Active carpets drive non-equilibrium diffusion and enhanced molecular fluxes

Biological activity is often highly concentrated on surfaces, across the scales from molecular motors and ciliary arrays to sessile and motile organisms. These ‘active carpets’ locally inject energy into their surrounding fluid. Whereas Fick’s laws of diffusion are established near equilibrium, it is unclear how to solve non-equilibrium transport driven by such boundary-actuated fluctuations. Here, we derive the enhanced diffusivity of molecules or passive particles as a function of distance from an active carpet. Following Schnitzer’s telegraph model, we then cast these results into generalised Fick’s laws. Two archetypal problems are solved using these laws: First, considering sedimentation towards an active carpet, we find a self-cleaning effect where surface-driven fluctuations can repel particles. Second, considering diffusion from a source to an active sink, say nutrient capture by suspension feeders, we find a large molecular flux compared to thermal diffusion. Hence, our results could elucidate certain non-equilibrium properties of active coating materials and life at interfaces.

Pore structure controls stability and molecular flux in engineered protein cages

Protein cages are a common architectural motif used by living organisms to compartmentalize and control biochemical reactions. While engineered protein cages have recently been featured in the construction of nanoreactors and synthetic organelles, relatively little is known about the underlying molecular parameters that govern cage stability and molecular flux through their pores. In this work, we systematically designed a 24-member library of protein cage variants based on the T. maritima encapsulin, each featuring pores of different size and charge. Twelve encapsulin pore variants were successfully assembled and purified, including eight designs with exceptional and prolonged thermal stability. Pores lined with anionic residues resulted in more robust assemblies than their corresponding cationic variants. We then determined seven cryo-EM structures of pore variants at resolutions between 2.5-3.6 Å. Together with stopped-flow kinetics experiments for quantifying cation influx, we uncover the complex interplay between pore size, charge, and flexibility that controls molecular flux in protein cages, providing guidance for future nanoreactor designs.Abstract Figure

Influence of radiation-stimulated discharges on the contamination of cover glasses of solar batteries of spacecraft

The results of an AFM study of changes in the surface structure of K-208 and CMG cover glasses after electron irradiation and exposure to molecular fluxes are presented. It is shown that contamination of glass surfaces irradiated with electrons at flux densities (φ) from 1010 to 8·1010 cm–2 s–1 occurs during electrostatic discharges accompanied by the release of plasmoids into the surrounding space, the particles of which are deposited on the glass. It has been experimentally established that the effect of preliminary irradiation of glass on the deposition of molecular flow components is most effective immediately after irradiation and decreases with time. This is due to the drainage of the charge injected into the glass and a decrease in the initially high reactivity of the substances in the discharge channels. It was also shown that the combined effect of electrons and molecular flux on glasses significantly increased the discharge frequency at a given value of φ and, as a result, led to an increase in the number of discharge channels on the sample surfaces. In this case, over time, the process of accumulation of molecular flow components begins to dominate the cleaning of the glass surface due to electron-stimulated desorption and mechanical desorption under the action of shock waves accompanying the discharges. To interpret the experimental results, a mathematical model of the deposition of molecular flow components on glass is proposed.

A novel voltage-clamp/dye uptake assay reveals saturable transport of molecules through CALHM1 and connexin channels

Large-pore channels permeable to small molecules such as ATP, in addition to atomic ions, are emerging as important regulators in health and disease. Nonetheless, their mechanisms of molecular permeation and selectivity remain mostly unexplored. Combining fluorescence microscopy and electrophysiology, we developed a novel technique that allows kinetic analysis of molecular permeation through connexin and CALHM1 channels in Xenopus oocytes rendered translucent. Using this methodology, we found that (1) molecular flux through these channels saturates at low micromolar concentrations, (2) kinetic parameters of molecular transport are sensitive to modulators of channel gating, (3) molecular transport and ionic currents can be differentially affected by mutation and gating, and (4) N-terminal regions of these channels control transport kinetics and permselectivity. Our methodology allows analysis of how human disease–causing mutations affect kinetic properties and permselectivity of molecular signaling and enables the study of molecular mechanisms, including selectivity and saturability, of molecular transport in other large-pore channels.

The 2D Flow Around Tilted Plate

The 2D problem on stratified flow around a strip is studied numerically and experimentally on the basis of the system of fundamental equations of incompressible viscous fluid mechanics taking into account diffusion effects and neglecting heat transfer. Strongly and weakly stratified fluid flows are considered, as well as potentially and actually homogeneous ones when the buoyancy effects, respectively, are assumed extremely weak or even neglected completely. Initial condition is the diffusion-induced flow on a motionless obstacle, which occurs as a result of interrupting the molecular flux of a stratifying agent on the plate surface. Influence of a set of problem parameters on the flow structure and dynamics is studied, including longitudinal and transverse dimensions of the plate, its shape, angle of attack, and velocity of movement. Analysis of the results shows that the unsteady problem does not have a stationary limit over the entire range of flow parameters due to its internal multiscale structure. The calculated field patterns, being specific for the basic physical variables and their gradients, are in a qualitative agreement with the laboratory data. In the extreme cases, the results converge to the well-known solutions, in particular, to the Blasius solution for the half-plane set in the direction of free stream.

Cretaceous dinosaur bone contains recent organic material and provides an environment conducive to microbial communities

Fossils were thought to lack original organic molecules, but chemical analyses show that some can survive. Dinosaur bone has been proposed to preserve collagen, osteocytes, and blood vessels. However, proteins and labile lipids are diagenetically unstable, and bone is a porous open system, allowing microbial/molecular flux. These ‘soft tissues’ have been reinterpreted as biofilms. Organic preservation versus contamination of dinosaur bone was examined by freshly excavating, with aseptic protocols, fossils and sedimentary matrix, and chemically/biologically analyzing them. Fossil ‘soft tissues’ differed from collagen chemically and structurally; while degradation would be expected, the patterns observed did not support this. 16S rRNA amplicon sequencing revealed that dinosaur bone hosted an abundant microbial community different from lesser abundant communities of surrounding sediment. Subsurface dinosaur bone is a relatively fertile habitat, attracting microbes that likely utilize inorganic nutrients and complicate identification of original organic material. There exists potential post-burial taphonomic roles for subsurface microorganisms.

Molecular flux control encodes distinct cytoskeletal responses by specifying SRC signaling pathway usage

Multi-domain signaling proteins sample numerous stimuli to coordinate distinct cellular responses. Understanding the mechanisms of their pleiotropic signaling activity requires to directly manipulate their activity of decision leading to distinct cellular responses. We developed an optogenetic probe, optoSRC, to control spatio-temporally the SRC kinase, a representative example of versatile signaling node, and challenge its ability to generate different cellular responses. Genesis of different local molecular fluxes of the same optoSRC to adhesion sites, was sufficient to trigger distinct and specific acto-adhesive responses. Collectively, this study reveals how hijacking the pleiotropy of SRC signaling by modulating in space and time subcellular molecular fluxes of active SRC kinases.