Exploring the Relationship between Skeletal Mass and Total Body Mass in Birds

Total body mass (TBM) is known to be related to a number of different osteological features in vertebrates, including limb element measurements and total skeletal mass. The relationship between skeletal mass and TBM in birds has been suggested as a way of estimating the latter in cases where only the skeleton is known (e.g., fossils). This relationship has thus also been applied to other extinct vertebrates, including the non-avian pterosaurs, while other studies have used additional skeletal correlates found in modern birds to estimate TBM. However, most previous studies have used TBM compiled from the literature rather than from direct measurements, producing values from population averages rather than from individuals. Here, we report a new dataset of 487 extant birds encompassing 79 species that have skeletal mass and TBM recorded at the time of collection or preparation. We combine both historical and new data for analyses with phylogenetic control and find a similar and well-correlated relationship between skeletal mass and TBM. Thus, we confirm that TBM and skeletal mass are accurate proxies for estimating one another. We also look at other factors that may have an effect on avian body mass, including sex, ontogenetic stage, and flight mode. While data are well-correlated in all cases, phylogeny is a major control on TBM in birds strongly suggesting that this relationship is not appropriate for estimating the total mass of taxa outside of crown birds, Neornithes (e.g., non-avian dinosaurs, pterosaurs). Data also reveal large variability in both bird skeletal and TBM within single species; caution should thus be applied when using published mass to test direct correlations with skeletal mass and bone lengths.     

Protein folding pathways and state transitions described by classical equations of motion of an elastic network model

Protein topology defined by the matrix of residue contacts has proved to be a fruitful basis for the study of protein dynamics. The widely implemented coarse-grained elastic network model of backbone fluctuations has been used to describe crystallographic temperature factors, allosteric couplings, and some aspects of the folding pathway. In the present study, we develop a model of protein dynamics based on the classical equations of motion of a damped network model (DNM) that describes the folding path from a completely unfolded state to the native conformation through a single-well potential derived purely from the native conformation. The kinetic energy gained through the collapse of the protein chain is dissipated through a friction term in the equations of motion that models the water bath. This approach is completely general and sufficiently fast that it can be applied to large proteins. Folding pathways for various proteins of different classes are described and shown to correlate with experimental observations and molecular dynamics and Monte Carlo simulations. Allosteric transitions between alternative protein structures are also modeled within the DNM through an asymmetric double-well potential.     

Structure of human thioredoxin exhibits a large conformational change

Thioredoxin is an oxidoreductase, which is ubiquitously present across phyla from humans to plants and bacteria. Thioredoxin reduces a variety of substrates through active site Cys 32, which is subsequently oxidized to form the intramolecular disulphide with Cys 35. The thioredoxin fold is known to be highly stable and conformational changes in the active site loops and residues Cys 32, Cys 35 have been characterized between ligand bound and free structures. We have determined a novel 2.0 Å resolution crystal structure for a human thioredoxin, which reveals a much larger conformational change than previously characterized. The principal change involves unraveling of a helix to form an extended loop that is linked to secondary changes in further loop regions and the wider area of the active site Cys 32. This gives rise to a more open conformation and an elongated hydrophobic pocket results in place of the helix. Buried residue Cys 62 from this helix becomes exposed in the open conformation. This provides a structural basis for observations that the Cys 62 sidechain can form mixed disulphides and be modified by thiol reactive small molecules.     

Modelling apical constriction in epithelia using elastic shell theory

Apical constriction is one of the fundamental mechanisms by which embryonic tissue is deformed, giving rise to the shape and form of the fully-developed organism. The mechanism involves a contraction of fibres embedded in the apical side of epithelial tissues, leading to an invagination or folding of the cell sheet. In this article the phenomenon is modelled mechanically by describing the epithelial sheet as an elastic shell, which contains a surface representing the continuous mesh formed from the embedded fibres. Allowing this mesh to contract, an enhanced shell theory is developed in which the stiffness and bending tensors of the shell are modified to include the fibres’ stiffness, and in which the active effects of the contraction appear as body forces in the shell equilibrium equations. Numerical examples are presented at the end, including the bending of a plate and a cylindrical shell (modelling neurulation) and the invagination of a spherical shell (modelling simple gastrulation).     

Vocal Repertoire of Golden-backed Uakaris (<Emphasis Type="Italic">Cacajao melanocephalus</Emphasis>): Call Structure and Context

The study of vocal behavior can reveal important aspects of how and why a species communicates in relation to ecological and social challenges. We here focus on vocal communication in golden-backed uakaris (Cacajao melanocephalus), diurnal, pitheciine monkeys that exhibit fission-fusion social organization and typically inhabit dense forests that limit the potential for visual communication. Moreover, the species spends little time engaged in tactile or olfactory communication, e.g., social grooming and scent marking, respectively. Hence, vocalizations may be very important for the coordination of social organization in these monkeys. We 1) categorized golden-backed uakari vocalizations, 2) ascertained their behavioral context, and 3) investigated whether golden-backed uakari calls can encode information about the signaler. We observed the monkeys during 2 wet seasons in the flooded igapó forest of Jaú National Park, Brazil. We showed that golden-backed uakaris have 9 call types in their vocal repertoire, all distinguishable by ear and from analysis of spectrograms. Some calls, e.g., play-specific calls, were used only in particular behavioral contexts, and by individuals of specific age, whereas others were emitted under a range of situations. The structure of the loud tchó call varied among individuals, and according to behavioral context, i.e., whether individuals were foraging/feeding, traveling, or performing agonistic interactions. This knowledge of the species’ vocal repertoire is valuable for surveying the monkeys acoustically in habitats where visual surveys are difficult.     

Echolocation behaviours of the Japanese pipistrelle batPipistrellus abramus during foraging flight

The acoustic structure of echolocation pulses emitted by Japanese pipistrellePipistrellus abramus (Temminck, 1840) bats during different phases of aerial hawking is described here for the first time. Behavioural observations of the foraging flight in conjunction with acoustical analysis of echolocation pulses indicated a flight path consisting of four distinct phases following the reconnaissance or search phase. Short (∼4.68 ms) and relatively broadband frequencymodulated (FM) pulses (∼23.55 kHz bandwidth) were emitted at a repetition rate of 15 Hz during presumed target approach. Presumed insect capture consisted of an early and a late buzz phase. Both buzz types were emitted at high repetition rates (111 Hz in early to 222 Hz in late) and consisted of very short, broadband FM pulses (1.26 ms in early to 0.3 ms in late). There was also a characteristically sharp drop in both the peak and terminal frequencies of each echolocation pulse during the transition from early to late buzz. No pulses were recorded during the final phase of foraging referred to as a “post-buzz pause”. Thus the foraging behaviour of this species consisted of five sequential phases involving four broad types of echolocation pulses.