SummaryRecently, a new regulatory circuitry has been identified in which RNAs can crosstalk with each other by competing for shared microRNAs. Such competing endogenous RNAs (ceRNAs) regulate the distribution of miRNA molecules on their targets and thereby impose an additional level of post-transcriptional regulation. Here we identify a muscle-specific long noncoding RNA, linc-MD1, which governs the time of muscle differentiation by acting as a ceRNA in mouse and human myoblasts. Downregulation or overexpression of linc-MD1 correlate with retardation or anticipation of the muscle differentiation program, respectively. We show that linc-MD1 “sponges” miR-133 and miR-135 to regulate the expression of MAML1 and MEF2C, transcription factors that activate muscle-specific gene expression. Finally, we demonstrate that linc-MD1 exerts the same control over differentiation timing in human myoblasts, and that its levels are strongly reduced in Duchenne muscle cells. We conclude that the ceRNA network plays an important role in muscle differentiation.

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Single-cell profiling methods have had a profound impact on the understanding of cellular heterogeneity. While genomes and transcriptomes can be explored at the single-cell level, single-cell profiling of proteomes is not yet established. Here we describe new single-molecule protein sequencing and identification technologies alongside innovations in mass spectrometry that will eventually enable broad sequence coverage in single-cell profiling. These technologies will in turn facilitate biological discovery and open new avenues for ultrasensitive disease diagnostics.

In this work, we study the wetting of a surface decorated with one nanogroove by a bulk Lennard-Jones liquid at various temperatures and densities. We used atomistic simulations aimed at computing the free energy of the stable and metastable states of the system, as well as the intermediate states separating them. We found that the usual description in terms of Cassie-Baxter and Wenzel states is insufficient, as the system presents two states of the Cassie-Baxter type. These states are characterized by different curvatures of the meniscus. The measured free energy barrier separating the Cassie-Baxter from the Wenzel state (and vice versa) largely exceeds the thermal energy, attesting the existence of Cassie-Baxter/Wenzel metastabilities. Finally, we found that the Cassie-Baxter/Wenzel transition follows an asymmetric path, with the formation of a liquid finger on one side of the groove and a vapor bubble on the opposite side.

In this Letter, we develop a continuum theory for the Cassie-Baxter-Wenzel (CB-W) transition. The proposed model accounts for the metastabilities in the wetting of rough hydrophobic surfaces, allows us to reconstruct the transition mechanism, and identifies the free energy barriers separating the CB and W states as a function of the liquid pressure. This information is crucial in the context of superhydrophobic surfaces, where there is interest in extending the duration of the metastable superhydrophobic CB state. The model is validated against free energy atomistic simulations.

We report on the ability to control the dynamics of a single peptide capture and passage across a voltage-biased, α-hemolysin nanopore (α-HL), under conditions that the electroosmotic force exerted on the analyte dominates the electrophoretic transport. We demonstrate that by extending outside the nanopore, the electroosmotic force is able to capture a peptide at either the lumen or vestibule entry of the nanopore, and transiently traps it inside the nanopore, against the electrophoretic force. Statistical analysis of the resolvable dwell-times of a metastable trapped peptide, as it occupies either the β-barrel or vestibule domain of the α-HL nanopore, reveals rich kinetic details regarding the direction and rates of stochastic movement of a peptide inside the nanopore. The presented approach demonstrates the ability to shuttle and study molecules along the passage pathway inside the nanopore, allows to identify the mesoscopic trajectory of a peptide exiting the nanopore through either the vestibule or β-barrel moiety, thus providing convincing proof of a molecule translocating the pore. The kinetic analysis of a peptide fluctuating between various microstates inside the nanopore, enabled a detailed picture of the free energy description of its interaction with the α-HL nanopore. When studied at the limit of vanishingly low transmembrane potentials, this provided a thermodynamic description of peptide reversible binding to and within the α-HL nanopore, under equilibrium conditions devoid of electric and electroosmotic contributions.

The Cahn–Hilliard model is increasingly often being used in combination with the incompressible Navier–Stokes equation to describe unsteady binary fluids in a variety of applications ranging from turbulent two-phase flows to microfluidics. The thickness of the interface between the two bulk fluids and the mobility are the main parameters of the model. For real fluids they are usually too small to be directly used in numerical simulations. Several authors proposed criteria for the proper choice of interface thickness and mobility in order to reach the so-called ‘sharp-interface limit’. In this paper the problem is approached by a formal asymptotic expansion of the governing equations. It is shown that the mobility is an effective parameter to be chosen proportional to the square of the interface thickness. The theoretical results are confirmed by numerical simulations for two prototypal flows, namely capillary waves riding the interface and droplets coalescence. The numerical analysis of two different physical problems confirms the theoretical findings and establishes an optimal relationship between the effective parameters of the model.

Protein and solid-state nanometer-scale pores are being developed for the detection, analysis, and manipulation of single molecules. In the simplest embodiment, the entry of a molecule into a nanopore causes a reduction in the latter’s ionic conductance. The ionic current blockade depth and residence time have been shown to provide detailed information on the size, adsorbed charge, and other properties of molecules. Here we describe the use of the nanopore formed by Staphylococcus aureus α-hemolysin and polypeptides with oppositely charged segments at the N- and C-termini to increase both the polypeptide capture rate and mean residence time of them in the pore, regardless of the polarity of the applied electrostatic potential. The technique provides the means to improve the signal to noise of single molecule nanopore-based measurements.