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!)

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

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)

Sunday Protist - Choreocolax: Shooting nuclei into foreign cytoplasm

The cell, the fundamental unit of life, consists of a package of information-bearing molecules (DNA) wrapped in some material that delineates it from the outer world (lipid membrane). Basically, a cell is a highly organised and compartmentalised bag of fat and acid. Nothing much to see here...

The story is not so simple however. Multiple nuclei occupying one cytoplasm is a fairly common situation, as are holes (channels) between cells in multicellular organisms. This has even led to discussions about using an alternative "Cell Body" concept instead of the conventional cell (Baluska et al. 2004 Annals Bot. (free access)) - although perhaps it's not worth the bother to panic over redefining everything.

Apparently, some coenocytic algal nuclei can survive plasma-membrane-less upon release from a wounded cell. The nucleoplasm is then surrounded by a gelatinous envelope and subsequently forms a plasma membrane and cell wall. (Ram & Babbar 2002, BioEssays). That could be just a special case, a byproduct of coenocytic wound repair mechanisms.

But there is an organism that specialises in firing its nuclei into the host to take it over! (kinda like installing trojans on your computer...) Meet Choreocolax, a filamentous red algal parasite that leeches off Polysiphonia (another red alga).

(Goff & Coleman 1984 PNAS; free access)

It forms 'planetic' nuclei which are then injected into Polysiphonia by forming pit connections. These planetic nuclei then multiply vigorously in the host cytoplasm and 'take over' the cell:
(PN - planetic nucleus; HN - host nucleus)


The molecular aspect of this process must be pretty awesome -- would love to see that thing's genome sequence (sadly unlikely; this thing isn't particularly popular or well-known. Yet.) and hear about the various pathways involved in taking over the host... and how the nucleus can survive in a foreign cytoplasm in the first place!

There's only one lab studying Choreocolax, it appears. That needs to change...

Sunday Protist resumed: Acetabularia

I've been thoroughly neglecting Archaeplastida... probably because I see its representatives everyday anyway. Archaeplastida is the superkingdom containing Glaucophytes, red algae, green algae and land plants*. Archaeplastids are characterised by primary plastid endosymbiosis, so most of them are photosynthetic. Hopefully I'll get around to discussing some exceptions later...

Since I like large complicated cells, today's menu features Acetabularia:

(UBC Botanical Garden)

Each of those umbrella-like things is a single uninucleate cell up to 6cm tall. At the base of the stalk is the rhizoid containing the nucleus. This little detail turned out to be extremely useful for establishing the cell organelle responsible for heredity back in the 30's by Hämmerling. A couple species of Acetabularia produce morphologically distinct caps, so Hämmerling cut off the caps and exchanged the stalks between the two species. The morphology of the regenerating cap was determined by the species of the nucleus-containing rhizoid, not the stalk: thereby strongly supporting the central role of the nucleus in heredity and the cell's 'information'.

I'd love to study cell morphogenesis in that thing! There seems to be a bit of work done on it here and there, but it is far from model organism status. Doesn't seem to have its genome sequenced yet, although I may be wrong on that. Being a unicellular organism relatively close to land plants, it could reveal some insights about plant cell development and evolution. The size would be wonderful for studying cytoskeletal dynamics. Acetabularia was at one point used as a model for circadian rhythm studies - it maintains its rhythm in the absence of the nucleus, implying a cytosolic component to biological clock regulations (briefly mentioned here).

However, for all I know, it may be hard to culture, do genetics with, etc.

(personally, I still prefer ciliates... ^_^ )

*Archaeplastida is also alternatively called Plantae, but I resent that naming. After being taught for so long that plants are the terrestrial multicellular green stuff, and being proud of recognising that 'seaweeds' aren't plants after all... they suddenly decide to name the whole freaking group Plants. Sorry, no. I find it rather unsettling when some protistologists refer to red algae or prasoniphytes as 'plants'. The conventional plants are refered to as 'land plants' (which I'm fine with to avoid confusion; although botanists give me funny looks when I do that...) Furthermore, the name Archaeplastida makes sense, since this group is defined by having plastids from primary endosymbiosis. Everything else got their plastids from them via secondary and tertiary endosymbiosis.
Sorry, but your Chlamydomonas is not a freaking plant, kthx.