Project description:Proteins recognize DNA sequences by two different mechanisms. The first is direct readout, in which recognition is mediated by direct interactions between the protein and the DNA bases. The second is indirect readout, which is caused by the dependence of conformation and the deformability of the DNA structure on the sequence. Various energy functions have been proposed to evaluate the contribution of indirect readout to the free-energy changes in complex formations. We developed a new generalized energy function to estimate the dependence of the deformability of DNA on the sequence. This function was derived from molecular dynamics simulations previously conducted on B-DNA dodecamers, each of which had one possible tetramer sequence embedded at its center. By taking the logarithm of the probability distribution function (PDF) for the base-step parameters of the central base-pair step of the tetramer, its ability to distinguish the native sequence from random ones was superior to that with the previous method that approximated the energy function in harmonic form. From a comparison of the energy profiles calculated with these two methods, we found that the harmonic approximation caused significant errors in the conformational energies of the tetramers that adopted multiple stable conformations.
Project description:How animals jump and land on diverse surfaces is ecologically important and relevant to bioinspired robotics. Here, we describe the jumping biomechanics of the planthopper Lycorma delicatula (spotted lanternfly), an invasive insect in the USA that jumps frequently for dispersal, locomotion and predator evasion. High-speed video was used to analyze jumping by spotted lanternfly nymphs from take-off to impact on compliant surfaces. These insects used rapid hindleg extensions to achieve high take-off speeds (2.7-3.4 m s-1) and accelerations (800-1000 m s-2), with mid-air trajectories consistent with ballistic motion without drag forces or steering. Despite rotating rapidly (5-45 Hz) about time-varying axes of rotation, they landed successfully in 58.9% of trials. They also attained the most successful impact orientation significantly more often than predicted by chance, consistent with their using attitude control. Notably, these insects were able to land successfully when impacting surfaces at all angles, pointing to the importance of collisional recovery behaviors. To further understand their rotational dynamics, we created realistic 3D rendered models of spotted lanternflies and used them to compute their mechanical properties during jumping. Computer simulations based on these models and drag torques estimated from fits to tracked data successfully predicted several features of the measured rotational kinematics. This analysis showed that the rotational inertia of spotted lanternfly nymphs is predominantly due to their legs, enabling them to use posture changes as well as drag torque to control their angular velocity, and hence their orientation, thereby facilitating predominately successful landings when jumping.
Project description:Bird pollination systems are diverse, ranging from narrow-tubed flowers pollinated by specialist nectarivores such as hummingbirds and sunbirds, to relatively open flowers pollinated by opportunistic (i.e. generalist) nectarivores. The role of opportunistic avian nectarivores as pollinators has historically been under-appreciated. A key aspect to understanding the importance of opportunistic birds as pollinators is to investigate how efficiently they transfer pollen among flowers. Here, we document the pollination and breeding systems of Schotia brachypetala, a southern African tree known as the 'weeping boer-bean' on account of its prolific production of dilute hexose-dominated nectar. The cup-shaped flowers of this tree attract a large number of bird species, including both opportunistic and specialist nectarivores. We identified floral visitors using observations and camera traps and quantified the floral traits responsible for animal attraction. We documented the breeding system, used selective pollinator exclusion to test the contribution of birds to fecundity, and performed supplemental pollination to test for pollen limitation. Single-visit pollen deposition trials were undertaken to determine the efficacy of bird pollinators. Controlled hand-pollination experiments showed that S. brachypetala is genetically self-incompatible and therefore dependent on pollinators for seed production. Supplemental hand-pollination experiments showed that natural fecundity is limited by either the amount and/or the quality of pollen on stigmas. Flowers from which birds but not insects were experimentally excluded set fewer seeds than open control flowers. Opportunistic birds deposited more pollen per visit than did specialist sunbirds. We conclude that S. brachypetala has a generalized bird pollination system that mainly involves opportunistic nectarivores.
Project description:The objective of this study was to investigate the prevalence of generalized joint hypermobility (GJH) in a university-aged population, whether young adults (aged 18-25 years) with GJH are prone to sustain more musculoskeletal injuries, and are more likely to suffer from chronic musculoskeletal pain. The study used an interactive survey to gather data; GJH was assessed using a cut-off Beighton score of ≥5 in accordance with the 2017 International Classification of EDS criteria. The analyzed sample consisted of 482 female and 172 male participants from Florida Gulf Coast University (USA). The prevalence of GJH in a university-aged population can be estimated at 12.5%. Women did not have higher rates of GJH than men. However, female participants showed significantly higher rates of hypermobility of the spine as well as the right knee and elbow joints. The Beighton scores did not differ by ethnicity/race. Female participants had a lower rate of self-reported injuries than male participants, although this difference was not significant. There was no difference in the proportion of all participants classified within different categories (0; 1-4; 5-9) of Beighton scores and whether or not they reported having been injured. Male and female participants reported chronic pain of joints and neck or back at the same rates across the Beighton score categories. Female participants, however, reported higher pain intensity for chronic neck and back pain. This study increases knowledge about a correlation between GJH, musculoskeletal injuries, and chronic pain of joints, neck, and back in a university-aged population.
Project description:The hindlimb of theropod dinosaurs changed appreciably in the lineage leading to extant birds, becoming more 'crouched' in association with changes to body shape and gait dynamics. This postural evolution included anatomical changes of the foot and ankle, altering the moment arms and control of the muscles that manipulated the tarsometatarsus and digits, but the timing of these changes is unknown. Here, we report cellular-level preservation of tendon- and cartilage-like tissues from the lower hindlimb of Early Cretaceous Confuciusornis. The digital flexor tendons passed through cartilages, cartilaginous cristae and ridges on the plantar side of the distal tibiotarsus and proximal tarsometatarsus, as in extant birds. In particular, fibrocartilaginous and cartilaginous structures on the plantar surface of the ankle joint of Confuciusornis may indicate a more crouched hindlimb posture. Recognition of these specialized soft tissues in Confuciusornis is enabled by our combination of imaging and chemical analyses applied to an exceptionally preserved fossil.
Project description:Physics-based predictive simulations of human movement have the potential to support personalized medicine, but large computational costs and difficulties to model control strategies have limited their use. We have developed a computationally efficient optimal control framework to predict human gaits based on optimization of a performance criterion without relying on experimental data. The framework generates three-dimensional muscle-driven simulations in 36 min on average-more than 20 times faster than existing simulations-by using direct collocation, implicit differential equations and algorithmic differentiation. Using this framework, we identified a multi-objective performance criterion combining energy and effort considerations that produces physiologically realistic walking gaits. The same criterion also predicted the walk-to-run transition and clinical gait deficiencies caused by muscle weakness and prosthesis use, suggesting that diverse healthy and pathological gaits can emerge from the same control strategy. The ability to predict the mechanics and energetics of a broad range of gaits with complex three-dimensional musculoskeletal models will allow testing novel hypotheses about gait control and hasten the development of optimal treatments for neuro-musculoskeletal disorders.
Project description:Selection and training practices for jumping horses have not yet been validated using objective performance analyses. This study aimed to quantify the differences and relationships between movement and muscle activation strategies in horses with varying jump technique to identify objective jumping performance indicators. Surface electromyography (sEMG) and three-dimensional kinematic data were collected from horses executing a submaximal jump. Kinematic variables were calculated based on equestrian-derived performance indicators relating to impulsion, engagement and joint articulation. Horses were grouped using an objective performance indicator-center of mass (CM) elevation during jump suspension (ZCM). Between-group differences in kinematic variables and muscle activation timings, calculated from sEMG data, were analyzed using one-way ANOVA. Statistical parametric mapping (SPM) evaluated between-group differences in time and amplitude-normalized sEMG waveforms. Relationships between movement and muscle activation were evaluated using Pearson correlation coefficients. Horses with the greatest ZCM displayed significantly (p < 0.05) shorter gluteal contractions at take-off, which were significantly correlated (p < 0.05) with a faster approach and more rapid hindlimb shortening and CM vertical displacement and velocity, as well as shorter hindlimb stance duration at take-off. Findings provide objective support for prioritizing equestrian-derived performance indicators related to the generation of engagement, impulsion and hindlimb muscle power when selecting or training jumping horses.
Project description:The generalized Born (GB) model is one of the fastest implicit solvent models and it has become widely adopted for Molecular Dynamics (MD) simulations. This speed comes with tradeoffs, and many reports in the literature have pointed out weaknesses with GB models. Because the quality of a GB model is heavily affected by empirical parameters used in calculating solvation energy, in this work we have refit these parameters for GB-Neck, a recently developed GB model, in order to improve the accuracy of both the solvation energy and effective radii calculations. The data sets used for fitting are significantly larger than those used in the past. Comparing to other pairwise GB models like GB-OBC and the original GB-Neck, the new GB model (GB-Neck2) has better agreement to Poisson-Boltzmann (PB) in terms of reproducing solvation energies for a variety of systems ranging from peptides to proteins. Secondary structure preferences are also in much better agreement with those obtained from explicit solvent MD simulations. We also obtain near-quantitative reproduction of experimental structure and thermal stability profiles for several model peptides with varying secondary structure motifs. Extension to non-protein systems will be explored in the future.
Project description:Predation is one of the main selective forces in nature, frequently selecting potential prey for developing escape strategies. Escape ability is typically influenced by several morphological parameters, such as morphology of the locomotor appendices, muscular capacity, body mass, or fluctuating asymmetry, and may differ between sexes and age classes. In this study, we tested the relationship among these variables and jumping performance in 712 Iberian green frogs Pelophylax perezi from an urban population. The results suggest that the main determinant of jumping capacity was body size (explaining 48% of variance). Larger frogs jumped farther, but jumping performance reached an asymptote for the largest frogs. Once controlled by structural body size, the heaviest frogs jumped shorter distances, suggesting a trade-off between fat storage and jumping performance. Relative hind limb length also determined a small but significant percentage of variance (2.4%) in jumping performance-that is, the longer the hind limbs, the greater the jumping capacity. Juveniles had relatively shorter and less muscular hind limbs than adults (for a given body size), and their jumping performance was poorer. In our study population, the hind limbs of the frogs were very symmetrical, and we found no effect of fluctuating asymmetry on jumping performance. Therefore, our study provides evidence that jumping performance in frogs is not only affected by body size, but also by body mass and hind limb length, and differ between age classes.
Project description:Ontogenetic locomotion research focuses on the evolution of locomotion behavior in different developmental stages of a species. Unlike vertebrates, ontogenetic locomotion in invertebrates is poorly investigated. Locusts represent an outstanding biological model to study this issue. They are hemimetabolous insects and have similar aspects and behaviors in different instars. This research is aimed at studying the jumping performance of Locusta migratoria over different developmental instars. Jumps of third instar, fourth instar, and adult L. migratoria were recorded through a high-speed camera. Data were analyzed to develop a simplified biomechanical model of the insect: the elastic joint of locust hind legs was simplified as a torsional spring located at the femur-tibiae joint as a semilunar process and based on an energetic approach involving both locomotion and geometrical data. A simplified mathematical model evaluated the performances of each tested jump. Results showed that longer hind leg length, higher elastic parameter, and longer takeoff time synergistically contribute to a greater velocity and energy storing/releasing in adult locusts, if compared to young instars; at the same time, they compensate possible decreases of the acceleration due to the mass increase. This finding also gives insights for advanced bioinspired jumping robot design.