funnel-shaped hole in their chorions called the micropyle at the animal pole, which is just big enough to allow a single sperm to enter, reducing the likelihood of polyspermy.

What’s also cool about the chorion is that it inflates and self-assembles. It lifts off the surface of the egg at fertilization and expands, and further, enzymes are released from cortical granules in the egg to harden and toughen the coat. Basically when the egg is fertilized it quickly blows up a fluid-filled bubble around itself.

In zebrafish, the chorion is thin and transparent, and relatively easy to tear and remove. Other fish species may differ; the first time I tried removing the chorion from medaka, it was like trying to rip through tough leather after after being used to peeling away soft toilet paper. Chorions may also be decorated with threads or spiky processes, especially in demersal (sinking) eggs that need to stick to rocks or grasses at the bottom of a stream. Zebrafish are rather mundane and plain in comparison.

There are complicated things going on in the chorion: it’s a barrier and a filter. It blocks some toxic or teratogenic agents — there are some substances, like steroid-like plant alkaloids (cyclopamine, jervine) that are much more potent if you remove or even just tear a small hole in the chorion.

So about that photo: you are looking at a very thin sheet of a glycoprotein matrix that forms a kind of eggshell around the embryo. Most of the time I just rip it off and throw it away, but in this case I was scanning embryos and left it on, and as always, it struck me as lovely and intricately patterned.

Bonsignorio D., et al., 1996. Structure and macromolecular composition of the zebrafish egg chorion. Zygote, 4(02), pp.101-108.

Iwamatsu T et al. 1995. Changes in chorion proteins induced by the exudate released from the egg cortex at the time of fertilization in the teleost, Oryzias latipes. Development, Growth & Differentiation, 37: 747–759.

Murata K et al. 2014. Identification of the Origin and Localization of Chorion (Egg Envelope) Proteins in an Ancient Fish, the White Sturgeon, Acipenser transmontanus. Biol Reprod 90(6): 132.

Rizzo E et al. Oocyte surface in four teleost fish species postspawning and fertilization. 1998. Braz. arch. biol. technol., Curitiba , 41(1):37-48.

Zebrafish are so pretty

I was tinkering in the lab this morning, trying out a new gadget, collecting embryos, and cleaning and fine-tuning my microscope, when I saw this. Can you guess what I’m looking at?

Hints: shot at 40x, it’s not part of the embryo itself, and every zebrafish pro is thoroughly familiar with it.

There was a guess that it was yolk. No! I took a quick picture of the yolk sac in this same embryo, at the same magnification.

Those boulders at the top are cells, blastomeres. The bright band across the middle is the yolk syncytial layer, cells that bridge the gap between the cellular embryo and the yolk mass at the bottom. See? Nothing alike.

A few of you got it right, or came close: it’s the chorion.

More like “wary coexistence”

Annalee Newitz writes about the domestication history of house cats. They’re odd in that they haven’t been bred away from the standard wildcat, so the idea is that they’ve only recently been domesticated, and haven’t yet undergone extensive genetic selection. Interesting, but I must disagree with her closing statement.

Or maybe cats will continue to defy domestication. They could carve out a place as one of the only animals to befriend humans without ever falling completely under our control.

“Befriend”? She hasn’t met my cat.

The Face of Evil

Raychelle Burks explains how chemists would get rid of a body

I always thought the idea of getting rid of a body by dumping it in an acid bath was impractical and inefficient — it would take such a long time to break down, and would require so much in the way of chemicals. Raychelle Burks does the test, dropping chunks of pork in beakers of hydrochloric acid or sodium hydroxide, and my suspicions were confirmed. This is a bad way to do it. It’s also really gross.

You really need to get a biologist’s expertise for this job. My first thought was dermestid beetles — clean it down to bare bones, then mount the skeleton and store it in plain sight in the anatomy lab. You don’t have any beetles? There’s always Lord Dunsany’s solution.

But for simple practicality, just find a crematorium.

A new claim from the quack decapitator

Sergio Canavero is now claiming to have achieved successful repair/regeneration of severed spinal cords by something he pompously calls The Gemini Protocol. This is simply severing the cord with a sharp knife (good to know he’s not using a dull one) and immediately squirting the cut with polyethylene glycol (which we’ve known for decades will cause cells to fuse). He has photos of rats that he said managed to start walking again two weeks after slicing through their spinal cords.

This is pretty much guaranteed bullshit.

More qualified experts than I say the same thing.

Critics of the proposed human head transplant have been vocal since it was first announced. Commenting on it in 2015, Chad Gordon, professor neurological surgery at Johns Hopkins University, told BuzzFeed : “There’s no way he’s going to hook up somebody’s brain to someone’s spinal cord and have them be functional. On the conservative side, we’re about 100 years away from being able to figure this out. If he’s saying two, and he’s promising a living, breathing, talking, moving human being? He’s lying.”

Jerry Silver, Professor of Neurosciences at Case Western Reserve University, Ohio, works on repairing spinal cords after injury. Commenting on the latest study, he tells Newsweek it is unclear whether to team had truly severed the cord completely. “I notice that in the last paragraph they state ‘In conclusion, we have shown that the paralysis following full severance of the dorsal spinal cord can be reversed—to a significant extent—by immediate application of a fusogen.’ Did they sever only the ‘dorsal’ cord?” he says.

He said the team also claims the axons—which form part of the spinal cord—had regenerated, but “they show no evidence for regeneration.”

“There is no histology [the study of the microscopic structure of tissues] which is the only way to assess what is really going on here,” Silver said, adding the BBB scores—the scoring system used to assess motor function in rats—were unrealistic.

“Two treated animals supposedly recover locomotor skills that are nearly normal (BBB scores of 19 and 20 out of a possible 21 total) and as a group they average a score of 12 which means that they can on average take multiple weight bearing steps. [This is] unbelievable. Too good to be true in my opinion, which mandates that these results will have be independently verified and properly analyzed before this work can be accepted as scientifically valid.”

No histology. Partial cuts? Poor documentation of supposed recovery. This guy is a quack.

By the way, he’s also abruptly dropped plans to do the first human experiment on a man with a degenerative disease, Valery Spiridonov, and is instead planning to do it on an unnamed Chinese victim patient, just as he has announced Chinese government support.

Don’t take Canavero seriously, unless it’s to drag him off to the Hague for prosecution. His proposal is a glory-seeking sham.