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Protists, memes and random musings
Psi Wavefunction
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- July 1, 2011
- 01:58 AM
- 466 views
A Tree of Eukaryotes v1.3a
by Psi Wavefunction in Skeptic Wonder
Time for a new tree, finally. Some groups have been fixed and the diagram has moved from Powerpoint to a real vector art program (Illustrator), so hopefully it looks a bit nicer now and has slightly fewer glaring errors. Have yet to fix all issues, the biggest (and hardest) being the proportions taken up by the various groups -- the tree appears dominated by Excavates for some reason. Due to lack of convenient taxa for the heteroloboseans and euglenids, I expanded them to the genus level in some cases to attempt to capture some of the diversity better, but that screwed things up for the rest of the tree. Since fixing that would require some hardcore structural changes to the whole tree, I'll do that later, in the next edition (which will not take over a year to come out this time). Given some conferences coming up this summer, and that people have asked, I'll release what I have done now as v1.3a. Enjoy! (And do complain if you spot anything awry...)Previous versions and discussions, along with trees by other people, can be found here.ReferencesA shit ton (see image). But ResearchBlogging.org doesn't allow indexing 'shit ton', so I'm gonna be pathetically lazy and just cite this:Keeling, P., Burger, G., Durnford, D., Lang, B., Lee, R., Pearlman, R., Roger, A., & Gray, M. (2005). The tree of eukaryotes Trends in Ecology & Evolution, 20 (12), 670-676 DOI: 10.1016/j.tree.2005.09.005
... Read more »
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
- May 21, 2011
- 11:47 AM
- 256 views
Sticky proteins, complexity drama and selection's blind eye
by Psi Wavefunction in Skeptic Wonder
*For your entertainment, rejected titles:[Sticky proteins and complex relationships][(protein) Relationship drama: promiscuous proteins in small populations][Not all is good that sticks: non-adaptive complexity gain through compensatory protein adhesion][Man, I suck at titles]NB: This post can be considered as part 2.5 of my In defense of constructive neutral evolution series; also recommended for some background are part 1, discussing selection, drift and Neutral Theory, and part 2, discussing Constructive Neutral Evolution; to answer a popular question, part 3 *will* materialise eventually once I get off my ass and write it.Constructive neutral evolution is one mechanism of complexity increase without any associated increase in fitness – or, in other words, non-adaptive complexity gain. Basically, a random interaction between two proteins can lead to a fixed dependency if this interaction compensates for a mutation that was otherwise lethal – termed 'pressuppression'. In this way, previously unnecessary dependencies accumulate to make a very bulky, bureaucratic system that essentially does the same thing. We've all seen it in our institutions, and evolution is about as efficient.Now, one bottleneck in this model is waiting for proteins to actually interact. Proteins are quite sticky and non-specific by nature, but usually not too much as that can be quite deleterious. Piling up a bunch of proteins on each other has a non-negligible chance of interfering with their function, and one would expect for chance interactions to not be excessively promiscuous, although those who have done regulatory genetics and protein work are probably aware just how annoyingly non-specific some of the protein binding can get. Luckily, there is now a possibly mechanism boosting these chance interactions, and thus alleviating that particular bottleneck in the Constructive Neutral Evolution process, rapidly accelerating complexification and protein network obfuscation to the extent where the interaction map looks like a web; not a finely organised web of an orb-weaver but rather one of those clumpy webs that are a clusterfuck of stickiness and silk. Enter this week's Fernández and Lynch 2011 Nature paper, from here onwards referred to as "the paper".Protein 'stickiness' can be enhanced by biochemical means. Proteins vary in stability, and themselves come in populations – generally, most are in the optimal conformation that is presumably functional, but some individuals are messed up. This happens well past the sequence and folding errors, and some perfectly 'normal' proteins can be in a suboptimal state at any given time. Clearly, this affects the overall efficiency of the protein – even if it's enzymatically awesome, the overall 'protein' as we biologists understand it (sans population aspect) would decline in efficiency if a large chunk of its population is in a misfolded state.One aspect that pushes around the proportion of the protein in the 'right' conformation is how well it plays with water. It shouldn't be too surprising that hydrophobic regions induce instability. What was new to me, but perhaps old news to those who actually understood chemistry, is that the exposure of the polar(hydrophilic) protein backbone to water also has a destabilising effect – and not only that, but often more significant than that of exposed hydrophobic regions! This may seem counterintuitive – doesn't water like hydrophilic regions? And there lies our problem.Water molecules are attracted to polar groups, and the amino acid backbone is quite polar. This means little water molecules wander in towards the backbone and form hydrogen bonds with it. The problem is twofold: first of all, the protein, like all molecules, likes to 'jiggle'. The more it can jiggle in its given conformation, the more favourable that conformation is thermodynamically since its satisfied by more states. Entropy, etc. (now we're *really* entering territory I know nothing about, since my phys chem experience is locked away by PTSD...). Hooking up this backbone with water molecules reduces its 'jiggle' room, and makes it less thermodynamically stable – making change to other conformations more probable, therefore possibly leading to more errors in the protein population.Secondly, as detailed further in the paper, water likes to hang out with more of itself. Water molecules are happiest in foursomes, sharing four hydrogen bonds with their neighbours. When a creepy protein backbone emerges and lures an unsuspecting water molecule away into the protein's murky depths, the water molecule cannot form as many bonds with its fellows (or as many hydrogen bonds, period), and is really sad and lonely. Or, in proper terms, the system becomes less stable, since thermodynamics will favour an arrangement where these water molecules are all happily coordinated with each other, and not being molested in a corner by an amino acid polar group. In other words, exposing the polar backbone (Solvent-Accessible Backbone Hydrogen Bonds, SABHBs in the paper) to water induces what is called Protein-Water Interfacial Tension (PWIT).One way this tension can be released and the backbone exposure ('coded for' by genes, by the way) can be compensated for is if a random other protein (or more of its own kind) are recruited to cover that exposed backbone. This would help stabilise the protein conformation, and allow this potentially deleterious drawback to be tolerated (and get fixed in the population). Ultimately, the second (and third, etc) protein can become exapted for something useful, although just an eventual dependency is good enough to make sure these proteins stick together permanently. The crazy web of interactions gets crazier.Fernández & Lynch's fig1a suffices perfectly but I like making diagrams, so I made one anyway. See text.(Disclaimer: I'm horrible at chemistry, this may all have been thoroughly wrong...read the paper.)Now I'm about the last person to willingly blog about biochemistry, and this seems to have little only a distant relevance to evolution, particularly the non-adaptive kind that fascinates yours truly. It will make sense in a bit. Recall from a few seconds ago (hey, already difficult for some of us) that protein instability leads to reduced protein efficiency. This reduction is generally tolerated, however, until it's bad enough to have a higher chance of being removed. Recall from [what should be] introductory population genetics that selection acts probabilistically, with true slightly deleterious mutations have a lesser, but still significant, chance of fixation than strongly deleterious mutations, which selection has a higher chance of taking care of before drift quietly fixes it. (more detail in older post here) Since proteins are, quite unsurprisingly, also governed by fundamental principles of population genetics, drift becomes involved there too.As populations get smaller, drift becomes a more dominant force relative to selection, and the window of 'effectively neutral' mutations – slightly beneficial and slightly deleterious, but unlikely to be dealt with by selection – increases. More mess is tolerated. This means more protein inefficiencies are allowed to fix in the population, those induced by backbone exposure among them. Since there are now more proteins that are no longer happy with themselves (or, rather, have an increased Protein-Water Interfacial Tension), they are more likely to stick together for biochemical stability. And here Constructive Neutral Evolution can come in too, allowing further deleterious mutations that are now presuppressed by the recruited proteins. In a way, this greases the presuppression process, rather than competing with it as this ... Read more »
Fernández, A., & Lynch, M. (2011) Non-adaptive origins of interactome complexity. Nature. DOI: 10.1038/nature09992
- May 17, 2011
- 10:05 AM
- 254 views
Ratcheting up some splice leaders: a note on directionality
by Psi Wavefunction in Skeptic Wonder
In the sea of eukaryotic genetic diversity also lurk different manners of doing day-to-day genome work itself. Ciliates run two nuclear genomes, trypanosome kinetoplasts contain a chainmail suit of RNA editing circles and dinoflagellates are just weird in every genome compartment they have. Their plastids contain tiny minicircles often containing but a single gene, capable of "rolling" transcription where the minicircle is much like a Mesopotamian cylindrical seal, leaving a concatenated repeated string of genes on the transcript. The mitochondria have linear genomes with short fragmented repeated chunks of important genes all over them. But the nuclear genome is the most fucked up: for one thing, dinoflagellates lack a few histones, and have enormous genomes stored in absolutely bizarre chromosomes. More importantly for our story: every single gene must be trans-spliced with a 'splice leader', a short sequence that attaches at the beginning of the mRNA transcript and brings to it the 3' cap necessary for transcription to work. Oddly enough, Euglenozoans like the trypanosomes and euglenids seem to have a very similar system, evolved entirely by chance* convergence (Lukes et al. 2009 PNAS goes over this remarkable convergence in more detail).*Or perhaps something happened to both that made them prone to evolve this bizarre system.Genomic quirks are not just interesting in their own right as some arcane oddities, but can reveal a great deal about the dynamics of genomes in general. The dinoflagellate splice leader system turns out to yield a very crisp illustration of the power of ratchets and the toll of reverse transcription on genomes.To reiterate, every single nuclear gene transcript in a dinoflagellate must be spliced with the 3'cap-bearing 'splice leader', or else it simply won't work. This means that the dino is full of mature transcripts with splice leaders attached to the transcribed genes. Enter reverse transcriptases, which are prevalent in probably most, if not all, eukaryotic genomes, thanks to viruses and their partners in genomic parasitism crimes, transposons. When they're not busy moving transposons around and helping viruses move in, they reverse transcribe random gene transcripts for fun, that may then, on occasion, be successfully recombined back into the genome. This process probably doesn't happen [successfully] every day, but over thousands or millions of years (and countless individuals) is rampant enough to leave a noticeable trace in the genome.So we have a load of transcripts floating around with an extra sequence stitched onto them from the splice leader. Do the reverse transcriptases care in the slightest? Of course not: to them, a ribonucleotide is a ribonucleotide, give or take some trace biophysical stuff that might make a couple people cringe at what I just said. (meaning, I wouldn't be surprised if there could be some slight but ultimately detectable biases there too) This means that splice leader, on occasion, actually makes its way back into the nuclear genome attached to the beginning of the gene.However, this splice leader does not substitute for the usual splice leader trans-splicing, since the 3' cap must be added again, or else the transcript will not be translated. That now-nuclear gene-attached splice leader ends up being completely useless, and is able to gradually degrade into benign junk, provided it doesn't mess with the translation of the gene. What is really cool is that one can actually see this gradual degradation, as shown in Slamovits and Keeling 2008 Current Biol:Mmmm, actual data! Note how the oldest SL piece closest to the gene (on the right) is the most degraded. (Slamovits & Keeling 2008 Curr Biol)Once the unnecessary splice leader chunk becomes part of the gene, the gene gets transcribed and trans-spliced like any other – meaning it is once again susceptible to replaying that same process of reverse transcription, except this time it already has a relict sequence. It can acquire a second one on top of that. This explains how there can be several concatenated splice leader relics tagging along, like in the above figure.Splice leader trans-splicing not necessarily promoting reverse transcription – only makes it easier to detect. In other words, it inadvertently makes for a wonderfully convenient system where you can actually track what happens to a gene after it gets reverse transcribed. Once the gene makes its new home, the old gene copy is still present and they generally would be functionally redundant, so the dual-copy state is extremely unstable as ultimately the loss of one of the copies will be tolerated. If the newly transcribed copy is lost, we never see it and thus don't talk about it in the first place. However, once the clean original is lost, only the gene with the crap from the splice leader remains, and reversal to the original state is so improbable it's practically impossible. In other words, this process is a wonderful example of an evolutionary ratchet.Ratchets are interesting because they confer intrinsic directionality to a system, even in the absense of external pressures (like selection). The accumulation of splice leader junk in the dinoflagellate's genes isn't particularly healthy, nor is it particularly deleterious – it's effectively neutral. However, one can argue that we do have an example of bloated complexity here. Since you can't go back and lose chunks of splice leaders, this ratchet essentially ensures that left to its own devices, this aspect of genome complexity will increase on its own. At a certain point, there will probably be ever-increasing selection against accumulating further splice leaders, and those lineages that go too far will simply die off – the central tendency doesn't care, and the ratchet will keep on going regardless of what selection 'wants'.This ratchet example is therefore an elegant case of evolutionary direction that's not particularly well explained by the central dogmas of Modern Synthesis or (neo)Darwinism, where selection is the force that crafts order and directionality, with mutation a mere passive provider of material to be molded. I will go into a deeper discussion of this in another post (there's a cool paper coming out soon), but I think it's worth briefly mentioning here too while we're at it. The "mutation" step (to which, I guess, this trans-splicing and reverse-transcription process can be awkwardly attached) here is what provides a drive, a push in a certain direction, and towards increasing complexity, no less (although that last detail is irrelevant). While selection is present and provides constraints (if both genes are lost, for example, the organism dies), it does not do the 'driving' or 'forcing' in this system. Very crudely put, selection here is the passive phenomenon, and mutation is at the wheel.Another case of intrinsic directionality, but where reversal is allowed, is your garden variety directional bias – where proceeding in one direction is more probable than going backwards. A very basic example of that is if the replication machinery favours a certain type of nucleic acid – left to its own devices, the genome base composition would be skewed in that direction. Boundaries can also induce an apparent directionality, but in this case it's no longer intrinsic... that's, again, a topic for another day.This idea was a part of the Mutationism theories in the early 20th century, which were a little extreme and perhaps premature, since mu... Read more »
Slamovits, C., & Keeling, P. (2008) Widespread recycling of processed cDNAs in dinoflagellates. Current Biology, 18(13). DOI: 10.1016/j.cub.2008.04.054
McShea, D. (2001) The minor transitions in hierarchical evolution and the question of a directional bias. Journal of Evolutionary Biology, 14(3), 502-518. DOI: 10.1046/j.1420-9101.2001.00283.x
Stoltzfus A. (2006) Mutationism and the dual causation of evolutionary change. Evolution , 8(3), 304-17. PMID: 16686641
- May 17, 2011
- 10:05 AM
- 236 views
Ratcheting up some splice leaders: a note on directionality
by Psi Wavefunction in Skeptic Wonder
In the sea of eukaryotic genetic diversity also lurk different manners of doing day-to-day genome work itself. Ciliates run two nuclear genomes, trypanosome kinetoplasts contain a chainmail suit of RNA editing circles and dinoflagellates are just weird in every genome compartment they have. Their plastids contain tiny minicircles often containing but a single gene, capable of "rolling" transcription where the minicircle is much like a Mesopotamian cylindrical seal, leaving a concatenated repeated string of genes on the transcript. The mitochondria have linear genomes with short fragmented repeated chunks of important genes all over them. But the nuclear genome is the most fucked up: for one thing, dinoflagellates lack a few histones, and have enormous genomes stored in absolutely bizarre chromosomes. More importantly for our story: every single gene must be trans-spliced with a 'splice leader', a short sequence that attaches at the beginning of the mRNA transcript and brings to it the 3' cap necessary for transcription to work. Oddly enough, Euglenozoans like the trypanosomes and euglenids seem to have a very similar system, evolved entirely by chance* convergence (Lukes et al. 2009 PNAS goes over this remarkable convergence in more detail).*Or perhaps something happened to both that made them prone to evolve this bizarre system.Genomic quirks are not just interesting in their own right as some arcane oddities, but can reveal a great deal about the dynamics of genomes in general. The dinoflagellate splice leader system turns out to yield a very crisp illustration of the power of ratchets and the toll of reverse transcription on genomes.To reiterate, every single nuclear gene transcript in a dinoflagellate must be spliced with the 3'cap-bearing 'splice leader', or else it simply won't work. This means that the dino is full of mature transcripts with splice leaders attached to the transcribed genes. Enter reverse transcriptases, which are prevalent in probably most, if not all, eukaryotic genomes, thanks to viruses and their partners in genomic parasitism crimes, transposons. When they're not busy moving transposons around and helping viruses move in, they reverse transcribe random gene transcripts for fun, that may then, on occasion, be successfully recombined back into the genome. This process probably doesn't happen [successfully] every day, but over thousands or millions of years (and countless individuals) is rampant enough to leave a noticeable trace in the genome.So we have a load of transcripts floating around with an extra sequence stitched onto them from the splice leader. Do the reverse transcriptases care in the slightest? Of course not: to them, a ribonucleotide is a ribonucleotide, give or take some trace biophysical stuff that might make a couple people cringe at what I just said. (meaning, I wouldn't be surprised if there could be some slight but ultimately detectable biases there too) This means that splice leader, on occasion, actually makes its way back into the nuclear genome attached to the beginning of the gene.However, this splice leader does not substitute for the usual splice leader trans-splicing, since the 3' cap must be added again, or else the transcript will not be translated. That now-nuclear gene-attached splice leader ends up being completely useless, and is able to gradually degrade into benign junk, provided it doesn't mess with the translation of the gene. What is really cool is that one can actually see this gradual degradation, as shown in Slamovits and Keeling 2008 Current Biol:Mmmm, actual data! Note how the oldest SL piece closest to the gene (on the right) is the most degraded. (Slamovits & Keeling 2008 Curr Biol)Once the unnecessary splice leader chunk becomes part of the gene, the gene gets transcribed and trans-spliced like any other – meaning it is once again susceptible to replaying that same process of reverse transcription, except this time it already has a relict sequence. It can acquire a second one on top of that. This explains how there can be several concatenated splice leader relics tagging along, like in the above figure.Splice leader trans-splicing not necessarily promoting reverse transcription – only makes it easier to detect. In other words, it inadvertently makes for a wonderfully convenient system where you can actually track what happens to a gene after it gets reverse transcribed. Once the gene makes its new home, the old gene copy is still present and they generally would be functionally redundant, so the dual-copy state is extremely unstable as ultimately the loss of one of the copies will be tolerated. If the newly transcribed copy is lost, we never see it and thus don't talk about it in the first place. However, once the clean original is lost, only the gene with the crap from the splice leader remains, and reversal to the original state is so improbable it's practically impossible. In other words, this process is a wonderful example of an evolutionary ratchet.Ratchets are interesting because they confer intrinsic directionality to a system, even in the absense of external pressures (like selection). The accumulation of splice leader junk in the dinoflagellate's genes isn't particularly healthy, nor is it particularly deleterious – it's effectively neutral. However, one can argue that we do have an example of bloated complexity here. Since you can't go back and lose chunks of splice leaders, this ratchet essentially ensures that left to its own devices, this aspect of genome complexity will increase on its own. At a certain point, there will probably be ever-increasing selection against accumulating further splice leaders, and those lineages that go too far will simply die off – the central tendency doesn't care, and the ratchet will keep on going regardless of what selection 'wants'.This ratchet example is therefore an elegant case of evolutionary direction that's not particularly well explained by the central dogmas of Modern Synthesis or (neo)Darwinism, where selection is the force that crafts order and directionality, with mutation a mere passive provider of material to be molded. I will go into a deeper discussion of this in another post (there's a cool paper coming out soon), but I think it's worth briefly mentioning here too while we're at it. The "mutation" step (to which, I guess, this trans-splicing and reverse-transcription process can be awkwardly attached) here is what provides a drive, a push in a certain direction, and towards increasing complexity, no less (although that last detail is irrelevant). While selection is present and provides constraints (if both genes are lost, for example, the organism dies), it does not do the 'driving' or 'forcing' in this system. Very crudely put, selection here is the passive phenomenon, and mutation is at the wheel.Another case of intrinsic directionality, but where reversal is allowed, is your garden variety directional bias – where proceeding in one direction is more probable than going backwards. A very basic example of that is if the replication machinery favours a certain type of nucleic acid – left to its own devices, the genome base composition would be skewed in that direction. Boundaries can also induce an apparent directionality, but in this case it's no longer intrinsic... that's, again, a topic for another day.This idea was a part of the Mutationism theories in the early 20th century, which were a little extreme and perhaps premature, since mu... Read more »
Slamovits, C., & Keeling, P. (2008) Widespread recycling of processed cDNAs in dinoflagellates. Current Biology, 18(13). DOI: 10.1016/j.cub.2008.04.054
McShea, D. (2001) The minor transitions in hierarchical evolution and the question of a directional bias. Journal of Evolutionary Biology, 14(3), 502-518. DOI: 10.1046/j.1420-9101.2001.00283.x
Stoltzfus A. (2006) Mutationism and the dual causation of evolutionary change. Evolution , 8(3), 304-17. PMID: 16686641
- April 4, 2011
- 11:42 AM
- 618 views
"Just another ciliate" – importance of sexy descriptions
by Psi Wavefunction in Skeptic Wonder
There are species descriptions, and then there are species descriptions. All too often, you come across a mention of some obscure but ridiculously cool-looking organism, with only a very scant description of what it looks like and what it does. Much less often, you can come across yet-another-new-species (usually of a ciliate), but a particularly nicely described one. Again, those super nice descriptions tend to be of ciliates, largely due to the likes of Wilhelm Foissner and his academic offspring. Descriptive detail can only make species more interesting, and eventually of great potential to be useful for science. (Conversely, many a taxon has been rendered invalid due to poor description)A sexy description is also a great way to lure readers into noticing your otherwise garden variety new species. Case in point – I see this random IJSEM paper on a couple new marine ciliate Frontonia species – nothing too earth shattering. Being rather compulsive about skimming over any mention of a protist I see in the literature, I click. Being rather lazy and a shallow-minded picture-loving type, I head straight for the figures. Unexpectedly, they dazzle me with sexiness. Desperate for something easy to blog about for the next little while (impending interview, exams, end-of-term chaos, etc), I suddenly find your otherwise-routine new species description quite exciting and blog about it. Here, Frontonia mengi and F.magna get screentime largely thanks to their authors.Some of us in science are that simple minded. If more people realised that and preyed upon our ilk with shiny pictures, think how much more presentable science as a whole would be!(That said, no amount of gloss and shine can make your data more or less wrong. But it can, and does, dazzle some of us into overlooking a flaw or three...)Actually, the above was just a long-winded elaborate excuse to post ciliate porn. Ah, check out the kineties on that ass!Frontonia mengi. See text. (Fan et al. 2010 IJSEM)Well, those were mostly just shots of its oral ciliature, but close enough. The root structures of the cilia are highlighted with silver nitrate and carbonate staining, yielding the pretty staining effect. a-c section through the 'mouth'; d shows the "membranelle" around the 'mouth'. e shows the area behind the mouth; arrowhead points to the cytopyge. 'Cytopyge'? Well, a cell's gotta get rid of its waste somehow, and ciliates actually have the cellular analogue of an asshole. Not the socially dysfunctional kind. So yeah, look at that ass. g shows detail of the cortex, h is the overall view of the ventral ciliature. At i, the rows of cilia "stitch together" at the 'anterior suture'. k shows the germline micronucleus (Mi) and somatic macronucleus (Ma).Now for some delicious DIC:Frontonia mengi. See text. (Fan et al. 2010 IJSEM)Crisp DIC intoxicates me. The seductive allure of polarisation-derived faux-3D relief is nearly impossible to resist, especially when you have the fine complex cell of a ciliate. In fact, good DIC is often better than staining, since you don't have to fix (kill) anything. Unfortunately in the case of some larger ciliates, some degree of squishing must be done otherwise the sample is too damn thick for crisp DIC. I think the gist of microscopy can be summarised as the never-ending compromise between care of specimen and care of the optical setup. The most powerful microscopy generally requires total destruction of the specimen, whereas the most natural and undisturbed data can only be attained with simple techniques and weak optics. It's like the Heisenberg principle of microscopy: the more accurately you determine the state of your specimen, the more mangled your specimen gets.I digress. In the above plate, a-e show general views of several individuals of F.mengi. Remember my rant a couple posts ago about the usefulness of depicting morphotypical (shape type) variation? I hope it is evident here how that can be useful. For example, if only figure a was published, one could be mislead to consider that large vacuole a characteristic feature of this particular ciliate species. The other four images, however, show that to be a feature of just that specimen instead (non-contractile vacuoles, in this case). Furthermore, the authors even invluded a table of morphometric data, measuring the body dimensions and some visible subcellular details (like numbers of kineties and nuclear size) of 23 individuals.The arrow in 1b points to a contractile vacuole – one could just make out the channel leading to the cell's exterior for expelling its contents. f-g show sections of the mouth, live. h shows detail of the cell surface, the oral apparatus quite visible (as is the cytopyge). i details the cytopharyngeal rods, which are specialised structures this genus of ciliates employs to devour long strands of algae. The characteristically massive ciliate nuclei are visible in j – the arrow points to the macronucleus while the arrowhead points to the micronucleus. No staining necessary, fuck yah.Frontonia, like many ciliates, is also armed and dangerous. The surface is loaded with extrusomes (k), which can fire leaving a trail, much like the cryptomonad ejectisomes (l). m and n show the contractile vacuole and its exit pore, respectively. The contractile vacuole is necessary for osmotic regulation, especially in freshwater species, and is somewhat analogous in function to our kidneys.The second species, Frontonia magna, is also well-described. In these specimens, one can make out the algal filament and its constituents – particularly in b, e and f. Like F.menga, it's also loaded with extrusomes (h). I particularly like i, which shows the ciliature of the anterior suture. It's quite hawt.Frontonia magna. See text. (Fan et al. 2010 IJSEM)Of course, no description is properly complete (in my opinion) without drawings to accompany the micrographs. Drawings highlight the important features observed by the authors, and are useful in combining information gathered from multiple sections and imaging techniques in a convenient summary. Making an accessible visual summary of a huge pile of microscopy data is no easy task, and is very much an art.Continuing with F.magna, a summarises the ventral view of a typical individual. b provides a sketch of the sutures, without the distracting detail. c shows the side view, along with the contractile vacuole. d shows the relative sizes and positions of the nuclei. e, again, emphasises variation – it shows the various ways a cell appears after overeating with algal filaments protruding all over the place. It's amazing how hard prey can try to make their predator look like an entirely new freaking domain of life, by stretching it out and colouring it in all sorts of funny ways. A similar phenomenon has... Read more »
Fan, X., Chen, X., Song, W., Al-Rasheid, K., & Warren, A. (2010) Two new marine Frontonia species, F. mengi spec. nov. and F. magna spec. nov. (Protozoa; Ciliophora), with notes on their phylogeny based on SSU rRNA gene sequence data. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY. DOI: 10.1099/ijs.0.024794-0
- March 28, 2011
- 09:26 AM
- 618 views
Dermamoeba – Having your coat and eating it too
by Psi Wavefunction in Skeptic Wonder
We've been neglecting the micro-squishies lately (filose amoebae ain't proper squishies – too many fine protrusions in the way). Amoebozoa is a eukaryotic supergroup comprised of predominantly lobose amoebae, meaning their pseudopods are rounded and not fine and pointy (like those in the preceding post's organism – Filoreta). Aside from the test-bearing Arcellinids, amoebozoans tend to be naked amoebae ('gymnamoebae'), like the well-known Amoeba proteus, often erroneously referred to as a 'primitive', 'simple' or 'ancient' organism. "Naked amoeba" is a bit of a misnomer – while they don't lug rocks and heavy dishware around like testate amoebae, they generally carry some sort of cover, as most cells do. Gymnamoebae just pack light. Some, like Cochliopodium, dress themselves in intricate scales, while others, like many Vannellids, are covered in thin, pointy glycostyles. Dermamoeba, in turn, wears a thick, heavy coat.5-8 Dermamoeba going about its business (n – nucleus, cv – contractile vacuole). 9 – Dermamoeba lounging about in cysts (c) upon devouring some algae (chain-forming diatom or some Trebonema-like thing). Nom nom nom. (Smirnov et al. 2011 EJP)Dermamoeba's fine coat consists of thick bi-layered glycocalyx (a covering of fluffy sugar-proteins), sometimes with additional 'dense matter' lining the cell membrane. Upon encystation, an extra layer, the cell wall, is formed, but the contraption is thick enough without it already, at about half a micron.EM sections through the intense Dermamoeba cell coat. m – cell membrane, gl – glycocalyx, adm – 'arrangement of dense material' (ie, "we don't know"). The glycocalyx often forms pretty patterns when sectioned. (15 is part of a Golgi body) (Smirnov et al. 2011 EJP)This thick coat poses some problems of its own. Amoebae eat by engulfing prey with their pseudopods – and this involves some degree of nudity and cell membrane exposure. Half a micron of glycocalyx wouldn't be particularly flexible, and and not much fun to digest. Dermamoeba has to nibble on its coat before the meal. Upon contacting prey (typically algae), the amoeba forms a concave food cup around it, from the centre of which the cell coat gradually disappears. As the food cup deepens, the prey is pulled in to meet its doom via thick bundles of actin microfilaments spanning much of the cell – another unusual feature of this process. The prey is consequently engulfed for eventual digestion. As a result, the prey-containing vacuole has no glycocalyx for the amoeba to choke on (or rather, presumably, waste energy digesting).Diagram of Dermamoeba's unusual feeding procedure. After the algal prey (al) is contacted by the amoeba (am), the glycocalyx (gl) is digested and the prey is drawn in by thick actin microfilament bundles (mf). The resulting food vacuole (fv) is conveniently devoid of coat material. (Smirnov et al. 2011 EJP)And here the food cup is 'live', or was before some electron microscopist brutally murdered it in osmic acid and sliced it up:EM sections through prey (al) being engulfed by the amoeba (am). Note the disappearance of the glycocalyx (gl) at the centre of the invagination. (Smirnov et al. 2011 EJP)How do some of the other coat-bearing amoebae get around their irremovable clothing? Without going into much detail (amoebozoan surface coverings are really cool...), the glycostyle-bearing Pellita simple sticks small 'subpseudopodia' through it for both moving about and feeding. In fact, some propose that the glycostyles may help it move by reducing the surface area in contact with the substrate – keeping the sticky cell membrane away on stilts.Top left: Pellita walking on stilts of glycostyles (depicted at the right). Bottom: extruding sub-feet across stilts for feeding. (Smirnov & Kudryavtsev 2005 EJP)I'm decidedly avoiding amoebozoan systematics here. Christopher Taylor did a nice overview of it at the Catalogue of Organisms a while back, but keep in mind that some of the groups did jump around since then, and the phylogenies are in the works. Maybe if more people cared, the taxonomy could be resolved sooner...PS: My committee* has voted to remove "Sunday Protist" from Sunday Protist titles, since:a) They seldom come out on Sundays anyway (lulz); andb) Takes up too much valuable headline real estate. Since we bloggers are supposedly playing pseudo-journalists or something, might as well play it right... ;-)(and c) Structure and I aren't the best of friends.)* Given how inefficient my brain is at accomplishing anything, I've concluded it can only be composed of a close neural approximation of a committee. Explains the indecisiveness as well. Probably requires a double majority to pass any major decisions, and hence is about as effective as the Californian government. Without the sovereign debt crisis, fortunately.References... Read more »
SMIRNOV, A., & KUDRYAVTSEV, A. (2005) Pellitidae n. fam. (Lobosea, Gymnamoebia) – a new family, accommodating two amoebae with an unusual cell coat and an original mode of locomotion, n.g., n.sp. and comb. nov. European Journal of Protistology, 41(4), 257-267. DOI: 10.1016/j.ejop.2005.05.002
Smirnov AV, Bedjagina OM, & Goodkov AV. (2011) Dermamoeba algensis n. sp. (Amoebozoa, Dermamoebidae) – An algivorous lobose amoeba with complex cell coat and unusual feeding mode. European Journal of Protistology. info:/10.1016/j.ejop.2010.12.002
- March 17, 2011
- 05:25 AM
- 423 views
Trypanosomatid plastids and uninentional scientific comedy
by Psi Wavefunction in Skeptic Wonder
One need not read past the abstract:"It is usually assumed that the trypanosomatid plastid shared a common origin with that of euglenids, but Δ4 desaturase phylogenies suggest that it could have originated via an independent, tertiary endosymbiosis involving a haptophyte alga. It is also possible that ancestors of the Trypanosomatidae initially possessed a primary plastid that later was replaced by a secondary or tertiary plastid." – Bodyl et al 2010 J Parasitol (pdf)I could go on for many, many pages about the implausibility of most entirely unnecessary serial plastid symbiosis theories; I could go on for pages yet on how little a single gene phylogeny means these days; I could go over the typical first few lectures on phylogenetic reconstruction and the fundamental principle of parsimony. But instead, I've quickly thrown together a diagram highlighting the KEY problem with Bodyl et al.'s hypothesis:Taxa in black – non-photosynthetic and non-plastid-bearing.Trypanosomes don't have plastids. Or any reason to suspect they might.*to be fair, they are (I hope) talking about a plastid in their ancestry, but those things are seldom lost completely due to inevitable strong dependencies.In fact, unlike apicomplexans, trypanosomes are nested firmly within a completely non-photosynthetic phylum in a predominantly non-photosynthetic subgroup of an almost-exclusively non-photosynthetic supergroup. Furthermore, the many possible phylogenies of euglenid evolution overwhelmingly support a single symbiotic event; character evolution supports this further, in one of the few cases where there's actually little room for dispute. Endosymbiosis may not be excessively rare, but it ain't common either, particularly in a full-fledged form involving vast transfer of plastid genes to the nucleus AND mechanisms of plastid targeting of the synthesised proteins. Too many an ambitious biologist completely forget about targeting, or that there's actual cell biology happening around their beloved gene sequences.For a properly scientific and civil demolition of an earlier iteration of this ridiculous idea, see Leander 2004 Tr Microbiol (pdf). That smell of something burning? No need to worry – probably just coming from the link.Lastly, as ridiculous as this hypothesis is and as amusing as it is that this actually survived peer review (no offense to J Parasitol, but phylogenies and evolution do not seem to be their strong point based on some other cases...), I fully support it being published. It is the excessive censorship of atypical theories rather than sketchy papers that "stiffles [scientific] thought"...(Note: I would've submitted this to the high IF Journal of Are You Fucking Kidding, but I'm out of hard liquor and would thereby fail the author instructions...)ReferencesBodył, A., Mackiewicz, P., & Milanowski, R. (2010). Did Trypanosomatid Parasites Contain a Eukaryotic Alga–Derived Plastid in Their Evolutionary Past? Journal of Parasitology, 96 (2), 465-475 DOI: 10.1645/GE-1810.1LEANDER, B. (2004). Did trypanosomatid parasites have photosynthetic ancestors? Trends in Microbiology, 12 (6), 251-258 DOI: 10.1016/j.tim.2004.04.001
... Read more »
Bodył, A., Mackiewicz, P., & Milanowski, R. (2010) Did Trypanosomatid Parasites Contain a Eukaryotic Alga–Derived Plastid in Their Evolutionary Past?. Journal of Parasitology, 96(2), 465-475. DOI: 10.1645/GE-1810.1
LEANDER, B. (2004) Did trypanosomatid parasites have photosynthetic ancestors?. Trends in Microbiology, 12(6), 251-258. DOI: 10.1016/j.tim.2004.04.001
- March 15, 2011
- 09:09 AM
- 630 views
Sunday Protist – Trimastix marina
by Psi Wavefunction in Skeptic Wonder
Before we begin, two things about [current] Trimastix marina – it has four flagella (not three) and is found in freshwater. The taxonomic author, Saville-Kent, is a bit notorious for some rather sketchy descriptions, and Trimastix is one of his 'trophies'. That said, it may be that Kent did actually see a three-flagellated and/or marine thing like this and it just hasn't been found or published yet. But for the time being, feel free to point and laugh at the double misnomer.This past fall I dumped a bunch of leaves in a dish and kept them wet for a while. Turns out, the abundance and diversity of microbes and meiofauna thriving in that pile of dead leaves in your yard is quite amazing – all sorts of ciliates, myxomycetes (slime moulds), tardigrades, rotifers, springtails, flagellates, amoebae – you name it. Some of this world can be seen with a simple dissecting scope; it helps to put a coverslip or some other piece of glass on the wet leaves to see better. This coverslip is also great for investigating what lives on the surface of the rotting leaves. The other impressive detail was how quickly the leaf tissues rot away, after a couple months leaving little more than the bare skeleton of the vascular system. Dead leaves are the whale falls of the terrestrial microbiome.Rotting tissues tend to have relatively low oxygen concentrations, and thus host some unique organisms. Among them was this peculiar flagellate that simply screamed "EXCAVATE" at the top of its lungs, but I couldn't quite figure out what it was:Trimastix marina. The cell body is about 25-30µm, with a prominent anterior flagellum sticking out in front, and three smaller flagella trailing behind. The nucleus is the little blob at the very anterior tip of the cell, in front of a large circular food vacuole. At the very posterior tip is the contractile vacuole characteristic of freshwater things in general. Along the side of the cell is an exceptionally conspicuous groove, through which one of the recurrent flagella runs – a characteristic feature of excavates. Anoxic, leaf litter moistened with ample water for a couple of weeks. 40x obj, DICThe part that screamed "EXCAVATE" at me was the distinctive groove (namesake of the supergroup) along the side of the cell. You can often discern it in other excavates like Jakobids, Retortamonads and Carpediemonas-like organisms (CLOs; hey, it beats "Clade B"...), but here you don't even have to look hard. Curiously, the closely related oxymonads (see Streblo, Saccinobaculus) seem to have lost the groove, but that's another story.Overview of 'basic' excavate cell types. Trimastix marina is the very distinctive one in the bottom middle. There's something distinctive and cute about its thick anterior flagellum and the way it moves. (Simpson et al. 2002 JEM)Thus far, Trimastix may seem like your garden variety peculiar flagellate. But there's something universally eukaryotic you might have difficulty finding – a proper mitochondrion.I mentioned earlier the sample was somewhat anoxic. It wasn't irrelevant, because I've never seen anything like this critter in regular pondwater or well-aerated soil. Like many of its excavate relatives, Trimastix has lost the necessity to maintain the elaborate complexity of aerobic pathways and their accompanying structures, like cristae. Furthermore, it lacks a mitochondrial genome. This led to the conclusion that Trimastix lacks anything mitochondrial altogether, and may have diverged prior to mitochondrial endosymbiosis – a perfectly reasonable assumption given the data at the time. This landed Trimastix (along with the better-known sister Oxymonads) a position in then-subkingdom/phylum Archezoa (Cavalier-Smith 1983)[NB: Archezoa = 'beginning/early animals', not ArchaEzoa, which would be 'ancient animals'. He seems particular about that.]Trimastix wasn't a major player in the Archezoa Hypothesis (wherein 'amitochondriate' lineages are contemporary representatives of pre-endosymbiotic eukaryotes) since it's rather obscure, but was still a piece of the puzzle. Eventually, better phylogenetic techniques and improved taxon sampling destroyed the Archezoa Hypothesis, particularly as mitochondrial genes and derived organelles (such as mitosomes and hydrogenosomes) were found. Trimastix's mitochondrial genes were found later than those of other anaerobes, perhaps owing to its obscurity – but they're there: mitochondrion-targetting genes in the nuclear genome (Hampl et al. 2008 PLoS ONE). Furthermore, the aftermath of mitochondrial reduction looks like a generic double-membrane bound blob in electron micrographs (Hampl & Simpson 2008 in Hydrogenosomes and Mitosomes: Mitochondria of Anaerobic Eukaryotes) – no wonder it was so hard to find!All that's left of Trimastix's mitochondrion, as the eons of anaerobic existence devoured its need to maintain one. It is uncertain whether it produces hydrogen gas – which would make it a hydrogenosome rather than a mitosome – though at least some of the necessary genes seem to be present in the nuclear genome. (Hampl & Simpson 2008)As an aside, there's no known case yet of a reduced mitochondrion that simply disappeared – in addition to aerobic respiration, eukaryotes have also become dependent upon it for some other vital metabolic pathways, such as those involving the Fe-S cluster. In fact, in at least one species of microsporidia, ATP is imported into the mitochondrial relic in order to keep the key metabolic pathways running. (I vaguely recall having written about this before, somewhere...)Lastly, Trimastix is host to some lateral gene transfer for its glycolytic pathway – it appears to have picked up and replaced at least four of the eukaryotic genes with bacterial versions (Stechmann et al. 2006 BMC Evol Biol). There was a discussion somewhere on the blogosphere lately (Coyne's blog, IIRC) about the relative importance of LGT – it sure as hell does happen in eukaryotes as well, though not crazy enough to wreak havoc on the phylogenies.And the rain hasn't stopped yet. But I can't skip a second night of sleep... as much as I'd love to keep blogging about stuff.References... Read more »
Hampl, V., Silberman, J., Stechmann, A., Diaz-Triviño, S., Johnson, P., & Roger, A. (2008) Genetic Evidence for a Mitochondriate Ancestry in the ‘Amitochondriate’ Flagellate Trimastix pyriformis. PLoS ONE, 3(1). DOI: 10.1371/journal.pone.0001383
Hampl, V, & Simpson, AGB. (2008) Possible Mitochondria-Related Organelles in Poorly-Studied “Amitochondriate” Eukaryotes. HYDROGENOSOMES AND MITOSOMES: MITOCHONDRIA OF ANAEROBIC EUKARYOTES. DOI: 10.1007/7171_2007_107
SIMPSON, A., RADEK, R., DACKS, J., & O'KELLY, C. (2002) How Oxymonads Lost Their Groove: An Ultrastructural Comparison of Monocercomonoides and Excavate Taxa. The Journal of Eukaryotic Microbiology, 49(3), 239-248. DOI: 10.1111/j.1550-7408.2002.tb00529.x
Stechmann, A., Baumgartner, M., Silberman, J., & Roger, A. (2006) The glycolytic pathway of Trimastix pyriformis is an evolutionary mosaic. BMC Evolutionary Biology, 6(1), 101. DOI: 10.1186/1471-2148-6-101
- March 2, 2011
- 07:34 AM
- 709 views
Cryptomonads: solar-powered armoured battleships
by Psi Wavefunction in Skeptic Wonder
I've been 'scoping around some pond water lately and came across some relatively big cryptomonads (g. Cryptomonas, I think). Cryptos aren't all that rare, but most of them whirl about rather hyperactively, rendering them as troublesome photo subjects. This specimen, on the other hand, had a convenient habit of pausing every once in a while to have its picture taken. Finally, I have my own cryptomonad shots!Cryptomonas(?) sp. The cell is about ~30µm long, pretty big for a cryptomonad. On its right side the cryptomonad has a furrow – or, in some species, an tube-like gullet – lined with ejectisomes (particularly visible in the top right image). The vesicle at the anterior tip of the cell is its contractile vacuole. Refractile stuff is the starch granules. 40x objective, DICDespite their small size and superficially generic algal appearance, cryptomonads do have quite a few awesome bits about them. From an evolutionary standpoint, they have pretty damn awesome plastids – products of secondary endosymbiosis of red algae, complete with a shrunken relict nucleus ("nucleomorph") of the red algal ex-host! The plastids also have four membranes, complicating the delivery of plastid-targetting proteins from the cryptomonad host nucleus. But I'll save that story for some other time, and instead keep it superficial. Literally: it has ejectile things lining its surface, and who doesn't like the idea of a microscopic solar-powered hyperactive battleship?Prior to embarking on some battle scenes, lets look around the ship's anatomy a little bit mostly as an excuse to show off a diagram. At its fore we have a pair of flagella, lined with little hairs – also a characteristic of many Alveolates and Stramenopiles, with whom Cryptomonads might share the secondary red algal symbiosis event with. Much of the cell is occupied with a single plastid, making the fucker a bit difficult to diagram. In all his/her/its infinite wisdom, the designer apparently failed to take into consideration the future pains of this student attempting to tame the wild beast that is Illustrator while drawing this cell. Asshole. Besides the plastid, there's also a single mitochondrion and a bunch of other small crap that a eukaryote ought to have. The plastid's outermost (fourth) membrane is contiguous with the endoplasmic reticulum system, presumably homologous to the original digestive vesicle that enveloped the 'enslaved'* red alga. The third membrane derives from the red algal cell membrane, whereas the inner pair are the usual plastid membranes. Pop quiz: where would you expect to find the relict endosymbiont's nucleus (the nucleomorph)? (Answer at the bottom of the post, or in the diagram if you're so inclined to 'cheat' ;p)*Google [scholar] "Cavalier-Smith" and "enslaved". When he likes certain words, he really likes them.Back to the surface. The cryptomonad surface is quite complex, consisting of an inner and surface periplast layers separated by the cell membrane. Sometimes the surface layer can be be covered in scales, sometimes fibrous matter. This periplast is perforated with pores for ejectisomes, much like battlements on a warship. Ejectisomes themselves consist of coiled proteinaceous ribbons that extend forcefully upon firing.Cryptomonad periplast. IPC – inner periplast layer, PM – plasma membrane, S – scales (of the surface periplast layer). On the right is a freeze fracture EM of the plasma membrane, which shows imprints of the surface scales (vaguely hexagonal) and pores for ejectisomes (E). In other words, the surface of an armoured warship with battlements. (Brett & Wetherbee 1986 Protoplasma)Ejectisomes – more generally, extrusomes – are not all that unusual in the protist world. Many ciliates are loaded with menacing trichocysts and green algae like Pyramimonas are not afraid to fire similar structures either. Some bacterial endo- and episymbionts also bear similar coiled structures, but that's a topic for some other day as well. Extrusomes can also be used more locally to glue prey to the organism – if you, upon finding yourself shrunk to microns, accidentally bump into a frail-looking centrohelid heliozoan, be afraid. Be very afraid. It will smother you in adhesive proteins from the extrusomes lining its fragile-looking axopodia and devour you alive and possibly paralysed.Ejectisomes in cryptomonads and their non-photosynthetic close relatives, katablepharids. Pyramimonas is only distantly related, and probably evolved its ejectisomes completely independently. (Kugrens et al. 1994 Protoplasma: nice review on protist ejectisomes in general, excluding ciliates)One of the poor cryptomonads got stuck as my slide was drying out, and in its agony, released an explosion of ejectisomes. As any other biologist excessively attached to their subjects, I hate seeing protists die; at least this one didn't die in vain but gave us a nice demonstration. Extrusome firing often accompanies stress in protists that have them, drying out definitely qualifying. The following images are quite graphic, and not for the faint of heart. At least because the image quality is seriously compromised by a random layer of air between the coverslip and the specimen covered with remnants of water – a total chaos of refraction indexes.... Read more »
Brett, S., & Wetherbee, R. (1986) A comparative study of periplast structure inCryptomonas cryophila andC. ovata (Cryptophyceae). Protoplasma, 131(1), 23-31. DOI: 10.1007/BF01281684
Kugrens, P., Lee, R., & Corliss, J. (1994) Ultrastructure, biogenesis, and functions of extrusive organelles in selected non-ciliate protists. Protoplasma, 181(1-4), 164-190. DOI: 10.1007/BF01666394
Purcell, E. (1977) Life at low Reynolds number. American Journal of Physics, 45(1), 3. DOI: 10.1119/1.10903
- February 21, 2011
- 12:48 AM
- 607 views
Sunday Protist – Gromia: beautiful predatory grapes of the sea
by Psi Wavefunction in Skeptic Wonder
And we're back. The protists and I, that is. Well, the protists never quite went anywhere but you know what I mean...You may have heard of Gromia a couple years ago when it hit the news by leaving tracks on the ocean floor resembling Ediacaran trace fossils (tracks). Or perhaps not; I tend to get overly excited the one time a year some protist makes the news. The giant (3cm) track-leaving Gromia in question sounded even cooler as it came from the great deep sea; other species of Gromia are in fact quite content with the more familiar shallow waters as well, crawling on the holdfasts of kelp in addition to thriving in the ice cold polar waters of McMurdo Sound (Antarctica), where the vibrantly colourful first specimen below comes from:Gromia, from various locales including Antarctica (A), Madeira in the Atlantic (B) and Guam (C). Big and colourful, what's not to like there? Scalebars: A - 1mm; B - 0.5mm; C - 0.1mm (Burki et al. 2002 Protist)For some time, there has been considerable confusion between Gromia and the cruelly similarly-named foraminiferan Allogromia, bad enough to warrant a Nature paper (Hedley 1958). At first glance, they do appear somewhat similar: a sizeable grape-like blob of a test surrounded by a mass of fine pseudopodia. While foram pseudopodia form a rather elaborate and extensive network of doom and terror for anything they come in contact with, Gromia uses more modest non-fusing alternative of pseudopodia. Thus, prior to molecular data, it was often considered a sort of a precursor to the more grown-up real forams, and assumed to have a rather simple test. They could hardly be more wrong, both with the assumed relation to forams and the simplicity of its test.Typically (using that word rather loosely), a protist test consists of the plasma membrane covered by some sort of an organic matrix (often sugary proteins and protein-y sugars), followed by the deposited structural material, be it agglutinated bits of rock from the environment (often carefully and specifically selected) or secreted calcium carbonate, siliceous scales or something else entirely. To my knowledge, the process of selecting material for the test in agglutinating species, and formation of the test in general, is still quite poorly understood. There is some understanding of how diatoms and some coccolithophorids build their extracellular wonders, but most amoebae have been largely ignored, even the more 'famous' representatives like the forams, euglyphids and arcellinids. The Allogromia mentioned earlier has the organic (non-calcified, non-agglutinated) test characteristic of Allogromiids at large, who form a vast paraphyletic sea of diversity from which the more popular lineages arise – the Protista of the foram world, if you will.Gromia also carries an organic test, hence the confusion with Allogromiids. But its test turns out to be a bit more elaborate, with an inner lining consisting of up to ten layers of odd honeycomb membranes, the whole thickness of the structure penetrated by multitudes of pores. The test surface is sometimes covered by attached bacteria (Aranda da Silva & Gooday 2009 DSR II). Furthermore, rather than simply a hole in the wall, its opening is surrounded by a complicated oral capsule which acts as a valve or a trap door: when the pseudopodia are withdrawn, the opening closes. One seldom thinks of movable structural parts on the microscopic level, but here you go:The structure of Gromia's test and oral capsule, in that order. The figure on the right shows a pseudopodium gradually protruding through the closed aperture. (Hedley & Bertaud 1962 J Protozool; Mazei & Tsiganov 2006 in Presnovodniye Rakoviye Amyobi (in Rus.))The pores make the test surface look quite pretty in reflected light:The giant deep sea Gromia sphaerica; note the complex test surface structure with prominent perforations. (Matz et al. 2008 Curr Biol)To make these mysterious 'grapes' of the sea even sexier, they are known to have sex. Upon conjugation, flagellated gametes are exchanged between the parents, producing amoeboid diploid swarmers that ultimately form a new test and complete the cycle. The parental shell and all the work that went into building one is abandoned in this process. Both forams and gromiids are 'mortal' in our sense – they spend a period of time building a body that eventually becomes abandoned by the next generation. Organisms like many flagellates, for example, are somewhat 'immortal' in that the cell is never abandoned between generations, but rather split up and shared by mostly clonal offspring. Extra structural complexity often bears the curse of losing 'immortality'.Gromia's life cycle. (Arnold 1966 J Protozool)Gromia shares some strangeness with giant deep sea ... Read more »
Aranda da Silva, A., & Gooday, A. (2009) Large organic-walled Protista (Gromia) in the Arabian Sea: Density, diversity, distribution and ecology. Deep Sea Research Part II: Topical Studies in Oceanography, 56(6-7), 422-433. DOI: 10.1016/j.dsr2.2008.12.027
Silva, A., Pawlowski, J., & Gooday, A. (2005) High diversity of deep-sea Gromia from the Arabian Sea revealed by small subunit rDNA sequence analysis. Marine Biology, 148(4), 769-777. DOI: 10.1007/s00227-005-0071-9
ARNOLD, Z. (1966) Observations on the Sexual Generation of Gromia oviformis Dujardin. The Journal of Eukaryotic Microbiology, 13(1), 23-27. DOI: 10.1111/j.1550-7408.1966.tb01863.x
Zach M. Arnold. (1952) Structure and Paleontological Significance of the Oral Apparatus of the Foraminiferoid Gromia oviformis Dujardin. Journal of Paleontology, 26(5), 829-831. info:/
BURKI, F. (2002) Phylogenetic Position of Dujardin inferred from Nuclear-Encoded Small Subunit Ribosomal DNA. Protist, 153(3), 251-260. DOI: 10.1078/1434-4610-00102
- December 4, 2010
- 11:04 AM
- 670 views
Walsby's Square Archaea! Haloquadratum walsbyi
by Psi Wavefunction in Skeptic Wonder
Procrastination and overwhelming itch to get back to blogging win over the more pressing obligations tonight. Fuck'em, it's Friday night, I can write about protists if I feel like it. Moreover, I can even write about non-protists, especially those I've been meaning to write about for a month now. Square Archaea!Despite their awesome morphological diversity, seldom do cells take the shape of a flat square. Or any other flat geometric shape. In fact, there are reasons for this – the cell cytoplasm is generally hypertonic relative to its surroundings (the cell contains more solute), so there is considerable osmotic pressure against the cell membrane, kind of like an inflated balloon. The optimal favoured geometry in this situation is a perfect sphere, so without cytoskeletal or cell membrane alterations, the cell swells up into a ball. Plant mutants deficient in wall cellulose tend to have very bubbly cells, as do plants treated with cellulose-inhibiting drugs, due to turgor pressure from within. Thus, it would take a lot of structural effort for a cell to take on a very flat shape, with a high length x width : height ratio. Normally. Except when they do just that: brought to us from a very salty pool on the Sinai Peninsula is Walsby's square archaeon, a thin rectangular sheet of cell:Left: Walsby's square archaeon, Haloquadratum walsbyi. A – phase contrast of archaean with conspicuous gas vesicles; B – TEM detail of gas vesicle; C – darkfield micrograph of large cell – their unusual flexibility means they're seldom found unfolded. (Bolhuis et al. 2004 Env Microbiol) Right: Original images of the square archaean, from Walsby 1980 (Walsby 2005 Tr Microbiol).These flat ~1.5 x 1.5 µm cells are only 0.1µm thick at most. The cell periphery is lined with conspicuous gas vesicles of undetermined function; they were previously thought to be involved in buoyancy, but experimental data cast doubt on that idea. Instead, they may participate in positioning cells parallel to the surface in order to optimise light exposure for their photoactive pigments (Oren et al. 2006 Saline Syst, OA). They may also play a role in buffering changes in turgor pressure (Walsby 2005). Some cells are unbelievably square, but most tend to be rectangular, due to growth. One can't really divide into squares unless some weird four-way cell division process is employed, so the non-square delinquents have a reason for their geometric imperfections.Left: Cryo TEM of H.walsbyi, showing prominent gas vesicle in the corner. The scalebar is 1µm. (Burns et al. 2007 IJSEM) Right: Electron tomography of a single H.walsbyi cell. Gas vesicles (GV) line the cell periphery, while electron-dense blobs of acidic polymers fill the inside of the cell. (Bolhuis et al. 2006 BMC Genomics, OA)Unlike protistologists, bacteriologists are blessed with small genomes, and can thus sequence whatever they like with little pain (relatively). This means they get to sequence all the cool things they want, which is a little unfair. Haloquadratum has been sequenced (Bolhuis et al. 2006 BMC Genomics); there is also unusually high amounts of polymorphisms in ribosomal DNA both within species and within the genomes themselves, thought to be an adaptation to their extreme environments (López-López et al. 2007 J Mol Evol), although the adaptation aspect is to be taken with a grain of salt as it is difficult to distinguish from consequence. Haloquadratum belongs to a large group of extreme halophilic archae, the Halobacteriales. Obligatory latest tree (note the taxonomic mess, and the swaths of poorly-understood organisms in need of attention):Phylogeny of salty extremophilic Halobacteriales; as with anything microbial, taxonomic chaos is inevitable. Unusually high rDNA polymorphism within single species doesn't help much either. (Modified... Read more »
Bolhuis, H., Poele, E., & Rodriguez-Valera, F. (2004) Isolation and cultivation of Walsby's square archaeon. Environmental Microbiology, 6(12), 1287-1291. DOI: 10.1111/j.1462-2920.2004.00692.x
Bolhuis, H., Palm, P., Wende, A., Falb, M., Rampp, M., Rodriguez-Valera, F., Pfeiffer, F., & Oesterhelt, D. (2006) The genome of the square archaeon Haloquadratum walsbyi : life at the limits of water activity . BMC Genomics, 7(1), 169. DOI: 10.1186/1471-2164-7-169
Burns, D., Janssen, P., Itoh, T., Kamekura, M., Li, Z., Jensen, G., Rodriguez-Valera, F., Bolhuis, H., & Dyall-Smith, M. (2007) Haloquadratum walsbyi gen. nov., sp. nov., the square haloarchaeon of Walsby, isolated from saltern crystallizers in Australia and Spain. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 57(2), 387-392. DOI: 10.1099/ijs.0.64690-0
Hamamoto, T., Takashina, T., Grant, W., & Horikoshi, K. (1988) Asymmetric cell division of a triangular halophilic archaebacterium. FEMS Microbiology Letters, 56(2), 221-224. DOI: 10.1111/j.1574-6968.1988.tb03181.x
Horikoshi, K., Aono, R., & Nakamura, S. (1993) The triangular halophilic archaebacteriumHaloarcula japonica strain TR-1. Experientia, 49(6-7), 497-502. DOI: 10.1007/BF01955151
López-López, A., Benlloch, S., Bonfá, M., Rodríguez-Valera, F., & Mira, A. (2007) Intragenomic 16S rDNA Divergence in Haloarcula marismortui Is an Adaptation to Different Temperatures. Journal of Molecular Evolution, 65(6), 687-696. DOI: 10.1007/s00239-007-9047-3
Minegishi, H., Kamekura, M., Itoh, T., Echigo, A., Usami, R., & Hashimoto, T. (2009) Further refinement of the phylogeny of the Halobacteriaceae based on the full-length RNA polymerase subunit B' (rpoB') gene. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 60(10), 2398-2408. DOI: 10.1099/ijs.0.017160-0
Oren, A., Pri-El, N., Shapiro, O., & Siboni, N. (2006) Buoyancy studies in natural communities of square gas-vacuolate archaea in saltern crystallizer ponds. Saline Systems, 2(1), 4. DOI: 10.1186/1746-1448-2-4
Walsby, A. (2005) Archaea with square cells. Trends in Microbiology, 13(5), 193-195. DOI: 10.1016/j.tim.2005.03.002
- November 1, 2010
- 05:51 AM
- 649 views
Sunday Protist - A sampling of Cercozoa Part I
by Psi Wavefunction in Skeptic Wonder
This post grew out of proportion, so I'm splitting it into two or three parts, to cater to our ever-shortening attention spans (mine included)...[Warning: Taxonomy. Of the harshest kind: involves Cavalier-Smith]At the moment, among my favourite supergroups is Rhizaria (tree). Rhizaria is generally where all the obscure, interesting, and outright weird eukaryotes get sent by molecular data these days. The group itself is fairly recent, having been formally spewed out declared by Cavalier-Smith in 2002, as a fusion of Cercozoa and Retaria(=forams and 'radiolarians'), as well as Heliozoa and Apusozoa, apparently because they had "a centrosomal core or radiating microtubules and two microtubular roots and soft surface, typically with reticulopodia." (TC-S 2002 IJSEM:297) Don't worry, I don't really know what that means either. That is, those are fairly common traits in many non-Rhizarians, even according to the TC-S 2002 classification.The name derives from the group's inclusion of many members of the then-defunct "Rhizopods" ('root-feet' - members typically had thin, branchy pseudopodia). Since then, Heliozoa died a horrible death with its limbs strewn all over the tree (Nikolaev et al. 2004 PNAS) and [many] Apusozoa now seem to enjoy their privileged life as the putative basal Opisthokonts (or their sisters). Ironically, many of the "Heliozoa" did return to Cercozoa later. Obligatory TC-S Diagram:The birth of Rhizaria. As the young supergroup struggles to open its eyes to the world for the first time, it is confronted by the glaring faces of frustrated readers threatening to ban the author from ever birthing another taxon, for the sake of global sanity. Yet, despite its weak, fragile synapomorphies, the newborn supergroup, heavily-medicated by state-of-the-art molecular phylogenies, rises to become a bona fide citizen of the taxonomic world. For now. As all other life forms on earth, the higher taxa themselves are mortal. (diagram slightly modified (red box added) from Cavalier-Smith 2002 IJSEM)"Radiolarians" (Acantharians+Taxopodids+Polycystines) and Forams (more generally, Granuloreticulosea) are massively diverse, complicated and awesome, but Cercozoa are more obscure to non-protistologists, and are a rather weird assemblage of stuff. I think the Amoebozoan taxon "Variosea" would have been quite fitting for them, were it not taken by amoebae instead. Cercozoa is older than Rhizaria, but not by much - it was formally established by Cavalier-Smith in 1998 (Biol Rev) as a modified successor of Rhizopoda:"The recently revised phylum Rhizopoda is modified further by adding more flagellates and removing some ‘ rhizopods ’ and is therefore renamed Cercozoa" (TC-S 1998 BiolRev:203)Of course, that was Tom's version of Rhizopoda to begin with. Taxonomy gets very fun when different people at different times mean different things by the same name. Can't seem to find the etymology of Cercozoa, but the formal description reads pretty much like 'miscellaneous eukaryotes with thin pseudopodia'. And that they are.While Cercozoa was initially based loosely on morphology and sketchy data from the dawn of molecular phylogenetics, it mostly survived intact over the years, and grew further (with various things shaved off too, of course). The original members were Phytomyxids (incl. the plant pathogen Plasmodiophora), Reticulofilosa (basically, Chlorarachniophytes) and Monadofilosa (Cercomonas, Gymnophrys, Euglypha and Spongomonas are given as original examples). Curiously, all of them survived the onslaught of molecular reality (or so we hope...). Stuff has been added, like Ascetosporea (paramyxids and haplosporidia; added in TC-S 2002 IJSEM) and the gromiids, as well as various obscure incertae sedis orphans and a few refugees from 'Heliozoa'.Eventually, the Cercozoa got 'sistered' to the forams (Keeling 2001 MBE) by ACTIN phylogenies, which got taxonomically recognised in the TC-S 2002 IJSEM revision of The Book of Tom by declaring the holy union of Retaria (forams and rads) and Cercozoa as Rhizaria. Going overboard as usual by adding in Heliozoa and Apusozoa, of course. We're talking about the mad taxonomist here ;-) (now someone needs to make that into a pop culture phenomenon to rival mad scientists..."And along comes the evil mad taxonomist...and RENAMES EVERYTHING!" *cue spooky music*) The group still lacks any solid synapomorphies (shared derived characters); the situation is such that even the use of obscure ultrastructural elements has been attempted, such as Cavalier-Smith's "transitional nonagonal fibre" (TC-S 2008 Protist) – even one of his own past students has no idea what he meant there!And a whole bunch of other stuff happened but I think that was enough Historical Taxonomy (would make the most popular course evar, srsly) for...the month. Ok, so have we lost everyone yet? Or have the wiser ones employed the high art of The Scrollbar and skimmed accordingly? In any case, I'd like to very briefly and shallowly run over a few of the major cercozoans to give you a taste of the phylum, and just how diverse and varied it is. Things will be skipped, including, quite possibly, The Most Interesting Thing Ever Because You Studied it for the Past Ten Years. Apologies in advance. TMITEBYSiftPTY will get its chance, someday.Some phylogeny and taxonomy sources: TC-S & Chao 2003; Bass & TC-S 2004; Bass et al. 2005; Pawlowski & Burki 2009; Chantangsi et al. 2010.(L: Pawlowski & Burki 2009; R: Chantangsi et al. 2010)To be continued in Part II – Endomyxa.References... Read more »
CAVALIER-SMITH, T. (1998) A revised six-kingdom system of life. Biological Reviews of the Cambridge Philosophical Society, 73(3), 203-266. DOI: 10.1017/S0006323198005167
Bass D, & Cavalier-Smith T. (2004) Phylum-specific environmental DNA analysis reveals remarkably high global biodiversity of Cercozoa (Protozoa). International journal of systematic and evolutionary microbiology, 54(Pt 6), 2393-404. PMID: 15545489
BASS, D. (2005) Polyubiquitin Insertions and the Phylogeny of Cercozoa and Rhizaria. Protist, 156(2), 149-161. DOI: 10.1016/j.protis.2005.03.001
Cavalier-Smith T. (2002) The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. International journal of systematic and evolutionary microbiology, 52(Pt 2), 297-354. PMID: 11931142
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
CAVALIERSMITH, T., LEWIS, R., CHAO, E., OATES, B., & BASS, D. (2008) Morphology and Phylogeny of Sainouron acronematica sp. n. and the Ultrastructural Unity of Cercozoa. Protist, 159(4), 591-620. DOI: 10.1016/j.protis.2008.04.002
Chantangsi, C., Hoppenrath, M., & Leander, B. (2010) Evolutionary relationships among marine cercozoans as inferred from combined SSU and LSU rDNA sequences and polyubiquitin insertions. Molecular Phylogenetics and Evolution, 57(2), 518-527. DOI: 10.1016/j.ympev.2010.07.007
Keeling PJ. (2001) Foraminifera and Cercozoa are related in actin phylogeny: two orphans find a home?. Molecular biology and evolution, 18(8), 1551-7. PMID: 11470846
Nikolaev, S. (2004) From the Cover: The twilight of Heliozoa and rise of Rhizaria, an emerging supergroup of amoeboid eukaryotes. Proceedings of the National Academy of Sciences, 101(21), 8066-8071. DOI: 10.1073/pnas.0308602101
PAWLOWSKI, J., & BURKI, F. (2009) Untangling the Phylogeny of Amoeboid Protists. Journal of Eukaryotic Microbiology, 56(1), 16-25. DOI: 10.1111/j.1550-7408.2008.00379.x
- September 30, 2010
- 05:17 AM
- 622 views
Sunday Protist – Scary nematode-eating forams and their amazing feet of doom
by Psi Wavefunction in Skeptic Wonder
Poor, poor nematodes...In the interests of public safety, I must reiterate once again what should be so painfully apparent from the last few posts on forams: If you ever find yourself shrunk to a milimetre or less, DO NOT fuck with forams. Ever.It's a fairly known fact around these parts that [unicellular] forams can devour [multicellular] animals. But thus far we've just had giant tree forams like Notodendrodes show us the terrifying force of microbial nature. Notodendrodes is notably bigger than its prey, so the embarrassed metazoa have an excuse there. As for giant planktonic forams – well, those eat things only slightly larger than themselves, you may say. In which case you must be almost insatiable. But, as usual, there's more: rather small, unassuming Ammonia tepida devouring nematodes, copepods and gastropods unarguably larger than itself.Like other forams, Ammonia uses its amazing reticulopodia (lit. "net-feet") to trap and entangle prey. Then, it penetrates its prey's exoskeleton or cuticle and forcefully rips apart the insides to shreds, bringing back phagocytosed chunks towards the main cell body for digestion. This process is creepy enough to warrant its own term: skyllocytosis (Bowser 1985 J Prootozool). All that's left behind is an empty cuticle with a hole. By the way, the prey are devoured within 24 hours. And apparently forams are pretty much always hungry. Imagine being violated by masses of dynamic and powerful net-like pseudopodia and torn to pieces from the inside. Doesn't sound fun. Feels good to be big, doesn't it?Ammonia tepida vs. nematodes. c and d show before and after shots of one such encounter. Sometimes a second foram joins for a threesome. (Dupuy et al. 2010 J Foram Res)As for copepods...the following sentence from the paper raises some concern: "Despite vigorous attempts to escape, copepods could not free themselves from the pseudopodial mesh."(Dupuy et al. 2010 J Foram Res) Most of us have seen copepods one time or another. For the world of their scale, they're quite strong. And yet they cannot escape. Neither can snails, whose shells are all that remains after a few hours. Have I mentioned foram reticulopodia are simply amazing?Ammonia tepida vs. copepod (a) and juvenile snails (b,c). Note how the copepod is partially eaten already towards the right. d,e - SEM view of the ventral (umbilical) end of the foram. Little bumps (pustules) are thought to potentially act as 'teeth' and used to grind tests and cuticles. Some other forams are thought to do this with diatoms as well. (Dupuy et al. 2010 J Foram Res)You may wonder how foram pseudopodia get to be so special. They possess many unique properties, many of which have yet to be understood. One of the more striking features is the rate of microtubule growth. @font-face { font-family: "Times New Roman"; }@font-face { font-family: "Courier New"; }@font-face { font-family: "Wingdings"; }@font-face { font-family: "ArialMS"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Times; }h1 { margin: 0in 0in 0.0001pt; page-break-after: avoid; font-size: 18pt; font-family: Times; }h2 { margin: 0in 0in 0.0001pt; page-break-after: avoid; font-size: 12pt; font-family: Times; }h3 { margin: 0in 0in 0.0001pt; page-break-after: avoid; font-size: 12pt; font-family: Times; color: blue; }h4 { margin: 0in 0in 0.0001pt; page-break-after: avoid; font-size: 12pt; font-family: Times; font-weight: normal; font-style: italic; }h5 { margin: 0in 0in 0.0001pt; page-break-after: avoid; font-size: 12pt; font-family: Times; color: blue; font-weight: normal; font-style: italic; }h6 { margin: 0in 0in 0.0001pt; page-break-after: avoid; font-size: 12pt; font-family: Times; color: blue; font-style: italic; }p.MsoHeading7, li.MsoHeading7, div.MsoHeading7 { margin: 0in 0in 0.0001pt; page-break-after: avoid; font-size: 16pt; font-family: ArialMS; color: blue; }p.MsoBodyText, li.MsoBodyText, div.MsoBodyText { margin: 0in 0in 0.0001pt; font-size: 10pt; font-family: Times; }p.MsoBodyText2, li.MsoBodyText2, div.MsoBodyText2 { margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Times; color: blue; }a:link, span.MsoHyperlink { color: blue; text-decoration: underline; }a:visited, span.MsoHyperlinkFollowed { color: purple; text-decoration: underline; }div.Section1 { page: Section1; }ol { margin-bottom: 0in; }ul { margin-bottom: 0in; }While microtubules of animal cells grow at about 1-15µm/min, microtubule assembly in some forams can reach a stunning 12µm per second (Bowser & Travis 2002 J Foram Res). They manage this by possessing a unique third conformation of tubulin: helical filaments (in addition to the usual protofilaments/'tubes and free dimers).Transformation of tubulin between helical filaments and free dimers appears to require no ATP, and thus would progress quite rapidly. Furthermore, tubulin of helical filaments can transform directly to the tubules, much faster than regular polymerisation from free dimers. The idea is that tubulin is stored in helical form (crystalised, if you will), and then transported to the site of active growth, and used for a quick and efficient supply of the growing 'tubes with fresh tubulin (Welnhofer & Travis 1996 Cell Motil Cytosk). Thus, it is perhaps not overly surprising that foraminiferan tubulins are highly diverged, suggesting selective pressure for the foram-specific modifications (Habura et al. 2005 MBE). This is yet another example of bizarre alterations by a protist of typically conservative aspects of eukaryotic biology.SEMs of foram pseudopodia entrapping prey; in this case, Artemia. (Bowser et al. 1992 J Protozool)To have an idea of what the microtubule cytoskeleton looks like in action, here's a stolen video of plant epidermis cortical microtubules marked with AtEB1:GFP:
... Read more »
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
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., ALEXANDER, S., STOCKTON, W., & DELACA, T. (1992) Extracellular Matrix Augments Mechanical Properties of Pseudopodia in the Carnivorous Foraminiferan Astrammina rara: Role in Prey Capture. The Journal of Eukaryotic Microbiology, 39(6), 724-732. DOI: 10.1111/j.1550-7408.1992.tb04455.x
Brandner, K., Sambade, A., Boutant, E., Didier, P., Mely, Y., Ritzenthaler, C., & Heinlein, M. (2008) Tobacco Mosaic Virus Movement Protein Interacts with Green Fluorescent Protein-Tagged Microtubule End-Binding Protein 1. PLANT PHYSIOLOGY, 147(2), 611-623. DOI: 10.1104/pp.108.117481
Dupuy, C., Rossignol, L., Geslin, E., & Pascal, P. (2010) PREDATION OF MUDFLAT MEIO-MACROFAUNAL METAZOANS BY A CALCAREOUS FORAMINIFER, AMMONIA TEPIDA (CUSHMAN, 1926). The Journal of Foraminiferal Research, 40(4), 305-312. DOI: 10.2113/gsjfr.40.4.305
Habura, A. (2005) Structural and Functional Implications of an Unusual Foraminiferal -Tubulin. Molecular Biology and Evolution, 22(10), 2000-2009. DOI: 10.1093/molbev/msi190
- September 8, 2010
- 06:39 AM
- 658 views
Clickable Tree of Eukaryotes (Katz Lab)
by Psi Wavefunction in Skeptic Wonder
For a while I've been contemplating on considering to con someone into making a clickable tree for me, allowing one to zoom in and click genus names leading to further info/pictures/whatever. Of course, I'd be far too lazy to actually execute such a project, especially given my lack of programming skills, and lack of faith in the stability of current phylogenies... luckily, I recently discovered some nice people already took care of that, and produced a really awesome tree:The genus names lead to their respective Micro*scope pages (with pictures)! (Parfrey and Katz, http://www.science.smith.edu/departments/Biology/lkatz/EuTree2009/Eutree09.html; relevant literature: Parfrey et al. 2006 PLoS Genet, 2010 Syst Biol)This is the eukaryotic tree of life sensu Katz Lab. Being on the opposite side of the continent, the people here have some differing opinions on the subject (my diagram – seriously due for an update – kind of reflects local influences). As you may have noticed from the bounty of polytomies (multiple branches at a single node indicating uncertainty in branching order), the Parfrey and Katz tree is quite conservative, which is probably a good thing. For pedagogical purposes, however, I still think it's better to go ahead with the supergroups, while mentioning the frailty of some, as it helps organise the organisms and dispells the common notion of Protista being just an amorphous grab-bag of microbial crap that doesn't fit. They run the show, it is WE who 'don't fit'...For research purposes, one must strive to keep track of the certainty of each and every piece of data or hypothesis one works with. Of course, that's overwhelming to n00bs people outside the field, so the shakiness of some models tends to be glossed over. Also, most people don't care.Speaking of things normal people don't care about, I was quite shocked by the disappearance of Archaeplastida as a clade -- the locals give off the impression Archaeplastida is among the healthier of the supergroups. Excavates, on the other hand, are acknowledged to be somewhat 'meh' as a clade by some of the people working on them. Hacrobia is rumoured to be practically dead anyway, so I'm just keeping that label for the sake of categorising things that may at best turn out to be paraphyletic (which I'm ok with informally), or at worst, grotesquely polyphyletic in ways that would make Heliozoa and Rhizopodia cry. Also, the Stramenopiles are sister to Rhizaria as opposed to Alveolata ("our" order goes (Rhiz,(Stram,Alv))). I find that weird. Although, on the second though, why the hell not. But local folklore has it that Stram+Alv are a pretty solid grouping. Then again, local folklore sings praises to the Chromalveolate Hypothesis... As an innocent, defenseless cell biologist, I'll just hide in the corner until this blows over...Also, note that the tattered remnants of the 'supergroups' themselves are horribly politomised. Recall how the animal phylogeny tends to have a comb-like branch structure along the 'base' -- ie, among the earlier divergence events, only one group went on to diversify in ways we notice. Then, shortly before the Cambrian diversification event ('explosion' my ass), a bunch of divergences happened that later did lead to multiple lineages that became diverse, in ways we notice. But prior to that, it seems that animal evolution proceeded at a fairly "gradual" pace, according to some anyway. In terms of extant descendants anyway. But in any case, there are ample opportunities for an illiterate journalist (or scientist) to commit the "primitive animal" fallacy.This error comes much more difficult in the eukaryotic evolution scenario, that is, if only those illiterates knew a thing or two about the modern phylogenies. This is because apparently, very few early-branching 'undiversified' taxa exist, if none at all. Hard to explain without a tree to show, but it seems like the major eukaryotic supergroups rapidly exploded, either soon after the origin of eukaryotes, or all the earlier-diverging clades disappeared without a trace.This is a question of the 'tempo and mode' of evolution -- the rate and extent of diversification. It's a rather fuzzy concept, as it's quite difficult to establish what diversity is and how to measure it. Considering we biologists don't even know what a species is (and linguists, I'm told, know not what a word (or language), is...), comparing diversity is very difficult. There are some vague tendencies, but that's all they are. Or so it seems anyway -- perhaps I missed something. I guess it's hard to compare the extent of diversity when you reject ranked taxonomy. Zoologists, at least in the past, have used phyla as an indicator, which were somewhat based on the body plan. Whether it's a valid indicator is a whole other topic, but we lack such luxuries in the microbial realm anyway. This topic deserves a proper post someday...What I was trying to get at, before almost drowning in caveats and disclaimers there, is that the major clades of eukaryotes have arisen rapidly and seem to have left no residual 'basal'/'stem' taxa, making it very difficult to resolve the relationships between them. Resolving recent 'explosions' is quite doable, as is resolving more gradual evolution in the distant past...rapid explosions in the distant past are one hell of a bitch to deal with, which is why much of the deep phylogeny remains a mystery.How I managed to go off on this tangent eludes me. I see trees, I start chatting about them, ain't nothin' I can do 'bout that.It being the start of the school year accompanied by an ominous influx of undergrad cooties *shudder*, I'm going to be on slow blogging mode for another week or so. So use that tree to entertain yourselves -- in fact, this tree and ToLweb make my blogging kind of redundant =P (shhh...) Fear not, since I still need to feel useful from time to time, my protists shall keep on coming.Relevant papers to the Parfrey & Katz tree: (should be accessible)Parfrey, L., Barbero, E., Lasser, E., Dunthorn, M., Bhattacharya, D., Patterson, D., & Katz, L. (2006). Evaluating Support for the Current Classification of Eukaryotic Diversity PLoS Genetics, 2 (12) DOI: 10.1371/journal.pgen.0020220Parfrey, L., Grant, J., Tekle, Y., Lasek-Nesselquist, E., Morrison, H., Sogin, M., Patterson, D., & Katz, L. (2010). Broadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life Systematic Biology DOI: 10.1093/sysbio/syq037... Read more »
Parfrey, L., Barbero, E., Lasser, E., Dunthorn, M., Bhattacharya, D., Patterson, D., & Katz, L. (2006) Evaluating Support for the Current Classification of Eukaryotic Diversity. PLoS Genetics, 2(12). DOI: 10.1371/journal.pgen.0020220
Parfrey, L., Grant, J., Tekle, Y., Lasek-Nesselquist, E., Morrison, H., Sogin, M., Patterson, D., & Katz, L. (2010) Broadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life. Systematic Biology. DOI: 10.1093/sysbio/syq037
- August 2, 2010
- 10:59 PM
- 723 views
Sunday Protist – Nematode-hunting amoebae: Theratromyxa
by Psi Wavefunction in Skeptic Wonder
A couple posts ago we saw how ecological relationships may refuse to obey the laws of their kingdoms: protists can hunt crustaceans. Protists can also farm bacteria, animals can parasitise unicellular protists, plants can parasitise fungi, fungi can hunt animals, animals can steal plastids and photosynthesise, as well as steal algae for their embryos, fungi parasitise protists, and perhaps plants may even feast on the occasional bacterium or two (though that's yet to be confirmed). It seems neither the organisms in question nor evolution itself received the memo wherein "plants photosynthesise, animals hunt, fungi decompose, protists are generic microbial slime subservient to all the former". Probably forget to staple cover sheets to their TPS reports as well.In the predatory foram case, you may be shrugging your shoulders and remarking that those forams are pretty damn huge anyway, so it's not that incredible. Alright, I'll grant you that. But what about a fairly small single-celled amoeba tackling nematodes in the soil?Life cycle of Theratromyxa, involving predation on food a little too large for its size followed by long-term digestion and slumber in cysts. Not a bad lifestyle. (Sayre 1973 J Nematol; Sayre & Wergin 1989 Can J Microbiol)Imagine you're living your life as a diminutive nematode, and suddenly a small creepy-looking branchy amoeba crawls toward you. Shivers descend down your non-existent spine as the amoeba extends its slender pseudopodia all over your body and gradually engulfs it. Your writhe in terror, but to no avail, for the creepy monster who just moments before appeared tiny and insignificant now has you inside a digestive vacuole full of acid and unfriendly enzymes. If you were lucky, some of your companions were engulfed along with you, so while packed in like sardines, you still have company. You wonder whether this is payback for all the evil you had wrought upon those poor plant roots. Little do you know your entire plight has been carefully planned by your self-proclaimed overlords from another phylum, just to get pretty pictures in the end:Light micrographs (left; Sayre 1973 J Nematol) and SEM of Theratromyxa (right; Sayre & Wergin 1989 Can J Microbiol). Image 6 shows quite nicely how Theratromyxa captures the nematode. This looks rather similar in principle to the feeding veil of dinoflagellate Protoperidium. Sometimes the amoeba can capture several nematodes at once. SEM shows amoeba enveloping a nematode.Theratromyxa has been considered for use as a biological control agent for the root-knot nematode (a very tiny group of nematodes, G. Meloidogyne. However, it wasn't particularly effective as excystment was rather slow, and there was no known method of speeding it up. Apparently, anastamosis (joining of numerous pseudopodia/amoebae) has been reported in previous studies, but Sayre 1973 did not observe any. But there still is the possibility of several Theratromyxa individuals (or their relatives) also ganging up on larger prey, as some other protists are known to do (eg. centrohelids cooperating in hunting larger ciliates).Theratromyxa is a Vampyrellid, a group of rather frightening amoebae, likely in the Endomyxa clade of Cercozoans/Rhizarians (see Pawlowski & Burki 2009 JEM; Parfrey et al. 2010 Syst Biol) (AFAIK, endomyxans are cercozoans, but considering the amount of stuff that's gradually settling in Endomyxa, perhaps the definition of cercozoa is bound to change eventually. I like 'Cercozoa' better than 'Filosea', the other subgroup of cercozoans; ie, it'd be nice to ditch 'Filosea', replace it with 'Cercozoa' and make Endomyxa not Cercozoans. Confused? Don't worry – just taxonomic musings.) Some other Vampyrellids are notorious for poking holes in fungi (Anderson & Patrick 1980 Soil Biol Biochem) and algae (life cycle), and then devouring the cells within. Not a very happy thought if you're a filamentous alga.By the way, some cercozoan amoeboflagellates can gang up on larger nematodes too, but I'll save that for another day.ReferencesSayre RM (1973). Theratromyxa weberi, An Amoeba Predatory on Plant-Parasitic Nematodes. Journal of nematology, 5 (4), 258-64 PMID: 19319347... Read more »
Sayre RM. (1973) Theratromyxa weberi, An Amoeba Predatory on Plant-Parasitic Nematodes. Journal of nematology, 5(4), 258-64. PMID: 19319347
Sayre, R., & Wergin, W. (1989) Morphology and fine structure of the trophozoites of Theratromyxa weberi (Protozoa: Vampyrellidae) predacious on soil nematodes. Canadian Journal of Microbiology, 35(5), 589-602. DOI: 10.1139/m89-094
- July 23, 2010
- 07:02 AM
- 841 views
Sunday Protist - Farming forams: a case of protistan agriculture
by Psi Wavefunction in Skeptic Wonder
"WTF, it's Friday already!" Friday? What Friday? You saw nothing.My previous two Sunday Protist attempts got derailed. With the first one, noticed there was quite a bit to say about them, and decided to postpone it for later as it was a big topic (and unrelated to my current work). Then I picked something relevant to my day job, y'know, two birds one stone, etc. And somehow that led me to paleontology. A warzone in paleontology. Complete and total clusterfuck. With potential inaccuracies here and there that I now need to sort out. Whilst we wait, I'll just do something quick: a case of a foraminiferan apparently growing bacteria and then eating them in perhaps one of the most non-human farming enterprises ever! (leafcutter ants are pretty much human at that phylogenetic distance...)Textularia blocki lives on seagrass. Many forams have interesting associations with seaweeds, ranging from internal parasitism to epiphytic attachment, usually via secretions of sulfated mucopolysaccharides, a fairly common material in the extracellular matrix. T.blocki, however, is a freely motile foram. It leaves peculiar 'grazing traces' as it crawls along the seagrass, without damaging the tissue beneath it:Left: T.blocki with grazing traces on blade of seagrass. Right: (Langer & Gehring 1993 J Foram Res)As made evident in the diagram, the traces consist of two parallel 'walls', consisting of pale whitish adhesive material, presumably containing mucopolysaccharides, devoid of sand grains or other contaminants. Curiously, some forams carried sand grains along, without depositing them. These secretions are formed by pseudopodia, or the 'business' part of the foram: an intricate network of reticulated feet with amazing cytoskeletal properties. When these secretions are left alone in seawater for 48h, a lush garden of bacteria sprung up specifically along the secretion traces:Bacterial gardens along the foraminiferan secretion traces. Note the relatively clean surface of the leaf outside the secretions, supporting that it is the adhesive mucous that attracts bacterial accumulation (Langer & Gehring 1993 J Foram Res)When released back into the medium containing the seagrass lined with traces, the forams approach the nearest trace and follow along it, suggesting they use some form of chemical sensing to determine where the secretions are and how they are oriented. The speed is then reduced, suggesting the foram is then busy grazing on their bacterial harvest.Thus, a 'mere' single celled organism can produce organised tracks of nutritious material, wait for their bacterial crop to grow, and subsequently harvest it. We like to think we invented agriculture. The more biologically-oriented among us point out leafcutter ant fungus gardens and aphid farming. Yet, agriculture has also evolved on the unicellular scale in a small humble foraminiferan living among blades of seagrass. Humbling, isn't it?Interestingly, a similar behaviour has been described gastropods like slugs and limpets, as their mucous also attracts bacterial growth. Convergence: when a good thing is chanced upon multiple times, it will likely be kept by several lineages independently. This applies to language and cultural evolution as well as that of biological organisms.We tend to have a deep conviction that cells are dumb blobs of goo, incapable of any sort of behaviour besides basic phototaxis or whatever. We think cells are just simple chemical response machines – which is true. But ultimately, so are we. There is no fundamental distinction between human social dynamics and the adventures of a crawling amoeba. The difference is all in the quantity and complexity of interactions – the higher the complexity, the more random (stochastic) the system appears (and to an extent, is). While I must concede that in terms of the number of components and pathways involved, human or ant behaviours are more complex than that of an amoeba, that does not mean the proverbial amoeba 'lacks' behaviour entirely.I've mentioned the cellular behaviour stuff before, probably too often for regular readers. Apparently, that idea needs restating though. Also, as a cell biologist, I find it quite...well, pleasing. It's nice that, ultimately, my subjects are no more or less machine-like than humans or plants. Furthermore, where I was heading with this originally, I think part of our notion of cells being 'stupid' comes from the obsession with our own cells. Animal cells are, in fact, quite simple and developmentally retarded. The cause is cell specialisation driven by multicellularity. Eg. an epithelial cell can now afford to lose the ability to hunt around for prey, it no longer needs to coordinate movement in any sophisticated manner, the life cycle can be simplified to terminal differentiation.Curiously, a similar problem plagues modern science and engineering: overspecialisation means that one must no longer have the same level of foundational education to survive, and thus we end up arguably knowing more about less, or perhaps knowing the same about less. I can suck at math or chemistry and get away with it. In the old days, people had to actually have a broader base just to function. Conversely, there was also less information floating around. Which is more efficient? Just as multicellularity vs. unicellularity, each system has its merits and drawbacks. So it's hard to tell.A while back I found a paper on cellular complexity in multicellular vs. unicellular organisms that needs to be discussed in greater detail eventually...---Random Link---ChrisM over at the wonderful Echinoblog (about the cooler deuterostomes; ok, hemichordates and ascidians are cool too) wrote about sperm-eating ciliates infesting starfish.Lots of things like sperm. For example, Monocystis is a gregarine with a penchant for earthworm sperm – infection rates are so high that if you slice up a worm from your backyard and smear the contents of its seminal vesicles on a slide, the chances are pretty good that you'll find some. And by 'some', I mean, LOTS. So if you're ever in the mood for some apicomplexans, all you need is an earthworm, a blade and a scope. There are parasites in pretty much anything and everything, so if you go around examining various animals, you may well find loads of cool protistan denizens in them. Many of which could be undescribed and, perhaps, new to science.Reference... Read more »
Langer, M., & Gehring, C. (1993) Bacteria farming; a possible feeding strategy of some smaller motile Foraminifera. The Journal of Foraminiferal Research, 23(1), 40-46. DOI: 10.2113/gsjfr.23.1.40
- July 14, 2010
- 07:42 AM
- 679 views
Carnivorous trees of the sea: Notodendrodes not as harmless as it looks
by Psi Wavefunction in Skeptic Wonder
Remember Notodendrodes and the spicule tree? Don't they look so much like harmless trees sitting around sunbathing like their plant counterparts? Not all tree forams are harmless. The microscopic marine world is full of surprises, like trees waving around their long sticky network 'feet' to trap and devour any traveler that happens by. Here's some wonderful shots of Notodendrodes caught in the act:The top left image shows a clump of Artemia caught by Notodendrodes, a big carnivorous tree foram. Note how the reticulopodia (pseudopodial networks) stretch between the branches like spiderwebs. Top right: SEM of the reticulopodial mesh of another species of Notodendrodes. Bottom: The tree foram in its natural setting, with a copepod attached (arrow). (Suhr et al. 2008 Mar Ecol Prog Ser)There some nice foram videos on this YouTube page, including shots of reticulopodia and a fairly large foram moving about in situ. This movie by a Japanese researcher includes clips of Artemia being captured starting at 0:50.Many forams are voracious predators, devouring anything from fellow protists to crustaceans and echinoderm and mollusc larvae. The following is Astrammina rara's rather impressive menu; all but two species were happily consumed:However, not all forams are carnivorous. Some are mediocre at best at capturing prey, and some, like Crithionina, are quite bad. This suggests a range of feeding habits from detritovory to carnovory to omnivory. Note how Gromia (not a foram, despite looking vaguely similar; placement somewhat uncertain, though most likely either close to forams or a cercozoan) fails to capture any prey. Also, dead specimens failed to catch prey, indicating the capture is intentional and requires a fully functioning cell, and not an accidental adhesion to something sticky. In fact, there is evidence for specific targetting of certain prey, which wouldn't be much of a stretch as many forams are quite picky in choosing their test material.I think this has some interesting – perhaps borderline philosophical – implications. Towards the end of the ciliate kleptoplasty post I mentioned how the traditional ecological terms often fail to describe the majority of life, which happens to be microscopic and play by some different rules. There's a greater problem in the approach of traditional ecology towards microbial life, however, and it even surfaced in a random chat with some ecology grad students. Namely, the treatment of all things microbial as the "bottom of the food web", ie. prey species created by evolution to feed cute fluffy animals. They have a similar attitude to plants as well: 'producers'. Fungi are 'decomposers'.Probably to people tracking bird migration out in the field, such crude terms do just fine, and we all must make crude approximations somewhere (or drown in details). However, as in any simplification, there's always a danger of skimming over interesting outliers. I disagree with the blanket treatment of protists (and bacteria, and anything else) as the "bottom of the food web" for two reasons:1. There are plenty of intricate interactions resulting in elaborate food webs (and, more generally, 'interaction webs'); a plethora of fascinating relationships is lost when one blurs them all into the 'prey for animals' category.2. Feeding by animals forms but a very tiny part of the overall diversity of microbe-animal interactions. An ecological framework must account for symbionts (mutualists, parasites and commensals) along with predation. Toxoplasma, arguably the most successful parasite of vertebrates ever, is a wonderful example of 'lower trophic levels' leeching 'up' the food web and running the show. You can't really draw an arrow from a cat or human to the modest apicomplexan, as it doesn't really consume its slaves. But you can't really not draw that arrow. It's complicated.(In fact, if organisms besides humans had Facebook, most of their relationship statuses would be set to "It's complicated". Groan all you want... =P)Lastly, our forams mentioned above also have ecological consequences on the megafauna in their environments. Astrammina rara is benthic, meaning it lives on the ocean floor (or, technically, any substrate). Suhr et al (2008) mention past studies indicating lower-than-usual densities of marine fauna in particular areas; these areas seem to match up with Astrammina's distribution. Presumably, the effects of predation on small fauna and larvae can be seen on the larger scale.Furthermore, the carnivorous forams seem to affect the survival strategies of the fauna around them (in hindsight, unsurprisingly): some echinoids have brood protection and settling strategies that may well have evolved in response to the lowly single celled protists they rightly fear. The authors suggest that the failure of Astrammina to capture larvae of the echinoid Acodontaster may be a result of the latter evolving a specific chemical defense against it.The 'scum' from the bottom of the foodweb can come up to bite some 'higher' organisms in the ass – whodathunk?ReferenceSuhr, S., Alexander, S., Gooday, A., Pond, D., & Bowser, S. (2008). Trophic modes of large Antarctic Foraminifera: roles of carnivory, omnivory, and detritivory Marine Ecology Progress Series, 371, 155-164 DOI: 10.3354/meps07693... Read more »
Suhr, S., Alexander, S., Gooday, A., Pond, D., & Bowser, S. (2008) Trophic modes of large Antarctic Foraminifera: roles of carnivory, omnivory, and detritivory. Marine Ecology Progress Series, 155-164. DOI: 10.3354/meps07693
- July 13, 2010
- 08:41 AM
- 938 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
- June 26, 2010
- 10:28 AM
- 864 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
- June 21, 2010
- 09:02 AM
- 935 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
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