Field of Science

Happy holidays to all, back in January!

I totally meant to do a kick-ass end-0f-the-year post, but that'll have to wait until January... was swamped with everything. Promise to return to regular, proper blogging in the new year! (after ScienceOnline2011!) Mostly away from internet until 05 Jan.

Almost late for my flight... so a happy and relaxing whatever-you-celebrate (protistmas? =P) to everyone!

Walsby's Square Archaea! Haloquadratum walsbyi

ResearchBlogging.orgProcrastination 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 from Minegishi et al. 2010 IJSEM (abbreviations deciphered in red))

The salty waters Haloquadratum inhabits are no regular salty waters – the salinity exceeds that of typical seawater by a factor of ten. In other words, really salty. Not only that, but Haloquadratum thrives in Mg-rich waters just below the lethal concentration (past which nothing lives). This extreme salinity means the cells are no longer hypertonic relative to the medium, and in fact may be hypotonic – recall classic experiments involving dipping onion cells in saltwater to show shrinkage. In fact, despite living in aqueous environments, these organisms have very little access to water, and the extremely saline muck is also highly anoxic (low in oxygen). In other words, not the ideal vacation spot for most life.

Presumably, there is considerable selective pressure to optimise for a very different surface-area-to-volume ratio, particularly to enhance gas exchange (otherwise severely hampered by salinity). Thus, not only does the non-hypotonic environment with respect to the cell enable it to easily deviate from its spherical tendencies due to lack of turgor (Walsby 2005), but in fact favours it to expand its surface area by being a flat sheet.

There are also triangular hypersaline Archaea, Haloarcula japonica:
Left: Triangular Haloarcula japonica cells under normal conditions. Right: H.japonica after lowering magnesium concentrations – the cells become rounded "spheroplasts". (Horikoshi et al. 1993 Cell Mol Life Sci, modified therein from Nakamura et al. 1992)

Quite fascinatingly, the decrease of magnesium concentrations in H.japonica cultures results in the cells becoming spherical! A specific glycoprotein appears to be responsible for maintaining H.japonica's triangular shape, and is released upon lowering magnesium levels, allowing the cells to spring back to their natural rounded selves (Horikoshi et al. 1993 Cell Mol Life Sci). This is also a cool case of membrane morphology being predominantly regulated by a single protein, which is not so common. There's a whole area of research based around the shaping of membranes with various proteins...really cool stuff too. Interestingly, the triangular H.japonica divides asymmetrically (Hamamoto et al. 1988 FEMS Microbiol Let), resembling the division of triangular stomatal lineage meristemoids in Arabidopsis...

Extreme environments can provide opportunity for some extreme geometric experimentation, as shown by a couple flat square and triangular archaeans here. While prokaryotes are notoriously dismissed for being morphologically 'plain', many are far from it, and even have elaborate cell structures within, but that's for another day. But zoologists and botanists take note: the little awesome that is left outside the protist kingdom is hoarded by prokaryotes, ha!

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) 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) 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

(h/t Opisthokont, who owes my boss few hours of my productive work time)

October Mushroom Foray

Felt a little guilty not posting, especially considering I'm mentioning the blog on applications and such. So have a low-maintenance post for now! It barely even features any protists, but rather some mushroom walk pictures I had lying about since October. Also, this should put me in the right mood to start possibly considering contemplating studying for that mycology lab final next week *shudder*. The rusts are on there, and perhaps some of you might now what that means: that's right, life cycle hell. And structures that vaguely look all the same but aren't.

Most of the fungi one can easily see with unarmed eye in the forest are basidiomycetes, with a few ascomycetes if you're attentive enough. Many more fungal phyla exist, of course. In case you care, the basic layout roughly looks like this: Chytrid-y things (paraphyletic mess at the "base" of the fungal tree; characterised by having retained flagellate zoospores; though apparently a lineage in the Zygomycetes also has flagellates spores – odd...); Zygomycetes (fast-growing fungi, you'd know them if you've ever let food go bad – some of them are the scary tall molds with black-ish heads on bread and fruit); Glomeromycetes (Vesicular Arbuscular Mycorrhizae) – form internal associations with roots; have cool multinucleate spores at one stage; Ascomycetes (moldy things and tiny cuppy things, generally) and Basidiomycetes (your garden variety mushrooms, and other things). Microsporidia – really cool single-celled intracellular parasites with tiny genomes and mitochondrial remains that import ATP, are somewhere in there too, either basal among the chytrids or somewhere around Zygomycetes.

I have only two of the phyla here; but someday, I'll go hunting for chytrid zoospores – parts of fungi that actually move and appear sentient! (partial to motile things here. Which is why I worked on plants for three years. Yeah...) So we begin with a wet log – the Northwest/West coast (depending on which side of the border) has lots of wet logs in the winter. And wet weather. And wet residents. On the left are tiny ascomycete cup fungi; on the right are also ascomycetes with perithecia – flask-like spore containers – (thus Sordariomycetes) or something else. Saw it with ID once before, completely forgot the genus...
(btw you should check out Haeckel's Ascomycota plate – some elaborate pretty cleistothecia there!)

Mushroom-like ascomycete Helvella lacunosa. I love these things – ascomycetes seldom get so conveniently large and common.

A mushroom expert of some sort already beat us to it, as suggested by the carefully trimmed stem of the Helvella to reveal a distinctive structure:

Jelly fungi – contrary to their non-mushroomy appearance, they are, in fact, basidiomycetes:

These are your conventional garden-variety basidiomycete mushrooms. I forget what these are, but there may be something cortina-like (a type of veil) on the second midground mushroom (left of the heavily springtail-infested one) – if that's what it really is, then these would be aCortinarius sp. EDIT: It's Hypholoma fasiculare, or Sulfur Tuft; thanks Emma!

A reishi mushroom – those are apparently prized for medicinal qualities in East Asia, particularly Japan. They're also quite pretty, this isn't the best specimen.

Who can walk by a puffball without feeling a dire obligation to poke it? Puffballs, earthballs et al. are pretty interesting – they're basically degenerate gill fungi where the gill structures become an enclosed mass of basidia and hyphae called a gleba. These 'degraded' mushrooms have arisen multiple times independently, often in dry regions – presumably, since forced basidiospore ejection requires water to work, the selective pressure to keep the gills parallel and well-organised disappears and the mushroom is quickly allowed to lose the structures. Furthermore, dispersal the way of most puffballs – being being hit with something or stepped on – is more effective in those conditions. But the first step was likely the loss of selective pressure driving the maintenance of well-formed gills...

A tick. It was very tiny. And removed and thrown very far away promptly after photo. Ticks are scary...

A big, pretty mollusc for Aydin at Snail's Tales: (anyone got the ID?)
Finally, we return to protist – a slime mould! A
Physarum-like thing, still in plasmodial stage but preparing to fruit soon:
And now I must return to procrastinating with life tackling the intimidating pile of duties for the next couple of weeks. Finals are trivial in comparison. That says something. Something terrifying...

If anyone else would like to organise a magical time warp by next week where we get an extra few days of time, I'm in! Can't we just stop the bloody calendar for a couple days?!

Personal Update

Dear readers-who-haven't-abandoned-the-place-yet,

You may have noticed that calling my recent blogging as 'spotty' would be a bit of an understatement. And it is. I don't like resorting to excuses, but the truth is, there's some agonising deadlines coming up, many of which are kind of important to my life after graduation. That is, if I want to have food(=instant ramen) to eat and occasional internet access (for blogging! =D) after the university kicks me out in May, these deadlines must be addressed. After all, one must work hard to deserve a life of academic poverty and eternal job insecurity. The good news is, many of these deadlines will pass, hopefully having received appropriate attention beforehand, around 01 Dec, after which I may have a sliver or two of free time to share some epic protist awesum with you.

Thus please don't think I've forgotten or have become too lazy to blog – the guilt eats me alive day and night, if that makes you feel any better. But there's scarier guilt competing with blogging guilt at the moment. In case it's not entirely obvious – I'm applying to graduate schools. Since the average PhD lasts longer than the average marriage in North America, this is a bit of an important decision.

For now, here's some amazing crafts (surface scales) created by a 'lowly' amoeba, Cochliopodium (second from left in my blog header images), arguably putting Haptophyte coccoliths to shame:

PS: If any of you are going to ScienceOnline2011 in January, I'll be there!
Room D - “But it’s just a blog!”Hannah Waters, Psi Wavefunction, Eric Michael Johnson, Jason Goldman, Mike Lisieski and Lucas Brouwers
Many young people are eager to communicate science despite their lack of scientific and/or journalistic credentials. While all science communicators face challenges, this subgroup has their own set of challenges including cultivating a following of readers from scratch, and high levels of self-doubt, often referred to as "imposter syndrome." What value does this rapidly-growing group of science communicators bring do the field? How can the science blogging community encourage and mentor young bloggers? How can we hold these individuals accountable to the high standards of science and journalism while simultaneously allowing them to make mistakes as part of the learning process? In addition, established and successful science communicators will be encouraged to share their tips and tricks with their newer colleagues. (Source: program)

Irremediable Complexity – Science piece

Just wanted to bring to your attention that a new Perspectives piece finally came out in Science this past week, nicely (and in a concise way) summarising Constructive Neutral Evolution – that is, the capacity of non-adaptive and neutral processes to drive a seemingly directed increase in complexity.

Since non-OA publishers are lame and don't let the unprivileged lower creatures to see their articles, I put up a (hopefully) freely accessible pdf here. Hope the link doesn't die. Read it, it's like my previous ramblings on the subject but more concise and accurate and written by people who know what they're talking about ;-) (I also blogged Ford Doolittle's talk here)


And yes, part III of my CNE post is coming, as well as the post on Mike Lynch's seminar talk. Let's just say that writing for work does not leave much guilt-free writing juices left for blogging about complicated topics. I mean, if I have the mind and energy to read papers and write about them, I feel guilty not spending that on the work I'm actually paid to do... Should catch up soon enough though, and then the blog monsters shall be unleashed and there will be no respite from the flood of intense protistiness that shall follow, bwahaha!

*The Dal is strong in this list...

Research proposal ramblings – Eukaryotic cellular evolution

Have a research proposal to do in a week for a graduate research fellowship (which also contributes to my spotty blogging as of late). Figured I'd try out Rosie's strategy of blogging to generate ideas and sort things out a bit. Would really appreciate feedback + discussion, particularly criticisms. This is my first time doing one of these, so I'm a total clueless n00b. This isn't my proposal, obviously, but rather a pre-draft of a pre-proposal draft, to lay out some thoughts ;-)

And this stuff needs to be narrowed down A. LOT. I'm well aware of that!

Topic: Eukaryotic cellular evolution
Or "cellular evo-devo"; of protists, obviously ;-)
Possible subtopics:
- The role of non-genomic ('cellular') inheritance in the broader context of evolution
- The relative extent of cellular inheritance in various unicellular and multicellular examples, in relation to size/"complexity", effective population size, mutation rates, whatever. (no idea how I'd do that yet though)
- Tracing the path of individual components in eukaryotic evolution, such as specific protein families, etc. Comparative work.
- ?

Early evolutionary biology focused on the macroscopic level, such as general morphology of an organism and its behaviours in relation to its ecology. Later developments in molecular techniques have largely shifted the focus of the field towards the molecular scale, focusing on genes and proteins. In doing so, the organisms have been reduced to mere genomes – their cellular and developmental contexts largely forgotten. While evo-devo aims to revive the developmental aspect of evolution in multicellular organisms, little has been done to approach evolutionary biology on the level of individual cells, particularly in unicellular lifeforms. Cellular biology is crucial to a properly holistic understanding of evolution, and since the vast majority of organisms on earth, both in quantity and in diversity, are cells, time is ripe to investigate the role of extra-genomic cellular hereditary processes and their role in organismal evolution as a whole.

The first requirement of studying cellular evolution is good sampling. This demands a good phylogeny, and well-understood cell biology among non-Animal/Fungal/Plant organisms. Phylogeny together with cell biology must then be used in attempt to reconstruct ancestral states in order to seek out potential patterns and correlations. These patterns must arise several times independently, in order to have a decent independent sample size. However, at this point it's still only comparative biology; to make it to the level of evolutionary theory, predictive models must be inferred and tested from these patterns – this would ultimately require tying it in with the entire range of biological topics, from biochemistry to population genetics and ecology.

Of the above steps, only the phylogeny has begun to more-or-less solidify, at least enough to begin doing comparative work, if enough well-developed model systems exist in the attention-starved areas of the tree. However, the organismal & cell biology side does not fare as well: of the non-Animal/Fungal/Plant eukaryotes, only the medically important intracellular parasites like Plasmodium, Giardia and Trypanosomes have been well-studied (in the molecular cell biology sense), as well as cellular slime mould Dictyostelium due to its assumed significance in the evolution of multicellularity. To a lesser degree, ciliates Tetrahymena and Paramecium have been studied, as well as diatoms and oomycetes. This leaves huge swaths of phyla severely underrepresented, including practically all of Rhizaria. It must first be established whether anything is salvageable from what has been done to date.

(It would be unwise to rely on developing a novel model system for a PhD project, as potentially awesome as some candidate species may be. Maybe on the side, somehow (I really want Allogromia!))

As an aside, the close relatives of a potential model system should be examined to evaluate how well this model represents the group – picking at outrageously derived system would not be preferred for comparative work, although it would be quite biologically informative in its own right. Some of model candidates may have annoying quirks for certain types of things – eg. Paramecium undergoes autogamy every couple of weeks and destroys its somatic nucleus, thereby being ill-suited for molecular work.

To summarise, studying cellular evolution would require further development of protistan model systems, as well as extensive comparative work between them. Project could focus either on using what's already there for widescale comparative and theoretical work, or picking a single system and working on it specifically.

Relevant examples
- directed assembly of ciliate cytoskeletal elements (Grimes & Aufderheide 1991; Sonneborn & Beisson 1965 PNAS; Frankel 1989) A substantial body of work exists on the topic of ciliate development and how a chunk of the cytoskeletal organisation and morphogenesis seem to depend on non-genomic factors; eg the vertical transmission of a surgically inverted row of cilia independently of genomic inheritance. Furthermore, during encystation, hypotrich ciliates lose all basal bodies, and morphogenesis must happen anew. Some altered traits are lost after encystation, some are not. A mysterious 'organising centre' seems to exist in Oxytricha that determines defining features of the new morphology.

- endosymbiotic bacteria (eg. Görtz 2006 The Prokaryotes) of ciliates as a model for cytoplasmic inheritance of more tangible/quantifiable things.

- organellar inheritance, but that's been done to death already. Relative to above two cases, I mean! (before they kick me out of the lab for saying that...)

Potential projects
A lone tumbleweed rolls across the vast expanses of the chilling mind desert as the ruins of a derelict ghost town stand as a ghastly reminder of the Mind's complete and total absense. A slanted cracked wooden door of the saloon creaks softly in the winds of confusion, seemingly bemoaning the long-gone days of vibrant endless drinking...OH, THERE, I GOT IT! I need beer, the cause of and solution to all research problems!

- Continue the ciliate morphogenesis work of the 60's-80's. Look for general evolutionary principles, if feasible. [something specific goes here]

- Cytoplasmic inheritance of endosymbiotic bacteria and their genomes; effects of various things on that; comparing patterns between different [independent] clades? [something specific and intelligent goes here]

- mapping known cell biological traits onto modern eukaryotic phylogeny, look for patterns. Protein trees, for starters. Eg, Jékély and Cavalier-Smith type of work.

- ?

- lock self in a dark closet microscopy 'room', grab Allogromia or Stentor or Oxytricha or something, work on its molecular cellular biology, screw the whole broad research questions thing. Play with new protists on the side. Be a real hardcore protistologist. Shun everyone else. Damn, so bloody tempting...

Considering the cytoskeleton is the best part of the cell, and tubulin kicks actin's sorry little ass, my hands are seriously itching to do some in vivo fluoresent labelling on various cytoskeletal components in foram reticulopodia, and...well, that's a career right there. Especially when their microtubules grow 10x faster than those of any other eukaryote. (not sure how foram genomes go – could be a pain to work with)

But ciliates are cool too. And Warnowiid dinoflagellates with their awesome 'camera eyes', and radiolarians, and all these other things that aren't even culturable yet. Damn.

Broader impacts, justification
...heh. Should probably have something vaguely resembling a faint outline of a potential project before even considering these. Content first, embellishments after, even if the latter can appear to be more important at times.


Problem with cellular evolution at the moment is that we don't even have a decent grasp of cell biology yet, even in multicellular model divas like Arabidopsis and C.elegans. Not even getting into the phylogenetic sampling issues and lack of extant theoretical framework.

And we haven't even mentioned the prokaryotic cells yet. Yes, they have cell biology too, not just bags of biochemistry. No, most people haven't realised that yet, and/or don't care. Yes, we're fucked.

The very idea of cellular evolution almost looks impossible at the moment. So I really want to do it!

Ok, now sink your teeth in and demolish my very dream of making it in my foolish career choice. Start discussion. I need ideas. My mind is full of arcane protist taxa to think straight anymore (did you know Pseudospora was reported in 1905 to produce uniflagellate gametes? Did you care? Lookie, I'm soooo employable! Transferrable skills galore!)

MolBiol Carnival #04

Welcome to the fourth edition the MolBiol Carnival!

With a GRE to write this Thursday, don't have much time or energy for creativity, so I'll just run the submitted posts on a gel this time. The submitted posts were measured for word count* and run on a gel in Excel (didn't know you could do that, did you?) – aside from a contaminant (and mysterious primer dimers despite not using any primers), the gel seems to have worked and is displayed below:
(Sorry, was too lazy to make a fake ladder too...)
*Ideally, one would use character count instead, but that requires extra clicking and I'm lazy energetically-challenged.

Now I'll do some gel extractions and run the resulting sketchy solution through a sequencer (ie dumped them off at the sequencing unit, to be glared at by the personnel as usual). Ooooh, it came back like this: nnnnnnynnnnnrmnnnnhrnnnnnnrannnnnn. That's right, I have a single base pair recognised! And that was my longest read! nnnn's are so easy to assemble into contigs. Am I doing it right? Nothing wrong with sequencing single posts without amplification, you see?

And this is why wise ones keep hardcore molecular biology preferrably in an entirely separate building from cell biologists like me. Preferably with security. For the greater good of Science.

So I have up on 'sequencing' the posts from scratch and went directly to 'GenBank' (reads, The Internet) where these posts were strangely already deposited. As they say, "Two months in the lab can save two hours in the library." – source unknown.

Saving the best for last, or going straight for the best first, we start with our friendly and not-so-friendly prokaryotes. First off we have an explanation of the effect of ATP on bacterial biofilms in the medical context by Michael Scott Long at Phased. Next we have another biofilm-forming bacterium, beautifully-named Golden Staph, with a really nice SEM, seen at the right. It has a close relative which may actually be quite helpful to us medially, explained at James Byrne's Disease of the Week!. Another post from his blog features Pseudomonas aeruginosa and amazing antiseptic honey action. Apparently, biofilms don't fell so well after being smothered with honey. Last item from Disease of the Week this issue comes just in time for flu season – an explanation of how vaccines work, in two parts.

Next up we hear about bacteria being 'floxed'. To find out what the Cre-lox system and Streptomyces have to do with each other, head over and read LabRat's post for your daily flox. She also has a nice post on bacterial division.

Taking a break from small things, we have a post on thoroughbred horses: turns out, while the pedigree of the stallions was well-maintained, it did not dawn upon the ancients that the mares contribute half of the phenotype. Thus, while the males were imported from various exotic locations, any local female was considered to suffice...find out more at GrrlScientist's Punctuated Equilibrium.

Next we have Lucas Brouwers on tinkering and the evolution of novelty at Thoughtomics, tracing the story of the metazoan nuclear receptor. Of course, this receptor could be misfolded upon formation, like any other protein. How are defect proteins removed before they wreck havoc upon the cell? Enter E3 ubiquitin ligases and their role in removing proteins originating from mRNAs devoid of stop codons, in a post by David Weinberg at You'd Prefer an Argonaute (a title that makes me feel oddly...silenced *groan*).

And last but not least, all the proteins must fit somewhere. Well, the genes that code for them anyway. Often, these genes have a very spacious home in a massive genome(amid piles of junk), as discussed in Iddo Friedberg's Byte Sized Biology. Here I must shamelessly add a plug for 'my' kingdom: the coolest genomic gymnastics happen among the protists, aka "the other 99% of eukaryotic diversity, that you don't hear about". We have the smallest eukaryotic genomes, called nucleomorphs, as relict algal nuclei remaining after secondary endosymbiosis (in cryptomonads and chlorarachniophytes). We also have [arguably] the largest eukaryotic genomes: Amoeba proteus and Amoeba dubia, the latter around 670GBp, as well as dinoflagellates with their unusual low-histone nuclei. And size is not all that matters – some nuclei, eg. of euglenozoans, have polycistronic messages consisting of many eukaryotic genes riding off a single promoter. They rely upon splice leader trans-splicing to work, and that is only the beginning of awesome... feel free to stick around here for more! ;)

That's it for this month's edition of The MolBio Carnival. You can check future hosts and past editions on the Carnival's home page. Be sure to subscribe to the RSS feed to receive notifications and summaries when new editions of the Carnival are posted. Also, you are welcomed to submit your best molbio blog articles to the next edition of The MolBio Carnival which will be hosted by LabRat. More info here. The previous edition was hosted by Alexander Knoll at Alles was lebt.

My favourite thing about carnivals is the exposure you get to various topics and writers as a reader, and the forced exposure to various topics as a host. Thus, submit, submit, submit – feel responsible for enlightening the next host as well as the readership about the existence of topics they never come across! Molecular biology is everywhere – let's see more of that!

PS: Carnival of Evolution #19 came out yesterday at Byte Sized Biology.
Also, if hungry and poor, Sci at Neurotic Physiology has an awesome compilation of recipes at her The Grad Student Eating in Style Carnival.

PPS: Apologies for slight delay. Reason – my life looks roughly like this comic. INTERNET! FOREVER...

Some cited references:
[Will add as soon as I wake up + get to a computer tomorrow. Don't want to be walked in on still being in the lab at 6am...]

Sunday Protist - A sampling of Cercozoa Part I

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]

ResearchBlogging.orgAt 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.

To be continued in Part II – Endomyxa.

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. (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

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

Scaled protists and bloated distractions

Ok, I was gonna just post this picture as filler, and then suddenly got sucked into the microbial biogeography debate – you know, "is everything everywhere?" etc. So I was going to write up a quick blurb on that, but it somehow grew out of control. As I don't have time for such epic digressions at this moment, esp w a promised post quite overdue, amidst other stuff, I'll just shelve that for later and simply post the pretty picture instead. Enjoy this lineup of protists scaled to the size of a pinhead:

How many protists can dance atop a pin? (Finlay 2002 Science)
I'm going to try to vaguely identify them, from left to right: Chaos sp.; Stentor sp.; some random amoebozoan; Amoeba sp.; Loxodes? man I suck at this; Bursaria sp.?; Paramecium sp.; Mayorella sp.?; a euglyphid; another bloody ciliate; Strombidium; Difflugia-like thing; Euplotes; Ophryscolex-like; heterotrophic euglenid; heterotrophic euglenid again (Peranema); het eugl (Entosiphon or Petalomonas), Chlamydomonas? too small; ?, pedinellid-like thing?; Bodo, non-descript small unknown flagellate? Bodo., last two look like those tiny non-photosynthetic stramenopiles everyone ignores.

This tangent was initiated by working on that long overdue post, by the way. Apparently, one graph is enough to lead me on a massive multi-window-tab-explosion journey into the wild unknowns, even if it involves ecology. Maybe this is why it's taking me like four months to write a single freaking chapter. I'm not sure the free version of Mendeley was meant to handle hundreds upon hundreds of references. Let's see what it does once I hit a thousand, which will be soon. At least researching flagellar root apparatuses doesn't typically lead me to Hooke's description of the first cell, unlike one particular reader here =P (who needs to update, by the way...)

Oh, and submit to the carnivals! The more posts I have, the lest posts I'd have to fake, and the less I must rickroll you with fake links...

Mystery Micrograph #25

The last one was cracked by 'Anonymous', suspiciously close to a well-known dinoflagellate lab... it was a Warnowiid ocelloid, which is pretty much the coolest thing ever. I shall definitely blog about it someday. Been procrastinating with it because I'm not sure I can do it justice. In short, it's an image-forming camera eye...of a unicellular alga. If only these things weren't present at about one individual per cubic metre of seawater...argh!

Onto the next one. Tell me what's going on here:

TEM; 2 - 2300x 3 - 3400x. To be referenced later.

Gluttonous amoeba

Was looking through some freshwater pond samples one day, and saw this amoeba (Polychaos?) which has managed to engulf an entire Phacus (a photosynthetic euglenid)!

How it managed to ensnare the Phacus with its pseudopodia is beyond me. Phacus is perfectly capable of swimming away. Then again, amoebae are actually kinda scary...

Or what if this euglenid wasn't actually being digested, and would have eventually become a permanent endosymbiont, forming a brand new lineage of photosynthetic amoebozoans with tertiary plastids? And just as this miracle was about to happen, some asshole biologist captures the poor amoeba and kills it. Oh well.

Call for submissions for MolBiol Carnival! (and CoE)

Have you written about fancy little molecules doing something biological lately? Have you written about biologists doings something molecular? Do you have pretty gels to show off, in a polite manner as to not offend those of us who chronically fail at PCR? Have you aligned some proteins into pretty super-neat colourful blocks screaming OCD! to the rest of the world? And written about it?

If so, you should submit your post to the high Impact Factor MolBiol Carnival. That way, not only will your wonderful exhibit be hosted amid members of the world's awesomest kingdom, but you'd reach a much wider readership than you would through Obscure Journal of Experimental Molecular Shit No-one Understands Anyway (Aka Journal of HAHAHA YOU'RE NOT IN CANCER RESEARCH SO WE DON'T CARE ABOUT YOU) And you thought that post was going to Nature, eh? What are you, an undergrad summer intern? ;-)
You can even cross-submit to the Carnival of Evolution, as evolution cannot be properly studied without molecular biology (Ha, suck on that, ecologists!*)

Was all of the above too much text for you? Too confusing? Lemme rephrase that:

CLICK HERE and SUBMIT YOUR POST to MolBiol Carnival NOW. Please ;) Scheduled for 01 Nov, 2010, here; please have the submissions in by 31 Oct. Make 'em spooky if you'd like.

Are you happy now, Alejandro?

*I'm perfectly cool with ecologists. I even have a friend who is one. It's kind of like the token 'gay friends' of flaming fundie Republicans. Except that I'm not actually an ecologist** myself. ;-)

** Please don't tell my cell biology peeps I'm applying to a graduate program with "ecology" in its title...I would get shunned by the entire field.

Speaking of evolution, Carnival of Evolution is alive and kicking too. You should submit. Next one is also 01 Nov at Byte Size Biology, and even though it won't be as cool as ours, it will still be totally awesome and the perfect place for you evolution posts.

Incidentally, I should probably write some real posts. Haven't done that in a while...