Field of Science

MM21 Hint

One more chance to crack it before I spill the beans - It's a relative of these fearsome things:

(to be referenced later)

(to be referenced later)

Obligatory synthetic genome post: clearing up some confusion

I wasn't gonna bother writing anything about this, considering that pretty much the entire blogging community has sucked the topic dry and written about it much better than I could've. But one little detail still bugs me enough to fail at keeping my trap shut: the phrases "synthetic cell" and "synthetic bacterium". And the brutal media misrepresentation of the whole thing. Also note there will be bias as I tend to be rather skeptical towards synthetic biology in general, partly because the sheer magnitude of their difficulties are underplayed in the media, and replaced with some naive fantasies about "custom life" or irrational fears of Frankenstein-like creatures taking over the world or something. I think we are faaaaar too behind in our understanding of biology attempts at understanding biology for any of these fantasies and fears to be worth considering.

With the recent hype about the synthesis of a new bacterial chromosome (based on an existing one with a few minor modifications), it seems like media and bloggers alike are confusing 'genome', 'cell' and 'organism', using all three interchangeably. In fact, one does get the feeling that lately the existence of the cell has been largely eclipsed by the genome. As it largely has been outside the field of cell biology, sadly. I think a nice sketch of this majority viewpoint can be represented in this quote from Pharyngula:
"So, if after a period of time, you've got a cell whose DNA was produced by a machine, and whose membranes, enzymes, structural proteins, and metabolic by-products were all produced by that machine-generated DNA or the protein products of that DNA, what makes it a non-synthetic cell?" PZ Myers 22 May 2010
Granted, this was said in defense before some utterly ridiculous claims by crazy people, eg. that this somehow proves creationism. Still, as a biologist, PZ Myers should know better - only the proteins and nucleic acids (incl. ribozymes) have been synthesised by the genome. The membranes and non-protein metabolic products, while influenced by genomic activity, also have a life of their own, having been inherited and modified since the origin of life itself. Furthermore, systems like cellular organisation are also not entirely 'programmed' by the genome, and are also inherited extragenomically.

In the paper, the authors use the word 'control' to describe what the genome does, which I think is also not entirely accurate -- would be close enough for most circumstances, but the topic here has become much too philosophical and thus demands careful semantics. Thus, normally I wouldn't've even noticed the slightly misused term. Strictly speaking, as mentioned before, the genome synthesises proteins and ribozymes which act in symbiosis with membranes and cytoplasm to form the cell, also the fundamental level of selection in most cases (eg. see the discussion near the beginning of Cavalier-Smith 2001 J Mol Evol). Thus, the genome cooperates with the rest of the cell, rather than controlling it. Both the extragenomic and intragenomic elements 'seek' to be propagated further, and are mutually co-dependent to achieve said goal, thereby acting as a unit. The gene-centred view popularised by the likes of Dawkins may well be parly responsible for the dismissal of heritable (and thus, evolvable) elements outside the nucleus. While the gene-centred view lays foundations for many important and useful models, one must not get too carried away with it.

There's also a point made that by inserting the synthetic M.mycoides genome into M.capricolum, the latter was essentially transformed into the former - that is, 'changed species', if you will. First of all, the M.capricolum-now-mycoides cell is quite possibly still not identical to M.mycoides, perhaps retaining some cytoplasmic features unique to M.capricolum - this depends on how truly different the two species were to begin with. Which leads us to the second point: the muck that is our attempt to define a species in prokaryotic (that is, asexual) populations. While I personally think that, philosophically, a case can be made for some form of species concept in prokaryotes -- eg. stable 'islands' in the 'fitness landscape' or 'design space' -- the authors have not provided a clear description of the difference between the species (or strains?) in question, and thus it is difficult to evaluate the claim about 'one species taking over another'.

The insertion of nuclei into foreign cytoplasm is not a novel concept. In fact, some red algae have mastered the technique millions of years ago, long before animal cloning and such (remember Dolly?). And genomic fragments overall often tend to be quite promiscuous and not too choosy about their cytoplasmic environment.

My intent is not at all to underplay the achievements. Creating long stretches of custom modified DNA is kind of nice, and could perhaps someday be helpful in, say, generating complex knockouts or modifying multiple gene expression patterns/fusing stuff to them/etc at once. Perhaps someday people will look upon our small-scale molecular genetics work in much the same way we now [try not to] laugh at people who spent years sequencing one gene by hand. I worry whether we are entirely prepared to handle such an onslaught of data, but perhaps 20 years ago they wondered the same thing about us. Perhaps someday organismal biologists will move from molecular genetics to molecular genomics (and thus it is imperative for us to understand both genomics and the tree of life itself!). Again, our current work was beyond fantasy just some two-three decades ago!

But I don't think Venter's paper signals any sort of new era of biological science just yet, let alone humanity or whatever. The world has not ended yet. Nor has utopia begun. Tomorrow is back to lab as usual!

I'm rather overwhelmed by offline stuff right now, especially in the reading and comprehension (and writing!) department, and thus have no time to read over what everyone has to say about the paper, let alone analyse the results in any particular detail, but here's a few recommended musings on the subject, much better written than mine:

- fellow protistologist who kind of scooped me on several points, grrr! =P
(I also wondered about the use of an obligate intracellular parasite in the search for 'minimal life'. Parasites are known to undergo rather extreme reductions both in genome complexity/size and cell structure, and tend to be obscenely derived.)

Lab Rat - bacteriologist who is also cautious about the findings. She also comments that implanting synthetic genomes into bacteria is unlikely to add much to the terrorist's arsenal at this point. She also points out just how much we have yet to know before attempting to create life, as even when an organism emerges from some deep resting stage, it is still equipped with various non-genetic elements necessary for its survival. For the rest, read it yourself! =P

A Russian science news site,, actually got the title somewhat accurate: "The first living organism with a synthetic genome was created" (rather than "OMG SYNTHETIC LIFE!!1!"), and then goes into a detailed history of the project itself, with some insightful comments - apparently at some point Venter's team had some issues with a random deletion in dnaA, kind of important for DNA replication! While I still disagree with their underappreciation of cytoplasmic inheritance, the article overall is well-written, if you speak Russian.

Completely irrelevant to the discussion, but my [poorly informed] impression of Craig Venter is along the lines of this music video from a slightly overfunded (;-)) Harvard lab.

On an unrelated note, Merry and Elio have compiled a summary of the first half-year of microbial blogging for 2010 at Small Things Considered. Anyone interested in microbiology, both nucleated and non, should read their blog if you don't already!

Ok, I've now exhausted my writing juices for the next little while. Hopefully not for long...

Sunday Protist -- Blue Mats of the deep sea: Folliculinopsis

ResearchBlogging.orgFar, far away, in the land of eternal darkness along the base of the deep sea hydrothermal vents of the Juan de Fuca Ridge lie stretches of surface covered by 'blue mats'.
These blue mats are produced by yet another tube-forming denizen of the hydrothermal vents. To non-tube-dwellers like us they may even look vaguely reminiscent of the much more famous giant tube worms, and the concept is quite similar up until that point.

However, if you look inside a tube with its live host, something distinctly non-annelid peers out:

This creature is, in fact, a ciliate - a relative of the elegant Folliculina (referred to in the good ol' days as the "bottle-animalcule"), Folliculinopsis sp., a heterotrich like the giant Stentor:

Folliculinopsis. The two long 'wings' or 'ears' sticking out are its peristomal lobes, which can be seen in the preceding SEM. (Ji et al. 2004 J Ocean Univ China)

Folliculinopsis is host to countless bacterial symbionts; in fact so lushly the bacteria thrive on it that one can barely see the ciliate beneath them! Presumably, these bacteria may be involved in chemical defense, protection from the rather toxic surrounding environment or assist in metabolism. Symbiosis with prokaryotes seems to be fairly common for eukaryotes living awkward (extreme) environments, in large part because prokaryotes are simply amazing at biochemistry unlike their metabolically-challenged nucleated counterparts.

SEMs and TEM of symbiotic bacteria on Folliculinopsis sp. The lorica is covered mostly with filamentous bacteria (top left) whereas the surface of the ciliate is entirely covered with coccoid and rod-shaped episymbionts (bottom two SEMs). Moreover, the inside of the ciliate is full of bacteria-containing vacuoles, as seen in the TEM (near the cortex). (Kouris et al. 2007 Mar Ecol)

In another folliculinid, Eufolliculina, the surface of the peristomal lobes has a peculiar feature: short membrane-covered pins at the base of each cilium. Mulisch (1991 Cell Tissue Res) proposes these pins may act as sensory organelles, perhaps to transmit oriented mechanical stimuli. The cilia have a swelling at the level of the pin, filled with peculiar granular particles with potential involvement in calcium regulation (as you may recall from intro-level physiology, Ca2+ is quite popular in signaling systems). Similar cilium-pin complexes have also been found in other folliculinids, suggesting it may be a shared feature.

Cilia with sensory pegs at the base (arrows). (Mulisch 1991 Cell Tissue Res)

The cilium-peg complex reminds me of sensory hairs or sensilla on insects. Mulisch relates it to the hydrozoan cnidocil in the cnidocyst, or the stereocilia (microvili) at the base of the kinocilium in vertebrate sensory hair bundles. Perhaps this is yet another instance of ultimate convergence, as there is ultimately a finite number of ways particular functions can be performed, and evolution's random walks are bound to chance upon some more than once.

The biology of protist sensory mechansims and overall behaviour is still vast, mysterious, murky territory desperately in need of serious investigation. Unicellular organisms have complex behaviours just like multicellular ones, and are no more 'mere automatic responders to stimuli' than we are (due to our cumbersome complexity, much more random noise tends to creep in; perhaps where creativity comes from...); somehow, without a brain or even a nervous system, many unicellular organisms are nevertheless quite capable of performing complex behaviours in response to various stimuli.

This topic was quite popular in the early 20th century, but seems to have been largely abandoned today (in unicellular organisms). Considering the volumes of papers published daily on cell motility in tissue cultures, would it be too much to ask for some investigation of more intelligent cell types, ie. those that also act as entire organisms? Surely a ciliate must be much more fascinating to work with than some confused helpless cells ripped out of context in some suspension? There's enough work to do in this corner of science to keep us busy for many more years to come...!

On that note, the sun is rising. I should respond to the stimulus. By sleeping... (spent a few more hours scratching my head over some potential centrohelids...freaking gaps in the literature are really annoying, especially when you can't access half of it as it lies under piles of dust in some obscure obsolete journals that have been forgotten for the past five decades or so. Fun times.

Ji, D., Lin, X., & Song, W. (2004). Complementary notes on a ‘well-known’ marine heterotrichous ciliate, Folliculinopsis producta (Wright, 1859) Frauré-Fremiet, 1936 (Protozoa, ciliophora) Journal of Ocean University of China, 3 (1), 65-69 DOI: 10.1007/s11802-004-0011-1

Kouris, A., Kim Juniper, S., Frébourg, G., & Gaill, F. (2007). Protozoan?bacterial symbiosis in a deep-sea hydrothermal vent folliculinid ciliate (Folliculinopsis sp.) from the Juan de Fuca Ridge Marine Ecology, 28 (1), 63-71 DOI: 10.1111/j.1439-0485.2006.00118.x

Mulisch, M. (1991). Ultrastructure and membrane topography of special ciliary organelles in the ciliate Eufolliculina uhligi (Protozoa) Cell and Tissue Research, 265 (1), 145-150 DOI: 10.1007/BF00318148

Snippets of the beauty of sliced axonemes

Look what I found in obscure ultrastructure literature!

It's a star! (Ringo 1967 J Cell Biol)

That's a cross section through the transitional zone of the Chlamydomonas flagellum. The geometric intricacy actually comes from the need to transition from nine triplets of the basal body to the flagellum's nine doublets and a central pair (of microtubules). As evident in the figure below, this can get quite tricky:

Cross-sections through a Chlamydomonas flagellum and basal body. (Ringo 1967 J Cell Biol)

This could be inspiration to some fun baking project...

Speaking of sliced flagella, there are some more wonderful patterns hidden away in the axonemes of rather obscure 'heliozoans' (centrohelids and actinophryids):
Left: Spiral arrangement of microtubules in the axoneme of actinophryid(?) Echinosphaerium. (Jones & Taylor 1981 JCS) Right: Cross section through an axopod of Actionosphaerum (actinoprhyid) containing an axoneme in the centre. m - mitochondrion. (Tilney et al. 1961 JCB)

(axonemes are the cytoskeletal support within axopodia, the long spikey protrusions that make the creatures appear like miniature suns)

And here's one so bizarre it takes three additional diagrams to explain it:

Axoneme of Cienkowskya mereschkovskyi*, a centrohelid 'heliozoan' reportedly closely related to Heterophrys. (Febvre-Chevalier + Febvre 1984 Origins of Life)

*To the slavic ear, this sounds painfully like a masculine adjective applied to a feminine genus name...owww.

And back to basal bodies, parabasalian TEMs are a work of art in their own right. Especially from Joeniids:

Rows of basal bodies in the ciliary region of Pachyjoenia howa. (Brugerolle & Bordereau 2004 Eur J Protistol)

This has nothing to do whatsoever with neither protists nor axonemes, but rather a funky-looking reject from my research images. It's cytoplasmic GFP in a partly lysed plant cell (normally the GFP should look diffuse) Not sure why it does that though, but often lysing cells become very bright, and squashed material is lush with autofluorescence.

My favourite colour is GFP.

Real posts to come soon... still mildly overwhelmed by stuff at the moment. Currently working on gathering up literature both new and old on a supergroup that may or may not actually exist, and is a complete and total mess either way (the new 'Hacrobia'). On top of other things.

To give you an idea, the previously incertae sedis centrohelids are in it, apparently, and their older grouping, "heliozoa", has only recently been dissolved (Nikolaev et al 2004 PNAS), so what is now spread out over at least two supergroups (centrohelids in 'Hacrobia' and actinophryids in Stramenopila) used to be lumped under one category and now you might as well rip all your hair out trying to figure anything out in there. It basically means you have to deal with the damn things on a genus-by-genus, taxon-by-taxon basis. (luckily, they're really cute so it's not that bad ^^) Also, a couple extensive papers happen to be written by The One We Fear, and I'm still denying the fact I may eventually have to actually read them. Grrr. Oh, and add to that the horrible and sometimes altogether lacking availability of older literature, requiring you to assemble epic shopping lists for the inter-library loan people...

Should probably also write another sentence of that manuscript to feel as if I've done something this week. Describe a couple more figures that don't actually exist yet... wish all my control pictures didn't totally suck. Redoing experiments again to get better images of...controls. Sigh. Working on projects in two completely unrelated fields (and different buildings) is a bit draining... /rant

On the non-Sunday-ness of Sunday Protist

Even at the very beginning, I sensed trying a regularly scheduled weekly anything wouldn't work well for me, as I tend to be rather haphazard like that. Furthermore, writing depends a lot on time and inspiration, and the two seldom operate on a regular weekly basis. Sometimes things like those pesky offline obligations (aka 'life', apparently) pile up. Gonna have to keep my blogging slow for a while as I currently have two bosses to satisfy and kind of failing at both. Apparently leaving a lab is no easier than getting into one...

So that's why Sunday Protists come out on random weekdays. The name kind of stuck so I don't really feel like renaming the series; the regulars are well aware of the non-Sunday-ness aspect by now, and the n00bs respected newcomers can suffer mwahaha pick up soon enough.

That said, here's a glimpse of the upcoming post, to keep you in suspense and guilt trip myself into hurrying the hell up to finish it:

(to be referenced later)

Maybe from now on they will start happening on actual Sundays, and that would be creepy and hilarious.

Also, pay absolutely no attention to the loads of Mystery Micrographs I still have to explain and write up. Speaking of which, we still have an outstanding Mystery Micrograph and a Mystery Flagellar Root Apparatus to resolve, both at the free beer* level of difficult by this point ;-)

*If/when budget and geography allow it.

Now if only I could get enough results to satisfy everyone. Science is not cooperating with me lately...grrr. Nor are my writing juices. (Must. finish. results *yawn* section...zzZZZ) Annoyingly enough, annoying complications exciting new data tends to come along just as you're writing up and leaving. Oh gamma-tubulin, why do you insist on getting yourself involved in our already ridiculously complicated plot? *sob* Just gonna pretend that experiment never happened, lalala... actually, just gonna sleep and deal with all this crap tomorrow. Maybe even stop whining about it, but that may be asking for a bit much. But afterwards -- Sunday Protist!

Skeptic Wonder has joined FoS! (and new header!)

In case you haven't yet left the comfort of your feed reader and noticed the changes, Skeptic Wonder has moved from to, hereafter known as FoS. The founder, Edward, has invited me very kindly and thus persuaded me to join. I feel quite honoured to be among the wonderful bloggers here, and hope I can pull my weight. Thank you, Edward!

Please let me know if anything's not working as well as it should, or if some element of formatting is tempting you to throw a sharp heavy object against the monitor. Or even if it only bugs you slightly. And, of course, speaking of which, various bugs too. The blog looks a bit funny via Safari on a Mac for me, does anyone else have the same problem? Or is that computer generally fucked? Via Firefox on PC seems fine though...

To celebrate the move, I finally set out to take care of a problem that has plagued this blog since conception, namely the long overdue customised header. I have spent many mL of brain juice pondering how to make the header several months ago, and never quite got anywhere. Today, I scrapped all prior planning and simply assembled some of my own micrographs together, intended to represent the eight major eukaryotic supergroups:

From left to right: Opisthokonta (nucleariid), Amoebozoa (Cochliopodium?), Excavata (Trichonympha), Archaeplastida (Eudorina?), Hacrobia (centrohelid Raphidiophrys), Rhizaria (euglyphid), Stramenopila (bicosoecid) and Alveolata (ciliate Cyclidium).

Ha, I have images for every supergroup! Would be nice to have one for each subgrouping, and then refine further and further until I get the whole tree covered. And then my plans for world protist domination shall be complete, bwahaha!

I've posted the Trichonympha image before, but haven't shared the whole stack. Admittedly, the poor creature is kind of bloated and dead, but I think the piece of undigested xylem lignin helix makes it all worth it:

I don't have any half-decent pictures of other parabasalians. Yet.

Also, the full picture of what I think may be Eudorina:

It's one of my earlier micrographs, and thus the DIC sucks badly. The colonies are still adorable though!

The other images hang out elsewhere on the blog, except for the euglyphid, which will be blogged about eventually soon. I've got more where that came from.

Public service announcement: animals-fungi-plants != eukaryote-wide

Was just perusing some high impact factor journals before going to sleep, and every other week or the following little detail makes my blood boil:

Someone claims to have done a eukaryote-wide analysis, or something pertaining to eukaryotic evolution, in the title; excitedly, I click, only to find out the eukaryote-wide analysis was metazoa-wide with some yeasts thrown on, maybe Arabidopsis if we're really lucky.

Since I'm in a rather grumpy mood today already, finally slapped together this quick little announcement I've been meaning to make in a while:

(yes I'm lazy and just modified the Tree of Roots published earlier...sue me.)

That's all. Just had to let it out. How can trained biologists be so ignorant about basic biology!? Shouldn't you know at least a little bit about the relatives and evolutionary history of the organisms you work with; shouldn't you be even a little bit curious, at least enough to actually know a thing or two about something as basic as the general scope of eukaryotic diversity? Is that asking for too much?! If an undergrad with a 2.0 GPA can swallow this, why can't tenured faculty at high-ranking famous instutitions?

At least I don't see implicit (animals,plants),fungi too much lately, only once in a blue moon. Maybe because I don't read as much hardcore cell biology literature anymore...

The thoughts of Aurigamonas

While literature surfing again, came across this adorable little cercozoan:

Aurigamonas solis. Diminutive amoeboflagellate, ambitious apetite. Seems to be a common theme in the protist world... (Vickerman et al. 2005 Protist)

That diagram was desperately asking for something to be done. It had to be. And so I did it:

True story: the phagocytic vacuole together with the nucleus express the cell's emotions. But seriously, why would it attack something so big and so armoured!? (Hope the authors wouldn't mind too much someone mutilating their drawings like that...)

On a more serious note, Aurigamonas seem very interesting in terms of cell structure:

The cell is biflagellated with multitudes of haptopodia sticking out and capped by haptosomes. The diagram shows them in varying stages of development (1-5). pno - paranuclear organelle (looks interesting!), cv - contractile vacuoles, sv - spicule-containing vacuoles, mt - microtubule rootlet system (reduced), m - mitochondrion, tv - thick-membraned vesicle. (Vickerman et al. 2005 Protist)

Don't you just wanna dangle this one by its 'tail'?

I hate Macs.

So. Much.

Please, are there any sane people left out there? Am I really alone? Is anyone else sick of getting owned by a stupid white/light grey box every 5 min because some morons are obsessed with making their products 'sleek' rather than something that actually works in a sensible way, and is compatible outside the small special cult they formed???

The only reason Macs are 'safer' in terms of viruses is because Apple has such a small percentage of the total market share that one would have to be a total idiot to write viruses for them. Although considering the arrogance of many Mac fanatics (bordering on religious fervor), it is somedays really fucking tempting to write one.

Can't wait to save up enough to finally get my own computer again. It will definitely be a PC. And all you mac users will save your files in sane formats to accomodate the other 99% of computer users. We are not inferior to you.

Maybe I should just go ahead and install GNU/Linux everywhere in the lab. MWAHAHA. Too bad I probably don't have sufficient computer skills to do so =(

Ok I think I can proceed with my work now. Writing this from a Mac right now... how does one autoclave a blog? Ewww the cooties...

Pwned by Euglena* earlier and now by a Mac. My day really sucks...

*I think I just discovered the first strain of those fuckers who are NEGATIVELY phototactic. That's right, they consistently move AWAY from the light, or ignore it altogether at lower intensities. Photosynthetic organisms displaying photophobia. Oh yeah, makes so much sense. Maybe tomorrow the laws of nature will hate me a little less...

Do giant deep sea isopods have protist endosymbionts?

Apparently not as of this [admittedly slim] description of intestinal microbes from 1982. Seems to be mostly bacteria and nematodes - though one wonders if there are some cool gregarine or something inside one of those.

On the topic of isopod gut endosymbionts (though not of the deep sea), there's a recent PNAS paper starring a wood-boring isopod devoid of cellulose-digesting gut microbes, capable of lignocellulose digestion all on its own! (King et al. 2010 PNAS "Molecular insight into lignocellulose digestion by a marine isopod in the absence of gut microbes") Limnoria quadripunctata, quite amazingly, actually lacks gut microbiota entirely (unlike the bivalve woodboring 'shipworms', which do have a flourishing gut culture) and as animals are known for failing at lignocellulose digestion on their own, raised some interesting questions about how they do it.

Turns out, Limnoria not only has unusually high glycosyl hydrolase (GH) expression levels in its transcriptome, but also the first described case of endogenously produced GH7 in metazoa. This was then followed up by finding GH7 expression in the Daphnia and Gammarus(both also crustacea) ESTs. Seems like the GH7 domain is key to self-sufficient cellulose digestion, in animals anyway. Another question did it get there? LGT from somewhere? The authors consider recent LGT unlikely as the metazoan sequences are quite distant from anything else in tree (and don't fall in the midst of another clade; though there's arguably too few sequences to judge at this point).

Thus, it seems that what most strikingly enables the gastromicrobially deprived Limnoria to digest wood on their own is GH7 (and potentially hemocyanins). Curiously, the most abundant cellulases in the termite gut, produced mostly by its protist symbionts, are GH7.

This little adventure, like most others on this blog, was completely unplanned and sporadic. Someone brought up deep sea isopods, thus I couldn't just ignore that very important question of ultra high priority. Mostly because giant isopods are fucking cool. Oh, and giant. Would make an adorable, wonderful pet, if it weren't for the whole deep sea thing.

Source: Ross Gwynn on Reddit. 2.5 feet long, or roughly 75cm, though that may be exaggerated.

Sunday Protist -- Tachyblaston: A suctorian parasite of suctorians[it's totally still Sunday in someone's mind somewhere...right?]

Reading old protistology books can be quite a frustrating exercise: image you come across a really cool-looking organism, try to follow up on what happened to it since, and discover it's only been written up once in the distant past and neglected ever since. This happens to a very annoying percentage of organisms described in those older books (newer books tend to forget the phantom and near-phantom species). Now this organism in particular at least has a very detailed source behind it, but alas! German. I saw it in Grell's (1973) Protozoology, and the original description comes from... Grell 1950 . The former I have an English copy of, the latter I do not. So don't expect much detail.

Ecologists often lump microorganisms together as 'decomposers' (at least in undergrad courses); those of us living in a different scale of things beg to differ. From an intro ecology text, you get the idea that ecology somehow ceases to happen once you reach a certain size or phylum, and everything's just a part of this amorphous blob that exists to recycle nutrients so that the rest of us can live on. Shockingly enough, this amorphous blob has a whole ecosystem of its own, complete with predators and photosynthesisers and those who do both, as well as parasites and mutualist endosymbionts and saprophytes, etc. They interact with each other in ways not in the slightest less interesting than fluffy animals. In the microscopic world, cells become bodies that, just like ours, can get hunted, infected or benefited by some other organism. Or host a pile of commensals (who do exist, by the way, by similar arguments that Nearly Neutral Theory employs for mutations)

*Zoological ecologists also tend to treat plants as 'those things that exist for animals to eat', which annoys the hell out of anyone dealing with plants. On the first day of ecology the instructor causally mentioned that 'plants don't do much in the way of behaviour', and thus the course will largely ignore them. I expressed disagreement after class, noting there is little fundamentally different between a plant biochemical response leading to, say, discharge of toxins or some regulatory change, and an animal biochemical response leading to observable [to our eye] mechanical change. Yeah, this is why I have difficulty talking to the more 'traditional' biologists sometimes...but that is completely off-topic.

Remember how crabs can sometimes be covered in sea anemonies? Many smaller crustaceans can often be covered in organisms superficially resembling miniature sea anemonies - namely, Suctorians - highly derived (=weird) ciliates covered in miniature tentacles. Suctorians also reproduce by budding, as opposed to conventional symmetrical mitosis employed by the canonical ciliate. Just like sea anemonies and other cnidarians, suctorians also have stalked and swarming forms, like the polyp vs. medusa destinction in the former. Which is quite unsurprising, really, as aquatic sessile organisms usually use specialised free-swimming forms to spread. But still another cool bit of ultimate convergence discussed a couple posts ago.

Top: A copepod covered in suctorians; an SEM of Ephelota gemmipara from the copepod. (Fernandez-Leborans et al. 2005 J Nat Hist) Bottom: Ephelota superba, suctorian episymbiont of Antarctic krill. Quite reminiscent of an anthozoan. (Stankovic et al. 2002 Polar Biol)

Now, imagine a microscopic sea anemone being parasitised by another. I'm not sure whether there are any cnidarian parasites of other cnidarians (wouldn't be too surprised), so the analogy stops around here. The awesome does not, however: parasites are never truly simple. Tachyblaston's infancy consists of finding an Ephelota, attaching itself and piercing the cell membrane to leech off the cytoplasm. Over time, the entire cell can become filled with parasites. During this stage, the parasite buds to produce swarmers.

Tachyblaston invading Ephelota cell body. Right: Tachyblaston budding. (Grell 1950 Z.Protistenk)

Afterwards, the swarmers swim around and attach themselves to an Ephelota stalk, where they themselves form a stalked cup structure. There the parasite buds multiple times, yielding a cup full of Tachyblaston, which is subsequently emptied as the buds (this time with a single thick tentacle, according to Martin 1909) evacuate and crawl up the stalk toward the main cell body of Ephelota to infect it and start the cycle over.
Left: Swarmers. The stage that actually sort of looks like a ciliate... Middle: Full 'cup' of Tachyblaston in stalked stage. Right: Empty cup after all (Grell 1950 Z.Protistenk)

To summarise Tachyblaston's life cycle, the cell-penetrating parasites of the Ephelota cell body bud to form swarmers, which, in addition to reminding us of suctorians' ciliate leanings, find another Ephelota and attach themselves to the stalk, forming a cup which they fill up by budding again, finally releasing single-tentacled forms that crawl up the stalk to the next victim. How's that for unicellular organisms having 'primitive' differentiation capabilities?

Overview of the whole life cycle of Tachyblaston. Oh the tentacles... (Grell 1950 Z.Protistenk)

Tachyblaston's original description by Martin 1909:380 J Cell Sci can be found here. The parasite was very distinctive due to a major refringent particle of unknown origin or function present within each Tachyblaston cell. The genus name reflects the extraordinary speed with which the parasite epidemic can sweep over an entire population of Ephelota, which end up a decimated forest of bare stalks. Creepy.

And last but not least, here's an obligatory tree to orient ourselves phylogenetically:

Tachyblaston and Ephelota are both suctorians in Phyllopharyngea, which contains some other bizarre (and somewhat obscure) creatures like Chonotrichs. (Gong et al. 2008 JEM)

PS: Blogging about ciliates is very difficult. They are too damn distracting - you start reading about one and come across ten others you suddenly must look up, and so on. About as bad as Wikipedia. Actually, since looking these things up is now actually relevant to my day job, the distractions get worse as I feel compelled to write down and follow anything potentially related to work. Just in case. Apparently, sort of using blogger as a reference manager... hence the exploding drafts folder. Sigh.

Fernandez-Leborans, G., Freeman, M., Gabilondo, R., & Sommerville, C. (2005). Marine protozoan epibionts on the copepod Lepeophtheirus salmonis , parasite of the Atlantic salmon Journal of Natural History, 39 (8), 587-596 DOI: 10.1080/00222930400001525

GONG, J., GAO, S., ROBERTS, D., AL-RASHEID, K., & SONG, W. (2008).
n. sp. (Ciliophora, Phyllopharyngea, Cyrtophoria): Morphological Description and Phylogenetic Analyses Based on SSU rRNA and Group I Intron Sequences
Journal of Eukaryotic Microbiology, 55 (6), 492-500 DOI: 10.1111/j.1550-7408.2008.00350.x

Grell, K. (1950). Der Generationswechsel des parasitischen Suktors Tachyblaston ephelotensis Martin Zeitschrift f�r Parasitenkunde, 14 (5) DOI: 10.1007/BF00260027

Martin, CH (1909). Some Observations on Acinetaria: Part I.—The " Tinctin-kbrper " of Acinetaria and the Conjugation of Acineta papillifera. Quarterly journal of microscopical science, 53 (2), 351-389

Tree of Roots

Flagellar roots, that is. Tree of phylogenetic roots would be another fun project though...

You know when you see a page full of diagrams and get overcome by this urge to map them onto some phylogeny just for the hell of it? Especially when your other option is to actually write up the results and discussion sections your supervisor's sort of waiting for? (wrote two whole paragraphs' worth today, so I can take the rest of the day off, right?) Anyway, here comes Sleigh 1988 BioSystems p279, modern phylogeny edition:

Phylogeny of Sleigh representations of flagellar root structures. Diagrams from Sleigh 1988 BioSystems; phylogeny based on A Tree of Eukaryotes v1.2 (complete references therein).

Sleigh came up with a way to represent the structure of flagellar root apparatuses in order to compare them between various groups. These diagrams are used today by people working with protist cytoskeletons, and are reportedly a pain in the ass to make (rather unkind on one's 3D imagination capabilities). The flagellar root was traditionally considered to be a reliable character for taxonomic work, although it seems to be rather dangerous in some cases, as morphological any traits often tend to be. The flagellar root apparatus is quite complicated, and very often is responsible for the organisation of the rest of the cell. An annoying thing about them is how little is often known about the biochemistry of the various root elements, as materials besides tubulin can be freely used. In fact, older literature is full of descriptions of various fibrillar systems that have yet to be followed up on with modern cell biology techniques.

Luckily, I somehow resisted the temptation to add other people's Sleigh diagrams onto the tree; hopefully won't succumb any time soon as I actually have real work to do. Hopefully fate won't take me to Simpson 2003 anytime soon...

Does anyone else find making diagrams quite...relaxing?

(Sunday Protist on its way...keep on getting distracted while looking stuff up for it)

SLEIGH, M. (1988). Flagellar root maps allow speculative comparisons of root patterns and of their ontogeny Biosystems, 21 (3-4), 277-282 DOI: 10.1016/0303-2647(88)90023-8

Mystery Flagellar Root Apparatus #01

This is mostly just to annoy someone =P

Have fun!

Deciphering abbreviations would only kill the fun. Obviously not expecting species-level identification. To be referenced later. Bwahaha.

Fine, I'll help a bit: this is in interphase.
Oh, and obligatory XKCD reference.

Edit 10.05.10 - Feeling generous today. Here's the rest of the figure:

(to be referenced later)

And it's not a Sleigh diagram, as the bulk of those have probably been seen by a certain reader already.

Convergent evolution between shrunken animals and bloated protists

ResearchBlogging.orgOur invertebrate zoology textbook, being a good couple decades behind schedule as any textbook ought to, felt rather heavily biased against molecular phylogenetic analysis, and rather conservative in sticking to traditional taxonomy in spite of contradicting molecular data. In fact, towards the end somewhere the authors rather explicitly pointed out that molecular phylogenies are not to be trusted, especially when in disagreement with embryological data.

Here we run into the age-old problem in evolutionary biology: how do you reconstruct the past is the models of evolution you use are based on your...reconstructions of the past? Hah, as with any other interesting problem in life, you have to do both simultaneously, devoid of simple algorithms. Dismissing molecular phylogenies because they disagree with your pet theories on morphological evolution is just stupid. The non-photosynthetic stramenopiles(=heterokonts), for example, include things that were once, based on morphology, considered as: yeast, filamentous fungi, 'heliozoa' (group now completely defunct) and ciliates. Molecular phylogenies, while definitely full of their own flaws, eventually resolved that mess.

Curiously, it seems there may be a bit of a problem with bacterial phylogenies being overrated in spite of the organisms and their biology. So while traditional taxonomy fails there as well, it's as if the field got a little carried away with sequences. Part of the reason may be that there seems to be very little communication between cell and evolutionary bacteriologists, emphasised by the stark absense of organism in evolutionary discussions and evolution in organismal ones. Which is another thing that makes protistology a pretty awesome field - there appears to be at least some semblance of balance and sanity between organismal and evolutionary protistologists, perhaps because there's so few of them to begin with.

Anyway, back to our invert zool text, one major drawback of clumping things together by morphology is that smaller things tend to go together that way. Obviously, sharing size does not imply any phylogenetic closeness; nor does the level of structural complexity. Plagued by past notions of a progression towards increased complexity, many taxonomists lumped the 'simpler' incertae sedis taxa together.

One such example was the acoelomate/pseudocoelomate/coelomate concept, where the inner body cavity (coelom) became progressively more complex as proto-bilaterians evolved into acoelomate flatworms, then pseudocoelomate nematode-like intermediates and finally acheived the true coelom of arthropods and vertebrates. From the morphological perspective, that makes sense. However, along came molecular data and cast this neat little story into the rubbish pile, revealing that many of the acoelomates and pseudocoelomates have secondarily reduced coeloms, derived from a true coelom. Thus, Acoelomata and Pseudocoelomata kind of exploded all over the tree. Much like 'yeasts' and 'heliozoans' and 'rhizopods' (amoebae, forams, etc).

Structural complexity is very dangerous, as evolution wanders about rather aimlessly and has little against losing complexity if it can. In fact, selective pressures tend to favour simplicity, and to put it crudely, reduction of complexity tends to be adaptive more often than bloating. I've rambled on about this before, but this is to emphasise that this concept is actually kind of important and useful, and not just idle philosophising. It is actually dangerous to assume some sort of adaptive search for complexity as shown in cases like those of Acoelomata and Archaezoa.

This leads us to the next taxonomic 'clump' - small metazoans, or 'meiofauna'. Meiofauna include Loriciferans, Rotifers, Gastrotrichs and the rather adorable Tardigrades. Many of them weren't clumped together seriously as much as simply due to lack of any information about them, considering they sadly don't fare well in the charismatic megafauna beauty contest. Turns out that meiofauna tend to be secondarily miniaturised. There is only so many ways an organism can be shrunk and still viable, thus convergence becomes a rampant feature in miniaturisation, the central theme of Rundell & Leander 2010 BioEssays:

Latest sketch of the metazoan phylogeny with representative meiofauna depicted in the images, where applicable. Very nice of them to put metazoa into the broader eukaryotic perspective in the top left corner! As meiofauna are quite widespread over the metazoan phyla, it is emphasised that a better understanding of these groups is crucial to properly reconstruct metazoan evolution and diversity. Microorganisms being important...another issue in need of reminders every five years or so? (Rundell & Leander 2010 BioEssays)

Rundell & Leander focus on interstitial organisms (those of the intertidal zone) and note the prevalence and importance of convergent evolution between various independently reduced animals, such as adult loriciferans and larval priapulids; and adult vs. larval ostracods and barnacles, respectively:

a) adult loriciferan b) larval priapulid c) adult ostracod d) barnacle larva (Cypris stage) Scalebars: a - 30um; b-d - 100um. (Rundell & Leander 2010 BioEssays)

Of course the comparisons at this stage are superficial, but still a good lesson in the prominence of convergent evolution and the dangers of morphological lumping. Furthermore, they proceed to point out convergent features shared with some protistan representatives from the same environment: ciliates. Meiofaunal taxonomy is plagued by cases of well-trained zoologists failing to distinguish ciliates from rotifers and cryptic small metazoa (there was one cryptic species mentioned in the textbook that was obviously a ciliate based on the description, especially the 'dispersal by transverse fragmentation' part... can't find it at the moment, perhaps someone might know what I'm talking about? Name starts with a C or an S...), and there may be good reasons for that:

a) A gastrotrich b) A [hypotrich] ciliate. Note the dorsal spines and dense ventral cilia on both. Incidentally, both are benthic, so this is rather unsurprising, but still cool considering the former is a case of size reduction whereas the latter is a case of a size increase. c-d) stalked rotiferConochilus e) stalked ciliate Epistylis. They are both capable of rapid contractions in a very similar manner. Again, only so many ways one can be a stalked colonial organism of this size and ecological niche. Scalebars - 10um. (Rundell & Leander 2010 BioEssays)

As shown above, the examples of convergence are quite striking, and also not too surprising - there are only so many ways one can survive under given conditions, especially when the conditions are extreme as in the intertidal case (or in case of parasitism as well). Extreme conditions generally imply stronger selective pressures which lead to greater streamlining and a reduced 'design space', to steal a term Dennett often uses in Darwin's Dangerous Idea (1995). What is quite intriguing is that parts of this design space are accessible to both unicellular and multicellular organisms, leading to striking convergence as in the stalked rotifer and ciliate examples above. While the 'function' (I use this word with fear...) is similar, the mechanisms underlying it are as different as can get, striking down the phylogenetically-limited argument that all convergent features are ultimately homologous in some way (see Leander 2008 JEM and an informative reply in 2008 TrEE here(both free access)).

Of course, the crux of all this is that microscopic organisms of all phylogenetic affiliations are infinitely awesome and desperately in need of research attention. If you insist on multicellularity, then metazoan 'meiofauna' are for you. If we can still find amitochondriate anaerobic animals in 2010, there must be plenty of other amazing stuff hidden within neglected, obscure and underexplored phyla.

And with that, I shall migrate back towards my protists - feels like I'm cheating on them. My past two 'meatier' posts have been about...metazoa. That's just...wrong =P

Gonna stop there as someone holds freakishly early lab meetings (9.30am! the cruelty...!) so someone else must be up early... yes, before noon is early, ok?

[completely off topic: someone besides TC-S agrees people have become a little too obsessed with the role of endosymbiosis in eukaryogenesis - essay by Poole & Penny 2007 Nature]

Rundell, R., & Leander, B. (2010). Masters of miniaturization: Convergent evolution among interstitial eukaryotes BioEssays, 32 (5), 430-437 DOI: 10.1002/bies.200900116