And we're back! The protists have never actually left, but some of us have pursued them (or rather, employment related to them) all the way into the cornfields of Indiana*. Apologies for the disappearance: I think it's more precise to say that I clumsily tumbled here in August (still a bit dazed), rather than having moved in a civilised fashion. For one thing, still had to finish my Bachelor's degree in Vancouver, while already taking a graduate course here -- thereby attending two geographically disparate universities at once! Must also admit there's a bit of a difference in setting between urban mountainous Canadian Pacific Northwest, and a small Mid"western" town of 80K. Will get back to that later... but n0w that I am no longer officially an undergrad as of last week... time is ripe to return to protists at last!

*Actually it's mostly forested hills around here with the occasional patch of corn and soybeans, but we can't let "facts" interfere with our stereotyping...

[caption id="attachment_113" align="aligncenter" width="626" caption="Cornfields! All there is in Indiana... don't let the camera lens fool you!"][/caption]

This means the only marine protists I'll be able to play with for the next little are fossilised forams (of which much of this town happens to be built), but fear not -- we've got plenty of freshwater and terrestrial critters to sample around here. Furthermore, I've got my hands on more Paramecium (a ciliate) stocks than one could ever dream of. Among them, KILLER Paramecia! I'll explain what they are in a later post, but let's just say they involve everything from violent murder to viruses, bacteria and mysterious coiled ribbons of unknown origin. Many of these Paramecium stocks are quite old and have historic value, being direct descendants of this very department's Tracy Sonneborn, notable for his work on epigenetic inheritance of cilia patterning, as well as discovering the killers and much outstanding Paramecium genetics work. For the speciation aficionados among you, the Paramecium aurelia species complex is a messy tale of multiple genome duplications and complicated sexual relations with love triangles of mating types.

[caption id="attachment_110" align="alignright" width="300" caption="A Paramecium cell with DNA in blue and prey E.coli bacteria in red and green. The big blue blob is the somatic 'macronucleus', the site of transcriptionally-active DNA. The pale blue-staining (artefactually) clumps are waste crystals, while what looks like a bubble of candy is a food vacuole full of freshly swallowed bacteria.   (63x oil, confocal)"][/caption]

Despite being known by many kids in school classrooms, Paramecium is quite a poorly-understood organism -- no doubt complicated further by pretty much everything about it being strikingly complicated. Depending on the species, this ciliate can get large for a single cell -- up to 350um, or more than a third of a millimetre. It has not one but two types of nuclei, and must have sex every few generations or die. Some species can make do with having sex with themselves, through a process called autogamy -- induced by starvation. Surely there must be a lesson in there somewhere for when life gets tough and suitable companions few and far between... but I digress. One species of Paramecium farms algal livestock inside it, while others largely subsist on devouring bacteria and whatever small flagellate is foolish enough to get in their way. You can see a video of the feeding process in action here. Just for fun, on the right is a micrograph we got while being trained on the confocal (there will surely be plenty more to follow over the months, or years): we have been feeding Paramecium shiny coloured bacteria to be able to track prey through their 'digestive tract'. The result was pretty and quite dazzling to the non-microscopists in the lab, much to our satisfaction...

Another component of what I do here is perhaps a bit less scenic. Every scientist must pass through a ruthless test of one's endurance (or two, or many, many... many), and a perfect task to satisfy that is a mutation accumulation experiment. In a nutshell, you start with a bunch of clonal lines and allow them to accumulate mutations while minimising the effects of selection. You can reduce the relative force of selection by decreasing the population size. You may have heard of some additional threats inflicted upon endangered species simply due to them being small in number -- not only is their gene pool impoverished (thereby making them vulnerable to change), but bad mutations begin to accumulate thanks to genetic drift. Essentially, we raise our organisms as 'endangered species' (while keeping the environment constant) by keeping their populations low and constantly bottlenecking them as often as we can, by randomly picking a single individual to go on to the next generation.

As you may begin to gather, when such an experiment works well, it really doesn't -- your lines start dying off left, right and centre due to deleterious mutations. Ideally, if anything survives the 2000-4000 generations you're forced to watch them through (and some better make it, else angry PI and no funding =( ), a several genomes get sequenced and you not only get an honest, accurate measurement of the mutation rate, but a sampling of the mutational spectrum freed from (most) selection. What's amazing is that even in the near-absense of selection (save for purifying selection of lethal mutations), you end up with drastic phenotypic changes rather quickly. While selection and adaptation have hoarded most of the attention in evolutionary biology, non-adaptive (and non-selective) forces like mutation (including mutational bias) and drift too play quite a major role in evolution. While mutation accumulation experiments are hard, frustrating work, they provide important data for grappling with evolution's very principles. But do appreciate that behind some modest numbers lie many grueling years of work and a sea of graduate student tears (and those of postdocs, RAs, technicians...)

By the way, this means that if anyone claims evolution can't be demonstrated in the lab... I can personally veto that, kthx.

Lastly, just for fun, my friends and I have taken the rocky road to time travel -- or digging around in Indiana's many fossil strata and remnants of a long-lost sea. There is something truly surreal about picking up corals and brachiopods in southern Indiana. Something is likewise surreal about driving past a giant billboard for the Kentucky creation museum en route to said fossils.

[caption id="attachment_119" align="aligncenter" width="640" caption="Ordovician (~520 million year old) fossils from southeastern Indiana! The tusk-like things are giant horn corals, and the rest are brachiopod shells, bits and pieces of trilobites, and corals. In the matrix around them is probably loads of ancient protist microfossils, but those take skill to extract."][/caption]

[caption id="attachment_120" align="aligncenter" width="547" caption="Adorable trilobite, partially rolled-up...for over half a billion years. By the way, these things apparently don't come pre-cleaned like the ones in museums. Actually, pretty sure the museum ones didn't come cleaned, assembled and coated either..."][/caption]