Mystery Micrograph #02 - last call!

Just guess something!

Should be enough hints here:

Hint #1: predation
Hint #2: protist
Scale: thing is ~5-10um long
Hint #3: parasitism
Hint #4: I have a fetish for complex cell structure
Hint #5: multicellular forms exist in this group
Hint #6: chromalveolate
Last hint: hyphal stramenopile (this should be easy-ish now!)

Genus or cell type name would do!

Extension until tomorrow evening, where I aim to post the answer, and the Sunday Protist...

100th post!

100^th post, yay! Time for something silly, to celebrate:

Let's meet our new mascots, Cer Ratium (pun avoidance order in effect) and [insert witty name here] the Protoperidinium:

(ARGH my shitty computer just can't handle the elite memory whore that is ImageJ...)

Cer Ratium has a special attack: for the anime geeks among us, remember Lust from Fullmetal Alchemist? Yeah... this thing is gonna grow unrealistically long finger[nail] things to pierce opponents with...

And Protoperidinium ("Protoper"?) has this epic pallium attack where it casts a pseudopodious veil upon its opponents and digests them. Size advantages are useless against this one!

And now some of the other cast members: (mostly borne of lecture note margin doodles...)

Left -> right: T-phage riding E.coli, Psi, perpetually hammered EtOH, Partial [derivative], hNu, perpetually abused Neuron, a couple dimensions (R³ with the Projection Lance, mwahaha), Caffeine, cute lil' Kinesin and Dynein chillin on a 'tube (microtubule)... Dynein is holding up a clathrin-coated vesicle.

("Эх, прокачу!" is a reference to a Russian novel, Золотой Телёнок...)

Note: I am not a nerd. I am not a nerd. I am not a nerd. I am not a nerd. I am not a nerd. I am not a nerd. I am not a nerd. I am not a nerd. I am not a nerd. I am not a nerd. I am not a nerd. I am not a nerd. I am not a nerd. I am not a nerd. I am not a nerd. I am not a nerd. I am not a nerd. I am not a nerd. I am not a nerd. I am not a nerd. I am not a nerd. I am not a nerd. I am not a nerd. I am not a nerd. I am not a nerd. I am not a nerd. I am not a nerd. I am not a nerd. I am not a nerd. I am not a nerd. I am not a nerd. I am not a nerd. I am not a nerd. I am not a nerd. I am not a nerd. I am not a nerd. I am not a nerd...

A quick note on flagella, and their evolution

First off, 'flagella' and 'cilia' tend to be used interchangeably. I prefer to call them flagella, out of habit, but there's some who argue 'flagellum' should be reserved for bacteria, who have a fundamentally different system from us; while we have 'cilia'. Another note: 'flagella' is spelled with two l's, 'cilia' with one. Took me about two months of protistology to learn that. (also, I consistently spelled 'axopodia' as 'auxopodia', thanks to a plant biology research background. Curse you, auxin!)

Interestingly the flagellar structures seem to be fairly conserved in evolution, and are often used in taxonomy. Most eukaryotes are fundamentally biflagellate, meaning their flagellar systems, whatever they are, are likely derived from modifications of an ancestral biflagellate form, and retaining the double basal bodies. Flagella can be lost, but the basal bodies that anchor them tend to remain behind. Conversely, basal bodies can be duplicated, as they have, for example, in parabasalia, which are tetraflagellate; entire basal body units (kinetids) can also be multiplied, up to extremes such as in ciliates. (the developmental organisation of ciliate flagella is an endlessly fascinating subject, and if all goes well, would be my research focus after BSc. =D *knocks on her head wood)

In contrast, a few eukaryotes have what is fundamentally a single flagellum - those are unikonts, which include amoebozoa (eg. cellular slime moulds) and opisthokonts (ass-tails, eg. fungi, choanoflagellates...and us). It is intuitive to think of flagella as propelling the organism forward. But not everything is about sperm: most eukaryotic organisms actually pull themselves by flagellar motion, thereby defining the location of the flagellum as the anterior end, rather than posterior. Another distinction is between isokonts (equal flagella) and heterokonts (unequal flagella) - in the former, the two flagella are structurally identical, whereas in the latter they differ, often with little protrusions (mastigonemes) lining one of them.

Actually, scratch everything I just said about opisthokonts and amoebozoa being unikonts together. Missed a memo... there's this amitochondriate amoeba Breviata (TCoO post here and picture here), previously of uncertain placement or classified as an archamoeba. Despite having a single flagellum, it seems to have a double basal body, one of them unflagellated (Walker et al. 2006 JEM). Turns out that evidence suggests it's a basal amoebozoan, which would kill TC-S' unikont/bikont division (indicated in grey below):

(Roger & Simpson 2009 Curr Biol; numbers indicate ancestral number of basal bodies/flagellar unit, asterisk indicates one basal body is unflagellated, and the 2+ in Breviata indicates there may have been more that two basal bodies/unit.)

So to summarise:
kinetid - unit of basal bodies + flagella; not all basal bodies must have a flagellum (but the flagella must be anchored to a basal body each)
opisthokont - organisms with posterior flagellation; most eukaryotes have flagella at the front of their movement.
heterokont - both (or more) flagella structurally different
isokont - both (or more) flagella are the same
unikont - organisms with single basal body/flagellum per kinetid
bikont - organisms with double (or more) basal body per kinetid
mastigonemes - little protrusions regularly lining a flagellum; for increasing a flagellum's surface area.
centriole/basal body - generally interchangeable
cilium/flagellum - generally interchangeable
(kont means tail, by the way)

I noticed I throw those terms a lot in other posts without really explaining them; so hopefully this post can be some sort of reference, just in case!

There's more to it, but someone has some protist-oriented microscopy for me to do. I love Saturday nights!


Roger, A., & Simpson, A. (2009). Evolution: Revisiting the Root of the Eukaryote Tree Current Biology, 19 (4) DOI: 10.1016/j.cub.2008.12.032

WALKER, G., DACKS, J., & MARTIN EMBLEY, T. (2006). Ultrastructural Description of Breviata anathema, N. Gen., N. Sp., the Organism Previously Studied as "Mastigamoeba invertens" The Journal of Eukaryotic Microbiology, 53 (2), 65-78 DOI: 10.1111/j.1550-7408.2005.00087.x

Which opisthokont amoeboflagellate is this!?

While looking through the developmental biol lecture notes yesterday, I came across this image:

(Developmental Biology 8th ed. Gilbert fig 7.2)
So I sit there, staring at it, thinking: "Ok, so it's an amoeboflagellate opisthokont capable of transforming between the two. Shit, what kind of protist is this!? Not a Heterolobosean (those famously form flagella+centrioles de novo) due to its posterior flagellum and continuously present centrioles. Can't be a nucleariid or ichthyosporid or anything..." for a good 5min, getting frustrating that I couldn't recognise this protist... (also wondering why there were protists in a classical developmental biol class)

...and then I read 'sperm head'.

I'm so gonna fail this class in 3...2...1...

Well, actually I was right: this -is- an amoeboflagellate opisthokont with de novo flagellar formation. To a cladist, we'd be protists too!

Finger-growing dinoflagellate (cute!)

Why must I spoil the plot by peeking into advance online publications instead of waiting for the damn issue to come out, like normal people do? Especially with an 8am class coming up so soon...

Anyway, apparently Ceratium ranipes, a photosynthetic dinoflagellate, decided to grow plastid-stuffed 'fingers' during daylight:

(Pizay et al. 2009 Protist, in press; light period)

And retracts them back in for the night:

(Pizay et al. 2009 Protist, in press; dark period)

In case you're not convinced these are the same organism:

(Pizay et al. 2009 Protist, in press; sequence from a single individual removed from light, T measures minutes of darkness) (a video of that would be so awesome...!)

Chloroplasts fluoresce red when hit by UV light (see my own example with a diatom); take a look at those fingers:

(Pizay et al. 2009 Protist, in press. Left: formalin-preserved C.ranipes with a daytime morphology; the inset shows UV autofluorescense of the plastids: note their concentration in the 'fingers'. The bluish/whitish subinset shows Calcofluor White staining, which indicates the presence of thecal plates on the fingers. Right: transitional morphology at the end of the day: note how the plastids migrated inwards away from the fingers.)

This raises some cell biology-related questions: how is plastid movement coordinated and regulated? What does the genetic developmental pathway look like for those fingers, and how does it interact with whatever immediately respond to light? More importantly, why does this thing seemingly waste its time growing and retracting fingers, when it could have just kept them protruded during dark hours?

Could be just a low cost glitch in the system, or perhaps there is something to it. After all, perhaps it wouldn't take much to lose the finger retraction ability - so is there some cost when that happens, thereby keeping this process going? Sinking may have something to do with it - many planktonic algae sink for the night and float back up during the day. Fingers may drastically slow down the sinking speed. However, there's no data yet showing any vertical migration in C.ranipes (Pizay et al. 2009 Protist). Could be a relic from an ancestor that did sink, but then why hasn't this behaviour been found earlier, and in more dinos?

Another idea in the same paper is that the fingers get in the way of directed swimming; during daylight hours, you sacrifice your swimming ability for a larger photosynthetic capacity, but it may be advantageous to put away the tackle in the absense of light.

This reminds me of two things: 1) plant leaves - increasing the surface area exposed to surroundings for gas exchange, as well as the area exposed to light. Sort of a convergence. 2) Many 'radiolaria' have algal symbionts they use for photosynthesis, and they too spread them out towards the tips of the host's filopodia during daytime, and retract them inwards for the night. So whatever you do, don't dangle your plastids in plain view when they're not in use.

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Pizay, M., Lemée, R., Simon, N., Cras, A., Laugier, J., & Dolan, J. (2009). Night and Day Morphologies in a Planktonic Dinoflagellate Protist DOI: 10.1016/j.protis.2009.04.003

More hints for Mystery Micrograph#2

As stated previously about the very obscure micrograph in question:
Hint #1: predation
Hint #2: protist
Scale: thing is ~5-10um long

More hints:
Hint #3: parasitism
Hint #4: I have a fetish for complex cell structure
Hint #5: multicellular forms exist in this group

Come on, guess something!

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New hint #6: chromalveolate
Last hint: hyphal stramenopile (this should be easy-ish now!)

Mystery Micrograph #02

Alright guys, get crackin':

(to be referenced later)
Hint: predation

Got plenty of time, let's say by 9pm PDT this coming Sunday. Reward scheme as vague and implausible as last time. Speaking of which, I guess I do owe someone a beer*. And it happens to be geographically plausible even. And a little bit weird.

Open to members and ex-members of a 'certain department' this time, as there shouldn't be any advantages.

*when I gets me a supplementary job that can, uhhh, cover food expenses and stuff. My current one barely covers rent in this damn expensive-yet-very-'sustainable' yuppieville corner of the Northwest. I guess pretending to save the world by buying organic lettuce is more important than affordable student housing... anyone need a spare biotic dishwasher/PCR monkey/data entry robot/slave?

Although, come to think of it... one could live off media for a while, eh? I think we have all the essential amino acids on the chemical shelves somewhere...and lab grade sucrose. Yeah, we're set. Pun intended.

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(09.09.09) HINT#2: protist
(10.09.09) Scale: thing is ~5-10um long

Butterfly = Worm + Insect (2009, PNAS)

Shit, is it really that easy to get published? Seriously, what the fuck:

Caterpillars evolved from onychophorans by hybridogenesis
PNAS 2009 AOP

I reject the Darwinian assumption that larvae and their adults evolved from a single common ancestor. Rather I posit that, in animals that metamorphose, the basic types of larvae originated as adults of different lineages, i.e., larvae were transferred when, through hybridization, their genomes were acquired by distantly related animals. “Caterpillars,” the name for eruciforms with thoracic and abdominal legs, are larvae of lepidopterans, hymenopterans, and mecopterans (scorpionflies). Grubs and maggots, including the larvae of beetles, bees, and flies, evolved from caterpillars by loss of legs. Caterpillar larval organs are dismantled and reconstructed in the pupal phase. Such indirect developmental patterns (metamorphoses) did not originate solely by accumulation of random mutations followed by natural selection; rather they are fully consistent with my concept of evolution by hybridogenesis. Members of the phylum Onychophora (velvet worms) are proposed as the evolutionary source of caterpillars and their grub or maggot descendants. I present a molecular biological research proposal to test my thesis. By my hypothesis 2 recognizable sets of genes are detectable in the genomes of all insects with caterpillar grub- or maggot-like larvae: (i) onychophoran genes that code for proteins determining larval morphology/physiology and (ii) sequentially expressed insect genes that code for adult proteins. The genomes of insects and other animals that, by contrast, entirely lack larvae comprise recognizable sets of genes from single animal common ancestors.

This? In PNAS of all places?

Basically, worm hybridised with insect to make grub-like larval forms. Yeah. I thought "k, maybe the paper itself may have some data, or something", and even VPN'd to get it. It actually wasn't really worth it. At all. There was nothing of substance there .I expected some grotesquely misinterpreted data. It was disappointing: a few drawings pointing out the visual similarities (very robust methodology, especially for constructing phylogenetic trees. Absolutely failproof.), some rather sketchy-looking tree I was too lazy to figure out in the 2min I could spare for that paper. And discussiony-looking text. Kinda reminiscent of a certain creationist 'journal' we do not speak of in fear of death by laughter...


Via Musings of The Mad Biologist, wherein the paper is gently chewed up (could be worse). I really like the phrase 'clusterfuck of genes'. I'll be sure to steal it when necessary. Because that's really the only argument you need against this paper. And also, genes don't work like that. Really, they don't.

Come to think of it, neither does evolution. Or decent science.

Sunday Protist - a slime mould

Too tired to write up a proper post this time; gonna slack off by posting a few pictures of a couple slime moulds (likely same species? were near each other...) I found this morning:
(plasmodium)

(fruiting bodies on a neighbouring shrub; anyone wanna ID those?)

For the uninitiated: myxomycetes generally start out from the spore as free-living amoebae (or amoeboflagellates, depending on environment) crawling about in wet soil/dead leaves/etc; then they have sex, and undergo multiple rounds of nuclear mitosis (without cell membrane division) resulting in giant multinucleate plasmodia, like the dripping yellow thing in the first photo. The plasmodia move around feeding on stuff (mainly bacteria) until conditions deteriorate (environment dries out or food runs out). Then, they form stalked fruiting bodies, sporulate and disperse away. They're actually quite more common than you'd think, it's just that they're seldom noticed, and generally ignored due to their slime-like appearance (to some people). To the initiated, they are just another embodiment of beauty. And quite exciting to come across!

Despite the 'mould' in the name, they have little to do with fungi. In fact, for more info on slime mould diversity, go read this post. Also, Jen@The Artful Amoeba is poised to produce us some more slime mould pictures. Meanwhile, I'm falling asleep at the keyboard, as I've just pretty much mixed up and hybridised dictyostelid (cellular slime mould) and myxomycete (plasmodial slime mould) life cycles, and had to rewrite the preceding paragraph... feel free to ignore any glaring inaccuracies left lying about in this post...they never 'happened'... 'night~

Back in Raincouver

Back in Vancouver with all the rain and start-of-term chaos; will pay off posting debts shortly...

While we're at it, PhDComics just summed up the story of my life:

I feel stalked... (and next time someone complains about my peculiar work hours, I am so citing this comic. And Phdcomics.com has the highest impact factor/citation index/LULz index of all scholarly publications EVAR, therefore they must be right.)

Sunday Protist is on its way...