Reticulose amoeba: cells can be fine nets too

Again, the protist kingdom is a special paradise for a cell biologist: as soon as one steps outside the plant and animal kingdoms (and yeast), diversity of cellular forms and structures explodes beyond reason. Cells can also take the shape of a fine net with no obvious cell body proper:

Cover slip floated ~ 1wk on marine sample from intertidal silt at Stanley Park. (40x obj, DIC and phase, resp.)
EDIT: Confirmed Filoreta.

Almost overlooked it thinking it was just slide gunk. Amoebae suffer all too often from that fate – apparently Parvamoeba, one of the most common and ubiquitous amoebae, was only described in the early 90's (Rogerson 1993 EJP) because it was tiny and no one noticed.

Could be something like Filoreta sp. (Rhizarian), but something feels off about it. Filoreta doesn't seem to stretch cytoplasm between filopodia like this specimen does. Maybe it's more like the amoebozoan Corallomyxa and Stereomyxa, or stramenopile Leukarachnion. Then again, amoebae are notoriously dynamic in their morphology. Something that's a far bigger issue in the microbial world is the necessity of getting a sense of the morphotype range of a species; one specimen doesn't quite cut it as it does for animal taxonomy.

In fact, perhaps instead of the ridiculious (for us) ICZN and ICBN requirements for submission of material for curation (many species neither like being cultured nor preserve all that well on a slide), for microbial species there should be a requirement for additional images of different specimens, if possible, to try to capture some of the morphological range. But then again, I'm not a taxonomist, so what do I know.

Right, midterm... (hey, at least I procrastinate productively!)

Mystery Micrograph #27

Busy week here, so have a mystery micrograph:

To be referenced later. Won't reveal the scale yet.

Kekeke. *evil grin*
Anyway, I have a "mid"term, almost two weeks before the term ends. Took the art of neglecting coursework to a whole new dimension this term – incredibly difficult to give a fuck in term 2 of year 5. Lots of catching up to do...

Trypanosomatid plastids and uninentional scientific comedy

One need not read past the abstract:

"It is usually assumed that the trypanosomatid plastid shared a common origin with that of euglenids, but Δ4 desaturase phylogenies suggest that it could have originated via an independent, tertiary endosymbiosis involving a haptophyte alga. It is also possible that ancestors of the Trypanosomatidae initially possessed a primary plastid that later was replaced by a secondary or tertiary plastid." – Bodyl et al 2010 J Parasitol (pdf)

I could go on for many, many pages about the implausibility of most entirely unnecessary serial plastid symbiosis theories; I could go on for pages yet on how little a single gene phylogeny means these days; I could go over the typical first few lectures on phylogenetic reconstruction and the fundamental principle of parsimony. But instead, I've quickly thrown together a diagram highlighting the KEY problem with Bodyl et al.'s hypothesis:

Taxa in black – non-photosynthetic and non-plastid-bearing.

Trypanosomes don't have plastids.

Or any reason to suspect they might.

*to be fair, they are (I hope) talking about a plastid in their ancestry, but those things are seldom lost completely due to inevitable strong dependencies.

In fact, unlike apicomplexans, trypanosomes are nested firmly within a completely non-photosynthetic phylum in a predominantly non-photosynthetic subgroup of an almost-exclusively non-photosynthetic supergroup. Furthermore, the many possible phylogenies of euglenid evolution overwhelmingly support a single symbiotic event; character evolution supports this further, in one of the few cases where there's actually little room for dispute. Endosymbiosis may not be excessively rare, but it ain't common either, particularly in a full-fledged form involving vast transfer of plastid genes to the nucleus AND mechanisms of plastid targeting of the synthesised proteins. Too many an ambitious biologist completely forget about targeting, or that there's actual cell biology happening around their beloved gene sequences.

For a properly scientific and civil demolition of an earlier iteration of this ridiculous idea, see Leander 2004 Tr Microbiol (pdf). That smell of something burning? No need to worry – probably just coming from the link.

Lastly, as ridiculous as this hypothesis is and as amusing as it is that this actually survived peer review (no offense to J Parasitol, but phylogenies and evolution do not seem to be their strong point based on some other cases...), I fully support it being published. It is the excessive censorship of atypical theories rather than sketchy papers that "stiffles [scientific] thought"...

(Note: I would've submitted this to the high IF Journal of Are You Fucking Kidding, but I'm out of hard liquor and would thereby fail the author instructions...)

References
Bodył, A., Mackiewicz, P., & Milanowski, R. (2010). Did Trypanosomatid Parasites Contain a Eukaryotic Alga–Derived Plastid in Their Evolutionary Past? Journal of Parasitology, 96 (2), 465-475 DOI: 10.1645/GE-1810.1

LEANDER, B. (2004). Did trypanosomatid parasites have photosynthetic ancestors? Trends in Microbiology, 12 (6), 251-258 DOI: 10.1016/j.tim.2004.04.001

Out in the field: freshwater microforay picture dump

I've probably accumulated about 10-20GB of protist pics by now. And a couple DV tapes' worth of video. Still got some work to do before I can catch up with my 80GB of Arabidopsis epidermis pictures (mostly of all sorts of mutilated stomata), but this is for fun rather than data, and thus accumulates much slower. Most of them are crap or uninteresting by now, but the others might as well get dumped here as raw data from 'field work'. The wonderful thing about microscopy is that the more you know, the more new things you observe, and the more interesting it gets. Eg. once you're no longer distracted by trying to identify unknown things, you pay more attention to behaviour. Anyway, I'll dump the photos in random installments here and there, hope there's at least something interesting for you from time to time.

To begin, a fuzzy ciliate of sorts. Prominent contractile vacuole, and I think in the left image I think you can make out its macronucleus or two. Can't see the mouth so IDing it is a bit difficult.

[to shave off some page loading time, the rest is below the jump (if it works)]

Sunday Protist – Trimastix marina

Before we begin, two things about [current] Trimastix marina – it has four flagella (not three) and is found in freshwater. The taxonomic author, Saville-Kent, is a bit notorious for some rather sketchy descriptions, and Trimastix is one of his 'trophies'. That said, it may be that Kent did actually see a three-flagellated and/or marine thing like this and it just hasn't been found or published yet. But for the time being, feel free to point and laugh at the double misnomer.

This past fall I dumped a bunch of leaves in a dish and kept them wet for a while. Turns out, the abundance and diversity of microbes and meiofauna thriving in that pile of dead leaves in your yard is quite amazing – all sorts of ciliates, myxomycetes (slime moulds), tardigrades, rotifers, springtails, flagellates, amoebae – you name it. Some of this world can be seen with a simple dissecting scope; it helps to put a coverslip or some other piece of glass on the wet leaves to see better. This coverslip is also great for investigating what lives on the surface of the rotting leaves. The other impressive detail was how quickly the leaf tissues rot away, after a couple months leaving little more than the bare skeleton of the vascular system. Dead leaves are the whale falls of the terrestrial microbiome.

Rotting tissues tend to have relatively low oxygen concentrations, and thus host some unique organisms. Among them was this peculiar flagellate that simply screamed "EXCAVATE" at the top of its lungs, but I couldn't quite figure out what it was:

Trimastix marina. The cell body is about 25-30µm, with a prominent anterior flagellum sticking out in front, and three smaller flagella trailing behind. The nucleus is the little blob at the very anterior tip of the cell, in front of a large circular food vacuole. At the very posterior tip is the contractile vacuole characteristic of freshwater things in general. Along the side of the cell is an exceptionally conspicuous groove, through which one of the recurrent flagella runs – a characteristic feature of excavates. Anoxic, leaf litter moistened with ample water for a couple of weeks. 40x obj, DIC

The part that screamed "EXCAVATE" at me was the distinctive groove (namesake of the supergroup) along the side of the cell. You can often discern it in other excavates like Jakobids, Retortamonads and Carpediemonas-like organisms (CLOs; hey, it beats "Clade B"...), but here you don't even have to look hard. Curiously, the closely related oxymonads (see Streblo, Saccinobaculus) seem to have lost the groove, but that's another story.

Overview of 'basic' excavate cell types. Trimastix marina is the very distinctive one in the bottom middle. There's something distinctive and cute about its thick anterior flagellum and the way it moves. (Simpson et al. 2002 JEM)

Thus far, Trimastix may seem like your garden variety peculiar flagellate. But there's something universally eukaryotic you might have difficulty finding – a proper mitochondrion.

I mentioned earlier the sample was somewhat anoxic. It wasn't irrelevant, because I've never seen anything like this critter in regular pondwater or well-aerated soil. Like many of its excavate relatives, Trimastix has lost the necessity to maintain the elaborate complexity of aerobic pathways and their accompanying structures, like cristae. Furthermore, it lacks a mitochondrial genome. This led to the conclusion that Trimastix lacks anything mitochondrial altogether, and may have diverged prior to mitochondrial endosymbiosis – a perfectly reasonable assumption given the data at the time. This landed Trimastix (along with the better-known sister Oxymonads) a position in then-subkingdom/phylum Archezoa (Cavalier-Smith 1983)
[NB: Archezoa = 'beginning/early animals', not ArchaEzoa, which would be 'ancient animals'. He seems particular about that.]

Trimastix wasn't a major player in the Archezoa Hypothesis (wherein 'amitochondriate' lineages are contemporary representatives of pre-endosymbiotic eukaryotes) since it's rather obscure, but was still a piece of the puzzle. Eventually, better phylogenetic techniques and improved taxon sampling destroyed the Archezoa Hypothesis, particularly as mitochondrial genes and derived organelles (such as mitosomes and hydrogenosomes) were found. Trimastix's mitochondrial genes were found later than those of other anaerobes, perhaps owing to its obscurity – but they're there: mitochondrion-targetting genes in the nuclear genome (Hampl et al. 2008 PLoS ONE). Furthermore, the aftermath of mitochondrial reduction looks like a generic double-membrane bound blob in electron micrographs (Hampl & Simpson 2008 in Hydrogenosomes and Mitosomes: Mitochondria of Anaerobic Eukaryotes) – no wonder it was so hard to find!

All that's left of Trimastix's mitochondrion, as the eons of anaerobic existence devoured its need to maintain one. It is uncertain whether it produces hydrogen gas – which would make it a hydrogenosome rather than a mitosome – though at least some of the necessary genes seem to be present in the nuclear genome. (Hampl & Simpson 2008)

As an aside, there's no known case yet of a reduced mitochondrion that simply disappeared – in addition to aerobic respiration, eukaryotes have also become dependent upon it for some other vital metabolic pathways, such as those involving the Fe-S cluster. In fact, in at least one species of microsporidia, ATP is imported into the mitochondrial relic in order to keep the key metabolic pathways running. (I vaguely recall having written about this before, somewhere...)

Lastly, Trimastix is host to some lateral gene transfer for its glycolytic pathway – it appears to have picked up and replaced at least four of the eukaryotic genes with bacterial versions (Stechmann et al. 2006 BMC Evol Biol). There was a discussion somewhere on the blogosphere lately (Coyne's blog, IIRC) about the relative importance of LGT – it sure as hell does happen in eukaryotes as well, though not crazy enough to wreak havoc on the phylogenies.


And the rain hasn't stopped yet. But I can't skip a second night of sleep... as much as I'd love to keep blogging about stuff.

References
Hampl, V., Silberman, J., Stechmann, A., Diaz-Triviño, S., Johnson, P., & Roger, A. (2008). Genetic Evidence for a Mitochondriate Ancestry in the ‘Amitochondriate’ Flagellate Trimastix pyriformis PLoS ONE, 3 (1) DOI: 10.1371/journal.pone.0001383

Hampl, V, & Simpson, AGB (2008). Possible Mitochondria-Related Organelles in Poorly-Studied “Amitochondriate” Eukaryotes HYDROGENOSOMES AND MITOSOMES: MITOCHONDRIA OF ANAEROBIC EUKARYOTES DOI: 10.1007/7171_2007_107

SIMPSON, A., RADEK, R., DACKS, J., & O'KELLY, C. (2002). How Oxymonads Lost Their Groove: An Ultrastructural Comparison of Monocercomonoides and Excavate Taxa The Journal of Eukaryotic Microbiology, 49 (3), 239-248 DOI: 10.1111/j.1550-7408.2002.tb00529.x

Stechmann, A., Baumgartner, M., Silberman, J., & Roger, A. (2006). The glycolytic pathway of Trimastix pyriformis is an evolutionary mosaic BMC Evolutionary Biology, 6 (1) DOI: 10.1186/1471-2148-6-101

Cryptomonads: solar-powered armoured battleships

I've been 'scoping around some pond water lately and came across some relatively big cryptomonads (g. Cryptomonas, I think). Cryptos aren't all that rare, but most of them whirl about rather hyperactively, rendering them as troublesome photo subjects. This specimen, on the other hand, had a convenient habit of pausing every once in a while to have its picture taken. Finally, I have my own cryptomonad shots!

Cryptomonas(?) sp. The cell is about ~30µm long, pretty big for a cryptomonad. On its right side the cryptomonad has a furrow – or, in some species, an tube-like gullet – lined with ejectisomes (particularly visible in the top right image). The vesicle at the anterior tip of the cell is its contractile vacuole. Refractile stuff is the starch granules. 40x objective, DIC

Despite their small size and superficially generic algal appearance, cryptomonads do have quite a few awesome bits about them. From an evolutionary standpoint, they have pretty damn awesome plastids – products of secondary endosymbiosis of red algae, complete with a shrunken relict nucleus ("nucleomorph") of the red algal ex-host! The plastids also have four membranes, complicating the delivery of plastid-targetting proteins from the cryptomonad host nucleus. But I'll save that story for some other time, and instead keep it superficial. Literally: it has ejectile things lining its surface, and who doesn't like the idea of a microscopic solar-powered hyperactive battleship?

Prior to embarking on some battle scenes, lets look around the ship's anatomy a little bit mostly as an excuse to show off a diagram. At its fore we have a pair of flagella, lined with little hairs – also a characteristic of many Alveolates and Stramenopiles, with whom Cryptomonads might share the secondary red algal symbiosis event with. Much of the cell is occupied with a single plastid, making the fucker a bit difficult to diagram. In all his/her/its infinite wisdom, the designer apparently failed to take into consideration the future pains of this student attempting to tame the wild beast that is Illustrator while drawing this cell. Asshole. Besides the plastid, there's also a single mitochondrion and a bunch of other small crap that a eukaryote ought to have. The plastid's outermost (fourth) membrane is contiguous with the endoplasmic reticulum system, presumably homologous to the original digestive vesicle that enveloped the 'enslaved'* red alga. The third membrane derives from the red algal cell membrane, whereas the inner pair are the usual plastid membranes. Pop quiz: where would you expect to find the relict endosymbiont's nucleus (the nucleomorph)? (Answer at the bottom of the post, or in the diagram if you're so inclined to 'cheat' ;p)

*Google [scholar] "Cavalier-Smith" and "enslaved". When he likes certain words, he really likes them.

Back to the surface. The cryptomonad surface is quite complex, consisting of an inner and surface periplast layers separated by the cell membrane. Sometimes the surface layer can be be covered in scales, sometimes fibrous matter. This periplast is perforated with pores for ejectisomes, much like battlements on a warship. Ejectisomes themselves consist of coiled proteinaceous ribbons that extend forcefully upon firing.

Cryptomonad periplast. IPC – inner periplast layer, PM – plasma membrane, S – scales (of the surface periplast layer). On the right is a freeze fracture EM of the plasma membrane, which shows imprints of the surface scales (vaguely hexagonal) and pores for ejectisomes (E). In other words, the surface of an armoured warship with battlements. (Brett & Wetherbee 1986 Protoplasma)

Ejectisomes – more generally, extrusomes – are not all that unusual in the protist world. Many ciliates are loaded with menacing trichocysts and green algae like Pyramimonas are not afraid to fire similar structures either. Some bacterial endo- and episymbionts also bear similar coiled structures, but that's a topic for some other day as well. Extrusomes can also be used more locally to glue prey to the organism – if you, upon finding yourself shrunk to microns, accidentally bump into a frail-looking centrohelid heliozoan, be afraid. Be very afraid. It will smother you in adhesive proteins from the extrusomes lining its fragile-looking axopodia and devour you alive and possibly paralysed.

Ejectisomes in cryptomonads and their non-photosynthetic close relatives, katablepharids. Pyramimonas is only distantly related, and probably evolved its ejectisomes completely independently. (Kugrens et al. 1994 Protoplasma: nice review on protist ejectisomes in general, excluding ciliates)

One of the poor cryptomonads got stuck as my slide was drying out, and in its agony, released an explosion of ejectisomes. As any other biologist excessively attached to their subjects, I hate seeing protists die; at least this one didn't die in vain but gave us a nice demonstration. Extrusome firing often accompanies stress in protists that have them, drying out definitely qualifying. The following images are quite graphic, and not for the faint of heart. At least because the image quality is seriously compromised by a random layer of air between the coverslip and the specimen covered with remnants of water – a total chaos of refraction indexes.

Lysed cryptomonad on a dried out slide, surrounded fired ejectisomes. The fibrils around the cryptomonad remains are the uncoiled ribbons propelling the ejectisomes (refractile granules seen well in phase contrast, bottom images). 40x obj, DIC and PC.

While the cryptomonad may use its ejectisomes for hunting (most photosynthetic unicellular protists tend to be predators as well), perhaps they play a larger role in defense. Partly in stabbing its own predators, but additionally in a way that's quite counterintuitive to large creatures like us – sudden movement.

You might notice there isn't really much projectile action per se happening at the microbial scale. The firing is closer to an extrusion of a structure rather than freely propelling it a far distance. Furthermore, unlike an actual battleship, the cryptomonad can stop and turn almost instantaneously, and doesn't have much inertia. There is a reason for that, and it lies in the physics of fluid dynamics, a topic few of us outside biophysical biology concern ourselves with. Luckily, Purcell took care of that for us in his rather interesting 1977 paper, "Life at low Reynold's Number*" – turns out, the effect of viscosity on the behaviour of an object depends on its size, and water from a microorganism's perspective is a very different substance than what it is to us. In fact, it helps to imagine that microbial creatures live in honey or molasses – while water's viscosity doesn't actually change, it acts on µm-size things in a manner somewhat similar to how highly viscous fluids would act on things of our scale. Biophysics is quite a bit different at that scale, and different strategies are required in dealing with it.

*Reynold's number = proportion between object's velocity*size*[fluid density] and the fluid's viscosity)

In highly viscous fluids, coasting is not really an option. Things stop as soon as the driving force ceases to be applied, as anyone who's paddled a canoe across a lake of molasses would know (Bostonians from the early 1900's, perhaps?). This is why you don't really see stiff fins on bacteria or single-celled eukaryotes, at least not for motility itself. There are many ways to use a flagellum – a topic deserving of its own post – the beating strategy requiring it to be flexible at the right times. More importantly to our topic, you can't realistically give something enough force for it to keep moving like a bullet, so shooting things is out of question. Instead, the projectile must keep being pushed, usually by something unfolding or unraveling – in the case of the cryptomonad, a coiled protein ribbon. Cryptomonad artillery is perhaps more similar to harpoons than cannons.

This means a fired ejectisome can be used to essentially "push off" in the opposite direction, providing the organism with a sudden, drastic movement it wouldn't be able to obtain by flapping its flagella. The armoury of a threatened cryptomonad may be more important in providing it with rapid escape than damaging its pursuers. The microbial art of war is seldom discussed in non-enzymatic terms, but it is too a diverse and fascinating area, peppered with counterintuitive surprises. Life, and war, are indeed very different at low Reynold's numbers.

References
Brett, S., & Wetherbee, R. (1986). A comparative study of periplast structure inCryptomonas cryophila andC. ovata (Cryptophyceae) Protoplasma, 131 (1), 23-31 DOI: 10.1007/BF01281684

Kugrens, P., Lee, R., & Corliss, J. (1994). Ultrastructure, biogenesis, and functions of extrusive organelles in selected non-ciliate protists Protoplasma, 181 (1-4), 164-190 DOI: 10.1007/BF01666394

Purcell, E. (1977). Life at low Reynolds number American Journal of Physics, 45 (1) DOI: 10.1119/1.10903

Answer to the nucleomorph scavenger hunt: between the third (red algal) and second (plastid outer) membranes. The nucleus was originally in the cytoplasm, within the red algal cell membrane and outside the plastid. Oh, and if you want real topological clusterfuck, may I recommend the tertiary endosymbiosis in Kryptoperidinium – also try to count the genomes!

Sunday Protist – Gromia: beautiful predatory grapes of the sea

And we're back. The protists and I, that is. Well, the protists never quite went anywhere but you know what I mean...

You may have heard of Gromia a couple years ago when it hit the news by leaving tracks on the ocean floor resembling Ediacaran trace fossils (tracks). Or perhaps not; I tend to get overly excited the one time a year some protist makes the news. The giant (3cm) track-leaving Gromia in question sounded even cooler as it came from the great deep sea; other species of Gromia are in fact quite content with the more familiar shallow waters as well, crawling on the holdfasts of kelp in addition to thriving in the ice cold polar waters of McMurdo Sound (Antarctica), where the vibrantly colourful first specimen below comes from:

Gromia, from various locales including Antarctica (A), Madeira in the Atlantic (B) and Guam (C). Big and colourful, what's not to like there? Scalebars: A - 1mm; B - 0.5mm; C - 0.1mm (Burki et al. 2002 Protist)

For some time, there has been considerable confusion between Gromia and the cruelly similarly-named foraminiferan Allogromia, bad enough to warrant a Nature paper (Hedley 1958). At first glance, they do appear somewhat similar: a sizeable grape-like blob of a test surrounded by a mass of fine pseudopodia. While foram pseudopodia form a rather elaborate and extensive network of doom and terror for anything they come in contact with, Gromia uses more modest non-fusing alternative of pseudopodia. Thus, prior to molecular data, it was often considered a sort of a precursor to the more grown-up real forams, and assumed to have a rather simple test. They could hardly be more wrong, both with the assumed relation to forams and the simplicity of its test.

Typically (using that word rather loosely), a protist test consists of the plasma membrane covered by some sort of an organic matrix (often sugary proteins and protein-y sugars), followed by the deposited structural material, be it agglutinated bits of rock from the environment (often carefully and specifically selected) or secreted calcium carbonate, siliceous scales or something else entirely. To my knowledge, the process of selecting material for the test in agglutinating species, and formation of the test in general, is still quite poorly understood. There is some understanding of how diatoms and some coccolithophorids build their extracellular wonders, but most amoebae have been largely ignored, even the more 'famous' representatives like the forams, euglyphids and arcellinids. The Allogromia mentioned earlier has the organic (non-calcified, non-agglutinated) test characteristic of Allogromiids at large, who form a vast paraphyletic sea of diversity from which the more popular lineages arise – the Protista of the foram world, if you will.

Gromia also carries an organic test, hence the confusion with Allogromiids. But its test turns out to be a bit more elaborate, with an inner lining consisting of up to ten layers of odd honeycomb membranes, the whole thickness of the structure penetrated by multitudes of pores. The test surface is sometimes covered by attached bacteria (Aranda da Silva & Gooday 2009 DSR II). Furthermore, rather than simply a hole in the wall, its opening is surrounded by a complicated oral capsule which acts as a valve or a trap door: when the pseudopodia are withdrawn, the opening closes. One seldom thinks of movable structural parts on the microscopic level, but here you go:

The structure of Gromia's test and oral capsule, in that order. The figure on the right shows a pseudopodium gradually protruding through the closed aperture. (Hedley & Bertaud 1962 J Protozool; Mazei & Tsiganov 2006 in Presnovodniye Rakoviye Amyobi (in Rus.))

The pores make the test surface look quite pretty in reflected light:

The giant deep sea Gromia sphaerica; note the complex test surface structure with prominent perforations. (Matz et al. 2008 Curr Biol)

To make these mysterious 'grapes' of the sea even sexier, they are known to have sex. Upon conjugation, flagellated gametes are exchanged between the parents, producing amoeboid diploid swarmers that ultimately form a new test and complete the cycle. The parental shell and all the work that went into building one is abandoned in this process. Both forams and gromiids are 'mortal' in our sense – they spend a period of time building a body that eventually becomes abandoned by the next generation. Organisms like many flagellates, for example, are somewhat 'immortal' in that the cell is never abandoned between generations, but rather split up and shared by mostly clonal offspring. Extra structural complexity often bears the curse of losing 'immortality'.

Gromia's life cycle. (Arnold 1966 J Protozool)

Gromia shares some strangeness with giant deep sea Xenophyophores (forams): they like to live in their own excrement. This may sound disturbing, but they're still fairly microscopic, so their shit is of a rather more chemical character. Curiously, both Xenophyophores and Gromia tend to lean toward the upper end of the protist size range, perhaps partly aided by their inability or lack of desire to part with their faeces – these faecal pellets, so-called stercomata, appear to play a structural role in the Xenophyophores, and may well contribute to structure in Gromiids as well. Waste accumulation is not too grave a problem for these organisms due to their habit of generating clouds of swarmers that ditch the parental shell forever.

As alluded to earlier, gromiids are fairly distantly related to forams, and definitely evolved their elaborate test independently. For some time, gromiids were thought to be closely related to filose amoebae with shells, ie cercozoan euglyphids and such. Turns out, while not too close to the euglyphids, Gromia is a cercozoan (Burki et al. 2002 Protist), and tends towards the endomyxean side with the plant parasite phytomyxids, vicious vampyrellid amoebae and the ornate haplosporidia. In other words, things that look little like them, aside from a tendency to form thin pseudopodia.

Gromiids probably have a bigger story to tell, as environmental sequence data reveal swaths of cryptic diversity, and new species are still being described from the deep sea as well as polar waters (eg. Rothe et al. 2009 Zool J Linn Soc; Gooday & Bowser 2004 Protist; Rothe et al. 2011 Polar Biol; and Aranda da Silva et al. 2006 Mar Biol for diversity porn). As for their ecological niche, the gromiids seem to play a similar role to allogromiids and other forams – versatile predators preying on algae and anything else that gets caught in their feet.

Aww, they even grow on trees! Gromia schmoozing with a tree-shaped foram, Pelosina, possibly in some sort of a symbiotic relationship. (Gooday & Bowser 2004 Protist)

Hopefully back to more regular blogging now. Quality of writing is at the mercy of my irritating writer's block, you have been warned...

References
Aranda da Silva, A., & Gooday, A. (2009). Large organic-walled Protista (Gromia) in the Arabian Sea: Density, diversity, distribution and ecology Deep Sea Research Part II: Topical Studies in Oceanography, 56 (6-7), 422-433 DOI: 10.1016/j.dsr2.2008.12.027

Silva, A., Pawlowski, J., & Gooday, A. (2005). High diversity of deep-sea Gromia from the Arabian Sea revealed by small subunit rDNA sequence analysis Marine Biology, 148 (4), 769-777 DOI: 10.1007/s00227-005-0071-9

ARNOLD, Z. (1966). Observations on the Sexual Generation of Gromia oviformis Dujardin The Journal of Eukaryotic Microbiology, 13 (1), 23-27 DOI: 10.1111/j.1550-7408.1966.tb01863.x

Zach M. Arnold (1952). Structure and Paleontological Significance of the Oral Apparatus of the Foraminiferoid Gromia oviformis Dujardin Journal of Paleontology, 26 (5), 829-831

BURKI, F. (2002). Phylogenetic Position of Dujardin inferred from Nuclear-Encoded Small Subunit Ribosomal DNA Protist, 153 (3), 251-260 DOI: 10.1078/1434-4610-00102

[Fuck this, the browser crashed TWICE and I'm not finding all the links again. Not tonight anyway. URLs are in the post.]

Eight supergroups on a table

Back, after a bit of a distraction and an irritating bout of writer's block (how do you get rid of those things, seriously?). While I go write up a post for the long-interrupted Sunday Protist series, have a protisty doodle. My friends have this makeshift coffee table from two pieces of wood, which serves as a canvas for procrastination painting and such; anyway, if you supply me with permission to doodle on something, it invariably ends up protisty (or anime characters, or a frightening mix of the two), so here are eight supergroups on a table: (flash gets a a sharper image but the colours get screwed up)

Watercolour, pencil and [lab] marker on painted wood. Really fun to do watercolours on top of paint – you're not sneered at by warped wet paper, and it's very easy to wash off mistakes.

The cast:
Archaeplastida – Acetabularia
Alveolata – dinoflagellate (eg. Protoperidinium)
Stramenopila – Chaetoceros
Rhizaria – Gromia
"Hacrobia" – centrohelid "heliozoan"
Amoebozoa – tubulinid amoeba
Opisthokonta – choanoflagellate with a chitinous basket
Excavata – photosynthetic euglenid

(Accuracy not guaranteed as I was too lazy to use references)

Deciphering protist shapes

A while ago, while rigorously procrastinating, I came across a slightly odd tiny freshwater flagellate that was sufficiently morphologically non-straightforward it lent itself well to 3D reconstruction/sketching practice. Figuring out cell shape from micrographs isn't as easy as it looks – for one thing, the bloody cell is three dimensional, while the images are flat and further complicated by DIC optics – and thus a very fun exercise! And then, once you've got a cell shape in your head, you have to figure out a way to draw it out for others to see. I still suck, but the sketches at the end looked kinda pretty together with the micrographs, so here they are:

I still have no idea what this thing is. Acts vaguely ancyromonad-like, but may well be a glissomonad or something else entirely. Pretty positive it's biflagellated. Probably nothing too earth-shattering (and may well be well-known by everyone but me), but if anyone has some sort of research interest in this thing, let me know – don't have time to deal with it myself. Not that I'm likely to find it again... Here's the pics and videos:

Science Online 2011 ramblings

By now, about every aspect of Science Online has been thoroughly blogged and overblogged, so for a comprehensive review, see the Science Online 2011 website, namely the Blog and Media Coverage page. I don't think I have much to add, but I'll ramble anyway. After all, this is why I have a blog, right? Plagued by an epic writer's block lately though, so lower your expectations accordingly. Even more so than you should normally when approaching this place. In fact, since this has been sitting in my drafts folder for about four five six days, I'm just going to hit random parts of the keyboard and hope the result resembles English somehow, while torturing you with a sequence of cumbersome, poorly linked clauses, so I can get back to regular blogging, ideally with readable sentences that time.


Cheesy as it sounds, the highlight of the conference was definitely the people. In a way, it's more of a 'reunion' than a conference sensu stricto, as some put it. A major aim of the conference is to humanise the blogosphere, as knowing each other personally should make the environment more pleasant and less aggressive, and I think it works. Without knowing the physical entity behind an online alias, it is sometimes easy to find yourself carried away with something they wrote, as opposed to evaluating the person as a whole. We all have our quirky opinions, and we all write stuff from time to time that can piss off someone, somewhere. Sometimes it's too easy to get fixated on a single idea you find personally irritating, and forget that there is more to the poster than that one comment. Knowing each other in a more personal manner could diffuse some of those conflicts.

I was pleasantly surprised by how little of the general blogosphere drama carried over into the physical conference. People generally seem more chill offline. Maybe I was just oblivious to the real picture, as I usually am (drama usually passes by me without even acknowledging my existence – I guess that has its own perks), but everyone was really friendly and full of energy. Combine that with Deep Sea partying and North Carolinean hospitality*, and great times were had!

*I'll ramble about 'surprising' non-homogeneity of North American cultures in a later post...

The group of attendees was surprisingly diverse in the professional/occupational sense, including a range from students and scientists to full-time writers and journalists to PIOs and librarians and some people behind things like PLoS and Mendeley. There were those with various artistic talents, from science illustration (eg @flyingtrilobite/Glendon Mellow) to music (eg. Adrian and Kevin's GFAJ-1 Arsenic Blues – though that recording does not do it justice) and comedy (@sciencecomedian/Brian Malow). Being somewhat locked up in the ivory tower by this point, it was great to meet people with real jobs who actually talk to people outside academia. Science Online is also unusual in that everyone was on a fairly even level, regardless of professional rank. Your professional hierarchy and reputation were irrelevant since there was hardly anyone from your own field. Thus, faculty, students, librarians, writers, postdocs, etc all spoke on equal ground, which was a wonderful experience in itself. As much as some try to suppress hierarchy at traditional academic conferences, it's still clearly there, and your rank in the field does matter. At Science Online, your online presence was more important, but that hierarchy is, thankfully, less rigid, and still rather nebulous in concept.

The use of Twitter at the conference was rather surreal...it's as if between all the smaller discussions and conversations in the physical realm was a broader conversation in the electromagnetic waves of Twitterland. The badges had a place for one's Twitter handle, along with a QR code for the website. It's as if we had multiple identities, and I did for sure. I went by my blogger alias (shocking plot twist: Psi Wavefunction is not my legal name ;p) since that's how people know me online. Given that, I still preferred by real name in offline conversations. Which made it even more awkward. Some people insisted on calling me Psi – I don't mind at all, but it was odd to be called by something other than my real name!


I won't even try to go over all the highlights regarding people and events, but I'll just casually mention some snippets, in a totally random manner and order. Mostly my own reactions to them, since others have already discussed the topics in greater detail (and insight).

First off, our keynote was Robert Krulwich, a journalist and co-host of Radiolab. In attempting to attract an audience who typically think they don't care about science, they have a very interesting approach to explaining complicated topics: acting stupid. Stupider than their listeners. We like feeling smarter than others, so it often works better when the teacher (sensu lato) speaks the language of a novice rather than an expert, and asks such questions of the guest experts that the audience would never 'stoop' to. Ie, very basic questions, prodding for very basic answers in return. That way, the audience doesn't feel like material is dumbed down for them (which may feel somewhat insulting, and definitely distanced), but rather for the host, ie Krulwich. Of course, there is also much humour involved, and the programmes are, as a result, entertaining. It's amazing what these people can do, as it is incredibly difficult to convince someone a topic is interesting once they've made up their mind it's not. Making it relevant is not enough – making it relevant and fun, without the feeling of distance (and definitely not lecturing!) is an art, and one we really need more of.

* This happened around hour 56** since I last had sleep, so I shamefully admit to not processing much information at that point

**let's see, got up around 9ish on Tuesday, hung out + packed all night, went to Seattle on Wed, hung out, flew out Wed night, horribly packed flight with stopover at Washington DC, too short to sleep much, arrived at RDU on Thu around 9am, couldn't check in or sleep, keynote around 8pm...yeah. Must've been a zombie by that point.

Went to the history of science panel, where we underlined the importance of understanding the context of scientific discoveries, and the richness that the extra dimension (time) adds to scientific stories overall. And historical context provided properly, not crudely mocking the past thinkers for coming up with such "ridiculous" hypotheses. Probably most of the stuff we think today will be laughed at in a couple centuries or so, if we as a species make it that far. The historical aspect includes not only the history of one's field, but also the sociopolitical context of the time, since science is not this purely 'objective' holy thing independent of human thought; science is a human process, and thus carries with it the stamps of every generation's worldviews. It can only make more sense that way. Where possible, good science writing should happen in four dimensions.

With John Logsdon and Julie we directed a discussion on improving public outreach for small and/or obscure "micro"-disciplines, with emphasis on internet presence. I'll make a separate post on this topic later.

I was also on a panel my awesome co-moderators on beginning blogging and issues like the impostor syndrome, which was a great lot of fun. Others have blogged about it already, and I'll add the links once I find them (soooo many #scio11 posts to catch up on...!).


There is currently some talk about compromised diversity in the blogosphere, but we must keep in mind that we are biased by being an anglophone blogsphere, and the conference was in North Carolina, which was difficult to get to even for those of us on the other coast, let alone from overseas. I personally doubt pushing labels could help much, and think the problem, where it truly exists, lies deeper than online presence. Yes, some races/ethnicities/groups are underrepresented in the English-speaking blogosphere, but that may have something to do with the same races/ethnicities/groups being underrepresented in the educational system in general, and not with the internet or the community.

When I read blog posts, I pay very little attention to the background of who writes them, aside from their field of expertise/activity. If I find the stories interesting, I'll read them regardless of the gender of the author, and I don't feel particularly obliged to read a story I wouldn't otherwise touch simply due to their background. On the internet, it is especially easy to be truly 'colourblind' (in the metaphorical sense too), since you don't even see the author unless you look. So the issues with diversity online are probably a direct result of the problems offline, which are much harder to fix with online means. Maybe instead of focusing on the skewed diversity of bloggers, we should first look at how blogging can help the problem closer to its root. Eg, are underprivileged groups even reading any of our stuff in the first place, and if so, what can we do to be more useful to them, etc.

But I'm not sure it's entirely helpful to start shelving ourselves into categories like "female blogger" or "white blogger" or whatever. I don't particularly care for being read as a "female immigrant Russian atheist blogger". I would prefer to be read as some person whose writing people occasionally find interesting. My background would be a digression, perhaps interesting for my regular readership, but far from necessary for the main goal. But then again, maybe as a scientist I underestimate the average reader's desire to understand the blogger's character – would love for my readership to chime in on this!

Anyway, those were my [somewhat obligatory] two cents on the diversity issue, and I'll probably leave the discussion there. It's not that I don't care, but rather that such topics are not my forte, so I prefer to lurk quietly. But, by all means, feel free to discuss here!


And lastly, before I forget, some nebulous panel ideas for #scio12:
- Online presence of non-English languages
- Issues/specifics of niche blogging
- Dealing with "writer's block" (successfully, unlike Upper 1974 J Appl Behav Anal)
- Making the most of course blogs

Next up, eventually I'll put up some pictures from the overall east coast journey. And post some fucking protists, at last! =D