Field of Science

Hiatus until 01 Sep + MORE random doodles!

Flying out very soon, for an underserved vacation smack in the middle of "OMG I don't have "all summer" anymore!!1! *flailing arms*" season. This is what happens when you let parents buy tickets for you. On the other hand, I really need the extra money so I can blow it all on my GREs. Yay.

So before I go and ditch you guys for a week and a half (really, I'd rather be here, blogging and working! =/), I'd like to share something bedroom ^^. I know, how risqué...! This naughty piece is a part of my...wall. That's right, my wall is covered in very shameful things, like even more protist doodles:

No, I don't actually need a life. It's all over my wall anyway.

Anyway, I'll be back 01 Sep. Hopefully the blogging will pick up then, as I'm beginning to discover that regardless how nicely undergrad-free it is, summer is just not conducive to extreme productivity or anything. Quite annoying, actually. Must compensate in fall.

[rant] Some asshat recalled the two specific books I was gonna bring home and read on my vacation to get two major sections of the chapter finished before it becomes evident how little I got done this month... and those aren't books of which you find many similar works lying about -- one of them is the ONLY book on the subject since the 1800's, and I absolutely cannot get by without it. So yeah, thanks, whoever it was. Not that they were supposed to know or anything. But I still retain the right to be irrationally pissed off about it. So much for catching up over the vacation. Now I'm really screwed come September. [/rant]

Must head off to airport soon... have a happy end of August, everyone!

Protist doodles

I like doodling things from time to time, especially protists. The fun aside, it's actually a nice way to acquaint oneself with how the look and behave. With protists, you get the choice of portraying the internal structures, as if viewing in transmission light microscopy, or only the surfaces, as if through SEM. Both are fun, although the former works better with ink doodles and the latter best suited for more serious shaded drawings, in my opinion. Anyway, a while ago I got home after reading and writing about Hacrobians all day, grabbed a beer and went doodling. From memory. Note that a lot of ultrastructure descriptions were read and incorporated into my work that day. Can anyone identify the organisms portrayed?

The image on the right comes from fucking around with a couple filters in ImageJ, and the result was kinda trippy. I smoothened the image, ran Find Edges on it and inverted the colours.
Oh, the image on the left was also post-processed: the original was a photo of a strip of paper with the drawings lying atop a horrible background, which was some random research paper that happened to be beneath it. The strip of paper was horribly slanted, and thus the background had to be edited out by hand, meaning I had to up the contrast until the drawing background was entirely evenly white, so I could blank out the background behind it. I really dislike post-processing besides cropping and slight change of brightness+contrast, but had little choice there. Thought I'd run this disclaimer anyway.

Post-it notes are fun to doodle on too. This is a fairly old one:

And a random trypanosome from a while ago: (the closest I'll ever get to biomedicine, ha!)

There's more, but they require being photographed or scanned, and that takes effort.

Also, I have a few posts in the making featuring protist-y things by people who can actually do art, so stay tuned. Also, if you know of some awesome protist/microbial/biology/sciencey, please do mention it here!

Ok, retreating back into my cave to work on blog posts as well as my actual writing stuff. Yay, guilt-zone!

Anoxic microforay part I: Aggregations and contractions

First I'll dump a few pictures of the strange bacterial swarming described in the earlier post, followed by some hawt ciliate action. First the bacterial swarming sequence; any suggestions/explanations/musings/factoids welcome and encouraged.

Stated the objectives used as opposed to magnification. No proper microscopist cares about mag anyway as it's rather meaningless. Also, I have no idea what the 'mag' is in this case anyway...the bacteria are small, about a couple microns or so. Sorry there are no timestamps - no idea how to put them on. Overall sequence spread out over about 5min. Phase contrast unless stated otherwise.

[Edit 20.08.10: Compressed pictures into a slideshow, thanks to Edward's helpful tips + tutorial; noticed the blog page is becoming harsh on the loading time, hope this helps]

EDIT 22.08.10 Moving pics to slideshow turned out more complicated than it should be, and don't have time to fix with an impending flight to internetlessness+vacation in a couple hours...really sorry, will fix + put up pictures ASAP once I get back!

I think the theory at the moment is that is may have something to do with optimal oxygen concentrations (ie low) towards the middle of the slide; oxygen would diffuse more at the edges of the cover slip, and this was an anoxic sample. However, it may have been near the centre as a coincidence; my sample size is kinda tiny here.

Was recording Vorticella generating feeding currents in phase contrast when another obnoxious ciliate rudely interrupted the shoot; these three frames are consecutive, note how near-instantaneous the stalk contraction is!

Here's another one contracting, in DIC:
There are more photos to come, but processing and identifying them is time-consuming, and I'm still ridiculously behind on my actual that should come later.

Random picture dump: Parabasalid mitosis

I actually went out and did stuff this weekend. Like, non-protist stuff involving geographical locations outside the lab. Incidentally, this weekend also happened to be about the hottest this summer, and heat and I aren't the best of friends. Reading isn't particularly fun on a headache, so I went over my random protist videos and got more screenshots. Most of them should end up in the upcoming 'microforay' sometime soon, but I also found something cool from an adventure way back in May. Not enough material for a microforay, but still wanted to dump it somewhere.

Had to do some stuff with termite (local Zootermopsis) gut symbionts, so I dumped them under DIC for fun. There was the usual gang: Streblomastix, Trichomitopsis, Trichonympha and miscellaneous smaller things. Watching Trichonymphas (they're big and cute enough to be a count noun) can get quite addicting, and the guilt from being responsible for their inevitable death by oxygen poisoning compels you to acquaint yourself with every individual on the slide. At that point, I noticed something was odd about the way some of them moved. Furthermore, their anterior ends appeared if there were two "heads"!

(Once again, apologies for the crappy image quality, but this is the best I can do until I actually have the time to sit down and learn the program.)

OMG, cell division! I still find dividing cells utterly awesome, even just conceptually - it's as if unicellular organisms regularly undergo a "Siamese twin" phase! This is especially evident in organisms who continue to move about and beat their flagella during division, thereby making the two-individuals-in-one concept even more apparent. The cell(s?) usually move(s) around in a fairly incoherent manner at that point, although that might depend on the species too.

Anyway, what's that thing in the middle, between the two "heads"?

As you may have guessed, that thing is indeed the nucleus in mitosis, with spindle fibres all over. With chromosomes. Roughly like these figures from Cleveland (1960 J Protozool):

Top: Whole Trichonympha in early anaphase. Bottom: Close-up of mitotic nucleus. The chromosomes are separated as the thick central spindle grows, pushing apart the centrioles which pull chromosomes along with them via the astral rays. (Cleveland 1960 J Protozool)

Parabasalian mitosis can be quite weird and awesome, but that's a topic for another day. At the moment, I can't even crop properly anymore...ignore that random line in 9a. Just thought I'd share pictures of weird organisms doing cool things.

Oh, and if I ever catch these critters mating, you'll hear it. Potentially even literally ^^

Microfieldwork and a couple mystery critters

My work-related productivity ran aground lately, and thus I feel too guilty to blog. I should probably sort out the stuff I get paid to do first, and until then, do not qualify for having "spare time", especially since I already did too much of that this weekend by going on a random sampling foray:

My friend apparently saw a bubbling pool with a nice stench of sulfur on a local beach, so we went hunting for extremophiles. She had just borrowed A Field Guide to Bacteria, and finally realised that microbial life is many orders of magnitude more awesome than anything easily visible to the naked eye. Far more exciting than her sticklebacks anyway =P (joking! please don't lynch me, fish people!)

Anyway, naturally our fieldwork had to be accompanied by the first rain in over a month, and we got soaked while wading through salty mud in search of the elusive bubbling pool. Unfortunately, the pool seems to have disappeared. Furtunately, the stench of sulfur hasn't. Nor has the blackish-greyish unappetising-looking gunk, or the patches of bright green algae. Being biologists, the yuckier and smellier the gunk, the more excited we got, and the more happily we sampled away. Now I have a plate of anoxic goo sitting on my bench -- could be a great teaching tool for training one not to open random plates and sniff them. Biologists are immune to such lessons, of course, especially microbiologists, who seem to be irresistibly attracted to nasty smelly stuff.

Anyway, gunk hit the slide and on the scope it went (the slide, not the gunk). It was AMAZING. I have found an excavate paradise! At least four varieties of diplomonads I could see! Swarms of bodonids and heterotrophic euglenids! For the saner people, there were loads of bacteria to oogle at too. For some reason, many assume all prokaryotes are too tiny to be detected by a light scope, but that is entirely not true -- you can see bacteria swimming around, even under low mag. Resolving inner structures is obviously nearly impossible (except for Epulopiscium), but you can definitely watch the cells themselves swimming around for hours, and see plenty of morphological diversity.

On the topic of bacteria, next time you put a coverslip on a rich anoxic sample (at least of the very surface layer, but maybe planktonic/benthic samples work too), wait a bit and go towards somewhere in the centre of the slide on medium mag. With phase contrast, you can even go to low mag. Somewhere on the slide, there may be a giant swarming ball of bacteria! The ball gets bigger and bigger as more bacteria accumulate inside, and becomes slightly visible to the naked eye! After a few minutes, the ball collapses into an ever-expanding ring, which keeps growing until it reaches the edges of the coverslip, by which point many of the bacteria die.

What's going on there? I've been told it's probably aerotaxis - microaerophilic/anaerobic bacteria scurrying the hell away from the poisonous oxygenated slide edges (while their aerophilic counterparts often form borders along the edges, if you look carefully after a few minutes). Thus, the bacteria eventually congregate in the local minimum of oxygen concentration, and form a ball. What is interesting is why this ball then collapses into a ring -- do some anaerobes produce oxygen waste, and thus poison their immediate vicinity? Alternatively, could they be secreting some other toxic product and fleeing from it? Seems like this is something that should have been well studied (and well-modeled - mathematical biologists love this kind of stuff, don't they? They get to whip out their gradients and differential equations and other fun stuff), but my unproductivity guilt stops me from looking it up myself ^^

Anyway, plenty of cool stuff has been seen, including a particularly weird flagellate that swims around in a corkscrew fashion and has a warped cell body morphology too difficult to describe at the moment. Might anyone know what it is? It's not too common, around 1-2 cells/slide, and seems to enjoy lower planktonic/benthic areas more than the surface. Roughly 10-15um, I'd say. Anyway, I grabbed some pics:

Sorry for the awful quality -- they're crude screenshots of stills from video, as the scope in question lacks a normal camera and I've yet to figure out how to use the software...those pixels have been through a lot. Be nice to them. The resolution abuse really bothers me though, so I'll try not to look at them myself...

Any ideas? Anoxic dense marine intertidal sediment, ~10um big, swims in a corkscrew fashion. Slightly more refractile than nearby bodonids and diplomonads of similar size. Two cells depicted above.

I'll get more images from the anoxic samples once the unproductivity guilt issue gets taken care of, but that flagellate has been nagging me too much. But in addition to excavates and this mysterious thing, there's also loads of cool ciliates, Naegleria (I think!), dinoflagellates, amoebozoans, and cercozoans. Speaking of which:

In addition to the anoxic wonderland, I also went on a grueling field work expedition to a nearby stagnant ditch-pond thing, an arduous journey that took me 10min including stair-climbing and door-opening. And the potential threat of being bitten by a feral stickleback or some roaming drunk undergrad. I almost sympathise with the field biologists - it is dangerous and difficult work, after all. Especially once the beer runs out.

Anyway, got loads of sample, dumped it into a petri dish, floated coverslips on it. I heard of this technique where coverslips are floated for a while and stuff grows on them, so I had to try it out. Was sort of relevant to my work too, to see how well it would work for an undergrad lab. Fairly quickly, you get 'benthic' ciliates crawling all over it. Curiously, the neuston (air-water interface layer) is full of benthic-looking things growing upside down on it. Amoebae crawl under the water (air?) surface, hypotrich ciliates 'walk' on it. While neuston has been studied a fair bit lately (under the glamour word "biofilms"), the protist component has, as usual, been entirely ignored, save for a couple old papers. Upside-down forest of stalked choanoflagellates, bicoecids and various ochrophytes? Hard to believe, eh?

This doesn't simulate the air-water interface per se, but the cover slips do show how easily small floating life can grow upside down and not even care. After about 4 days, you start seeing some really cool stuff, like this peculiar cercozoan:

Peculiar cercozoan. Freshwater 'pond' sample, collected in early August, cover slip floated on sample for about 4 days. Organism growing on the cover slip glass.
The doughnut-shaped thing is the nucleus with the large nucleolus (I think - plenty of cercozoans do that anyway), the large circle beneath that is the contractile vacuole. From the cell body proper to the shell/test/lorica opening leads some strange 'neck' structure with longitudinal striations. From the shell extend numerous branched filopodia exhibiting bidirectional streaming of granules (extrusomes?) and what appears to be bacterial prey (the large-ish lump in a filopodium near the shell)

I doubt this is a freshwater foram, as the foram reticulopodia look quite different (less thin, and fuse together a lot). There are apparently freshwater gromiids (remember the giant track-leaving Gromia in the news a couple years ago?), but something feels off about its pseudopodia -- they don't appear to anastamose (fuse together) in the ones I saw. Alternatively, I thought it could be a Granofilosean cercozoan, like Limnofila(Bass et al. 2009 Protist fig 5) or something, but those lack tests, so that's stupid. And now I'm all out of ideas. Would appreciate some help from anyone into this kind of thing =D (could also be an stramenopile amoeba, not a cercozoan...a thraustochytrid, perhaps? Cell body structure doesn't seem right; also, do thraustrochytrids do bidirectional streaming of granules and prey?)

I probably lost most of my readers by about there. Sorry about that, but I really want to know what these things are! They nag me! In my sleep! (seriously -- never read a detailed taxonomy paper, especially a Cavalier-Smith taxonomy paper, along with a beer just before going to sleep; so many gliding amoeboflagellates went through my head last night...creepy. Unless you like that kind of thing. Looking forward to my bedtime beer + Cavalier-Smith paper tonight =D)

Anyway, my guilt is back, so I must go and read stuff so I can finally make progress in writing stuff. I'm still alive and blogging though, and hopefully will get back on track soon ^^ And you have some more protist pictures (and maybe even videos!) to look forward to!

Sunday Protist – Nematode-hunting amoebae: Theratromyxa

ResearchBlogging.orgA 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.

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