Description and interpretation of interphalangeal lines in tetrapods

A previously unnoticed geometric pattern is present in the extremities of all tetrapods. Sets of straight and typically uninterrupted hinge lines pass through neighboring interphalangeal joints and across ungual tips. Four sets of these lines appear in basal polydactyl tetrapods, two medial sets, a transverse set and a lateral set. The two medial sets merge in primitive pentadactyl tetrapods. The resulting three line sets persist in later taxa, even when digits shrink and disappear. Primitively and typically the lines in each set are more or less parallel, but lines may converge, merge and shift as phalanges disappear or phalangeal proportions change. Confirming this geometric pattern, complex interphalangeal joint surfaces typically align with hinge lines and pad divisions parallel them. In addition, unguals rarely cross extensions of hinge lines and longer unguals may divert medially or laterally rather than cross them. Exceptions occur most commonly on ungual II. Line sets may exist because phalanges appear to flex and extend most efficiently in unison. Hinge line patterns appear to identify clades so they may, to a limited extent, be used taxonomically. Hinge lines also have predictive value in that missing phalanges, including unguals, can be reconstructed with confidence using hinge lines as size guides. Correct digit spread and metapodial configuration can also be determined in extinct taxa by seeking the appearance of continuous interphalangeal hinge lines in tested reconstructions.     

In defence of parallel interphalangeal lines

Virtually parallel lines can be drawn through the interphalangeal joints and across the ungual tips of every tetrapod manus or pes, including wings and flippers. Their presence indicates that phalanges operate in sets sharing common hinges, whether for walking (extension) or climbing (flexion). A recent paper has attempted to dismantle both the observation and utility of parallel interphalangeal lines. Here, I rebut those spurious arguments and report additional evidence.     

Terrestrial tetrapods and the end Permian event: A comparison of analyses

Previous analyses of changes in diversity of Permo‐Triassic tetrapods are reviewed and compared. Biases inherent in such studies which distort the picture of diversity change are discussed. A new analysis of change in generic diversity of the tetrapods of the Karoo Basin, South Africa is presented. Various factors which could bias the results, namely, inconsistent taxonomy, insensitive stratigraphy, area of exposure per time interval, and differing intensity of collecting are addressed and corrections made for them. The results of the new analysis are compared to those of previous ones. In particular it is noted that, contrary to the results of other studies, large decreases in generic number are recorded not once, but twice in the Late Permian sediments, the second occurring in sediments dating from well before the close of that Period. It is concluded that stratigraphic sensitivity is the most important biasing factor in the present analysis and the implications of this for other diversity studies, and for explanations of diversity change, are emphasized.     

Holocene footprints in Namibia: The influence of substrate on footprint variability

We report a Holocene human and animal footprint site from the Namib Sand Sea, south of Walvis Bay, Namibia. Using these data, we explore intratrail footprint variability associated with small variations in substrate properties using a “whole foot” analytical technique developed for the studies in human ichnology. We demonstrate high levels of intratrail variability as a result of variations in grain size, depositional moisture content, and the degree of sediment disturbance, all of which determine the bearing capacity of the substrate. The two principal trails were examined, which had consistent stride and step lengths, and as such variations in print typology were primarily controlled by substrate rather than locomotor mechanics. Footprint typology varies with bearing capacity such that firm substrates show limited impressions associated with areas of peak plantar pressure, whereas softer substrates are associated with deep prints with narrow heels and reduced medial longitudinal arches. Substrates of medium bearing capacity give displacement rims and proximal movement of sediment, which obscures the true form of the medial longitudinal arch. A simple conceptual model is offered which summarizes these conclusions and is presented as a basis for further investigation into the control of substrate on footprint typology. The method, model, and results presented here are essential in the interpretation of any sites of greater paleoanthropological significance, such as recently reported from Ileret (1.5 Ma, Kenya; Bennett et al.: Science 323 (2009) 1197–1201). Am J Phys Anthropol 151:265–279, 2013. © 2013 Wiley Periodicals, Inc.     

Limb‐bone histology of temnospondyls: implications for understanding the diversification of palaeoecologies and patterns of locomotion of Permo‐Triassic tetrapods

The locomotion of early tetrapods has long been a subject of great interest in the evolutionary history of vertebrates. However, we still do not have a precise understanding of the evolutionary radiation of their locomotory strategies. We present here the first palaeohistological study based on theoretical biomechanical considerations among a highly diversified group of early tetrapods, the temnospondyls. Based on the quantification of microanatomical and histological parameters in the humerus and femur of nine genera, this multivariate analysis provides new insights concerning the adaptations of temnospondyls to their palaeoenvironments during the Early Permian, and clearly after the Permo‐Triassic crisis. This study therefore presents a methodology that, if based on a bigger sample, could contribute towards a characterization of the behaviour of species during great evolutionary events.     

Crenulations of the hinge plate of pectinoideans

Checa, A.G., Esteban‐Delgado, F.J. and Salas, C. 2010. Crenulations of the hinge plate of pectinoideans. —Acta Zoologica (Stockholm) 92 : 344–354. Crenulations are a succession of micron‐sized elongated ridges and troughs with a general dorsoventral pseudo‐labyrinthine pattern that are present on the hinge plate of most pectinoideans. The crenulations of opposing valves are complementary and interpenetrate in a hinge‐like fashion. They are also imprinted in the dorsal mantle, although there is evidence that the mantle adheres only at the ridges, but not at the troughs. Those mantle areas that secrete the ridges contain cells that are richer in structures, indicating an active metabolism than those facing the troughs. Crenulations are formed because the dorsal mantle expands allometrically along the anteroposterior direction. The excess length is accommodated by creasing. Crenulations initiate at the anterior and posterior ends of the hinge plate as shallow spheruliths, which increase in height with time until the mantle on both sides detaches from the shell areas forming the neighbouring troughs. A contact differentiation of the mantle into actively and passively secreting bands follows. This genetic model explains the general pattern as well as the changes in the morphology of crenulations that occur during growth. Crenulations are secondary postlarval structures unrelated to the provinculum. Their presence in the earliest pectinoideans makes crenulations a plesiomorphic character of the group.     

CO2‐metabolism in early tetrapods revisited: inferences from osteological correlates of gills,skin and lung ventilation in the fossil record

One of the most important physiological changes during the conquest of land by vertebrates was the increasing reliance on lung breathing, with the concomitant decrease in importance of gill breathing. The main problem involved here was to cope with the excessive accumulation of CO₂ in the body and to avoid respiratory acidosis. In the past, several often mutually contradicting hypotheses of CO₂‐elimination via skin, lungs and gills in early tetrapods have been proposed, based on theoretical physiological considerations and comparison with extant air‐breathing fishes and amphibians. This study proposes a revised scenario of CO₂‐elimination in early tetrapods based on fossil evidence, that is recently identified osteological correlates of gills, skin structure and mode of lung ventilation. In stem tetrapods of the Devonian and Carboniferous, O₂‐uptake via the lungs by buccal pumping was decoupled from CO₂‐release via internal gills, and the rather gas‐impermeable skin played a minor role in gaseous exchange. The two main lineages of crown‐group tetrapods, the amphibian and amniote lineage, used different strategies of CO₂‐elimination. As in stem tetrapods, O₂‐uptake and CO₂‐release remained always largely decoupled in temnospondyls, which ventilated their lungs via buccal pumping and relied mainly on their internal gills for CO₂‐release. Temnospondyls were not able to reduce their internal gills before their skin became more gas permeable and their body size was reduced, to shift from internal gills to the skin as the major site of CO₂‐elimination, a pattern that is retained in most lissamphibians. In contrast, internal gills were lost very early in stem amniote evolution. This was associated with the evolution of the more effective aspiration pump that allowed the elimination of the bulk of CO₂ via the lungs, leading to a coupled O₂‐uptake and CO₂‐loss in stem amniotes and later in amniotes.     

铰链结构对抗菌肽生物活性的影响及在分子设计中的应用研究进展

铰链结构,又称铰链区或转角,是部分抗菌肽序列中存在的一种特殊结构。但目前抗菌肽结构的研究多集中于标准的α-螺旋和β-折叠二级结构,对于铰链结构及其作用总结较少。铰链结构对抗菌肽生物活性有重要影响,主要原因是铰链结构能够提高抗菌肽的结构灵活性,促进其对细菌细胞膜的破坏作用或与胞内作用靶点的结合效率,进而提高抗菌肽的抗菌活性。同时,降低的抗菌肽结构刚性,消减了抗菌肽对真核细胞的毒性。文中结合了笔者课题组相关工作,就铰链结构特点、对抗菌肽生物活性的影响以及在抗菌肽分子设计方面的应用进行了综述,以期为新型抗菌肽的设计和开发提供参考。     

Thermal physiology and the origin of terrestriality in vertebrates

The adaptive reasons for the evolutionary transition between obligatorily aquatic lobe-finned fish and facultatively terrestrial early tetrapods have long been debated. The oldest adequately known amphibians, Acanthostega and Ichthyostega , from the final stage in the Upper Devonian (Famennian), can be clearly distinguished from the most advanced choanate sarcopterygian fish from the next older stage (Frasnian) by the presence of large pectoral and pelvic girdles, limbs generally resembling those of later Palaeozoic land vertebrates, and the absence of bones linking the back of the skull with the shoulder girdle. Upper Devonian and most Lower Carboniferous amphibians, like their aquatic predecessors, differed significantly from modern amphibians in their much larger size, up to a metre or more in length. Animals of this size, resembling modern crocodiles and the marine iguana, could have raised their body temperatures by basking in the sun and sustained them upon re-entry into the water. It is hypothesized that the physiological advantages of thermoregulation were a major selective force that resulted in the increasing capacity for the ancestors of tetrapods to move into shallow water, and later to support their bodies against the force of gravity and increase the size and locomotor capacities of the limbs.  © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society , 2005, 143 , 345–358.     

Crystal structure of the E. coli dipeptidyl carboxypeptidase Dcp: further indication of a ligand-dependent hinge movement mechanism

Dcp from Escherichia coli is a 680 residue cytoplasmic peptidase, which shows a strict dipeptidyl carboxypeptidase activity. Although Dcp had been assigned to the angiotensin I-converting enzymes (ACE) due to blockage by typical ACE inhibitors, it is currently grouped into the M3 family of mono zinc peptidases, which also contains the endopeptidases neurolysin and thimet oligopeptidase (TOP). We have cloned, expressed, purified, and crystallized Dcp in the presence of an octapeptide "inhibitor", and have determined its 2.0A crystal structure using MAD methods. The analysis revealed that Dcp consists of two half shell-like subdomains, which enclose an almost closed two-chamber cavity. In this cavity, two dipeptide products presumably generated by Dcp cleavage of the octapeptide bind to the thermolysin-like active site fixed to side-chains, which are provided by both subdomains. In particular, an Arg side-chain backed by a Glu residue, together with two Tyr phenolic groups provide a charged anchor for fixing the C-terminal carboxylate group of the P2' residue of a bound substrate, explaining the strict dipeptidyl carboxypeptidase specificity of Dcp. Tetrapeptidic substrates are fixed only via their main-chain functions from P2 to P2', suggesting a broad residue specificity for Dcp. Both subdomains exhibit very similar chain folds as the equivalent but abducted subdomains of neurolysin and TOP. Therefore, this "product-bound" Dcp structure seems to represent the inhibitor/substrate-bound "closed" form of the M3 peptidases, generated from the free "open" substrate-accessible form by a hinge-bending mechanism. A similar mechanism has recently been demonstrated experimentally for ACE2.     

HingeMaster: normal mode hinge prediction approach and integration of complementary predictors

Protein motion is often the link between structure and function and a substantial fraction of proteins move through a domain hinge bending mechanism. Predicting the location of the hinge from a single structure is thus a logical first step towards predicting motion. Here, we describe ways to predict the hinge location by grouping residues with correlated normal-mode motions. We benchmarked our normal-mode based predictor against a gold standard set of carefully annotated hinge locations taken from the Database of Macromolecular Motions. We then compared it with three existing structure-based hinge predictors (TLSMD, StoneHinge, and FlexOracle), plus HingeSeq, a sequence-based hinge predictor. Each of these methods predicts hinges using very different sources of information-normal modes, experimental thermal factors, bond constraint networks, energetics, and sequence, respectively. Thus it is logical that using these algorithms together would improve predictions. We integrated all the methods into a combined predictor using a weighted voting scheme. Finally, we encapsulated all our results in a web tool which can be used to run all the predictors on submitted proteins and visualize the results.     

Essential dynamics sampling study of adenylate kinase: comparison to citrate synthase and implication for the hinge and shear mechanisms of domain motions

Essential dynamics sampling simulations of the domain conformations of unliganded Escherichia coli adenylate kinase have been performed to determine whether the ligand-induced closed-domain conformation is accessible to the open unliganded enzyme. Adenylate kinase is a three- domain protein with a central CORE domain and twoflanking domains, the LID and the NMPbind domains. The sampling simulations were applied to the CORE and NMPbind domain pair and the CORE and LID domain pair separately. One aim is to compare the results to those of a similar study on the enzyme citrate synthase to determine whether a similar domain-locking mechanism operates in adenylate kinase. Although for adenylate kinase the simulations suggest that the closed-domain conformation of the unliganded enzyme is at a slightly higher free energy than the open for both domain pairs, the results are radically different to those found for citrate synthase. In adenylate kinase the targeted domain conformations could always be achieved, whereas this was not the case in citrate synthase due to an apparent free-energy barrier between the open and closed conformations. Adenylate kinase has been classified as a protein that undergoes closure through a hinge mechanism, whereas citrate synthase has been assigned to the shear mechanism. This was quantified here in terms of the change in the number of interdomain contacting atoms upon closure which showed a considerable increase in adenylate kinase. For citrate synthase this number remained largely the same, suggesting that the domain faces slide over each other during closure. This suggests that shear and hinge mechanisms of domain closure may relate to the existence or absence of an appreciable barrier to closure for the unliganded protein, as the latter can hinge comparatively freely, whereas the former must follow a more constrained path. In general though it appears a bias toward keeping the unliganded enzyme in the open-domain conformation may be a common feature of domain enzymes.     

Intrachain disulfide bond in the core hinge region of human IgG4.

IgG is a tetrameric protein composed of two copies each of the light and heavy chains. The four-chain structure is maintained by strong noncovalent interactions between the amino-terminal half of pairs of heavy-light chains and between the carboxyl-terminal regions of the two heavy chains. In addition, interchain disulfide bonds link each heavy-light chain and also link the paired heavy chains. An engineered human IgG4 specific for human tumor necrosis factor-alpha (CDP571) is similar to human myeloma IgG4 in that it is secreted as both disulfide bonded tetramers (approximately 75% of the total amount of IgG) and as tetramers composed of nondisulfide bonded half-IgG4 (heavy chain disulfide bonded to light chain) molecules. However, when CDP571 was genetically engineered with a proline at residue 229 of the core hinge region rather than serine, CDP571 (S229P), or with an IgG1 rather than IgG4 hinge region, CDP571(gamma 1), only trace amounts of nondisulfide bonded half-IgG tetramers were observed. Trypsin digest reversephase HPLC peptide mapping studies of CDP571 and CDP571(gamma 1) with on-line electrospray ionization mass spectroscopy supplemented with Edman sequencing identified the chemical factor preventing inter-heavy chain disulfide bond formation between half-IgG molecules: the two cysteines in the IgG4 and IgG1 core hinge region (CPSCP and CPPCP, respectively) are capable of forming an intrachain disulfide bond. Conformational modeling studies on cyclic disulfide bonded CPSCP and CPPCP peptides yielded energy ranges for the low-energy conformations of 31-33 kcal/mol and 40-42 kcal/mol, respectively. In addition, higher torsion and angle bending energies were observed for the CPPCP peptide due to backbone constraints caused by the extra proline. These modeling results suggest a reason why a larger fraction of intrachain bonds are observed in IgG4 rather than IgG1 molecules: the serine in the core hinge region of IgG4 allows more hinge region flexibility than the proline of IgG1 and thus may permit formation of a stable intrachain disulfide bond more readily.     

Substrate binding modifies the hinge bending characteristics of human 3‐phosphoglycerate kinase: A molecular dynamics study

3‐Phosphogycerate kinase (PGK) is a two domain enzyme, with a binding site of the 1,3‐bisphosphoglycerate on the N‐domain and of the ADP on the C‐domain. To transfer a phosphate group the enzyme has to undergo a hinge bending motion from open to closed conformation to bring the substrates to close proximity. Molecular dynamics simulation was used to elucidate the effect of ligand binding onto the domain motions of this enzyme. The simulation results of the apo form indicate a hinge bending motion in the ns timescale while the time period of the hinge bending motion of the complex form is clearly over the 20 ns simulation time. The apo form exhibits several hinge points that contribute to the hinge bending motion while upon binding the ligands, the hinge bending becomes strictly restrained with one dominant hinge point in the vicinity of the substrates. At the same time, ligand binding results in an enhanced correlation of internal domain motions. Proteins 2009. © 2009 Wiley‐Liss, Inc.     

Coral bleaching: one disturbance too many for near-shore reefs of the Great Barrier Reef

The dynamic nature of coral communities can make it difficult to judge whether a reef system is resilient to the current disturbance regime. To address this question of resilience for near-shore coral communities of the Great Barrier Reef (Australia) a data set consisting of 350 annual observations of benthic community change was compiled from existing monitoring data. These data spanned the period 1985–2007 and were derived from coral reefs within 20 km of the coast. During years without major disturbance events, cover increase of the Acroporidae was much faster than it was for other coral families; a median of 11% per annum compared to medians of less than 4% for other coral families. Conversely, Acroporidae were more severely affected by cyclones and bleaching events than most other families. A simulation model parameterised with these observations indicated that while recovery rates of hard corals were sufficient to compensate for impacts associated with cyclones and crown-of-thorns starfish, the advent of mass bleaching has lead to a significant change in the composition of the community and a rapid decline in hard coral cover. Furthermore, if bleaching events continue to occur with the same frequency and severity as in the recent past, the model predicts that the cover of Acroporidae will continue to decline. Although significant cover of live coral remains on near-shore reefs, and recovery is observed during inter-disturbance periods, it appears that this system will not be resilient to the recent disturbance regime over the long term. Conservation strategies for coral reefs should focus on both mitigating local factors that act synergistically to increase the susceptibility of Acroporidae to climate change while promoting initiatives that maximise the recovery potential from inevitable disturbances.     

Leporid immunoglobulin G shows evidence of strong selective pressure on the hinge and CH3 domains

Immunoglobulin G (IgG) is the predominant serum immunoglobulin and has the longest serum half-life of all the antibody classes. The European rabbit IgG has been of significant importance in immunological research, and is therefore well characterized. However, the IgG of other leporids has been disregarded. To evaluate the evolution of this gene in leporids, we sequenced the complete IGHG for six other genera: Bunolagus, Brachylagus, Lepus, Pentalagus, Romerolagus and Sylvilagus. The newly sequenced leporid IGHG gene has an organization and structure similar to that of the European rabbit IgG. A gradient in leporid IgG constant domain diversity was observed, with the CH1 being the most conserved and the CH3 the most variable domain. Positive selection was found to be acting on all constant domains, but with a greater incidence in the CH3 domain, where a cluster of three positively selected sites was identified. In the hinge region, only three polymorphic positions were observed. The same hinge length was observed for all leporids. Unlike the variation observed for the European rabbit, all 11 Lepus species studied share exactly the same hinge motif, suggesting its maintenance as a result of an advantageous structure or conformation.     

A reconsideration of the origins of the 'typical' Cretaceous inoceramid calcitic hinge plate in the light of new ultrastructural observations from some Jurassic 'inoceramids'

Abstract:  Marked differences occur between the hinge plates of Jurassic and Upper Cretaceous British 'inoceramid' species. Albian and Upper Cretaceous inoceramids had the poiriform calcite hinge plate with closely spaced resiliifers that is widely associated with this extinct bivalve family. The whole structure was dominated by compressible ligament. Jurassic species, in contrast, had an ultrastructurally less familiar aragonite hinge plate with widely spaced resiliifers and a ligament reminiscent of Isognomon with equally spaced elastic and compressional components. The wider taxonomic relationships of the Inoceramidae still remain uncertain, although the majority of the evidence links the family to the Pterioida. This study, however, suggests that the ancestral inoceramid did not necessarily have a calcitic hinge plate, but rather that a Jurassic 'inoceramid' species could have been developing such a structure via an aragonite precursor. Observations on British Kimmeridgian 'inoceramid' specimens indicate that calcite was being incorporated into the aragonite hinge plate by these times. Structures in the ligamentat of Jurassic species suggest that the fundamental change in mineralogy was initiated by valve architectural modification at the byssal notch, linked to inoceramid epifaunalism. Worldwide poor preservation of Lower Cretaceous inoceramids makes it very difficult to further prove this hypothesis via intermediate evolutionary stages leading to the fully poiriform calcite hinge plate observed in Albian and Upper Cretaceous species of Inoceramidae.     

Observations on the formation and persistence of radiopaque transverse lines

The formation and persistence of radiopaque transverse lines have been assessed in the living in clinical studies of growth, nutrition, and disease. Lines have also been used by many researchers in the analysis of patterns of childhood stress in prehistoric skeletal materials, although most of this research has been undertaken on adult bones. However, how reliable and useful are transverse lines for interpretations of stress? The precise etiologies for their appearance are varied and controversial, and lines are also known to resorb during both childhood and the adult years. Sex differences in both their formation and persistence have also been reported. To assess better the viability of lines as indicators of stress, the present research analyzes rates of formation, distribution frequencies, and the persistence of transverse lines in individuals aged birth to 50 + years from a single archaeological population. The results suggest that while transverse lines may be analytically useful as subsidiary criteria for more fully understanding the biological well-being of prehistoric populations, caution should be exercised in the interpretations made concerning childhood stress, particularly when using adult bones.     

New cases of orangoid hand: Carpopetal main lines of the palm

New cases of orangoid hand are described in two unrelated, normal, Spaniard women. This dermatoglyphic particularity is characterized by an unusual trajectory of the main lines of the palm, which tend to the proximal border of the palm, therefore a new terminology is proposed: ‘carpopetal main lines’. The author passed away while the present paper was in press.