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

Snippets of the beauty of sliced axonemes

Look what I found in obscure ultrastructure literature!

It's a star! (Ringo 1967 J Cell Biol)

That's a cross section through the transitional zone of the Chlamydomonas flagellum. The geometric intricacy actually comes from the need to transition from nine triplets of the basal body to the flagellum's nine doublets and a central pair (of microtubules). As evident in the figure below, this can get quite tricky:

Cross-sections through a Chlamydomonas flagellum and basal body. (Ringo 1967 J Cell Biol)

This could be inspiration to some fun baking project...

Speaking of sliced flagella, there are some more wonderful patterns hidden away in the axonemes of rather obscure 'heliozoans' (centrohelids and actinophryids):

Left: Spiral arrangement of microtubules in the axoneme of actinophryid(?) Echinosphaerium. (Jones & Taylor 1981 JCS) Right: Cross section through an axopod of Actionosphaerum (actinoprhyid) containing an axoneme in the centre. m - mitochondrion. (Tilney et al. 1961 JCB)

(axonemes are the cytoskeletal support within axopodia, the long spikey protrusions that make the creatures appear like miniature suns)

And here's one so bizarre it takes three additional diagrams to explain it:

Axoneme of Cienkowskya mereschkovskyi*, a centrohelid 'heliozoan' reportedly closely related to Heterophrys. (Febvre-Chevalier + Febvre 1984 Origins of Life)

*To the slavic ear, this sounds painfully like a masculine adjective applied to a feminine genus name...owww.

And back to basal bodies, parabasalian TEMs are a work of art in their own right. Especially from Joeniids:

Rows of basal bodies in the ciliary region of Pachyjoenia howa. (Brugerolle & Bordereau 2004 Eur J Protistol)

This has nothing to do whatsoever with neither protists nor axonemes, but rather a funky-looking reject from my research images. It's cytoplasmic GFP in a partly lysed plant cell (normally the GFP should look diffuse) Not sure why it does that though, but often lysing cells become very bright, and squashed material is lush with autofluorescence.

My favourite colour is GFP.

Real posts to come soon... still mildly overwhelmed by stuff at the moment. Currently working on gathering up literature both new and old on a supergroup that may or may not actually exist, and is a complete and total mess either way (the new 'Hacrobia'). On top of other things.

To give you an idea, the previously incertae sedis centrohelids are in it, apparently, and their older grouping, "heliozoa", has only recently been dissolved (Nikolaev et al 2004 PNAS), so what is now spread out over at least two supergroups (centrohelids in 'Hacrobia' and actinophryids in Stramenopila) used to be lumped under one category and now you might as well rip all your hair out trying to figure anything out in there. It basically means you have to deal with the damn things on a genus-by-genus, taxon-by-taxon basis. (luckily, they're really cute so it's not that bad ^^) Also, a couple extensive papers happen to be written by The One We Fear, and I'm still denying the fact I may eventually have to actually read them. Grrr. Oh, and add to that the horrible and sometimes altogether lacking availability of older literature, requiring you to assemble epic shopping lists for the inter-library loan people...

Should probably also write another sentence of that manuscript to feel as if I've done something this week. Describe a couple more figures that don't actually exist yet... wish all my control pictures didn't totally suck. Redoing experiments again to get better images of...controls. Sigh. Working on projects in two completely unrelated fields (and different buildings) is a bit draining... /rant

On the non-Sunday-ness of Sunday Protist

Even at the very beginning, I sensed trying a regularly scheduled weekly anything wouldn't work well for me, as I tend to be rather haphazard like that. Furthermore, writing depends a lot on time and inspiration, and the two seldom operate on a regular weekly basis. Sometimes things like those pesky offline obligations (aka 'life', apparently) pile up. Gonna have to keep my blogging slow for a while as I currently have two bosses to satisfy and kind of failing at both. Apparently leaving a lab is no easier than getting into one...

So that's why Sunday Protists come out on random weekdays. The name kind of stuck so I don't really feel like renaming the series; the regulars are well aware of the non-Sunday-ness aspect by now, and the n00bs respected newcomers can suffer mwahaha pick up soon enough.

That said, here's a glimpse of the upcoming post, to keep you in suspense and guilt trip myself into hurrying the hell up to finish it:

(to be referenced later)

Maybe from now on they will start happening on actual Sundays, and that would be creepy and hilarious.

Also, pay absolutely no attention to the loads of Mystery Micrographs I still have to explain and write up. Speaking of which, we still have an outstanding Mystery Micrograph and a Mystery Flagellar Root Apparatus to resolve, both at the free beer* level of difficult by this point ;-)

*If/when budget and geography allow it.

Now if only I could get enough results to satisfy everyone. Science is not cooperating with me lately...grrr. Nor are my writing juices. (Must. finish. results *yawn* section...zzZZZ) Annoyingly enough, annoying complications exciting new data tends to come along just as you're writing up and leaving. Oh gamma-tubulin, why do you insist on getting yourself involved in our already ridiculously complicated plot? *sob* Just gonna pretend that experiment never happened, lalala... actually, just gonna sleep and deal with all this crap tomorrow. Maybe even stop whining about it, but that may be asking for a bit much. But afterwards -- Sunday Protist!