The evolution of cranial form and function in theropod dinosaurs: insights from geometric morphometrics

Theropod dinosaurs, an iconic clade of fossil species including Tyrannosaurus and Velociraptor, developed a great diversity of body size, skull form and feeding habits over their 160+ million year evolutionary history. Here, we utilize geometric morphometrics to study broad patterns in theropod skull shape variation and compare the distribution of taxa in cranial morphospace (form) to both phylogeny and quantitative metrics of biting behaviour (function). We find that theropod skulls primarily differ in relative anteroposterior length and snout depth and to a lesser extent in orbit size and depth of the cheek region, and oviraptorosaurs deviate most strongly from the "typical" and ancestral theropod morphologies. Noncarnivorous taxa generally fall out in distinct regions of morphospace and exhibit greater overall disparity than carnivorous taxa, whereas large-bodied carnivores independently converge on the same region of morphospace. The distribution of taxa in morphospace is strongly correlated with phylogeny but only weakly correlated with functional biting behaviour. These results imply that phylogeny, not biting function, was the major determinant of theropod skull shape.     

3D reconstruction of the pelvis from bi-planar radiography

3D personalized models are more and more requested for clinical and biomechanical studies. Techniques based on bi-planar X-rays present the advantage of a low radiation dose for the patient. However, up to now, such techniques have shown limited accuracy in the case of pelvis reconstruction. This study proposes and validates a method providing accurate 3D personalized model of the pelvis from bi-planar X-rays. The algorithm is based on the fast computation of an initial solution followed by local deformations based on 2D anatomical points and contours that are digitized in both radiographs. Results were close to CT-scan reconstructions (mean difference 1.6 mm and differences under 4.3 mm for 95% of the points). Moreover, 3D morphometry of the pelvis could be obtained with an accuracy of 5%. This technique provides 3D patient specific model with a low radiation dose.     

Pure moment testing for spinal biomechanics applications: fixed versus 3D floating ring cable-driven test designs

Pure moment testing has become a standard protocol for in vitro assessment of the effect of surgical techniques or devices on the bending rigidity of the spine. Of the methods used for pure moment testing, cable-driven set-ups are popular due to their low requirements and simple design. Fixed loading rings are traditionally used in conjunction with these cable-driven systems. However, the accuracy and validity of the loading conditions applied with fixed ring designs have raised some concern, and discrepancies have been found between intended and prescribed loading conditions for flexion-extension. This study extends this prior work to include lateral bending and axial torsion, and compares this fixed ring design with a novel "3D floating ring" design. A complete battery of multi-axial bending tests was conducted with both rings in multiple different configurations using an artificial lumbar spine. Applied moments were monitored and recorded by a multi-axial load cell at the base of the specimen. Results indicate that the fixed ring design deviates as much as 77% from intended moments and induces non-trivial shear forces (up to 18 N) when loaded to a non-destructive maximum of 4.5 Nm. The novel 3D floating ring design largely corrects the inherent errors in the fixed ring design by allowing additional directions of unconstrained motion and producing uniform loading conditions along the length of the specimen. In light of the results, it is suggested that the 3D floating ring set-up be used for future pure moment spine biomechanics applications using a cable-driven apparatus.     

Geometric morphometrics of the skull of various murid rodents (Mammalia, Rodentia): relation of the skull shape to the trophic specialization

Presented is a brief overview of basic principles and notions of geometric morphometrics, a new approach to quantitative analysis of shape variations. This approach is applied to analysis of variation of the skull shape in the sample of 18 muroid genera belonging to the families Cricetidae, Arvicolidae and Gerbillidae. The skull shape is described by landmarks, and skulls are compared by resistant fit and superimposition methods. Under consideration is relation of skull shape to the trophic specialization, to family belonging, and to body size. Axial skull reveals more conspicuous relation to each of the factor analyzed as compared to mandible. Zygomatic region and tooth raw are most differentiable, while change of auditory bulla is of secondary effect. Transition from omnivorous through granivorous to grass-eating specialization involves the same trend in each of the family studied in the case of axial skull but not of mandible. Most dependent of trophic specialization appeared to be shape of axial skull rather then of mandible. Arvicolines are most specific in respect to the skull shape. Shape to size relation, although rather slight, also involves the same zygomatic-dental region. The results obtained indicate probably that geometric morphometrics does reveal variations in the skull shape that are free of the size effect.     

Creating physical 3D stereolithograph models of brain and skull

The human brain and skull are three dimensional (3D) anatomical structures with complex surfaces. However, medical images are often two dimensional (2D) and provide incomplete visualization of structural morphology. To overcome this loss in dimension, we developed and validated a freely available, semi-automated pathway to build 3D virtual reality (VR) and hand-held, stereolithograph models. To evaluate whether surface visualization in 3D was more informative than in 2D, undergraduate students (n = 50) used the Gillespie scale to rate 3D VR and physical models of both a living patient-volunteer's brain and the skull of Phineas Gage, a historically famous railroad worker whose misfortune with a projectile tamping iron provided the first evidence of a structure-function relationship in brain. Using our processing pathway, we successfully fabricated human brain and skull replicas and validated that the stereolithograph model preserved the scale of the VR model. Based on the Gillespie ratings, students indicated that the biological utility and quality of visual information at the surface of VR and stereolithograph models were greater than the 2D images from which they were derived. The method we developed is useful to create VR and stereolithograph 3D models from medical images and can be used to model hard or soft tissue in living or preserved specimens. Compared to 2D images, VR and stereolithograph models provide an extra dimension that enhances both the quality of visual information and utility of surface visualization in neuroscience and medicine.     

Two different template replicators coexisting in the same protocell: stochastic simulation of an extended chemoton model

The simulation of complex biochemical systems, consisting of intertwined subsystems, is a challenging task in computational biology. The complex biochemical organization of the cell is effectively modeled by the minimal cell model called chemoton, proposed by Gánti. Since the chemoton is a system consisting of a large but fixed number of interacting molecular species, it can effectively be implemented in a process algebra-based language such as the BlenX programming language. The stochastic model behaves comparably to previous continuous deterministic models of the chemoton. Additionally to the well-known chemoton, we also implemented an extended version with two competing template cycles. The new insight from our study is that the coupling of reactions in the chemoton ensures that these templates coexist providing an alternative solution to Eigen's paradox. Our technical innovation involves the introduction of a two-state switch to control cell growth and division, thus providing an example for hybrid methods in BlenX. Further developments to the BlenX language are suggested in the Appendix.     

3D electron microscopy of biological nanomachines: principles and applications

Transmission electron microscopy is a powerful technique for studying the three-dimensional (3D) structure of a wide range of biological specimens. Knowledge of this structure is crucial for fully understanding complex relationships among macromolecular complexes and organelles in living cells. In this paper, we present the principles and main application domains of 3D transmission electron microscopy in structural biology. Moreover, we survey current developments needed in this field, and discuss the close relationship of 3D transmission electron microscopy with other experimental techniques aimed at obtaining structural and dynamical information from the scale of whole living cells to atomic structure of macromolecular complexes. Presented at the joint biannual meeting of the SFB-GEIMM-GRIP, Anglet France, 14–19 October, 2006.     

ROC analysis: applications to the classification of biological sequences and 3D structures

ROC ('receiver operator characteristics') analysis is a visual as well as numerical method used for assessing the performance of classification algorithms, such as those used for predicting structures and functions from sequence data. This review summarizes the fundamental concepts of ROC analysis and the interpretation of results using examples of sequence and structure comparison. We overview the available programs and provide evaluation guidelines for genomic/proteomic data, with particular regard to applications to large and heterogeneous databases used in bioinformatics.     

Hawaiian craniofacial morphometrics: Average Mokapuan skull,artificial cranial deformation,and the “rocker” mandible

Craniofacial morphology and cultural cranial deformation were analyzed by the computer morphometric system in 79 adult Hawaiian skulls from Mokapu, Oahu. The average Hawaiian male was large, but similar in shape to the female. Both were larger than the present Caucasian, showed a greater dental protrusion, and possessed a larger ANB angle, flatter cranial base, and larger facial heights. Correlations in Hawaiian craniofacial structure were found between an increasing mandibular plane angle and (1) shorter posterior facial height, (2) larger gonial angle, (3) larger cranial base angle, and (4) smaller SNA and SNB angles. Of the 79 skulls studied, 8. 9% were found to have severe head molding or intentional cranial deformation. Significant statistical differences between the molded group and the nonmolded group are, in decreasing significance: (1) larger upper face height, (2) smaller glabella to occiput distance, and (3) increased lower face height with deformation. The morphometric differences were readily seen by graphic comparison between groups. It is postulated that external forces to the neurocranium result in redirection of the growth vectors in the neurocranial functional matrix, including the cranial base, and secondarily, to the orofacial functional matrix. There is a possibility that the cranial deformation is a retention of the normal birth molding changes. The Polynesian “rocker jaw” was found in 81% to 95% of this populace. This mandibular form occurs only with attainment of adult stature and craniofacial form. This data agrees with the hypothesis that mandibular form is modified by the physical forces present and their direction in the orofacial functional matrix.     

重庆晚侏罗世两处兽脚类足迹组合与四川盆地侏罗纪地层(英文)

重庆市已报道了4处侏罗纪的恐龙足迹点,包括下侏罗统珍珠冲组的大足化石点,该地点发现了中国迄今最古老的蜥脚类行迹;另外两处化石点(南岸和金鸡)的层位曾被视为中或上侏罗统,这里首次将其确认为上侏罗统上沙溪庙组;第4处化石点(成渝), 本文全部作者目前都未曾观察,这里不做描述。南岸化石点是南岸重庆足迹(Chongqingpus nananensis)模式标本的所在地,位于重庆市中心,曾发现过大量兽脚类足迹,如今已消逝在城市化进程中。幸运的是,这批标本被保存于重庆自然博物馆,本文作者曾前后两次对其进行研究,并得出文中的结论。南岸重庆足迹为中型足迹(平均长约29 cm), 最可能被卡岩塔足迹(Kayentapus)所囊括,这批标本中有一些保存着边界不清的拇趾迹。该化石点的其他足迹被归于似异样龙足迹(cf. Anomoepus)。其他较小的、来自重庆市周边中侏罗统中部的足迹此前已被归于跷脚龙足迹(Grallator)。金鸡化石点保存了一条孤立的兽脚类行迹,因其粗壮的特征而被暂时归于似窄足龙足迹(cf. Therangospodus)。金鸡点的行迹也保存了非连续出现的拇趾迹。虽然重庆市和四川盆地及其周边更广泛地区之侏罗纪地层发现的兽脚类足迹日渐增多,但要明确其确切地质年龄及有效的足迹分类依然需要进一步工作。这是因为侏罗纪的恐龙足迹尽管丰富,但显示出连续变化的形态学特征,而保存状况的变化更使其难以在时间与空间上做出定义与鉴别。     

Morphology and morphometrics of the appendicular musculature in geckoes with different locomotor habits (Lepidosauria)

 In this study a ground-dwelling (Eublepharis macularius) and a highly specialised climbing (Gekko gecko) lizard were chosen as study objects. The fore- and hindlimbs of two individuals of each species were dissected, and muscle masses, mean fibre lengths, cross-sectional areas and moment arms were determined. Special attention was paid to general muscle architecture (origin, insertion, fibre orientation, etc.) and pennation angles. Using these variables (cross sectional areas and moment arms), maximal moments exertable across the shoulder/hip, elbow/knee and wrist/ankle were calculated for both species. In accordance with the biomechanical predictions related to the preferred locomotor substrate of each species (i.e. level running for E. macularius and climbing for G. gecko), the results of this study indicate that climbers such as G. gecko generally possess powerful retractor muscles crossing the shoulder and hip joints. Additionally, the specialised climber is able to exert higher flexion moments across the elbow, which prevents the animals from falling backwards. However, G. gecko appears to be constrained in its ankle extension capabilities by the presence of the adhesive toe pads. The level-running species, on the other hand, shows a relatively stronger development of the extensor muscles in the lower limbs, allowing these lizards to run in an erect posture. In general, both species show large similarities on a gross morphological level as expected when considering their phylogenetic relatedness. Adaptations to their preferred locomotor substrate only become apparent when considering the functional properties (i.e. joint moments) of the appendicular musculature. Accepted: 30 November 1998     

Synthesis and biological activity of 3 beta-fluorovitamin D3: comparison of the biological activity of 3 beta-fluorovitamin D3 and 3-deoxyvitamin D3

The alteration in the biologic activity of the vitamin D3 molecule resulting from the replacement of a hydrogen atom with a fluorine atom is a subject of fundamental interest. To investigate this problem we synthesized 3 beta-fluorovitamin D3 6 and its hydrogen analog, 3-deoxyvitamin D3 7, and tested the biologic activity of each by in vitro and in vivo methods. Contrary to previous reports which showed that 3 beta-fluorovitamin D3 was as active as vitamin D3 in vivo, we found that the fluoro-analog was less active than vitamin D3. With regard to stimulation of intestinal calcium transport and bone calcium mobilization in the D-deficient hypocalcemic rat, 3 beta-fluorovitamin D3 showed significantly greater biologic activity than its hydrogen analog, 3-deoxyvitamin D3. In the organ-cultured, embryonic chick duodenum, 3 beta-fluorovitamin D3 was approx 1/1000th as active as the native hormone, 1,25-dihydroxyvitamin D3, while 3-deoxyvitamin D3 was inactive even at microM concentrations, in the induction of the vitamin D-dependent, calcium-binding protein. With regard to in vitro activity in displacing radiolabeled 25-hydroxyvitamin D3 from vitamin D binding protein and radiolabelled 1,25-dihydroxyvitamin D3 from a chick intestinal cytosol receptor, 3 beta-fluorovitamin D3 and 3 beta-deoxyvitamin D3 both showed very poor binding efficiencies when compared with vitamin D3. Our results show that the substitution of a fluorine atom for a hydrogen atom at the C-3 position of the vitamin D3 molecule results in a fluorovitamin 6 with significantly more biological activity than its hydrogen analog, 3-deoxyvitamin D3 7.     

The recent development and applications of fluidic channels by 3D printing

The technology of “Lab-on-a-Chip” allows the synthesis and analysis of chemicals and biological substance within a portable or handheld device. The 3D printed structures enable precise control of various geometries. The combination of these two technologies in recent years makes a significant progress. The current approaches of 3D printing, such as stereolithography, polyjet, and fused deposition modeling, are introduced. Their manufacture specifications, such as surface roughness, resolution, replication fidelity, cost, and fabrication time, are compared with each other. Finally, novel application of 3D printed channel in biology are reviewed, including pathogenic bacteria detection using magnetic nanoparticle clusters in a helical microchannel, cell stimulation by 3D chemical gradients, perfused functional vascular channels, 3D tissue construct, organ-on-a-chip, and miniaturized fluidic “reactionware” devices for chemical syntheses. Overall, the 3D printed fluidic chip is becoming a powerful tool in the both medical and chemical industries.     

Frequency of interspecific mating in salamanders of the plethodontid genus Desmognathus: different experimental designs may yield different results

Heterosexual courtship trials were staged between dusky salamanders of two species ( Desmognathus fuscus and D. santeetlah ) from two allopatric populations in the southern Appalachian Mountains of eastern North America. Two experiments were conducted in order to test for effects of experimental design on estimates of the strength of sexual isolation between these species. In Experiment 1, frequencies of interspecific mating were determined when: (1) a male was presented with a conspecific and a heterotypic female successively; and (2) both types of females were presented simultaneously to a male. The frequency of interspecific mating by male D. fuscus was greatest when females were presented successively. The frequency of interspecific mating by male D. santeetlah was not influenced by method of female presentation. An index of sexual isolation of +0.29 was obtained between D. fuscus and D. santeetlah when females were presented successively, and of +0.63 when females were presented simultaneously. In Experiment 2, interspecific mating frequencies were determined in courtship arenas of two different sizes. No significant effect of arena size on frequency of interspecific mating was found for D. fuscus. In D. santeetlah , a trend towards greater mating frequency in small arenas was almost significant. These results suggest that interspecific mating frequencies (and thus estimates of the strength of sexual isolation between populations or species) may be sensitive to the experimental design employed. The validity and generality of this conclusion for other animals is an urgent, empirical issue.     

Two mcm3 mutations affect different steps in the initiation of DNA replication

Mcm3 is a subunit of the hexameric MCM2-7 complex required for the initiation and elongation of DNA replication in eukaryotes. We have characterized two mutant alleles, mcm3-1 and mcm3-10, in Saccharomyces cerevisiae and showed that they are defective at different steps of the replication initiation process. Mcm3-10 contains a P118L substitution that compromises its interaction with Mcm5 and the recruitment of Mcm3 and Mcm7 to a replication origin. P118 is conserved between Mcm3, Mcm4, Mcm5, and Mcm7. An identical substitution of this conserved residue in Mcm5 (P83L of mcm5-bob1) strengthens the interaction between Mcm3 and Mcm5 and allows cells to enter S phase independent of Cdc7-Dbf4 kinase (Hardy, C. F., Dryga, O., Pahl, P. M. B., and Sclafani, R. A. (1997) Proc. Natl. Acad. Sci. U. S. A. 94, 3151-3155). Mcm3-1 contains a G246E mutation that diminishes the efficiency of replication initiation (Yan, H., Merchant, A. M., and Tye, B. K. (1993) Genes Dev. 7, 2149-2160) but not its interaction with Mcm5 or recruitment of the MCM2-7 complex to replication origin. These observations indicate that Mcm3-10 is defective in a step before, and Mcm3-1 is defective in a step after the recruitment of the MCM2-7 complex to replication origins.     

Biodiversity and evolution in the light of morphometrics: From patterns to processes

Disparity (shape diversity) is a key aspect of biodiversity, both present and past. The shapes of organisms are usually quantified by means of morphometrics. In this article, after a short review of recent advances and applications of morphometric methods, examples are presented as an overview of morphometric studies undertaken at the Biogéosciences research unit of Burgundy University. They concern both works on shape differentiation and evolution of disparity through time, and work aiming to infer, from the shapes of the organisms, any developmental stresses, constraints or processes which could explain in part the resulting disparity. The objective is to demonstrate how useful morphometrics can be for research in evolutionary and developmental biology.     

Refocusing revisited: An optimized,gradient-enhanced refocused HSQC and its applications in 2D and 3D NMR and in deuterium exchange experiments

Summary 2D ¹⁵N-¹H correlation spectra are ideal for measuring backbone amide populations to determine amide exchange protection factors in studies of protein folding or other structural features. Most protein NMR spectroscopists use HSQC, which has been shown to be generally superior to HMQC in both resolution and sensitivity. The refocused HSQC experiment is intrinsically less sensitive than the regular HSQC, due to T₂ relaxation during the refocusing delays. However, we show here that, when high ¹⁵N resolution is needed, an optimized refocused HSQC sequence that utilizes a semi-constant time evolution period and pulsed field gradients has better signal-to-noise ratio and resolution, and integrates more accurately, than a similar HSQC. The differences are demonstrated on a 20 kDa protein. The technique can also be applied to 3D NOESY experiments to eliminate strong NH₂ geminal peaks and their truncation artefacts at a modest cost in sensitivity.     

East Greenland and Barents Sea polar bears (Ursus maritimus): adaptive variation between two populations using skull morphometrics as an indicator of environmental and genetic differences

A morphometric study was conducted on four skull traits of 37 male and 18 female adult East Greenland polar bears (Ursus maritimus) collected 1892-1968, and on 54 male and 44 female adult Barents Sea polar bears collected 1950-1969. The aim was to compare differences in size and shape of the bear skulls using a multivariate approach, characterizing the variation between the two populations using morphometric traits as an indicator of environmental and genetic differences. Mixture analysis testing for geographic differentiation within each population revealed three clusters for Barents Sea males and three clusters for Barents Sea females. East Greenland consisted of one female and one male cluster. A principal component analysis (PCA) conducted on the clusters defined by the mixture analysis, showed that East Greenland and Barents Sea polar bear populations overlapped to a large degree, especially with regards to females. Multivariate analyses of variance (MANOVA) showed no significant differences in morphometric means between the two populations, but differences were detected between clusters from each respective geographic locality. To estimate the importance of genetics and environment in the morphometric differences between the bears, a PCA was performed on the covariance matrix derived from the skull measurements. Skull trait size (PC1) explained approx. 80% of the morphometric variation, whereas shape (PC2) defined approx. 15%, indicating some genetic differentiation. Hence, both environmental and genetic factors seem to have contributed to the observed skull differences between the two populations. Overall, results indicate that many Barents Sea polar bears are morphometrically similar to the East Greenland ones, suggesting an exchange of individuals between the two populations. Furthermore, a subpopulation structure in the Barents Sea population was also indicated from the present analyses, which should be considered with regards to future management decisions.