Mystery Micrograph #05 hint

From my pond microforay: (Edit: the organism below is NOT the mystery organism. Follow the link below instead! I fail at making sense lately...)

The mystery organism is special with respect to this form of motion. That was a very massive hint.

Also, not this:

(Leander et al. 2001 Evolution)

The protist geeks among you better get it this time!

Pond Microforay part 1.5

More pond pictures (part 0.5 is here). The first hour or so was dedicated to putting up with very shitty DIC because some moron decided to 'frobnicate' with the bottom polariser, which is not meant to be touched very often. Luckily, I eventually managed to out-'twiddle' their frobnication and adjust the scope properly. In that first hour I did find some cool stuff, so please excuse the embarassingly shitty image quality. The polariser was misaligned, grrr!

So here's some Difflugia-like amoebozoan. They're amoebae which ingest and secrete random particles to make a test. (sometimes, those can even be diatom valves!)

A random amoeba. Don't expect me to ID amoebae... especially with shitty lightning! (still sore about that, yes!)

Then the slide was drying out, so I decided to add a drop of water.

Everything stopped moving, and finally I got a shot of a euglenid (remember that our camera is painfully sloooow!) By stopped moving, I mean I could even get an awesome shot of a flagellum, and a badly deformed cell (another euglenid):

By now I was confused. I look at the water dropper - it's labelled 50% glycerol. Shit. Who knows what was actually in it, as it induced a diatom to blow up rather impressively:

Somehow I doubt glycerol is supposed to do that. Probably screwed up the osmotic pressure drastically - I'm guessing typically one uses ~10% glycerol to slow things down in microscopy? Anyone know? Plants don't need slowing, so the glycerol there is added to help match the refractive index more than anything else...

Made a fresh slide. First off, Difflugia-like amoeba in mitosis(? or not...do they redistribute test material during division?):

(REALLY sore about the shitty image quality - this would've been so amazing under proper DIC!!!)
Something vaguely looking like an Actinophryid... (although not as vacuolated as it should be, but who knows...)

And what appears to be an abandoned Bicosoecid lorica:

And then I had an encounter with what appears to be a dividing ciliate!

Damn I want my DIC by this point. A ciliate in mitosis - how cool is that!? Grrrr! You could even see the oral ciliature! Can't wait to work on ciliate morphogenesis/development (if they're crazy enough to let me in, that is...)

Speaking of ciliates, the armoured Coleps:

A few random amoeboid things:

Random flagellates: (there were a lot of Cyclidium (ciliate)):

And I really need to brush up on my euglenids!

Being beyond fed up with the lack of DIC, and knowing our scope is actually quite good, I finally twiddled my way to the problematic polariser. Suddenly, life was good again!

"HOLY SHIT, IT ACTUALLY WORKS NAO!" I even allowed some blatant overexposure to creep in... >_>

So here my images actually started to suck less. And more cool stuff was seen. Now that we're all waiting in suspense for marginally acceptable microscopy, I'll call it a day here. Stay tuned for part 2.5: This time with DIC! ^_^

Pond Microforay part 0.5

Don't have the time to process all the images, but here's a heliozoan and some flagellates from today. By the way, our ancient CCD camera is too slow to capture pictures of...amoebae. Yeah, you know your imaging equipment needs to upgrading when... (it's a decent camera for plants though. Just really fucking slow.)

Actinophryid or a Centrohelid? Actinophrys is a bit more 'bubbly', if I recall... (Heliozoa is not a real [monophyletic] group) Edit: most likely centrohelid...

Mystery flagellate. A non-photosynthetic euglenid, perhaps? Or something that's been rather mangled?

Wow this image is shitty... but Bicosoeca is brutal for imaging... this is a small sessile heteroflagellate with a lorica (the little barely-visible cup-like structure). And it hunts:

Captured this image just as the flagellate retracted back into its lorica after seemingly grabbing something. I don't know much about its hunting tactics, may be worth looking into someday...

I spent 2h looking for bicosoecids and choanoflagellates (no success with the latter) since I've seen them before in that sample. Which is, by the way, a freshwater one from a local pond. That may actually be useful information for ID purposes...

Got more coming later, eventually, hopefully soon-ish... (apparently, offline life needs tending to from time to time)

Microscopists can get grumpy...

Dear Whoever-the-Fuck-Decided-it-was-a-Great-Idea-to-Fuck-up-the-Light-Path-on-my-Scope,

I just spent an HOUR taking shitty images wondering why the fuck no amount of fiddling with my usual knobs could get me a half-decent DIC image. I was very confused - I fiddle with A LOT of stuff when setting up the scope, and don't expect to be easily outfiddled. Especially by a new undergrad. I was getting decent images yesterday, and today everything looked like shit. My condenser was set up perfectly, analyser and prism set up the way I always do when it works, and my sample was even better than usual. It was fucking annoying.

So then I finally snapped, and started fiddling with shit I usually don't fiddle with. With good reason. And guess what I find... the very first fucking polariser is completely misaligned somehow. Seriously, how the fuck did you even FIND that knob??? No one EVER touches it, because you just don't. You never need to. That's why it's hidden in a rather inconspicuous place. You notice how the focus knobs are like RIGHT THERE? That's because you use them a lot. They have to be accessible. Same with the stage control. And the condenser height. And then we get to the slightly more obscure stuff, like the analyser and prism - also must be set up, but not as critical, and you don't really need to fiddle with them constantly.

And then there's the REALLY obscure shit. Stuff you set up once, and never ever think of ever again. While a nice chunk of microscopy can be clueless artistic fiddling, some stuff you just leave alone, because there IS an optimal setting for it, and any deviation from that fucks shit up. This includes the alignment of the bottom polariser. It was set up once, everyone was happy, and no one ever needed to look at it ever again. Until you, most likely one of our new clueless undergrads, decided to find that knob, and give it a fucking twirl, thereby fucking up my DIC light path. And since I don't usually reach there, I had no idea what the fuck was going wrong. Now I know. After an HOUR of perplexed shitty imaging.

How about we introduce a new rule: If you don't know what it is, DO NOT FUCKING TOUCH IT. If you REALLY wanna screw with it, then make sure you put it back EXACTLY the way it was, to the hundreth of a degree/micron/radian/kelvin/mV/WHATEVER. If you don't know, then fucking ASK. Srsly, you look a LOT fucking dumber by doing stupid shit than by asking stupid shit. I ask stupid shit all the time, and they still haven't clued in kicked me out.

This applies far beyond microscopy - what if you decided to twirl some potentially exciting/excitable chemical one day? The consequences could get more dire than an angry labmate, believe it or not. As scary as we may seem, nature can be much worse. Also, nature doesn't give a fuck about you. Just fyi. It really doesn't. It doesn't care you're new and don't know shit - stuff can still explode in your face without warning. After all, this is a LAB for fuck's sake, and we're licensed to have some pretty hazardous shit in here. We may be only BSL1, but we still have stuff than can kill you. Some stuff that you probably shouldn't really touch too much. At all.

So ASK next time. You'll seem a much greater idiot stark naked in the emergency shower because you didn't know what that chemical was than while asking questions of ANY level of stupidity. Also, we're labrats - we lack social skills. Pissing us off too much by doing idiotic shit can lead to the psychological equivalent of standing naked under an emergency shower. Have I mentioned that you should ASK before touching anything? Don't make me do it again.

Signed,
Angry Labmate

Mystery Micrograph #05

Ok, sane people seem to be too intimidated, or perhaps actually in posession of lives and stuff, and thus deprived of any yearning to go on a nightlong Google/journal hunt adventure. As a matter of fact, I suppose not everyone voluntarily leeches off the high speed VPN-free journal access at a lab computer at interesting hours of the night. Some might even go all the way home and resort to slow pdf-loading ordeals. Or maybe even skip the whole academic article thing altogether. Especially on a Friday night. So I'll just go back to doing super hard ones, and perhaps occasionally space them out with something publicly-accessible. But don't count on it. =P Actually, this way I get an excuse to learn about some REALLY obscure stuff. Some stuff so obscure it finds some protistology faculty clueless. Mwahaha. Stuff I should totally dump on my CV/Resume - to bewilder potential future employers with the sheer uselessness of my knowledge! ^_^

This one is open to everyone; AND I've made a whole chunk of various images available:

(to be referenced later; 12 - DAPI-stained DNA)

Due Sunday noon-ish, I guess. Feel free to ask questions - I may or may not answer them ^_~

Winner gets to feel good about themselves. I don't think this one is particularly beer-worthy.

Btw, summary of past Mystery Micrograph winners:
#01 - Rosie Redfield (protist with episymbiotic bacteria/Streblomastix)
#02 - nobody... (Haptoglossa)
#03 - Alastair Simpson (unaware of this blog's existence), Jan (after ridiculously revealing clues) (Bicosoecid)
#04 - Opisthokont (Euglyphid)
#05 - You? ^_^

Phylodeities and clade spirits now happily accepting beer sacrifices.

Freaky coincidence...

In the previous post, I just mentioned in passing Blackburn and the discovery of Tetrahymena telomeres and telomerase:

Like what ciliate genomic madness has done for the discovery of telomeres (Blackburn & Gall 1978) and telomerase (Greider & Blackburn 1985)

While looking at those papers, I thought "I wonder if she ever got a Nobel prize for that. The findings seem prize-worthy, and it's about time anyway."

...And then, a few hours later, I see this post on Jonathan Eisen's blog; and it turns out... they JUST won a Nobel for exactly that!

I may have a sixth sense. Or it may well be a random coincidence. Sigh, probably the latter. But I still think it's hilarious!

Sunday Protist - Euglyphids

I'm going to be lazy and leech off the Mystery Micrograph again. None of you saner people (non-protistgeeks) seem to have taken advantage of the massive handicap, and subsequent hint. Seriously, type in "testate amoebae" in Google image search, and it's on the first page! Perhaps I should do a tutorial on some methods of attacking those mystery images...

Quite shockingly(not!), Opisthokont got the last one. I agree with his statement that that was like shooting fish in a barrel, but easier since fish are actually difficult to shoot at from air due to refraction, etc. The organism behind the shell in the mystery micrograph was...

Euglypha!

(Wikipedia; Euglyphid test)

Euglypha morphologically belongs to the polyphyletic 'testate amoebae', but is phylogenetically quite distant from your garden variety test-building amoebozoans, like Arcella and Difflugia. Euglyphids are cercozoan rhizarians. Since those words likely mean nothing to the vast majority of the human population, here's a 'map' of Rhizaria in my Coelodiceras (Phaeodaria) post, and an overall tree of eukaryotes can be found here. They can often be found in moss samples, but are also present in soil and freshwater environments. Their test scales are made of silica, and preserve quite decently as fossils. Speaking of which, I apparently may have a slight fetish for unicellular microfossils:

(Javaux 2007 in Eukaryotic Membranes and Cytoskeleton: Origins and Evolution ed. Jékely; 10 - fossil; 11 - modern Euglyphid; 12 - VSM - 'vase-shaped microfossil' (micropaleontological equivalent of mycologists' LBM - 'little brown mushroom' ?) with holes possibly caused by predation; fossils ~750My old)

Fast forward 750My back to the present, the modern euglyphids are about as diverse as they are understudied:

(Lara et al. 2007 Protist; tree of Euglyphids)

Images of Euglyphid diversity, shamelessly stolen from the same paper:

(Lara et al. 2007 Protist; Euglyphid SEMs, scalebar 50um except for E,F,H, where it's 10um. A - Assulina; B- Placocista; C,D - Euglypha ciliata & compressa; E - Corythion; F - Trinema; H,G - Euglypha penardi)

Unfortunately, finding nice plates full of euglyphids is rather difficult, since until quite recently, they were lumped together with testate Amoebozoans. Also, since euglyphids fossilise, they seem to be mostly studied by paleontologists, who seem to have an 'interesting' relationship with systematics of the living. Where 'interesting' entails being at least a couple decades out of date. Well, they are millions of years in the past...

Paulinella can be argued to be particularly interesting - it is a case of an independent event of primary plastid endosymbiosis. Why this is interesting can be seen in this really nice overview:

(Keeling 2oo4 Am J Bot (free access); overview of plastid endosymbiosis - the 'Pacmen' are pretty awesome! Interestingly, if the Chromalveolate Hypothesis is correct, this would mean that Paulinella already had a plastid in its ancient past. However, it would've been a red algal plastid of a different cyanobacterial origin, not a Synechococcus-derived cyanelle)

Cyanelles are photosynthetic endosymbionts/organelles - they differ from plastids by retaining some prokaryotic features like the peptidoglycan wall. Among the conventional plastid-bearing algae, glaucophytes carry cyanelles from the primary cyanobacterial endosymbiotic event which eventually led to plant chloroplasts and most algal plastids. In sequence comparisons, Paulinella cyanelles branch with the cyanobacterium Synechococcus, and retain much of the gene order, suggesting a fairly recent endosymbiosis with Synechococcus (Yoon et al. 2006 Curr Biol). The authors predict a transfer of plastid division genes to the host nucleus; however, while the plastid genome has been sequenced (Nowack et al. 2008 Curr Biol), the nuclear genome is yet to be investigated, to my knowledge.

(Lauderborn 1895 (L) Melkonian (R) in Keeling & Archibald 2008 Curr Biol; Paulinella with cyanelles)

So are the Paulinella cyanelles to be considered as endosymbionts or organelles? As with the Perkinsela case discussed a while ago, who cares? Keeling & Archibald (2008) and Bodył et al. (2007) argue that the distinction between organelles and endosymbionts is too vague and fuzzy to obsess over, while Theissen & Martin (2006) seem to have nothing better to do. Well, to be fair, they argue that gene transfer to the host nucleus is the necessary rite of passage to become an organelle. But that is a rather arbitrary cut off, since you can also say that a complete disappearance of a certain class of genes, or the endosymbiont genome altogether, are necessary to be called an organelle. Alternatively, you could also argue that as soon as an endosymbiont spends its entire life cycle within the host cell, it's sufficient to be called an organelle. With lateral gene transfer turning out to be more ubiquitous than it first seemed, perhaps gene transfer isn't that significant of an event after all. Meanwhile, how about we just accept that nature doesn't particularly care for the artefacts of our reasoning -- ie. the obsessive-compulsive yearning to categorise the world around us -- and just enjoy the biology?

Nowack et al. (2008) avoid the whole Paulinella organelle vs. endosymbiont debate by settling for 'chromatophore'.

But just to annoy fellow cell biologists, I sometimes insist on referring to plastids and mitochondria as 'endosymbionts'. Speaking of which, from Theissen & Martin (2006):

"Calling the Paulinella endosymbiont a plastid or an organelle might make a story more exciting, but at the cost of scientific accuracy. Some proteobacterial endosymbionts of aphids have genomes smaller than those of some plastids 16 A. Nakabachi, A. Yamashita, H. Toh, H. Ishikawa, H.E. Dunbar, N.A. Moran and M. Hattori, The 160-kilobase genome of the bacterial endosymbiont Carsonella, Science 314 (2006), p. 267. Full Text via CrossRef | View Record in Scopus | Cited By in Scopus (86)[16]. Would anyone call those endosymbionts ‘mitochondria’? Hardly."

First of all, why 'mitochondria'?! Those are specifically defined as endosymbionts/organelles of that one alpha-proteobacterial endosymbiosis event ancestral to all known eukaryotes. Second of all, I would totally call them organelles. I see no problem with it. I guess I'm just special then, according to those guys. Actually, I'll go around intentionally calling them 'organelles' just to piss them off.

So mitochondria and cyanobacterial plastids = endosymbionts; Paulinella cyanelles and Wolbachia bacterial endosymbionts = organelles. I think that pisses off just about everyone. My job here is done. =D


I hope this post has helped cast some familiarity upon yet another obscure group of Rhizarians. There's probably volumes more to say about them, but [insert rant about biomed crushing real biology here], so they're as understudied as the rest of Rhizaria. And much of the rest of Eukarya. Who knows how much biology weirdness lurks behind some of those obscure taxon names. Perhaps that 'Obscurius obscura' may hold the perfect properties to help us sort out some biological connundrum or other. Like what ciliate genomic madness has done for the discovery of telomeres (Blackburn & Gall 1978) and telomerase (Greider & Blackburn 1985). Come on guys, let's do something!

What if each lab was to take on a (culturable) obscure organism as a small side project? Even the big biomed labs... if each scientist played with a random organism long enough, perhaps we could unearth a freaking Pandora's box-worth of discoveries and new research directions? And the mixing of disciplines would do wonders to our overall understanding of biology! This may even be *gasp* slightly more efficient than 10 labs staring at one protein and barricading their labs from rampant scoopage... but I'll stop here with my heretic thoughts.


I have several posts in the works at the moment, among them one on origins of eukaryotes and a series on Heterolobosea, which Christopher Taylor challenged be to blog about. But first, a couple midterms, a talk I'm giving on Tuesday which I have yet to start working on, and a whole wad of research- and seminar course-related stuff. Learning seems to happen predominantly outside of class, which I find rather debilitating to grades. So multitasking must happen, and generally the class-related stuff gets cut. Which is bad. There's a dilemma between developing your mind/knowledge and getting decent marks - the former is essential for any reasonable progress in research/other professions, the latter is necessary to actually get anywhere after graduating. And they conflict with each other. Yay. [/rant]

And I seriously intended this post to be like "Hi, this is Euglypha. It is pretty. Gotta go. Bye." Cannot resist the allure of journal surfing at odd hours of the night...

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

Javaux EJ (2007). The early eukaryotic fossil record. Advances in experimental medicine and biology, 607, 1-19 PMID: 17977455

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

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

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

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

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

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

Japan is a special place: The Manga Guide to Molecular Biology

Holy shit, two epic geekdoms blended into one awesome compilation -- The Manga Guide to Molecular Biology:

Really really curious...anxious to read it... internet, can we make this happen? *wink*

Now I really need to go to Japan. Considering I'm so going to have loads of cash flowing around for the next 10 or so years of slavery grad school and post docs... =(
Although, rumour has it this coming summer the Arabidopsis meeting is in Japan somewhere... brb, must make earth-shattering discovery. Of sorts. Where do I begin? *opens cytotoxic drug box* hmmm!

It seems like the Manga Guide to Protistology will be free of competition for the next little while. Hello there, Cer Ratium! ^_^

Mystery Micrograph #04 - open to everyone!

Since yesterday noon... no one seemed to take advantage of the handicap so now anyone can tell us what this thing is!

Could make it a bit more challenging and ask for genus/species, but meh. I suck at IDing species level myself, and frankly could care less. So, dig in, ye protist geeks!

Carnival of Evolution #16 now on Pleiotropy

Bjørn Østman over at Pleiotropy is hosting this month's Carnival of Evolution - go check it out for some extra procrastination web surfing educational reading opportunities! (well-organised too)

I do dig the ultra-geeky histogram of words/post distribution...mmm, data!

---

On an unrelated note, my post rate should be sacrificed a bit in the name of oncoming midterms. If you catch me writing up 5000 word posts on obscure organisms and evolutionary concepts, feel free to remind me of that 'school' thing I'm currently enslaved entrapped enrolled in. Apparently, getting a degree is supposed to be kind of useful, or something. Should probably go check out this 'studying' concept.

[rant]Also, since when does Developmental Biology entail memorising parts of vertebrate embryonic development? I don't ever recall signing up for ANIMAL development either, for that matter. Why does the entire course focus on vertebrates, with a small digression about basics of Drosophila? Shouldn't we go the other way around - focus on models like C.elegans and Drosophila, and THEN briefly mention spined things, leaving the rest of the latter for an actual embryology course? Furthermore, since we never specified the ANIMAL part, wouldn't it be nice to explore, you know, other regions of that massive phylogenetic tree of life? Do plants not develop? (if so, then what's my current research about? I guess stomatal development doesn't count for development, in the eyes of Zoology...) Do unicellular eukaryotes not develop? Do prokaryotes not develop?

Seriously... what's the damn big deal about glorified coenobia with segregated germ lines? Multicellularity is simply clumps of clonal cells responding to various environmental cues (eg. from neighbouring cells), using many of the same mechanisms free-living unicells employ. Oh, and metazoa have gone extra stupid where the germline can only segregate once, and stay there for life. You can't randomly decide to grow ovaries on your head. That's just dumb. Seriously. Lose your germline organs and you're screwed. Forwever. Most other forms of multicellularity (eg plants, fungi, some seaweeds, slime moulds) seem to have gotten around that. Plants are laughing as we speak. (and prokaryotes sneer at the whole concept altogether, save for Myxobacteria, Streptomyces et al.) 'Intelligent design' my ass.

So yeah, if you're going to call a course 'Developmental Biology', then you should probably include examples from the other >99% of life. Otherwise, let's just stick with 'Animal Development', ok?
[/rant]