Sunday Protist - Assorted oddballs

As I scramble to finish a chapter before my supervisor notices his hiring mistake, instead of writing out a mini-review paper about a single group of sorts, I'll use the opportunity to point out a few of the oddballs I've accumulated lately. Many of them have just a single paper, or a passing mention and a reference to a paper I can't get easily (and that would likely be in some language I can't read to begin with...), and thus they don't really make good weekly protists by themselves. But yet, many are too cool to ignore mentioning.

Our first exhibit is a peculiar association between a coccolithophorid haptophyte (small phytoplankton), Reticulofenestra sessilis, and a centric diatom, Thalassiosira sp.:

The thing in the centre is the centric diatom. The scaley things around are the coccoliths, or calcified scales, of the haptophytes Reticulofenestra clustering around it. The exact nature of this relationship is unknown, though presumably beneficial for the haptophyte, as R.sesslis is found almost exclusively attached to diatoms. Image by from nannotax.org; original citation - Gaarder & Hasle 1962 Nyü Mag Bot (which doesn't exist online *gasp*)

Speaking of haptophytes, here's another cool-looking one. There is quite a bit to say about haptophytes overall, just too lazy to do it right now. There is a post in the making though...

Umbellosphaera. The things on the surface are its coccoliths, of which each individual is intricately crafted into a chanterelle/trumped-like shape. SEM on the left from a nice image repository/course supplement by Isao Inouye from U Tsukuba, one of the Meccas of protistology. (Website is in Japanese, unfortunately for [most of?] us. I really need to learn Japanese someday...) Image of single coccolith on the right from eol.org.

Now for an obligatory ciliate. Trichodina is a cute little peritrich (group that includes the coiled-stemmed-trumpet Vorticella) that deserves more attention than just a pretty picture, but its looks can't wait to be exposed. Both the top and bottom sides have cilia, and the creature is like a miniature robotic vacuum cleaner, vacuuming the fish gills (or other substrates, like jellyfish) of bacteria and various other prey that accumulate there. In doing so, it causes fish disease, but the cute lil' thing didn't mean to!

Left: Trichodina 'vacuuming' fish gills (source). Middle: DIC image of the Trichodina 'sucker' (surprisingly from National Geographic, of all places). Right: Drawing of the ciliate. (HJ Clark 1866 Am J Sci) Will surely come back to it someday!

And last for today, this little critter is absolutely adorable. There's actually quite a bit to say about it, but I'm not gonna do it because some other blogger is far more qualified to write it up. Perhaps after the conference season calms down a little, said blogger could share their wonderful stories with us...

Apusomonas proboscidea. To paraphrase Opisthokont, 'cute Apusomonas' would be redundant. You see that little protrusion at the top? It wiggles 'spastically' as the critter crawls forward along its flagellum. If you're really keen check out the movies in this recent paper on apusomonads (TC-S alert!). Left: Karpov & Myl'nikov 1989 Zoologicheskiy Zhurnal (in Russ.) Right: Flemming Ekelund at ToLWeb (Apusomonas is really tiny...)

That's it for today. Am going out of town until middle of next week, will likely lack internet (eeek, how will I live?!), so if comments are mysteriously ignored, that's why.

Criminally photosynthetic: Myrionecta, Dinophysis and stolen plastids

The microbial world is full of vicious beasts. Yes, much of microbial life is cute and cuddly in one way or another. But that doesn't stop many of them from making wolverines seem docile by comparison. There is an entire mafia out there built around...organ theft; including some multicellular players as well, in case you thought animals were saintly. Today we'll look at some famous thieving masterminds of the plastid black market, but keep in mind that there are many more fascinating relationships involving keeping entire organisms or their parts alive within the host, and vastly more oddities that have still escaped human attention (not hard to do, actually).

Let's start off the messy subject with a pretty diagram summarising the major plastid hoarding events of the [moderately] distant past:

Pac-Man!* Today all we need to do is appreciate the overall big picture: there were numerous symbiotic events and by about tertiary endosymbiosis, it gets messy. Not pictured are the cases of more-or-less transient kleptoplasty (plastid-theft), which would do serious harm to the readability and aesthetic qualities of this diagram. (Keeling 2004 Am J Bot; free access) For those keen on extra gory details of plastid endosymbiosis, see this recent review.
*If somebody were to make a game of Pac-Man: Endosymbiosis Edition...

Today's plastidial saga will involve an arduous journey from the cyanobacterium to the red algal endosymbiont of the cryptomonad, to the subsequent ingestion by a ciliate and a dinoflagellate. In fact, just keep in mind that the cryptomonad itself is the result of a hungry heterotroph getting a habit of devouring red algae and developing a case of terminal indigestion, ultimately gaining a plastid and plastid-targetting genes in its own nucleus. The cryptomonad in particular happens to be really awesome in another way: it actually still retains the original, eukaryotic, red algal nucleus of its former prey! That nucleus has been badly shrunk in the wash, and the genome is essentially on crack, but that's a long story for some other day.

Just so you get an idea of what a cryptomonad roughly looks like:

Cryptomonas. Note its very diminutive size. Source: Micro*scope.

We're about to move on to the sleazy thieving ciliates and dinoflagellates. But first, we must establish how kleptoplasty (lit. plastid theft) differs from endosymbiosis. To clarify, I use 'symbiosis' as a general term for an intimate interaction between two different species, including parasitism, mutualism and commensalism. Thus, an endosymbiont needn't feel the same way about the relationship as its host, and very often doesn't. Keep in mind that it is often not very obvious which exact category the symbiosis falls into, as nature doesn't particularly care for our naming fetish.

Endosymbiosis, in the context of organelles and other intracellular stuff, typically entails the complete engulfment of another organism by the cell. Once gene transfer occurs between the genomes of the two organisms, some declare the endosymbiont is now officially an organelle. The endosymbiont-organelle debate is old, stale and utterly pointless; thus, as I have declared in a previous post, I like to call plastids and mitochondria 'endosymbionts' and the more questionable cases, like Perkinsela, 'organelles'. That way, I can piss off just about everyone. Ha!

Then there is the much-awaited plastid theft, where only the plastid itself of the failed endosymbiont is retained, with the rest of it typically digested away. The katablepharid Hatena which Labrat wrote a wonderful post about (as well as Merry at Small Things Considered), is a striking case of kleptoplasty (and only discovered this past decade!). The intensity of kleptoplasty, as well as endosymbiosis, vary greatly from transient plastids (or endosymbionts) that are not essential to the host, to mostly permanent plastids or endosymbionts that are retained indefinitely, capable of reproducing on their own, and completely obligatory for the host's survival. This is nicely summarised in this diagram from a recent review on acquired photosynthesis by Stoeker et al 2009:

Two ways to get a plastid: 1) steal a plastid-bearing alga and lock it in your basement keep it alive within you (endosymbiosis); 2) mug the alga, steal its plastid and try to keep it alive yourself. Along the two paths lie multitudes of intermediate steps different in the persistence of the plastid (how long it lasts) and how dependent the host is upon it. (Stoecker et al. 2009 Aquat Microbiol Ecol)

In the endosymbiotic pathway, nucleomorphs (and the original plastidial prokaryotic genome) suggest the permanent associations we know among the 'normal' algae come from the endosymbiotic path, as there is evidence for whole host retention at some point. However, the data do not entirely rule out some independent secondary plastid acquisition via kleptoplasty rather than endosymbiosis. As for tertiary plastidial symbionts, it gets fun. The classic persistent cases like Kryptoperidinium tend to have a whole endosymbiont, nucleus and all, so the endosymbiotic pathway is also more likely, cut things like Dinophysis, on the other hand, are just weird.

Now, at last, our long-awaited thief: the ciliate Myrionecta rubra (=Mesodinium rubrum):

Myrionecta rubra (originally Mesodinium rubrum); c - cirri; ChC - chloroplast complexes; ECB - equatorial ciliary band (Taylor et al. 1969 Nature) Right: SEM of Myrionecta by Takayama Haruyoshi (more awesome micrographs here)

As you can see, this ciliate bears plastids - a rather non-ciliate activity. In fact, if you slice it up, you'll find that the plastids are very carefully arranged at the periphery:

N - cryptomonad nucleus; M - ciliate macronucleus (note the difference in chromatin organisation); note how the plastids are not only predominantly on the cell periphery but also tend to all face outward! (Oakley & Taylor 1978 Biosyst)

The ciliate captures a cryptophyte, takes its plastids -- along with the nucleomorphs, pyrenoids and other plastid-associated stuff, as well as cryptomonad mitochondria -- and packages them up in their own little compartments. Furthermore, the nucleus is also retained and consistently packaged in an entirely separate package from the plastids. Quite remarkably, the cryptomonad nucleus remains transcriptionally active! (Apparently, Elio beat me to it in 2007. Grrr) Presumably, maintaining an active host nucleus would help keep the plastids functional longer.

Oddly enough, I have difficulties finding anything on the exact process of crypto acquisition - I initially thought it just phagocytoses them, but a friend of mine studying weird plastid aquisition thinks they may actually employ myzocytosis - sucking out the contents of its prey through a 'straw', like many other alveolates do: this may explain the segregation and separate enveloping of the plastid and crypto nucleus. This would require Myrianecta to be quite fast and well-coordinated; the speed is there as it tends to jump instead of moving gradually (details here).


There is a plot twist to this story. A stroke of irony, or poetic justice, or karma if you're into such things. The thieving ciliate itself gets mugged...by a dinoflagellate!

At first glance, Dinophysis caudata is a normal photosynthetic dino, which isn't particularly surprising as roughly half of them are (most with their own plastids). Dinophyceans are quite trippy morphologically, which made it even more frustrating that Dinophysis appeared impossible to culture, despite being photosynthetic. For a while, no one could figure out what exactly was wrong with it. Turns out, its plastids aren't its own, and are rather cryptomonad-like. Great, so it kleptoplasties the cryptos, let's just grow it in a jar full of them! Again, no luck - for some reason, Dinophysis appeared incapable of ingesting the cryptomonads!

It was all rather perplexing until someone figured out the problem in the 2000's, publishing the first successful culturing attempt in 2006 (Park et al. 2006 Aquat Microbiol Ecol). Here's what was missing:

Dinophysis (the jug-like thing with a conspicuous flagellum) sucking the plastids out of Myrionecta, who's rolled up into a small, whimpering ball by this point. (Park et al. 2006 Aquat Microbiol Ecol)

Not only is Dinophysis caudata a stinkin' thief, but it can't even do the primary stealing itself - the dino requires Myrionecta to do all the dirty work of packaging up the plastids. But it gets messier. First, a summary of the plastid's plight:

Dinophysis ingests plastids from the ciliate Myrionecta, who in turn stole them from a cryptomonad. Who, if you recall, obtained it a long time ago as a red algal endosymbiont. Who, of course, obtained the original plastid as a cyanobacterial symbiont. I think it ends there though. That poor cyanobacterial genome has been through a lot! (Wisecaver & Hackett 2010 BMC Genomics)

Now, whether Dinophysis also bears proper plastids of its own is up to heated debate at the moment. It looks like I'm not the only one thoroughly confused by it, and sorting out this issues is slightly beyond the responsibilities of a mere blogger at the moment, so let's leave this part of the story explicitly vague. It seems like Dinophysis may somehow supplement its own stock with the stolen plastids, as it appears to have plastid-targetting genes in its own genome (Wisecaver & Hackett 2010 BMC Genomics). However, there are also cases of Dinophysis carrying plastids that appeared very non-cryptomonad, and most likely to be of dinoflagellate origin (Garcia-Cuetos et al. 2009 Harmful Algae).

The chaos is quite understandable: it is actually very difficult to determine the nature of a relationship between two organisms, especially on the microscopic scale, and especially when one is inside another. It's often hard to distinguish a permanent from a transient relationship, and a mutualistic from a parasitic one. While there is strong direct evidence that the dino sucks plastids out of Myrionecta, that does not necessarily mean all of its plastids originated there. Or that it lacks its own (though that would make sense). Or more importantly, that the various research teams are even looking at the same bloody organism! Speaking of which, Myrionecta and Dinophysis appear to be in a 'bit' of taxonomic mess too, so I'll just let the professionals fight it out amongst themselves.

While that's going on, one cannot help but wonder how many such 'unconventional' relationships there really are. Food webs are not as direct as people think, the once one peers a little further than the usual stereotyped interactions (predator, parasite, prey, producer, whatever), ecology actually becomes an interesting (admittedly, fascinating!) subject. On that note, I think we should really be careful when trying to force terrestrial and macroscopic ecological terms onto the microbial world -- and by careful, I think we should perhaps come up with a system specialised for microbial life from the very beginning. While we seldom see one animal rip out an organ of another and keep it alive for itself, organelle theft is actually not all that uncommon. Life on the cellular level is weird to us, and many traditional terms simply fail to describe it.

There's a whole black market of utterly bizarre microbial interactions out there. We are only scratching the surface.

References
Garcia-Cuetos, L., Moestrup, �., Hansen, P., & Daugbjerg, N. (2010). The toxic dinoflagellate Dinophysis acuminata harbors permanent chloroplasts of cryptomonad origin, not kleptochloroplasts Harmful Algae, 9 (1), 25-38 DOI: 10.1016/j.hal.2009.07.002

Johnson, M. (2010). The acquisition of phototrophy: adaptive strategies of hosting endosymbionts and organelles Photosynthesis Research DOI: 10.1007/s11120-010-9546-8

Johnson, M., Oldach, D., Delwiche, C., & Stoecker, D. (2007). Retention of transcriptionally active cryptophyte nuclei by the ciliate Myrionecta rubra Nature, 445 (7126), 426-428 DOI: 10.1038/nature05496

Keeling, P. (2004). Diversity and evolutionary history of plastids and their hosts American Journal of Botany, 91 (10), 1481-1493 DOI: 10.3732/ajb.91.10.1481

OAKLEY, B., & TAYLOR, F. (1978). Evidence for a new type of endosymbiotic organization in a population of the ciliate Mesodinium rubrum from British Columbia Biosystems, 10 (4), 361-369 DOI: 10.1016/0303-2647(78)90019-9

Park, M., Kim, S., Kim, H., Myung, G., Kang, Y., & Yih, W. (2006). First successful culture of the marine dinoflagellate Dinophysis acuminata Aquatic Microbial Ecology, 45, 101-106 DOI: 10.3354/ame045101

Stoecker, D., Johnson, M., deVargas, C., & Not, F. (2009). Acquired phototrophy in aquatic protists Aquatic Microbial Ecology, 57, 279-310 DOI: 10.3354/ame01340

TAYLOR, F., BLACKBOURN, D., & BLACKBOURN, J. (1969). Ultrastructure of the Chloroplasts and Associated Structures within the Marine Ciliate Mesodinium rubrum (Lohmann) Nature, 224 (5221), 819-821 DOI: 10.1038/224819a0

Wisecaver, J., & Hackett, J. (2010). Transcriptome analysis reveals nuclear-encoded proteins for the maintenance of temporary plastids in the dinoflagellate Dinophysis acuminata BMC Genomics, 11 (1) DOI: 10.1186/1471-2164-11-366

Ciliate-in-a-test-tube

Who said test-tube babies were 'unnatural'?

Undella hyalina, a tintinnid ciliate. Tintinnids craft wonderful loricas out of organic materials, often studding them with bits of random gunk (but not in this case).
http://www.obs-vlfr.fr/gallery/album316/undellopsis_hyalina

There's something quite adorable about a ciliate who willingly crawls into a test-tube by itself. In fact, it actually makes its own test-tube. If only all the protists could just grown their own flasks, fill them with optimal media, and culture themselves*...

More to come soon!

*Technically, they do culture themselves, quite successfully too. Just not in conditions convenient for researchers...

Sunday Protist - Lagynion: bottled algae

Quick one today as I should really be writing a chapter, as well as the post on plastid thiefs some of you wanted. And haptophytes. Have I mentioned my ADD tendencies?

While I find ochrophytes (large group including diatoms and kelps) a bit too phycological for my tastes, some of them are actually really cool, especially Chrysophytes - the 'golden algae'. Chrysos include things like scaly flagellates (Paraphysomonas) and Dinobryon which makes colonies that look like trees of stacked wine glasses. A while ago we had bottled ciliates, and this time the Chrysophytes offer us a few bottled algae, especially the flask-shaped Lagynion.

A happy(?) clump of photosynthetic flasks, of Lagynion. Source: Micro*scope.

The lorica consists of organic material. The progeny following division are released as little zoospores bearing the ridiculously complicated flagella characteristic of ochrophytes (one of them too short to be easily visible). Then the zoospores settle down, become amoeboid and grow themselves a new flask. As far as I could gather, that's pretty much all there is to say about Lagynion at the moment. But it still looks pretty cool!

1. Side view. Arrowheads indicated a rib structure surrounding the 'flask'. 2 and 3: top views of three Lagynion cells showing optical sections through the base and the neck regions, respectively. 4. TEM of 'flask'. Note the plastids (C) and the nucleus (N). V - peripheral vesicles. In short, plastids in a bottle. (O'Kelly & Wujek 2001 Eur J Protistol)

In fact, there's a whole family of bottled, and often amoeboid, algae called Stylococcaceae (eg. see Nicholls 1987 J Phycol), but they are so obscure it's painful to find much literature on them, or even decent pictures. Especially since by the time they get digitised, a lot of the old images become completely illegible. But here's another member of the family bearing slightly different glassware, Chrysopyxis:

Source: Micro*scope

Now to do real work and then write up some of the really exciting stuff I came across lately. And crush my writer's block with something sharp and heavy. Really annoying when you can't write anything because, well, you can't write anything. Wish brains came with instruction manuals...

References
Nicholls, K. (1987). CHRYSOAMPHIPYXIS GEN. NOVA A NEW GENUS IN THE STYLOCOCCACEAE (CHRYSOPHYCEAE) Journal of Phycology, 23 (3), 499-501 DOI: 10.1111/j.1529-8817.1987.tb02537.x

O'Kelly, C., & Wujek, D. (2001). Cell structure and asexual reproduction in Lagynion delicatulum (Stylococcaceae, Chrysophyceae) European Journal of Phycology, 36 (1), 51-59 DOI: 10.1080/09670260110001735198

PS: Hardly relevant but kind of newsworthy: First Phaeophyte genome sequenced! (Cock et al. 2010 Nature) Until now, the only complete Stramenopile(=Heterokont) genomes were a couple diatoms and oomycetes. Ok, there's still many more to go but Phaeophytes can be interesting in terms of studying the evolution of multicellularity. Also, the ochrophyte clade is a phylogenetic mess; not that single whole genome data means much but could perhaps helps calm the harsh seas somewhat.

Intermission [hopefully] over...

Hey guys,
Sorry about the lack of posting lately. Discovered that actual writing (ie not rambling blogging in my style) is kind of slow and painful and difficult, at least at the start anyway. First thing that happened when I got my chapter assigned was one hell of an epic writer's block. I spent hours staring at the damn outline. And being miserable. Thus I had to make up for it on the weekend...

Becoming easier, but still full of headbanging and frustration in places, especially where the field gets a little messy. The annoying thing about protist writing is the massive holes in the literature and instances of absolute chaos that no one's bothered to resolve since it transpired half a century ago or so. Like phantom species. And phantom cellular structures. And other phantom factoids. Being obsessive compulsive in a way, I feel obliged to investigate. Which eats up a lot of time, etc. Am trying to learn the art of ignoring not-quite-so-relevant literature. And the art of containing browser tab explosions...

Anyway, I should probably get back to blogging to keep my other stuff from getting too dry (or that's the idea anyway). Otherwise my other writing reads like ultrastructure descriptions. Middle ground between my style here and there would be awesome. (Right now I only have two settings of formality: bloggy and research papery. Grrr. Or, more accurately, zzzZZ.)

Anyway, some of you are probably sitting there snickering at this n00b. Meh.

Feel free to ask me anything about Hacrobians/"Craptophytes". Come on, I dare you =P


Just to keep track of what I need to do here eventually, in no particular order:

- reduce percentage of posts being about lack of posting...
- update Tree of Euks (prerequisite: learn shiny new toy Adobe Illustrator)
- finish part III of Constructive Neutral Evol series
- new Mystery Micrograph
- write up the 10 or so neglected past MMs
- Sunday Protists (maybe even on Sundays! *gasp*)
- Haptophytes (started writing up a mini-series on them)
- Neomura and Eukaryogenesis (Hahaha. Ha. Must read a couple more TC-S novels "papers" first...)
- Bacterial evol: comparing TC-S stories with trees and so on. Leaving that for later. Much later.
- Stomatal development + diversity (related to my old lab project; might as well share some cool tidbits before I forget completely)

Anything I missed? Hard to keep track of blogging obligations on top of everything else...

Coming up next: Dinos mugging ciliates for their stolen algal plastids. Which the latter dismembered and packaged up into neat little compartments.

Clearing up eukaryotic life histories

I can still vaguely recall the horrid hell that was my second year "non-vascular 'plant'" course (valid contender for most polyphyletic course in existence...) - amid the poorly explained phylogenetic clusterfuck, we also had to cram life cycle diagrams from hell. Ever thought red algae looked cute? Not quite so much after realising you get three fundamental life cycle phases to plow through...the night before a final, as it always is. In hindsight, it actually makes a lot of sense, once you grasp some basic principles. Somehow, I missed those the first time around, and then wondered what the hell went wrong.

Warning: This is a bit of a rant. For the meat, skip to the figure.

The damnation

One of those key concepts is the haploid-diploid variation found in many, if not most (if not, secretly, all) eukaryotes. You know the whole thing with syngamy and meiosis and gametic vs. zygotic vs. sporic life histories. You may even wish I hadn't reminded you. Click here if you'd like to experience the wonderful feeling of intense confusion again. So basically, eukaryotes can be haploid or diploid. Typically they have ways of switching between the two phases: diploid --> haploid = meiosis (typically), haploid --> diploid = syngamy (again, roughly). To make things more fun, there may also be several distinct diploid and haploid stages, but let's ignore those for now. Now, it logically follows that there may be variation in how 'prevalent' a certain stage is for various organisms. Let's call it the 'dominant' stage, just for kicks.

Now, how do you define 'dominant'? Well, for humans, it's obviously the part of your life you're an 'individual'. Ok this gets weird when said 'individuals' can clone themselves; also, a bit too philosophical. Let's reword that: It's obviously the stage in your life you're multicellular and big and stuff. Baker's yeast, for example... hang on, what's the big multicellular stage in yeast? Errr... scratch that. Ok, the stage an organism spends most of its time in. Great, works so far. Yeast is most usually haploid. What about moss? It's roughly equal (for the sake of the argument) in both haploid and diploid stages. So it's sporic.

I admit to being a little slow at times, but that seriously confused the fuck out of me -- it seemed arbitrary! How exactly do you decide whether an organism has one or multiple "dominant" stages?

We've been told to "look where meiosis happens". Now this is where it becomes absolute and total mindfuck, on steroids and LSD. Remember the 'gametic', 'zygotic' and 'sporic' life histories? You know what else they're officially(!) called? Gametic, zygotic and sporic...MEIOSES. That's right. We have gametic meiosis, zygotic meiosis and sporic meiosis. Now, sit back and savour the absolute chaos that this naturally incites in young minds yet to be protected by the hard-ass defensive shell your brain produces from years of bitter academic cynicism.

Done? Borderline mental abuse, ain't it?

Of course, while none of those terms have a single redeeming quality besides being physically pronounceable, the worst, by far, is 'gametic meiosis'. Last time I checked, there are no documented case of haploid cells consistently/normally undergoing meiosis. (allowing it has somehow been induced artificially in haploids - who knows) So that's absurd. Even speaking from a field where biological "laws" need not apply. I'm happy to know that someone with qualifications agrees with this, and also has a nice rant on the topic. Of course, I'd say we should do away with 'gametic', 'zygotic' and 'sporic' altogether, but more on that later.

We've also been told "the big, obvious stage [presumably, multicellular] is dominant" Again, last time I checked, Chlamydomonas doesn't exactly jump out of the culture medium and grow before you into a giant... SuperChlamy... or something. That would be really cool for a cartoon character, but most life doesn't exactly strive to be visible to the human eye or anything. In fact, it's much better to not be...

A slightly more sensible point was "look where feeding happens". Great, so sperm are now a dominant stage? If I recall, they do absorb nutrients. Are we gonna go as far as define what manner the nutrients must be obtained in? The lesser known life of Dictyostelium involves cuddling up with a mate, fusing, forming a cyst and then baiting unsuspecting haploid dictys with cAMP...to devour them!

How about "the stage that can live freely"? Well, then many parasites now have no life, and are very sad. Or "the stage that lasts the longest". Well, many things can fuck, encyst, and hang out for what is an eternity compared to their mitotic cycles. Some organisms can spend more time in resting stages than in active ones - ever wondered how a puddle can come back to life as quickly as it dries up?

In the end, I figured this was more of a fuzzy philosophical question, with ultimately everything being somewhat sporic-

Salvation at last!

-until randomly wandering across this neat little diagram today:

A sensible summary of a) Haplontic, b) Haplodiplontic and c) Diplontic life histories. ( Houdan et al 2004 Syst Biodiv based on (and greatly improved from, IMO) Valero et al. 1992 TrEE)

Do you see the difference? At last, a clear, crisp definition! The dominant stage is the one where mitosis occurs, duh! Perhaps it'd help to add 'reproductive' meiosis, to take care of those pesky little exceptions (some multicellular lineages). And personally, I prefer 'haplontic' vs. 'zygotic'. Zygotic sounds very diploid to me. That term owes me a nice chunk of my grade for that 'non-vascular plant' course. 'Haplodiplontic' is wonderful too as you don't have to sit there wondering what a 'spore' is. It's straightforward, concise and universally applicable.

Humans? Diplontic - sperm and eggs don't reproduce mitotically. Dictyostelium? Haplontic - diploid stage quickly followed by meiosis without any mitotic divisions. Moss? Haplodiplontic - both haploid and diploid forms divide mitotically, in this case to form large multicellular organisms. Our favourite beer-making Saccharomyces? Haplodiplontic, actually - it can happily reproduce mitotically in haploid and diploid stages! Red algae? Don't ever remind me. But haplodiplontic as well. A very convoluted form thereof. Pfiesteria-aka-lets-cram-every-possible-eukaryotic-way-of-being-into-one-organism? (yup, that was [reportedly; some doubts RE amoebae] 24 distinct life cycle stages) Appears to be haplontic as a typical dino.)

The original source of the above diagram still makes the usual mistakes of skipping stages taken for granted and relying much too heavily on metazoa, fungi and land plants for explanation (and using Margulis' 'protoctists', ewww...) As per usual, a protistologist comes along and makes everything better! =D

Ah the legacies biology's phylogenetically myopic traditions have left us!

Yet another rant about teaching...

I'm slowly beginning to believe in the following principle: If [caring] students don't understand something, it's either wrong or taught poorly. Usually, but not always, the latter. Science is seriously not that complicated. At all. Just that we humans are fucking abysmal at explaining it. And since most teaching seems to be vertically inherited, poor approaches to certain topics are often maintained due to purely historical reasons. All too often it is perpetrated in the same form the teacher once received it as a student; and since those who make it in academia tend to be those who can grasp concepts despite the poor teaching (sigh...doesn't bode well for me =( ), they are perhaps somewhat oblivious to how cumbersome their inherited approach is.

As much as I love research, I still think teaching is a more pressing priority for academic science.

(Personally, I tend to think of everything from a cellular perspective. Furthermore, if you tell me something that only applies to a small polyphyletic assemblage of conspicuously sized organisms, I tend to file it away as an exception and forget. (I like exceptions, but only when aware of the general principles that go along with them) Furthermore, that 'non-vascular plants' course revolved predominantly around terminology, most of which I immediately forgot after the final. Or even before the final. Hell if I remember what an 'archaegonium' is, and how it differs from a 'sporocarp' or whatever. Especially when the same things get different names depending on who studies them. In fact, don't expect me to remember taxon-specific terms for general things even for organisms I actively study (and like!). I won't. Even though everyone claims to 'know' this, students (and conference attendees, etc) tend to take away concepts, not terminology. Seriously. We all have our favourite jargon, but please pity the uninitiated!)

Now, food for thought: how did a student just plow through four years of biology courses without properly understanding eukaryotic life histories? Our education system is truly scary...

References

Houdan, A., Billard, C., Marie, D., Not, F., Sez, A., Young, J., & Probert, I. (2003). Holococcolithophore-heterococcolithophore (Haptophyta) life cycles: flow cytometric analysis of relative ploidy levels Systematics and Biodiversity, 1 (4), 453-465 DOI: 10.1017/S1477200003001270

Valero, M. (1992). Evolution of alternation of haploid and diploid phases in life cycles Trends in Ecology & Evolution, 7 (1), 25-29 DOI: 10.1016/0169-5347(92)90195-H

Carnival of Evolution #24 is up at Neurodojo

Go check it out (I'm in it, uncategoriseable as any true protistologist ought to be...). Vandalised logo included

(I think those black things around the brain are Toxoplasma afflicting Dr. Zen's rational decision-making, driving skills as well as design sense...=P Just joking!)

In personal/blogging news, I just got back from a random trip to Calgary (where it snowed and hit -2C on the 29th of May... wonderful variety of climate!), and for no comprehensible reason volunteered myself to write a chapter in a week and a half. Felt like I couldn't ask for too much time from someone who's rumoured to be fully capable of writing an entire paper within 24h... anyway, since this blog is not that said chapter, won't be able to do much aside from a Sunday Protist or two, and maybe some random post if something comes up.

Hmmm... or maybe I should write parts of the chapter here first? Anyone wanna hear about Hacrobians (cryptophytes, haptophytes, centrohelids, telonemids, katablepharids and biliphytes)?

Oh, and does anyone have access to Cell Motility and the Cytoskeleton, eg. this article? Every once in a while I come across interesting- and relevant-sounding papers from there, and we apparently don't subscribe to the archives, but not sure I'm bothered/desperate enough to order them through interlibrary loan...

MM21 Hint

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

(to be referenced later)

(to be referenced later)

Obligatory synthetic genome post: clearing up some confusion

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

With the recent hype about the synthesis of a new bacterial chromosome (based on an existing one with a few minor modifications), it seems like media and bloggers alike are confusing 'genome', 'cell' and 'organism', using all three interchangeably. In fact, one does get the feeling that lately the existence of the cell has been largely eclipsed by the genome. As it largely has been outside the field of cell biology, sadly. I think a nice sketch of this majority viewpoint can be represented in this quote from Pharyngula:

"So, if after a period of time, you've got a cell whose DNA was produced by a machine, and whose membranes, enzymes, structural proteins, and metabolic by-products were all produced by that machine-generated DNA or the protein products of that DNA, what makes it a non-synthetic cell?" PZ Myers 22 May 2010

Granted, this was said in defense before some utterly ridiculous claims by crazy people, eg. that this somehow proves creationism. Still, as a biologist, PZ Myers should know better - only the proteins and nucleic acids (incl. ribozymes) have been synthesised by the genome. The membranes and non-protein metabolic products, while influenced by genomic activity, also have a life of their own, having been inherited and modified since the origin of life itself. Furthermore, systems like cellular organisation are also not entirely 'programmed' by the genome, and are also inherited extragenomically.

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

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

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

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

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


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

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

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

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

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


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

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

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

Far, far away, in the land of eternal darkness along the base of the deep sea hydrothermal vents of the Juan de Fuca Ridge lie stretches of surface covered by 'blue mats'.

(Kouris et al. 2007 Mar Ecol)

These blue mats are produced by yet another tube-forming denizen of the hydrothermal vents. To non-tube-dwellers like us they may even look vaguely reminiscent of the much more famous giant tube worms, and the concept is quite similar up until that point.

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

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

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

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

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

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

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

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

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

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

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

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

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

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