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Int’l Congress of Protistology follow-up and overview

The views expressed are those of the author and are not necessarily those of Scientific American.


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(I’m a month late on writing this — apologies, getting settled in at a new job in a marine station, until December)

A few weeks ago, about 300 of us had a total blast in Vancouver, savouring the once-a-year opportunity to talk protists at each other and not get total blank stares in return! Blank stares only came from other people at the hotel for more serious conferences — jealousy, of course, right? Vancouver’s also my home turf, which was a mix of awesome and sucky — awesome that I knew where to go for food and such, awful in that I had to ignore most of my non-protist friends and never leave downtown in order to focus on the conference. Those should really be held in the middle of nowhere, so we have no one but each other… and holy crap that sounds creepy. Retraction.

Afterwards, I took a couple ferries to hole myself up on a remote island in Washington State, so apologies for the late return. I found me a habitat smaller and more remote than Bloomington, Indiana — by more than an order of magnitude. I thought 80 000 was a small town… but nope, we haven’t even reached 2500 here yet, in Friday Harbor[sic]. That’s excluding the ocean critters, of course — the two whale pods bring us about 10-15 closer to 2500 (haven’t inquired about their populations yet, but there are two families! Of whales, not townies… though don’t cite me on the latter).  But the critters I care about are far more numerous — definitely elevate Friday Harbour’s population past the billions! Anyway, I’m at the marine biology station here until December (funding allowing), protistologising the high seas of San Juan islands.

And I’ve started saying “Washington State” instead of just the proper “Washington”… what has the Midwest done to me!?

Anyway, here’s the transcript of live tweets from the conference. Several of these will be elaborated upon, and I’d love to hear if there’s any specific public interest in one talk or another! There’s a ton of cool posters too, but I’ll need permission to post anything from those. There should be guest posts along the way too. Many talks blew me away… it was an overall awesome conference, everyone was very happy, it seems! And the next congress, in 4 years, is in Prague, so we’re all super stoked for the cheap amazing beer SCIENCE!

So for now… hope you enjoy the notes, until I get off my ass and start putting real posts up! ;-)

ICOP 2013 Twitter transcript  — via @ocelloid

David Bass on “rampant rhizarian parasites”

DB: haplosporidia. Annelid hosts ignored b/c industry doesn’t care! Other hosts too, incl molluscs, echinoderms, crustaceans

DB: Mystery crab parasite. Epithelial cells infected.

DB: Parasite phylo position: Long branch is looooong.

RT @Paraphyso: Follow RT @ejaminter: Plastids from Lepidodinium sp. Were once a pedinophyte, full plastid genome almost complete

DB: Microcytos — new parasite + group within haplosporidia

DB: New emerging crab and oyster diseases. A whole world of new commercially-relevant parasites found.

DB: Paramyxeans now. (they’re AWESOME: http://t.co/e5Cf3cR14H)

DB: Ascetosporea (cont haplos and paramyxids) branches with gromia…?

DB: A lot more cercozoan parasite lineages worked on and found. Should be very exciting to follow! (and useful too)

Simdyanov on phylogeny of parasitic apicomplexans

S: Parasitic apis largely ignored in inverts. Coccidia: transition to blood parasitism.

S: protococcidia eg. eleutheroschizon. Attachment organelles. Creepy track left in host epithelium…

S:Agamococcidia: eg rhytidocystis. [going over how various stages absent and present in various lineages].

S: HAemosporidia. Synapomorphy: loss of conoid. Cryptosporidia form parasitophorous sac in/on host.

…this speaker is SO Russian. Lecture style, intonation, and all. It’s epic.

S: Gregarines: Arche-, Neo- Eu-gregarinida. Abberant archigregarines: Platyproteida. Very dynamic pellicle (looks vaguely euglenoid)

Anderi Diakin on agamoccoccidian Rhytidocystis in white sea polychaete

AD: Agamoccoccidians: gemmocystis in corals. Rhytidocystis is new, in polychaete intestine epithelium.

AD: Surface morphol really weird. Small ridges form transverse rows like ////

AD: Micropore openings as well. Developmental stages observed. (pretty TEMs of ultrastruc!)

AD: Vesicular nucleus, Unusual mito on periphery of cell. Ampullalike cristae at periphery of mitochondria. Opaque matrix. Weird.

AD: 2nd dev stage, also at base of epithelium. Dense cytoplasm, fewer inclusions.

AD: 3rd stage: more vesiculaty, nucleus heterogenous. Many many inclusions. lots of RER, golgis, etc.

AD: Host epithelium forms cyncitia (can’t spell now) nuclei surrounding parasite. Seem to be degrading around the parasite

AD: [seems like membrane between epithelial cells where the parasite is get degraded... if I understood]

Kevin Wakeman on marine gregarine apicomplexan evolution

KW: Invert parasitic apicomplexans. Est. only about 1% of apis described. Most are gregarines — extremely understudied.

KW: [time to liberate the 99%!) Gregarines found even in butterflies, dragonfly (large single celled trophozoite!) (will look)

KW: In earthworms, sexually transmitted disease gregarines. Exchange cysts.| Myzocytosis, in colpodellids + perkinsids -- ancestral

KW: Cool video of bendy twisty Platyproteum, a eugregarine. Only in marine intestines. Weird sex.

KW: Gorgeous diversity of eugregarines slide. In all sorts of marine inverts. Marine and terrestrial gregarines form nice clades

KW: Elusive deep relationships

KW: Also looking at evol of terrestrial gregarines from marine, happened many times convergence

KW: Selenidium terebellae: Ultrastructure, x-section, few folds, nucleus occupies a lot of this particular section.

KW: Tubulin corresponding to folds/strips, and in mucron

KW: Another life stage of same org: outer surface of gut. Many folds, fibrils underneath instead of MTs. SAME organism!!!

KW: Apical cluster of tubular material.Corresponded to tubulin staining earlier of the mucron."morphotypes"turned out to be diff spp

Conclusion: Gregarines are awesomest apis.

Sonja Rueckert on more gregarines, gonna be similarly exciting!

SR: Slides are sooooo full of gorgeous pics!!!

SR: Marine crustaceans this time. A nice clade of eugregarine crustacean specialists

SR: Long gregarine, 1mm -- very narrow. Surface folds, no septum.

SR: Skeleton shrimp -- septate, surface folds, look different in their own ways. Tree, cephaloidophorideae superfamily, crustacean

SR: Need more good molecular and morphol ID on these gregarines. More work led to more confusion...

SR: [REALLY need pictures via twitter... wow]

SR: [Protists really need to stop screwing with our phylogenies]

RT @ejaminter: Now for one of the coolest discoveries this Year: Paulinella, a recent and novel primary endosymbiosis even, by Hwan Su Yoon…

Wyth Marshall on Ichthyosporids (Opisthokonts, on animal/choano side of things).

RT @cslamo: Ichthyosporea: one of the words that bothers me every time i have to write it. Â

@cslamo Ichthyophtyrius is even better.

WM: Ichthyophonida and dermocystida, two clades of ich-sporeans

Ichthyophonids: sphareical, form hyphal-like structures,amoieboid, some pathogens, some commensal; often unknown. mostly invert host

WM: Ichthyophonida and dermocystida, two clades of ich-sporeans

WM: Posteriorly flagellated zoospores (as exp from opisthos). Also reproduce by endospores

WM: Dermocystida: cysts filled with multinucleate spore. Multinucleate coenocytic stages. Cell walls (several layers often)

WM: spindle pole bodies described from some, obv MTOCs present

(remembered how to spell syncitium all of the sudden, I think… still looks wrong though)

WM: Motile plasmodia, hyphal like shapes, and leaving trails of extracellular slime

WM: Membrane-bound tubules present — fixation artefact? — Sometimes organised in pits or winding through inner layers of cell wall

WM: Impressive morphol diversity of a _single isolate_! Shape changing as hell…

WM:”Reproduction parallels some form of anarchy” Colony morphol is insane

WM: Ich-sp host interaction. Tendency towards broad host range in some lineages

WM: Can take infected herring, feed to salmon, pass on infection.

WM: Emergent disease potential. Introduced species also a problem. Oh yeah, this is in fish — we care about that!

WM: Motile stages common. Secrete attachment material. Membrane-bound tubules– why? Causing disease emergence. Awesome critters!

{Ichthyosporids often neglected by protistologists, too close to animals…)

Gong on a nov sp. of proteriochromonas, and chrysophyte predator of chlorella cultures

G: Proterioochromonas responsible for crashing of chlorella culture (a problem if you care about chlorella)

G: Chlorella cells gradually disappear into proterioochromonas

G: Not only voracious feeder, but can also digest it completely

Up next: Susanne Menden-Deuer on cell-cell interactions and their effect on plankton dynamics.

SM: Cell-cell interactions feed into large scale ecological phenomena

SM: (I like this approach — we need to get behaviour back into protistology!!!)

SM: 3D movement behav of indiv plankton; growth and grazing rates, etc

RT @cslamo: Ganymedes. I loved that genus name.

SM: Movement of plankton considered random, aimless. Turns out to be non-random, ballistic, persistent.

SM: (protists move with intent!)

SM: “protist migration” — right, why should birds and mammals have a monopoly on that?

SM: Eg. Heterosigma / favella: latter likes bottom layers; het-sigma likes it too; when predator present, swims predominant UP.

SM: Response to predator signals; heterosigma actively swims away from ciliate predator.

SN: Fleeing behaviour does lead to higher growth rate despite presence of predator. It matters.

SM: On larger time scales, plankton (protist) motility non-random and much more coordinated than normally assumed.

SM: Swimming behaviour also changes by prey preference.

SM: (cute 3D model of Heterosigma (dino) on last slide, moving about!)

Matthias Fischer on virus-affected swarming in Cafeteria (a bicosoecid flagellate, not the site of horrible food…)

MF: Cafeteria perform complex coordinated behaviour in response to viral infection

MF: Tiny heterotrophic flagellate, transformed by giant virus into a virion factory dominating much of the cell!

MF: (NB: this virus for a while had the largest viral genome known…)

MF: Infects other flagellates too. >300nm viral diameter (=”giant”), 730kb dsDNA genome; 544 protein coding genes;has its own virus!

MF: virophage — can only replicate in cafeteria infected by Cafeteria virus

MF: increases host survival in doing that. Blocks CroV (Cafeteria virus, the giant on) replication

MF: Those who survive virus, called CroV survivor strains, found new population

MF: More motile than original. Don’t settle down no more. Wild ones settle.

MF:While motile, cells accumulate in one particular spot — form a swarm with dense centre, then move away — form  a ring!

MF: Flagellates move around periphery of ring, avoid the centre. Ring is gradually expanding, reaches a certain size

MF: 1-20min after cells added to slide, time to swarm

MF: Rings remain stable. (awesome — and “simple” experiment with just haemocytometer and droplet of cells)

MF: Amazing videos of swarming — 2 rings form, grow, overlap and fuse, make larger ring!

MF: After disturbance (shaking cover slip) — congregate again in centre, and gradually form ring again!

MF: CroV survivors tolerant to CroV — virus has no effect. Not dying. CroV still replicates, but latently.

MF: After time,survivor strains can lose this ability to swarm eventually.

CroV swarming story reminds me of something I saw in bacteria once:http://t.co/9y9FyuAlCy

MF: WT can also form patterns, but they settle and don’t swarm

Fenchel explained my bacteria phenomenon — microaerophilic, form ball to deplete oxygen, deplete too much, ring expands!

Nisbet on polycistronic transcription inapicomplast (plastid) of plasmodium

EN: Dinos have poly u tails on mRNA, and polycistronic. Chromera does too. Apis — no poly-U tails. What about polycist transcripts?

EN: Extensive polycistronic transcription; through rolling transcription as in dinoflagellates, perhaps?

EN: MAny antisense transcripts too — rolling circle transcription in the opposite direction as well?

Jan Janouskovec on the Twirling Disk (an organism =) )

JJ: A bunch of subcultures left on bench by leaving postdoc. Looking through it while cleaning out… something colponema-like!

JJ: Turns out to not be colponema, but deep branching near telonemid (though prob long branch)

JJ: Looks like a twirling disk. Had to ditch culture for going on trip, was only ONE cell left upon return — and SURVIVED!!!

JJ: Large posterior vacuole (like telonema!), extrusomes (ultrastructure by Myl’nikov)

JJ: Complex pellicle, except for where phagocytosis happens. Extrusomes completely novel for euks

JJ: Fairly gene-rich mitochondrion; deep branching… maybe some ancestral characters?

JJ: Clarification — deep branching at base of archaplastids and SAR. Like, DEEP.

That’s one hell of an awesome organism…

Ivan Cepicka (apologies for lack of accents over C) on new anaerobic marine amoeba, Anaeramoeba.

IC: Many WEIRD marine and freshwater free-living anaerobic protists. Today, anaeramoeba.

IC: Very few anaerobes known in Amoebozoa. Weird. Some amoeboid things in other groups. But not much.

IC: Forms pseudopods: lovose, tubular projections, or very fine/skinny flat lamellopodium.

IC: Big round plasmodia formed too, several nuclei. Granuloplasm full of mitochondria and bacterial endosymbs

IC: Not excessively flattened, and moves somehow without the fine pseudopod projections

IC: Two marine strains, from Aus and indonesia. A.ignava — ignava = “lazy”,not as compact/well defined. (love the name!)

IC:[Hand-drawn amoeba porn by Bovee... mmmm! Gorgeous.]

IC: Acristate mitochondrion-related organelles (MROs). B/c anaerobic. PRob related to the symbiotic bacteria too. No large nucleolus

IC: Multiple small nucleoli — granular. Nucleus w paranuclear body — present in every cell. Fibrillar structure inside.

IC: “If somebody knows what this is, please tell me” hah!

IC: Paranuclear body as small tubules can extend all throughout the cell.

IC: PHylogenetic position within amoebozoa is still confusing and weird and annoying. Thus, fascinating novel lineage

Renate Radek on new oxymonads from termites

RR: Oxymonads of drywood termites. 5 families. Polymastix and Saccinobacculus move, the rest attach to the wall (eg oxymonas)

RR: OXymonads: 4 flagella arranged into pairs, axostyle, anterior cell cone.

RR: In cryptotermes dudleyi — only one large species still described. Microrhopalidina multinucleata

RR: Looking at sample — different sizes of “one species”. Same with Oxymonas. Tinier versions unknown.

RR: Probably not one species. Now, species from Neotermes jouteli, another termite.

RR:In SEMs, spirochaetes attach to surface, and cells are covered by weird scales!

RR: In TEM, scales still visible: like a cylinder w lid. Bacteria inside nucleus (why of course…) Weird new root structure too

RR: Next species: Opisthomitus. Smaller, thinner than oxymonas. 50um flagella to 10um body!!! Weirdproportions…

RR: SEM — Holy crap the flagella are still soooo very long that’s weird…

RR: SEM: Deep invaginations (pits) but no lids, unlike oxymonas — no scales

RR: recurrent flagellum attached. Nocellulose inside (usually in termite = wood-eating) so must be osmotrophic

RR: Of course, once again, bacteria in nucleus.

RR: Lots and lots of microtubules. Many microtubules. Wow.

RR: Molecular results do not support what root ultrastructures suggest. Oh great.

Tomas Panek (again, apologies for accentlessness) on anaerobic jakobids in marine/brackish sediments.

TP: Jakobids: small heterotrophic flagellates in excavata. Few species described originally, look similar to each other.

TP: The cool part: Mitochondrial genomes of Jakobids are the most gene-rich, most bacterial-like. Also jakobids branch deeeeply

TP: Andalucia: two species — aerobic and anaerobic. No mito cristae in latter, and prob no genome! What contrast within “genus”…

TP: Obviously, we might be missing a thing or two about jakobid diversity. Need more. Sequencing suggests hidden diversity

TP: Jakobid phylotypes quite abundant in anoxic marine sediments

TP: ‘Stygiella trypanoides’ (Jakobids have 2 morphs — attached and swimming. Swimming lacks feeding groove, diff length flagellum)

TP: Difference b/w andalucia and stygiella (5sp in latter, 1 in former) is presence/absence of mitochondrial cristae, respectively

TP: Stygiella incarcerata complex — hard to ID spp within, but group itself IDable

Vasily Zlatogurski on centrohelid heliozoan evolution — namely, raphidophrys w Unusual combo in cell covering.

VZ: Scales on cell surface very diverse, and useful morphological characters for ID and taxonomy.

TP: Ancestral state is to be completely naked (eg.oxnerella), then spicule-bearing (heterophrys) then siliceous scales…and spines.

TP: Of course, aforementioned progression to perfection gets shat on by reality.

TP: Ancestral reconstruction: both radial and tangential spicules. Loss is secondary. (deja vu… of a deja vu…)

TP: Spiculation is just loss of biomineralisation (from scales) with organic matrix remaining.

TP” Spicules are organic matrices, do not mineralise anymore, unlike scales.

Fuck, wrong abbreviation… habit…

TP is VZ since heliozoans entered the scene.

VZ: No silica in raphidiophrys sp — combined organic and siliceous skeletal element

VZ: (Raphidiophrys sp. = heterophrypoides)

VZ: (emphasises difference between spiculation and speculation ;-) )

VZ: SpIculation is loss of biomineralisation; radial-only scales through loss of tangential scales.

VZ: R.heterophryoidea not a missing link. (don’t tell the creationists…)

VZ: R. heterophryoidea — unusual. Specimens w GIANT scales found. Subclones all had normal scales. 20 of ‘em. Mmmm.

VZ: SEM deployed. The giant scales are polygonal (not oval), and attached to each other. Special interlinking system (jigsaw puzzle)

VZ: Mega-scales involved in encystment — cyst scales!

VZ: Another mystery: in a few clonal cultures — finding huge colonies, attached to substrate via scale-covered pseudopod!!!

VZ: Skeletal elements a good marker for phylogeny, but some restrictions apply (of course). No ‘progression’, simple = derived here.

Remember, guys: simple does not mean primitive! Quite often — the exact opposite!

Denis Tikhonenkov on colpodellids (deep-branching alveolates)

DT: Colponemids: deep-branching predatory alveolates. Attack other flagellates. Hyperactively twirling when move.

TD: Question is how predators became parasites on apicomplexan side of things (and some dinos too)

TD: Colponemids (colponema sp. peru) branch next to dinos+apis.. Colponema sp. vietnam branches at BASE of alveolata!!!

TD: (now, if you ever needed ancestral characters… you should be drooling.)

TD: No ventral groove in Colponema peru as opposed to sp. vietnam — supports separate groupings.

TD: Mitochondrial genome of colponemids has large gene set, genes other alveolates don’t have –> ancestral mito state

TD: Colponemids don’t suck — literally, they lack myzocytosis, or the ability to attack prey and ‘drink’ them.

TD: Colponema sp. peru thus important for understanding evolution of myzocytosis and the origin of the apical complex.

TD: Ancestor of all alveolates: biflagellate predator feeding by phagocytosis, w extrusive organelles.

Alex de Mendoza on evol of multicellularity via transcription factor diversification

AM: Most animals have homogenous TF (transcription factor) profile

AM: [Heat maps are hard to tweet...]

AM: Basically, other multicellular groups have different clumps of diversified TF families

AM: Reconstructed repertoire of TFs in ancestral euk; diversification has been been step-wise.

AM: Why more TFs in animals and plants than other multicel lineages? — model organism bias! We just don’t know!

AM: TFs used as proxy for # cell types in org — false, some unicellulars have more TFs than multicellulars

AM: TFs activity highest in gastrulation (but embryonic dev’t overall). Not so much in plants. Plants always keep growing…

AM: …so early dev’t is not as much of a big deal

Susan Sharpe on new organism, Pygsuia, a Breviate, and integrin evol

SS: Integrins — cell cell adhesion — important in animal multicellularity

SS: Transmembrane proteins, 2 subunits (alpha, beta)

SS: Binds collagen, etc etc etc — form a complex.

SS: Integrins activated by scaffolding proteins.

SS: Integrins involved in intercellular signalling. Cell motility in some cell types too.

SS: Know what integrins do in animals. What about in unicel protists? Motility, predation, something else?

SS: Not present in multicellulars aside from animals, assumed not to exist in protists. Turns out — WRONG.

SS: First, choanos found to have it, then the whole group of non-multicellular opisthokonts.

SS: Thecamonas, just outside opisthokonts — has integrin, though missing some associated proteins. Fungi had gradual LOSS after

SS: Pygsuia, a breviate, just outside Thecamonas + Opisthokonts. Evolutionarily handy.

SS: Tree. Groups with Breviata, type for breviates.

SS: Breviates, thought amoeboid, not on amoebozoan side, but rather sister to apusomonads + opisthos

SS: Let’s look for integrins!

SS: So guess what… Pygsuia has integrins! One alpha and one beta — both subunits. Similar integrin adhesive protein collection…

SS: …to apusomonad. A couple missing though. Now domain architecture. Integrin alphas in protists longer — looong in Pygsuia

SS: Integrin beta also longer in protists!

SS: Elongated stalk, more repeats. 27-29 in Pygsuia!

SS: Vinculin, integrin-adhesing protein, lost secondarily in Pygsuia, binding regions included

SS: Pygsuia pushes back the origin of the integrin adhesome.

SS: Further questions: what do these integrins do? What do they interact with? Why adhesion molecules w/o cell-cell interaction

Jan Janouskovec (again!) on colpodellids. overlapping session slots, coming in half-way…

JJ: Colpodellids and origin of apicoplast, that is

JJ:Refresher: apicoplast evolved deep in alveolates, many secondary losses and cryptic plastids

JJ: Colponema represents deep branching alveolates (paraphyletic but shhh). See the colponema talk yesterday

JJ: Voromonas, colpodella, psammosa, alphamonas — predators, hard to culture. Quite diverse cell types, alveolae included

JJ: Colpodella groups with voromonas and chromera. “Chromeriid” Vitrella groups separately, not in clade!!!

JJ: Chromera is thus a colpodellid. Vitrella and chromera have plastids, so why none in other colpodellids?

Miroslav Obornik on Chromera encystation and excystation

MO: Chromera isolated as coccoid cells from Sydney harbour. Forms sporangia, cysts and flagellates. Contain functional plastid

MO: Found unusual rod-like structur, ‘chromerosome’

MO: Chromera’s vegetative form coccoid, makes autosporangium with a wall around, Then either big sporangium (enclosed) or zoospore

MO: Zoospore forms in 10min from autosporangium. Vitrella has a lot more zoospores and autospores in sporangia

MO: Culture since 2004, but only this year giant cells found.

MO: (if I got that correctly)

MO: Zoosporangia excystation movie. Zoospores apparently LOVE running around hyperactive in circles. Cute!

MO: Lots of rotation of spores at first, then released one by one (and then circles!)

MO: Compared to rosette of zooites of plasmodium — similar residual body in centre while the spores go around

MO: Chromera — chromerosome structure in the middle of coccoid — transforms into the residual body!

MO: Zoospore formation induced by light — circadian rhythms

MO: Under constant light, appear at same time — circadian clock inside!

MO: Now interested in Chomera clocks. Some plant clock homologues found. cca1 (circadian clock assoc. prot too divergent in chromera

MO: ie — trouble making tree. Cryptochromes switched to blue light receptors in some organisms. Has them. many rel to other algae.

MO: RT-PCR — max transcription at 8am (start of excystation)

MO: Under constant light and dark — same thing, at 8am.

MO: Btw, chromerosome is likely homologous to residual body in apicomplexans

Gillian Gile, my undergrad protistology lab TA, on colpodellids having retained the plastid!

GG: (refer to previous tweets for more colpodellid and chromera stuff). Also @LaneLabURI is tweeting…

GG: Since apis and allies have plastids,as well as dinos and some allies; ut colpodellids,in the middle, do not seem to.True or not?

GG: Genes in oxyrrhis (friend of dinos) seems to have something resembling plastid targetting genes

GG: Voromonas (colpodellid) transcriptome: found Fe-S cluster biosynth genes, 4 systems. Mito, plastid, etc.

GG: Cannot transfer Fe-S cluster across membranes, it seems. Must generate own in plastid. Look for plastid Fe-S system

RT @LaneLabURI: Gile: fe-s cluster (ISC, SUF,NIF, CIA) and isoprenoid biosynthesis proteins found. N-terminal signal on SufB.

GG: Not yet found plastid FeS synth system.But a sequence that’s LGT’d from bacteria is there

GG: An isoprenoid pathway indicative of plastids. 3 related enzymes found in voromonas.

GG: Heme biogenesis. A photosynthetic and non-photosynthetic paradigm exists. Whole thing in plastid in photosynthetic orgs

GG: Apis+chromera have hybrid pathway — first stem in mitochondrion, the rest in plastid, then cytoplasm, then mito again (efficiency!)

GG: Apis+chromera have hybrid pathway — first step in mito, the rest in plastid, then cytoplasm, then mito again (efficiency!)

GG: Plastidic phosphate transporter. Monophyletic group, In apis, 2 copies in plasmodium, others can get complicated; toxo has 1

GG: seems to be a transporter similar to apis’ apicoplast one. NEED LOCALISATION!

GG: Seeming presence of plastid-associated parthhways, and caniddate genes associate with api counterparts!

Just voted on whether Voromonas has a plastid. Decided it does. Case closed. SCIENCE!

Anesi on changes in lipid composition in ciliate Euplotes based on thermal conditions

A: 4 Euplotes spp.. Lots of different lipids — rich “lipidome” Differs b/w the spp.

A: Ether forms of phospholipds found. Common in marine organisms (thought ether forms only in Archaea… oops)

A: Ether phospholipids more resistant to lipolytic enzymes (that attack lipids). Defense against chemical conditions?

Slabodnick on revival of Stentor for cell regeneration studies! (lots of awesome old experiments there, google Vance Tartar)

MS: [this talk will be rich in microporn... fuck yah]

MS: [Grrr... that ciliate image is not from my blog, have original reference right there...]

MS: Stentor very strongly defined developmental axes. Also HUGE. Classic model for morphogenesis and regeneration.

MS: Takes 8-10h to divide! New cell buds from top of the other.

MS: Initiate division every 4-5 days.

MS: Cell can be cut along any axis, if remaining fragments have portion of macronucleus — can regenerate completely!

MS: [Stentor don't need no health insurance...]

MS: Regeneration completed within 48h tops. Ok, but now, with new tools… let’s break it! RNAi to the rescue.

MS: Just feed dsRNA containing Ecoli — and voila!

MS: Oral apparatus regeneration looks bit like it in cell division.This also stage in cell div where MAC condenses — same in regen

MS: Might even share genetic pathway b/w oral apparatus regeneration, and formation in cell division

MS: Mob1 in tetrahymena — knock down, defect in cytokeniss. Knock down in stentor — also defect in cytokinesis.

MS: The cell in normal conditions also weirdly shaped, more cylindrical, in stentor knockdown of mob1

MS: RNAi also results in ridiculous messy monster of Stentors!!! (fun fact: was courting that lab at one point. LOVE “monsters”!!!)

MS: Regeneration of oral apparatus results in abnormal morpholodies in mob1 knockdown.

MS: Seems to  be hung up at stage before developing multiple poles. Continues trying to regenerate though, even though can’t

RT @LaneLabURI: Every protist meeting I go to, dinoflagellates just get weirder.

MS: Fails to repair oral apparatus, then forms posterior protrusions from anterior end. Or both ends look indistinguishable.

RT @LaneLabURI: Dinoflagellates are the Chuck Norris of Eukaryotes: we all just exist because they allow it

MS: Cutting off head and tail results in much more severe phenotype than just head or tail in the knockdown

MS: Just the middle portion, unlike in wild type, cannot regenerate either end in the mob1 knockdown

MS: First protein characterised involved in morphology and regeneration in stentor

RT @LaneLabURI: On acid, maybe. RT @Ocelloid: @LaneLabURI She went over it for me during lunch… INCREDIBLE! And dinos are SOOOO apis ;-)

MS: Mob1 localised along ridges…

Portman on relationship between apical complex and flagellum

P: Flagellar biogenesis in apicomplexa: cytosolic in some.

P: Intraflagellar transport protein (IFT) incolved in flagellar biogenesis. Present in chromera.

P: Flagella reach full length prior to excystation. Have some compartmentalised growing to get there.

P: Once flagellum outside cell, that is. Possibly role for IFT. Now: how is apical complex involved?

P: Flagella are part of complicated complex at the apex. Apical complex associated with weird noose-shaped membrane system

P: Flagella and apical complex appear at the same time within cell and are interconnected!

Ross Waller on dinoflagellate nuclear organisation evolution

RW: Dino nucleus huge, permanently condensed chromosomes — ‘dinokaryon’. Crapton of DNA, no nucleosomal packing, histones absent

RW: Roughly 10:1 DNA to protein ratio (vs more normal 1:1 in other things

RW: Back in the good ol’ days, dino nucleus so weird it was considered intermediate b/w prokes and euks

Grrrr, stop hating on ciliates, people!!! They’re protists too! And fucking awesome ones at that, thank you! >.<

RW: Perkinsus and Hematodinium early branching dinos. Parasitic. Convenient detail — infect fisheries stuff, so funding cares ;-)

RW: Perkinsus 28Mb, Hematodinoium 2400Mb (2.4Gb) — getting big!

RW: Do either of their nuclei use nucleosomes to package DNA?

RW: PErkinsus normal, also in histone department. Hematodinium weird — apparently no histones

RW: Dinos do have the genes for histones, but extremely diverged and lowly expressed

RW: Alternative nuclear protein found to localise to chromosome — DVNP. In Hematodinium!

RT @LaneLabURI: Waller: Hematodinium has odd histones and a 2400mb genome. Dinos lacking histones get bigger.

RW: DVNP exclusive to dinos and algal viruses!

RT @LaneLabURI: Waller: posttranslational modification of alt histones gives rise to several species of the protein.

RW: Multiple isoforms of DVNP encoded and expressed.

RW: A ton of changes quickly happened between the divergence of perkinsus and Hematodninium +rest of dinos

No outlet in room (WTF), might randomly stop tweeting…

Next: Bachvaroff on more dinokaryon biology. Let’s see how far my battery makes it.

TB: Dinokaryon — extremely refractile. And yes, that image does indeed make me reach for the DIC prism…

Plenary lecture: my to-be MSc advisor Alastair Simpson on deep eukaryotic relationships and unusual free-living anaerobic excavates

AS: Excavates key for resolving what Last Euk Common Ancestor (LECA) looked like. Carpediemonas — key excavate. Culture croaked =(

AS: Need to look for it again. Found Carpediemonas-like organisms (CLOs). Something like carpediemonas finally re-found

AS: A whole group of these CLOs. From anaerobic saline samples. All similar in structure, appearance. Contain flagellar vanes.

AS: Have mitochondrion-like organelles, reminiscent of hydrogenosomes and mitosomes in other anaerobes. Tiny — 3 microtubules long!

AS: Well, guess what… all these similar-looking CLOs… not related to each other. Paraphyletic but relatives of diplomonads

AS: Once again, free-living obscure forms inform us about parasitic ones

AS: Trimastix marine — organism w FOUR flagella living in freshwater environments

AS: (PS: Carpediemonads not only related to diplomonads (think giardia)  but ancestral state!)

AS: MEtamonads not parasitic inherently as thought. Other lineages, eg oxymonads, have paraphyletic free-living associates

AS: Again, free-living modest-looking cells redraw our understanding of ancestral states of a group

AS:(A call for hunting NEW ORGANISMS. GOGOGO!)

AS: Second topic — Deep-level eukaryotic evolution

AS: Starts with same organisms: diplomonads, parabasalids, oxymonads

AS: Old SSU tree: excavates paraphyletic at base of eukaryotes. Picking crappy genes can still lead to that. But suspicious result

AS: Old SSU tree full of artefacts: long branch attraction. Highly divergent sequences like each other and outgroup.

AS: (STOP USING THE WOESE TREE, ESPECIALLY FOR EUKARYOTES!!!)

AS: Enter retortamonads — free-living metamonads. Trimastix, carpediemonas and retorts have feeding groove — hence, excavates

AS: Flagellum pushes current through feeding groove, to posterior end where doomed prey get eaten

AS: Obscure feeding-groove containing organisms: Jakobids and MAlawimonas

AS: These tiny cells look simple, but slicing for TEM reveals a very complex cytoskeleton

AS: Excavates still share similar flagellar aparatus structure. But can look for subtle differences

AS: Jakobids, typical-looking excavates, group with heteroloboseans, who don’t have a groove

AS: Throwing enough genes at the phylogenetic analysis makes the problem go away.

AS: But worrisome. Jakobids and malawimonas have looong branches. Remind you of something?

AS: Free-living euks tend to be less divergent than parasitic lineages, so, weird. Need to add short-branching representatives

AS: Can remove long branching taxa, and trees become more reliable. Give consistent results

AS: Now all excavates form a clade, under these analyses. So excavates appear to be a group

AS: 3 groups of eukaryotes “three musketeers”: Unikonts, “Bikonts”, Excavates.

AS: Enter collodictyon, weird free-living flagellate. Suddenly, starts dragging Malawimonas away from Collodictyon.

AS: Maybe Malawimonas isn’t an excavate — maybe convergence! Morphological work all based on one study, one strain.

AS: Malawimonad cytoskeleton. Not obviously related to other excavates looking at flagellar root components

AS: “I don’t see any way this cannot be interesting.”

AS: Now, functional morphology of LECA (last euk common ancestor)

AS: Assumption was that LECA was simple… turns out, had all euk components. And very boring — a bag with flagellum

AS: Or… as assumed anyway. Can infer anything real about its morphology?

AS: And ancestors of Amorphea and unikonts — ARE boring, simpler flagellar cytoskeletons than excavates (someone has an agenda)

AS: For unikonts — use apusomonas, ancyromonas and breviates — group just outside

AS: PRecise relationships still sketchy, but within amorphea (opistho+amoebozoa_

AS: @Opisthokont did first detailed flagellar root apparatus study of ancyromonas. Awesome 3D reconstructions based on real TEMs

AS: 3D recon of anterior half, showing indiv MTs. Turns out, amorphea actually not boring, just looked atboring cytoskeletons

AS: Similarities b/w amorphea and some stramenopiles and excavates in flagellar root apparatus

AS: One particular microtubule seems to have been with eukaryotes since a billion years ago!

AS: Euk cytoskeletons evolve slowly enough that reconstructing LECA

AS: (sorry… can recon LECA cytoskeleton)

AS: “typical” euk in cell biol + microbiol textbooks–bag with flagellum. Protistologists have access to much more interesting cells

AS: =DDD Protistologist’s version of cell. I LOVE THIS!  http://t.co/gS0oKV9eRW

Chris Howe on plastid endosymbioses in dinoflagellates

CH: Photosynthesis is dangerous — generates free radicals

CH: Takes out a shopping bag w muffins, socks and copy of Protist. Even though says [store name], comes from 3 different sources

CH: Shopping bag model is mixture of replacing plastid contributions

CH: [this talk is awesome but going a little too fast to tweet... and I'm not as familiar with the stuff]

RT @cslamo: If you are a cell biologist you should look at this pic (by Alastair Simpson)  http://t.co/vt3xjs4ixF

CH: Mitochondrial genomes of lice are remarkable similar to those of dino plastid!!! Similar fragmentation process. #WTF

CH: Shopping bag model — mosaic genome and proteome

CH: Replacement plastids contain mosaic proteomes and borrow predescessor pathways; indicating the plastids coexisted for a while

CH: Not likely to be due to LGT from food. Shopping bag model beats one-stop-shop model

CH: One stop shop = everything worked out right away, but seems unlikely. Intermediate: multiple failed attempts at acquisition

CH: Shopping bag — colection of bits from previous as well as most recent acquisition.

CH: Dinoflagellate studies suggest the latter is what happens.Endosymb not a one-off event, outcome of a long process

CH: Not just a sudden accident, a single event. Culmination of the process of plastid eventually settling in.

Mike Gray on mitochondrial evolution, genome vs proteome

MG: Consequences of mito acquisition: insane genomic organisation — “anything goes” — many novelties like split genes, trna import

MG: Andalucia, a jakobid, has largest gene repertoire of mito genomes — let’s use to find Last Mito Common Ancestor (LMCA) traits

MG: Mito genetic fxn became highly specialised — formation of functional respiratory chain. Most genes in nucleus though.

MG: Origin of mitochondrion. Proteobacterium entrance coincident w origin of euk, or euk first and then ate mitochondrion

MG: Both models seem inadequate.

MG: Core mito proteome already there in LMCA. Functioned as contemporary aerobic mito. Anaerobes are derived.

MG: Yeast mitochondrial proteome overwhelmed by non-alphaproteobacterial genes, full of imports. Euk-like and unique as well.

MG: Pattern repeated in Tetrahymena as in yeast — again, only 11% alphaproteobacteria, convincingly

MG: Mito proteome is an evolutionary mosaic

MG: Non proteobacterial compopnent is bulk of mito proteome! Evol origin is obscure — how and why is it there?

MG: Nonproteobacterial stuff could also be alphaprot but so derived… but many euk ‘inventions’ like TOM/TIM transport channel

MG: Large part of nonproteobacterial stuff might have been present in host before mito arrived. Euk first? Take that, Bill Martin!

MG: Another model: Euks did not evolve from prokes, separate lineage, archae and eubac together (Harish et al. 2013 Biochimie)

MG: Not necessarily believing it, but alternative views raise possibility that nonalphaprot mitochondrial proteome was before mito

MG: If present in host cell, not waiting for endosymb to arrive and begin eukaryifying

MG: Might hjave had a premitochondrion (own invention!) with own prot import apparatus, and then replacement

MG: Compartmentalisation does happen in bacteria anyway. ‘Prepared’ cell for mito endosymb. Compartment perhaps non ATP making

MG: Alphaprot endosymbiont contributing alphaprot component, and premitochondrion contributed the rest!

RT @UKProtistology: Protist art is good for the heart -  art exhibition Thursday afternoon http://t.co/lhYfnTmEvS

MG: Advantage of model: allowing transformation of organelle to happen more directly and rapidly (not just sudden accident)

MG: (parallel to plastid acquisition talk previously by Chris Howe, see below)

Today’s take home seems to be:endosymbiosis not a sudden event, but a long process with much ‘preparation’

This talk makes me so happy, makes me feel better after getting argument scars from Bill Martin at SMBE earlier. Fuck yes.

MG: Premitochondrion — a replicating populating extra membrane surface that can be put inside cell, increase surface for ATP prof

MG: Thus, rescues from the bioenergetic (ATP) restriction against euk cell hypoethsis of Bill Martin and Nick Lane.

Ohkuma on termite gut flagellates and their relationship with endosymbiotic bacteria!

O: MAtryoshka-type evolution — multilayered relationships between hosts and various endosymbionts

O: Pretty tetrahymena with fluorescence! Love seeing fluorescence in protists…

O: Termite gut endosymbiont 1 (noncultured): small genome, lots of pseudogenes, reductive evol (oooh, low Ne?)

O: Second endosymb of pseudotrichonympha. 70-80% of gut bacteria. Cospeciated w protist hosts.

O: Major role is nitrogen fixation to host. Host provides cellulose and stable habitat. Endosymbs: cellulose fermentation; acetate

O: “Triplex symbiosis” Co-speciate, N fixation gene an get absent if host changes feeding habits, seen in phylogeny

O: Nitrogen fixation — in sound wood eating termites (dry-wood); lacking N fix in decayed wood eating (damp-wood).

O: Euk-proke association localisation — where are they? More pretty fluorescence pictures!

O: Single cell sorting of bacteria, select one sp. for genome sequencing  — endosymbiont seems to have come from ectosymbionts

O: So, interesting for looking at process of endosymbiosis.

O: Ooooh… TEM of bacteria within flagella, very regularly arranged

O: Tetrahymena ectosymbiont only in apical end of cell, where flagella are

O: An alphaproteobacterium in a belt just below the flagellar region. Friggin weird.

O: Endonuclear verrucomicrobial symbionts common in termite gut protists. 10-80% of host protists have ‘em

O: (prokes tend to love nuclei…envy?)(nah, just tasty chromatin ;p)

O: Oh shock, LGT on steroids among symbionts

Yamamoto on Toxoplasma manipulation of host functions

Y: Parasitophorous vacuole employed by parasite to avoid fusion w acidic and lytic vacuoles of host, escape digestion

T: Strain-dependent suppression of host genome; ROPs determine this, localised in rhoptry and then secreted

T: How to rhoptry proteins (ROPs) suppress host immune response?

T: Rop16 suppresses proinflammatory protein production in infected macrophages. Anti-inflamation.

Y: Stat3 activation in host requires ROP16 interaction. [confused what stat3 does... but some signalling thing

Y: ROP16 required for suppressing host immunity. Secretion of ROP16 to activate stat3 required.

Y: ROP18 required for virulence of toxo. In mice, toxo rop18 knockdown resulted in enhanced immune response.

Y: Rop18 bait for host protein interaction. ATF6beta reacts, involved in host stress response. In atf deficient mice, toxo stronger

Y: So Rop18 supresses ATF6beta in host. Makes more susceptible to toxo. (IFN, interferingamma production) as proxy for immune resp

Y: Via activating stat3 by Rop16 --> decreased immunie response. Rop18 disrupts ATF-dependent adaptive immunity

Geoff McFadden on plasmodium apicoplast evolution and function

GM: Fatty acid synthesis essential only in liver (during malaria, that is; Plasmodium is malaria parasite etc)

GM: During intercourse humans use an average of 1.5kg of ATP (Casazza et al N End J Med 2013) -- sex is vigorous business

GM: Back to Plasmodium sex. Kreb's cycle activated in gametocytes -- to get ready for sex, presumably

GM: ATP synthesis (rather than just theft) essential for sex in plasmodium

GM: IPP synthesis in blood and liver -- prob best therapeutic target. Heme biosynth essential in mosquitoes,maybe block transmission

GM: fatty acid only essential in liver; can only be used to stop liver from getting damaged

GM: fatty acid biosynth mutants work as attenuated vaccination strain in mice -- vaccination against malaria?

Yuichiro Kashiyama on chlorophyll detox in predators

YK: Chlorophylls can be fatal phototoxins for cell. Degradation controlled in plants. Protists must also do so.

RT @sinaadl: Name the ICOP emblem, with nucleus, crystal skeleton, endosymbipnts, and feeding tentacles http://t.co/0rmtflV10M

YK: Protection strategies: scavenging singlet oxygen released from nasty photosynthesis waste; Detox chlorophylls.

YK: Massive amounts of chlorophyll degraded all the time on the global scale.

YK: Eating algae in illuminated and oxygenated environment is dangerous. But how do clear heterotrophs do it?

YK: Chlorophyll autofluorescence disappears in early phagocytosis,  (btw, see #protist2012 for last year's version)

YK: Cyclo-enol destroys chlorophyll, protects againsy toxicity, and widely distributed among protists

YK: Being an alga in illuminated/oxygenated environments is also risky -- you have that plastid yourself, and it's dangerous

YK: Old euglena cells accumulate cycloenols -- plastid number reduced. Seems like alga gradually degrades chlorophyll to cycloenols.

YK: Cyclo-enol thing should be inherited from colourless ancestors

Ed Glucksman on apusozoan diversity and ecology

EG: BioMarKs dataset. MArine coastal sites sampled. Result: a crapton of new planomonad, apusomonad and mantamonad lineages

EG: Planomonad lineages detected in Biomarks are new -- previously undetected under different techniques

EG: Apusomonads: most lineages new as well.A couple known but a tiny minority. Only20% of lineages detected in more than one dataset

ED: Each approach leads to different resaults, must use several when assaying diversity of a group

EG: Mantamonads -- found one new lineage, no described species detected. Rarely detected and in low abundance.

EG: Most apusozoan lineages detected in aerobic sediments. Anoxic layer -- lowest diversity, but mostly new lineages!Uncharacterised

EG: Lineages with most reads found at multiple levels in the ocean.

EG (@edglucksman): Now looking at european freshwater sites. Low general apusomonad detection rate, low relative abundance.

EG: Marine-freshwater crossover -- many apusomonads found in mar environments can also be found in freshwater

EG: Stepwise approach: detect novel diversity, verify molecular only findings and targetted approach to ecology -- important

ED: @ukprotistology -- British protistological society, next meeting in Lancaster 23-25 April; focus on parasite microbial ecology

Matt Parrow on dinoflagellate phototrophy caught in the act

MP: Esoptrodinium -- case study in plastid loss?

MP: Esopterodinoium -- rare incomplete cingulum (girdle flagellum around it) posessed, conflicted description.

MP: Can see prey-filled phagosomes. Chloroplasts actually less so.

MP: Got first culture of this critter. Is there an obvious chloroplast? Are the morphospecies related to each other? Mixotrophy?

MP: Hatch-door phagotrophy -- voraciously feed on algae. Do they have plastids? Need to starve cells, then squish (oww!)--seems yes

MP: Cell autopsy. Found extraplastidal eyespot, naked dino. Another pond isolate -- squash: never plastid pigment.

(cell squashing might be a cool tool for teaching people about cell components... dangerous w/o experience though)

MP: Another isolate: has some plastids, but look degraded. Consistent within cultures throughout time

MP: ISolates with plastids a d internal eyespots, extraplastid plastid, no plastid but eyespot, plastid(?) and eyespot

MP: Inter or intra specific diversity

MP: All isolates form well-supported clade.Most have obvious plastids, but some do not. Can phototroph?

MP: Degenerate plstids hard to show; hunt for psbA. Found in most isolates except one. Looks like 2 independent plastid degeneration

RT @sinaadl: Confirmed genus by sequence and tree w/out plastid but both need light eventhough all are phagotroph on microalgae MParrow

MP: psbA mutation in RP strain (non-phototroph) occured recently if it's a cryptic species -- not excessively divergent

Sebastian Gornik: Endosymbiosis undone --  parasitic dinoflagellate haematodinium gives up on plastid

SG: Hematodiniumis a basal non-photosynth dino, can be cultured indefinitely in dark. Crustacean blood parasite, within bloostream

SG: So prevalent in shellfish, we've all probably eaten some by now

SG: Infected lobster blood is a gross shade of yellow

SG: Life cycle is insane --has some weird multinucleate branchy blob stage -- you're telling me it's a dinoflagellate?! ;-)

SG: Parasite can keep plastids -- for other essential metabolic processes -- eg in apicomplexans

SG: How to lose plastid and become independent from all metabolic capacities of plastid -- eg. cryptosporidium in apicomplexans

SG: Does hematodinium have a remnant plastid? expected. Any nuc-encoded plastid targetting prots? Eg.plastid-like isoprenoid pathway

SG: 2.4GB genome(not too big,phew) and: lack of plastid-derived transcripts, rDNA subunits lost,no plastid-type sequence similarity

SG: So, no sign of plastid

SG: No plastid-targetting proteins similar to apicomplexan ones found. And no plastid leader sequences

SG: No plastid isoprenoid pathway -- but also no cytosolic pathway genes!!!

SG: No molecular evidence for presence of plastid -- both on genome and proteome level. And no isoprenoid pathway at all -- WTF?

SG: Hematodinium ditched its plastid!

Andrew Roger on deep structure of euk tree and phylogenies

AR: Groups now: Amorphea, Diaphoretickes (let's pretend this one doesn't exist... >.<) and Excavata

AR: Root still not pinpointed; roots go everywhere. Subtle reference to TC-S 2010's collection of ad hoc rationalisms for root...

AR: piece of unresolved deep euk phylogeny:"orphan"lineages."I always use the term because a reviewer specifically told me not to

AR: "I don't know why [reviewer] hates orphans”

AR: Orphans: apusomonads, breviates, ancyromonads and collodictyon

AR: Breviata anathema — thought within or sister to amoebozoa, deep-branching. Ultrastructure: Apusomonads?

AR: Enter Pygsuia. Biflagellate breviate (usually uniflagellate) — anaerobe, Where does it go?

AR: Pygsuia branching with breviata, and sister to apusomonads + opisthokonts (breviates and apusozoa are paraphyletic to opisthos

AR: “Obazoa” = Opisthokonts + breviata + apusomonadida

AR: Removing noisy data: removing — fastest evolving sites, genes or taxa

Next up: @AncestralState Tom Richards on gene fusions, cytoskeleton evol and complexity in last euk common ancestor (LECA)

TR: General views of euk compleity: starts out simple at root, then diverges and compexifyies

TR: Example — archezoa hypothesis, showcases simpler euk ancestor gaining and increasing complexity of mitochondrion

TR: Another idea (TCSism): unikont bikont root, celll started with single flagellum

TR: Are gene fusions useful synapomorphies?

TR: Polarised gene fusions and fissions on fugnal tree — fusions and fissions not as stable as assumed. High rate of gene fision

TR: Gene fissions more common: separation, degeneration and duplication. Gene fusions are not stable characters

TR: (I might be mixing up fusions with fissions… @AncestralState)

TR: Fissions and fusions of genes could be unreliable synapomorphies; maybe can identify more stable ones, but hard.

TR: LECA assumption: minimal set of orthologues proceeeding to gain in orthologues. Is this a valid way of thinking?

TR: LECA has high kinesin and myosin complexity reconstructed from phylogeny. Thus, had a complex and diversified cytoskeleton

TR: DNA replisome — mopst of it present in LECA. Once again,

TR: DNA replisome — mopst of it present in LECA. Once again, LECA complex.

TR: Maybe the minimal setof orthologues (Simple cell) not the best model for LECA

TR: Root possibilities in two categories: small LECA repertoire (euglenozoa or metamonad root) — the rest suggest a large one

TR: By reperoitre, orthologue diversityn is meant

TR: “Where you root has massive implications for LECA orthologue complexity” (Aussies must love this…)

TR: Excavate roots make LECA simple — be mindful of that!

TR: What does orthologue mapping tell us about historically contentious supergroups?

TR: Little orthologue support for historically contentious groups(excavata,metamonads, etc–looks like bigbang diversification model

Fabien Burki on evidence for a mitosome in Rhizaria! Mikrocytos sp.

FB: Mitochondrion-related organelles: mitosomes, hydrogenosomes — different. Mitosomes — no role in ATP synth, no H2 synth

FB: Most mitosomes involved in Fe-S cluster formation

FB: Mikrocytos mackini — intracellular parasite in pacific oyster of unknown affinity. Restricted to WA-BC, the northwest!!!

FB: Denman ISland disease — killed 17-35% of oysters, when first discovered in 1960s

FB: Very simple morphology, no defining features, lacks canonical mitochondria

FB: Mikrocystis not related to any eukaryotes — in a couple of the 18S trees ;p

FB: Goes at basalmost branch of euks — but long branch

FB: Mikrocystis branch is looooooooooooooooooooooooooooooooooong, sticks out of euks. Literally.

FB: Famous fast-evolving lineages: diplomonads, nucleomorphs, look unimpressive compared to this critter

FB: Fucked up alignment? Nope. Well, fuck. But fits in rhizaria with strong support. But INSANELY long.

FB: (Never seen a branch this long before…this is insane… my head hurts)

FB: Data corroborated with fastest-evolving taxon removal, and fiddling with other taxa. Still holds.

FB: Looking for presence of mitochondrion in long branching bastard–a whole FOUR (4, yes, four) proteins of mitochondrial function.

FB: All 4 proteins involved in Fe-S cluster formation. The last remnants. No coincidence. But seriously… holy fuckballs.

FB: Only unifying feature of mitosome, hydrogenosome and mitochondrial proteins — Fe=S pathway

FB: Parasite can’t be cultured, can only get once a year in March – May… well, lovely. Just lovely.

FB: Interestingly — host mitochondria packed tightly against the parasite. Mitochondria stolen from host

FB: Very close association between host mitochondria and parasite — a tubelike structure goes from mito into parasite cytoplasm!

FB: A convergence with microsporidian mitosome, independent.

FB: First case of reduced mitochondria in Rhizaria. 4 mt genes, only in FeS cluster formation. Incredible.

Next up: Yuji Inagaki on Tsukubamonas globosa and Palpitomonas — phylogenetic position

YI: “Simple story: Found, isolated grew, observed,sequenced (a lot) and treed (a lot)”

YI: EST data “provoked” hacrobia hypothesis. EST data for raphidiophrys and telonema exist…

YI: “Later, Fabien disfavoured this Hacrobia hypothesis, but that’s ok, for me”

YI: Palpitomonas described,a new flagellate branching with archaeplastids of cryptomonads+haptos

YI: Palp groups with roombia and cryptomonads — neither hacrobia not archaeplastid are paraphyletic

YI: Now, Roombia, goniomonas, cryptos and palp seem to be together, near archaeplastids. HAcrobia blows up.

YI: Putative phylo: (((crypto,gonio)katablepharids)palpitomonas)

YI: Diversity of group still not sufficiently covered by phylo analyses.

YI: Now, Tsukubamonas. Related to excavates. Maalawimonads and discoba are mitochondriate, metamonads not

YI: Metamonads important for understanding evolution of mitochondria

YI: Dysnectes — also hydrogenosome-like organelle. Discoba — most “ancestral” (ie gene rich) mito genomes — eg. Jakobids.

YI: Tsukubamonas isolated from a dirty pond on campus in Tsukuba U.

Ts-monas has large food vacuoles, a very excavatey flagellar apparatus.

YI: Ts-monas groups with special affinity for discoba. (hlobos and jakobids)

YI: Ts-monas doesn’t group with any of the major lineages within Discoba. Novel deep lineage in discoba

YI: Ts-monas Mt genome: expected largest Mt genome, but not =( heartbreaking. But has rare genes. Parallel gene loss in Discobid Mts

Chris Lane (@LaneLabURI ) on lifestyle effect on secreted oomycete proteome

CL: New saprolegniaceae genome  CC: @KamounLab

CL: Protein families of ‘secretome’ (an apology was issued, @phylogenomics))– ancestral states, gains and losses reconstructed

CL: About 20 LGTs from fungi to oomycete group!

Vittorio Boscaro on obligate bacterial endosymbiont of Euplotes (ciliate), Polynucleobacter. Really cool, btw — should go see it

VB: Cytoplasmic endosymbiont — polynucleobacter. Weird ultrastructure — multiple nuclei w one copy of genome each

VB: Ciliate cannot survive for more than a few days without this endosymbiont! Nor can symbiont live without host

VB: A lot of free-living polynucleobacter strains (abundant), but distinct from this particular species — so not life cycle stage

VB: Euplotes endosymbiosis derived more than once. Comparing free-living vs. endosymbiont genomes now

VB: Genome reduction (of endosymbiont, vs. free-living) not the same in all categories. No repetitive sequences.

VB: Metabolism of free-living polynucleobacter; so much lost in the endosymbiont — devastated pathways

VB: Symbiont relies on host for carbon, organic N and S, and amino acids. Severely reduced environmental sensing genes — can’t live

VB: Can’t live on its own, that is. Probably will not be cultured. So why does Euplotes need this thing?

VB: Probably not metabolites needed from endosymbiont — euplotes has a healthy diverse diet

VB: Can rely on each others effector genes — but no support in genome. Exception: non-fxnal bacterial secretion systems.

VB: Weird because common in invasion and inhabiting inside things. 12 pseudogenised LGTd bacterial secretion genes

VB: BActerial secretion genes go there to die.

VB: Genome evolution. Driven by neutral evol — weakened selection, increased drift b/c bottlenecking during vertical transmission

VB: Leads to non-functionalisation, including of DNA repair genes (wow, vicious cycle)

VB: Nancy Moran’s (and McCutcheon’s) model of bacterial genome reduction in insects largely does apply to polynucleobacter case

VB: But… huge number of pseudogenes; no mobile elements — latter thus not required for the rapid genome decay

VB: Emphasise role of trans-lesion DNA polymerase (mismatch repair) loss. Leads to exacerbated mutation and gene decay

VB: But… if all DNA repair falls apart, threat for immediate survival! Are there alternatives to compensate?

VB: Genome reduction can lead to reduction of sites for mutation hazard(less targets)and thus compensate for increased mutation rate

VB: Could be adaptive drive for genome reduction in endosymbionts — reduction in mutational target size. (Mike Lynch’s stuff)

VB: Polynucleobacter endosymbiont reduction is probably recent due to high sequence similarity — not an ancient symbiosis

Yuki Kodama on Chlorella attachment and dettachment in Paramecium bursaria (the symbiotic green Paramecium

YK: In typical endosymbiosis,endosymbionts lose ability to live without host. But not in this chlorella case

YK: Paramecium gets maltose and oxygen; and provides nitrogen, CO2 and enhanced C fixation.

YK: Aposymbiotic (lost endosymbiont) cells very easily re-acquire the symbiotic algae. Can’t get over each other ;-)

YK: Algal reinfection process: algae get resistance to host digestion system. Bud membrane into cytoplasm, then docked to membrane

YK: that is, cell cortex — among the trichocysts

YK: A natural mutant exists where the chlorella does not dock to cortex. Is in cluster. When divides, can lose the symbiotic algae.

YK: Can ultracentrifuge the hell out of the cells and un-dock the algae.

YK: After centrifugation — the algae redistribute properly within 10min

YK: During re-docking, cytoplasmic streaming much faster than usual. A driving force in algal recovery

YK: Add nocodazole(microtubule inhibiting drug)–fails to distribute properly all over cell cortex.  Cytoplasmic streaming essential

YK: Digestive vesicles also dislocated during ultracentrifugation — then gradually redistributed along with chlorella

Courtesy of @Opisthokont RT @edglucksman: Never seen a 3D poster before! (Aaron Heiss et al – Malawimonads)  http://t.co/OAi2VvLOb2

YK: Alga-free bursaria mixed with algae, centrifuged. 10min later — localise. Nascent membrane around chlorella already can dock

YK: Ultracentrifugation — method for synchronising docking and undocking of chlorella. Useful technique!

Masahiro Fujishima on Holospora in Paramecium caudatum.

(This is also going to be reeeeeally cool!!!)

MF: Gram neg alphaproteobac. Endonuclear symbiont! Species and nucleus specificity. Different morphologies. Distinguishes MIC + MAC

MF: Cytoplasmic and periplasmic region of bacterium,about half-half. Invasive form, that is. Has an invasive tip!

MF: Life cycle — Ingested into digestive vacuole, then escape. Move to MAC (or MIC), find nuclear envelope and target.

MF: MIC vs. MAC species-dependent. Can detect what type of nuclear membrane they’re invading

MF: Identify receptor. Then penetrate, differentiate, undergo a ton of cell division, become infectious form, and escape

MF: Escape from digestive vacuole (dv from now on) — disrupt membrane, or bud out and have own mini membrane until get to nucleus

MF: Apply concanamycin A –inhibits vacuolar ATPase. Can’t target nucleus. Acidification of host dv necessary for escape

MF: 89kDA prtein, tip localised. tREAT W NaOH for a minute — localised a tip. In non-treated dv — protein goes outside the tip!

MF: Translocation of 89kDa protein by acidification. Goes throyugh outer membrane upon pH change

MF: Interaction of 89kD prot w host actin. Pokes out of dv, prot goes outside tip, then bacterium goes to cytoplasm

MF: 89kD protein maintained outside tip, interacts with host actin. Latrunculin B (actin inhibitor) — blocks nuclear invasion

MF: How do they distinguish MAC from MIC? Lipopolysaccharide antibody around bacterial membrane.

MF: [confused... giving talk like a paper, with figures from paper. I'm too hungover for this...]

Aaron Turkewitz on EVOLUTIONARY CELL BIOLOGY!!! Endomembrane evol in ciliates  #evolcellbiol

or #evolcell…. we need a hashtag for the coolest emerging field in all of biology…

AT: Tetrahymena — ciliate. Very complex endomembrane system, several systems

AT: Comparing pathways to those of plants and animals and yeast.What’s conserved, and what’s innovated.

AT: Didinium and Paramecium — relationship happens by regulated secretion.Each releases its own proteins, a battle

AT:Similar process in Tetrahymena (Tt from now on) mucocysts — positioned everywhere, fuses w plasmid membrane and secretes

AT: Contents as crystal, and then rapidly extruded — crystal is a calcium-driven spring!!!

AT: Proteolytic lysing happens in spring action, reminiscent of human insulin granule secretion. Let’s compare.

AT: proteins bound for core granules cp=aggregate om secretory [athway. Sorting via receptor independent processes.

AT: No receptors involved in sorting!!! Similar in Tt mucosysts

AT: Mucocysts have two families of  cargo proteins. GRT and GRL, unrelated. GRT proteins do not aggregate — must sort differently

AT: Transcriptional profiling. Co-regulated genes–14candidates focused on genes w homologues in non-alveolates,esp membrane traffic

AT: Tt encodes four sortilin/vps10 receptors.sor4 KO strong mucocyst secretion defect

AT: sor4 KOs still make mucocysts with GRL proteins — sorting does not depend on sor4. GRT missing though.

AT: sor4 could act directly as receptor for grt1.

AT: Mucocysts in sor4 ko still look different — completely lack elongated crystaline structres

AT: Core built up by GRL proteins to make a crystal. Protein gets processed, sor4 required. Delivers something to mucocysts

AT: Deliver proteases? Not previously identified though. Any coregulated with GRL proteins? One KO did kill GRL processing!

AT: Cathepsin 3 sorted to mucocysts (this is the protease) — in sor4 ko, no longer targeted to mucocysts

AT: Sor4 acts as grt protein receptor, and sortilin required fpr GRL maturation — keyproteases

AT: sor4 dependent branch resembles lysosome biogenesis pathways. Tt borrowing lysosome targetting pathway to generate mucocysts!

AT: Trichocyst formation involves two classes of vesicles. (Haussman 1977)

AT: Sor4 localises to a mobile endosomal compartment — transGolgi in the cells? Doesn’;t localise to golgi. Ammonium chloride…

AT: …neutralises acid… behaves like trans golgi networkl (ignore the ammonia…)

AT: So, do all ciliate extrusome share these biosynthetic pathways?

AT: Mark Slabodnick of Stentor affinity: Stentor has pigment granules. Canfollow exocytosis — autofluoresce, can follow in realtime

(Neo- and subfunctionalisation.– no valid argument against that being a major driving force in evolution)

AT: Convergence between insulin granule secretion and ciliate mucocyst secretion!!!

Arthur Grossman on organellar evolution in Paulinella.

AG: To establish endosymb: gene transfer, metabolic transport (must be there), exciotation energy management (reactive oxygen)

AG: protein import as well

AG: Paulinella chromatophora — early evol of photosynth organelles (primary). Also Angomonas deani — new model tryp

AG: Paulinella — miserable organism to work with — grows slowly — cyanelles — carboxysomes, bacterial wall, phycobilisomes

AG: Basically, cyanobacteria trapped eternally inside cell. Division is synchronised, by do energetics coordinate? Why slow-growing?

AG: Why does it dislike light? Probably too early in evol — the connection b/w endosymbiont and host not yet well developed

AG: Cyanelle genome is reduced — to 1Mb (plastidisusually 150kb)

AG: A bunch of cyanelle metabolic pathways now missing — incl many aminoacids, co-factors, TCA cycle, N uptake, no N transporter

AG: Transporters must be coming from host then — so gene transfer happened

AG: Elements of photosystem not found in cyanelle — but still does photosynthesis. Thus must be in host

AG: Molecular evidence for gene transfer from cyanelle to host — about 30 genes. Adapted codon usage and introns for nuclear env

AG: Many photosynthesis proteins involved. Tiny light harvesting-looking proteins. But also found in energy  dissippation

AG: Regulate light energy dissippation. How good is this connection between host and symbiont?

AG: 15 genes for energy dissipation — required for dealing with poor host-symbiont connection?

AG: Is PsaE (photosystem?) localised in EM — localises to the cyanelle. On it and also on thylakoid membranes

AG: Do the Psa components assemble with PSI in cyanelle? Are they there? Assemble after entry in cyanelle, w/o presequence

AG: How do they get in? Enriched in the golgi.Perhaps in secretory pathway

AG: Only two membranes separate cynalle from, cytoplasm — plausible to be mediated via vesicular transpport

AG: Tryps now. Angomonas deanei. beta-proteobacterial endosymbiont (Taylorella spp. relative)

AG: Angomonas formerly crythidia. Faster growing (16h doubling), can grow on plates, axenic, no plates, small host genome (20mb)

AG: With genome and transcriptome, looking for gene transfer. Candidates present.

Mark Field on “breaking the fourth wall using proteomics” of evol cell biol

MF: Problem of asymetry — know more about opisthokonts, plants to some extent, prob w trying to infer ancestral states and evol

MF: Majority of genes in a random chunk of tryp genome have unknown function

MF: Phylogenetics only gets us so far. Have no idea what it does; we know if it’s there or not, but not function.

MF: Promiscuous as far as interactions go. Trying to reassemble these relationships phylogenetically is nearly impossible

MF: produced gorgeous atlas of tryp endosomal trafficking system! awesome stuff.

MF: Extremely fast endocytosis in tryps, 20s to fill up. 5min to recycle back. Much faster than a macrophage;awesome at phagocytosis

MF: Coulson plot generator (for comparing presence/absence of complex components): http://t.co/Aff7XOz8DZ

MF: Tryp epigenetics and nuclear envelope. Nuclear pores. A ton of complex members. Much conserved, but also novel!

MF: The lamina was thought to be restricted to metazoa. Cryptic in other system. Lamin found in ditcty

MF: Cannot find lamins in genomes of other things — but a lamin-like distinct protein restricted to tri-tryps

MF: Errr, no resemblance to lamin, but convergent function to that of a thing in C.elegans — knockdown leads to nuc pore clustering

MF: Need a broader range of cell biology, phylogenetically!

Jeremy Wideman on evolution of ER-mitochondrial associations

JW: ERMES — ER-mito interaction complex. Previously thought to be fungal-specific. None in animals.

JW: Take basal fungal homologues to look for it elsewhere. Found in dicty, acanthamoeba; parts found in thecamonas. Pre-Unikont

JW: Found in T.vaginalis (remember:reduced mitochondrion!)–maintained in hydrogenosome containing orgs, but not mitosome cont ones!

JW: Is ERMES present in the SAR+Arch+CCTH group? No!

JW: Ermes arose early in eukaryote evol, common ancestor of excavayes, amoebozoa, opisthokonts.

JW: Only lost in animals and mitosome-bearing organisms — must be hard to lose!

JW: So according to these ERMES data — root between Excavates+Unikonts and the rest of euks!!!

Let’s see how long this root lasts…

JW: New taxa: uberphyta and uberzoa ;p

JW: No ERMES in choanos either — but mito-ER  interactions still there — another complex, or replaced?

NExt: Sven Gould on intermediate filaments in protists!!!!

SG: IFs underexplored. Main feature is central coiled-coil (I heard those are extra fun for bioinformatics + BLASTing…)

JW: PEllicle proteome of Tetrahymena: A compl;ex rang eof structures in tetrahymena localised, particularly basal bodies

SG: Only one localises cytoplasmically, everything else to pellicle. Repeat motifs — evolution rate on steroids.

SG: Lots of convergence and homology mess with differently named fibrous proteins

SG: HArd to tag  some — tag interferes with protein polymerisation. Still… TtAlv2 knockdown affects pellicle integrity.

SG: So many IFs localise around basal bodies — IF organising centres? Start at basal bodies, and then complex structures grow out

SG: Definition of IFs too constrained at the moment.Fast evolving–phylo issues. Ciliary basal bodies appear to organise in ciliates

Alex Schlacht on endomembrane secretory and endocytic system evolution

AS: Major protein families of endocytic system are well-conserved.

AS: COPII coat formation components seem to have been present in LECA (last euk ancestor)

AS: Sec27 domain: two copies in LECA. ERGIC (ER-Golgi traffic system) also conserved.

AS: CopII ubiquotously conserved, ERGIC more ancient than proposed, and secretory system has lower plasticity than endocytic.

ISOP-ISEP in Banff next year, 03-08 August.  #protists

Rebecca Pearce (an undergrad!!!) on Rhizarian slime moulds! ‘Rosculus’ and Guttulinopsis

RP: Rosculus and guttullinopsis — free-living, small, thought to be excavates b/c blunt eruptive pseudopods and flattened cristae

RP: Hlobos typically have ER around mito, these guys don’t

RP: Gutt aggregates into a slime mould. (slime moulds in Rhizaria… oh, and a strameno one found too!)

RP: Gutt and Rosc group convincingly within Rhizaria. Not morphologially similar to any Rhizarians!!!

JP: Sainouroidea (incl helkisemastix) also have discoid cristae, but also rare

RP: Are Rosc and Gutt related as sisters? Where do they fit within Rhizaria? SSU very divergent.

RP: Rosc from camel cricket, Gutt from dung. And I just left the habitat range of cave crickets…

RP: Fall with Helkisemastix and Sainouron, also w discoid cristae. A couple Rosc isolates not rosc actually, of course (via phylo)

RP: Another “Rosculus” falls within Amoebozoa. Non-rosculus have finer pseudopodia, less fan-shaped, move differently. Barely move!

RP: 100% bootstrap support for sisterhood with Helkisemastix (flagellate)

It simply blows my mind how little we know of the eukaryotic world. Still. We’re barely scratching the surface. Amazing.

RP: Is ffruiting ability a character of guttullinopsis, or is guttullinopsis actually Rosculus?

RP: Vice versa, actually — Guttullinopsis is older.

Second last talk: Jana Szabova on MAT (methionin adenosyltransferase) locus evolution in euglenids

JS: Highly conserved metabolic protein. MATX present in photosynthetic eulgenids, dinos, diatoms, haptophytes, a plant, an animal

JS: Deep paralogy vs. LGT to explain patchy distribution of MATX among unrelated lineages

JS: Inherited from secondarily endosymbiosed green algal plastid?

JS: MATX only in photoautotrophs; when looking for mixotrophs (eg rapaza) — only has MAT

JS: Can MATX substitute for counterpart MAT function? (reminiscent of EFL case)

Last speaker! Cam Grisdale on pre-mRNA splicing in two protists

CG: Pre-mRNA splicing in microsporidian Encephalitozoon cuniculi

CG: E. cuniculi — 2000 protein-coding genes.37introns. Tiny genomes. Other organism: Cyanidioschizon merolae–27 introns 5300 genes

CG: How efficient is pre-mRNA splicing in reduced eukaryote’s splicing? normal euk — 80% efficiency of splicing. E.cuniculi: lower!

CG: Many junctions spliced with under 50% efficiency

CG: Average splicing levels very low. Majority of introns poorly spliced. Reduced spliceosome?

CG: Compormised decay pathways for mis-spliced mRNA decay might lead to longer halflife of defects

CG: different types of alternative splicing events — all happen. A fair bit of alternative splicing.

CG: Splicing active without U1 snRNA — apparently not found in any other eukaryote so far.

CG: Surprisingly high alternative splicing levels for a reduced genome (tolerated, rather than ‘alternative splicing = good’ theory)

Apparently Bigellowiella natans (chlorarachniophyte) also has high intron retention rate (ie, shitty splicing)…

 

Psi Wavefunction About the Author: Psi Wavefunction is a graduate of the University of British Columbia working as a protist researcher (soon to be graduate student) at Dalhousie University in Halifax, Nova Scotia, and blogs about protists and evolution at The Ocelloid as well as at Skeptic Wonder. Follow on Twitter @Ocelloid.

The views expressed are those of the author and are not necessarily those of Scientific American.



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