EFNA3 long noncoding RNAs induced by hypoxia promote metastatic dissemination

The presence of hypoxic regions in solid tumors is an adverse prognostic factor for patient outcome. Here, we show that hypoxia induces the expression of Ephrin-A3 through a novel hypoxia-inducible factor (HIF)-mediated mechanism. In response to hypoxia, the coding EFNA3 mRNA levels remained relatively stable, but HIFs drove the expression of previously unknown long noncoding (lnc) RNAs from EFNA3 locus and these lncRNA caused Ephrin-A3 protein accumulation. Ephrins are cell surface proteins that regulate diverse biological processes by modulating cellular adhesion and repulsion. Mounting evidence implicates deregulated ephrin function in multiple aspects of tumor biology. We demonstrate that sustained expression of both Ephrin-A3 and novel EFNA3 lncRNAs increased the metastatic potential of human breast cancer cells, possibly by increasing the ability of tumor cells to extravasate from the blood vessels into surrounding tissue. In agreement, we found a strong correlation between high EFNA3 expression and shorter metastasis-free survival in breast cancer patients. Taken together, our results suggest that hypoxia could contribute to metastatic spread of breast cancer via HIF-mediated induction of EFNA3 lncRNAs and subsequent Ephrin-A3 protein accumulation.

Consensus on the solubility of NaCl in water from computer simulations using the chemical potential route

The solubility of NaCl in water is evaluated by using three force field models: Joung-Cheatham for NaCl dissolved in two different water models (SPC/E and TIP4P/2005) and Smith Dang NaCl model in SPC/E water. The methodology based on free-energy calculations [E. Sanz and C. Vega, J. Chem. Phys. 126, 014507 (2007)] and [J. L. Aragones et al., J. Chem. Phys. 136, 244508 (2012)] has been used, except, that all calculations for the NaCl in solution were obtained by using molecular dynamics simulations with the GROMACS package instead of homemade MC programs. We have explored new lower molalities and made longer runs to improve the accuracy of the calculations. Exploring the low molality region allowed us to obtain an analytical expression for the chemical potential of the ions in solution as a function of molality valid for a wider range of molalities, including the infinite dilute case. These new results are in better agreement with recent estimations of the solubility obtained with other methodologies. Besides, two empirical simple rules have been obtained to have a rough estimate of the solubility of a certain model, by analyzing the ionic pairs formation as a function of molality and/or by calculating the difference between the NaCl solid chemical potential and the standard chemical potential of the salt in solution.

Free energy calculations for molecular solids using GROMACS

In this work, we describe a procedure to evaluate the free energy of molecular solids with the GROMACS molecular dynamics package. The free energy is calculated using the Einstein molecule method that can be regarded as a small modification of the Einstein crystal method. Here, the position and orientation of the molecules is fixed by using an Einstein field that binds with harmonic springs at least three non-collinear atoms (or points of the molecule) to their reference positions. The validity of the Einstein field is tested by performing free-energy calculations of methanol, water (ice), and patchy colloids molecular solids. The free energies calculated with GROMACS show a very good agreement with those obtained using Monte Carlo and with previously published results.

Phase diagram of water under an applied electric field

Simulations are used to investigate for the first time the anisotropy of the dielectric response and the effects of an applied electric field E(ex) on the phase diagram of water. In the presence of electric fields ice II disappears from the phase diagram. When E(ex) is applied in the direction perpendicular to the ac crystallographic plane the melting temperatures of ices III and V increase whereas that of ice Ih is hardly affected. Ice III also disappears as a stable phase when E(ex) is applied in the direction perpendicular to the ab plane. E(ex) increases by a small amount the critical temperature and reduces slightly the temperature of the maximum density of liquid water. The presence E(ex) modifies all phase transitions of water but its effect on solid-solid and solid-fluid transitions seems to be more important and different depending on the direction of E(ex).

Single-step assembly of asymmetric vesicles

Asymmetric vesicles are membranes in which amphiphiles are asymmetrically distributed between each membrane leaflet. This asymmetry dictates chemical and physical properties of these vesicles, enabling their use as more realistic models of biological cell membranes, which also are asymmetric, and improves their potential for drug delivery and cosmetic applications. However, their fabrication is difficult as the self-assembly of amphiphiles always leads to symmetric vesicles. Here, we report the use of water-in-oil-in-oil-in-water triple emulsion drops to direct the assembly of the two leaflets to form asymmetric vesicles. Different compositions of amphiphiles are dissolved in each of the two oil shells of the triple emulsion; the amphiphiles diffuse to the interfaces and adsorb differentially at each of the two oil/water interfaces of the triple emulsion. These middle oil phases dewet from the innermost water cores of the triple emulsion drops, leading to the formation of membranes with degrees of asymmetry up to 70%. The triple emulsion drops are fabricated using capillary microfluidics, enabling production of highly monodisperse drops at rates as high as 300 Hz. Vesicles produced by this method can very efficiently encapsulate many different ingredients; this further enhances the utility of asymmetric vesicles as artificial cells, bioreactors and delivery vehicles.

How rotating ATP synthases can modulate membrane structure

F1Fo-ATP synthase (ATP synthase) is a central membrane protein that synthetizes most of the ATP in the cell through a rotational movement driven by a proton gradient across the hosting membrane. In mitochondria, ATP synthases can form dimers through specific interactions between some subunits of the protein. The dimeric form of ATP synthase provides the protein with a spontaneous curvature that sustain their arrangement at the rim of the high-curvature edges of mitochondrial membrane (cristae). Also, a direct interaction with cardiolipin, a lipid present in the inner mitochondrial membrane, induces the dimerization of ATP synthase molecules along cristae. The deletion of those biochemical interactions abolishes the protein dimerization producing an altered mitochondrial function and morphology. Mechanically, membrane bending is one of the key deformation modes by which mitochondrial membranes can be shaped. In particular, bending rigidity and spontaneous curvature are important physical factors for membrane remodelling. Here, we discuss a complementary mechanism whereby the rotatory movement of the ATP synthase might modify the mechanical properties of lipid bilayers and contribute to the formation and regulation of the membrane invaginations.

Artificial tribotactic microscopic walkers: walking based on friction gradients

Friction, the resistive force between two surfaces sliding past each other, is at the core of a wide diversity of locomotion schemes. While such schemes are well described for homogeneous environments, locomotion based on friction in inhomogeneous environments has not received much attention. Here we introduce and demonstrate the concept of tribotaxis, a motion that is guided by gradients in the friction coefficient. Our system is composed of microwalkers that undergo an effective frictional interaction with biological receptors on the substrate, which is regulated by the density of such receptors. When actuated stochastically, microwalkers migrate to regions of higher friction, much like a chemotactic cell migrates to regions of higher chemoattractant concentration. Simulations and theory based on biased random walks are in excellent agreement with experiments. We foresee important implications for tribotaxis in artificial and natural locomotion in biological environments.

Aggregation dynamics of active rotating particles in dense passive media

Active matter systems are able to exhibit emergent non-equilibrium behavior due to activity-induced effective interactions between the active particles. Here we study the aggregation and dynamical behavior of active rotating particles, spinners, embedded in 2D passive colloidal monolayers. Using both experiments and simulations we observe aggregation of active particles or spinners whose behavior resembles classical 2D Cahn-Hilliard coarsening. The aggregation behavior and spinner attraction depend on the mechanical properties of the passive monolayer and the activity of spinners. Spinner aggregation only occurs when the passive monolayer behaves elastically and when the spinner activity exceeds a minimum activity threshold. Interestingly, for the spinner concentrations investigated here, the spinner concentration does not seem to change the dynamics of the aggregation behavior. There is a characteristic cluster size which maximizes spinner aggregation by minimizing the drag through the passive monolayer and maximizing the stress applied on the passive medium. We also show a ternary mixture of passive particles and co-rotating and counter-rotating spinners that aggregate into clusters of co and counter-rotating spinners respectively.

Rolling vesicles: From confined rotational flows to surface-enabled motion

Friction forces are essential for cell movement, yet they also trigger numerous active cellular responses, complicating their measurement in vivo. Here, we introduce a synthetic model designed to measure friction forces between biomimetic membranes and substrates. The model consists of a vesicle with precisely controlled properties, fabricated via microfluidics, encapsulating a single ferromagnetic particle that is magnetically driven to rotate. The rotation of the particle generates a confined rotational flow, setting the vesicle membrane into motion. By adjusting the magnetic field frequency and vesicle size, the rotation frequency of the vesicle can be finely controlled, resulting in a rolling vesicle that functions as an effective tribological tool across a wide frequency range. At low frequencies, molecular contact between the membrane and substrate dominates frictional interactions, which enables determination of the contact friction coefficient. At higher frequencies, lubrication becomes predominant, causing the vesicles to slip rather than roll. Adjusting membrane fluidity and incorporating specific ligand-receptor interactions within this model will enable detailed studies of frictional forces in more complex biomimetic systems, providing key insights into the mechanisms of cell movement and mechanotransduction.

Aqueous Two-Phase Systems within Selectively Permeable Vesicles

An aqueous two-phase system (ATPS) encapsulated within a vesicle organizes the vesicle core as two coexisting phases that partition encapsulated solutes. Here, we use microfluidic technologies to produce vesicles that efficiently encapsulate mixtures of macromolecules, providing a versatile platform to determine the phase behavior of ATPSs. Moreover, we use compartmentalized vesicles to investigate how membrane permeability affects the dynamics of the encapsulated ATPS. Designing a membrane selectively permeable to one of the components of the ATPS, we show that out-of-equilibrium phase separations formed by a rapid outflow of water can be spontaneously reversed by a slower outflow of the permeating component across the vesicle membrane. This dynamics may be exploited advantageously by cells to separate and connect metabolic and signaling routes within their nucleoplasm or cytoplasm depending on external conditions.