Role of development in the evolution of the scapula of the giant sthenurine kangaroos (Macropodidae: Sthenurinae)

Extinct giant sthenurine kangaroos possessed scapulae morphologically distinct from those of all other extant and extinct adult macropodids, but qualitatively resembling those of newborn macropodids. The similarity between adult sthenurine and neonatal macropodid scapulae suggests that a developmental process, such as heterochrony, might have been behind the evolution of the unique sthenurine scapular morphology. By incorporating adult and ontogenetic data, this study examines the evolution and development of the sthenurine scapula. This study quantitatively upholds the previous qualitative morphological observations of macropodid scapulae and finds that ontogenetic and evolutionary morphological changes are correlated in macropodids. The similarity of scapula morphology in sthenurines and newborn macropodids, the correlation between ontogenetic and evolutionary morphological change, and information from other sources (i.e., sthenurine evolutionary history) suggests that pedomorphic shifts in morphology, most likely due to neotenic processes, occurred within the development of the scapula of giant sthenurines.     

Transformation methods for estimation of subject-specific scapular muscle attachment sites

The parameters that describe the soft tissue structures are among the most important anatomical parameters for subject-specific biomechanical modelling. In this paper, we study one of the soft tissue parameters, namely muscle attachment sites. Two new methods are proposed for transformation of the muscle attachment sites of any reference scapula to any destination scapula based on four palpable bony landmarks. The proposed methods as well as one previously proposed method have been applied for transformation of muscle attachment sites of one reference scapula to seven other scapulae. The transformation errors are compared among the three methods. Both proposed methods yield significantly less (p < 0.05) prediction error as compared to the currently available method. Furthermore, we investigate whether there exists a reference scapula that performs significantly better than other scapulae when used for transformation of muscle attachment sites. Seven different scapulae were used as reference scapula and their resulting transformation errors were compared with each other. In the considered statistical population, no such a thing as an ideal scapula was found. There was, however, one outlier scapula that performed significantly worse than the other scapulae when used as a reference. The effect of perturbations in both muscle attachment sites and other muscle properties is studied by comparing muscle force predictions of a musculoskeletal model between perturbed and non-perturbed versions of the model. It is found that 10 mm variations in muscle attachments have more significant effect on muscle force predictions than 10% variations in any of the other four analysed muscle properties.     

中国人肩胛骨的观察

对西安地区收集的202副(男115,女87)中国成年人肩胛骨进行了观察。中国人肩胛冈可分五型,肩胛骨脊柱缘的形状与种族和性别有关。     

Brief communication: Morphological effects of captivity: A geometric morphometric analysis of the dorsal side of the scapula in captive‐bred and wild‐caught hominoidea

Many osteological collections from museums and research institutions consist mainly of remains from captive‐bred animals. The restrictions related to the space of their enclosures and the nature of its substrate are likely to affect the locomotor and postural behaviors of captive‐bred animals, which are widely considered uninformative regarding bone morphology and anatomical adaptations of wild animals, especially so in the case of extant great apes. We made a landmark‐based geometric morphometrics analysis of the dorsal side of the scapular bone of both wild‐caught and captive‐bred great apes to clarify the effect of captivity on the morphology of a bone greatly involved in locomotion. The comparison suggested that captivity did not have a significant effect on the landmark configuration used, neither on average scapular shape nor shape variability, being impossible to distinguish the scapulae of a captive‐bred animal from that of a wild‐caught one. This indicates that the analyzed scapulae from captive Hominoidea specimens may be used in morphological or taxonomic analyses since they show no atypical morphological traits caused by living conditions in captivity. Am J Phys Anthropol 152:306–310, 2013. © 2013 Wiley Periodicals, Inc.     

Morphometric study of the fetal development of the human hip joint: significance for congenital hip disease.

Hip joints (280) from 140 human fetuses, obtained from abortions and deaths in the perinatal period, were studied. The fetuses ranged from 8.7 to 40 cm in crown-rump length and are believed to be between 12 and 42 weeks in age. The joints were dissected, morphology inspected, and measurements taken of the depth and diameter of the acetabulum, the diameter of the femoral head, length and width of the ligament of the head, the neck-shaft, and torsion angles of the proximal femur. Regression models were fitted to determine which would best predict the growth pattern. Multivariate analysis of variance showed no significant differences between males and females or between the right and left sides. Acetabular depth was shown to be the slowest-growing hip variable, increasing less than fourfold in the period studied. Acetabular indices less than 50 percent indicate a shallow socket at term. Femoral head and acetabular diameter demonstrated a strong relationship (r = 0.860) and in many joints the femoral head diameter exceeded that of the acetabulum. Considerable variability was demonstrated in both femoral angles. The femoral angles showed only low correlation with the other hip variables. These observations indicate that soft tissue structures about the joint must play an important role in neonatal joint stability. The explanation of greater female and left side involvement in congenital hip disease must lie in factors other than growth changes of hip dimensions. Neither angle appears to be a useful indicator of normal joint development.     

Statistical and conformational analysis of the electron density of protein side chains

Protein side chains make most of the specific contacts between proteins and other molecules, and their conformational properties have been studied for many years. These properties have been analyzed primarily in the form of rotamer libraries, which cluster the observed conformations into groups and provide frequencies and average dihedral angles for these groups. In recent years, these libraries have improved with higher resolution structures and using various criteria such as high thermal factors to eliminate side chains that may be misplaced within the crystallographic model coordinates. Many of these side chains have highly non-rotameric dihedral angles. The origin of side chains with high B-factors and/or with non-rotameric dihedral angles is of interest in the determination of protein structures and in assessing the prediction of side chain conformations. In this paper, using a statistical analysis of the electron density of a large set of proteins, it is shown that: (1) most non-rotameric side chains have low electron density compared to rotameric side chains; (2) up to 15% of chi1 non-rotameric side chains in PDB models can clearly be fit to density at a single rotameric conformation and in some cases multiple rotameric conformations; (3) a further 47% of non-rotameric side chains have highly dispersed electron density, indicating potentially interconverting rotameric conformations; (4) the entropy of these side chains is close to that of side chains annotated as having more than one chi(1) rotamer in the crystallographic model; (5) many rotameric side chains with high entropy clearly show multiple conformations that are not annotated in the crystallographic model. These results indicate that modeling of side chains alternating between rotamers in the electron density is important and needs further improvement, both in structure determination and in structure prediction.     

Control for small-speed lateral flight in a model insect

Controls required for small-speed lateral flight of a model insect were studied using techniques based on the linear theories of stability and control (the stability and control derivatives were computed by the method of computational fluid dynamics). The main results are as follows. (1) Two steady-state lateral motions can exist: one is a horizontal side translation with the body rolling to the same side of the translation by a small angle, and the other is a constant-rate yaw rotation (rotation about the vertical axis). (2) The side translation requires an anti-symmetrical change in the stroke amplitudes of the contralateral wings, and/or an anti-symmetrical change in the angles of attack of the contralateral wings, with the down- and upstroke angles of attack of a wing having equal change. The constant-rate yaw rotation requires an anti-symmetrical change in the angles of attack of the contralateral wings, with the down- and upstroke angles of attack of a wing having differential change. (3) For the control of the horizontal side translation, control input required for the steady-state motion has an opposite sign to that needed for initiating the motion. For example, to have a steady-state left side-translation, the insect needs to increase the stroke amplitude of the left wing and decrease that of the right wing to maintain the steady-state flight, but it needs an opposite change in stroke amplitude (decreasing the stroke amplitude of the left wing and increasing that of the right wing) to enter the flight.     

Histochemical studies on the amphibian opercularis muscle (Amphibia)

Summary Histochemical studies of the opercularis muscle of the bullfrog (Rana catesbeiana) and the tiger salamander (Ambystoma tigrinum) provide evidence that the opercularis muscle of anurans is a specialized, tonic portion of the levator scapulae superior muscle. Staining results for myosin adenosine triphosphatase (ATPase) and succinate dehydrogenase (SDH), combined with measurements of muscle fiber diameters, demonstrate that the opercularis/levator scapulae superior muscle mass of both the tiger salamander and bullfrog consists of an anterior tonic portion, a middle fast oxidative-glycolytic (FOG) twitch portion, and a posterior fast-glycolytic (FG) twitch portion. In R. catesbeiana the tonic fibers represent 57.3% of the fiber total and (because they have relatively narrow diameters) about 29% of the cross-sectional area of the muscle mass, and form that part of the muscle (=opercularis muscle) that inserts on the operculum. In Ambystoma the tonic fibers represent only 8.8% of the fiber total and represent about 4% of the cross-sectional area. In the tiger salamander, the entire levator scapulae superior muscle inserts on the operculum and therefore represents the opercularis muscle. The bullfrog differs from the tiger salamander, therefore, in that the anterior tonic part of the opercularis/levator scapulae superior complex is greatly enlarged and the insertion on the operculum is limited to these tonic fibers. No evidence of a columellar muscle was found in R. catesbeiana. Previous reports of one in this species and in other anurans may be based on the tripartite nature of the opercularis/levator scapulae superior muscle mass. The middle FOG portion of the muscle may have been considered a muscle distinct from the anterior tonic portion (=opercularis muscle) and the posterior FG portion.     

Anthropometric studies of the long bones of the "shell mound" Indians

The “shell mound” Indians exhibit both sexual and bilateral variations in comparative long bone lengths. Mean long bone lengths are shortest in the Indian group when compared to those reported for both Caucasians and Negroes. The radiohumeral and humero-femoral indices of the “shell mound” Indians are higher than those reported for either Caucasians or Negroes. There is a relatively high degree of anterior-posterior curvature of the femur in the Indian group when compared to the femora of Caucasian and Negroes. There is apparently no correlation between maximum femoral length and trochanter length in comparing right and left sides in either sex. The collo-diaphyseal angles are greater on the average on the left side in both sexes. The femora of male “shell mound” Indians exhibits greater average collo-diaphyseal angles than do the femora of male Caucasians.     

The mobility of the side chains of His57 and other amino acid residues in the active center of chymotrypsin

Using the "hard-sphere" atom-atom approximation with consideration of the available X-ray data, the possibility of free rotation of the side chain of His57 residue in the active center of chymotrypsin was studied. It was shown that there is a significant rotational freedom of the imidazole ring on chi1 and chi2 torsional angles. The rotation is accompanied by the movement of the side chains of Tyr94, Ile99 and Ser195 residues. It was assumed that the four residues act as movable parts of the motor of the enzymatic machinery. Amino acid residues that contact the cavity around the His57 imidazole ring were identified.     

Theoretical conformational analysis of methylamide N-acetyl-L-arginine]

The spatial structure of methylamide N-acetyl-L-argine was studied taking into account the non-valent and electrostati interactions, the torsion energy, and the distorsion of valency angles. Calculation of the favourable conformations of the molecule was carried out with the use of all the combinations of angles phi, psi, chi1 divided by chi4 as an intital approximation. These correspond to the low energy forms of the main chain and to the minima of the torsion potentials of the side chain. Conformational possibilities of arginine and lysine were compared. The calculated stable conformation of N-acetyl-L-arginine-methylamide are compared with the geometry of arginine residues in the proteins with known structure.     

Rotamer libraries and probabilities of transition between rotamers for the side chains in protein-protein binding

Conformational changes in the side chains are essential for protein-protein binding. Rotameric states and unbound- to-bound conformational changes in the surface residues were systematically studied on a representative set of protein complexes. The side-chain conformations were mapped onto dihedral angles space. The variable threshold algorithm was developed to cluster the dihedral angle distributions and to derive rotamers, defined as the most probable conformation in a cluster. Six rotamer libraries were generated: full surface, surface noninterface, and surface interface-each for bound and unbound states. The libraries were used to calculate the probabilities of the rotamer transitions upon binding. The stability of amino acids was quantified based on the transition maps. The noninterface residues' stability was higher than that of the interface. Long side chains with three or four dihedral angles were less stable than the shorter ones. The transitions between the rotamers at the interface occurred more frequently than on the noninterface surface. Most side chains changed conformation within the same rotamer or moved to an adjacent rotamer. The highest percentage of the transitions was observed primarily between the two most occupied rotamers. The probability of the transition between rotamers increased with the decrease of the rotamer stability. The analysis revealed characteristics of the surface side-chain conformational transitions that can be utilized in flexible docking protocols.     

Determination of local conformation of proteins from 1H-NMR spectroscopy data

A method is proposed to determine conformations of amino acid residues of the protein and effective correlation time tau c from cross-peak intensities in two-dimensional nuclear Overhauser enhancement (NOESY) spectra. The method consists in fitting complete relaxation matrix of dipeptide unit protons to experimental cross-peak intensities by varying phi, psi, chi torsional angles and tau c. To verify the method, NOESY spectra of basic pancreatic trypsin inhibitor (BPTI) were theoretically generated at mixing times tau m = 25-300 ms and tau c = 4 ns and used for local structure determination. The method works well with optimum for measurement of NOE intensities tau m 100-200 ms. As a result, the backbone phi, psi torsion angles were unambiguously determined at tau m = 100 ms for all but Gly residues of BPTI, and chi 1 angles were determined for the majority of side chains. The obtained dipeptide unit conformations are very close to the BPTI crystallographic structure: root mean square deviation (RMSD) of interproton distances within dipeptide units, on the average, is 0.08 A (maximal deviation 0.44 A), and RMSD of phi and psi angles are 18 and 9 degrees, respectively (maximal deviations are 44 and 22 degrees).     

Serine and threonine residues bend alpha-helices in the chi(1) = g(-) conformation

The relationship between the Ser, Thr, and Cys side-chain conformation (chi(1) = g(-), t, g(+)) and the main-chain conformation (phi and psi angles) has been studied in a selection of protein structures that contain alpha-helices. The statistical results show that the g(-) conformation of both Ser and Thr residues decreases their phi angles and increases their psi angles relative to Ala, used as a control. The additional hydrogen bond formed between the O(gamma) atom of Ser and Thr and the i-3 or i-4 peptide carbonyl oxygen induces or stabilizes a bending angle in the helix 3-4 degrees larger than for Ala. This is of particular significance for membrane proteins. Incorporation of this small bending angle in the transmembrane alpha-helix at one side of the cell membrane results in a significant displacement of the residues located at the other side of the membrane. We hypothesize that local alterations of the rotamer configurations of these Ser and Thr residues may result in significant conformational changes across transmembrane helices, and thus participate in the molecular mechanisms underlying transmembrane signaling. This finding has provided the structural basis to understand the experimentally observed influence of Ser residues on the conformational equilibrium between inactive and active states of the receptor, in the neurotransmitter subfamily of G protein-coupled receptors.     

Electromyography of the opercularis muscle of Rana catesbeiana: An amphibian tonic muscle

The opercularis muscle of Rana catesbeiana originates on the suprascapular cartilage of the shoulder girdle and inserts on the otic opercular element. It is part of the levator scapulae musculature and lies dorsomedial to the levator scapulae superior and inferior muscles. Bipolar electrode recordings from all three muscles show electrical activity linked to cyclical firing of the posterior intermandibularis muscle, an important ventilatory muscle. The opercularis muscle shows low amplitude, erratic signals when animals are sumerged. Upon emergence of the snout region, the opercularis muscle shows rhythmic low amplitude activity at twice the rate of buccal pumping. Lung ventilation is synchronized with this rhythm and at ventilation the opercularis muscle shows higher amplitude activity. Upon submergence, opercularis activity again shows low level activity with no rhythmic pattern. Opercularis muscle activity has a major low frequency component (about 30 Hz) that probably corresponds to activity of tonic muscle fibers. Higher frequency signals (about 200–250 Hz) comparable to those of the levator scapulae muscles are also present and probably represent activity of phasic muscle fibers. Activity of the opercularis muscle is correlated with conditions in which aerial respiration is possible, and this pattern of activity supports an opercularis role in aerial hearing and/or detection of substrate vibrations. As far as we know, this is the first report of electromyographic analysis of a vertebrate tonic muscle.     

Influence of glenohumeral mismatch on bone strains and implant displacements in implanted glenoïds. An in vitro experimental study on cadaveric scapulae

In shoulder arthroplasty, there is no consensus about the ideal mismatch between a prosthetic humeral head and a glenoïd component. Thus, investigations into mismatch effects from a biomechanical point of view can be useful. The aim of this in vitro study was to help us understand mismatch influence on bone strains, translational forces in the joint and implant/bone displacements in implanted scapulae.

Five fresh cadaveric scapulae were implanted with a cemented keeled polyethylene implant. The lower part of the scapulae was embedded and the loadings were carried out using five metallic spheres simulating mismatches of 0, 2, 4, 5 and 6 mm. Loadings included a constant compressive preload of 392 N and an anterior, posterior, inferior and superior translation of 2.5 mm. We measured the transversal force necessary to produce the imposed translation, the strains at six locations around the peripheral cortex of the glenoïd using strain gages and the relative implant/bone displacements using CCD cameras.

Generally, the increase of mismatch reduced the translational forces, the strains around the glenoïd and, except for the anterior loading, the relative implant/bone displacements. Few and even no significant differences were observed when the mismatch varied from 0 to 2 mm; the number of significant differences increased when the mismatch varied from 0 to 4 mm and from 0 to 5 mm; the results obtained for a 0–6 mm variation in mismatch were comparable to those obtained for a 0–5 mm variation.

This study underlines that the mismatch has a significant effect on bone strains, relative implant/bone displacements and induced translational forces when a compressive preload and imposed translations were applied on implanted scapulae.     

Prediction of side chain orientations in proteins by statistical machine learning methods

We develop ways to predict the side chain orientations of residues within a protein structure by using several different statistical machine learning methods. Here side chain orientation of a given residue i is measured by an angle Omega(i) between the vector pointing from the center of the protein structure to the C(i)(alpha) atom and the vector pointing from the C(i)(alpha) atom to the center of its side chain atoms. To predict the Omega(i) angles, we construct statistical models by using several different methods such as general linear regression, a regression tree and bagging, a neural network, and a support vector machine. The root mean square errors for the different models range only from 36.67 to 37.60 degrees and the correlation coefficients are all between 30% and 34%. The performances of different models in the test set are, thus, quite similar, and show the relative predictive power of these models to be significant in comparison with random side chain orientations.     

Gravitropism of Primary Roots of Zea mays L. at Different Displacement Angles

Primary roots of Zea mays were oriented at various angles fromthe vertical ranging from 99° to 1° and their subsequentbending analysed from filmed records. The maximum rate of bendingand the time before bending commenced both varied two-fold,but showed no correlation with the initial angle of tip displacement.Roots orientated to small initial angles (< 40°) oftenovershot the vertical and proceeded to oscillate around thisorientation, whereas roots oriented to large initial angles(> 60°) often failed to achieve the vertical. Roots inthis latter group resumed bending after an indeterminate time,or did so immediately after a second displacement of their tip,showing that they were not intrinsically unable to bend. Theapparently spontaneous resumption of bending after a temporaryplagiogravitropic phase is suggested as being due to noise inthe graviperception system in the root cap. The tips of rootsgrowing vertically downwards showed oscillatory bending movementsup to 10° either side of vertical. This angle correspondsto the minimum angle of displacement which induces gravitropicbending. Only when roots were oriented 10-20° from verticaldid they begin unequivocally to show a gravitropism since atsuch angles the deflection of their tips exceeded that due totheir natural oscillation.Copyright 1993, 1999 Academic Press Gravitropism, roots, Zea mays     

Tag location and risk assessment for passive integrated transponder‐tagging passerines

Understanding changes in body temperature is central to several fields in biology, but determining these changes accurately without harming or restraining individuals can be challenging, particularly for small species. We tested first whether body temperature readings differed between passive integrated transponder (PIT) tags injected subcutaneously inter‐scapulae (i.e. solely through the skin) and intra‐peritoneally (through the skin and abdominal muscle wall) and, secondly, whether intra‐peritoneal tag injuries differed among three weight classes of passerines. We found no significant difference in body temperature readings between subcutaneous inter‐scapulae and intra‐peritoneal PIT‐tags, and observed that the intra‐peritoneal injection of PIT‐tags may cause adverse effects among smaller (<25 g) birds. Our findings suggest a reduced gradient between core and peripheral body temperature in small species, which to the best of our knowledge has not yet been quantified. We further show that the risk of detrimental injury was greatest in small species, and thus recommend implanting PIT‐tags subcutaneously between the scapulae for smaller birds.