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Protists, memes and random musings

Psi Wavefunction
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  • July 1, 2011
  • 02:58 AM

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........ 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
  • 12:47 PM

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........ Read more »

  • May 17, 2011
  • 11:05 AM

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 repeate........ Read more »

  • May 17, 2011
  • 11:05 AM

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 repeate........ Read more »

  • April 4, 2011
  • 12:42 PM

"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 offspr........ Read more »

  • March 28, 2011
  • 10:26 AM

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 '........ Read more »

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
  • 06:25 AM

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, m........ Read more »

  • March 15, 2011
  • 10:09 AM

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 du........ Read more »

  • March 2, 2011
  • 08:34 AM

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 rig........ Read more »

  • February 21, 2011
  • 01:48 AM

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 fa........ Read more »

  • December 4, 2010
  • 12:04 PM

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 cytopla........ 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  

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  

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
  • 06:51 AM

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........ 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  

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  

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
  • 06:17 AM

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........ Read more »

  • September 8, 2010
  • 07:39 AM

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 t........ 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
  • 11:59 PM

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 neit........ Read more »

  • July 23, 2010
  • 08:02 AM

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 an........ Read more »

  • July 14, 2010
  • 08:42 AM

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. ........ Read more »

  • July 13, 2010
  • 09:41 AM

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 seriou........ 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:/

  • June 26, 2010
  • 11:28 AM

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 rela........ Read more »

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  

  • June 21, 2010
  • 10:02 AM

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......... Read more »

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