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Find video protocols related to scientific articles indexed in Pubmed.
The geometry of taking flight: Limb morphometrics in Mesozoic theropods.
J. Morphol.
PUBLISHED: 08-02-2014
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Theropoda was one of the most successful dinosaurian clades during the Mesozoic and has remained a dominant component of faunas throughout the Cenozoic, with nearly 10,000 extant representatives. The discovery of Archaeopteryx provides evidence that avian theropods evolved at least 155 million years ago and that more than half of the tenure of avian theropods on Earth was during the Mesozoic. Considering the major changes in niche occupation for theropods resulting from the evolution of arboreal and flight capabilities, we have analyzed forelimb and hindlimb proportions among nonmaniraptoriform theropods, nonavian maniraptoriforms, and basal avialans using reduced major axis regressions, principal components analysis, canonical variates analysis, and discriminant function analysis. Our study is the first analysis on theropod limb proportions to apply phylogenetic independent contrasts and size corrections to the data to ensure that all the data are statistically independent and amenable to statistical analyses. The three ordination analyses we performed did not show any significant groupings or deviations between nonavian theropods and Mesozoic avian forms when including all limb elements. However, the bivariate regression analyses did show some significant trends between individual elements that suggested evolutionary trends of increased forelimb length relative to hindlimb length from nonmaniraptoriform theropods to nonavian maniraptoriforms to basal avialans. The increase in disparity and divergence away from the nonavian theropod body plan is well documented within Cenozoic forms. The lack of significant groupings among Mesozoic forms when examining the entire theropod body plan concurrently suggests that nonavian theropods and avian theropods did not substantially diverge in limb proportions until the Cenozoic. J. Morphol., 2014. © 2014 Wiley Periodicals, Inc.
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Synchrotron imaging reveals bone healing and remodelling strategies in extinct and extant vertebrates.
J R Soc Interface
PUBLISHED: 01-01-2014
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Current understanding of bone healing and remodelling strategies in vertebrates has traditionally relied on morphological observations through the histological analysis of thin sections. However, chemical analysis may also be used in such interpretations, as different elements are known to be absorbed and used by bone for different physiological purposes such as growth and healing. These chemical signatures are beyond the detection limit of most laboratory-based analytical techniques (e.g. scanning electron microscopy). However, synchrotron rapid scanning-X-ray fluorescence (SRS-XRF) is an elemental mapping technique that uniquely combines high sensitivity (ppm), excellent sample resolution (20-100 µm) and the ability to scan large specimens (decimetre scale) approximately 3000 times faster than other mapping techniques. Here, we use SRS-XRF combined with microfocus elemental mapping (2-20 µm) to determine the distribution and concentration of trace elements within pathological and normal bone of both extant and extinct archosaurs (Cathartes aura and Allosaurus fragilis). Results reveal discrete chemical inventories within different bone tissue types and preservation modes. Chemical inventories also revealed detail of histological features not observable in thin section, including fine structures within the interface between pathological and normal bone as well as woven texture within pathological tissue.
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Intra-trackway morphological variations due to substrate consistency: the El Frontal dinosaur tracksite (Lower Cretaceous, Spain).
PLoS ONE
PUBLISHED: 01-01-2014
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An ichnological and sedimentological study of the El Frontal dinosaur tracksite (Early Cretaceous, Cameros basin, Soria, Spain) highlights the pronounced intra-trackway variation found in track morphologies of four theropod trackways. Photogrammetric 3D digital models revealed various and distinct intra-trackway morphotypes, which reflect changes in footprint parameters such as the pace length, the track length, depth, and height of displacement rims. Sedimentological analyses suggest that the original substrate was non-homogenous due to lateral changes in adjoining microfacies. Multidata analyses indicate that morphological differences in these deep and shallow tracks represent a part of a continuum of track morphologies and geometries produced by a gradient of substrate consistencies across the site. This implies that the large range of track morphologies at this site resulted from similar trackmakers crossing variable facies. The trackways at the El Frontal site present an exemplary case of how track morphology, and consequently potential ichnotaxa, can vary, even when produced by a single trackmaker.
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Finite element modelling versus classic beam theory: comparing methods for stress estimation in a morphologically diverse sample of vertebrate long bones.
J R Soc Interface
PUBLISHED: 05-02-2013
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Classic beam theory is frequently used in biomechanics to model the stress behaviour of vertebrate long bones, particularly when creating intraspecific scaling models. Although methodologically straightforward, classic beam theory requires complex irregular bones to be approximated as slender beams, and the errors associated with simplifying complex organic structures to such an extent are unknown. Alternative approaches, such as finite element analysis (FEA), while much more time-consuming to perform, require no such assumptions. This study compares the results obtained using classic beam theory with those from FEA to quantify the beam theory errors and to provide recommendations about when a full FEA is essential for reasonable biomechanical predictions. High-resolution computed tomographic scans of eight vertebrate long bones were used to calculate diaphyseal stress owing to various loading regimes. Under compression, FEA values of minimum principal stress (?(min)) were on average 142 per cent (±28% s.e.) larger than those predicted by beam theory, with deviation between the two models correlated to shaft curvature (two-tailed p = 0.03, r(2) = 0.56). Under bending, FEA values of maximum principal stress (?(max)) and beam theory values differed on average by 12 per cent (±4% s.e.), with deviation between the models significantly correlated to cross-sectional asymmetry at midshaft (two-tailed p = 0.02, r(2) = 0.62). In torsion, assuming maximum stress values occurred at the location of minimum cortical thickness brought beam theory and FEA values closest in line, and in this case FEA values of ?(torsion) were on average 14 per cent (±5% s.e.) higher than beam theory. Therefore, FEA is the preferred modelling solution when estimates of absolute diaphyseal stress are required, although values calculated by beam theory for bending may be acceptable in some situations.
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The role of cross-sectional geometry, curvature, and limb posture in maintaining equal safety factors: a computed tomography study.
Anat Rec (Hoboken)
PUBLISHED: 02-05-2013
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The limb bones of an elephant are considered to experience similar peak locomotory stresses as a shrew. "Safety factors" are maintained across the entire range of body masses through a combination of robusticity of long bones, postural variation, and modification of gait. The relative contributions of these variables remain uncertain. To test the role of shape change, we undertook X-ray tomographic scans of the leg bones of 60 species of mammals and birds, and extracted geometric properties. The maximum resistible forces the bones could withstand before yield under compressive, bending, and torsional loads were calculated using standard engineering equations incorporating curvature. Positive allometric scaling of cross-sectional properties with body mass was insufficient to prevent negative allometry of bending (F(b) ) and torsional maximum force (F(t) ) (and hence decreasing safety factors) in mammalian (femur F(b) ?M(b) (0.76) , F(t) ?M(b) (0.80) ; tibia F(b) ?M(b) (0.80) , F(t) ?M(b) (0.76) ) and avian hindlimbs (tibiotarsus F(b) ?M(b) (0.88) , F(t) ?M(b) (0.89) ) with the exception of avian femoral F(b) and F(t) . The minimum angle from horizontal a bone must be held while maintaining a given safety factor under combined compressive and bending loads increases with M(b) , with the exception of the avian femur. Postural erectness is shown as an effective means of achieving stress similarity in mammals. The scaling behavior of the avian femur is discussed in light of unusual posture and kinematics.
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Manus track preservation bias as a key factor for assessing trackmaker identity and quadrupedalism in basal ornithopods.
PLoS ONE
PUBLISHED: 01-22-2013
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The Las Cerradicas site (Tithonian-Berriasian), Teruel, Spain, preserves at least seventeen dinosaur trackways, some of them formerly attributed to quadrupedal ornithopods, sauropods and theropods. The exposure of new track evidence allows a more detailed interpretation of the controversial tridactyl trackways as well as the modes of locomotion and taxonomic affinities of the trackmakers.
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Dynamic similarity in titanosaur sauropods: ichnological evidence from the Fumanya dinosaur tracksite (southern Pyrenees).
PLoS ONE
PUBLISHED: 01-21-2013
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The study of a small sauropod trackway from the Late Cretaceous Fumanya tracksite (southern Pyrenees, Catalonia) and further comparisons with larger trackways from the same locality suggest a causative relationship between gait, gauge, and body proportions of the respective titanosaur trackmakers. This analysis, conducted in the context of scaling predictions and using geometric similarity and dynamic similarity hypotheses, reveals similar Froude numbers and relative stride lengths for both small and large trackmakers from Fumanya. Evidence for geometric similarity in these trackways suggests that titanosaurs of different sizes moved in a dynamically similar way, probably using an amble gait. The wide gauge condition reported in trackways of small and large titanosaurs implies that they possessed similar body (trunk and limbs) proportions despite large differences in body size. These results strengthen the hypothesis that titanosaurs possessed a distinctive suite of anatomical characteristics that are well reflected in their tracks and trackways.
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Morphological and geochemical evidence of eumelanin preservation in the feathers of the Early Cretaceous bird, Gansus yumenensis.
PLoS ONE
PUBLISHED: 07-20-2011
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Recent studies have shown evidence for the preservation of colour in fossilized soft tissues by imaging melanosomes, melanin pigment containing organelles. This study combines geochemical analyses with morphological observations to investigate the preservation of melanosomes and melanin within feathers of the Early Cretaceous bird, Gansus yumenensis. Scanning electron microscopy reveals structures concordant with those previously identified as eumelanosomes within visually dark areas of the feathers but not in lighter areas or sedimentary matrices. Fourier transform infrared analyses show different spectra for the feathers and their matrices; melanic functional groups appear in the feather including carboxylic acid and ketone groups that are not seen in the matrix. When mapped, the carboxylic acid group absorption faithfully replicates the visually dark areas of the feathers. Electron Paramagnetic Resonance spectroscopy of one specimen demonstrates the presence of organic signals but proved too insensitive to resolve melanin. Pyrolysis gas chromatography mass spectrometry shows a similar distribution of aliphatic material within both feathers that are different from those of their respective matrices. In combination, these techniques strongly suggest that not only do the feathers contain endogenous organic material, but that both geochemical and morphological evidence supports the preservation of original eumelanic pigment residue.
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Pelvic and hindlimb myology of the basal Archosaur Poposaurus gracilis (Archosauria: Poposauroidea).
J. Morphol.
PUBLISHED: 05-10-2011
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The discovery of a largely complete and well preserved specimen of Poposaurus gracilis has provided the opportunity to generate the first phylogenetically based reconstruction of pelvic and hindlimb musculature of an extinct nondinosaurian archosaur. As in dinosaurs, multiple lineages of basal archosaurs convergently evolved parasagittally erect limbs. However, in contrast to the laterally projecting acetabulum, or "buttress erect" hip morphology of ornithodirans, basal archosaurs evolved a very different, ventrally projecting acetabulum, or "pillar erect" hip. Reconstruction of the pelvic and hindlimb musculotendinous system in a bipedal suchian archosaur clarifies how the anatomical transformations associated with the evolution of bipedalism in basal archosaurs differed from that of bipedal dinosaurs and birds. This reconstruction is based on the direct examination of the osteology and myology of phylogenetically relevant extant taxa in conjunction with osteological correlates from the skeleton of P. gracilis. This data set includes a series of inferences (presence/absence of a structure, number of components, and origin/insertion sites) regarding 26 individual muscles or muscle groups, three pelvic ligaments, and two connective tissue structures in the pelvis, hindlimb, and pes of P. gracilis. These data provide a foundation for subsequent examination of variation in myological orientation and function based on pelvic and hindlimb morphology, across the basal archosaur lineage leading to extant crocodilians.
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Biomechanics of dromaeosaurid dinosaur claws: application of X-ray microtomography, nanoindentation, and finite element analysis.
Anat Rec (Hoboken)
PUBLISHED: 08-28-2009
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Dromaeosaurid theropod dinosaurs, such as Velociraptor, possess strongly recurved, hypertrophied and hyperextensible ungual claws on the pes (digit II) and manus. The morphology of these unguals has been linked to the capture and despatching of prey. However, the mechanical properties or, more importantly, the mechanical potential of these structures have not been explored. Generation of a 3D finite element (FE) stress/strain contour map of a Velociraptor manual ungual has allowed us to evaluate quantitatively the mechanical behavior of a dromaeosaurid claw for the first time. An X-ray microtomography scan allowed construction of an accurate 3D FE mesh. Analogue material from an extant avian theropod, the pedal digit and claw of an eagle owl (Bubo bubo), was analyzed to provide input data for the Velociraptor claw FE model (FEM). The resultant FEM confirms that dromaeosaurid claws were well-adapted for climbing as they would have been resistant to forces acting in a single (longitudinal) plane, in this case due to gravity. However, the strength of the unguals was limited with respect to forces acting tangential to the long-axis of the claw. The tip of the claw functioned as the puncturing and gripping element of the structure, whereas the expanded proximal portion transferred the load stress through the trabeculae and cortical bone. Enhanced climbing abilities of dromaeosaurid dinosaurs supports a scansorial phase in the evolution of flight.
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Mineralized soft-tissue structure and chemistry in a mummified hadrosaur from the Hell Creek Formation, North Dakota (USA).
Proc. Biol. Sci.
PUBLISHED: 07-01-2009
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An extremely well-preserved dinosaur (Cf. Edmontosaurus sp.) found in the Hell Creek Formation (Upper Cretaceous, North Dakota) retains soft-tissue replacement structures and associated organic compounds. Mineral cements precipitated in the skin apparently follow original cell boundaries, partially preserving epidermis microstructure. Infrared and electron microprobe images of ossified tendon clearly show preserved mineral zonation, with silica and trapped carbon dioxide forming thin linings on Haversian canals within apatite. Furthermore, Fourier transform infrared spectroscopy (FTIR) of materials recovered from the skin and terminal ungual phalanx suggests the presence of compounds containing amide groups. Amino acid composition analyses of the mineralized skin envelope clearly differ from the surrounding matrix; however, intact proteins could not be obtained using protein mass spectrometry. The presence of endogenously derived organics from the skin was further demonstrated by pyrolysis gas chromatography mass spectrometry (Py-GCMS), indicating survival and presence of macromolecules that were in part aliphatic (see the electronic supplementary material).
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Estimating mass properties of dinosaurs using laser imaging and 3D computer modelling.
PLoS ONE
PUBLISHED: 01-13-2009
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Body mass reconstructions of extinct vertebrates are most robust when complete to near-complete skeletons allow the reconstruction of either physical or digital models. Digital models are most efficient in terms of time and cost, and provide the facility to infinitely modify model properties non-destructively, such that sensitivity analyses can be conducted to quantify the effect of the many unknown parameters involved in reconstructions of extinct animals. In this study we use laser scanning (LiDAR) and computer modelling methods to create a range of 3D mass models of five specimens of non-avian dinosaur; two near-complete specimens of Tyrannosaurus rex, the most complete specimens of Acrocanthosaurus atokensis and Strutiomimum sedens, and a near-complete skeleton of a sub-adult Edmontosaurus annectens. LiDAR scanning allows a full mounted skeleton to be imaged resulting in a detailed 3D model in which each bone retains its spatial position and articulation. This provides a high resolution skeletal framework around which the body cavity and internal organs such as lungs and air sacs can be reconstructed. This has allowed calculation of body segment masses, centres of mass and moments or inertia for each animal. However, any soft tissue reconstruction of an extinct taxon inevitably represents a best estimate model with an unknown level of accuracy. We have therefore conducted an extensive sensitivity analysis in which the volumes of body segments and respiratory organs were varied in an attempt to constrain the likely maximum plausible range of mass parameters for each animal. Our results provide wide ranges in actual mass and inertial values, emphasizing the high level of uncertainty inevitable in such reconstructions. However, our sensitivity analysis consistently places the centre of mass well below and in front of hip joint in each animal, regardless of the chosen combination of body and respiratory structure volumes. These results emphasize that future biomechanical assessments of extinct taxa should be preceded by a detailed investigation of the plausible range of mass properties, in which sensitivity analyses are used to identify a suite of possible values to be tested as inputs in analytical models.
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Chemical mapping of paleontological and archeological artifacts with synchrotron X-rays.
Annu Rev Anal Chem (Palo Alto Calif)
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The application of the recently developed synchrotron rapid scanning X-ray fluorescence (SRS-XRF) technique to the mapping of large objects is the focus of this review. We discuss the advantages of SRS-XRF over traditional systems and the use of other synchrotron radiation (SR) techniques to provide corroborating spectroscopic and diffraction analyses during the same analytical session. After reviewing routine techniques used to analyze precious specimens, we present several case studies that show how SR-based methods have been successfully applied in archeology and paleontology. For example, SRS-XRF imaging of a seventh-century Qur?n palimpsest and an overpainted original opera score from Luigi Cherubini is described. We also review the recent discovery of soft-tissue residue in fossils of Archaeopteryx and an ancient reptile, as well as work that has successfully resolved the remnants of pigment in Confuciusornis sanctus, a 120-million-year-old fossil of the oldest documented bird with a fully derived avian beak.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

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We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

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In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.