Eight supergroups on a table

Back, after a bit of a distraction and an irritating bout of writer's block (how do you get rid of those things, seriously?). While I go write up a post for the long-interrupted Sunday Protist series, have a protisty doodle. My friends have this makeshift coffee table from two pieces of wood, which serves as a canvas for procrastination painting and such; anyway, if you supply me with permission to doodle on something, it invariably ends up protisty (or anime characters, or a frightening mix of the two), so here are eight supergroups on a table: (flash gets a a sharper image but the colours get screwed up)

Watercolour, pencil and [lab] marker on painted wood. Really fun to do watercolours on top of paint – you're not sneered at by warped wet paper, and it's very easy to wash off mistakes.

The cast:
Archaeplastida – Acetabularia
Alveolata – dinoflagellate (eg. Protoperidinium)
Stramenopila – Chaetoceros
Rhizaria – Gromia
"Hacrobia" – centrohelid "heliozoan"
Amoebozoa – tubulinid amoeba
Opisthokonta – choanoflagellate with a chitinous basket
Excavata – photosynthetic euglenid

(Accuracy not guaranteed as I was too lazy to use references)

Deciphering protist shapes

A while ago, while rigorously procrastinating, I came across a slightly odd tiny freshwater flagellate that was sufficiently morphologically non-straightforward it lent itself well to 3D reconstruction/sketching practice. Figuring out cell shape from micrographs isn't as easy as it looks – for one thing, the bloody cell is three dimensional, while the images are flat and further complicated by DIC optics – and thus a very fun exercise! And then, once you've got a cell shape in your head, you have to figure out a way to draw it out for others to see. I still suck, but the sketches at the end looked kinda pretty together with the micrographs, so here they are:

I still have no idea what this thing is. Acts vaguely ancyromonad-like, but may well be a glissomonad or something else entirely. Pretty positive it's biflagellated. Probably nothing too earth-shattering (and may well be well-known by everyone but me), but if anyone has some sort of research interest in this thing, let me know – don't have time to deal with it myself. Not that I'm likely to find it again... Here's the pics and videos:

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 from...my 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!

Snippets of the beauty of sliced axonemes

Look what I found in obscure ultrastructure literature!

It's a star! (Ringo 1967 J Cell Biol)

That's a cross section through the transitional zone of the Chlamydomonas flagellum. The geometric intricacy actually comes from the need to transition from nine triplets of the basal body to the flagellum's nine doublets and a central pair (of microtubules). As evident in the figure below, this can get quite tricky:

Cross-sections through a Chlamydomonas flagellum and basal body. (Ringo 1967 J Cell Biol)

This could be inspiration to some fun baking project...

Speaking of sliced flagella, there are some more wonderful patterns hidden away in the axonemes of rather obscure 'heliozoans' (centrohelids and actinophryids):

Left: Spiral arrangement of microtubules in the axoneme of actinophryid(?) Echinosphaerium. (Jones & Taylor 1981 JCS) Right: Cross section through an axopod of Actionosphaerum (actinoprhyid) containing an axoneme in the centre. m - mitochondrion. (Tilney et al. 1961 JCB)

(axonemes are the cytoskeletal support within axopodia, the long spikey protrusions that make the creatures appear like miniature suns)

And here's one so bizarre it takes three additional diagrams to explain it:

Axoneme of Cienkowskya mereschkovskyi*, a centrohelid 'heliozoan' reportedly closely related to Heterophrys. (Febvre-Chevalier + Febvre 1984 Origins of Life)

*To the slavic ear, this sounds painfully like a masculine adjective applied to a feminine genus name...owww.

And back to basal bodies, parabasalian TEMs are a work of art in their own right. Especially from Joeniids:

Rows of basal bodies in the ciliary region of Pachyjoenia howa. (Brugerolle & Bordereau 2004 Eur J Protistol)

This has nothing to do whatsoever with neither protists nor axonemes, but rather a funky-looking reject from my research images. It's cytoplasmic GFP in a partly lysed plant cell (normally the GFP should look diffuse) Not sure why it does that though, but often lysing cells become very bright, and squashed material is lush with autofluorescence.

My favourite colour is GFP.

Real posts to come soon... still mildly overwhelmed by stuff at the moment. Currently working on gathering up literature both new and old on a supergroup that may or may not actually exist, and is a complete and total mess either way (the new 'Hacrobia'). On top of other things.

To give you an idea, the previously incertae sedis centrohelids are in it, apparently, and their older grouping, "heliozoa", has only recently been dissolved (Nikolaev et al 2004 PNAS), so what is now spread out over at least two supergroups (centrohelids in 'Hacrobia' and actinophryids in Stramenopila) used to be lumped under one category and now you might as well rip all your hair out trying to figure anything out in there. It basically means you have to deal with the damn things on a genus-by-genus, taxon-by-taxon basis. (luckily, they're really cute so it's not that bad ^^) Also, a couple extensive papers happen to be written by The One We Fear, and I'm still denying the fact I may eventually have to actually read them. Grrr. Oh, and add to that the horrible and sometimes altogether lacking availability of older literature, requiring you to assemble epic shopping lists for the inter-library loan people...

Should probably also write another sentence of that manuscript to feel as if I've done something this week. Describe a couple more figures that don't actually exist yet... wish all my control pictures didn't totally suck. Redoing experiments again to get better images of...controls. Sigh. Working on projects in two completely unrelated fields (and different buildings) is a bit draining... /rant

Microbial Art

Several clans of geeks profs and their students put together an awesome collection of art done on plates with bacterial and fungal cultures - go check it out at MicrobialArt.com!

Of course, this one had to be one of my favourites:

(Gregory Lab; exhibit #12)

Perhaps 'tis about time I start plating my bacteria 'creatively'...