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Posts Tagged ‘dem bones’

Uh oh, a “why?” question in biology! There are many potential, and not mutually exclusive, answers to such questions. Ultimately there is a historical, evolutionary answer that underpins it all (“ostriches evolved two kneecaps because…”). But we like ostrich knees and their funky double-kneecaps (patellae; singular = patella) so we wanted to know why they get so funky. One level of addressing that question is more like a “how?” they have them. So we started there, with what on the surface is a simple analysis. And we published that paper this week, with all of the supporting data (CT, MRI, FEA).

Stomach-Churning Rating: 6/10 because there is a gooey image of a real dissection later in the post, not just tidy 3D graphics.

First author Kyle Chadwick was my research technician for 2 years on our sesamoid evolution grant, and we reported earlier on the detailed 3D anatomy of ostrich knees (this was all part of his MRes degree with me, done in parallel with his technician post). Here, in the new paper with Sandra Shefelbine and Andy Pitsillides, we took that 3D anatomy and subjected it to some biomechanical analysis in two main steps.

Ostrich (right) knee bones. The patellae are the two knobbly bits in the knee.

First, we used our previous biomechanical simulation data from an adult ostrich (from our paper by Rankin et al.) to estimate the in vivo forces that the knee muscles exert onto the patellar region during moderately large loading in running (not maximal speed running, but “jogging”). That was “just” (Kyle may laugh at the “just”– it wasn’t trivial) taking some vectors out of an existing simulation and adding them into a detailed 3D model. We’ve done similar things before with a horse foot’s bones (and plenty more to come!), but here we had essentially all of the soft tissues, too.

Ostrich knee with muscles as 3D objects.

Second, the 3D model that the muscular forces were applied to was a finite element model: i.e., the original 3D anatomical model broken up into a mesh, whose voxels each had specific properties, such as resistance to shape change under loading in different directions. The response of that model to the loads (a finite element analysis; FEA) gave us details on the stresses (force/area) and strains (deformations from original shape) in each voxel and overall in anatomical regions.

Finite element model setup for our study. If you do FEA, you care about these things. If not, it’s a pretty, sciencey picture.

The great thing about a computer/theoretical model is that you can ask “what if?” and that can help you understand “how?” or even “why?” questions that experiments alone cannot address. Ostriches aren’t born with fully formed bony kneecaps; indeed those patellae seem to mature fairly late in development, perhaps well after hatching. We need to know more about how the patellae form but they clearly end up inside the patellar (knee extensor) tendon that crosses the knee. So we modelled our adult ostrich without bony patellae; just with a homogeneous patellar tendon (using the real anatomy of that tendon with the bony bits replaced by tendon); and subjected it to the loading environment for “jogging”.

The right knee of an ostrich hatchling. The patellae have yet to form; indeed there is little bone around the knee region at all, yet.

We then inspected our FEA’s results in light of modern theory about how tissues respond to loading regimes. That “mechanobiology” theory, specifically “tissue differentiation”, postulates that tendon will tend to turn into fibrocartilage if it is subjected to high compression (squishing) and shear (pushing). Then, the fibrocartilage might eventually be reworked into bone as it drops the compression and shear levels. So, according to that theory (and all else being equal; also ignoring the complex intermediate states that would happen in reality), the real ostrich’s kneecaps should be located in the same positions where the FEA, under the moderately large loads we applied, predicts the homogeneous tendon to have high compression and shear. But did the real anatomy match the mechanical environment and tissue differentiation theory’s predictions?

Tissue differentiation diagram displaying the theoretical pathways for transformation of tissues. If tendon (red) experiences high shear (going up the y-axis) and high compression (going toward the left), it should turn into fibrocartilage (purple). Transformation into bone (diagonally to the bottom right) would reduce the shear and compression.

Well, sort of. The image below takes some unpacking but you should be able to pick out the red areas on the bottom row where the patellae actually are, and the yellow shaded regions around some of those patellar regions are where the compression and shear regimes are indeed high and overlapping the actual patellar regions. The upper two rows show the levels of compression (or tension; pulling) and shear, but the bottom row gets the point across. It’s not a bad match overall for the first (“real”; common to all living birds) patella, located on top of the upper knee (femur). It’s not a good match overall for the second (unique to ostriches) patella, located below the first one (and attached to the tibia bone).

FEA results! (click to embiggen)

Kyle says, “Being a part of this project was exciting because of the application of engineering concepts to interesting biological (including evolutionary) questions. Also, it never gets old seeing people’s reactions when I tell them I study ostrich knees.

The study had a lot of nuances and assumptions. We only looked at one instant in slow running and only at one adult ostrich, not at the full development of ostrich anatomy and loading. That’s harder. We started simple. The tissue differentiation theory is used more for fracture healing than for sesamoid bone formation but there’s some reason to suspect that similar mechanisms are at play in both. And there’s much more; if you want the gory details see the paper.

So did we solve why, or how, ostriches have two kneecaps? We felt that the mechanical environment of our FEA was a good theoretical explanation of where the first patella forms. We originally expected the second patella, which evolved more recently and might be more mechanically sensitive as a result, to be a better match than the first one, but it was the opposite. C’est la science!

Enough models, let’s have some reality! I warned you this post would get messy, and here it is. Left leg (skinned) of an ostrich showing the muscles around the knee. The patellar region would be in the gloved hand of the lucky individual shown.

This study, for me, was a fun experience in moving toward more fusion of “evo-devo” and biomechanical analyses, a research goal of mine lately– but there’s still a ways to go with the “how?” and “why?” questions even about ostrich kneecaps.

We felt that the best conclusion supported by our analyses was that, rather than have homogeneous stresses and strains throughout their knee tissues (e.g. the patellar tendon), ostriches have a lot of regional diversity in how those tissues are loaded (in the condition we modelled, which is adequately representative of some athletic exertion). Look at the complex FEA coloured results above again, the top two rows: there are a lot of different shades of compression/tension and shear; not homogeneous strains. That diversity of regional loading sets those tissues up for potential transformation throughout growth and development. And thus ONE of the reasons why ostriches might have two kneecaps is that the heterogeneous loading of their knee tendon favours formation of heterogeneous tissue types.

Another, compatible, explanation is that these different tissues might have consequences for how the muscles, tendon and joint operate in movement behaviours. In due time there will be more about that. In the meantime, enjoy the paper if this post makes you want to know more about the amaaaaaazing knees of ostriches!

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A Confuciusornis fossil; not the one from our study but prettier (more complete).

Today almost three years of collaboration come together in a publication that is a fun departure from my normal research, but also makes sense in light of it. Professor Baoyu Jiang from Nanjing University in China has been being working on the taphonomy of the Early Cretaceous Jehol biota from northeastern China (Manchuria) for a while, and he found a lovely Confuciusornis (early bird) fossil; one of thousands of them; from the volcanic pyroclastic flow-based lake deposits there.

Although at first glance the skeletal remains of that fossil are not fabulous compared with some other Confuciusornis, what makes this one lovely is that, on peering at it with multiple microscopic and other imaging techniques, he (and me, and a China-UK collaboration that grew over the years) found striking evidence of very well-preserved fossil soft tissues. Our paper reporting on these findings has gone live in Nature Communications so I can blog about it now.

Reference: Jiang, B., Zhao, T., Regnault, S., Edwards, N.P., Kohn, S.C., Li, Z., Wogelius, R.A., Benton, M., Hutchinson, J.R. 2017. Cellular preservation of musculoskeletal specializations in the Cretaceous bird Confuciusornis. Nature Communications 8:14779. doi: 10.1038/NCOMMS14779

Stomach-Churning Rating: 3/10; gooey, but fossil gooey, except for some colourful, gastrically-tolerable histology of bird tissue.

Front view of the ankle/foot of our specimen.

Back view of the ankle/foot of our specimen.

What has been fun about this collaboration is that, for one, it fits in perfectly with my prior work. Ever since my PhD thesis I’d been wondering about odd bones in the legs of birds, including a very puzzling and very, very neglected bit of bone called the tarsal sesamoid, on the outside of the upper end of the ankle joint. Furthermore, a tunnel of tissue called the tibial cartilage sits next to that sesamoid bone, and then across the ankle joint there is a bony prominence with grooves and tunnels that vary highly among bird species; that is called the hypotarsus. These structures are all known in living birds and, to a degree, in extinct fossil cousins. Our specimen seems to reveal an earlier stage in how these little features of bird ankles originated, which we concluded to be a step along the transition to the more crouched legs that modern birds have.

This study has also challenged me to broaden my horizons as a scientist. Although this was a big collaboration and thus we had several specialists to apply supercharged technological techniques to our fossil, I had to learn something about what all that meant. My kind colleagues helped me learn more about tissue histology, scanning electron microscopy, synchrotron mapping, FTIR and mass spectrometry and more. I won’t go through all of these techniques but there are some pretty pictures sprinkled here and in the paper, and a lot more detail in the paper for those who want the gory techno-detail. Basically we threw the kitchen sink of science at the fossil to crack open some of its secrets, and what we found inside was nifty.

Scanning electron micrograph image of probable tendon or ligament fibres (arrow) in cross-section, from near the ankle joint.

We found preserved cells and other parts of connective tissues including tendons and/or ligaments, fibrocartilage (the tougher kind) and articular cartilage (the softer joint-padding kind). That’s great, although not unique, but the kitchen sink also flushed out even more reductionist data: those tissues included some organic residues, including what appear to be bits of proteins (amino acids); particularly the collagen that makes up tendons.

Fibrocartilage (“fc”) from the ankle joint region.

Hopefully we’re right, and we included as much of the data as we could manage so that others can look at our findings. The specimen is crushed into nearly two dimensions, like all Jehol biota organisms, so its anatomy was hard to interpret but we think we got it right. All of the other kitchen-sinky tools have their own nuances and pitfalls but we did our best with a superb team of experts. We’ve had to wait 125 million years to uncover this specimen and a few more years to find out if we’ve looked at the right way is no greater test of patience.

I thank my coauthors, especially Baoyu Jiang for the kind invitation to participate and the very fun experience of collaborating. I think I’ll remember this study for a long time because, for me, it takes a step beyond just describing Another Case of Jaw-Dropping Fossilization (can you hear the hipsters recounting the excitement and cynicism of the 1990s when this all was dawning? I was there and maybe now I’m one of them). By combining all of those methods we learned new things about the palaeobiology of birds and the evolution of traits within birds. Confuciusornis, not shockingly, had ankles that should have functioned in ways intermediate between those of bog-standard non-avian theropods and modern birds.

Same anatomical regions in an extant bird as in the main fossil specimen. Left distal tibiotarsus (TT; below) and proximal tarsometatarsus (TMT; above) from an adult helmeted guineafowl (Numida meleagris) after formalin fixation. (from our paper’s Supp Info)

I’m hopeful that more synthesis of molecular/cellular, imaging, biomechanical and other tools (not to mention good old palaeontology and anatomy!) can wash away some more of this mystery. And it was fun to be a part of a study that adds to overwhelming evidence that was heretical ~25 years ago: some hardy biomolecules such as collagen and keratin can survive hundreds of millions of years, not just thousands. Pioneers such as Prof. Mary Schweitzer led the original charge that made reporting on discoveries like ours much easier today.

I know how the birds fly, how the fishes swim, how animals run. But there is the Dragon. I cannot tell how it mounts on the winds through the clouds and flies through heaven. Today I have seen the Dragon.“– Confucius, ca. 500 BCE.

Let’s finish with some images of a living bird’s ankle region, by co-author and PhD student Sophie Regnault. We considered these for inclusion in the paper but they didn’t fit quite right. I love them anyway so here they are:

Patchwork of histology slide images, from a guineafowl’s ankle (as per photo above). The numbered squares correspond to zoomed-in images below. The tibiotarsus is on the proximal end (bottom left); the tarsometatarsus is on the distal end (right side); and the enigmatic tarsal sesamoid is at the top. Magnification: 20x overall.

Region 1. nice (fibro)cartilage-bone inferface at ligament insertion.

Region 2: longitudinal slice through ligaments connecting the tibiotarsus to the tarsometatarsus across the ankle joint.

Region 3: front (bottom) of the tibiotarsus/upper ankle.

Region 4: tendon fibres in longitudinal section; on the back of the tibiotarsus. Some show mineralization into ossified tendons (“metaplasia”); another curious feature of modern birds.

Region 5: muscle attachment to the back of the upper tarsometatarsus bone. Small sesamoid fragment visible.

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The early, hippo-like mammal Coryphodon. I didn’t know it had a patella but it does. From Yale Peabody Museum.

I’m not shy about my fondness for the patella (kneecap) of tetrapod vertebrates, and neither are the other members of RVC’s “Team Patella”. We’ve had a fun 3+ years studying these neglected bones, and today we’ve published a new study of them. Our attention has turned from our prior studies of bird and lepidosaur kneecaps to mammalian ones. Again, we’ve laid the groundwork for a lot of future work by focusing on (1) basic anatomy and (2) evolutionary history of these sesamoid bones, with a lot of synthesis of existing knowledge from the literature; including development and genetics. This particular paper is a sizeable monograph of the state of play in the perusal of patellae in placental and other synapsids. Here’s what we did and found, focusing mostly on bony (ossified) patellae because that allowed us to bring the fossil record better to bear on the problem.

Reference: Samuels, M., Regnault, S., Hutchinson, J.R. 2016. Evolution of the patellar sesamoid bone in mammals. PeerJ 5:e3103 https://doi.org/10.7717/peerj.3103

Stomach-Churning Rating: 1/10; bones and more bones.

The short version of the story is that mammals evolved bony kneecaps about five times, with marsupials gaining and losing them (maybe multiple times) whereas monotremes (platypus and echidna) and placentals (us and other mammals) didn’t do much once they gained them, and a couple of other fossil groups evolved patellae in apparent isolation.

Evolution of the patella in mammals: broad overview from our paper. Click to zoom in.

The marsupial case is the most fascinating one because they may have started with a fibrocartilaginous “patelloid” and then ossified that, then reduced it to a “patelloid” again and again or maybe even regained it. There needs to be a lot more study of this group to see if the standard tale that “just bandicoots and a few other oddballs have a bony patella” is true for the Metatheria (marsupials + extinct kin). And more study of the development of patellae in this group could help establish whether they truly do “regress” into fibrocartilage when they are “lost” in evolution, or if other, more flexible patterns exist, or even if some of the cases of apparent “loss” of a bony patella are actually instances of delayed ossification that only becomes evident in older adults. Our paper largely punts on these issues because of an absence of sufficient data, but we hope that it is inspiration for others to help carry the flag forward for this mystery.

The higgledy-piggledy evolution of a patella in Metatheria, including marsupials. Click to zoom in.

Some bats, too, do funky things with their kneecaps, analogous to the marsupial “patelloid” pattern, and that chiropteran pattern also is not well understood. Why do some bats such as Pteropus fruit bats “lose” their kneecaps whereas others don’t, and why do some bats and other species (e.g. various primates) seem to have an extra thing near their kneecaps often called a “suprapatella”? Kneecap geeks need to know.

The short-nosed bandicoot (marsupial) Isoodon, showing a nice bony patella as typifies this group. From Yale Peabody Museum.

Otherwise, once mammals evolved kneecaps they tended to keep them unless they lost their hindlimbs entirely (or nearly so). Witness the chunky patellae of early whales such as Pakicetus and join us in wondering why those chunks persisted. The evolutionary persistence of blocky bits of bone in the knees of various aquatic animals, especially foot-propelled diving birds, may help answer why, as the hindlimbs surely still played roles in swimming early in cetacean evolution. Ditto for sea cows (Sirenia) and other groups.

Early whale Ambulocetus, showing hefty kneecaps.

But I’m still left wondering why so many groups of land vertebrates (and aquatic ones, too) never turned parts of their knee extensor tendons into bone. We know a bit about the benefits of doing that, to add leverage to those joints that enables the knee muscles to act with dynamic gearing (becoming more forceful “low gear” or more speedy “high gear” in function). Non-avian (and most early avian/avialan) dinosaurs, crocodiles, turtles, amphibians, early mammal relatives, and almost all other known extinct lineages except for those noted above got by just fine without kneecaps, it seems, even in cases where a naïve biomechanist would expect them to be very handy, such as in giant dinosaurs.

A quoll, Dasyurus, with what is probably a fibrocartilaginous “patelloid”. From Yale Peabody Museum.

However, tendons don’t turn to bone unless the right stresses and strains are placed upon them, so maybe kneecaps are a “spandrel” or “exaptation” of sorts, to abuse Gould’s ghost, whose adaptive importance is overemphasized. Maybe that adaptive myopia overshadows a deeper ontogenetic story, of how tissues respond to their history of mechanical loading environment. It has been speculated that maybe (non-marsupial) mammals have broadly “genetically assimilated” their kneecaps, fixing them into semi-permanence in their genetic-developmental programmes, whereas in contrast the few studies of birds indicate more responsiveness and thus less assimilation/fixation. That “evo-devo-mechanics” story is what now fascinates me most and we’ve poked at this question a bit now, with some updates to come- watch this space! Regardless, whether an animal has a bony vs. more squishy soft tissue patella must have consequences for how the knee joint and muscles are loaded, so this kind of question is important.

Giant marsupial Diprotodon (at NHM London); to my knowledge, not known to have had kneecaps- why?

In the meantime, enjoy our latest contribution if it interests you. This paper came about when first author Dr. Mark Samuels emailed me in 2012, saying he’d read some of my old papers on the avian musculoskeletal system and was curious about the evolution of patellae in various lineages. Unlike many doctors and vets I’ve run into, he was deeply fascinated by the evolutionary and fossil components of patellae and how those relate to development, genetics and disorders of patellae. We got talking, found that we were kindred kneecap-spirits, and a collaboration serendipitously spun off from that, soon adding in Sophie. It was a blast!

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A quick heads-up that we just posted on our sister blog Anatomy To You, about a new open-access paper we’ve published on the skeletal anatomy of the tuatara Sphenodon. Lots of cool images you can’t see anywhere else are there!

In focus: The big picture of little bones in tuatara

I give it a Stomach-Churning Rating of 3/10- some picked specimens of tuatara but they’re still cute, not nasty, I’d say.

AND, like the Cool-Whip or vanilla ice cream atop your leftover pumpkin pie, there’s an added delicious bonus: a huge dataset of microCT scans from 19 tuatara specimens, free to access here:

https://osf.io/bds35/

We are VERY pumped up about getting this paper and dataset released, so we are spreading the word as wide as we can!

Sayonara.

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(Marcela with some furry friends; photo by Oliver Siddon)

(Marcela with some felid friends; photo by Oliver Siddon)

A guest post by Marcela Randau (m.randau@ucl.ac.uk)

Stomach-Churning Rating: 1/10; just bones and data plots!

It is often said that all cats are very similar in terms of their skeletal morphology (“a cat is a cat is a cat”). But is this really the case? It may be if only gross, qualitative anatomy is taken into consideration, i.e., if you just eyeball the skeletons of tigers and lions you might find yourself not knowing which one is which. But with huge advances in technology that allows for extracting detailed shape information off a structure (e.g., a skull) and for analysing this information (‘Geometric Morphometrics’), it has become more and more possible to distinguish between relatively similar forms – which may be from distinct species, separate sexes, or even just different populations of the same taxon.

And it is reasonable to think that cat skeletons might be a lot more different than what meets the eye, as for a lineage of apparently similarly built animals, with not that much variation in diet  (all cats are hypercarnivores) there is substantial variation in body mass (over 300-fold just in living species!) and in ecology across cat species. From the cursorial cheetah to the arboreal clouded leopard, felids present a wide range of locomotory adaptations. Yes, all cats can climb, but some do it better than others: think lion versus margay (yes, they do descend trees head-first). As hypercarnivores, all cats are meat specialists, but they also change with regards to how big their prey is, with a general and sometimes-not-so-black-and-white three-tier classification into small, mixed and large prey specialists. The rule of thumb is ‘if you are lighter than ~20-25 kg, hunt small stuff. If you are heavier than that, hunt BIG BIG things; bigger than yourself. And if you are in the middle ground, hunt some small-ish things, some big-ish things, and things about your size. Well, -ish’ – their prey size preference has a lot to do with energetic constraints (have a look at Carbone et al. 1999; and Carbone et al. 2007, if you’re interested in this). But the fun bit here is that form sometimes correlates quite strongly with function, so we should be able to find differences in some of their bones that carry this ecological signal.

Indeed, for a while now, we have known that the shape of the skull and limbs of felids can tell us a lot about how they move and how big their prey is (Meachen-Samuels and Van Valkenburgh 2009, 2009), but a large proportion of their skeleton has been largely ignored: we don’t know half as much about ecomorphology and evolution of the vertebral column. Well, it was time we changed this a bit! As the PhD student in the Leverhulme-funded ‘Walking the cat back’ (or more informally, “Team Cat”) project, I’ve spend a big chunk of my first two years travelling around the world (well, ok, mainly to several locations in the USA) carrying a heavy pellet case containing my working tool, a Microscribe, to collect 3-D landmarks (Fig. 1) across the presacral vertebral column of several cat species. And some of first results are just out! Check them out by reading our latest paper, “Regional differentiation of felid vertebral column evolution: a study of 3D shape trajectories” in the Organisms Diversity and Evolution journal (Randau, Cuff, et al. 2016).

cheetah-verts

Fig. 1: Different vertebral morphologies and their respective three-dimensional landmarks. Vertebral images are from CT scans of Acinonyx jubatus (Cheetah, USNM 520539)

Building from results based on our linear vertebral data from the beginning of the year (Randau, Goswami, et al. 2016), the 3-D vertebral coordinates carry a lot more information and we were able to describe how this complex shape-function relationship takes place throughout the axial skeleton (in cats at least) in much better detail than our prior study did. One of the difficulties in studying serial structures such as the vertebral column is that some clades present variation in vertebral count which makes it less straightforward to compare individual vertebrae or regions across species. However, mammals are relatively strongly constrained in vertebral count, and Felidae (cats; living and known fossils) show no variation at all, having 27 presacral vertebrae. So adaptation of the axial skeleton in mammals has been suggested to happen by modification of shape rather than changes in vertebral number.

Using a variety of geometric morphometric analyses, under a phylogenetically informative methodology, we have shown that there is clear shape and functional regionalisation across the vertebral column, with vertebrae forming clusters that share similar signal. Most interestingly, the big picture of these results is a neck region which is either very conservative in shape, or is under much stronger constraints preventing it from responding to direct evolutionary pressures, contrasting with the ‘posteriormost’ post-diaphragmatic tenth thoracic (T10) to last lumbar (L7) vertebral region, which show the strongest ecological correlations.

We were able to analyse shape change through functional vertebral regions, rather than individual vertebrae alone, by making a novel application of a technique called the ‘Phenotypic Trajectory Analysis’, and demonstrated that the direction of vertebral shape trajectories in the morphospace changes considerably between both prey size and locomotory ecomorphs in cats, but that the amount of change in each group was the same. It was again in this T10-L7 region that ecological groups differed the most in vertebral shape trajectories (Fig. 2).

pta-cats

Figure 2: Phenotypic trajectory analysis (PTA) of vertebrae in the T10 – L7 region grouped by prey size (A) and locomotory (B) categories.

So in the postcranial morphology of cats can be distinguished, changing its anatomy in order to accommodate the different lifestyles we see across species. But the distinct parts of this structure respond to selection differently. The next step is figuring out how that might happen and we are working on it.

While Team Cat continues to investigate other biomechanical and evolutionary aspects of postcranial morphology in this interesting family, we’ve been able to discuss some of these and other results in a recent outreach event organised by the University College of London Grant Museum of Zoology and The Royal Veterinary College. We called it “Wild Cats Uncovered: movement evolves”. Check how it went here: (https://blogs.ucl.ac.uk/museums/2016/11/17/cheetah-post-mortem/) and here (http://www.rvc.ac.uk/research/research-centres-and-facilities/structure-and-motion/news/wild-cats-uncovered), with even more pics here (https://www.flickr.com/photos/144824896@N07/sets/72157676695634065/).

References used here:

Carbone, C., Mace, G. M., Roberts, S. C., and Macdonald, D. W. 1999. Energetic constaints on the diet of terrestrial carnivores. Nature 402:286-288.

Carbone, C., Teacher, A., and Rowcliffe, J. M. 2007. The costs of carnivory. PLoS biology 5 (2):e22.

Meachen-Samuels, J. and Van Valkenburgh, B. 2009. Craniodental indicators of prey size preference in the Felidae. Biol J Linn Soc 96 (4):784-799.

———. 2009. Forelimb indicators of prey-size preference in the Felidae. Journal of morphology 270 (6):729-744.

Randau, M., Cuff, A. R., Hutchinson, J. R., Pierce, S. E., and Goswami, A. 2016. Regional differentiation of felid vertebral column evolution: a study of 3D shape trajectories. Organisms Diversity and Evolution Online First.

Randau, M., Goswami, A., Hutchinson, J. R., Cuff, A. R., and Pierce, S. E. 2016. Cryptic complexity in felid vertebral evolution: shape differentiation and allometry of the axial skeleton. Zoological Journal of the Linnean Society 178 (1):183-202.

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It has been almost three months since my last post here, and things have fallen quiet on our sister blog Anatomy to You, too. I thought it was time for an update, which is mostly a summary of stuff we’ve been doing on my team, but also featuring some interesting images if you stick around. The relative silence here has partly been due to me giving myself some nice holiday time w/family in L.A., then having surgery to fix my right shoulder, then recovering from that and some complications (still underway, but the fact that I am doing this post is itself evidence of recovery).

Stomach-Churning Rating: 4/10; semi-gruesome x-rays of me and hippo bits at the end, but just bones really.

X-ray of my right shoulder from frontal view, unlabelled

X-ray of my right shoulder from frontal view, unlabelled

Labelled x-ray

Labelled x-ray

So my priorities shifted to those things and to what work priorities most badly needed my limited energy and time. I’ve also felt that, especially since my health has had its two-year rough patch, this blog has been quieter and less interactive than it used to be, but that is the nature of things and maybe part of a broader trend in blogs, too. My creative juices in terms of social media just haven’t been at their ~2011-2014 levels but much is out of my control, and I am hopeful that time will reverse that trend. Enough about all this. I want to talk about science for the rest of this post.

My team, and collaborators as well, have published six recent studies that are very relevant to this blog’s theme- how about we run through them quickly? OK then.

  1. Panagiotopoulou, O., Pataky, T.C., Day, M., Hensman, M.C., Hensman, S., Hutchinson, J.R., Clemente, C.J. 2016. Foot pressure distributions during walking in African elephants (Loxodonta africana). Royal Society Open Science 3: 160203.

Our Australian collaborators got five African elephants together in Limpopo, South Africa and walked them over pressure-measuring mats, mimicking our 2012 study of Asian elephants. While sample sizes were too limited to say much statistically, in qualitatively descriptive terms we didn’t find striking differences between the two species’ foot pressure patterns. I particularly like how the centre of pressure of each foot (i.e. abstracting all regional pressures down to one mean point over time) followed essentially the same pattern in our African and Asian elephants, with a variable heelstrike concentration that then moved forward throughout the step, and finally moved toward the outer (3rd-5th; especially 3rd) toes as the foot pushed off the ground, as below.

African elephant foot COP traces vs. time in red; Asian elephant in orange. Left and right forefeet above; hindfeet below.

African elephant foot COP traces vs. time in red; Asian elephant in orange-yellow. Left and right forefeet above; hindfeet below.

Gradually, this work is moving the field toward better ability to use similar techniques to compare elephant foot mechanics among species, individuals, or over time– especially with the potential of using this method (popular in human clinical gait labs) to monitor foot (and broader musculoskeletal) health in elephants. I am hopeful that a difference can be made, and the basic science we’ve done to date will be a foundation for that.

  1. Panagiotopoulou, O., Rankin, J.W., Gatesy, S.M., Hutchinson, J.R. 2016. A preliminary case study of the effect of shoe-wearing on the biomechanics of a horse’s foot. PeerJ 4: e2164.

Finally, about six years after we collected some very challenging experimental data in our lab, we’ve published our first study on them. It’s a methodological study of one horse, not something one can hang any hats on statistically, but we threw the “kitchen sink” of biomechanics at that horse (harmlessly!) by combining standard in vivo forceplate analysis with “XROMM” (scientific rotoscopy with biplanar fluoroscopy or “x-ray video”) to conduct dynamic analysis of forefoot joint motions and forces (with and without horseshoes on the horse), and then to use these data as input values for finite element analysis (FEA) of estimated skeletal stresses and strains. This method sets the stage for some even more ambitious comparative studies that we’re finishing up now. And it is not in short supply of cool biomechanical, anatomical images so here ya go:

fig5-vonmises

Above: The toe bones (phalanges) of our horse’s forefoot in dorsal (cranial/front) view, from our FEA results, with hot colours showing higher relative stresses- in this case, hinting (but not demonstrating statistically) that wearing horseshoes might increase stresses in some regions on the feet. But more convincingly, showing that we have a scientific workflow set up to do these kinds of biomechanical calculations from experiments to computer models and simulations, which was not trivial.

And a cool XROMM video of our horse’s foot motions:

  1. Bates, K.T., Mannion, P.D., Falkingham, P.L., Brusatte, S.L., Hutchinson, J.R., Otero, A., Sellers, W.I., Sullivan, C., Stevens, K.A., Allen, V. 2016. Temporal and phylogenetic evolution of the sauropod dinosaur body plan. Royal Society Open Science 3: 150636.

I had the good fortune of joining a big international team of sauropod experts to look at how the shapes and sizes of body segments in sauropods evolved and how those influenced the position of the body’s centre of mass, similar to what we did earlier with theropod dinosaurs. My role was minor but I enjoyed the study (despite a rough ride with some early reviews) and the final product is one cool paper in my opinion. Here’s an example:

fig6a-bates-sauropod-com-evol

The (embiggenable-by-clicking) plot shows that early dinosaurs shifted their centre of mass (COM) backwards (maybe related to becoming bipedal?) and then sauropods shifted the COM forwards again (i.e. toward their forelimbs and heads) throughout much of their evolution. This was related to quadrupedalism and giant size as well as to evolving a longer neck; which makes sense (and I’m glad the data broadly supported it). But it is also a reminder that not all sauropods moved in the same ways- the change of COM would have required changes in how they moved. There was also plenty of methodological nuance here to cover all the uncertainties but for that, see the 17 page paper and 86 pages of supplementary material…

  1. Randau, M., Goswami, A., Hutchinson, J.R., Cuff, A.R., Pierce, S.E. 2016. Cryptic complexity in felid vertebral evolution: shape differentiation and allometry of the axial skeleton. Zoological Journal of the Linnean Society 178:183-202.

Back in 2011, Stephanie Pierce, Jenny Clack and I tried some simple linear morphometrics (shape analysis) to see how pinniped (seal, walrus, etc) mammals changed their vertebral morphology with size and regionally across their backbones. Now in this new study, with “Team Cat” assembled, PhD student Marcela Randau collected her own big dataset for felid (cat) backbones and applied some even fancier techniques to see how cat spines change their shape and size. We found that overall the vertebrae tended to get relatively more robust in larger cats, helping to resist gravity and other forces, and that cats with different ecologies across the arboreal-to-terrestrial spectrum also changed their (lumbar) vertebral shape differently. Now Marcela’s work is diving even deeper into these issues; stay tuned…

fig2-randau-measurements

Example measurements taken on felid vertebrae, from the neck (A-F) to the lumbar region (G-J), using a cheetah skeleton.

  1. Charles, J.P., Cappellari, O., Spence, A.J., Hutchinson, J.R., Wells, D.J. 2016. Musculoskeletal geometry, muscle architecture and functional specialisations of the mouse hindlimb. PLOS One 11(4): e0147669.

RVC PhD student James Charles measured the heck out of some normal mice, dissecting their hindlimb muscle anatomy, and using microCT scans produced some gorgeous images of that anatomy too. In the process, he also quantified how each muscle is differently specialized for the ability to produce large forces, rapid contractions or fine control. Those data were essential for the next study, where we got more computational!

mouse-mimics

  1. Charles, J.P., Cappellari, O., Spence, A.J., Wells, D.J., Hutchinson, J.R. 2016. Muscle moment arms and sensitivity analysis of a mouse hindlimb musculoskeletal model. Journal of Anatomy 229:514–535.

James wrangled together a lovely musculoskeletal model of our representative mouse subject’s hindlimb in the SIMM software that my team uses for these kinds of biomechanical analyses. As we normally do as a first step, we used the model to estimate things that are hard to measure directly, such as the leverages (moment arms) of each individual muscle and how those change with limb posture (which can produce variable gearing of muscles around joints). James has his PhD viva (defense) next week so good luck James!

mouse-simm

The horse and mouse papers are exemplars of what my team now does routinely. For about 15 years now, I’ve been building my team toward doing these kinds of fusion of data from anatomy, experimental biomechanics, musculoskeletal and other models, and simulation (i.e. estimating unmeasurable parameters by telling a model to execute a behaviour with a given set of criteria to try to perform well). Big thanks go to collaborator Jeff Rankin for helping us move that along lately. Our ostrich study from earlier this year shows the best example we’ve done yet with this, but there’s plenty more to come.

I am incredibly excited that, now that my team has the tools and expertise built up to do what I’ve long wanted to do, we can finally deliver the goods on the aspirations I had back when I was a postdoc, and which we have put enormous effort into pushing forward since then. In addition to new analyses of horses and mice and other animals, we’ll be trying to push the envelope more with how well we can apply similar methods to extinct animals, which brings new challenges– and evolutionary questions that get me very, very fired up.

Here we are, then; time has brought some changes to my life and work and it will continue to as we pass this juncture. I suspect I’ll look back on 2016 and see it as transformative, but it hasn’t been an easy year either, to say the least. “Draining” is the word that leaps to mind right now—but also “Focused” applies, because I had to try to be that, and sometimes succeeded. I’ve certainly benefited a lot at work from having some talented staff, students and other collaborators cranking out cool papers with me.

I still have time to do other things, too. Once in a while, a cool critter manifests in The Freezers. Check out a hippo foot from a CT scan! It’s not my best scan ever (noisy data) but it shows the anatomy fairly well, and some odd pathologies such as tiny floating lumps of mineralized soft tissue here and there. Lots to puzzle over.

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Sorry about the title. It’s the best I could do. In case you missed it on our Anatomy to You blog, we unleashed a hefty database of CT (and some MRI) scans of our frozen crocodile cadavers last week, for free public usage. In total, it’s about 34 individuals from 5 species, in 53 databases constituting around 26,000 individual DICOM file format slices of data. This page has a table of what the data/specimens are. I am writing this post to share some more images and ensure that word gets out. We’re thrilled to be able to finally release this first dataset. We have plans to let loose a LOT more such data in the future, for various organisms that we study.

Stomach-Churning Rating: 2/10- be glad that these data don’t come with an olfactory component, especially the five rotten, maggot-ridden Morelet’s croc specimens, which are among the stinkiest things I’ve dealt with.

Crocodiles are no strangers to this blog, of course, as these past links testify. Indeed, most of the crocodile images I’ve blogged with come from specimens that are in this scan dataset. We even released a “celebrity crocodile, “WCROC” or FNC7 in our dataset, which is the 3.7m long Nile croc from “Inside Nature’s Giants”. It broke our CT scanner back in ~2009 but we got the data, except for the torso, and we also got some MRI scans from it, so we’re chuffed.

Above: The only spectacled caiman (Caiman crocodilus); and indeed the only alligatorid; in our dataset. To watch for: stomach contents/gastroliths, and all the damn osteoderms that I did/didn’t segment in this quickly processed file. This specimen had its limbs dissected for one of our studies, so only the right limbs are visible.

There are some more specimens to come- e.g. five baby Nile crocs‘ datasets (“GNC1-5”) are hiding somewhere in our drives and we just need to dig them up. You might also know that we published some scan data for crocodile vertebral columns (including fossils) in our recent paper with Julia Molnar et al. (and related biomechanical data discussed here), and we published all of our anatomical measurements for a huge set of crocodylian species in our papers by Vivian Allen et al. And then I had an enjoyable collaboration with Colleen Farmer and Emma Schachner on the lung anatomy of various crocodylian species, using these same specimens and related scan datasets.

 

Above: rotating Crocodylus moreletii (specimen FMC5 from our database) in a happy colour.

Sharing these kind of huge datasets isn’t so easy. Not only do few websites host them cheaply, and with reasonable file size limits, and limited headaches for what info you have to provide, and with some confidence that the websites/databases will still exist in 5-20 years, but also we were hesitant to release the dataset until we felt that it was nicely curated. Researchers can now visit my lab and study the skeletons (or in some cases, the still-frozen specimens) matched up with the scan data, and known body masses or other metadata. We’re not a museum with dedicated curatorial staff, so that was not trivial to reliably organize, and I still worry that somewhere in the dataset we mis-identified a specimen or something. But we’ve done our best, and I’m happy with that for now.

Above: rotating Osteolaemus tetraspis (specimen FDC2 from our database), which was obviously dissected a bit postmortem before we could scan it, but still shows some cool features like the extensive bony armour and the cute little doglike (to me, anyway) skull. I worked with these animals (live) a bit >10 years ago and came to love them. Compared to some other crocodiles we worked with, they had a pleasant demeanour. Like this guy:

Osteolaemus (resting) set up with motion capture markers for a yet-to-be-published study that we did in 2005 (ugh!). It wasn't harmed by this.

Osteolaemus (resting) set up with motion capture markers for a yet-to-be-published gait study that we did in 2005 (ugh!). It wasn’t harmed by this.

Anyway, as a person who likes to maintain quality in the science we do, I also was hesitant to “just” release the DICOM file data rather than beautiful segmented 3D skeletal (or other tissue) geometry that is ready for 3D printing or animation or other uses, or interactive online tools like Sketchfab. Other labs (e.g. Witmerlab) do these kind of things better than we do and they inspire us to raise our game in the future, but I am sure that we will be forgiven for releasing big datasets without gorgeous visuals and more practical, processed files — this time. 🙂  We agree with many other scientists that sharing data is part of modern, responsible science– and it can be fun, too! Oddly enough, in this case we hadn’t used the CT/MRI data much for our own studies; most of the scans were never fully digitized. We just scan everything we get and figured it was time to share these scans.

Enjoy. If you do something cool with the data that we’ve made accessible, please let us know so we can spread the joy!

And if you’re a researcher headed to ICVM next week, I hope to see you there!

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