2015

Tracheal compression in pupae of the beetle Zophobas morio.

Pendar*, H., M. Kenny*, and J.J. Socha. Biology Letters. 11 (6): 20150259.

Science Shot | Cover image | Video abstract | Movies | Dryad data | Supplement | Download: [pdf]


How animals glide: from trajectory to morphology.

Socha, J.J., F. Jafari*, Y. Munk, and G. Byrnes. Online version, March 13, 2015. Canadian Journal of Zoology.

| Download: [pdf]


2014

Of snakes and robots.

Socha. J.J. 2014. Science. 346 (6206): 160-161.

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A theoretical analysis of gliding in flying snakes.

Jafari, F.*, S.D. Ross, P.P. Vlachos, and J.J. Socha. 2014. Bioinspiration and Biomimetics. 9(2): 025014.

| Download: [pdf]


Variation in tensile properties of tracheal tubes in the American cockroach.

Becker, W.*, M.R. Webster*, J.J. Socha, and R. De Vita. 2014. Smart Materials and Structures. 23 (5): 057001.

| Download: [pdf]


Effects of VR system fidelity on analyzing isosurface visualization of volume datasets

Laha, B.*, D.A. Bowman, and J.J. Socha. 2014. IEEE Transactions on Visualization and Computer Graphics (Proceedings of Virtual Reality 2013). 20 (4): 513-522.

| Download: [pdf]


Lift and wakes of flying snakes

Krishnan, A.* J.J. Socha, P.P. Vlachos, and L.A. Barba. 2014. Physics of Fluids. 26: 031901

| Download: [pdf]


Aerodynamics of the flying snake, Chrysopelea paradisi: how a bluff-body cross-sectional shape contributes to gliding performance

Holden, D.*, J.J. Socha, N. Cardwell, and P.P. Vlachos. 2014. Journal of Experimental Biology. 217 (3): 382-394.

Video abstract | Journal supplementary video (free via pdf) | Movie 1 | Movie 2 | Movie 3 | Download: [pdf]


2013

Hypoxia-induced compression in the tracheal system of the tobacco hornworm caterpillar, Manduca sexta L

Greenlee, K.J., J.J. Socha, H.B. Eubanks, G. Thapa, P. Pedersen, W.-K. Lee, and S.D. Kirkton. 2013. Journal of Experimental Biology. 216: 2293-2301.

Journal supplementary video (free via pdf) | Movie 1 | Movie 2 | Download: [pdf]

This paper looks at the tracheal systems of caterpillars under various atmospheric conditions. In normal circumstances, the tracheal system does nothing: the tracheal tubes do not deform, and oxygen and carbon dioxide are transported diffusively. But when oxygen levels are decreased, the caterpillar begins pumping its body, resulting in compression of parts of the tracheal system. This effect becomes more pronounced as oxygen becomes more scarce. This experiment clearly shows that—at least for these caterpillars—there exists an ability to turn on a second mode of gas exchange when the going gets tough.


Dynamics of tracheal compression in the horned passalus beetle

J.S. Waters*, W.-K. Lee, M.W. Westneat, and J.J. Socha. 2013. American Journal of Physiology: Regulatory, Integrative and Comparative Physiology. 304: R621-R627.

Movie S1.mov | Movie S2.mov | Movie S3.mov | Download: [pdf]

This paper documents a new form of tracheal compression, in which the compression “rolls” in one direction when compressing, and “rolls” in the opposite when re-inflating. Furthermore, some of these compressions took place when a local spiracle was closed, indicating that air must have been being pushed inward within the tracheal system, rather than outward to the outside air. We also do some theoretical modeling to compare transport by bulk flow vs. diffusion.


How locusts breathe

Harrison, J.F., J.S. Waters, A.J. Cease, J.M. VandenBrooks, V. Callier, C.J. Klok, K. Shaffer, and J.J. Socha. 2013. Physiology. 28: 18-27.

Download: [pdf]

As the title suggests, this is an overview of how locusts (grasshoppers) breathe, focusing on the mechanisms that produce deformation of the tracheae and air sacs to induce ventilation. In addition to the review, we present new data on tracheal system behavior based on synchrotron x-ray data, and present a new hypothesis of body compartmentalization.


Biomechanics of turtle shells: how whole shells fail in compression

Magwene, P.M. and J.J. Socha. 2013. Journal of Experimental Zoology A. 319A:86-98. [published online, 2012]

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The turtle’s shell is a robust structure that provides great protection for the turtle, but it is not infallible.  For instance, we know that some predators are able to breach the shell. How does the shell react to compressive loading, such as in a bite from an alligator? Here we present the first study that examines the behavior of turtle shells under such forces, including the resistance of native soft tissues. Four turtle species were studied. In addition to whole-shell loading, we also examined the material properties of the bony tissue of the plastron.


2011

Multigenerational effects of rearing atmospheric oxygen level on the tracheal dimensions and diffusing capacities of pupal and adult Drosophila melanogaster

Klok, C.J., A. Kaiser, J.J. Socha, W.-K. Lee, and J. F. Harrison. 2011.  In: Hypoxia and Cancer.  Eds. R.C. Roach et al., Springer, New York.

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This is a study led by Jaco Klok and Jon Harrison from Arizona State, another in a line of research that aims to test the hypothesis that the design of insect respiratory systems is physiologically limiting, particularly in regard to body size.  This study shows that the leg tracheae respond to rearing effects in different oxygen environments as one might expect from a purely diffusive-based system.  This contrasts with patterns in other tracheae in the body.


Gliding flight in Chrysopelea: Turning a snake into a wing

Socha, J.J.  2011. Integrative and Comparative Biology. 51(6): 969–982.

Movie 1 | Movie 2 | Download: [pdf]

A review of gliding flight in snakes Chrysopelea paradisi, including some new data on body shape change and landing.  This paper is a contribution from the symposium “The Biomechanics and Behavior of Gliding Flight” presented at the annual meeting of the Society for Integrative and Comparative Biology in 2011, organized by Robert Dudley & Steve Yanoviak.


Mechanical properties of tracheal tubes in the American cockroach (Periplaneta americana)

Webster, M.*, R. De Vita, J. Twigg, J.J. Socha. 2011.  Journal of Smart Materials and Structures, 20 (2011) 094017.

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The first measurements of mechanical properties of insect tracheal tubes, as far as we know.  We care because we’re trying to understand why tracheal tubes collapse (or don’t) in insects.  Currently highlighted as a “Featured article”.


2010

Non-equilibrium trajectory dynamics and the kinematics of gliding in a flying snake

Socha, J.J., K. Miklasz, F. Jafari*, and P.P. Vlachos. 2010. Bioinspiration and Biomimetics, 5 (2010) 045002.

Summary video | Journal supplementary video | Press | Download: [pdf]

A study of the kinematics and dynamics of fully developed gliding in the snake Chrysopelea paradisi.  We show that the snake maintains an angled posture relative to the glide path, and discuss theoretical issues of glide trajectories. 


Visceral-locomotory pistoning in crawling caterpillars (Manduca sexta)

Simon, M.A., W.A. Woods, Y.V. Serebrenik, S.M. Simon, L.I. van Griethuijsen, J.J. Socha, W.-K. Lee, and B.A. Trimmer. 2010.  Current Biology 20: 1-6.

Video abstract | Movie S1 | Movie S2 | Movie S3 | Download: [pdf]

We document a serendipitous discovery: when caterpillars crawl, their digestive system slides forward, independent of the movement of the surrounding body wall.  Weird stuff. 


Issues of convection in insect respiration: Insights from synchrotron x-ray imaging and beyond

Socha, J.J., T. Förster, and K.J. Greenlee. 2010. Respiratory Physiology and Neurobiology, 173S (2010) S65–S73.

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This paper is a symposium overview from the 2nd International Congress of Respiratory Science.  The symposium was organized by J. Socha, with speakers Thomas Förster, Kendra Greenlee, Wah-Keat Lee, John Lighton, and Thilo Wasserthal. 


Effects of body cross-sectional shape on flying snake aerodynamics

Miklasz, K.*, M. LaBarbera, X. Chen, and J.J. Socha. 2010. Experimental Mechanics , 50 (9): 1335-1348.

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It is unknown what particular features of snake gliding behavior contribute to the animal’s glide performance.  Here we present the first study of flying snake aerodynamics, isolating body shape in particular.


Canaliculi in the tessellated skeleton of cartilaginous fishes

Dean, M.N., J.J. Socha, K.M. Claeson, B.K. Hall, and A.P. Summers. 2010. Journal of Applied Ichthyology 26(2):263-267.

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We used synchrotron microtomography (SR-µCT) to investigate the lower jaw cartilage of a stingray.  Led by Mason Dean, this work identified never before appreciated internal structures, namely passages connecting the lacunar spaces within tesserae.  These passages may be used for transport, helping explain how chondrocytes remain viable despite being encased by mineral.    


2009

Synchrotron x-ray visualisation of ice formation in insects during lethal and non-lethal freezing

Sinclair, B.J., A.G. Gibbs, W.-K. Lee, A. Rajamohan, S.P. Roberts, and J.J. Socha. 2009. PLoS One 2009 4(12):e8259.

Movies | Press release | Download: [pdf]

Here we used synchrotron x-rays to directly visualize ice formation in real time in fruit fly larvae, including a species that is tolerant of freezing down to -14 C.  According to our data, the ability to withstand such freezing must lie in biochemical or cellular specializations, rather than physical differences. 


A plesiosaur containing an ichthyosaur embryo as stomach contents from the Sundance Formation of the Bighorn Basin, Wyoming

O’Keefe, F.R., H.P. Street, J.P. Cavigelli, J.J. Socha, and R.D. O’Keefe. 2009. Journal of Vertebrate Paleontology 29(4): 1306-1310.

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The first reported evidence of predation of ichthyosaurs by plesiosaurs; in this case, an embryo.  Both were marine reptiles found in the Sundance Sea, a large body of water covering parts of the western US and Canada during the Jurassic.


Direct visualization of hemolymph flow in the heart of a grasshopper (Schistocerca americana)

Lee, W.-K. and J.J. Socha. 2009. BMC Physiology 2009 9:2.

Movies | Download: [pdf]

Little is known about what flows occur in the insect heart, or how these flows are produced.  In this study, we used microbubbles as a tracer to directly observe heartflow in living grasshoppers using synchrotron x-ray phase contrast imaging.  This is the first time that microscale heartflow patterns have been visualized in any insect.


2008

Correlated patterns of tracheal compression and convective gas exchange in a carabid beetle

Socha, J.J., W.-K. Lee, J.F. Harrison, J.S. Waters*, Fezzaa, K., M.W. Westneat. 2008. Journal of Experimental Biology 211: 3409-3420.

Movies | Cover image | Download: [pdf]

Some insects rhythmically compress large segments of their tracheal systems, and the carabid beetle Pterostichus stygicus is a prime suspect.  Here we used synchrotron x-ray phase contrast imaging to visualize internal tracheal dynamics in living P. stygicus beetles.  Concurrent respiratory recordings show that one function of rhythmic tracheal compression is to convectively expel air from the body.



Advances in biological structure, function and physiology using synchrotron x-ray imaging

Westneat, M.W., J.J. Socha, and W.-K. Lee. 2008.  Annual Review of Physiology 70: 119-142.

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   This is a review of synchrotron full-field imaging, focusing on 2-D live imaging of small animals (particularly insects) and 3-D tomographic imaging of static samples (ie, things that are dead or otherwise really still). 



Use of synchrotron tomography to image naturalistic anatomy in insects

Socha, J.J. and F. De Carlo. 2008. In: Developments in X-Ray Tomography VI: 2008, San Diego, CA, USA: SPIE; 2008: 70780A-70787.

Download: [pdf]

A conference proceedings paper that demonstrates how to image fresh insect anatomy in 3D using synchrotron microCT (SR-µCT).         

                               

2007

Increase in tracheal investment with beetle size supports hypothesis of oxygen limitation on insect gigantism

Kaiser, A., C.J. Klok, J.J. Socha, W.-K. Lee, M.C. Quinlan, and J.F. Harrison. 2007.  Proceedings of the National Academy of Sciences 104 (32): 13198-13203.

Press release | Commentary | Download: [pdf]

  Although the correlation between the Carboniferous/Permian atmospheric oxygen rise and insect gigantism is well known, there has been no mechanistic explanation of its basis.  We provide one hypothesis: that space available for tracheae in the leg is limiting. 


Real-time phase-contrast x-ray imaging: a new technique for the study of animal form and function

Socha, J.J., M.W. Westneat, J.F. Harrison, J.S. Waters, and W.-K. Lee. 2007.  BMC Biology 2007 5:6.

Movies | Download:  [pdf]  

  It’s possible to visualize the internal morphology of living insects with micron-scale resolution using synchrotron x-rays.  This paper describes how it’s done, and scratches the surface of understanding the effects of such targeted x-rays on the animals. 


2006

Becoming airborne without wings: the kinematics of take-off in a flying snake, Chrysopelea paradisi

Socha, J.J. 2006.  Journal of Experimental Biology 209 (17): 3358-3369.

Movies | Cover image | Download:  [pdf]   [pdf with cover]

It’s a challenge to become airborne if you have no legs.  Flying snakes do it by hanging from a branch in a loop and jumping into the air. This paper shows how.


2005

A three-dimensional kinematic analysis of gliding in a flying snake, Chrysopelea paradisi

Socha, J.J., M. LaBarbera, and T. O’Dempsey. 2005.  Journal of Experimental Biology 208 (10): 1817-1833.

Movies | Cover image | Download: [pdf]  [pdf with cover]  [Inside JEB]

  This paper is a longer version of the Nature brief communication from 2002 (below).  It describes in detail how the paradise tree snake, C. paradisi, moves through the air during its entire trajectory. 



Effects of size and behavior on aerial performance of two species of flying snakes (Chrysopelea)

Socha, J.J. and M. LaBarbera. 2005.  Journal of Experimental Biology 208 (10): 1835-1847.

Movies | Cover image | Download: [pdf]  [pdf with cover]  [Inside JEB]

  Size matters.  In general smaller snakes make better gliders--from a given height, they travel farther and at a slower speed (admittedly a mixed bag; slower speed makes landing softer but faster speed makes for better escape from predators).



Chrysopelea ornata, C. paradisi (Flying Snakes). Behavior

Socha, J.J. and C.A. Sidor. 2005.  Herpetological Review 36(2): 190-191.

Download: [pdf]

  Flying snakes watch airplanes. (Not a joke!)  The C. ornata in the figure is tracking a passenger jet fly overhead.  I also observed C. paradisi tracking birds in the same way.  From these simple observations it can be inferred that Chrysopelea have good vision, and that birds may be one of their major predators.


2002

Gliding flight in the paradise tree snake

Socha, J.J. 2002. Nature 418: 603-604.

Download: [pdf]

  C. paradisi, the paradise tree snake, is a real glider. Its glide performance is on par with other vertebrate gliders such as flying squirrels, flying lizards (Draco), and flying frogs.  This snake can even turn in mid-air.




 

Publications

*Indicates student author.