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.

- ?

Background

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.

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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!)