Field of Science

Mystery Micrograph #24

Ok, last one was too easy – Braarudosphaera, a rather polyhedral coccolithophorid (haptophyte) which serves as strong evidence that our Creator was a D&D geek. Apparently he/she/it liked their tabletop RPGs microscopic. Who knew.

Time for an evil one, then. Oh, how can one be evil with micrographs...oh right, TEMs! Those tend to drive everyone crazy. Bwahahaha...

Oh what could this be? If only you knew... (to be referenced later)

Have fun! Again, if you're some sort of protistologist and immediately recognise what this is, stay the hell away. Stand back and savour some painful guesswork first – see, everyone wins!

Sunday Protist – Scary nematode-eating forams and their amazing feet of doom

ResearchBlogging.orgPoor, poor nematodes...

In the interests of public safety, I must reiterate once again what should be so painfully apparent from the last few posts on forams: If you ever find yourself shrunk to a milimetre or less, DO NOT fuck with forams. Ever.

It's a fairly known fact around these parts that [unicellular] forams can devour [multicellular] animals. But thus far we've just had giant tree forams like Notodendrodes show us the terrifying force of microbial nature. Notodendrodes is notably bigger than its prey, so the embarrassed metazoa have an excuse there. As for giant planktonic forams – well, those eat things only slightly larger than themselves, you may say. In which case you must be almost insatiable. But, as usual, there's more: rather small, unassuming Ammonia tepida devouring nematodes, copepods and gastropods unarguably larger than itself.

Like other forams, Ammonia uses its amazing reticulopodia (lit. "net-feet") to trap and entangle prey. Then, it penetrates its prey's exoskeleton or cuticle and forcefully rips apart the insides to shreds, bringing back phagocytosed chunks towards the main cell body for digestion. This process is creepy enough to warrant its own term: skyllocytosis (Bowser 1985 J Prootozool). All that's left behind is an empty cuticle with a hole. By the way, the prey are devoured within 24 hours. And apparently forams are pretty much always hungry. Imagine being violated by masses of dynamic and powerful net-like pseudopodia and torn to pieces from the inside. Doesn't sound fun. Feels good to be big, doesn't it?

Ammonia tepida vs. nematodes. c and d show before and after shots of one such encounter. Sometimes a second foram joins for a threesome. (Dupuy et al. 2010 J Foram Res)

As for copepods...the following sentence from the paper raises some concern: "Despite vigorous attempts to escape, copepods could not free themselves from the pseudopodial mesh."(Dupuy et al. 2010 J Foram Res) Most of us have seen copepods one time or another. For the world of their scale, they're quite strong. And yet they cannot escape. Neither can snails, whose shells are all that remains after a few hours. Have I mentioned foram reticulopodia are simply amazing?

Ammonia tepida vs. copepod (a) and juvenile snails (b,c). Note how the copepod is partially eaten already towards the right. d,e - SEM view of the ventral (umbilical) end of the foram. Little bumps (pustules) are thought to potentially act as 'teeth' and used to grind tests and cuticles. Some other forams are thought to do this with diatoms as well. (Dupuy et al. 2010 J Foram Res)

You may wonder how foram pseudopodia get to be so special. They possess many unique properties, many of which have yet to be understood. One of the more striking features is the rate of microtubule growth. While microtubules of animal cells grow at about 1-15µm/min, microtubule assembly in some forams can reach a stunning 12µm per second (Bowser & Travis 2002 J Foram Res). They manage this by possessing a unique third conformation of tubulin: helical filaments (in addition to the usual protofilaments/'tubes and free dimers).

Transformation of tubulin between helical filaments and free dimers appears to require no ATP, and thus would progress quite rapidly. Furthermore, tubulin of helical filaments can transform directly to the tubules, much faster than regular polymerisation from free dimers. The idea is that tubulin is stored in helical form (crystalised, if you will), and then transported to the site of active growth, and used for a quick and efficient supply of the growing 'tubes with fresh tubulin (Welnhofer & Travis 1996 Cell Motil Cytosk). Thus, it is perhaps not overly surprising that foraminiferan tubulins are highly diverged, suggesting selective pressure for the foram-specific modifications (Habura et al. 2005 MBE). This is yet another example of bizarre alterations by a protist of typically conservative aspects of eukaryotic biology.

SEMs of foram pseudopodia entrapping prey; in this case, Artemia. (Bowser et al. 1992 J Protozool)

To have an idea of what the microtubule cytoskeleton looks like in action, here's a stolen video of plant epidermis cortical microtubules marked with AtEB1:GFP:
In vivo timelapse of cortical microtubules marked with (+)-end binding GFP growing in a tobacco leaf epidermis. Picked this one because it has a scalebar (10µm) and a timestamp (in seconds; movie is sped up, but the whole thing lasts a minute); I do happen to have my own, but finding + editing them would be a pain right now. This should give you an idea of how dynamic the cytoskeleton really is, though keep in mind it's not the best example by far. Noticed interesting recent developments in the plant cell morphogenesis/cytoskeleton story, wish I had time to keep up. (Source: Brandner et al. 2008 Plant Physiol Movie S1)

Now for the video of foram microtubules growing and fluorescing in vivo... oh wait, there is none. =(

There are no foram model organisms. Yet. As far as I know, there's no genome yet either. That should be taken care of. And someone needs to figure out how to transform/transfect (genetically) the buggers too. "Must have pretty movies of rapid microtubule growth" should look great on a grant app. Seriously, it's even shiny and glowy and stuff. Don't they like things that look like cancer/immunology research? (And this is probably why they don't let me write grants yet; not that I'm in any hurry to become a bureaucrat...)

Another foram teaser: some species (eg. Rotaliella heterocaryotica) possess two types of nuclei – germline and somatic – just like ciliates. Actually, no one has any idea how much like ciliates they are, as very little molecular work has been done. Might be another case of crazy genomic dimorphism with ridiculous epigenetic machinery, etc.

Or, just like forams themselves, it may be something else altogether.

BOWSER, S. (1985). Invasive Activity of Allogromia Pseudopodial Networks: Skyllocytosis of a Gelatin/Agar Gel The Journal of Eukaryotic Microbiology, 32 (1), 9-12 DOI: 10.1111/j.1550-7408.1985.tb03005.x


BOWSER, S., ALEXANDER, S., STOCKTON, W., & DELACA, T. (1992). Extracellular Matrix Augments Mechanical Properties of Pseudopodia in the Carnivorous Foraminiferan Astrammina rara: Role in Prey Capture The Journal of Eukaryotic Microbiology, 39 (6), 724-732 DOI: 10.1111/j.1550-7408.1992.tb04455.x

Brandner, K., Sambade, A., Boutant, E., Didier, P., Mely, Y., Ritzenthaler, C., & Heinlein, M. (2008). Tobacco Mosaic Virus Movement Protein Interacts with Green Fluorescent Protein-Tagged Microtubule End-Binding Protein 1 PLANT PHYSIOLOGY, 147 (2), 611-623 DOI: 10.1104/pp.108.117481

Dupuy, C., Rossignol, L., Geslin, E., & Pascal, P. (2010). PREDATION OF MUDFLAT MEIO-MACROFAUNAL METAZOANS BY A CALCAREOUS FORAMINIFER, AMMONIA TEPIDA (CUSHMAN, 1926) The Journal of Foraminiferal Research, 40 (4), 305-312 DOI: 10.2113/gsjfr.40.4.305

Habura, A. (2005). Structural and Functional Implications of an Unusual Foraminiferal -Tubulin Molecular Biology and Evolution, 22 (10), 2000-2009 DOI: 10.1093/molbev/msi190

Mystery Micrograph #23

...and they're back! (last one was a TEM of Joenoides' sexy parabasal fibres)

Let's see what you've got on this sucker:

(to be referenced later)

Several people excluded from this one. You know who you are.

Diagrams that make me cry, part LargeNumber

I was calmly blogging about real content, of course procrastinating simultaneously by writing pieces of stuff for work, as well as planning on possibly contemplating actually doing the readings for tomorrow's paleontology class. In the intro chapter titled "Fossils and Evolution", we get shown the following figure as The Taxonomic System, with a mention in passing the there have been some minor adjustments in the past, such as Three Domains, etc. Of course, such trivial taxonomic nitpicking is apparently of no use to paleontology students, so we'll use the horribly outdated Whittaker 1963 classification which should never be seen outside history of science lectures...

Aaaaaaaaaaah! Gotta love the 3:2 vertebrate:invert ratio too. Apparently bryophytes and 'pteridophytes' don't actually exist either. My own kingdom makes me weep. Also, for personal sanity, ignore the "Protoctista". That's just Margulis trying to feel special. And somehow succeeding outside her own field. (Levin 1999 Ancient Invertebrates and Their Living Relatives. Prentice Hall, NJ)

'Oh but the textbook's from 1999, cut 'em some slack with the volatile ever-changing taxonomy mess!' If they had used the Woese tree, which I have other personal issues with, I'd be fine with it. Of course, Woese tree in 2010 is a bit irritating, but I can still live with that. But...what truly adds insult to the injury, and rubs various salts even deeper into the bleeding wounds of my inner soul – THAT FUCKING PIE CHART!

"Proportions of members of each kingdom living today"

Hang on, gonna go break some furniture with energetic *headdesk* maneuvers. And my forehead with epic *facepalming*. BRB.

...ok, back. Lab benches are quite sturdy, it turns out. I'll just let Star Trek and internet memes take care of this:

Source: The Internets. All of them.

And they teach this as an uncontroversial, neutral fact. When, in fact, reality looks more like this:

Proportions of total marine biomass and abundance occupied by the only noticeable taxonomic groupings. Also, anyone who replaces "eukaryotes" with "protists" must be pretty freaking awesome. And/or actually understand biodiversity. (Suttle 2007 Nature Rev Microbiol)

I don't mean to bash the textbook itself. Aside from the little taxonomical issue there, the rest of the book seems quite interesting and perhaps a great source for paleontology (not being of that field, I have little idea). It just bothers me when something so cheap and simple to fix is left ignored and perpetrated on and on as students fail to learn any better, and teach what the learned, and further students learn that, and so on, ad infinitum, until we're left wondering why modern anthropology graduates seem to think evolutionary biology progressed little since Darwin's time. It's kind of annoying. And detrimental to efficient progress in all relevant fields. Not even asking for a new section in the book; just fix what's already there!

Ok, my blogging spirit is back now. Time to write up actual posts, relying on the creative writing juices (if any) unlocked by the power of RANT.

Taxonomic tidbit: parabasalids and strippers

Sometimes the taxonomist's character lies concealed in the etymology of a new taxon name:

"The arrangement of the long cilia, clothing the body, reminded him of the nymphs in a recent spectacular drama, in which they appeared with their nakedness barely concealed by long cords suspended from the shoulders, and this arrangement has suggested the name applied to the parasite." Leidy 1877 Proc Acad Nat Sci Philadelphia (h/t PJK)

So yes, Trichonympha (third from left in the blog header), reminded some proper Victorian scientist of his latest stripper experience. And this is why it sometimes pays to read the original taxonomic descriptions.

Also, apparently it wasn't too weird for the author to refer to himself in third person back then...

Adorable apusomonads

Behold, purveyors of tiny soil flagellates: today, Santa brings you not one, but two whole species of Apusomonas. In fact, both described species of this, poor neglected genus. That's right, I've seen 'em all*, and after this post, you will too.

*I'm sure there's plenty more out there who've yet to encounter the microscope. Or be paid any attention to if seen. In fact, these may in fact be new species for all I know. They do fit their respective described ones quite nicely though, I think.

Apusomonas is a member of the Apusomonads, a group that includes Apusomonas, Amastigomonas, then Thecamonas, etc (as of Cavalier-Smith & Chao 2010 Protist) and, according to David Patterson (presumably) at Micro*scope, Etceterix etcetera (noticed by Opisthokont). Apusomonads seem to lean towards branching as sister to opisthokonts. They make their living by nibbling on bacteria, which they crawl over and ingest at their posterior ventral surface. Apusomonads are fascinating from both morphological and evolutionary perspectives, and perhaps if you prod Opisthokont persistently enough, he'll eventually dust off his blog and give these adorable creatures their deserved publicity.

For now, enjoy their strange and amusing mode of motility. By the way, the flagellar basal bodies are located at the kink in the proboscis, not within the cell body proper as in normal eukaryotes. Considering there's a strong tendency for the flagellar basal bodies to be fairly closely associated with nucleus among normal, non ass-tailed (opisthokont) eukaryotes, this is quite odd.

A.proboscidea Type species. First described in 1922.
video video

Differs from A.proboscidea in having a bit of a kink on the left side of its body. (it's crawling on the coverglass here, so it's upside down/ventral side up). Seems to have only been reported in Australia thus far. Now we know it lives in North America too (or some sort of new species, but I doubt it).

A.proboscidea (left) and A.australiensis (right) from their respective Micro*scope pages:

Want to find your own? Grab some soil, put in a dish and fill with some water. Let it stand for a couple of days, and the apusomonads should crawl out of their cysts. I placed coverslips on the surface, which tends to attract benthic-y crawly things. After about 3 days, the coverslips were transferred to the slide, and there was about one apusomonad per cover slip (n=2, heh). Careful though: they're pretty small – around 10µm. A.australiensis is slightly bigger, at least of my two specimens. Good luck!

Anoxic microforay Part II: Everything looks like Bodo

To the untrained eye, all tiny heteroflagellates look the same. To the slightly trained eye, all tiny heteroflagellates look like Bodo.

Anyway, here's a continuation of the smelly marine anoxic sludge microforay I should've finished over a month ago. Taking a break from the much too long Sunday Protist post...

There were lots of bodonids (kinetoplastids, see phylogeny in this post). A lot. Plenty of other excavates around too.

They tend to move about by twisting around their anterior-posterior axis with the anterior flagellum sticking in front, the posterior often wrapping around the body as it trails behind.

Free-living bodonids are quite common and diverse. Also quite understudied, as they don't cause disease. This makes them kind of annoying, as there's so many of them and so little to say. They do have interesting mitochondrial genomes, constituting the kinetoplasts, the group's namesake.

This next thing is another excavate. It reminds me of Carpediemonas (a basal fornicate, near diplomonads et al.), but I'm not entirely sure.

Chilomastix-y thing? Can't tell if there's supposed to be more flagella there...

Unidentifiable mess, but there appears to be a peculiar ridge or line of vesicles or something:

Presumably another bodonid. Wasn't moving quite like the others though...

Trigonomonas or something like it. Hard to catch the bugger in its distinctive pose.

Heteroloboseans! They showed some dramatic eruptive pseudopodial motion; will put up a video once I figure out how to. Though I can't currently rule out their being amoebozoans with eruptive pseudopodia (there are some). The human eye isn't particularly great at distinguishing apart amoeboid things.

Another interesting excavate with a very obvious oral groove. It apparently noticed being noticed, and immediately swam away into a pile of debris, and sneered at me from there. That bastard. The second image shows it from its side. Hard to ID anyway... perhaps some Enteromonad-y thing? Hard to tell how many flagella this one has...

A few more shots of that weird flagellate I mentioned earlier. I think it has four flagella now. Who knows how many tomorrow shall bring...

A heterotrophic euglenid, perhaps Petalomonas sp; it feels its way around with its thick anterior flagellum as it crawls around. The posterior flagellum remains inside the flagellar pocket. The cytostome is also visible inside the cell as the wedge-looking thing.

*shrug* Could be some cercozoany thing. Or maybe not.

Bacterial jungle the above critters seem to thrive in:

Next installment: Misc. non-excavate stuff.

Oh, on the topic of excavates, a jakobid from a freshwater (pond) sample. At least I think it is – looks like Reclinomonas americana. Do they form small stalked colonies like that?