Probing the (H3-H4)(2) histone tetramer structure using pulsed EPR spectroscopy combined with site-directed spin labelling

The (H3-H4)2 histone tetramer forms the central core of nucleosomes and, as such, plays a prominent role in assembly, disassembly and positioning of nucleosomes. Despite its fundamental role in chromatin, the tetramer has received little structural investigation. Here, through the use of pulsed electron-electron double resonance spectroscopy coupled with site-directed spin labelling, we survey the structure of the tetramer in solution. We find that tetramer is structurally more heterogeneous on its own than when sequestered in the octamer or nucleosome. In particular, while the central region including the H3-H3′ interface retains a structure similar to that observed in nucleosomes, other regions such as the H3 αN helix display increased structural heterogeneity. Flexibility of the H3 αN helix in the free tetramer also illustrates the potential for post-translational modifications to alter the structure of this region and mediate interactions with histone chaperones. The approach described here promises to prove a powerful system for investigating the structure of additional assemblies of histones with other important factors in chromatin assembly/fluidity

The histone chaperones Nap1 and Vps75 bind histones H3 and H4 in a tetrameric conformation

Histone chaperones physically interact with histones to direct proper assembly and disassembly of nucleosomes regulating diverse nuclear processes such as DNA replication, promoter remodeling, transcription elongation, DNA damage, and histone variant exchange. Currently, the best-characterized chaperone-histone interaction is that between the ubiquitous chaperone Asf1 and a dimer of H3 and H4. Nucleosome assembly proteins (Nap proteins) represent a distinct class of histone chaperone. Using pulsed electron double resonance (PELDOR) measurements and protein crosslinking, we show that two members of this class, Nap1 and Vps75, bind histones in the tetrameric conformation also observed when they are sequestered within the nucleosome. Furthermore, H3 and H4 trapped in their tetrameric state can be used as substrates in nucleosome assembly and chaperone-mediated lysine acetylation. This alternate mode of histone interaction provides a potential means of maintaining the integrity of the histone tetramer during cycles of nucleosome reassembly

Editorial:Metformin: Beyond Diabetes

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Quadratic BSDEs driven by a continuous martingale and application to utility maximization problem

In this paper, we study a class of quadratic Backward Stochastic Differential Equations (BSDEs) which arises naturally when studying the problem of utility maximization with portfolio constraints. We first establish existence and uniqueness results for such BSDEs and then, we give an application to the utility maximization problem. Three cases of utility functions will be discussed: the exponential, power and logarithmic ones

Empirical likelihood estimation of the spatial quantile regression

The spatial quantile regression model is a useful and flexible model for analysis of empirical problems with spatial dimension. This paper introduces an alternative estimator for this model. The properties of the proposed estimator are discussed in a comparative perspective with regard to the other available estimators. Simulation evidence on the small sample properties of the proposed estimator is provided. The proposed estimator is feasible and preferable when the model contains multiple spatial weighting matrices. Furthermore, a version of the proposed estimator based on the exponentially tilted empirical likelihood could be beneficial if model misspecification is suspect

3D lithium ion batteries—from fundamentals to fabrication

3D microbatteries are proposed as a step change in the energy and power per footprint of surface mountable rechargeable batteries for microelectromechanical systems (MEMS) and other small electronic devices. Within a battery electrode, a 3D nanoarchitecture gives mesoporosity, increasing power by reducing the length of the diffusion path; in the separator region it can form the basis of a robust but porous solid, isolating the electrodes and immobilising an otherwise fluid electrolyte. 3D microarchitecture of the whole cell allows fabrication of interdigitated or interpenetrating networks that minimise the ionic path length between the electrodes in a thick cell. This article outlines the design principles for 3D microbatteries and estimates the geometrical and physical requirements of the materials. It then gives selected examples of recent progress in the techniques available for fabrication of 3D battery structures by successive deposition of electrodes, electrolytes and current collectors onto microstructured substrates by self-assembly methods

The spatial effect of protein deuteration on nitroxide spin-label relaxation:implications for EPR distance measurement

This work was supported by a Wellcome Trust Senior Fellowship (095062) to T.O.-H. The Authors would also like to acknowledge funding from The MRC – United Kingdom, Grant G1100021.Pulsed electron-electron double resonance (PELDOR) coupled with site-directed spin labeling is a powerful technique for the elucidation of protein or nucleic acid, macromolecular structure and interactions. The intrinsic high sensitivity of electron paramagnetic resonance enables measurement on small quantities of bio-macromolecules, however short relaxation times impose a limit on the sensitivity and size of distances that can be measured using this technique. The persistence of the electron spin-echo, in the PELDOR experiment, is one of the most crucial limitations to distance measurement. At a temperature of around 50 K one of the predominant factors affecting persistence of an echo, and as such, the sensitivity and measurable distance between spin labels, is the electron spin echo dephasing time (Tm). It has become normal practice to use deuterated solvents to extend Tm and recently it has been demonstrated that deuteration of the underlying protein significantly extends Tm. Here we examine the spatial effect of segmental deuteration of the underlying protein, and also explore the concentration and temperature dependence of highly deuterated systems.Publisher PDFPeer reviewe

Biomimetic bluff body drag reduction by self-adaptive porous flaps

The performances of an original passive control system based on a biomimetic approach are assessed by investigating the flow over a bluff-body. This control device consists in a couple of flaps made from the combination of a rigid plastic skeleton coated with a porous fabric mimicking the shaft and the vane of the bird's feathers, respectively. The sides of a square cylinder have been fitted with this system so as to enable the flaps to freely rotate around their leading edge. This feature allows the movable flaps to self-adapt to the flow conditions. Comparing both the uncontrolled and the controlled flow, a significant drag reduction (up to 22%) has been obtained over a broad range of Reynolds number. The investigation of the mean flow reveals a noticeable modification of the flow topology at large scale in the vicinity of the controlled cylinder accounting for the increase of the pressure base in comparison with the natural flow. Meanwhile, the study of the relative motion of both flaps points out that their dynamics is sensitive to the Reynolds number. Furthermore, the comparative study of the flow dynamics at large scale suggest a lock-in coupling of the flap motion and the vortex shedding.Comment: 19 pages, 17 figures, submitted to Comptes-Rendus de l' Acad\'emie des Sciences (M\'ecanique

Parameter extraction for a superconducting thermal switch (hTron) SPICE model

Efficiently simulating large circuits is crucial for the broader use of superconducting nanowire-based electronics. However, current simulation tools for this technology are not adapted to the scaling of circuit size and complexity. We focus on the multilayered heater-nanocryotron (hTron), a promising superconducting nanowire-based switch used in applications such as superconducting nanowire single-photon detector (SNSPD) readout. Previously, the hTron was modeled using traditional finite-element methods (FEM), which fall short in simulating systems at a larger scale. An empirical-based method would be better adapted to this task, enhancing both simulation speed and agreement with experimental data. In this work, we perform switching current and activation delay measurements on 17 hTron devices. We then develop a method for extracting physical fitting parameters used to characterize the devices. We build a SPICE behavioral model that reproduces the static and transient device behavior using these parameters, and validate it by comparing its performance to the model developed in a prior work, showing an improvement in simulation time by several orders of magnitude. Our model provides circuit designers with a tool to help understand the hTron's behavior during all design stages, thus promoting broader use of the hTron across various new areas of application.Comment: Supplementary material (LTspice schematics and symbol) available on GitHub: https://github.com/vkaram/hTron-behavioral-mode

Rac1 drives intestinal stem cell proliferation and regeneration

Adult stem cells are responsible for maintaining the balance between cell proliferation and differentiation within self-renewing tissues. The molecular and cellular mechanisms mediating such balance are poorly understood. The production of reactive oxygen species (ROS) has emerged as an important mediator of stem cell homeostasis in various systems. Our recent work demonstrates that Rac1-dependent ROS production mediates intestinal stem cell (ISC) proliferation in mouse models of colorectal cancer (CRC). Here, we use the adult Drosophila midgut and the mouse small intestine to directly address the role of Rac1 in ISC proliferation and tissue regeneration in response to damage. Our results demonstrate that Rac1 is necessary and sufficient to drive ISC proliferation and regeneration in an ROS-dependent manner. Our data point to an evolutionarily conserved role of Rac1 in intestinal homeostasis and highlight the value of combining work in the mammalian and Drosophila intestine as paradigms to study stem cell biology