So what’s actually going on in the mitochondrial video? Well, I’m not sure of every detail, but as a former biochemistry TA, I can give you a lot of educated guesses. The movie appears to begin with mitochondria — sub-cellcular power stations — inching along a part of the cellular skeleton called microtubules. The job of mitochondria is to finish the process of turning the energy stored in the bonds of glucose into useable power through respiration. As energy is harvested from the electrons prised off glucose, they are finally passed to oxgen, which accepts them along with some hydrogen ions to form water. Meanwhile, the carbon that was tied up in glucose ends up as carbon dioxide. This forms the basis of your inhalation of oxygen and exhalation of carbon dioxide with each breath you take. Anyway, back to our film.

Then an (?)amino acid chain (fragment of a protein) of some sort escorted by (?)chaperone proteins enters a mitochondrion via a pore through its double membranes*. Then you see the contents of the mitochondrion: an asteroid field of colorful proteins zipping about amid strands of the mitochondrion’s DNA.

Then, looming in the distance like the Pillars of Hercules (or the warship encrusted columns inside the motherships in Independence Day — which seems to be the point. They are going for cinematic here.) are tubular mitochondrial cristae, or folds of the inner membrane. These folds increase the surface area available for respiration.

Embedded in these columns are the rotary engines of mitochondria — enzymes called ATP synthases. These proteins are fascinating feats of natural selection that rotate as they charge their substrates (the molecules they will act upon): namely, ADP. Swarming around these proteins like fireflies are hydrogen ions (H⁺ — essentially, a proton, but often surrounded by three oxygens in aqueous solutions) generated by stripping glucose of electrons like a car in chop shop.

Without going too deep into the gory details, when a cell burns glucose, it performs some preliminary reactions in the cytoplasm (glycolysis) and sends the remaining energy-bearing bits into the mitochondrion for full processing. After enzymes performing the Citric Acid cycle in the interior of the mitochondrion (called the matrix) squeeze more power out and release what’s left of the glucose as carbon dioxide (CO2), the electrons glucose has yielded are passed down the electron transport chain of proteins embedded in the inner membrane, which use the energy thus released to pump hydrogen ions out of the matrix into the space between the mitochondrion’s two membranes. I think you can see this happening at about 1:08.

The inner membrane, unlike the outer, is highly impermeable to most molecules — even to tiny hydrogen ions. The resulting ionic gradient can only flow back downhill through a rotating pore in ATP synthases**.  The passing hydrogen ions powers their rotation and their charging of ADP to ATP, the cell’s energy currency (an explanation of this fascinating mechanical process can be found here under “binding change mechanism”). It’s such a clever system that engineers have designed engines (called the Wankel Engine) based on the same principle and built them into working cars — namely, the Mazda RX-7 and RX-8. I know this because one of my biochemistry professors at Cornell had actually owned one of these for that very reason (You know you are a nerd when . . . ).You can see the biological version of this process happening at about 1:15, where small molecules enter the head of the synthase, light up to let you know they’ve been charged, and then are released to please go play nicely with the rest of the cell.

Here is a conventional representation of what I just described — I, II, III, and IV are proteins of the electron transport chain, NADH is an electron ferry that shuttles said particles from ex-glucose pieces to the electron transport chain, and succinate is an intermediary in the citric acid cycle (for those that remember, this is the step that generates FADH2):

During all this action in the movie, the camera also passes once or twice through the undulating lipid bilayer of membranes, where the kinky double-tailed (and faintely spermish) phospholipids jostle against each other to keep the membrane fluid. Mitochondrial membranes actually contain many fewer sterols (cholesterol is one — they are molecules that help stabilize membranes) than the cell membrane, giving the mitochondrion greater shape-shifting powers.

I think the next-to-last scene is an ATP/ADP transport protein that actively shuttles ADP into the matrix and ATP out. Finally, you see all the mitochondria swarming toward some big shiny thing (centrosome? endoplasmic reticulum? Who knows! Scene list please, Harvard!) like star cruisers converging on a galactic rendezvous. Actually, mitochondria do sometimes cluster near where they are most needed. For example, in cells with flagella, they may cluster near the base of the tail.

All in all, the mitochondrion’s a tightly run ship. Lest the ID community use these incredible little machines as evidence of “stasis” or “irreducible complexity”, let it be known that anaerobic (non-oxygen breathing and non-mitochondrial) bacteria alive today have proteins almost identical to ATP synthase that function in reverse: powered by ATP, they serve to detox the bacteria of H⁺ to rid them of the acidic by-products of the less-efficient but still-better-than-nothing energy-producing process of fermentation. The cytochrome complexes (aka I, II, III, and IV, the cogs of the electron transport chain) may have evolved for similar detox purposes in other ancient bacteria before being combined with ancient ATP synthase by natural selection to form the well-greased respiratory engines we have today.

Typical plant and animal cells contain hundreds or thousands of such mitochondria, though their number ranges from one bizarro giant in a few single-celled protists to several hundred thousand in well-provisioned egg cells. I’m not certain why the directors of this film chose to show this mitochondrion with tubular cristae. Most vertebrates have regular laminar, or sheetlike, cristae (remember that it was unusual that alvaeolates (the paramecia, ciliates, dinoflagellates, and apicomplexans) had tubular cristae), though plants have both sheets and tubes in their mitochondria, and are more irregularly shaped and sized.

Of course, proteins inside mitochondria don’t really float around looking like someone blew up a box of Trix in the space station. In reality, my understanding is they’re all sort of, well, clearish at that scale. And in this thorough NYT article on recent advances in molecular animation, scientists acknowledge that molecular animators also take liberties with space.

“Some animations are clearly more Hollywood than useful display,” says Peter Walter, a Howard Hughes Medical Institute investigator at the University of California, San Francisco. “It can become hard to distinguish between what is data and what is fantasy.”

But clearish molecules and vast distances would make for a pretty dull movie, so I don’t begrudge them their colors. This situation reminds me of the Peter Jackson Conundrum: was the Lord of the Rings better before your head was filled with Peter Jackson’s version of everything? And wasn’t it better when only the people who actually took the trouble to do all the reading were in on the magic?

My gut feeling is that these movies are a good thing, as is sharing the wonder with the masses. If we wish to make the case to society that science is important and worthy of time and money even on its own terms, animations like these help. It is also unquestionably cool to see it all in such detail — revealing things we could not easily foresee without seeing everything together in glorious living color — even if our imaginations are a bit impoverished for it. It’s a worthy sacrifice, in my opinion, if our appetites are whetted.

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* The outer membrane is a product of a long-ago engulfment of a bacteria by a predatory cell — the inner membrane is the ancient bacterial membrane and the outer membrane is the erstwhile vacuole. Further evidence for endosymbiosis includes that mitochondria (and chloroplasts) have their own single, circular (like most bacteria) DNA-based chromosome without a nuclear membrane from which they manufacture their own proteins and bacterial-sized ribosomes (which can even be interchanged with bacterial ribosomes in some cases) and replicate by division. They’re bacterially-sized too: 1.5 by 2-8 micrometers.

** In high-magnification photos of mitochondria, you can actually see the ATP synthases poking into the matrix like lollipops.

Video is, unfortunately, in German. If you don’t speak German, consider making up your own (PG) translations to key scenes and sharing them with us in the comments! : )

In the beginning you see the free-living amoebae (I think) happily wandering about on their own with some fungal filaments (called hyphae, high’-fee) growing at the top of the screen. Then the ameobae start aggregating — crowding after each other like sports fans filling a stadium. The species uses a famous signaling molecule called cyclic AMP (cAMP) to coordinate their union, and it passes through the swarms in pulsing, spiraling waves noticeable at about 1:35. If I’m using my extremely poor knowledge of German correctly, the narrator is nothing that hundreds of thousands of amoebae join together in the process. They do not fuse membranes; they retain their cellular identity.

Notice that some amoebae get left behind or lost in the process. At 2:47 you can actually see some break out of line and go back to being  little amoebae at the very tail end. After the spiraling and pulsating business is done, the mass stretches into a slug and crawls off. At some point between forming the slug (also called a grex) and making the sporangium (the house where spores are made), the amoebae get it on and mix some genes.

When the slug decides conditions are perfect, it stops, puddles up, and then stretches skyward. The lucky amoebae who will become spores riding up the stalk like an elevator. Those stalk cells get the rotten end of the deal — they must sacrifice themselves to ensure their comrades can reproduce. This little detail has led scientists to study these organisms in order to better understand altruism and cheating in nature. What they’ve found is that, as ever, things are not always as they seem. Some would-be stalk cells indeed give their lives, but others buck the system by cheating. Yet if everyone did, the system would break down entirely. There are, as you may imagine, some very interesting dynamics and mathematics governing this system.

Finally, a roving madsnail goes on a rampage wantonly destroying the beautiful slime mold gardens. Stupid animals.

Incidentally, D. discoideum is the species I wrote about in January in which some strains were recently discovered to practice agriculture, or something close to it, by taking bacteria of their preferred noshing type with them in their spores so they have a guaranteed food source when they land. And still more recently, scientists published an article in Science (see here and here) they may even have tissues — and use two signaling or regulatory proteins related to the ones animals use to organize their embryos during development. This seems to mean the common ancestor of slime molds and animals (whatever *that* might have looked like) was using ancient versions of these proteins to arrange itself, and its descendants — both slime molds, and you — inherited these same proteins and are still using them to organize their bodies, in their different ways.

Cellular slime molds represent one of life’s many experiments in multicellularity. You are the product of another. So are plants. And so are fungi, and brown and red algae and some blue-green algae — and there are many more. Other experiments seem to have been abortive; recently this article revealed that blue-green bacteria (aka cyanobacteria) dabbled in multicellularity many times. Remember: evolution isn’t a goal-directed endeavor, although in certain etremely successful groups (vertebrates, beetles) it may seem that way.

To see a different cellular slime mold species that makes violet sporangia on slime mold candelabra, see here. Spectacular.

Finally, I’d like to note I have a new favorite German word : Schelim. As in “schleim mold”. : )

HT to this post at Small Things Considered for the discovery of this wonderful and educational German film.

You are witnessing one of nature's most incredible migrations that never gets shown on the Discovery Channel. Believe it or not, each one of those little dots is a solitary amoeba. But not for long.

Note: This post contains a prize inside! It will await those patient enough to dig to the bottom. : )

Regular readers of this blog know well about my weakness for the protists formerly known as slime molds (scientists know apparently prefer the more PC and sexy “social amoebae”, although how you can get much sexier than “slime mold” I really don’t know). Exciting news came this past week that a species of cellular slime mold — Dictyostelium discoideum — contains members who have taken up bacterial farming (or at least husbandry — more on that distinction later). I ask again — slime molds: is there anything they can’t do*?

Before we get into their new status as potential FFA members, let’s talk a little bit about this particular group of slimes. So far on this blog, I’ve told you primarily about a group informally called “plasmodial slime molds”. This is the kind that make big, colorful slimy slicks that rove the forest floor wreaking microbial havoc as they vacuum up any bacteria, yeasts, and protists in their path, and then blossom into beautiful bright fruiting bodies like the one in the masthead of this blog.

But there is another kind of slime mold. One that, while perhaps less glamorous, is even more crafty and incredible: the dictyostelids, or cellular slime molds. What is the difference? Well, if plasmodial slime molds are amoebas that discovered living large, cellular slime molds are amoebas that discovered living social. In a plasmodial slime mold (also called myxomycete or myxogastrid), two amoebae meet, decide to spend the rest of their lives together, fuse, and then that fused cell starts dividing mitotically, or asexually, like it’s going out of style to churn out hundreds or thousands of genetically identical nuclei inside one big happy bag of cytoplasm.

In a cellular slime mold, something even more remarkable happens: a single amoeba called a myxamoeba suddenly decides it is starving. As a result, it secretes a molecule called cAMP as a distress call**. And suddenly, hundreds, thousands, hundreds of thousands of amoebae amplify the call by emitting their own cAMP, and begin streaming in toward Amoeba Zero in pulsating waves. They get sticky, climb on top of each other, and cling together. The pile towers up. And then, if it’s not sufficiently bright enough, the tower topples and begins sliming around like a slug. It’s now a single multicellular organism — made of 10,000 to 125,000 amoebae who still retain their individual membranes and identities. Yes, like the Borg — if they were all crazy-glued together. And if they intermittently all lived happily on their own before feeling an irresistible pull to join something called a “collective”.

Take a look at this process:

That aggregation star at left is a schematic of what you're seeing in the image at the top of this page. Tijmen Stam, IIVQ (SVG conversion) - user:Hideshi (original version) GFDL + CC-BY-SA, click image for link.

After crawling far enough to reach an area deemed suffienctly light (I imagine this it to raise the odds of being in a windy, spore-dispersally spot), the slug coalesces into a sombrero-shaped mass from which some of the cells begin gliding upward along a stalk like an elevator. At the apex, the elevator cells convert themselves to spores. Ultimately, they blow away in the breeze to (hopefully) more bacterial pastures.

Now take a look at this process in action.

• First, here’s an overview from my alma mater — the Plant Pathology department at Cornell (Try the downloadable versions if the player doesn’t automatically load or if you want to watch a high-res version (recommended)). Watch the perimeter and the background. Note slugs wandering about looking lost.

• Now let’s look at it up close — scroll down and press play on video at right. Note straggler amoebae.

And it gets better — or worse, depending on your perspective. Some of the amoebas in the slug must voluntarily sacrifice themselves (a process called programmed cell death, or apoptosis. It’s basically microbe seppuku) to form the long stalk. This seems to be determined primarily by what phase of the cell cycle they were in when they reached the forming slug; the last cells to arrive will form the tail of the slug, and the early-arrivers at the head of the slug will become the sacrificed cells of the stalk.

But in an entity where not all cells are genetically identical, you can see how it might be tempting (and much more reproductively successful) to shirk stalk duty and climb your way to the top come hell or high water — that is, to cheat. And in fact, it turns out cellular slime mold myxamoebae do sometimes cheat their way to reproductive success. Scientists fascinated by this have studied it a lot.

That brings us back to farming. Because in addition to being cheaters, some Dictyostelium also appear to plan ahead in other ways. Like packing lunch — or perhaps the seed of lunch. They bring their preferred bacteria with them and seed the soil where their spores land. It’s a little too early to tell if they just eat what they brought or wait sufficiently long for what they brought to reproduce a bit. But the evidence so far seems pretty conclusive: some D. discoideum spores are packin’ bacteria. Though whether they are packin’ them inside or outside the spore wasn’t entirely clear to me either. Only 1/3 of the samples they tested were farming amoebae, but that may be because it does come with a price. Farming amoebae are fitter in times of starvation, but less competitive than non-farmers in times of plenty. Having both strains around makes sense in a world of changing conditions.

Because they don’t weed, water, or fertilize their future food, some scientists suggest it might be better termed husbandry than farming. Whatever you call it, these are the first microbes ever known to do it. Cool***. And the reason, scientists told National Geographic, is that these are also the only microbes that are social — being social enables wind-blown, stalk-borne dispersal, which makes bringing bacteria worth it at all. And so far as we know, all the planet’s other farmers are all social organisms as well. EEEN-teresting.

From Science magazine’s writeup:

Koos Boomsma, an evolutionary biologist at the University of Copenhagen who did not work on the study, is not surprised that farming is scattered through the tree of life. “But if I would’ve had to predict where I would have next expected farming to be discovered, I would never have predicted a slime mold,” he says.

See, this is exactly what happens when we underestimate slime molds. And you all thought I was kidding about that world domination thing . . .

This discovery got full court press coverage; you can read more about it here, here, here, here, here, and here.

When first discovered, slime molds — both plasmodial and cellular — were thought to be fungi, hence the “mold” bit. But unlike fungi, they have cellulose cell walls (like plants and some other protists, but not chitin, like fungi) and cellular organelles called centrioles (like animals). Moreover, the two groups were not thought to be closely related to each other****. Now we know that although there are other types of slime molds that do not fit into these two groups, the plasmodial and cellular slime molds are true taxonomic groupings reflecting common ancestry, and that the two groups are fairly closely related: they are both in the same taxon as free-living amoebas — the Amoebazoa (look for the group on this tree, and then click on it to explore. Notice on the big tree they’re on the same branch with animals and fungi). Which makes sense — slime molds all begin life as ordinary looking amoebas.

Now bear in mind Dictyostelium, for all its transcendent coolness, is but one species among many — perhaps hundreds or thousands. What are other cellular slime molds like? Well, we may not know what many or most of them are like, since so few people study them. But below are videos (your treat for making it all the way to the end of this post) of a spectacularly beautiful other species of cellular slimes, Polysphondylium violaceum (Paul-ee-sfon-dil’-ee-um vie-o-lace’-ee-um — say that three times fast). Unlike Dictyostelium, it does not make roving slugs (though it does aggregate), and it uses a chemical called glorin, and not cAMP, as its chemoattractant. Watch the complex fruiting bodies — or sporocarps — form in these time-lapse movies again from my old buds in the Plant Path department at Cornell.  Notice in particular the branching and the purple pigment — it’s like a fireworks display in slow motion. Try pausing the videos just before the end for a nice still. And again, try the downloadable versions — they’re much higher quality images anyway.

• Video 1 — close up
• Video 2 — wider angle, different sample, even more spectacular display

Yes. Ameobas can do that.

Finally, ponder this: Dictyostelium, and the cellular slime molds as an entire group — was not discovered until 1935 in a North Carolina forest. 1935. Now ponder all the other amazing stuff that must still be out there, just waiting.

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*Perhaps home decorating.

**cAMP is a ubiquitous Earth signaling protein found in organisms from humans to bacteria. It’s a stripped down ATP ( the energy currency of the cell) used, essentially, as one of several master switches for turning circuits (metabolic pathways) on and off in the bioreaktor/ Brownian chaos computer of the cell (Many, if not most, of the biochemical reactions of the cell are governed merely by the rate at which molecules happen to randomly bump into one another (implication: more molecules will make the reaction go faster). Even proteins chaperoned to important reactions by other proteins must bump into their chaperones in the first place.) In social amoebae, cAMP takes up the somewhat novel role of chemical attractant — that is, a pheromone.

***There are a few more lurid and/or fascinating bits to the cellular slime mold story. For one, lest you think their asexual reproduction was the only weird thing about them, Dictyostelium sex is also kinda creepy. It starts out normally: two amoebae meet and fuse. But things get weird fast: the zygote (diploid, or double-chromosomed) offsprings goes on a cannabilistic rampage, engulfing all nearby amoebae as fast as it can. When sated, the cell wall thickens with cellulose to form the resting spore, or macrocyst, that can survive tough conditions. Before it germinates, the cell undergoes meiosis, or reductive cell division, to get back to one copy of chromosomes per cell, and then several mitotic, or regular, cell divisions before it releases its little myxamoebas when conditions are good.

**** From my late-90s botany book: “The plasmodial slime molds, or myxomycetes, are a group of about 700 species that seems to have no direct relationship to the cellular slime molds, the fungi, or any other group.”

If all goes according to plan, this website will be making its move this weekend from frazer.northerncoloradogrotto.com to being truly hosted at theartfulamoeba.com (right now I employ masking to make that work). That may mean the feed will change and you will need to resubscribe, but I’m not certain yet as I have yet to consult with my volunteer tech department. Rest assured I’ll do my best to make the transition as seamless as possible, and the feed may not need any updating on your end at all. If for some reason it does stop working, just go to theartfulamoeba.com and hit the little orange RSS feed subscribe button at the upper right to resubscribe this blog to your feed reader.

In addition, if you have any links to my blog on your site, the links will break unless you sub theartfulamoeba.com for frazer.northerncolorado.grotto in the root once the transition happens. Finally, if you have a link to this blog in general from your blogroll, etc .(thank you! Very honored by that!), make sure the link is to theartfulamoeba.com and not frazer.northerncoloradogrotto.com

I’m making this move to make things less confusing for readers (what the heck is frazer.northerncoloradogrotto.com?!) and in preparation for some big changes: I hope to attempt join to the Nature Blog network and Researchblogging.org soon and I figured it would be best to get the tech stuff squared away before I complicate things further.

In any case, theartfulamoeba.com, artfulamoeba.com, theartfulamoeba.org, etc., will all continue working no matter what happens. Bear with me, faithful readers, and in the meantime, enjoy this movie of an amoeba strutting its stuff. This phenomenon by which amoebae move is called “cytoplasmic streaming“. I love that the amoeba seems to “change its mind” several times about whether that top pseudopod (arm) should be expanding or contracting. : )

The poor little guy who gets it in this video is a little ciliate flagellate(single-celled organism with a long propeller-like propulsive tail) named Chilomonas, according to Psi Wavefunction (thanks Psi!). This little drama is one example of the billions of such daily struggles that go on every day in the soil and water all around you. With our daily lives so full, it’s easy to forget.

This process of eating by engulfment is called “endocytosis” by biologists, which is a fancy term for “into the cell”. Specifically, this is “phagocytosis”, or cellular eating. Many cells can also perform pinocytosis, or cellular drinking, where cells can ingest small bubbles of water. Plasmodial slime molds (oft mentioned and beloved at this blog) start out as single amoebae like this, doing pretty much this the exact same thing in the soil. When they fuse to form a plasmodium, they’re feeding the same way — just at 5 Jillion X.

But lucky for you, it started raining! And guess what, it’s raining genes! (Cue The Weather Girls) Which is great news, because your species is all female and hasn’t had sex in 100 million years. Hallelujah!

Scanning electron micrographs showing morphological variation of bdelloid rotifers and their jaws. We're going to need a bigger microscope (apologies to Roy Scheider and Peter Benchley). Photo by Diego Fontaneto, available under a Creative Commons Attribution license. Click photo for link.

As described in this little article over at discovermagazine.com, without a way to exchange and recombine genetic information, many animal species tend to degenerate and disappear over time (thus the joy of sex) because they lack efficient ways to generate novelty that can help them adapt to changing environments. That’s OK — when you’re a bdelloid rotifer, you can do it Hoover style: just vacuum up whatever stray DNA happens to be in your environment, including the genes of whatever it was you might have recently had for dinner (note to self: glad am not bdelloid rotifer). Plants, animals, bacteria, fungi, and who knows? — you might even get lucky. You might manage to incorporate some variant versions of your own species’s genes, thus escaping the cruel grind of creeping genetic obsolescence.

Coming soon: Part 2: So what is a bdelloid rotifer anyway?

In spite of what you're thinking, this is not the love child of a squid and a kernel of corn.

Also known as *cough* beaver fever (since the dam rodents are common carriers) to those hikers unlucky enough to have a run-in with this extremely unpleasant organism. Symptoms include such pleasantries as “projectile vomiting” and “explosive diarrhea”. Fortunately, I do not speak from personal experience.

This baby is the primary reason that all you outdoorspeople have to bother with bulky or foul-tasting water decontamination apparati. Unfortunately, it’s more than just annoying to people in countries with raw sewage washing down the street, who would probably gladly bother with bulky or foul-tasting water decontamination apparati if they could afford it.

So an article in the New York Times last week described a fascinating new vaccine strategy for defeating this and many protozoan parasites that rely on “coat switching”. Giardia has about 190 coat protein genes. It only needs one to function. Normally, it cycles through them one at a time about every 10 generations, yanking the rug out from your immune system each time. Someone had the bright idea to make the organism express them all at once, vastly condensing the time required for your immune system to learn them all from several lifetimes to several weeks.

Neat!

http://www.nytimes.com/2008/12/16/science/16giar.html

Its coat protein selection system is a prime example of how evolution has produced plenty of inefficiencies and life is not “perfect” (as if we needed a reminder). Instead of selecting one of its coat protein genes and only transcribing that, it transcribes *all* of them, and destroys all but the one it wants. Kinda like making dinner by cooking every recipe in the cookbook, and then tossing all the dishes but the one you’re actually having. And that’s not the only weird redundancy, according to the article. Giardia has two nuclei. No one knows why.

Many of you know about my slightly (ok, entirely) unnatural slime mold obsession. They’re weird, cool-looking, and semi-sentient. And they’re even here in Colorado! I found three or four different species when on the Mycoblitz in August up at Rocky Mountain National Park. They’ve even been used as robot brains. (see http://www.newscientist.com/article/dn8718)

A yellow slime mold at Olympic National Park.

Not bad for a giant crawling multinucleate bag of protoplasm. Well, here’s further proof of just how cool they are: http://discovermagazine.com/2009/jan/071

Even slime molds can remember.

So how on Earth is a feat like this possible for an organism that’s never even heard of a neuron? I’ll leave that for us to ponder. . . because no one really knows.