A Bayesian inference scheme to extract diffusivity and potential fields from confined single-molecule trajectories

Currently used techniques for the analysis of single-molecule trajectories only exploit a small part of the available information stored in the data. Here, we apply a Bayesian inference scheme to trajectories of confined receptors that are targeted by pore-forming toxins to extract the two-dimensional confining potential that restricts the motion of the receptor. The receptor motion is modeled by the overdamped Langevin equation of motion. The method uses most of the information stored in the trajectory and converges quickly onto inferred values, while providing the uncertainty on the determined values. The inference is performed on the polynomial development of the potential and on the diffusivities that have been discretized on a mesh. Numerical simulations are used to test the scheme and quantify the convergence toward the input values for forces, potential, and diffusivity. Furthermore, we show that the technique outperforms the classical mean-square-displacement technique when forces act on confined molecules because the typical mean-square-displacement analysis does not account for them. We also show that the inferred potential better represents input potentials than the potential extracted from the position distribution based on Boltzmann statistics that assumes statistical equilibrium.     

Postnatal Dynamics of Developmental Stability and Canalization of Lizard Head Shape Under Different Environmental Conditions

Developmental stability (DS) and canalization are key determinants of phenotypic variation. To provide a better understanding of how postnatal growth is involved in determining the effects of DS and canalization on phenotypic variation, we studied within- and among-individual variation in head shape in ontogenetic series of lizards inhabiting urban and rural environments. Urban lizards exhibited increased fluctuating asymmetry during the early postnatal stages, but asymmetry levels decreased during growth. By contrast, asymmetry remained constant across the investigated size range in the rural population. In addition, urban juveniles were more variable for symmetric shape and deviated more from the group shape-size allometric trajectory, but both indices declined across ontogeny. Congruent patterns of within- and among-individual variation suggest that both DS and canalization may rely on similar underlying mechanisms. Further, the ontogenetic reduction of variation in the urban population suggests that compensatory growth may aid in buffering phenotypic variation and correcting deviances from the established developmental path. Alternatively, passive mechanisms and population dynamics may also explain the decrease of phenodeviants in urban populations. Significant correlations between symmetric and asymmetric shape, as well as similar integration patterns between the two populations, suggest that similar developmental mechanisms regulate head shape in both environments. Overall, these results highlight the relevance of both pre- and post-natal dynamics in determining levels of phenotypic variation, enhancing our understanding of how organisms respond to perturbations to DS and canalization under stressful conditions.     

Delta-like Ligand-4-Notch Signaling Inhibition Regulates Pancreatic Islet Function and Insulin Secretion

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Locomotor Mode and the Evolution of the Hindlimb in Western Mediterranean Anurans

Evolutionary Biology - The evolutionary association between morphology, locomotor performance and habitat use is a central element of the ecomorphological paradigm, and it is known to underlie the...     

Maintenance of the keratocyte phenotype during cell proliferation stimulated by insulin

Keratocytes normally express high levels of aldehyde dehydrogenase and keratocan. They proliferate and lose their keratocyte markers when they become fibroblastic during corneal wound healing. Keratocytes cultured in fetal bovine serum also become fibroblastic, proliferate, and lose these markers. In this report, we studied the effects of three serum growth factors, fibroblast growth factor-2, insulin, and platelet-derived growth factor-BB, on keratocyte proliferation and the maintenance of the keratocyte markers in 7-day cultures in cells plated at low (5,000 cells/cm2) and high (20,000 cells/cm2) density in serum-free medium. Keratocyte proliferation was measured by [3H]thymidine incorporation and by DNA content of the cultures. Cytosolic aldehyde dehydrogenase and keratocan accumulated in the medium were quantified by Western blot. The results showed that all the growth factors stimulated proliferation, but insulin stimulated proliferation more consistently. The keratocyte markers aldehyde dehydrogenase and keratocan were maintained after 7 days in culture in all growth factors, but keratocyte cell morphology was only maintained in medium containing insulin. Most of the proteoglycans were degraded in cultures of keratocytes plated at low density and cultured in the absence of growth factors. This degradation was prevented when keratocytes were cultured in the presence of the growth factors or when keratocytes were plated at high density. The results of this study show that insulin can expand keratocytes in vitro, maintain their phenotype, and prevent proteoglycan degradation.     

A Primer on the Bayesian Approach to High-Density Single-Molecule Trajectories Analysis

Tracking single molecules in living cells provides invaluable information on their environment and on the interactions that underlie their motion. New experimental techniques now permit the recording of large amounts of individual trajectories, enabling the implementation of advanced statistical tools for data analysis. In this primer, we present a Bayesian approach toward treating these data, and we discuss how it can be fruitfully employed to infer physical and biochemical parameters from single-molecule trajectories.