Quick ImageJ Tutorial: Scalebar calibration

Due to popular demand, I'll sporadically write up a series of posts on some ImageJ basics. For those not in the loop, ImageJ is a popular open source image processing program for microscopy; due to the availability of some rather sophisticated plugins, it can be a very powerful tool in the right hands. Also, the customiseable shortcuts are a blessing (and a curse for one's muscoloskeletal system, especially in the wrist region). I'm by no means anywhere near an expert with ImageJ (and don't do anything sophisticated, like macros or even much 3D/4D work), but there's a few basic things that I had to learn, and would like to share with anyone interested.

I put the rest of the post under the fold as most of you probably don't care...

Live Hypermastigote clips

To compensate for crappy blogging as of late (and the delays in the Great Review of Heterolobosea aka 'cruel and unusual punishment'), here's some random parabasalian swimming around: (Trichonympha methinks)

And a Spirotrichonympha?

Since I'm too lazy to ID this thing for sure at the moment, it would be great if some resident extreme excavate experts (XXX for short...?) could perhaps blurt it out. You know who you are. Also, are those Monocercomonoides, the little things swimming around?

I lack video editing software, so apologies for random background noise.
Got plenty more clips of Saccinobaculus, by the way. Should show up when I have time to re-blog about that wonderful organism (I think it deserves a much better post...) For now, enjoy the suspense =P
(and go hang out at the Mystery Micrograph - should be more interesting now that we've established it's a case of a multicellular parasite of a unicellular organism. Hint: As far as I know, there's only one documented case of that. )

It's probably time to take a break when...

I just failed to realise pAP3::GUS is a transcriptional fusion reporter and therefore only expresses if and only if there is transcriptional activity of its promotor (hence pAP3); thus 35S driven expression of the same protein would not necessarily result in GUS activity, unless shit exists to activate it, including itself, if it is thus inclined. Should I take a break from my slides and go home now?

(this is for a class. Will never look at goddamn flowers the same way every again. I hate you, ABC genes. Past 3am the morning a talk is due about them anyway...)

PISTEFUCKINGLATTA*! SEPALLATA! (those look really scary about now...)

Also, Nature papers become unbearably dense when you have to present about every single fucking sentence in them...

*grumble grumble*

*Does the FUCKING insertion have to be italicised too? What do gene naming conventions say about expletive inclusions?

PS: For those of you who have absolutely no fucking clue what I just rambled on about -- lucky bastards!!! [ok the HTML got fucked; I'm not rewriting that, no fucking way] is AP3 expression, but that's just shitty wording and is getting me really bloody confused at this hour. Grrrrrr. I was like "WTF won't it show GUS if the fucking same thing is constitutively expressed via 35S!?" and then hung my head in deep shame and embarassment. And profanity.

5am update: Screw this I'm off to bed... been working on this for the past 12h pretty much non-stop... can totally wing it tomorrow if I have to. Actually, I'd do a lot less preparation if it wasn't a group project. Other people seem to have phobias of 'winging it'. Too bad, because all you really need to do is sound convincing. I mean, it works for me in lab meetings... isn't that how science really works anyway? (oh shit, the secret's out now!)

And yes, I made all the slides myself despite it being a group project. Did I ever mention groupmates can actually somehow manage to slow you down rather than help sometimes? Even if they're willing to help, they can still be fucking useless? Well, now I have. Grrrr.

Sunday Protist -- Hydrodictyon: The water net

This time, the Sunday Protist will be short, and not involve [too much] scholarly literature -- for real. No, seriously.

Let's do another Archaeplastid. Here, have a Hydrodictyon:

(source: algaebase.org; H.reticulatum in DIC)

(Source: Lewis Lab webpage)

It's a water-net of cells! Perhaps you could even use that to fish for copepods or something! It's basically a coenobium of coenocytic cells, meaning it's a network of multinucleate cells arising from a common zygote. It's actually related to Scenedesmus from last week, as you can see in this tree. Nearby net-forming neighbours include Pediastrum and Sorastrum, the former seeming a bit paraphyletic. Interestingly, just as in Scenedesmus, the 'colony' is to some extent 'preformed' in the mother cell prior to release - the zoospores (from a single parent) swarm and later form the net; the growth of each cell depends on how many points of contact it has with other cells. Isolated cells don't grow at all, whereas those that touch several grow extensively. Thus, the growth itself is initated by pressure (McReynolds 1961 Bull Torrey Bot Club), as is the shape of the cell, as far as I can tell.

This organism would be interesting to explore morphogenesis and self-organisation; and seems to have been rather neglected. The more recent papers on Hydrodictyon seem to be either of the biochemical/bioremediation nature, or the "we stared at some algae in central Pakistan" variety. I say we explore its potential as a fishing net for copepods. MASSIVE business potential, srsly. ^_^

Phew, now I've done enough of Archaeplastida to forget about them for a few more months until my conscience starts eating me up again. Yeah, Archaeplastids aren't exactly my favourite kingdom... Kinda weird for someone who works on plants at the moment... (although many True Botanists(tm) claim Arabidopsis is not a plant...)

Should be on a bit of a blogging hiatus this week -- presentation and a midterm this Friday, among other things. Also, boss wants data. Should probably go generate make gather some. Trying to find a way to make my numbers say what I want them to. Ah, the art of graph manipulation and creative statistics...

By the way, in all seriousness, I treat my data well. Or try to anyway. Even in spite of pressure to get publishable results ASAP... it's interesting how once you get an idea of what you want to publish, and go into the confirmation phase, your objectivity becomes an inverse function of how much effort was put into a project and how much pressure you have to get it done. I wonder if there's a higher chance of poor data gathering or massive misinterpretation during those later stages in the Publication [vicious] Cycle. Perhaps the best science actually happens during the 'fooling around in hopes of stumbling across something interesting' phase... any thoughts?

Ok, make sure I don't blog too much this week. Also, go do the Mystery Micrograph! Ask questions! It's a really weird one... (which should narrow it down. Then again, everything's weirder the more you look!)

MM#07 Answer: Haplosporidia -- spores with lids

Johan, our resident micropaleontologist, got this past week's Mystery Micrograph - congratulations! The answer was: Haplosporidia. Johan went the extra mile and identified its genus: Minchinia. This one is M.mercenariae, from Ford et al. 2009 JEM:

Minchinia mercenariae (Haplosporidian) from the clam Mercenaria mercenaria; 13 - SEM of spore with arrow pointing to the opening; 12 - spore with a closed hinged lid; 2 - Minchinia's 'habitat' in the clam connective tissue (which it has taken over), while the digestive epithelia (DE) remain untouched. (Ford et al. 2009 JEM)

Haplosporidia are unicellular parasites known for their peculiar jug-with-a-lid spores. Presumably those spores get inside the host and the hinged lid opens (cute!), releasing the organism, but I was unable to find any details of their invasion process. After finding their way inside the host and excysting, they exist in an amoeboid stage for a while, perhaps to quickly spread throughout the host. They then proceed to form multinuclear plasmodia inside host tissues and form spores via palintomy (cellularisation) (kinda like apicomplexans and some dinos), and release the spores.

Many of them are commercially important due to their taste in shellfish. However, they seem to linger in obscurity despire that fact. In fact, one wonders whether their complete life cycles are known yet. Parasites are notorious for spanning multiple species at times, and it's hard to rule out a secondary host of some sort. However, the presence of what seems to be a complete set of life cycle stages within one sample suggest a single host at the moment, but intermediates remain possible (Azavedo et al. 2008 J Parasitol).

TEM of Haplosporidium lusitanicum; Nu - nucleus; Sp - 'spherule' (multivesicular body) Hp - haplosporosome; Op - operculum ('lid'). Right: drawing of H.montforti; w- spore wall, F - filament (Left: Azevedo 1984 J Parasitol; Right: Azavedo et al. 2006 J Invert Pathol)

There are three major genera of Haplosporidia, which are quite distinct morphologically. See this nice page describing them, with pictures (thanks, Johan!). They used to be categorised based on spore ornamentation, but that turned out to be rather messy. Haplosporidia reside in Rhizaria (TC-S & Chao 2002), close to Cercozoa, as shown in the aforementioned website and in the Pawlowski & Burki 2009 tree. Rhizarians have gote so much cool stuff it ain't funny.

Next up we will have a glimpse of Paramyxids, which seem to be related to today's topic. They also have really interesting lifestyles. TC-S and Chao (2002, 2003) place them in "Ascetosporea" (Sprague 1979), sister to Haplosporidians, and Pawlowski (2008) doesn't seem to mind, so that's enough excuse to talk about them. I mean, I just READ a few paragraphs of TC-S, we can't let that effort go to waste! Besides, not like a little bit of long branch attraction has ever harmed anyone...

But that'll be later this week. I shouldn't really be reviewing Rhizaria right now or anything, even though that would be kinda fun!

References:
Azevedo, C. (1984). Ultrastructure of the Spore of Haplosporidium lusitanicum sp. n. (Haplosporida, Haplosporidiidae), Parasite of a Marine Mollusc The Journal of Parasitology, 70 (3) DOI: 10.2307/3281564

AZEVEDO, C., BALSEIRO, P., CASAL, G., GESTAL, C., ARANGUREN, R., STOKES, N., CARNEGIE, R., NOVOA, B., BURRESON, E., & FIGUERAS, A. (2006). Ultrastructural and molecular characterization of Haplosporidium montforti n. sp., parasite of the European abalone Haliotis tuberculata Journal of Invertebrate Pathology, 92 (1), 23-32 DOI: 10.1016/j.jip.2006.02.002

Azevedo, C., Casal, G., & Montes, J. (2008). Ultrastructural Developmental Cycle of Haplosporidium montforti (Phylum Haplosporidia) in its Farmed Abalone Host, Haliotis tuberculata (Gastropoda) Journal of Parasitology, 94 (1), 137-142 DOI: 10.1645/GE-1177.1

Cavalier-Smith, T., & Chao, E. (2003). Phylogeny of Choanozoa, Apusozoa, and Other Protozoa and Early Eukaryote Megaevolution Journal of Molecular Evolution, 56 (5), 540-563 DOI: 10.1007/s00239-002-2424-z

FORD, S., STOKES, N., BURRESON, E., SCARPA, E., CARNEGIE, R., KRAEUTER, J., & BUSHEK, D. (2009). Minchinia mercenariae n. sp. (Haplosporidia) in the Hard Clam
Mercenaria mercenaria Implications of a Rare Parasite in a Commercially Important Host
Journal of Eukaryotic Microbiology, 56 (6), 542-551 DOI: 10.1111/j.1550-7408.2009.00432.x

Windows is evil!

In other news, water is wet.

But srsly, you're sitting there, writing stuff, and suddenly... THIS FUCKING WINDOW RANDOMLY POPS UP SAYING YOU'VE GOT 15MIN TO LIVE SAVE ALL YOUR SHIT BEFORE THE COMPUTER AUTOMATICALLY RESTARTS TO INSTALL A FUCKING UPDATE YOU NEVER ASKED FOR IN THE FIRST PLACE!!! And the best part of this: YOU HAVE NO OPTION TO STOP IT!

Don't they have principles of some sort in compsci and robotics where the user must retain rights to override the machine at any time, ever? Isn't it a bit of an ethical (not to mention, PRACTICAL) violation to deprive an intelligent user of a dumb fucking machine the right to control when and if it does things? I mean, seriously, this is like IN YOUR FACE rude -- for no necessary reason, it randomly tells me, without any warning, that the computer is going to shut off. No, not because of a software glitch, or some safety concerns, no. It's just randomly going to restard. To install a fucking update. And you have no choice. Ever.

And I just lost like 20 tabs of papers I took all this time to find... fuck you, whatever idiot decided this automatic restart without override thing was a good idea. IT'S NOT.

GRRRRRRR!!!

I've deactivated that shit on my own computer, but lack privileges/desire to fiddle with the innards of the one in the lab. Perhaps that's a mistake. Sigh.

Sunday Protist - Scenedesmus: Of coenobia and cell cycles

Busy starting working on slides for a lab meeting talk tomorrow, so today's Sunday Protist will be very brief and undetailed. And thoroughly uninformative. For real this time. Seriously, I say this every freaking time and end up writing a minireview on the damn thing... it's just so damn alluring to go and read up random stuff on these organisms!

We've been ignoring Archaeplastids again. Here, have some Scenedesmus:

Scenedesmus dimorphus(?) 40x obj, DIC

Ok, my images are shitty (damn thing is motile!), let's look at a professional one:

Source here; Scenedesmus in DIC

What you see here is a green alga that divides multiple times without splitting off to form a coenobium - a clonal 'colony' of cells sharing an immediate ancestry. The sizes of coenobia depend on environmental conditions, such as availability of nutrients and sunlight, as well as presence of predators (they grow bigger to avoid being eaten). Often the end cells grow spikes (like the ones in the lower image).

Actually, this thing is somewhat relevant to the slides I'm working on - regulation of mitosis (and 'counting' cell divisions) is a very important aspect of multicellular development, since it's not helpful to have cells that divide too much or too little. Actually, of extreme interest to humans is this slight issue that arises when cells divide too much - we call it cancer. As some may sadly know personally, the effects of uncontrolled division can lead to rather dire consequences.

In Arabidopsis, stomata consist of a pair of guard cells surrounding a pore. Those guard cells come from a common precursor, called a guard mother cell (GMC). The stomatal lineage has a few specific genes seemingly responsible for enhancing the regulation of GMC division to ensure it happens once and only once. A double mitosis at that stage would result in guard cell clusters (which poses a problem to their opening and closing). There are some mutants where the regulation of this division gets screwed up - in some lines, you get single guard cells (ie no mitosis, and no pore); in others, you get clusters, sometimes massive ones. The molecular and genetic details behind cell cycle regulation are a fucking mess, and make one's head spin. Which is what makes giving talks on the subject so much [evil] fun! XP bwahahaha!

Now another question regarding those clusters is whether the nuclei go wild first, and then cell division follows to ensure each is separated off (sorta like palintomy), or whether the cells fail to exit the cell cycle upon division, and keep going into mitosis over and over again (with the complete set of mitotic events). When speaking of division, one must be careful to keep track of nuclear ploidy levels (DNA replication), karyokinesis (nuclear division) and cytokinesis (cell division). Now 'mitosis' is one of those words that's used to describe most, some, or all of the above, as if the cell cycle isn't confusing enough as is. Note that each of these proceses interact with a million other things, and have regulatory checkpoints and so on. Which results in wonderful diagrams like this or papers like this or this Annual Review from hell. Seriously, you do NOT want that latter paper as a first intro to cell cycle. You just don't.

If any of the above confuses you, the point is that the cell cycle is bloody complicated.

Back to Scenedesmus. The coenobium produced offspring inside each of its cells, which then vacate their parent cells and go on to explore the great world beyond. The characteristic divisions happen while the daughter colony coenobium is still inside the parent cell. (Pickett-Heaps & Staehelin 1975 J Phycol), and depend on the conditions present during the division. The details are descibed in (Zachleder et al. 2002 Eur. J. Phycol), which I'll try to walk you through (and hopefully not fail too badly). So this is roughly how Scenedesmus regulates its length (in terms of cell number) in response to the length of light periods:

Cell cycle events in daughter coenobia under various conditions.
A) Typical cell cycle. G1 - 'gap' one (main growth phase), S - 'synthesis' (DNA replication), G2 - 'gap' two (post replication growth phase), M- mitosis.
B) Cell cycle of Scenedesmus under high temperature and low irradiance. CP - commitment point, where the cell 'commits' to divide regardless of environmental conditions to follow. Unlike the canonical model (A), where the cell immediately undergoes cytokinesis after karyokinesis, the daughter coenobium undergoes another growth phase (G3) prior to undergoing cell division. Thus, this is a nice model for separating nuclear mitosis and cytokinesis.
C) Placing the synchronised cells into the dark after the first commitment point results in only one round of mitotic divisions. (the bar above represents amount of time spent in light and dark) (presumably, the cells don't divide in the dark)
D) Cells placed in the dark after the second commitment point. This results in two rounds of mitotic divisions, which also overlap (so the S of the second stage hits the nuclei when the first division stage is at M; ie during mitosis, the nuclei undergo replication. It would be so much fun to prod at this at the molecular level! *drools*
E)Darkness after the third commitment point. Three overlapping cell cycles. Note how G3 of the first cycle is elongated in order to undergo cytokinesis after all the nuclear divisions have been carried out. Seriously, how does the organism coordinate its cell cycles carefully enough to allow this madness to proceed smoothly?
(Zachleder et al. 2002 Eur. J. Phycol)

So what happens under constant light? (something that never happens in nature save for the polar regions)

The 4th commitment point is activated, but the G3 of the first cycle fails to proceed long enough to allow for the fourth nuclear mitosis to occur prior to cytokinesis. The cell divides while the nuclea still have twice the proper ploidy. The nucleus then divides after the cells are released from the parent, and you end up with a dikaryotic/binucleate organism. (Zachleder et al. 2002)

And of course, how can you do anything cell cycle related without drugs?

Cell cycle arrest via 3h cyclohexamide treatment (which halts protein synthesis) results in longer cell cycle and increase in the number of commitment points within a single division cycle (from main text). Under constant light, the mitotic phase in each of the cycles was postpones, even in the third and fourth cycles, whose commitment points occured after inhibitor removal. Thus, this drug affected the regulation of all of the overlapping cell cycles within that generation. Furthermore, even though the fourth cycle was initiated after the inhibitor removal, it had a greatly elongated G2 phase and still underwent mitosis after cytokinesis and release of the daughter coenobium! (thereby resulting in binucleate cells yet again). (Zachleder et al. 2002)

Of course, when you have one drug, why not try another? (the gateway drug concept works quite well in cell biology research, perhaps even better than in 'real life'...)

A) Constant treatment with FdUrd (fluorodeoxyuridine), which blocks the S-phase, causes the cells to grow in size, but fail to undergo replication (thereby leaving the nucleus at the normal G1 levels). Interestingly, the pathways regulating cell size remain oblivious to the failure of nuclear replication.
B) The removal of FdUrd after the second commitment point results in a highly unusual (for Scenedesmus) division patterns, where the G3 phase disappears altogether, and cytokinesis happens immediately following nuclear mitosis. While the cell cycles still overlap, they are no longer coordinated to 'wait' for the last nuclear division to be complete. This pattern is quite normal for its relatives, including Chlamydomonas. (Zachleder et al. 2002)

Interestingly, the adult organism still develops properly, suggesting that perhaps this strange mode of division may be a byproduct of other changes in cell cycle regulation. I can't say much more about this, as evolutionary biologists seem to REALLY not care about cell cycle regulation. They already tend to neglect the existence of cells (ie, organisms are more than just their genomes!), and it will be a while before we realise that those cells have clocks, which also evolved through time. Wait, but what about irreducible complexity? Not the clocks!!! (that was a really cool animation of simulation of clock evolution!)

So now I wonder whether the mutant stomatal clusters undergo something weird similar to this, or if something else is going on entirely. Being a systematics-loving cell biologist guarantees that I'll never have any friends, but I'm still surprised and disappointed by my colleague's strict aversion to anything that is not their pet model organism. I think comparative cell biology could do wonders to our understanding of the mainstream systems, as well as the very fundamentals of how the unit of life can function. Actually, Scenedesmus got me thinking just now...the most likely thing would be your usual "cell forgets it shouldn't divide" scenario, ie. a differentiation/cell cycle exit lag. But the overlapping cell cycles and a palintomy-like division remains a competing hypothesis that must be dealt with.

Another interesting detail (and now I'm pulling crap out of my ass) is the presence of spikes on the ends of the Scenedesmus coenobium -- somehow, the end cells 'know' they're at the end. Now what is interesting is whether they sense some intercellular morphogen gradient (unlikely), or can sense some signals from neighbouring cells, and the absense of this signal on the end may promote spike growth. Again, this ties in with the stomatal pathway - stomata are generally spaced out without [ideally] any of them touching (although that may happen once or twice per wild type leaf, by accident). Since they rely on opening and closing to function, being stuck together creates a bit of a hinderence to proper functioning. There are several mechanisms to ensure that when a precursor cell divides to form a stomatal precursor (a meristemoid), the meristemoid is on the opposite side of another stomatal lineage cell. Perhaps Scenedemus terminal cells use a similar method of 'neighbour sensing'.

Would be fun just to assemble a showcase of the diversity of the various cell cycles throughout both eukaryotic and prokaryotic domains of life. The cell cycle is fundamental to anything that divides and propagates (that is, anything biological), and there are some truly fascinating deviations from the canonical models!

WE NEED COMPARATIVE CELL BIOLOGY TO HAPPEN! Come on guys, don't leave it to the idiots like me to dabble in on our spare time! DO SOMETHING. Srsly. People are choking each other in biomed because there's simply no space for everyone to be there, whereas comparative cell biology and cellular evolution seem to be overgrown by weeds, with an occasional ball of tumbleweed rolling by, to the chorus of crickets in the background, and TC-S solitarily strolling by and churning out his Univeral Theories of Everything with no one to argue with. He must feel very lonely there. He may even want company.

This must be the strangest advertisement ever. ^_^

Anyway, here was my very short, completely-devoid-of-scholarly-literature Sunday Protist entry. Is it a problem when you just can't resist the tempation to read random crap about random crap? Damn. It's wrecking my undergrad performance! (Seriously. No one in those classes gives a damn that you've read hundreds of papers more than any other undergrad around. Grrr. Fucking pre-meds and those who cater to their whims. Grrrr.)

Anyway, now to skip over a couple phyla to my plant cycle... must prepare slides to I can pretend I've actually done something lately during the lab meeting. Ummm... lots of background should be able to confuse them long enough to not realise none of that is actually my own work! =P Especially if we stop to discuss the convoluted cell cycle diagrams at every opportunity (and with my boss, we will!) also, I'm armed with a couple (incomplete) graphs at the moment! Graphs are powerful creatures in biology. "I think your theory may be flaw-..." "I QUANTIFIED STUFF!" "Oh...ok! =D"

*Also, a small rant (can a blog post ever be complete without a rant?): could people please take the effort to discriminate between a true colony and a coenobium? If a bunch of organisms of different ancestries congregate together, that would be a colony; if an organism reproduces a bunch of times but the offspring don't split off, that's a coenobium. A coenobium is clonal, and a much more likely form of cooperation. Although coenobium generally applies to unicellular organisms, so it gets murky when similar stuff happens in clonal colonies of multicellular organisms. Perhaps one should make it mandatory to specify whether the 'colony' is clonal or not in those cases? It makes a difference from the evolutionary perspective... also, my understanding is that random stuff congregating together is actually a pretty unlikely occurence compared to clonal stuff not bothering to break apart. Would that be true?

PS: this thing is kinda cool-looking; also unicellular and multinuclear! (ie. coenocytic) Btw, if anyone is confused with regards to multinucleate/coenocytic/plasmodial, they all mean pretty much the same thing, except the former tends to be used by zoologists, the middle by botanists and phycologists, and the latter by mycologists (and to some extent, developmental zoologists). Since we don't really ever talk to each other, there's plenty of opportunity for the language to diversify into multitudes of mutually unintelligible dialects - would this be an example of sympatric or allopatric speciation then? Is a discipline more like a niche or a geographically isolated location? Or both?

References
Pickett-Heaps, J., & Staehelin, L. (1975). THE ULTRASTRUCTURE OF SCENEDESMUS (CHLOROPHYCEAE). II. CELL DIVISION AND COLONY FORMATION1 Journal of Phycology, 11 (2), 186-202 DOI: 10.1111/j.0022-3646.1975.00186.x

ZACHLEDER, V., BI??OV??, K., V??TOV??, M., KUB??N, ?., & HENDRYCHOV??, J. (2002). Variety of cell cycle patterns in the alga Scenedesmus quadricauda (Chlorophyta) as revealed by application of illumination regimes and inhibitors European Journal of Phycology, 37 (3), 361-371 DOI: 10.1017/S0967026202003815

Mystery Micrograph #07 hints

You guys need to get on this, the poor organism feels neglected and may soon develop abandonment issues. You must save its mental well-being by solving its little identity crisis. That would make you its personal hero - wouldn't that be an awesome feeling?

An SEM, and a glimpse of its habitat:

(scalebars: A - 2um, B - 200um; to be referenced later)

The thing in the SEM is a resting stage.

EDIT 02.11.09: This is giving it away big time - it's a Rhizarian...

Of random rotifers and vicious amoebae

Still procrastinating with the Heterolobosea posts (no, I haven't forgotten). Real protistologists give me sorry looks when I mention being stuck writing about that rather obscure and messy group. I don't want to just do a taxonomic overview - I like to mention odds and ends about their cell biology as well. Sadly, the cell biology of most of those things is a sorry neglected mess. Even the eruptive pseudopodia that are quite characteristic of this group (although present in some amoebozoans as well) seem to not have been examined on a molecular level - I cannot find a single paper describing the cytoskeletal dynamics behind this peculiar mode of motility, and my sources point out a severe shortage of attention in that area. But I'm still scraping things together, so eventually something will appear...

Now for something completely different...since someone just sent me scouring piles of archaic metazoan 'mesozoan' literature to identify that damn bug (an orthonectid of some sort), I have a random metazoan of my own to show off a bit, from the latest pond microforay:

Rotifer. (Mine =P 40x* DIC) Note the contractile vacuole-like structure (actually its bladder, but appears to function in a very similar way. Another case of ultimate convergence?).

I can't quite key this one out, especially since this damn sucker is on its side. Probably the only reason I was able to capture a photo of it, since they tend to be quite hyperactive normally. This one appears to be immobilised by the cover glass. Perhaps it may be Aspelta or something from the Lepadellidae. Or might it be a Bdelloid? Perhaps a certain taxonomist could help out. Especially the one who made me browse orthonectids for the past few hours. ^^

*40x here, and onwards, refers to objective rather than magnification. We don't actually care about mag, it's the other properties of the optical system that matter much more when dealing with professional instruments. (Such as numerical aperture and field of view, focal length, focal depth, which type of immersion medium its calibrated for, etc) Technically, I should be writing down the NA and such, but we're not that meticulous crazy around here.
**Randomly found out there's a rotifer that lives inside colonies of Volvox, as a parasite...

Much of my resentment towards metazoa simply comes from them being overstudied and overemphasised, to the neglect of other phyla. That said, they are still interesting and still poorly understood lifeforms, especially among the spineless things. While representing but a mere sliver of life's overall diversity -- contrary to what our senses tell us -- metazoa are nevertheless, like all life, fascinating and weird. Metazoan multicellularity, as mundane and ubiquitous as it may seem to our rather biased eyes, is about as weird and insane as kinetoplastid kDNA editing, or the convoluted ciliate nuclear genomes, or the breathtakingly massive, and seemingly pointlessly so, nuclear genomes of dinoflagellates and some amoebozoa. I'm quite disappointed at the absense of the 'perspective of strangeness', if you will, that seems to dominate many animal-oriented classes (especially those catering to pre-meds. Must. not. rant.)

Interestingly, off all taxonomic and phylogenetic literature, I find metazoan papers to be the most difficult to follow* - we actually have common names to refer to quite a few animals metazoa. Furthermore, the obsession with ranked hierarchy is driving me insane - you DO NOT have to name every single possible grouping you can come up with, seriously! That makes searching for stuff an absolute disaster, as you have to look for the relevant subfamily, family, superfamily, suborder, order, superorder, hypersuperorder, subclass... etc. All named differently enough to not fit into one convenient Google (or PubMed, or WebofScience) search. And you have to find all of them. And they change. And your life becomes a living hell. Please stop, seriously! WHYYYYY!? Did TC-S write their taxonomies or something?! And they listened to ALL of it?! [/rant]

Another fascinating facet of biodiversity that seems to be thoroughly ignored is the interface between kindoms: the breathtaking diversity and strangeness of the possible relationships between the many corners of life. Of course we get the 'animals eat plants' story**, occasionally hear of animal-earing plants. Then we hear of fungi and bacteria as decomposers. If you hang out on the botany side of the Great Divide, you also hear of algae as the aquatic producers and fungi as mycorrhyzal symbionts (plant-fungal relationships are a fascinating world of awesome, by the way). But that's pretty much all ecology you ever get (outside of ecology programs anyways. I hope!), and frankly, it's pretty boring.

What about the vast 'multicultural' realm of the customs and ways of the parasites? What about the unexpected mutual endosymbioses, both of multicellular and unicellular things, on both multicellular and unicellular levels? What about multicellular predators, and parasites(!) of unicellular organisms? Or unicellular predators(!) of multicellular organisms? For a case of the latter, let's turn back to our rotifers. By the way, if you're desperate for a tree, or sexy SEMs of rotifer morphological features, this paper could come in handy(free access).

*Well, that and any prokaryotic literature. Bacteria are...complicated. Unlike Eukaryotes. ^_^
**A while ago while writing a biochem exam, I came across a question starting off with plant lipid synthesis. I got excited (OMG they're mentioning PLANTS!!!). Then I read on: "...which is then consumed by a herbivore." and wanted to throw something at whoever wrote that question. That pretty much sums up the biochemists' and zoologists' view of plants.

Quick aside: the border between parasite and predator is quite fuzzy and arbitrary, especially once you venture outside familiar grounds. Generally, people tend to call something a parasite when it feeds of something bigger than itself, and a predator when it feeds off something smaller.

Rotifers, like anything else out there, have no choice but to participate in the great web of things eating things. As is the case for many small pond organisms, their predators are plentiful. In fact, there's some rather embarassing ones. Including a relative of this slow thing:

(Mine again. Having my own photo stock would save me so much search and citation time. Of course, making my own stock might kind of negate that.)

Yeah, rotifers can get chomped on by Difflugia, of all things.

NOT mine this time. Han et al. 2008 Hydrobiologia. I wish I could see this live! See text for description.

The [planktonic thecate(!)] amoeba senses the thecate rotifer, quickly extends its pseudopodium along its length as if to 'measure' it, positions itself with its 'mouth' towards the rotifer's foot, somehow makes a hole in its protective jelly, and slurps in the rotifer's contents, while grasping the shell of its prey with the pseudopodia. All within 20min. Amazingly, this amoeba is not a rotifer specialist - it only eats them upon a rare chance encounter. Thus, the amoeba actually has complex behavioural patterns, enabling it to detect the type of prey, sense its shape and decide on an attack strategy.

Many protist predators are actually quite picky, sifting through the various detritus they come across and deciding on what to engulf. Combine that with eyespots and ocelli (Warnowiid dino camera eyes!), along with other oddities of the unicellular world, and we've got ourselves a whole field of Protist Behavioural Biology.

As we look more and more carefully at the unicellular world, it becomes increasingly more apparent that cells can 'think' -- not in the woo-ey "OMG feelings and consciousness!!1!" kind of way (in fact, I HATE that shit) -- but in terms of processing information from their environment in a rather complex way. Doesn't seem like much is known about cellular 'molecular intelligence' (or 'molecular instinct' - the line between canonical behaviour and genetic/biochemical pathways is quite blurry, it seems), and the field is dominated by junk thinking at the moment. And computer scientists, who don't seem to be bothered by biological reality. But hopefully as more and more results pile up suggesting some sort of 'cellular intelligence*', some fundamentally interesting stuff may come out of that research.

*I feel I may end up hating myself for using that term, but I can't think of anything better at the moment...sadly, too many good words get hijacked by sloppy thinking.

If you ever find yourself randly shrinked to the micron scale some day: Stay the fuck AWAY from amoebae. They may look slow and stupid and oozy, but they're out to fucking get you. They vicious. They don't care what unicellular or multicellular phylum you happen to be a proud member of: if they can hug you, they WILL squish you with nasty enzymes. Or make holes in you. They're freaking SCARY! o_O

Same goes for forams and "radiolaria", by the way. Actually, on the micron scale, if something doesn't eat you from the outside, chances are, it's patiently waiting to devour you from the inside. The microbial world tends to be quite innovative. And we haven't even gotten to the lethal veil of pallium...

Starting to feel good about your size yet?

As much as I'm obsessed with the microscopic world, it feels much safer to be a mere observer, rather than a participant. There's some truly terrifying monsters in those waters!

References
Han, B., Wang, T., Lin, Q., & Dumont, H. (2007). Carnivory and active hunting by the planktonic testate amoeba Difflugia tuberspinifera Hydrobiologia, 596 (1), 197-201 DOI: 10.1007/s10750-007-9096-z

Riemann, O., Kieneke, A., & Ahlrichs, W. (2009). Phylogeny of Dicranophoridae (Rotifera: Monogononta) - a maximum parsimony analysis based on morphological characters Journal of Zoological Systematics and Evolutionary Research, 47 (1), 61-76 DOI: 10.1111/j.1439-0469.2008.00482.x

Could this be a foram?

Edit: No. Turns out to be a pollen grain. Thanks Chris!
(pollen morphology is quite fascinating and breathtakingly diverse, btw! Plant sex is weird...)

Found this in a marine benthic sample this past spring, never got around to cropping it:

(40x DIC; obsessive-compulsive optical sectioning alert...)

Could this be some sort of foraminiferan? Reminds me of something Globigerina-oid, but if I recall it's planktonic, not benthic - although those things are quite capable of 'littering' once they die. Any thoughts?

(can provide a higher res image if interested)