75 posts · 71,163 views

Undergratuate hoping to someday study cell biology and development of various unicellular protists. Currently working on plant development, as well as exploring some evolution of biological, as well as cultural and linguistic, organisms as a hobby on the side. Considers public outreach of science to be crucial to both research funding and research progress itself, as teaching and learning are highly dependent on one another. Hopes to improve own communication skills via blogging. Wonders why she is referring to self in third person...

Skeptic Wonder
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April 25, 2010
08:28 AM
3,034 views

Social onychophorans!

by Psi Wavefunction in Skeptic Wonder

As much as I'm obsessed with protists, I'm a rather promiscuous type when it comes to academic relationships, and thus can find the occasional non-protist cute and interesting. Forgive me if that is 'immoral', but I'm not Christian and thus am not obligated to be intellectually monogamous. So there.Onychophorans (velvet worms) are fucking adorable. Now, whether they are more or less adorable than, say, hypotrich ciliates or Apusomonas proboscidea, is open to debate (I remain loyal to my tribal academic affiliations in that regard), but there's no way you can look at this wonderful creature and not think it's damn cute:Something about onychophoran morphology resonates quite nicely with our innate aesthetic senses...or maybe it's just me. Some of them have really pretty patterns too, or come in absolutely bizarre colours. (Mayer & Herzsch 2007 BMC Evol Biol)A while back someone was waxing poetic about social spiders in class, which led me on quite an adventure. Since I had something very important to do that night, like an exam the following day or something, I got a lot of procrastination done: read about various social spiders (who also have an interesting story of evolutionary dead ends and conflicting levels of selection; oh, and a species with observed cooperative transport of large prey -- apparently fairly rare in arthropods), made my way to social pseudoscorpions (some of them apparently disperse by riding large insects like bugs or beetles), and then I hit upon this paper:Social behaviour in an Australian velvet worm, Euperipatoides rowelli (Onychophora: Peripatopsidae) (Reinhard & Rowell 2005 J Zool)Social behaviour in onychophorans? Seriously!? On a second thought, why the hell not? And then came a complete overload of cute that could've only been enhanced by better images...velvet worms who cuddle!Awww =D Reinhard & Rowell 2005 J ZoolAs cuddly as they may seem, these guys also have a strict social hierarchy involving an alpha female. Reinhard and Rowell (2005) describe a feeding process where a cricket was thrown into the petri dish and attacked by the adult onychophorans (who trap their prey with sticky salivary secretions). After subduing the cricket, the first female fed on the prey for nearly an hour, biting and chasing off any other individual that would approach. After that hour, other females were allowed to feed, and then eventually males and juveniles. Most of the males were feeding after the females left. A feminist's paradise.The interactions between individuals were observed and classified into dominant vs. subordinate: biting and chasing were done by the dominant individual (with the subordinate fleeing) whereas climbing was done by the subordinate and up to the decision of the dominant whether or not to be tolerated:Juveniles were generally left alone and tolerated. Meanwhile, the adults were involved in a constant display of aggression and submission. Females were dominant to the males. When groups of onychophorans from different logs (thus, different social groups) were pairs, individuals of both groups acted aggressively to each other, and despite the males insisting on climbing, no aggregations were formed as they were ruthlessly rejected. Thus, the social groups are stable and at least these onychophorans seem to be capable of kin recognition.The dominance hierarchy seemed largely size-dependent, with smaller females almost always being subservient to the larger individuals. It is believed that as in many other instances of sociality, social behaviour here aids in the cooperative capture of large prey. Curiously, the strict hierarchy when it comes to feeding, with the alpha female hoarding the entire prey, is not known in any other invertebrate.Onychophoran behaviour doesn't receive much attention, perhaps at least partly due to the onychophoran's idea of a perfect habitat not coinciding all too well with that of an ethologist: velvet worms love cold, damp places. So it wouldn't be too surprising if an entire group of social species were eventually discovered, perhaps even with separate origins. In fact, Reinhard and Rowell (2005) state that it is not even known whether sociality may be common for onychophorans in general. On the topic of behaviour, despite their cute and almost fluffy appearance, onychophorans can also be quite vicious. This one devoured a spider bigger than itself:Sticky spit vs. sticky silk. Quite surprisingly, the spit won this battle. (while checking whether this spider actually produces silk, found out that apprently tarantulas secrete adhesive silk from their feet...)It is thought that in order to partake in such complex social behaviours, the onychophoran must have a fairly well-developed region for higher level sensory processing. (considering the complexity of the visual and olfactory cues likely involved in this case, it seems quite plausible. That said, there may well be fairly intricate social interactions out there that do not rely on complex neurology, by executing much simpler rules...) Curiously, they seem to have structures similar to 'mushroom bodies' in arthropods responsible for visual and olfactory processing and regulating complex behaviours. Actually, that was just an excuse to show this stunning image:Onychophoran nervous system. Pseudocoloured to reflect the nerve depth in the confocal projection. Parts of the nervous system arise in a segmented fashion (eg. leg innervation), parts are repeated but not in a segmented way, and they also lack segmental ganglia as those in arthropods. Thus, onychophorans are slightly segmented in some respects, if you will, but still quite different fr... Read more »

Dias, S., & Lo-Man-Hung, N. (2009) First record of an onychophoran (Onychophora, Peripatidae) feeding on a theraphosid spider (Araneae, Theraphosidae). Journal of Arachnology, 37(1), 116-117. DOI: 10.1636/ST08-20.1

Mayer, G., & Harzsch, S. (2007) Immunolocalization of serotonin in Onychophora argues against segmental ganglia being an ancestral feature of arthropods. BMC Evolutionary Biology, 7(1), 118. DOI: 10.1186/1471-2148-7-118

Mayer, G., & Whitington, P. (2009) Neural development in Onychophora (velvet worms) suggests a step-wise evolution of segmentation in the nervous system of Panarthropoda. Developmental Biology, 335(1), 263-275. DOI: 10.1016/j.ydbio.2009.08.011

Reinhard, J., & Rowell, D. (2005) Social behaviour in an Australian velvet worm, Euperipatoides rowelli (Onychophora: Peripatopsidae). Journal of Zoology, 267(01), 1. DOI: 10.1017/S0952836905007090

November 27, 2009
06:44 AM
1,569 views

Heterolobosea II - 'Split Morphology Disorder': amoebo-flagellate transformation in Naegleria

by Psi Wavefunction in Skeptic Wonder

Earlier, in Heterolobosea I, I promised brain-eating amoebae with a split morphology disorder. Having a bit of a morphology fetish, I find the latter topic fascinating, so bear with me as we get into some gory details of cell biology, which I strive to make at least somewhat readable to sane human beings. As always, please let me know if anything is unclear, or *gasp* inaccurate...Fundamentals of cellular morphologyMost organisms strive to have some semblance of shape (including bacteria). To crudely simplify matters, in the style of biochemistry, cells are sphaerical double membraned lipid vesicles. Thus, by default, a cell 'wants' to be a round blob. That would be it's natural state.But most cells are not round blobs. In fact, they can have some rather complex shapes like metazoan neurons, forams, parabasalians or the endlessly weird and sophisticated ciliates. The deeper you venture into the realm of protist diversity, the more awe-inspiring the cornucopia of variety that is cell morphology. Luckily, this vast variety also has some order to it, for much of it happens to fall into two fundamental 'genres' of cellular morphology: flagellates and amoebae*. Of course, as with anything in biology, there are exceptions, and things that have a comfortable niche in-between. Unicellular organisms also have this tendency to construct cortical of extracellular structures, which can have a large influence on their shape. But the key determinant of cellular morphology remains the cytoskeleton, and the composition of the cytoskeleton largely determines which of the two categories the cell allies to. The cytoskeleton is an intricate, often highly dynamic, complex system; it is a misconception to see cells as bags of cytoplasm with organelles floating about -- the innards of a cell are strictly regulated and usually connected to various cytoskeletal and membraneous elements. Things don't just float about aimless inside there.*There's also a third type, the cyst, which is basically a lack of morphology (rounded up cell) usually with external protection of some sort. It often lacks any elaborate cytoskeletal organisation, both actin- and tubulin-based. Cysts are often used for mitosis or meiosis, as well as resting through periods of unfavourable conditions.There are two main component systems of the cytoskeleton: actin and tubulin, ignoring the plethora of miscellaneous proteins that have been used for various structural jobs. You are likely familiar with microtubules as spindle fibres during mitosis. You may also be familiar with actin as a key player in cell motility and morphology in animal systems. Tubulin is also important for the flagellar apparatus -- we've yet to find one composed of actin (and probably with good reason). Actin is involved heavily in endomembrane trafficking within a cell, as well as endo- and exocytosis. If interested, this week's issue of Science has a nice overview of actin in morphogenesis and cell movement.Their roles in morphogenesis, the formation of morphology (in this case, cellular), are much less clearly defined. Furthermore, it depends largely on the species -- plants, for example, rely very heavily upon microtubules for morphology, with actin being a minor player. Interestingly, plants also lack centrioles or basal bodies, except for in some gametes if I recall. Thus, the mitotic spindle in plants (and diatoms) forms entirely without centrioles. Yeast cells can also do mitosis without basal bodies if you surgically remove them. It seems like the characteristic centriole arrangement at mitosis is a way to ensure their inheritance in both daughter cells, rather than organising the spindle. More on this later, it will become relevant.Amoeboid cells, as you may know, are primarily actin-based. In fact, amoebozoans tend to suck at internal microtubules, except for spindle formation at mitosis. They hate tubulin about as much as plants hate actin. Actin-based cells don't have to be amorphous -- they are still able obtain complex morphologies like that of neurons (although there may be some serious tubulin involvement in that. My knowledge of animal cell biol is rather pathetic). But there is a positive correlation between amoeboid-ness and actin-ness ('actinity'?). Turns out, the entire unikont clade, if it exists (ok, opisthokonts and amoebozoans), seems to really prefer actin over tubulin.In contrast, flagellates are primarily tubulin-based -- of course, they still use actin for some intracellular work, but the shape depends largely on the whims of the 'tubes (microtubules, in the slang of our local plant cytoskeleton lab...). Perhaps not relying much on flagella in the amoeboid case allows them to lose so microtubule organisation pathways, thereby switching to actin; flagellates tend rely heavily on intact tubulin systems, and may thus be less prone to losing their structure. Also, if you're a flagellate, you kind of need shape for a modicum of streamlining -- try swimming around as a flattened reticulate blob of some sort! Keep in mind that life at that scale is very different -- viscosity becomes a crucial factor when considering unicellular motility. Perhaps being hydrodynamic isn't even as important as simply retaining shape. Otherwise you'd be like a blob of molasses trying to swim through a sea of maple syrup. Not gonna get very far.Whatever the reason, amoeboid cells tend to have a predominantly actin-based cytoskeleton; whereas flagellates have a penchant for tubulin. Of course, not all organisms are decisive enough to make this committment, so we've got amoeboflagellates in the middle:But your conventional amoeboflagellates are only the beginning -- plenty of cells, especially Cercozoans for some reason, fancy transitioning between being more amoeboid or more flagellate. But few cells actually dispense with flagella and basal bodies altogether, only to form them anew when special conditions arise.As we've seen earlier, de novo centriole formation was until recent considered fairly impossible (ignoring the organism we're about to prod at). As we all know, there must be a reason for the guaranteed inheritance of centrioles at mitosis, and they must be hard to form. After all, tubulin nucleation doesn't happen randomly very often, and new microtubules seldom start without some sort of 'seed' (gamma-tubulin), as the tubulin has to form a ring prior to growing into a tube, which isn't likely to happen on its own. (Actin, on the other hand, is only two monomers wide, and can form spontaneously relatively easily) Thus, for basal bodies to pop out of nowhere is also rather unlikely, but, as we're about to see (and as several more recent experiments show in yeasts and animals), de novo centriole formation can and does happen.Naegleria and Tetramitus: Heteroloboseans with 'split morphology disorder'Several paragraphs into our journey, we've yet to see any Heteroloboseans. Let's change that. Meet Naegleria, famous to medical biologists as a brain-eating opportunist, and to real biologists as the master of de novo flagellar creation:Naegleria gruberi. (by Jonckheere at ToLWeb)And before someone accuses me of focusing on biomedically relevant organisms, Tetramitus,... Read more »

Dingle AD, & Fulton C. (1966) Development of the flagellar apparatus of Naegleria. The Journal of cell biology, 31(1), 43-54. PMID: 5971974

Fulton C, & Walsh C. (1980) Cell differentiation and flagellar elongation in Naegleria gruberi. Dependence on transcription and translation. The Journal of cell biology, 85(2), 346-60. PMID: 6154711

González-Robles, A., Cristóbal-Ramos, A., González-Lázaro, M., Omaña-Molina, M., & Martínez-Palomo, A. (2009) Naegleria fowleri: Light and electron microscopy study of mitosis. Experimental Parasitology, 122(3), 212-217. DOI: 10.1016/j.exppara.2009.03.016

Outka DE, & Kluss BC. (1967) The ameba-to-flagellate transformation in Tetramitus rostratus. II. Microtubular morphogenesis. The Journal of cell biology, 35(2), 323-46. PMID: 4861775

WALSH, C. (2007) The role of actin, actomyosin and microtubules in defining cell shape during the differentiation of Naegleria amebae into flagellates. European Journal of Cell Biology, 86(2), 85-98. DOI: 10.1016/j.ejcb.2006.10.003

October 5, 2009
05:20 AM
1,543 views

Sunday Protist - Euglyphids

by Psi Wavefunction in Skeptic Wonder

I'm going to be lazy and leech off the Mystery Micrograph again. None of you saner people (non-protistgeeks) seem to have taken advantage of the massive handicap, and subsequent hint. Seriously, type in "testate amoebae" in Google image search, and it's on the first page! Perhaps I should do a tutorial on some methods of attacking those mystery images...Quite shockingly(not!), Opisthokont got the last one. I agree with his statement that that was like shooting fish in a barrel, but easier since fish are actually difficult to shoot at from air due to refraction, etc. The organism behind the shell in the mystery micrograph was...Euglypha!(Wikipedia; Euglyphid test)Euglypha morphologically belongs to the polyphyletic 'testate amoebae', but is phylogenetically quite distant from your garden variety test-building amoebozoans, like Arcella and Difflugia. Euglyphids are cercozoan rhizarians. Since those words likely mean nothing to the vast majority of the human population, here's a 'map' of Rhizaria in my Coelodiceras (Phaeodaria) post, and an overall tree of eukaryotes can be found here. They can often be found in moss samples, but are also present in soil and freshwater environments. Their test scales are made of silica, and preserve quite decently as fossils. Speaking of which, I apparently may have a slight fetish for unicellular microfossils:(Javaux 2007 in Eukaryotic Membranes and Cytoskeleton: Origins and Evolution ed. Jékely; 10 - fossil; 11 - modern Euglyphid; 12 - VSM - 'vase-shaped microfossil' (micropaleontological equivalent of mycologists' LBM - 'little brown mushroom' ?) with holes possibly caused by predation; fossils ~750My old)Fast forward 750My back to the present, the modern euglyphids are about as diverse as they are understudied:(Lara et al. 2007 Protist; tree of Euglyphids)Images of Euglyphid diversity, shamelessly stolen from the same paper:(Lara et al. 2007 Protist; Euglyphid SEMs, scalebar 50um except for E,F,H, where it's 10um. A - Assulina; B- Placocista; C,D - Euglypha ciliata & compressa; E - Corythion; F - Trinema; H,G - Euglypha penardi)Unfortunately, finding nice plates full of euglyphids is rather difficult, since until quite recently, they were lumped together with testate Amoebozoans. Also, since euglyphids fossilise, they seem to be mostly studied by paleontologists, who seem to have an 'interesting' relationship with systematics of the living. Where 'interesting' entails being at least a couple decades out of date. Well, they are millions of years in the past...Paulinella can be argued to be particularly interesting - it is a case of an independent event of primary plastid endosymbiosis. Why this is interesting can be seen in this really nice overview:(Keeling 2oo4 Am J Bot (free access); overview of plastid endosymbiosis - the 'Pacmen' are pretty awesome! Interestingly, if the Chromalveolate Hypothesis is correct, this would mean that Paulinella already had a plastid in its ancient past. However, it would've been a red algal plastid of a different cyanobacterial origin, not a Synechococcus-derived cyanelle)Cyanelles are photosynthetic endosymbionts/organelles - they differ from plastids by retaining some prokaryotic features like the peptidoglycan wall. Among the conventional plastid-bearing algae, glaucophytes carry cyanelles from the primary cyanobacterial endosymbiotic event which eventually led to plant chloroplasts and most algal plastids. In sequence comparisons, Paulinella cyanelles branch with the cyanobacterium Synechococcus, and retain much of the gene order, suggesting a fairly recent endosymbiosis with Synechococcus (... Read more »

BODYL, A., MACKIEWICZ, P., & STILLER, J. (2007) The intracellular cyanobacteria of Paulinella chromatophora: endosymbionts or organelles?. Trends in Microbiology, 15(7), 295-296. DOI: 10.1016/j.tim.2007.05.002

Javaux EJ. (2007) The early eukaryotic fossil record. Advances in experimental medicine and biology, 1-19. PMID: 17977455

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

KEELING, P., & ARCHIBALD, J. (2008) Organelle Evolution: What's in a Name?. Current Biology, 18(8). DOI: 10.1016/j.cub.2008.02.065

LARA, E., HEGER, T., MITCHELL, E., MEISTERFELD, R., & EKELUND, F. (2007) SSU rRNA Reveals a Sequential Increase in Shell Complexity Among the Euglyphid Testate Amoebae (Rhizaria: Euglyphida). Protist, 158(2), 229-237. DOI: 10.1016/j.protis.2006.11.006

NOWACK, E., MELKONIAN, M., & GLOCKNER, G. (2008) Chromatophore Genome Sequence of Paulinella Sheds Light on Acquisition of Photosynthesis by Eukaryotes. Current Biology, 18(6), 410-418. DOI: 10.1016/j.cub.2008.02.051

THEISSEN, U., & MARTIN, W. (2006) The difference between organelles and endosymbionts. Current Biology, 16(24). DOI: 10.1016/j.cub.2006.11.020

Yoon, H., Reyes-Prieto, A., Melkonian, M., & Bhattacharya, D. (2006) Minimal plastid genome evolution in the Paulinella endosymbiont. Current Biology, 16(17). DOI: 10.1016/j.cub.2006.08.018

November 4, 2009
07:17 AM
1,394 views

MM#07 Answer: Haplosporidia -- spores with lids

by Psi Wavefunction in Skeptic Wonder

Johan, our resident micropaleontologist, got this past week's Mystery Micrograph - congratulations! The answer was: Haplosporidia. Johan went the extra mile and identified its genus: Minchinia. This one is M.mercenariae, from Ford et al. 2009 JEM:Minchinia mercenariae (Haplosporidian) from the clam Mercenaria mercenaria; 13 - SEM of spore with arrow pointing to the opening; 12 - spore with a closed hinged lid; 2 - Minchinia's 'habitat' in the clam connective tissue (which it has taken over), while the digestive epithelia (DE) remain untouched. (Ford et al. 2009 JEM)Haplosporidia are unicellular parasites known for their peculiar jug-with-a-lid spores. Presumably those spores get inside the host and the hinged lid opens (cute!), releasing the organism, but I was unable to find any details of their invasion process. After finding their way inside the host and excysting, they exist in an amoeboid stage for a while, perhaps to quickly spread throughout the host. They then proceed to form multinuclear plasmodia inside host tissues and form spores via palintomy (cellularisation) (kinda like apicomplexans and some dinos), and release the spores.Many of them are commercially important due to their taste in shellfish. However, they seem to linger in obscurity despire that fact. In fact, one wonders whether their complete life cycles are known yet. Parasites are notorious for spanning multiple species at times, and it's hard to rule out a secondary host of some sort. However, the presence of what seems to be a complete set of life cycle stages within one sample suggest a single host at the moment, but intermediates remain possible (Azavedo et al. 2008 J Parasitol).TEM of Haplosporidium lusitanicum; Nu - nucleus; Sp - 'spherule' (multivesicular body) Hp - haplosporosome; Op - operculum ('lid'). Right: drawing of H.montforti; w- spore wall, F - filament (Left: Azevedo 1984 J Parasitol; Right: Azavedo et al. 2006 J Invert Pathol)There are three major genera of Haplosporidia, which are quite distinct morphologically. See this nice page describing them, with pictures (thanks, Johan!). They used to be categorised based on spore ornamentation, but that turned out to be rather messy. Haplosporidia reside in Rhizaria (TC-S & Chao 2002), close to Cercozoa, as shown in the aforementioned website and in the Pawlowski & Burki 2009 tree. Rhizarians have gote so much cool stuff it ain't funny.Next up we will have a glimpse of Paramyxids, which seem to be related to today's topic. They also have really interesting lifestyles. TC-S and Chao (2002, 2003) place them in "Ascetosporea" (Sprague 1979), sister to Haplosporidians, and Pawlowski (2008) doesn't seem to mind, so that's enough excuse to talk about them. I mean, I just READ a few paragraphs of TC-S, we can't let that effort go to waste! Besides, not like a little bit of long branch attraction has ever harmed anyone...But that'll be later this week. I shouldn't really be reviewing Rhizaria right now or anything, even though that would be kinda fun!References:Azevedo, C. (1984). Ultrastructure of the Spore of Haplosporidium lusitanicum sp. n. (Haplosporida, Haplosporidiidae), Parasite of a Marine Mollusc The Journal of Parasitology, 70 (3) DOI: 10.2307/3281564AZEVEDO, C., BALSEIRO, P., CASAL, G., GESTAL, C., ARANGUREN, R., STOKES, N., CARNEGIE, R., NOVOA, B., BURRESON, E., & FIGUERAS, A. (2006). Ultrastructural and molecular characterization of Haplosporidium montforti n. sp., parasite of the European abalone Haliotis tuberculata Journal of Invertebrate Pathology, 92 (1), 23-32 DOI: 10.1016/j.jip.2006.02.002Azevedo, C., Casal, G., & Montes, J. (2008). U... Read more »

Azevedo, C. (1984) Ultrastructure of the Spore of Haplosporidium lusitanicum sp. n. (Haplosporida, Haplosporidiidae), Parasite of a Marine Mollusc. The Journal of Parasitology, 70(3), 358. DOI: 10.2307/3281564

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

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

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

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

July 21, 2009
04:24 AM
1,311 views

Sunday Protist - Dinoflagellate eats Chaetoceros (gory) (for real this time!)

by Psi Wavefunction in Skeptic Wonder

(Yesterday's attempts were derailed by having to shred some New Age BS instead)The media seems to be obsessed with posting pictures/videos of things eating things; apparently that generates a lot of revenue interest. Since I'm neck deep in syntactic trees and X-bar theory (Yes, I voluntarily, by my own will, as an elective, take third year syntax & grammar courses. Also, I dislike Chomsky. Clearly, I am very sane), I'm going to resort to posting gory pictures: (and yes, I mixed up Chaetoceros with Skeletonema in the previous post. Sue me. =P Not that I pursued the topic any further over there)Following images from Jacobson & Anderson 1986 J. Phycol, unless otherwise stated)A dino (Protoperidinium) extends its pallium (feeding pseudopod) to devour a sizeable chain of diatoms (Chaetoceros); why bother bringing food to your mouth/gut when you can bring your gut to your food instead?Yes, it eats that whole thing! Super Big Macs and 12" subs would be no problem for Protoperidinium, although this fine diner probably actually has standards.More gore:So cute, yet so voracious! NOM NOM NOM /memeplexDetail of feeding apparatus:(Jacobson & Anderson 1992, J Phycol)The pallium can be described as a 'feeding' veil, a feature found in some thecate (armoured) predatory dinos, which cannot devour large prey as their expansion is limited by the thecal plates (an alternative is myzocytosis, or 'drinking through a straw'). The dino then proceeds to digest its prey much like a fungus - by secreting digestive enzymes and consuming the useful products (from ToLweb Dino page).Diversity of dining etiquette among knightly armoured dinoflagellates:Dinoflagellate feeding is a fascinating topic in itself, but I should probably abstain until after the upcoming final. Added to post topic queue.I honestly intended for this post to consist of one picture; then I got carried away. Scholarly literature is addicting (that's normal, right? *crickets*)/massive procrastination forayJacobson, D., & Anderson, D. (1986). THECATE HETEROPHIC DINOFLAGELLATES: FEEDING BEHAVIOR AND MECHANISMS Journal of Phycology, 22 (3), 249-258 DOI: 10.1111/j.1529-8817.1986.tb00021.xJacobson, D., & Anderson, D. (1992). ULTRASTRUCTURE OF THE FEEDING APPARATUS AND MYONEMAL SYSTEM OF THE HETEROTROPHIC DINOFLAGELLATE PROTOPERIDINIUM SPINULOSUM1 Journal of Phycology, 28 (1), 69-82 DOI: 10.1111/j.0022-3646.1992.00069.xAlso see: Gaines & Taylor 1984 J Plankton Research "Extracellular Digestion in Marine Dinoflagellates"... Read more »

Jacobson, D., & Anderson, D. (1986) THECATE HETEROPHIC DINOFLAGELLATES: FEEDING BEHAVIOR AND MECHANISMS. Journal of Phycology, 22(3), 249-258. DOI: 10.1111/j.1529-8817.1986.tb00021.x

Jacobson, D., & Anderson, D. (1992) ULTRASTRUCTURE OF THE FEEDING APPARATUS AND MYONEMAL SYSTEM OF THE HETEROTROPHIC DINOFLAGELLATE PROTOPERIDINIUM SPINULOSUM1. Journal of Phycology, 28(1), 69-82. DOI: 10.1111/j.0022-3646.1992.00069.x

September 12, 2009
09:45 PM
1,253 views

A quick note on flagella, and their evolution

by Psi Wavefunction in Skeptic Wonder

First off, 'flagella' and 'cilia' tend to be used interchangeably. I prefer to call them flagella, out of habit, but there's some who argue 'flagellum' should be reserved for bacteria, who have a fundamentally different system from us; while we have 'cilia'. Another note: 'flagella' is spelled with two l's, 'cilia' with one. Took me about two months of protistology to learn that. (also, I consistently spelled 'axopodia' as 'auxopodia', thanks to a plant biology research background. Curse you, auxin!)Interestingly the flagellar structures seem to be fairly conserved in evolution, and are often used in taxonomy. Most eukaryotes are fundamentally biflagellate, meaning their flagellar systems, whatever they are, are likely derived from modifications of an ancestral biflagellate form, and retaining the double basal bodies. Flagella can be lost, but the basal bodies that anchor them tend to remain behind. Conversely, basal bodies can be duplicated, as they have, for example, in parabasalia, which are tetraflagellate; entire basal body units (kinetids) can also be multiplied, up to extremes such as in ciliates. (the developmental organisation of ciliate flagella is an endlessly fascinating subject, and if all goes well, would be my research focus after BSc. =D *knocks on her head wood)In contrast, a few eukaryotes have what is fundamentally a single flagellum - those are unikonts, which include amoebozoa (eg. cellular slime moulds) and opisthokonts (ass-tails, eg. fungi, choanoflagellates...and us). It is intuitive to think of flagella as propelling the organism forward. But not everything is about sperm: most eukaryotic organisms actually pull themselves by flagellar motion, thereby defining the location of the flagellum as the anterior end, rather than posterior. Another distinction is between isokonts (equal flagella) and heterokonts (unequal flagella) - in the former, the two flagella are structurally identical, whereas in the latter they differ, often with little protrusions (mastigonemes) lining one of them.Actually, scratch everything I just said about opisthokonts and amoebozoa being unikonts together. Missed a memo... there's this amitochondriate amoeba Breviata (TCoO post here and picture here), previously of uncertain placement or classified as an archamoeba. Despite having a single flagellum, it seems to have a double basal body, one of them unflagellated (Walker et al. 2006 JEM). Turns out that evidence suggests it's a basal amoebozoan, which would kill TC-S' unikont/bikont division (indicated in grey below):(Roger & Simpson 2009 Curr Biol; numbers indicate ancestral number of basal bodies/flagellar unit, asterisk indicates one basal body is unflagellated, and the 2+ in Breviata indicates there may have been more that two basal bodies/unit.)So to summarise:kinetid - unit of basal bodies + flagella; not all basal bodies must have a flagellum (but the flagella must be anchored to a basal body each)opisthokont - organisms with posterior flagellation; most eukaryotes have flagella at the front of their movement.heterokont - both (or more) flagella structurally differentisokont - both (or more) flagella are the sameunikont - organisms with single basal body/flagellum per kinetidbikont - organisms with double (or more) basal body per kinetidmastigonemes - little protrusions regularly lining a flagellum; for increasing a flagellum's surface area.centriole/basal body - generally interchangeablecilium/flagellum - generally interchangeable(kont means tail, by the way)I noticed I throw those terms a lot in other posts without really explaining them; so hopefully this post can be some sort of reference, just in case!There's more to it, but someone has some protist-oriented microscopy for me to do. I love Saturday nights!Roger, A., & Simpson, A. (2009). Evolution: Revisiting the Root of the Eukaryote Tree Current Biology, 19 (4) DOI: 10.1016/j.cub.2008.12.032WALKER, G., DACKS, J., & MARTIN EMBLEY, T. (2006). Ultrastructural Description of Breviata anathema, N. Gen., N. Sp., the Organism Previously Studied as "Mastigamoeba invertens" The Journal of Eukaryotic Microbiology, 53 (2), 65-78 DOI: 10.1111/j.1550-7408.2005.00087.x... Read more »

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

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

October 26, 2009
04:48 AM
1,232 views

Sunday Protist - Nucleariids

by Psi Wavefunction in Skeptic Wonder

While exploring the various corners of the protistan world, I've been neglecting our close relatives - the Opisthokonts. Let's quickly remedy the situation.A couple weekends ago I had some pond water on hand, and it turned out to be quite productive. I was on a bit of a heliozoan and amoeba spree when I encountered these things:At first it seemed like a 'heliozoan'*, but wasn't quite round enough. Then I noticed filopodia. Heliozoa with filopodia? Nah. But it didn't quite qualify for your typical amoebozoan either, so I was rather confused. To make it even more fun, some of them had spicules sticking out (see the optical section through the top in the rightmost image above). Then I started seeing similar things without spicules, and they seemed to be related:So I spent an hour or so trying to figure this one out**. They turned out to be Nucleariids, a group of filose amoebae basal to fungi. The top one appears to be Rabdiophrys, which has been, in fact, confused with or considred as heliozoa; the bottom one may well be Nuclearia itself - some mixed images of Nuclearia and Rabdiophrys can be found here.Nucleariids are filose amoebae, meaning they produce long thin thread-like pseudopodia without internal microtubule bundles (which would be axopodia, like those of 'heliozoa'). They are on the fungal side of the great cauldron of Miscellaneous Opisthokonts sometimes called 'Choanozoa' by TC-S. Other times, he seems to reserve Choanozoa for those on the animal side of opisthokonts. Yet other times, he seems to fail to piss off cladists and actually use monophyletic terms. Which one of those is 'in season' likely depends on the monsoon patterns in Bangladesh. Or the temperature fluctuations on one of Jupiter's moons. Further research needs to be done. Materials include ethanol and acid, if I recall. Anyway, here's a damn tree already:(Ruiz-Trillo et al. 2007 Trends Genet; Opisthokonta - our fellow ass-tailed relatives)The Choanozoa/Misc Opisthokonts actually tend to be insignificant-looking amoeboid things most of the time, except for Choanoflagellates, which are these really cute lorica-building flagellates with a cone of microvili surrounding the flagellum on their asses. Speaking of which, opisthokont means 'posterior flagellum', or, less pretentiously, ass-tail. Some fungi (chytrids) have flagellated motile spores, and their flagellum happens to be on the posterior relative to the cell's swimming direction. As mentioned earlier, in most eukaryotes the flagellum performs a pulling action, whereas the opisthokont flagellum pushes the cell. This actually poses some problems for filter-feeding organisms, which use flagella for propelling food particles towards their 'mouth', and may be part of the reason some Choanoflagellates started aggregating into colonies - to stop themselves from moving away from their prey when using flagella.Here's another specimen of putative Rabdiophrys:And yet another:I can keep going:Seriously, I've got A LOT of those guys!Switching to Nuclearia now:Note the absense of spicules:Hey, it could be worse: I also have a freaking pile of non-descript random amoeboid things. SMALL non-descript random amoebae.There's a 'cellular' slime mould that turns out to be among the nucleariids: Fonticula (Brown et al. 2009 MBE; advance publication). The poor thing has been lumped with everything from Acrasids to cellular slime moulds, and subsequently neglected for a couple decades. This is the first documented case of slime mould aggregation in opisthokonts, which may contribute a thing or two to the evolution of fungal and metazoan multicellularity. (off topic note: ciliates can aggregate too!)So now we've finally covered an opisthokont. Phew. That was bugging me.* Just FYI, heliozoa are not a real group - they're united by their sun-like morphology, axopodia and nothing else...** Being too impatient to use dichotomous keys (which also simply fail to exist for some organisms), I use a combination of papers, websites and Google image search to find stuff. Basically, you find something that lists a bunch of organisms in the vicinity of what you think it might be, and then look to see if any of the pictures might match. If it's something so obscure that even Google is unaware of its existence, you have to sift through ancient forlorn journal articles sometimes, but usually it doesn't take that long to cross another name off the list.If completely stumped, I'll just start googling random morphological descriptions in both scholar and image search, until hitting something familiar. As random and haphazard and unprofessional as this method is, it's actually much more effective than figuring out dichotomous keys, in my opinion. Especially when you're unfamiliar with the ... Read more »

Brown, M., Spiegel, F., & Silberman, J. (2009) Phylogeny of the "forgotten" cellular slime mold, Fonticula alba, reveals a key evolutionary branch within Opisthokonta. Molecular Biology and Evolution. DOI: 10.1093/molbev/msp185

RUIZTRILLO, I., BURGER, G., HOLLAND, P., KING, N., LANG, B., ROGER, A., & GRAY, M. (2007) The origins of multicellularity: a multi-taxon genome initiative. Trends in Genetics, 23(3), 113-118. DOI: 10.1016/j.tig.2007.01.005

September 19, 2009
05:06 AM
1,231 views

'Crhaptophytes' and the Chromalveolate Hypothesis

by Psi Wavefunction in Skeptic Wonder

Procrastination with about a million things (including overdue blog posts) is the perfect time to blog a freshly published paper. Although I can't quite figure out how to make the preceding sentence make any sense syntactically...Warning: This post contains copious amounts of obscure phylogeny and taxonomy. Discussed by a cell biologist. Proceed with caution.I've probably carelessly alluded before to the Chromalveolate Hypothesis by Cavalier-Smith (eg. 2002 Curr Biol). In any case, I tend to go by the assumption it may be correct, since I'm a cell biologist and therefore required by federal law not to care about evolution. There's powerful/annoying(depending which side you're on) evidence pointing both ways, so the thing is a bit of a mess. I know, mess in protistological taxonomy? No fucking way!Let's zoom in to one of Tom Cavalier-Smith's many warzones:(based on Keeling et al 2005 Trends Ecol Evol; bonus marks for recycling diagrams from past talks, ignore box)The green dots indicate the presence of photosynthesis in respective lineages. This is just to get an idea of where these things are - members of Chromalveolata include ciliates, dinoflagellates, apicomplexans (eg. Plasmodium, responsible for malaria), diatoms, kelps, oomycetes (eg. Phytophthora, the other organism behind the Irish famine, besides H.sapiens and their sadistic and incompetent governance.) and the possibly less familiar Haptophytes (chalk in cliffs of Dover).Now that seems like a rather diverse mix of stuff to have in one kingdom, and it is. You have multiple independent instances of multicellularity, lifestyles from parasitism to phagotrophy to photosynthesis to osmotrophy (think fungi) to myxotrophy (eg. photosynthetic predators) and beyond. It's rather hard to believe that the entire grouping may be held together by... a single red algal plastid endosymbiosis event. (TC-S 2002) And some don't. In fact, the evidence is rather strong both for and against what is called the Chromalveolate Hypothesis: where 'chromists' (stramenopiles + cryptophytes and haptophytes) and alveolates share a single secondary endosymbiosis event.If the Chromalv. hypothesis is accurate, you would expect many lineages to be photosynthetic or contain relic plastids. Furthermore, you'd expect lineages devoid of plastids to at least contain some relic plastid-derived genes in their genome. Those characters should also point towards a single origin, as opposed to two or more independent endosymbiosis events (eg. from different red algae).I've prepared an overview of what the Chromalv. hypothesis 'looks like', hopefully not plagued by too many inaccuracies:(This almost looks like a TC-S diagram. I guess that's just inevitable. Red - groups containing photosynthetic lineages with a red-algal derived plastid; Green - group with green algal secondarily derived plastid.)Going clade by clade, some evidence that supports single chromalv. plastid origin is:- Apicomplexa, a vast group of intracellular parasites such as not-so-friendly(to us) critters like Plasmodium and Toxoplasma, have been found to posess reduced plastids, called apicoplasts (eg. reviewed in Waller & McFadden 2005 Curr Issues Mol Biol). Malaria turns out to be an algal disease. There's plenty of other examples of algae-turned-parasites, but we've got a TC-S hypothesis to cover...- Basal to Apicomplexa is a photosynthetic alga called Chromera, with a red-algal-derived plastid, which further supports an algal origin of 'Apies'. (Moore, Oborník, Janouškovec et al. 2008 Nature)- Dinoflagellates, Ochrophytes (group containing kelps and diatoms), Cryptomonads and Haptophytes all have photosynthetic members with a certain red-algal derived plastid. Now, the fuss is about whether they all got their plastids once, with the plastid-less lineages having lost them through time, or multiple times within the Chromalveolate kingdom.- (more evidence is discussed in Keeling 2009 JEM)Refer to the diagram below. Endosymbiosis is accepted by everyone but Marguilis to be a very unlikely event, and therefore very unparsimonious to postulate for every photosynthetic lineage you see. You would expect some lineages to lose their photosynthetic ability, and even their plastids altogether. However, since endosymbiosis usually results in gene transfer to the host, you should be able to find plastid-derived genes in most lineages. This means that both plastid-bearing and plastid-less lineages should be distributed fairly haphazardly, without too much non-photosynthetic stuff clumping around basally. Unfortunately, that is annoyingly not the case entirely:Prior to the discovery of Chromera and apicoplasts, the Chromalv. hypothesis was rather weak in Alveolata, with ciliates and apies both being non-photosynthetic. Furthermore, the basal lineages of Stramenopiles are also non-photosynthetic, with things like 'fungal' oomycetes, labyrinthulids, opalinids ('ciliat... Read more »

Moore, R., Oborník, M., Janouškovec, J., Chrudimský, T., Vancová, M., Green, D., Wright, S., Davies, N., Bolch, C., Heimann, K.... (2008) A photosynthetic alveolate closely related to apicomplexan parasites. Nature, 451(7181), 959-963. DOI: 10.1038/nature06635

Cavalier-Smith, T. (2002) Chloroplast Evolution: Secondary Symbiogenesis and Multiple Losses. Current Biology, 12(2). DOI: 10.1016/S0960-9822(01)00675-3

KEELING, P., BURGER, G., DURNFORD, D., LANG, B., LEE, R., PEARLMAN, R., ROGER, A., & GRAY, M. (2005) The tree of eukaryotes. Trends in Ecology , 20(12), 670-676. DOI: 10.1016/j.tree.2005.09.005

KEELING, P. (2009) Chromalveolates and the Evolution of Plastids by Secondary Endosymbiosis. Journal of Eukaryotic Microbiology, 56(1), 1-8. DOI: 10.1111/j.1550-7408.2008.00371.x

Okamoto, N., Chantangsi, C., Horák, A., Leander, B., & Keeling, P. (2009) Molecular Phylogeny and Description of the Novel Katablepharid Roombia truncata gen. et sp. nov., and Establishment of the Hacrobia Taxon nov. PLoS ONE, 4(9). DOI: 10.1371/journal.pone.0007080

REYESPRIETO, A., MOUSTAFA, A., & BHATTACHARYA, D. (2008) Multiple Genes of Apparent Algal Origin Suggest Ciliates May Once Have Been Photosynthetic. Current Biology, 18(13), 956-962. DOI: 10.1016/j.cub.2008.05.042

August 18, 2009
05:27 AM
1,227 views

The Myth of Evolutionary Ascent

by Psi Wavefunction in Skeptic Wonder

Many physicists whine about the public's grotesque misunderstanding of basic concepts like centripetal force and electromagnetism. Some of those very physicists often like to consider biology to be a simple subject, delivering profound lines like "people still study evolution???". Of course, how can anyone have any problems understanding something that barely uses any formulas! Of all sciences, biology uses the smallest portion of the Greek alphabet, and hasn't even moved on to Hebrew yet. How can there be much work in a field unless Norse runes must be invoked to complete a PhD thesis without assigning multiple meanings to symbols? Life is a giant differential equation, and unless you're cracking your skull open over one you're not doing it right! Quantify and model everything!!oneBut seriously, how can any one misunderstand something as simple as evolution? Let's go on a bit of a rant adventure and find out!The Ladder to ApocalypseThere is a classical image frequently used to represent evolution. This appears on the cover of some editions of The Origin:We really like this picture. It's polite to our fragile feelings. It dares not offend (too much) our sanctum of superiority. Fine, the abyss between Man and Animal may not be so sharp after all - we may actually be related to the beasts. Fine, we'll even let Man arise from Animal, and none other than the coarse graceless ape. But at least we can still keep our final tatter of self-importance: for while but a small chapter in the story of life, this story was written for us. We are the ultimate Species, the crown of the tree of life. How flattering seems the depiction of progress, this procession of life from the lowly ape to the fully-formed proudly-standing masterpiece of evolutionary craftsmanship!This view is reflected in the vernacular use of 'evolution'; exposed blatantly in cases like the Russian phrase "through hard work monkeys lost their tail and became man" (although that may be just my family, who knows...) and more the familiar Japanese phenomena like this:You may laugh, but this is a rather accurate representation of the public's (and some biologists') understanding of evolution. One may recall the oft-recited progression of life from bacteria to amoebae to sponges, fish, monkeys, and us. While preparing a talk for some compsci students, I realised Toxoplasma may have a slightly different opinion: (and almost got an aneurysm making this)Since our good friend Toxo actually managed to parasitise most mammals and birds, it clearly must preside over the crown of our lineage. Opisthokonts(well, unikonts) are but a basal lineage to Chromalveolata, of which Toxo is a proud empress. All hail T.gondii, the fierce goddess of the crown eukaryotes!But seriously, does anyone else get a bit tired of constantly hearing about how the stupid lowly amoebae somehow congregated together and became multicellular and wise and awsome? For the record, the sister group to animals is choanoflagellates, who are not amoebae! Our amoeboid cell types arose secondarily, since after all there isn't that much of a problem in doing both... (see Naegleria, which can switch between amoeboid and flagellate forms in our particular path, outlined in blue here:Homonids being basal to chimps, of course. We stopped evolving, they moved on. So how does it feel to be a basal lineage anyway? Still 'primitive'?Furthermore, the generation span in the animal lineage tends to be much longer, and among the larger animals we have rather insanely long time periods between heritable genetic modifications (and thus material for selection to play with). This means bacteria, some of which can replicate multiple times a day, until present day have passed through many orders of magnitude more 'versions' of themselves than animals have. In some ways, one can argue bacteria are more advanced than large metazoa. And this view is quite objective, if we only use the number of generations to go by.Now that we've established that prokaryotes rule the world, we could simply concede defeat and go home. However, there still remains a nagging thorn in the side: complexity. If we define complexity strictly as the number of components involved in a given system, one must agree metazoa do have far more components than their bacterial counterparts. That does not make us superior; however, it does raise some further points and misconceptions about directionality of evolution.The evolutionary 'ladder' may be a valid model for one thing: the history of a single lineage, with height representing nothing more than simply the time axis. Complexity has nothing to do with it. Nor does that ladder reach anywhere but the inevitable demise of our Earth at the end of biological time.Evolutionary DirectionalityEvolutionary directionality is a myth, a massive misunderstanding of evolutionary processes. I like to call it 'evolutionary creationism', for it eerily mimics the fairy tale put forth by the 'Intelligent' Design movement, albeit devoid of a few supernatural elements. Often, 'evolutionary creationism' and religiosity can be seen to go hand-in-hand, eg. Simon Conway Morris*. Even some brilliant, quite rational thinkers like Dennett have fallen for the appeal of anthropocentrism, emphasising the rise of human 'consciousness' in the discussion of memetics and devoting an entire chapter to the importance of the intentional stance in evolutionary thinking (1995 Darwin's Dangerous Idea). Consciousness is a topic for another day, but intentionality must be used with great care.Perhaps in some cases it may be useful to assume nature strives towards perfection and survival in order to deduce the 'function' of a certain trait (as in Dennett 1995), but even if this may help, it must be kept in mind that the concept of 'function' itself is an artefact of the human mind. We say the bird's wings are 'for' flying, but this is just a shorthand way of saying "the bird would not be capable of flying without this feature, therefore it is essential for that activity. Furthermore, it seems that flying would suffer the most in the absence of this feature, thus we shall denote this structure's purpose as 'for flying'."This can get murky upon deeper examination. What if these structures have multiple functions? Wings help maintain balance while walking; thus we can add that an additional 'function' of the wings is exactly that. However, if you chop those wings off, the bird's circulatory system would fail. Is a function of wings to keep blood from spilling out? That sounds a bit off. Ok, let's say it never had them in the first place. Then how about escaping predators? The bird would likely fail miserably without its... Read more »

DC Dennett. (1995) Darwin's Dangerous Idea. Darwin's Dangerous Idea. info:/

Collins RA, & Lambowitz AM. (1985) RNA splicing in Neurospora mitochondria. Defective splicing of mitochondrial mRNA precursors in the nuclear mutant cyt18-1. Journal of molecular biology, 184(3), 413-28. PMID: 2413216

LEANDER, B. (2008) Different modes of convergent evolution reflect phylogenetic distances: a reply to Arendt and Reznick. Trends in Ecology , 23(9), 481-482. DOI: 10.1016/j.tree.2008.04.012

LEANDER, B. (2008) A Hierarchical View of Convergent Evolution in Microbial Eukaryotes. The Journal of Eukaryotic Microbiology, 55(2), 59-68. DOI: 10.1111/j.1550-7408.2008.00308.x

SLAMOVITS, C., & KEELING, P. (2008) Widespread recycling of processed cDNAs in dinoflagellates. Current Biology, 18(13). DOI: 10.1016/j.cub.2008.04.054

Stoltzfus, A. (1999) On the Possibility of Constructive Neutral Evolution. Journal of Molecular Evolution, 49(2), 169-181. DOI: 10.1007/PL00006540

July 15, 2009
08:52 AM
1,215 views

"Sunday" Protist - Trichonympha returns!

by Psi Wavefunction in Skeptic Wonder

Finally published today: Extreme Trichonympha sexiness:(Carpenter, Chow and Keeling 2009. Morphology, Phylogeny, and Diversity of Trichonympha (Parabasalia: Hypermastigida) of the Wood-Feeding Cockroach Cryptocercus punctulatus. J Euk Microbiol 56:305-313I stole these while the manuscript was in advance online publication, before the images were shrunk and butchered to fit print quality:The little rod shaped things in 12-15 are some bacteria on the posterior end of the cell. 26-28 - after removing the anterior 'cap' (operculum). Scale bar is 10um in #2, for size comparison.Trichonympha is this giant and utterly adorable wood-eating gut endosymbiont of early-branching dictyoptera (cockroaches and termites). Sadly, it's anaerobic and thereby difficult to play with unless you have a steady supply of termites going on in your lab, like those guys do. As for the wood roach from which these particular critters come from, it has to be ordered. This roach also has the amazing Saccinobaculus...Trichonympha can also be found in basal termites; we're lucky to have some native ones here in Vancouver (alas, devoid of Saccinobaculus =( )It seems like cockroaches and termites formed endosymbiotic relationships with the protists before the two diverged - both groups have endosymbionts in their basal lineages, and lose them later on. The protistan endosymbiont diversity is wonderful: you have the aforementioned and much beloved 'snake-in-a-bag' (Saccinobaculus; can you tell I'm obsessed yet?) and fellow oxymonad companions like Streblomastix - a long cell with 'docking' for even longer episymbiont bacteria on it; Trichomitopsis and its protruding axostyle when it curls up into a ball; accompanied by loads of symbiont and parasitic bacteria.The wood-eating dictyoptera require endosymbionts to digest cellulose, since we metazoans suck at it. The more derived termites can get by with bacteria it seems; but interestingly the protists are actually doing the digesting themselves in the basal termites - killing off the gut bacteria does not prevent the termite from being able to digest the wood, if I recall correctly from class... (was a while ago since we sliced up some termites and cockroaches). Either way, you end up with this complex society with protists of all sorts with bacterial endo- and episymbionts, as well as free-living forms. I find it amazing how this system survived locked inside the termite/roach guts for millions of years; it would not survive without them!Most of the protists are anaerobic and lack conventional mitochondria, instead carrying highly reduced relics as mitosomes or hydrogenosomes; the latter produce hydrogen gas as a byproduct of their metabolic pathways. It was once thought those organisms were primarily amitochondriate, thus shoving them to the base of the eukaryotic tree, also known as theArchezoan Hypothesis, put forth by Tom Cavalier-Smith; later this hypothesis was rejected as relics of ancient mitochondrial gene transfers were found in some of the host nuclei and the evidence accumulating for one of the prime archaezoans, microsporidia, being found to branch smack in the middle of fungi (beginnings of demise of Archaezoa discussed in Keeling 1998 BioEssays; free access).It's 4am and I should stop procrastinating with my assignment... but here ya go. Aren't protists so cute and awesome? ^.^CARPENTER, K., CHOW, L., & KEELING, P. (2009). Morphology, Phylogeny, and Diversity of Trichonympha(Parabasalia: Hypermastigida) of the Wood-Feeding Cockroach Cryptocercus punctulatus Journal of Eukaryotic Microbiology, 56 (4), 305-313 DOI: 10.1111/j.1550-7408.2009.00406.x... Read more »

CARPENTER, K., CHOW, L., & KEELING, P. (2009) Morphology, Phylogeny, and Diversity of Trichonympha(Parabasalia: Hypermastigida) of the Wood-Feeding Cockroach Cryptocercus punctulatus . Journal of Eukaryotic Microbiology, 56(4), 305-313. DOI: 10.1111/j.1550-7408.2009.00406.x

September 11, 2009
03:45 AM
1,204 views

Finger-growing dinoflagellate (cute!)

by Psi Wavefunction in Skeptic Wonder

Why must I spoil the plot by peeking into advance online publications instead of waiting for the damn issue to come out, like normal people do? Especially with an 8am class coming up so soon...Anyway, apparently Ceratium ranipes, a photosynthetic dinoflagellate, decided to grow plastid-stuffed 'fingers' during daylight:(Pizay et al. 2009 Protist, in press; light period)And retracts them back in for the night:(Pizay et al. 2009 Protist, in press; dark period)In case you're not convinced these are the same organism:(Pizay et al. 2009 Protist, in press; sequence from a single individual removed from light, T measures minutes of darkness) (a video of that would be so awesome...!)Chloroplasts fluoresce red when hit by UV light (see my own example with a diatom); take a look at those fingers:(Pizay et al. 2009 Protist, in press. Left: formalin-preserved C.ranipes with a daytime morphology; the inset shows UV autofluorescense of the plastids: note their concentration in the 'fingers'. The bluish/whitish subinset shows Calcofluor White staining, which indicates the presence of thecal plates on the fingers. Right: transitional morphology at the end of the day: note how the plastids migrated inwards away from the fingers.)This raises some cell biology-related questions: how is plastid movement coordinated and regulated? What does the genetic developmental pathway look like for those fingers, and how does it interact with whatever immediately respond to light? More importantly, why does this thing seemingly waste its time growing and retracting fingers, when it could have just kept them protruded during dark hours?Could be just a low cost glitch in the system, or perhaps there is something to it. After all, perhaps it wouldn't take much to lose the finger retraction ability - so is there some cost when that happens, thereby keeping this process going? Sinking may have something to do with it - many planktonic algae sink for the night and float back up during the day. Fingers may drastically slow down the sinking speed. However, there's no data yet showing any vertical migration in C.ranipes (Pizay et al. 2009 Protist). Could be a relic from an ancestor that did sink, but then why hasn't this behaviour been found earlier, and in more dinos?Another idea in the same paper is that the fingers get in the way of directed swimming; during daylight hours, you sacrifice your swimming ability for a larger photosynthetic capacity, but it may be advantageous to put away the tackle in the absense of light.This reminds me of two things: 1) plant leaves - increasing the surface area exposed to surroundings for gas exchange, as well as the area exposed to light. Sort of a convergence. 2) Many 'radiolaria' have algal symbionts they use for photosynthesis, and they too spread them out towards the tips of the host's filopodia during daytime, and retract them inwards for the night. So whatever you do, don't dangle your plastids in plain view when they're not in use.---Pizay, M., Lemée, R., Simon, N., Cras, A., Laugier, J., & Dolan, J. (2009). Night and Day Morphologies in a Planktonic Dinoflagellate Protist DOI: 10.1016/j.protis.2009.04.003... Read more »

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

June 21, 2010
09:02 AM
1,203 views

Sunday Protist - Lagynion: bottled algae

by Psi Wavefunction in Skeptic Wonder

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*scopeNow 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...ReferencesNicholls, 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.xO'Kelly, C., & Wujek, D. (2001). Cell structure and asexual reproduction in Lagynion delicatulum (Stylococcaceae, Chrysophyceae) European Journal of Phycology, 36 (1), 51-59 DOI: 10.1080/09670260110001735198PS: 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.... Read more »

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

July 13, 2010
08:41 AM
1,177 views

Sunday Protist - Giant tree of spicules: Spiculidendron

by Psi Wavefunction in Skeptic Wonder

Christopher Taylor over at Catalogue of Organisms has a nice post on agglutinated Saccamminid foraminifera, and very recently wrote on the taxonomy and morphology of Pelosina, Pilulina and Technitella, wherein he brought up a fascinating paper on one hell of a bizarre foram: the 'spicule tree', initally mistaken for a gorgonian (sea fan). I'm going to leech off his find as he didn't specifically mention this tree foram in his post. Also, he mentioned Komokians before I did. Meanie. In all seriousness, go read his posts. For the phylogenetically inclined protistologists, the Komokian post is good food for thought.I'm going to slack off a bit this time. For an overview of the huge clade of awesome that is Foraminifera, see my earlier post here; for another tree foram, see Notodendrodes here.Foraminiferans are amazing creatures: some of them can be best described as giant cannibalistic carnivorous wads of sticky reticulated pseudopodia, capable of snaring and devouring small metazoans and Volvox colonies. They have the fastest microtubule growth rates in the eukaryotic kingdom - a whole two orders of magnitude greater than those of animals at a stunning 12µm/s! (animal cells grow microtubules at around 1-15µm/min.) (Bowser & Travis 2002 J Foram Res) Their pseudopodia are themselves capable of shearing flesh in a process so unique it deserved its own name: 'skyllocytosis' (Bowser 1985 J Protozool). Do not screw around with forams. They are scary.Most of them also have shells, but that's a story for some other day. Well, many stories, for many days. Forams are a huge and diverse group.The following specimen belongs to Astrorhizidae, a group of agglutinating forams - meaning their tests are composed of material from the environment, often very selectively picked. As implied by its name, the spicule tree, or Spiculidendron, composes its test entirely out of sponge spicules. Furthermore, this contraption reaches a stunning 60mm (6cm) in height, as a single-celled organism!Plant, animal or protist? A foram tree to shame all foram trees. A giant spicule-covered monster from the Caribbean tropics. (Rützler & Richardson 1996 Biologie)The paper mentions difficulties in determining whether the spicule tree bears a single nucleus or is coenocytic. Presumably, if it was that hard to find (though they had few specimens to work with), it may well be uninucleate like Notodendrodes. This would be quite cool as 6cm is one hell of a giant cell to be supported by a single nucleus. The cytoplasm also contains symbiotic dinoflagellates, making this tree foram even more like an actual tree.Note that this strange monster of a foram was only described in 1996. The age of exploration is far from over.ReferencesRützler, K., & Richardson, S. (1996). The Caribbean spicule tree: a sponge-imitating foraminifer (Astrorhizidae) Bulletin de l'Institut Royal des Sciences Naturelles de Belgique 66 (Suppl.), 143-151Bowser, S. (2002). RETICULOPODIA: STRUCTURAL AND BEHAVIORAL BASIS FOR THE SUPRAGENERIC PLACEMENT OF GRANULORETICULOSAN PROTISTS The Journal of Foraminiferal Research, 32 (4), 440-447 DOI: 10.2113/0320440BOWSER, S. (1985). Invasive Activity of Allogromia Pseudopodial Networks: Skyllocytosis of a Gelatin/Agar Gel The Journal of Eukaryotic Microbiology, 32 (1), 9-12 DOI: 10.1111/j.1550-7408.1985.tb03005.x... Read more »

Rützler, K., & Richardson, S. (1996) The Caribbean spicule tree: a sponge-imitating foraminifer (Astrorhizidae). Bulletin de l'Institut Royal des Sciences Naturelles de Belgique 66 (Suppl.), 143-151. info:/

Bowser, S. (2002) RETICULOPODIA: STRUCTURAL AND BEHAVIORAL BASIS FOR THE SUPRAGENERIC PLACEMENT OF GRANULORETICULOSAN PROTISTS. The Journal of Foraminiferal Research, 32(4), 440-447. DOI: 10.2113/0320440

BOWSER, S. (1985) Invasive Activity of Allogromia Pseudopodial Networks: Skyllocytosis of a Gelatin/Agar Gel. The Journal of Eukaryotic Microbiology, 32(1), 9-12. DOI: 10.1111/j.1550-7408.1985.tb03005.x

October 19, 2009
06:26 AM
1,168 views

Sunday Protist - Diplonemids: Metaboly without a pellicle and the dawn of kDNA?

by Psi Wavefunction in Skeptic Wonder

Took you guys a while to get the past Mystery Micrograph, which gave me ample excuses to procrastinate with last week's Sunday Protist. Of course, no one noticed, so it's all good, right? Opisthokont finally got it after every single other discicristate lineage has been eliminated, and grotesquely revealing hints have been given away. Johan guessed their sister clade, Kinetoplastida. More importantly, we need fresh blood on this blog, and thus far, the Mystery Micrograph winners have been an incestuous group, all linked in the present or past with a single department. Srsly. So half the win goes to Johan for getting sort of close-ish enough, as well as being somebody I don't actually know outside the blogosphere...So the correct answer for MM#05 was...Rhynchopus, a diplonemid. (Roy et al. 2007 JEM) Note the odd writhing movement in the timelapse (1-8) as well as absense of flagella in most figures. This group is very obscure - check out Table 1 in the above mentioned publication if you can, and marvel at the sea of question marks regarding the various diplonemids...That's right, yet another obscure protist, Rhynchopus, a genus of diplonemids. And everyone knows what those are, right? *crickets* Well, hang in there and find out! Feel free to point and laugh any time you see 'Rhyncopus' - apparently, I have serious issues spelling that one... (although it's definitely not as bad as Barleeiidae) Speaking of taxonomy, Diplonema was formerly known as 'Isonema', in case anyone gets the urge to scour ancient protistology literature...Cell StructureI assumed that the absense of flagella in the SEM was due to them falling off due to stress or just being generally shitty specimens for EM prep. Turns out, that's actually how they roll - flagella are only visible in swarmer cells produced in hungry (starved) cultures. The flatness is also a characteristic attribute of this cell, not so much a dehydration artefact. (Roy et al. 2007 JEM). The cell contains a large flagellar apparatus and a cytostome (cell mouth), generally oriented parallel to each other, with a lip protruding outside the opening:Drawings of Rhynchopus cell structure (Roy et al. 2007 JEM). Hopefully this makes the above paragraph make a little more sense...Not much is really known about the diplonemid nuclear genome organisation, although the chromosomes appear to be permanently condensed, just like in the euglenids. Weird chromosome structure is often correlated with genomes on crack, so one can only wonder what kind of oddities could be concealed in their chromatin. However, the nuclear genome does seem to contain a splice leader gene (Sturm et al. 2001 JEM), a characteristic feature of kinetoplastids, which are famous for their polycistronic primary mRNA transcripts - they have several genes following a single promotor, which are then broken up by trans-splicing 5' cap-containing splice leaders before each gene. Rumour has it, euglenids might also be capable of splice leader trans-splicing, so this may well be a general euglenozoan trait.Diplonemids are interesting from an evolutionary perspective. While sharing some distinctive features with many euglenids (metaboly, condensed nuclear chromatin, cytopharynx structure), they are actually basal to kinetoplastids, with the euglenids basal to both kinetoplastids AND diplonemids. Together, they form the Euglenozoa*:(Simpson et al. 2004 Protist; tree of Euglenozoa; note diplonemids branching basal to kinetoplastids, and not to euglenids.)* By the way, Euglenozoa = large group of excavates containing kinetoplastids (eg. Trypanosomes), euglenids (eg. Euglena) and diplonemids (subject of this post). We like to recycle fragments of Latin lexicon wherever possible. MetabolyMany euglenids share a characteristic form of motility called 'metaboly', which is essentially a writhing motion of a cell, where it twists and turns like mad, moving a blog of cytoplasm from one end to the other. Euglenids are covered with protein pellicle strips arranged longitudinally from one end of the cell to the other. Among many euglenids, those strips have a very complex structure, which enables them to slide against each other and allow metaboly to occur. Beneath each stript is a bundle of microtubules. (This page pretty much has nearly everything you ever wanted to know about Euglenids.)[rant]One anoying thing about Euglenid biologists (that is, people studying euglenids, not euglenids who have chosen a questionable career path...) is their referring to the pellicle strips as 'cytoskeleton', which the rest of us reserve strictly for microtubules, actin filaments and intermediate fibres. As cool as your strips might be, they do not consist of actin, 'tubes OR intermediate fibres, and are therefore NOT cytoskeleton. Otherwise anyone outside 'Euglenology' becomes very confused. Thanks. [/rant]Anyway, you may wonder why we're rambling about Euglenids all of the sudden. Thing is, diplonemids also have metaboly-like motility. Except that they lack pellicle strips altogether. However, they still have ... Read more »

Leander, B., Witek, R., & Farmer, M. (2001) TRENDS IN THE EVOLUTION OF THE EUGLENID PELLICLE. Evolution, 55(11), 2215. DOI: 10.1554/0014-3820(2001)055[2215:TITEOT]2.0.CO;2

Marande, W., Lukes, J., & Burger, G. (2005) Unique Mitochondrial Genome Structure in Diplonemids, the Sister Group of Kinetoplastids. Eukaryotic Cell, 4(6), 1137-1146. DOI: 10.1128/EC.4.6.1137-1146.2005

ROY, J., FAKTOROVÁ, D., BENADA, O., LUKEŠ, J., & BURGER, G. (2007) Description of Rhynchopus euleeides n. sp. (Diplonemea), a Free-Living Marine Euglenozoan. The Journal of Eukaryotic Microbiology, 54(2), 137-145. DOI: 10.1111/j.1550-7408.2007.00244.x

Roy, J., Faktorová, D., Lukeš, J., & Burger, G. (2007) Unusual Mitochondrial Genome Structures throughout the Euglenozoa. Protist, 158(3), 385-396. DOI: 10.1016/j.protis.2007.03.002

Simpson AG, Lukes J, & Roger AJ. (2002) The evolutionary history of kinetoplastids and their kinetoplasts. Molecular biology and evolution, 19(12), 2071-83. PMID: 12446799

SIMPSON, A. (2004) Early Evolution within Kinetoplastids (Euglenozoa), and the Late Emergence of Trypanosomatids. Protist, 155(4), 407-422. DOI: 10.1078/1434461042650389

STURM, N., MASLOV, D., GRISARD, E., & CAMPBELL, D. (2001) Diplonema spp. Possess Spliced Leader RNA Genes Similar to the Kinetoplastida. The Journal of Eukaryotic Microbiology, 48(3), 325-331. DOI: 10.1111/j.1550-7408.2001.tb00321.x

SWALE, E. (1973) A study of the colourless flagellate Rhynchomonas nasuta (Stokes) Klebs. Biological Journal of the Linnean Society, 5(3), 255-264. DOI: 10.1111/j.1095-8312.1973.tb00705.x

VICKERMAN, K. (1977) DNA Throughout the Single Mitochondrion of a Kinetoplastid Flagellate: Observations on the Ultrastructure of Cryptobia vaginalis (Hesse, 1910). The Journal of Eukaryotic Microbiology, 24(2), 221-233. DOI: 10.1111/j.1550-7408.1977.tb00970.x

February 9, 2010
05:56 AM
1,156 views

ToE Expansion pack: Foraminifera!

by Psi Wavefunction in Skeptic Wonder

After getting over my little moment of rage there, I decided to go ahead and redo the forams while I could still vaguely remember the phylogeny, sort of. So here comes the Tree of Eukaryotes Expansion Pack: Forams!I hope somebody is happy now, after nagging me about the freaking forams for the past two weeks! I know they deserve more space, and I did them an awful injustice by shrinking the entire group to just 'Forams'. Since I still haven't figured out the space problem (should I just shrink everything to 8pt font and add another 100 taxa or so?), I decided to make a special little expansion pack by crudely offending the Radiolaria and Cercozoa. I'd add more images, but it's almost 3am so...later. Also, this tree is liable to be very wrong, so perhaps I don't really need to polish it up just yet. Some groups seemed a bit confusing...Apparently it's unknown whether Komokians are forams or not, as no living specimen have been recovered (damn suckers insist on living at the very bottom of the ocean), and it's uncertain whether they even have reticulopodia, although presumably they should. Komokians are so awesome...!No time to finish the Sunday Protist to'night', but I totally just spoiled the surprise. Yes, it'll be a foram. And yes, it will be weird.Flakowski, J. (2005). ACTIN PHYLOGENY OF FORAMINIFERA The Journal of Foraminiferal Research, 35 (2), 93-102 DOI: 10.2113/35.2.93HABURA, A., GOLDSTEIN, S., PARFREY, L., & BOWSER, S. (2006). Phylogeny and Ultrastructure of Miliammina fusca: Evidence for Secondary Loss of Calcification in a Miliolid Foraminifer The Journal of Eukaryotic Microbiology, 53 (3), 204-210 DOI: 10.1111/j.1550-7408.2006.00096.xLONGET, D., & PAWLOWSKI, J. (2007). Higher-level phylogeny of Foraminifera inferred from the RNA polymerase II (RPB1) gene European Journal of Protistology, 43 (3), 171-177 DOI: 10.1016/j.ejop.2007.01.003Pawlowski, J. (2003). The evolution of early Foraminifera Proceedings of the National Academy of Sciences, 100 (20), 11494-11498 DOI: 10.1073/pnas.2035132100... Read more »

Flakowski, J. (2005) ACTIN PHYLOGENY OF FORAMINIFERA. The Journal of Foraminiferal Research, 35(2), 93-102. DOI: 10.2113/35.2.93

HABURA, A., GOLDSTEIN, S., PARFREY, L., & BOWSER, S. (2006) Phylogeny and Ultrastructure of Miliammina fusca: Evidence for Secondary Loss of Calcification in a Miliolid Foraminifer. The Journal of Eukaryotic Microbiology, 53(3), 204-210. DOI: 10.1111/j.1550-7408.2006.00096.x

LONGET, D., & PAWLOWSKI, J. (2007) Higher-level phylogeny of Foraminifera inferred from the RNA polymerase II (RPB1) gene. European Journal of Protistology, 43(3), 171-177. DOI: 10.1016/j.ejop.2007.01.003

Pawlowski, J. (2003) The evolution of early Foraminifera. Proceedings of the National Academy of Sciences, 100(20), 11494-11498. DOI: 10.1073/pnas.2035132100

August 24, 2009
08:01 AM
1,137 views

Sunday Protist - Perkinsela: Life as an organelle

by Psi Wavefunction in Skeptic Wonder

We've all heard of the primary endosymbiosis of bacteria that eventually became mitochondria* and plastids, on two separate occasions (three if you count Paulinella plastid origin). Some have heard of secondary, and maybe even tertiary, plastid endosymbiosis (eg. brown algae with red algal plastids). There's a fascinating case of tertiary endosymbiosis where an entire diatom inhabiting a dino (Kryptoperidinium), etc. Another interesting phenomenon is the endosymbiosis resulting in other essential 'organelles', eg. Polynucleobacter in Euplotes(Görtiz 2006 in Prokaryotes 1:364-402). While plastids have been transferred about the tree several times, secondary endosymbiosis of mitochondria or whole non-photosynthetic eukaryotes seems to be extremely rare. Thus, the following case of an endosymbiosis of a kinetoplastid by an amoeba I find to be rather interesting.*Well, there's still remnants of a crackpot adherence to the autogenous model of mitochondrial origin...Meet Perkinsela (formerly Perkinsiella; Dyková et al. 2008b), an endosymbiont of amoebae that took until Hollande 1980 to be recognised as an organism rather than organelle! (although Grell 1973 Protozoology (p.363) does suggest a link to the endosymbiosis theory that was just becoming established at that time). Here's the amoebozoan host Neoparamoeba with an arrow pointing to Perkinsela:(Eva Dyková, Tolweb Perkinsiella page)This endosymbiont's life cycle has become completely confined within the host cell, as it is perpetrated along with nuclei upon host cell division. It is often found in a strange 'bipolar' form, with nuclei opposite of each other across the massive mitochondrion (which contains the kinetoplast - a dense disk of mitochondrial DNA unique to Kinetoplastids, which include Trypanosomes, the cause of African Sleeping Sickness), and in close association with the host nucleus:(Dyková et al. 2003 Eur J Protistol; 8 shows Neoparamoeba with its endosymbiont (NN - host nucleus, K - kinetoplast (mitochondrial DNA), n - Perkinsela nucleus; 9 - Perkinsela itself. Note the two nuclei across the kinetoplast from each other (c- cytoplasm))The nature of this endosymbiotic relationship remains unknown, although it seems to be mutualistic as the host and the endosymbiont both die without each other (Dyková et al. 2008b).The endosymbiont is a sister group to Ichthyobodo, and even contains the splice leader sequences characteristic of Euglenozoa (the larger containing group of kinetoplastids, diplonemids and euglenids (remember Euglena?)) (Dyková et al. 2003; 2008b). Here's a tree to orient yourselves: (because everyone knows what Jakobids and Diplonemids are...feel free to go here for the bigger picture ^.^)(Simpson et al. 2006 Trends Parasitol.; family tree of creatures with 'hockey puck' mitochondrial DNA...the intelligent designer was definitely tripping out on some serious stuff when he made this clade ^.^)(Let's just say Neoparamoeba is an Amoebozoan. I have no desire to sort out Amoebozoan taxonomy at this hour, as it's a fucking mess. I have three trees before me from various periods, and the burning urge to rip all my hair out is a little too much. Seriously, Amoebozoa are just fucked up, as morphology-based classification failed more abysmally than usual there. It's hard to determine morphological features of something so...amoeboid ^^. I challenge a certain taxonomist who reads this to blog about their phylogeny! Have fun =P)Interstingly, both Neoparamoeba and Ichthyobodo are fish gill parasites. While Neoparamoeba is an opportunistic parasite (Young et al. 2007) (ie it can also live freely; a more vicious example of opportunistic parasitism is Naegleria, which is harmless until it accidentally gets into a brain - it happens to love neural tissue!), Ichthyobodo is an obligatory ectoparasite. ('ectoparasite' means it attaches to the surface of the host cell to drain it of its 'juices', instead of going completely inside).Fish gills seem to be rather fertile ground for parasites of all levels of devotion; for the chances of passing by one when you live in water are pretty good. It seems like the long-term close association between Neoparamoeba and Ichthyobodo parasitising off the same host has led to this intimate endosymbiosis - would be interesting to know the approximate timescale of the divergence between Perkinsela and Ichthyobodo, to see how long it can take for such relationships to evolve.Here's the Neoparamoeba opportunist in action:(Lovy et al. 2007 Vet Pathol; A - amoeba, E - fish epithelial layer; bar = 3um) To summarise what I'm talking about:... Read more »

DYKOVA, I. (2003) -like endosymbionts of spp., relatives of the kinetoplastid. European Journal of Protistology, 39(1), 37-52. DOI: 10.1078/0932-4739-00901

DYKOVA, I., FIALA, I., DVORAKOVA, H., & PECKOVA, H. (2008) Living together: The marine amoeba Thecamoeba hilla Schaeffer, 1926 and its endosymbiont Labyrinthula sp. European Journal of Protistology, 44(4), 308-316. DOI: 10.1016/j.ejop.2008.04.001

DYKOVA, I., FIALA, I., & PECKOVA, H. (2008) Neoparamoeba spp. and their eukaryotic endosymbionts similar to Perkinsela amoebae (Hollande, 1980): Coevolution demonstrated by SSU rRNA gene phylogenies. European Journal of Protistology, 44(4), 269-277. DOI: 10.1016/j.ejop.2008.01.004

Liu, B., Liu, Y., Motyka, S., Agbo, E., & Englund, P. (2005) Fellowship of the rings: the replication of kinetoplast DNA. Trends in Parasitology, 21(8), 363-369. DOI: 10.1016/j.pt.2005.06.008

Lovy J, Becker JA, Speare DJ, Wadowska DW, Wright GM, & Powell MD. (2007) Ultrastructural examination of the host cellular response in the gills of Atlantic salmon, Salmo salar, with amoebic gill disease. Veterinary pathology, 44(5), 663-71. PMID: 17846238

SIMPSON, A., STEVENS, J., & LUKES, J. (2006) The evolution and diversity of kinetoplastid flagellates. Trends in Parasitology, 22(4), 168-174. DOI: 10.1016/j.pt.2006.02.006

YOUNG, N., CROSBIE, P., ADAMS, M., NOWAK, B., & MORRISON, R. (2007) Neoparamoeba perurans n. sp., an agent of amoebic gill disease of Atlantic salmon (Salmo salar)☆. International Journal for Parasitology, 37(13), 1469-1481. DOI: 10.1016/j.ijpara.2007.04.018

December 22, 2009
07:24 AM
1,125 views

Sunday Protist -- Oligotrich Ciliates: another morphological acid trip

by Psi Wavefunction in Skeptic Wonder

Of course, no one noticed any delays in the posting of the Sunday Protist, because that never happened. Actually, I've been rather frazzled by this little fun activity that happens around this time of the year called 'finals', and thus had to desperately avoid any material I may find myself actually interested in, lest it hijacks my attention for too long. Also, I'll be mostly internetless starting tomorrow, and thus unable to blog. Coming back on 03 January. May or may not schedule a post, depending on time, but wish you all a very happy holiday and see you next year!But before I take off, let's oogle at some ciliates. Don't have much time (last final tomorrow), so this post will be very superficial. Just sit back, relax and enjoy the Cornucopia of awesome strangeness that is ciliate morphology. Today's special features Oligotrichs, conspicuous by their tuft of cilia at one end.Let's meet the prime representative, Strombidium:Strombidium inclinatum; the weird frayed flat-looking things at the top are actually flagella linked together into polykinety, formerly known as a 'membranelle' for its membrane-like appearance in light microscopy. Those usually constitute the oral ciliature, which are involved in feeding. G is the girdle kinety, basically a single row of flagella wrapped around the cell. It has very few kinety (which, btw, consists of kinetIDs, or basal bodies. Try not getting them mixed up on a lab exam...) compared to something like Paramecium or Tetrahymena, which are covered in rows of kinety. (Modeo et al. 2003 JEM)For a reminder of where ciliates are on the Big [sub]Tree of Life, they're alveolates here:I was playing with tree software this weekend. And then, to cleanse myself of the shame, I downloaded a cellular pathway modeling program and played around with some networks. This is the scheme we go by at this blog, at the moment (see the list of organisms towards the bottom of the side bar --) "Craptophyte" was shamelessly stolen from some real protistologists. Proper term is 'Hacrobia'.[disclaimer]By the way, while alveolates+stramenopiles and amoebozoa+opisthokonts are pretty good together, the other branchings may or may not bear any resemblance to reality. Furthermore, the rooting of the tree is highly contested, but I'll go along with what TC-S says these days (what Tom says is quite subject to change though...), since it'll be harder for you to argue with me as you'd have to read his stuff yourselves. And most of you are too lazy to do that, so I'm safe. I am in no way liable for any damage or deaths that may result from the use of this tree. [/disclaimer]Here's another sampler of Oligotrichs and their neighbouring Choreotrichs (which we should explore at a later date):(Gao et al. 2009 Sys & Biodiv)And how they relate to each other:Oligotrich (and Choreotrich) phylogeny. We'll briefly look at Strombidium, Laboea and Pseudotontonia.(Gao et al. 2009 Sys & Biodiv)I may have something oligotrich-like in this old sequence of images documenting a random ciliate exploding while I was taking an optical stack... the image quality is kinda crappy, so I could probably get away with calling it Strombidium or something. I don't even remember where this sample came from, may well have been marine, hence the explosion in water.Let's wander about the Oligotrich tree some more.The first glimpse of Laboea made me double-check it wasn't actually some sort of tiny snail:These SEMs are so nice I'm having trouble cropping them... (Agatha et al. 2004 JEM)It also a rather unusual-looking (for a ciliate) cell division pattern:Dividing Laboea sp. (Agatha et al. 2004 JEM)If you've ever wondered how to tell a dividing ciliate from a conjugating couple, it's pretty easy: Ciliates divide transversely along the anterior-posterior axis, ie like Trichonympha is almost the polar opposite -- they divide laterally and have sex like this: Kama sutra of protists must definitely be written someday! See the bottom of this post for more ciliate sex.Which is why Laboea looks a little weird, although here it must simply have a different longitudinal axis from what it first appears as. As much as I love morphogenesis/cellular development, and as much as tomorrow's final is Developmental Biol, ciliate morpho won't help much with chick gastrulation, sadly enough. Although it would be fun to draw parallels between various processes of development on morphogenesis to derive some fundamental principles, which I'm pretty sure (though only as much as a scientist can be sure about anything...) should repeat both on the unicellular and multicellular levels. After all, there's only so many ways to build a shape. So we'll have to pass on the cell division/morphogenesis stuff for now *sob*Pseudotontonia. Ok, this thing is weird:... Read more »

Agatha S. (2004) A cladistic approach for the classification of oligotrichid ciliates (Ciliophora: Spirotricha). Acta Protozoologica , 43(3), 201-217. info:/

AGATHA, S. (2004) Evolution of ciliary patterns in the Oligotrichida (Ciliophora, Spirotricha) and its taxonomic implications. Zoology, 107(2), 153-168. DOI: 10.1016/j.zool.2004.02.003

AGATHA, S., STRUDER-KYPKE, M., & BERAN, A. (2004) Morphologic and Genetic Variability in the Marine Planktonic Ciliate Laboea strobila Lohmann, 1908 (Ciliophora, Oligotrichia), with Notes on its Ontogenesis. The Journal of Eukaryotic Microbiology, 51(3), 267-281. DOI: 10.1111/j.1550-7408.2004.tb00567.x

Gao, S., Gong, J., Lynn, D., Lin, X., & Song, W. (2009) An updated phylogeny of oligotrich and choreotrich ciliates (Protozoa, Ciliophora, Spirotrichea) with representative taxa collected from Chinese coastal waters. Systematics and Biodiversity, 7(02), 235. DOI: 10.1017/S1477200009002989

MODEO, L., PETRONI, G., ROSATI, G., & MONTAGNES, D. (2003) A Multidisciplinary Approach to Describe Protists: Redescriptions of Novistrombidium testaceum Anigstein 1914 and Strombidium inclinatum Montagnes, Taylor, and Lynn 1990 (Ciliophora, Oligotrichia). The Journal of Eukaryotic Microbiology, 50(3), 175-189. DOI: 10.1111/j.1550-7408.2003.tb00114.x

Skovgaard, A., & Legrand, C. (2005) Observation of live specimens of Pseudotontonia cornuta (Ciliophora: Oligotrichida) reveals new distinctive characters. Journal of the Marine Biological Association of the United Kingdom, 85(4), 783-786. DOI: 10.1017/S0025315405011707

March 28, 2010
03:49 AM
1,113 views

Sunday Protist -- Trichotokara nothriae: Guitar-shaped gregarine

by Psi Wavefunction in Skeptic Wonder

This post turned into a bit of a hodgepodge of various gregarine-related trivia. Proceed with caution.Gregarines are a group of apicomplexans (='Sporozoa', a vastly diverse group famous for the malarial parasite Plasmodium and the behaviour-altering Toxoplasma) characterised by a monoxenous (single host) lifestyle that is quite different from that of other 'apis'. Christopher Taylor wrote a nice post about them here.Apicomplexa are alveolates along with ciliates and dinoflagellates; you can find them on the left side of this tree . The apicomplexan phylogeny is a complete mess at the moment; the old coccidian-haematozoan-gregarine divisions aren't too well-supported and the relationships of stuff within them are even murkier. As an aside, many apis have an 'apicoplast', or a relic plastid of red algal origin -- their ancestors were once photosynthetic! In fact, a paraphyletic group of organisms basal to apicomplexa (Chromera et al.) are currently photosynthetic, further supporting the photosynthetic ancestry of these weird mostly-intracellular parasites, most of whom rarely ever see the light of day!Gregarines are typically invertebrate parasites and unlike other apicomplexans, tend to spend most of their lives extracellularly; in fact, their cellular penetration consists of attaching themselves to a cell via the mucron (holdfast-like structure). You can read more about their biology and life cycle on their ToLWeb page. (also a review in Tr Parasitol: Leander 2007) If you want to see some for yourself, kidnapping and slicing up an earthworm is an easy way to do so: Monocystis is a parasite of earthworm seminal vesicles (feeds on sperm), and a rather abundant one. It may actually be quite easy to find various apicomplexan parasites in insects -- it is estimated that most of them may have an api specialised in parasitising them, which hints at the total apicomplexan diversity being something outrageously vast! Such a project would also be a good excuse to learn insect anatomy, which I find to be quite complicated.Right, you wanted to see a new genus of guitar-shaped gregarines: Trichotokara from the intestine of an onuphid tubeworm. a-e: trophozoites (feeding forms). M - mucron ('holdfast'), CB - cell body. Arrow - junction between mucron and cell body, which can be seen extending further into the mucron in (e; arrowheads). f: gamonts in syzygy, or gregarine sex. Scalebars: a-e 10um; f 25um. (Rueckert & Leander 2010 J Invert Pathol)By the way, if anyone asks you for a six-letter word in English 'devoid of any vowels', keep 'syzygy' in mind. Technically it does have vowels, as any phonologist would tell you, but most people insist on equating letters with sounds, and y 'is not a vowel'. Regardless, it's still a really awesome word. Syzygy!More gregarine awesomeness. Note how the cell surface seems to strive for increased surface area, especially in the mucron which gets inserted into a cell:SEM of Trichotokara. b - close-up of hair-like projections of the mucron. c - junction between mucron and cell body. d - folds along the cell body. Scalebars: a - 10um; b-d - 1um. (Rueckert & Leander 2010 J Invert Pathol)This gives me an excuse to mention a paper on proximate vs. ultimate convergence by the senior author on the above gregarine paper: Leander 2008 JEM (free access). Among several other examples of ultimate convergence between multicellular and unicellular organisms inhabiting similar environments, gregarines and nematodes are compared in terms of their structural organisation. While nematodes have longitudinal muscles just beneath the elastic epidermis, gregarines have subpellicular bands of longitudinal microtubules running just underneath the elastic cortex (although used differently -- see gliding motility below). Curiously, in both cases the result is a sinusoidal (wiggling) pattern of movement. Additionally, tapeworm and Haplozoon (dinoflagellate) surface morphology are noted to be similar (covered with microvili), for the obvious purpose of increasing surface area. It's probably not much of a stretch to add gregarine surface structure to that list. (see Leander et al. 2003 J Parasitol for more gregarine surfaces) Interesting case of structural ultimate convergence between nematodes and gregarines. Purple - bands of muscle and microtubules, respectively. Blue - elastic epidermis and tri-layered cortex, respectively. The three cortical layers consist of the plasma membrane at the very surface, with two alveolar membranes immediately below. (Leander 2008 JEM)Before we proceed to a digression on apicomplexan motility, oblicatory phylogeny of Trichotokara and relatives. Note its extremely diverged SSU sequence resulting in a hellishly long branch:ML tree of SSU rDNA sequences. Probably wouldn't trust its exact placement among the gregarines just yet... (Rueckert & Leander 2010 J Invert Pathol)Apicomplexans are generally aflagellate in their trophic stage (I say 'generally' just in c... Read more »

Baum, J., Papenfuss, A., Baum, B., Speed, T., & Cowman, A. (2006) Regulation of apicomplexan actin-based motility. Nature Reviews Microbiology, 4(8), 621-628. DOI: 10.1038/nrmicro1465

G. E. Gates. (1926) Preliminary Note on a New Protozoan Parasite of Earthworms of the Genus Eutyphœus. Biological Bulletin, 51(6), 400-404. info:/

LEANDER, B. (2008) Marine gregarines: evolutionary prelude to the apicomplexan radiation?. Trends in Parasitology, 24(2), 60-67. DOI: 10.1016/j.pt.2007.11.005

LEANDER, B. (2008) A Hierarchical View of Convergent Evolution in Microbial Eukaryotes. Journal of Eukaryotic Microbiology, 55(2), 59-68. DOI: 10.1111/j.1550-7408.2008.00308.x

Molino, P., & Wetherbee, R. (2008) The biology of biofouling diatoms and their role in the development of microbial slimes. Biofouling, 24(5), 365-379. DOI: 10.1080/08927010802254583

Purvis, A., & Hector, A. (2000) Getting the measure of biodiversity. Nature, 405(6783), 212-219. DOI: 10.1038/35012221

Rueckert, S., & Leander, B. (2010) Description of Trichotokara nothriae n. gen. et sp. (Apicomplexa, Lecudinidae) – an intestinal gregarine of Nothria conchylega (Polychaeta, Onuphidae). Journal of Invertebrate Pathology. DOI: 10.1016/j.jip.2010.03.005

Soldati, D., & Meissner, M. (2004) Toxoplasma as a novel system for motility. Current Opinion in Cell Biology, 16(1), 32-40. DOI: 10.1016/j.ceb.2003.11.013

June 26, 2010
10:28 AM
1,111 views

Criminally photosynthetic: Myrionecta, Dinophysis and stolen plastids

by Psi Wavefunction in Skeptic Wonder

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, 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 ... Read more »

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, 101-106. DOI: 10.3354/ame045101

Stoecker, D., Johnson, M., deVargas, C., & Not, F. (2009) Acquired phototrophy in aquatic protists. Aquatic Microbial Ecology, 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), 366. DOI: 10.1186/1471-2164-11-366

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