About X-frogs and failing at regeneration

Not the usual mad squee, but here’s a neat little system for studying regeneration that I quite liked today. I normally think about regeneration in terms of amputated limbs, mutilated hearts, decapitated flatworms. But you can induce a kind of “regeneration” in a less drastic and rather more tricksy way, at least in some animals. In newts and salamanders, you can create a small, superficial wound on the side of a limb, then manipulate a nearby nerve into it and add some skin from the other side of the limb.

The poor hurt limb then decides you’ve actually cut something off and tells the wound to grow a new limb. If you don’t add skin, regeneration begins but doesn’t progress very far; if you don’t add a nerve, nothing happens. IIRC you can also make extra heads in some worms in a similar way, but I digress. The figure below from Endo et al. (2004) illustrates just how well the procedure can work. The top row shows stages in the development of the extra limb, while D shows the stained skeletons of the original and new limbs. I’d say that’s a pretty good looking forearm and hand!



That this trick works is in itself a very interesting insight into the nature of regeneration, as it helps us figure out exactly what it is that triggers various steps of regeneration as opposed to a simple healing process (Endo et al., 2004).

Clawed frogs (Xenopus) have been staples of embryology for a long time, but they are also quite fascinating from a regeneration point of view. One, they can regrow their limbs while they are tadpoles, but mostly lose the ability as they mature. They also have a really weird thing going on with their tadpole tails, which they can regenerate early on, then can’t, then can again (Slack et al., 2004). Huh? O.o

Two, their adult limb regeneration ability is not totally absent: it’s somewhere between salamanders’ (oh, whatever, fine, I can do that!) and ours (uh… as long as I’m a baby and it’s just a fingertip?). In a frog, an amputated arm or leg doesn’t simply heal over, but the… thing that grows out of the stump is just a simple cartilaginous spike with no joints or muscles. It’s as if the system was trying very hard to remember how to form a limb but kind of got distracted.

We are obviously interested in creating superhumans with mad regeneration skillz, which also makes us interested in how and why animals lose this seemingly very useful ability*. (Bely (2010) wrote a lovely piece on this not at all simple question.) So: Xenopus yay!

Now, Mitogawa et al. (2014) have devised a skin wound + nerve deviation system to grow little extra limb buds in adult frogs. As you might expect, it doesn’t work nearly as well as it does in axolotls: you need three nerves rather than one, and it only induces a bud about half the time, but it works well enough for research purposes.

The bud (technically, a blastema when you’re talking about regeneration) looks like a good regeneration blastema: it’s got the seemingly undifferentiated cells inside, it’s got the thickened epidermis at the tip that teams up with the nerves to give developmental instructions to the rest of the thing, and it expresses a whole bunch of genes that are turned on in normal limb blastemas.

(Totally random aside: thanks to Chrome’s spell checker, I have discovered that “blastema” is an anagram for “lambaste”.)

One area where this blastema-by-trickery fails is making cartilage, which is one of the few proper limb things the defective spike regenerates in frogs do contain. There’s no simple way of coaxing a complete spike out of these blastemas. The researchers tried the skin graft thing from axolotls (which can already form cartilage without the skin graft), but they still only got a little blastema with no cartilage. To get a skeleton, however crappy,  you need to cut out muscles and crack the underlying bone, which kind of defeats the purpose of the whole exercise IMO. At that point, you might as well just chop off the arm.

Below: the best a frog can do. Development of blastema-like bumps and “spike limbs” on the upper arm from Mitogawa et al. (2014). Compared to the fully formed accessory limbs of axolotls, the things you can see in B-D here are not terribly impressive, but they may be just the “transitional form” we need!

The failure of skin grafts alone at inducing cartilage, however, does hint at the things that go wrong with regeneration in frogs. Mitogawa et al. speculate that newt and axolotl limbs produce factors that frogs can only get from damaged bone. Broken bones even in us form a cartilaginous callus as they begin to heal, and unlike the cartilage in the extra limbs of axolotls, the cartilage in frog spikes is directly attached to the underlying bone.

They also point out that if you add proteins called BMPs to amputated mouse arms, which are otherwise even shitter at regeneration than frog arms, a surprising amount of bone formation occurs. (“BMP” stands for bone morphogenetic protein, which is a big clue to their function.) So it looks like there may be a kind of regeneration gradient from mammals (need bone damage AND extra BMP), through frogs (need bone damage, take care of BMPs themselves) to salamanders (don’t need either).

I should point out that salamanders and frogs are equally closely related to us, so this isn’t a proper evolutionary gradient, but given all the ways in which we and amphibians are fundamentally similar, our loss of regenerative ability may well have evolved through a similar stage to where frogs are now. Neat!

(I just wish they stopped calling us “higher vertebrates”. That phrase annoys me right up the fucking wall, because, and I may have said this before, EVOLUTION IS NOT A GODDAMNED LADDER. The group they are referring to has a perfectly good name that doesn’t imply ladder thinking. Amniotes, people. Or mammals, if you mean mammals, but I think if they’d meant mammals they would have said mammals. End grump.)


*I mean “us” in a very general sense. I think regenerative medicine is the coolest thing in medicine since vaccines and antibiotics, but I personally don’t think that the evolution of regenerative ability needs medical considerations to make it interesting. Whatever. I’m not exactly a practically minded person 😛



Bely AE (2010) Evolutionary loss of animal regeneration: pattern and process. Integrative and Comparative Biology 50:515-527

Endo T et al. (2004) A stepwise model system for limb regeneration. Development 270:135-145

Mitogawa K et al. (2014) Ectopic blastema induction by nerve deviation and skin wounding: a new regeneration model in Xenopus laevis. Regeneration 2:11

Slack JMW et al. (2004) Cellular and molecular mechanisms of regeneration in Xenopus. Philosophical Transactions of the Royal Society B 359:745-751

Catching up

So I felt like I couldn’t put off the sixteen hundred articles twiddling their thumbs and tapping their feet in my RSS reader any longer. This is the first part of the crop that has accumulated since late December (yikes!). Legless axolotls, homing starfish, secretly related proteins, and more!

1. Axolotls are good at regenerating – until you make them grow up.

(Portrait of a pale lab/aquarium variety axolotl by Orizatriz, Wiki Commons.)

It’s probably not exactly obvious from my posting record, but a large part of my PhD work is about regeneration. It’s something we humans are pretty shit at, but many other vertebrates aren’t. Axolotls, these adorably dumb-faced salamanders, can easily regrow their legs. However, lab axolotls are kind of permanent babies. Although they can grow up in the sense that they are able to breed, they normally keep larval characteristics like gills throughout their lives. It’s reasonable to suspect that this influences their regenerative ability – after all, tadpoles lose their ability to regrow limbs the moment they turn into frogs.

It’s possible to make axolotls metamorphose, too, if you treat them with thyroxine (the same hormone that induces metamorphosis in “normal” amphibians). And when they turn into proper adult salamanders, they suddenly become much poorer regenerators. They can still replace a limb – kind of. But they take twice as long as non-metamorphosed axolotls of the same age and size, and they invariably wind up with small, malformed limbs, often missing bones. After amputation, new skin is slower to grow over their wounds, and the cells that gather under the new skin are sluggish to divide. Something about metamorphosis – that isn’t simply age – dramatically changes how they respond to amputation.

Reference: Monaghan JR et al. (2014) Experimentally induced metamorphosis in axolotls reduces regeneration rate and fidelity. Regeneration advance online publication, doi: 10.1002/reg2.8


2. Similar cells repair muscles in crustaceans and vertebrates

“Regeneration” can cover a lot of different processes. For example, depending on the creature and the organ you’ve damaged, regenerated body parts can come from totally different kinds of cells. In planarian flatworms, a single kind of stem cell can replace anything else in the body. In the eyes of newts, mature cells of the iris transform into lens cells to replace a missing lens. In our muscles, there are special cells called satellite cells that are held in reserve specifically to make new muscle cells when needed.

This recent study of a little crustacean called Parhyale hawaiensis suggests that muscle regeneration in the fingernail-sized arthropod works in much the same way. Konstantinidis and Averof shot early embryos of Parhyale with DNA encoding a fluorescent marker, which randomly integrated into the genomes of some of the cells it hit. In a few “lucky” individuals, the marker ended up labelling just one cell lineage, and the pair used these animals to figure out which cells made which tissues in a regenerated limb.

It turned out that cells in Parhyale are limited in their potential. Descendants of the ectodermal lineage could make skin and nerves but not muscle, and the mesodermal lineage built muscle but not skin or nerves. Moreover, labelled cells only contributed to regeneration near their original location – animals with their left sides labelled never regrew glowing limbs on the right side. This is starting to sound a lot like vertebrates, but it’s still a very general observation. However, the similarities don’t end there.

Like vertebrate muscles, the muscles of the little crustaceans contain satellite-like cells derived from the mesodermal lineage that sit beside mature muscle cells and express the Pax3/7 gene. When the researchers transplanted some of these cells from animals with the glowy label into leg stumps of non-glowy animals, there were glowing muscle cells in some of the regenerated limbs. So like satellite cells, these cells can turn into muscle during regeneration. There’s little question that muscle cells have a common origin in vertebrates and arthropods like Parhyale, but it’s really cool to see that their mechanisms of regeneration also might.

Reference: Konstantinidis N & Averof M (2014) A common cellular basis for muscle regeneration in arthropods and vertebrates. Science, published online 02/01/2014, doi: 10.1126/science.1243529


3. Convergent evolution is a poor explanation of rhodopsins

Proteins can be difficult. I mean, sometimes they do their darnedest to hide their family ties. A protein is a chain of amino acids (on average about 300 of them) often folded into a complex shape. Closely related proteins have obviously similar amino acid sequences. However, more distant relatives can be harder to identify. There are about 20 different kinds of amino acids in proteins, so the number of possible sequences is unimaginably vast. The same function can be carried out by very different sequences, and therefore enough evolution can completely erase sequence similarity.

Protein structures are generally thought to be more conserved than sequences. Like function, structure allows for a huge amount of sequence variation without significantly changing. However, theoretically, it’s possible that two unrelated proteins have similar structures because of their similar functions, not because of common ancestry. Apparently, this has been argued for the two types of rhodopsins – proteins that harvest light in systems as different as a the “solar generator” of a salt-loving microbe and the photoreceptors of our own eyes.

If Type I and Type II rhodopsins are similar despite being unrelated, one would assume that this is because they need to be that way to capture light. There are, after all, astronomical numbers of possible protein structures, and the chances of two protein families accidentally stumbling onto the same one without selection steering are slim to say the least. But, in fact, you can rearrange the structure of a rhodopsin in all kinds of cunning ways without destroying its function. This rather weakens the case for convergent evolution, and suggests that similarity of structure does indicate common ancestry here.

Reference: Mackin KA et al. (2014) An empirical test of convergent evolution in rhodopsins. Molecular Biology and Evolution 31:85-95


4. Starfish can see their way back home

(Blue starfish, the beast featured in the paper, in its natural habitat. Richard Ling, Wiki Commons.)

Starfish aren’t widely known as visual creatures, but they do have eyes at the tips of their arms. The eyes are a bit… basic – no lenses, just a hundred or two little units filled with photoreceptors. Garm and Nilsson set out to find out how the starfish used their eyes. They measured or calculated the eyes’ visual fields (five arm-eyes together can see pretty much everywhere around the animal), resolution (very coarse), reaction speed (slow), and their sensitivity to various wavelengths (they are colour-blind, most sensitive to ocean blue).

Then they took some poor starfish and dumped them a little way off the coral reefs they like staying on. The creatures could walk home from short distances (about 2 m or less), but if you take them too far away, they just wander around in random directions. Likewise if you take off their eyes (don’t worry, they regenerate) or do the experiment in the dark. In conclusion: starfish eyes aren’t exactly top-end cameras, but they are definitely useful to the animals. And what would a slow, brainless mopper-up of coral reef rubbish do with eagle eyes anyway?

(The paper states the walking speed of these starfish as about 4-5 cm per minute. I have a feeling this wasn’t the most exciting fieldwork these guys have done…)

Reference: Garm A & Nilsson D-E (2014) Visual navigation in starfish: first evidence for the use of vision and eyes in starfish. Proceedings of the Royal Society B 281:20133011


5. What makes wormies settle

OK, Shikuma et al. (2014) one isn’t so much for its own news value, but I hadn’t known that my favourite worms need bacteria to settle until I saw this paper, so I think it deserves a mention. (Besides, it has beautiful pictures of baby Hydroides in it, which I couldn’t resist posting below. They are So. Cute. Yes, I’m weird.)


Tubeworms of the serpulid family have swimming larvae which are in many ways like the acorn worm larvae mentioned in my previous post (except cuter). They are tiny, look nothing like an adult worm, have bands of cilia for swimming and feeding, and live in the plankton until they’re ready to metamorphose. When they find a place they like, they settle and turn into adult worms. And apparently, this particular species (Hydroides elegans) not only needs a specific bacterium to like a place, it needs specific proteins produced by that bacterium.

The proteins in question are the components of a nasty device bacteria probably stole from viruses and then used to poke holes in one another. But to Hydroides larvae, they appear to be necessary for metamorphosis. Put healthy bacteria together with worm babies in a dish, and you’ll get happily settled little worms. Do the same with bacteria with damage to the relevant genes, and nothing happens. Use an extract containing the proteins but not the bacteria, and you still get metamorphosing worms. Use too much, though, and they start dying. Everything in moderation…

(Maybe my dismal failure at raising happy young worms years ago could have been remedied with the right bacteria?)

Reference: Shikuma NJ et al. (2014) Marine tubeworm metamorphosis induced by arrays of bacterial phage tail-like structures. Science 343:529-533


6. Relative of animals does strange multicellularity with familiar genetics

Although this idea probably hasn’t reached popular perception, animals are surrounded by other multicellular lineages in the tree of life. Sure, most of them are only part-time multicellular, but that’s beside the point. What’s clear is that multicellularity, at least in its simpler forms, is rampant in our extended family. Slime moulds do it, fungi do it, our closest relatives choanoflagellates do it, and our next closest relatives, filastereans and ichthyosporeans also do it.

These latter two groups are really poorly known (the fact that only a taxonomist could like the latter’s name probably doesn’t help), but the situation is getting better with the attention they are receiving as relatives of animals. There are now genome sequences out, and some people are looking at the life cycles of the little creatures to search for clues to our own origins.

Iñaki Ruiz-Trillo recently published a paper describing an ichthyosporean that can form a weird kind of colony with many nuclei in the same membrane starting from a single cell (Suga and Ruiz-Trillo, 2013). Now his team describe a different kind of multicellularity in a filasterean, Capsaspora owczarzaki. Rather than developing from a single cell, this guy does something more akin to the slime mould way: take a load of individual cells and bring them together. (Below: a clump of Capsaspora cells from Sebé-Pedros et al. [2013]. On the right is a regular photograph of the colony. The two-coloured fluorescence on the left indicates that the colony formed by different cells coming together rather than a single cell dividing.)


But, interestingly, some of the genetics involved is similar to what animals use, despite the different ways in which the two groups achieve multicellularity. For example, we’ve known since all those genomes came out that the proteins animals use to glue cells together and make them talk to each other are often older than animals. Well, Ruiz-Trillo’s filasterean appears to ramp up the production of some of these when it goes multicellular. It also uses a gene regulation strategy that animals are really big on: it edits the RNA transcribed from many genes in different ways depending on cell type/life stage before it’s translated into protein.

A lot of the details are going to need further investigation, since this was a global RNA-sequencing study with a bird’s-eye view of what genes are doing. It’s still a nice reminder that, like most other innovations in evolutionary history, the multicellularity of animals didn’t spring fully formed out of nowhere.


Suga H & Ruiz-Trillo I (2013) Development of ichthyosporeans sheds light on the origin of metazoan multicellularity. Development 377:284-292

Sebé-Pedros A et al. (2013) Regulated aggregative multicellularity in a close unicellular relative of metazoa. eLife 2:e01287

Fanworm fandom

In all my meanderings so far, I have never talked about my work in more than vague references to my connection to biominerals. Well, today won’t be the day I really start, but I would like to introduce the animals I work with. Because they are beautiful, awesome, and I love them (except when they’re sabotaging my experiments :-P). They are fan worms.

“Fan worm” is a bit of a loose term, and I’m still not entirely sure what group of worms it is/isn’t supposed to apply to. The group of fan worms I’d like to talk about today is family Serpulidae. (Call them “serps”. They won’t mind.)

Serpulidae are, if the latest phylogenetic research is to be believed, a subgroup of another “family”, the Sabellidae or feather duster worms (Kupriyanova and Rouse, 2008). All sabellids are sedentary filter-feeders. They live in tubes, putting a feathery crown of tentacles out into the water to catch their microscopic food. This is the fan in fan worm, and it’s all that most people ever see of these gorgeous creatures. It’s also today’s excuse to post some Nick Hobgood Christmas tree worms from Wikipedia, although their crazy spiralling tentacle crowns are not all that fan-like. (Bottle brush worms? :D)

These guys in the photo are mostly buried in a coral colony, with only their tentacle crowns sticking out.

Ancestrally, sabellid tubes are made of hard particles like sand and shell fragments glued together with mucus secreted by the worm. Serpulids are special in that they make their own hard material – calcium carbonate – instead of picking stuff up from the environment.

Serpulid tubes can have a highly organised structure that betrays sophisticated tube-building mechanisms (Vinn et al., 2008). Incidentally, some of them are pretty awesome if you look close enough. Below are the rather bland-looking tubes of Ditrupa arietina lying on the seafloor (from ten Hove and Kupriyanova [2009]). Then an electron microscope image of the outer tube layer showing the cool jigsaw-like cross sections of the calcareous rods it’s made of (Olev Vinn via Wiki Commons).


The general anatomy of the animal inside the tube is demonstrated quite nicely in the photograph below, from ten Hove and Kupriyanova (2009):


This is Serpula vermicularis, the species that gave its name to the family. The head end, obviously, is the one with the tentacles. Below it is a rather elegant thorax wearing a jacket of skin flaps (technically, “thoracic membranes”), with a wide collar folding down over the top. The collar builds the tube: when the worm wants to expand its home, it pokes its head out, wraps its collar over the rim, and deposits a new layer of material from glands under the collar.

The weird funnel-shaped thingy sticking out Serpula‘s head above is called an operculum. It’s another speciality of (most) serpulids, functioning in defence against predators. It’s used to close off the tube, but – at least in my species – it’s also a sacrifice body part that pops off at a predetermined point if you tug or prod it too hard. A bit like a lizard’s tail. (Or a sea cucumber’s guts, because gross examples are always better.) Also like the lizard’s tail, the operculum regrows easily, but unlike lizards, serps can regenerate a perfect new operculum. Some serps, including mine, have upgraded their defences further by reinforcing the operculum with calcium carbonate. A calcified body part that you can make develop on demand. What more can you dream of? 😉

Serpulids are found all over the world. Most of the 300+ species live in the sea, all the way from tidal rock pools to deep sea vents. There are a few that can handle brackish water, and there’s a single species that somehow found its way into freshwater-filled limestone caves along the Adriatic coast. According to Kupriyanova et al. (2009), this little explorer is closely related to the brackish-water species, so serps probably only figured out how to deal with lower salinity once.

They are nowhere near as famous as corals, but a few serpulid species are prolific reef builders. Ficopomatus enigmaticus (one of the brackish serps) can grow in roundish reefs made of generations of worm tubes. Although the individual tubes are only a few cm long, reefs can reach several metres across.

F. enigmaticus is an invasive species. Hitchhiking from their European homeland on boats and spawning wherever they felt happy enough, the worms have spread across the warm, shallow, brackish waters of the world. Below, their reefs are shown polka dotting the Mar Chiquita lagoon over in Argentina (photos: Alejandro Bortolus, in Schwindt et al. [2001]). Note the scale bar!


F. enigmaticus reefs have a pretty big ecological impact in their new territory. Their filter-feeding makes the water less murky (Bruschetti et al., 2008), which is good for the seafloor community, not so great for the phytoplankton that caused the murkiness. The reefs provide hiding places for native predators, changing the composition of the seafloor community (Schwindt et al., 2001), and they can also serve as resting stops and hunting grounds for birds (Bruschetti et al., 2009).

And finally, let’s talk a bit about serpulid babies, because baby worms are the best. I don’t know about other serps, but my species has very stylish BABY PINK EGGS. The moment you remove an adult worm from its tube, it panic-spawns all over the place. If you mix the pink eggs with the boring white sperm in some seawater, by the next day the dish will be full of tiny, zipping white balls. (At this point you’d better feed them, since unlike some other baby polychaetes, they don’t get a lot of food from mum. In nature, they’d swim off and live in the plankton, hunting tiny algae until they are ready to settle.)

In another day or two, the little balls grow quite a bit and turn into textbook examples of the type of larva known as the trochophore. If you’re good to them and give them enough food, they’ll keep growing like crazy. You can always see whether they’re hungry or not, since they are transparent and the colourful algae they like to eat show through their skin. This one, from McDougall et al. (2006) via Wiki Commons, was clearly well-fed when it fell victim to science:

They look all hairy around the broadest part – those are the cilia they use to swim. They are very good at swimming! Within a couple of weeks, they’ve transformed into a more mature form with three newfangled segments and a lovely pair of eyes, like this other one from the same paper:

They are now sniffing along the bottom, looking for a place to settle. When they find a spot they like, they lie down, secrete a tiny tube (made of just mucus at first), and metamorphose into transparent baby worms complete with an operculum and everything. This is what Pomatoceros lamarckii looks like mid-metamorphosis (again from McDougall et al.):


At this point, they are a bit ugly, but don’t worry, the ugly wormling stage doesn’t last long. I’ll finish off with one of my own photos what they turn into:


These are slightly over three weeks old, and they have tiny, iridescent tentacles and minute, transparent opercula. Their now-calcified baby tubes are just a few mm long.

Aren’t they lovely? 😀



Bruschetti M et al. (2008) Grazing effect of the invasive reef-forming polychaete Ficopomatus enigmaticus (Fauvel) on phytoplankton biomass in a SW Atlantic coastal lagoon. Journal of Experimental Marine Biology and Ecology 354:212-219

Bruschetti M et al. (2009) An invasive intertidal reef-forming polychaete affect habitat use and feeding behavior of migratory and locals birds in a SW Atlantic coastal lagoon. Journal of Experimental Marine Biology and Ecology 375:76-83

Kupriyanova EK & Rouse GW (2008) Yet another example of paraphyly in Annelida: molecular evidence that Sabellidae contains Serpulidae. Molecular Phylogenetics and Evolution 46:1174-1181

Kupriyanova EK et al. (2009) Evolution of the unique freshwater cave-dwelling tube worm Marifugia cavatica (Annelida: Serpulidae). Systematics and Biodiversity 7:389-401

McDougall C et al. (2006) The development of the larval nervous system, musculature and ciliary bands of Pomatoceros lamarckii (Annelida): heterochrony in polychaetes. Frontiers in Zoology 3:16

Schwindt E et al. (2001) Invasion of a reef-builder polychaete: direct and indirect impacts on the native benthic community structure. Biological Invasions 3:137-149

ten Hove HA & Kupriyanova EK (2009) Taxonomy of Serpulidae (Annelida, Polychaeta): The state of affairs. Zootaxa 2036:1-126

Vinn O et al. (2008) Ultrastructure and mineral composition of serpulid tubes (Polychaeta, Annelida). Zoological Journal of the Linnean Society 154:633-650

Heads are rolling in Nature

The Nature website has been overrun with headless flatworms, my RSS feed tells me! These adorable guys called planarians are known for their ability to regenerate from almost any little scrap of their squishy bodies. (And yes, I find lots of things adorable.) More than a century ago, TH Morgan, who invented like half of modern biology, observed that a whole planarian complete with a head, tail, eyes, brain, and digestive system can regrow itself from a fragment as tiny as 1/279th of the original animal*.

If you’re not familiar with these neat creatures, here’s one of regeneration expert Alejandro Sánchez Alvarado’s pet planarians from Wikipedia:

(OK, “pet” is probably the wrong word. Unless your concept of pets involves frequent mutilation and poisoning.)

Of course, once humanity discovered that planarians can do that, we just had to try and figure out how. Solana_etal2012-ctrlheadWho knows, one day the knowledge might even help us boost our own pathetic regeneration abilities. (Well, aside from the fact that planarian regeneration is pretty weird compared to what vertebrates do. But they are dead easy to keep and you can do lots of fancy things with them.) I felt like I should include some pictures of head regeneration in action, so here’s a few shots from Solana et al. (2012). Watch the eyes!

When you chop bits off a planarian, the remainder of the body has to know a couple of things to repair itself correctly. First, of course, it has to recognise that something is missing. This happens when tissues that don’t normally meet come into contact as the wound closes. The system can be fooled – if you cut off a piece of worm, turn it upside down, and stick it back on, things start growing out even though technically nothing is missing (Kato et al., 1999). The next step is to recognise precisely what needs to be replaced. An example of failing at this step is this two-headed flatworm obtained from a chemical treatment (from Nogi et al. [2012] via Wikipedia):

Making heads or tails

So how does a headless planarian know whether it needs a new head or tail? There’s a venerable theory (apparently also TH Morgan’s) according to which the body of the animal has a sort of built-in molecular coordinate system. Some molecules are more abundant at one end of the beast, while different molecules mark the other end. The anterior (head) and posterior (tail) signals would interact negatively, banishing each other from their respective head(or tail)quarters and resulting in opposing gradients. So any particular point along the head to tail axis would have a precise level of “headness” and “tailness”, and a wounded worm would “know” exactly where it was cut based on this information.

The tail end has long been known to be a seat of an ancient signalling pathway. Wnt (pronounced “wint”) genes are really, really important in a variety of developmental processes; in fact, it’s been proposed that they were involved in defining the head to tail axes of animals long before the more famous Hox genes (Guder et al., 2006). (The merits of that proposition are a discussion for another day. :)) Similar to their axis-defining developmental role, they – or rather, one of the several pathways they act through – also signal “tail” in adult planarians (Gurley et al., 2008).

Butts rule?

In one of the three new planarian studies, Umesono et al. (2013) set out mainly to figure out how the less well-understood head signal worked, but they managed to chuck in something vastly more interesting (to me, evolution nerd that I am) in an almost throwaway paragraph towards the end of the paper. Not all planarians have awesome regeneration superpowers. In particular, many species have difficulty regrowing heads while they can still regenerate tails just fine. Umesono et al. found out why.

Knowing how important Wnt signalling is in making tails, they wondered if an over-enthusiastic Wnt system might be behind some species’ head regeneration defects. They took members of such a species, demolished their Wnt pathway by hijacking their own gene regulatory mechanisms, and proceeded to hack off their heads. A couple of weeks later, shiny new heads started appearing!

It’s not just that one species, either. The other two new headless worm studies (Sikes and Newmark, 2013; Liu et al., 2013) basically did the exact same thing with two other kinds of regeneration-deficient planarian, and got the exact same result. So it looks like the same failure to overcome tailness underlies head regeneration failure in these three species.

The latter two papers examined worms from the same family, and the two animals proved to fail at regeneration in eerily similar ways. Everything up to a point goes correctly: the wound heals properly, stem cells across the body start dividing and gather at the amputation site… and then it stops. Wnts run rampant, heady genes remain silent, and nothing regenerates.

What I’d like to know is why it’s nothing rather than a second tail. After all, the molecular makeup of their wounded parts is screaming “tail!”, and they can regenerate missing tail ends. If you overactivate Wnt signalling in better regenerators among planarians, you still get something growing out at the front, it’s just not a very good head. (Umesono et al., in fact, did a couple of experiments like that in the process of figuring out heads.)

I thought the key was in the Umesono paper, because their prime suspect for “head stuff” as they call it is actually briefly needed in tail regeneration as well, so if it’s not activated at all due to too much Wntiness, then nothing will happen. But if you can turn that on in the middle of a tail in one species, why can’t the same thing happen in the others, which are also perfectly capable of regenerating their tails? Does tail regeneration work differently in them?

Did I mention that living things are complicated?

(And this is the part where I don’t start discussing the whole issue of how and why regeneration is lost in evolution. ‘Tis beautiful, but the night’s getting old ;))


*I can’t for the life of me find the original source, even though I distinctly remember having read Morgan’s account. The 1/279th figure is cited, among others, by Newmark and Sánchez Alvarado (2001).



Guder C et al. (2006) The Wnt code: cnidarians signal the way. Oncogene 25:7450-7460

Gurley KA et al. (2008) β-catenin defines head versus tail identity during planarian regeneration and homeostasis. Science 319:323-327

Kato K et al. (1999) The role of dorsoventral interaction in the onset of planarian regeneration. Development 126:1031-1040

Liu SY et al. (2013) Reactivating head regrowth in a regeneration-deficient planarian species. Nature advance online publication 24/07/2013, doi: 10.1038/nature12414

Newmark PA and Sánchez Alvarado A (2001) Regeneration in Planaria. In: Encyclopedia of Life Sciences. John Wiley & Sons Ltd, Chichester. http://www.els.net; doi: 10.1038/npg.els.0001097

Nogi T et al. (2009) A novel biological activity of praziquantel requiring voltage-operated Ca2+ channel β subunits: subversion of flatworm regenerative polarity. PLoS Neglected Tropical Diseases 3:e464

Sikes JM & Newmark PA (2013) Restoration of anterior regeneration in a planarian with limited regenerative ability. Nature advance online publication, 24/07/2013, doi: 10.1038/nature12403

Solana J et al. (2012) Defining the molecular profile of planarian pluripotent stem cells using a combinatorial RNA-seq, RNA interference and irradiation approach. Genome Biology 13:R19

Umesono Y et al. (2013) The molecular logic for planarian regeneration along the anterior-posterior axis. Nature advance online publication, 24/07/2013, doi: 10.1038/nature12359

So… much… STUFF!

Gods, this is what I’m faced with all the time. Someone needs to tell me how proper science bloggers pick articles to discuss, because I just get my RSS alerts, start squeeing, and end up not writing about anything because damn, I WANT TO WRITE ABOUT EVERYTHING!

I give up. I’ll just dump all the cool stuff that’s accumulated on my desktop and bookmark bar here and return to lengthy meandering whenever I don’t feel like I’ve been caught in a bloody tornado 😉

So, here is some Cool Stuff…

(1) A group measured the rate of DNA decay in 158 moa bones of known age from three sites. Really cool stuff, to go out and directly measure how ancient DNA disappears from dead things under more or less identical conditions. The unsurprising result is that DNA decays exponentially, a bit like radioactive material. This suggests that the main cause of the decay is random breaking of the strands. The surprising bit is that this happens much more slowly than previously estimated, suggesting that in ideal (read: frozen) conditions, it might be worth looking for preserved DNA in samples as old as a million years.

(On a side note, if you ever get a chance to see a talk by Eske Willerslev, one of the authors and a leading expert on ancient DNA, don’t miss it. The man is absolutely hilarious.)

– Allentoft ME et al. (2012) The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils. Proceedings of the Royal Society B FirstCite article, available online 10/10/2012, doi: 10.1098/rspb.2012.1745

(2) The beaks of the finches, or mixing and matching developmental recipes. This study examines the genetic basis of beak shape in three little birds closely related to Darwin’s famous finches. The three finches, just like Darwin’s, share the same basic beak shape, only bigger or smaller. However, there seem to be two distinct developmental programs at work, using different genes and parts of the skeleton to orchestrate beak development. One of the three newly investigated species (the one most closely related to Darwin’s finches) apparently uses the same developmental program as its more famous relatives, even though its beak is shaped more like the other two birds studied here. I told you – genetics, development and homology are complicated 😉

– Mallarino R et al. (2012) Closely related bird species demonstrate flexibility between beak morphology and underlying developmental programs. PNAS 109:16222–16227

(3) Armoured fossil links worm-like molluscs to chitons. There’s a little-known group (or groups) of molluscs called aplacophorans that have only a coat of tiny spicules instead of shells and look more like worms than “proper” molluscs. Exactly where they fit into our picture of mollusc evolution has been controversial to say the least – they could represent an old lineage separate from other molluscs, they could be related to cephalopods, they could be related to chitons, they could be one group or they could be two lineages in completely different places on the tree… Well, a new fossil named Kulindroplax seems to argue for the chiton connection: the animal has the characteristic armour plates of a chiton on an aplacophoran-like body. Similar creatures have been discovered before, but this guy with its detailed 3D preservation provides the clearest evidence of the link so far.

– Sutton MD et al. (2012) A Silurian armoured aplacophoran and implications for molluscan phylogeny. Nature 490:94-97

(4) More cool fossils – this time straight from my beloved Cambrian. Nereocaris, a newly described Burgess Shale arthropod, suggests to its discoverers that the earliest arthropods weren’t predators prowling the seafloor, but swimmers who might have been filter feeders and certainly weren’t predators. The animal has a bivalved shell around its front end, similar to many other Cambrian swimming arthropods, and a long abdomen with paddles at the end. It bears the arthropod hallmark of a hardened and jointed exoskeleton, but it lacks specialised limbs such as antennae or mouthparts. In a cladistic analysis of arthropods and their nearest relatives, the new species comes out on the first branch within true arthropods, and the next few branches as we move towards living arthropods all contain similar shelled, swimming creatures. Since the non-arthropods closest to the real thing (i.e. anomalocaridids) were also fin-tailed swimmers, this arrangement makes the transition between them and true arthropods smoother than previously thought. It also suggests that the hard exoskeleton so characteristic of arthropods originally functioned in swimming – perhaps as an anchor for swimming muscles.

– Legg DA et al. (2012) Cambrian bivalved arthropod reveals origin of arthrodization. Proceedings of the Royal Society B FirstCite article, available online 10/10/2012, doi: 10.1098/rspb.2012.1958


And … there was also

… but it’s almost bedtime, and if I wanted to summarise every one of those, I’d be here all weekend 😦

See, this is why being a science nerd today is both amazing and frustrating. There’s just so. Much. Stuff.