Competition shapes the landscape of X-chromosome-linked genetic diversity.

X chromosome inactivation (XCI) generates clonal heterogeneity within XX individuals. Combined with sequence variation between human X chromosomes, XCI gives rise to intra-individual clonal diversity, whereby two sets of clones express mutually exclusive sequence variants present on one or the other X chromosome. Here we ask whether such clones merely co-exist or potentially interact with each other to modulate the contribution of X-linked diversity to organismal development. Focusing on X-linked coding variation in the human STAG2 gene, we show that Stag2variant clones contribute to most tissues at the expected frequencies but fail to form lymphocytes in Stag2WT Stag2variant mouse models. Unexpectedly, the absence of Stag2variant clones from the lymphoid compartment is due not solely to cell-intrinsic defects but requires continuous competition by Stag2WT clones. These findings show that interactions between epigenetically diverse clones can operate in an XX individual to shape the contribution of X-linked genetic diversity in a cell-type-specific manner.

Endogenous bioluminescent reporters reveal a sustained increase in utrophin gene expression upon EZH2 and ERK1/2 inhibition.

Duchenne muscular dystrophy (DMD) is an X-linked disorder caused by loss of function mutations in the dystrophin gene (Dmd), resulting in progressive muscle weakening. Here we modelled the longitudinal expression of endogenous Dmd, and its paralogue Utrn, in mice and in myoblasts by generating bespoke bioluminescent gene reporters. As utrophin can partially compensate for Dmd-deficiency, these reporters were used as tools to ask whether chromatin-modifying drugs can enhance Utrn expression in developing muscle. Myoblasts treated with different PRC2 inhibitors showed significant increases in Utrn transcripts and bioluminescent signals, and these responses were independently verified by conditional Ezh2 deletion. Inhibition of ERK1/2 signalling provoked an additional increase in Utrn expression that was also seen in Dmd-mutant cells, and maintained as myoblasts differentiate. These data reveal PRC2 and ERK1/2 to be negative regulators of Utrn expression and provide specialised molecular imaging tools to monitor utrophin expression as a therapeutic strategy for DMD.

3D Concentric Electrodes-Based Alternating Current Electrohydrodynamics: Design, Simulation, Fabrication, and Potential Applications for Bioassays.

Two-dimensional concentric asymmetric microelectrodes play a crucial role in developing sensitive and specific biological assays using fluid micromixing generated by alternating current electrohydrodynamics (ac-EHD). This paper reports the design, simulation, fabrication, and characterization of fluid motion generated by 3D concentric microelectrodes for the first time. Electric field simulations are used to compare electric field distribution at the electrodes and to analyze its effects on microfluidic micromixing in 2D and 3D electrodes. Three-dimensional devices show higher electric field peak values, resulting in better fluid micromixing than 2D devices. As a proof of concept, we design a simple biological assay comprising specific attachment of streptavidin beads onto the biotin-modified electrodes (2D and 3D), which shows ~40% higher efficiency of capturing specific beads in the case of 3D ac-EHD device compared to the 2D device. Our results show a significant contribution toward developing 3D ac-EHD devices that can be used to create more efficient biological assays in the future.

On the spurious resonance modes of time domain integral equations for analyzing acoustic scattering from penetrable objects.

The interior resonance problem of time domain integral equations (TDIEs) formulated to analyze acoustic field interactions on penetrable objects is investigated. Two types of TDIEs are considered: The first equation, which is termed the time domain potential integral equation (TDPIE), suffers from the interior resonance problem, i.e., its solution is replete with spurious modes that are excited at the resonance frequencies of the acoustic cavity in the shape of the scatterer. Numerical experiments demonstrate that, unlike the frequency-domain integral equations, the amplitude of these modes in the time domain could be suppressed to a level that does not significantly affect the solution. This is achieved by increasing the numerical solution accuracy through the use of a higher-order discretization in space and the band limited approximate prolate spheroidal wave function with high interpolation accuracy as basis function in time. The second equation is obtained by linearly combining TDPIE with its normal derivative. The solution of this equation, which is termed the time domain combined potential integral equation (TDCPIE), does not involve any spurious interior resonance modes but it is not as accurate as the TDPIE solution at non-resonance frequencies. In addition, TDCPIE's discretization calls for treatment of hypersingular integrals.

Efficient discontinuous Galerkin scheme for analyzing nanostructured photoconductive devices.

Incorporation of plasmonic nanostructures in the design of photoconductive devices (PCDs) has significantly improved their optical-to-terahertz conversion efficiency. However, this improvement comes at the cost of increased complexity for the design and simulation of these devices. Indeed, accurate and efficient modeling of multiphysics processes and intricate device geometries of nanostructured PCDs is challenging due to the high computational cost resulting from multiple characteristic scales in time and space. In this work, a discontinuous Galerkin (DG)-based unit-cell scheme for efficient simulation of PCDs with periodic nanostructures is proposed. The scheme considers two physical stages of the device and models them using two coupled systems: a system of Poisson and drift-diffusion equations describing the nonequilibrium steady state, and a system of Maxwell and drift-diffusion equations describing the transient stage. A "potential-drop" boundary condition is enforced on the opposing boundaries of the unit cell to mimic the effect of the bias voltage. Periodic boundary conditions are used for carrier densities and electromagnetic fields. The unit-cell model described by these coupled equations and boundary conditions is discretized using DG methods. Numerical results demonstrate that the proposed DG-based unit-cell scheme has the same accuracy in predicting the THz photocurrent as the DG framework that takes into account the whole device, while it significantly reduces the computational cost.

An explicit marching-on-in-time scheme for solving the time domain Kirchhoff integral equation.

A fully explicit marching-on-in-time (MOT) scheme for solving the time domain Kirchhoff (surface) integral equation to analyze transient acoustic scattering from rigid objects is presented. A higher-order Nyström method and a PE(CE)m-type ordinary differential equation integrator are used for spatial discretization and time marching, respectively. The resulting MOT scheme uses the same time step size as its implicit counterpart (which also uses Nyström method in space) without sacrificing from the accuracy and stability of the solution. Numerical results demonstrate the accuracy, efficiency, and applicability of the proposed explicit MOT solver.

An FMM-FFT Accelerated SIE Simulator for Analyzing EM Wave Propagation in Mine Environments Loaded With Conductors.

A fast and memory efficient three-dimensional full-wave simulator for analyzing electromagnetic (EM) wave propagation in electrically large and realistic mine tunnels/galleries loaded with conductors is proposed. The simulator relies on Muller and combined field surface integral equations (SIEs) to account for scattering from mine walls and conductors, respectively. During the iterative solution of the system of SIEs, the simulator uses a fast multipole method-fast Fourier transform (FMM-FFT) scheme to reduce CPU and memory requirements. The memory requirement is further reduced by compressing large data structures via singular value and Tucker decompositions. The efficiency, accuracy, and real-world applicability of the simulator are demonstrated through characterization of EM wave propagation in electrically large mine tunnels/galleries loaded with conducting cables and mine carts.

Epigenetic reprogramming enables the transition from primordial germ cell to gonocyte.

Gametes are highly specialized cells that can give rise to the next generation through their ability to generate a totipotent zygote. In mice, germ cells are first specified in the developing embryo around embryonic day (E) 6.25 as primordial germ cells (PGCs). Following subsequent migration into the developing gonad, PGCs undergo a wave of extensive epigenetic reprogramming around E10.5-E11.5, including genome-wide loss of 5-methylcytosine. The underlying molecular mechanisms of this process have remained unclear, leading to our inability to recapitulate this step of germline development in vitro. Here we show, using an integrative approach, that this complex reprogramming process involves coordinated interplay among promoter sequence characteristics, DNA (de)methylation, the polycomb (PRC1) complex and both DNA demethylation-dependent and -independent functions of TET1 to enable the activation of a critical set of germline reprogramming-responsive genes involved in gamete generation and meiosis. Our results also reveal an unexpected role for TET1 in maintaining but not driving DNA demethylation in gonadal PGCs. Collectively, our work uncovers a fundamental biological role for gonadal germline reprogramming and identifies the epigenetic principles of the PGC-to-gonocyte transition that will help to guide attempts to recapitulate complete gametogenesis in vitro.

Quantum-corrected transient analysis of plasmonic nanostructures.

A time domain surface integral equation (TD-SIE) solver is developed for quantum-corrected analysis of transient electromagnetic field interactions on plasmonic nanostructures with sub-nanometer gaps. "Quantum correction" introduces an auxiliary tunnel to support the current path that is generated by electrons tunneled between the nanostructures. The permittivity of the auxiliary tunnel and the nanostructures is obtained from density functional theory (DFT) computations. Electromagnetic field interactions on the combined structure (nanostructures plus auxiliary tunnel connecting them) are computed using a TD-SIE solver. Time domain samples of the permittivity and the Green function required by this solver are obtained from their frequency domain samples (generated from DFT computations) using a semi-analytical method. Accuracy and applicability of the resulting quantum-corrected solver scheme are demonstrated via numerical examples.

Transient analysis of electromagnetic wave interactions on plasmonic nanostructures using a surface integral equation solver.

Transient electromagnetic interactions on plasmonic nanostructures are analyzed by solving the Poggio-Miller-Chan-Harrington-Wu-Tsai (PMCHWT) surface integral equation (SIE). Equivalent (unknown) electric and magnetic current densities, which are introduced on the surfaces of the nanostructures, are expanded using Rao-Wilton-Glisson and polynomial basis functions in space and time, respectively. Inserting this expansion into the PMCHWT-SIE and Galerkin testing the resulting equation at discrete times yield a system of equations that is solved for the current expansion coefficients by a marching on-in-time (MOT) scheme. The resulting MOT-PMCHWT-SIE solver calls for computation of additional convolutions between the temporal basis function and the plasmonic medium's permittivity and Green function. This computation is carried out with almost no additional cost and without changing the computational complexity of the solver. Time-domain samples of the permittivity and the Green function required by these convolutions are obtained from their frequency-domain samples using a fast relaxed vector fitting algorithm. Numerical results demonstrate the accuracy and applicability of the proposed MOT-PMCHWT solver.

Ordered chromatin changes and human X chromosome reactivation by cell fusion-mediated pluripotent reprogramming.

Erasure of epigenetic memory is required to convert somatic cells towards pluripotency. Reactivation of the inactive X chromosome (Xi) has been used to model epigenetic reprogramming in mouse, but human studies are hampered by Xi epigenetic instability and difficulties in tracking partially reprogrammed iPSCs. Here we use cell fusion to examine the earliest events in the reprogramming-induced Xi reactivation of human female fibroblasts. We show that a rapid and widespread loss of Xi-associated H3K27me3 and XIST occurs in fused cells and precedes the bi-allelic expression of selected Xi-genes by many heterokaryons (30-50%). After cell division, RNA-FISH and RNA-seq analyses confirm that Xi reactivation remains partial and that induction of human pluripotency-specific XACT transcripts is rare (1%). These data effectively separate pre- and post-mitotic events in reprogramming-induced Xi reactivation and reveal a complex hierarchy of epigenetic changes that are required to reactivate the genes on the human Xi chromosome.

Mirror-backed Dark Alumina: A Nearly Perfect Absorber for Thermoelectronics and Thermophotovotaics.

We present here a broadband, wide-angle, and polarization-independent nearly perfect absorber consisting of mirror-backed nanoporous alumina. By electrochemically anodizing the disordered multicomponent aluminum and properly tailoring the thickness and air-filling fraction of nanoporous alumina, according to the Maxwell-Garnet mixture theory, a large-area dark alumina can be made with excellent photothermal properties and absorption larger than 93% over a wide wavelength range spanning from near-infrared to ultraviolet light, i.e. 250 nm-2500 nm. The measured absorption is orders of magnitude greater than other reported anodized porous alumina, typically semi-transparent at similar wavelengths. This simple yet effective approach, however, does not require any lithography, nano-mixture deposition, pre- and post-treatment. Here, we also envisage and theoretically investigate the practical use of proposed absorbers and/or photothermal converters in integrated thermoelectronic and/or thermophotovoltaic energy conversion devices, which make efficient use of the entire spectrum of ambient visible to near-infrared radiation.

Jarid2 Coordinates Nanog Expression and PCP/Wnt Signaling Required for Efficient ESC Differentiation and Early Embryo Development.

Jarid2 is part of the Polycomb Repressor complex 2 (PRC2) responsible for genome-wide H3K27me3 deposition. Unlike other PRC2-deficient embryonic stem cells (ESCs), however, Jarid2-deficient ESCs show a severe differentiation block, altered colony morphology, and distinctive patterns of deregulated gene expression. Here, we show that Jarid2(-/-) ESCs express constitutively high levels of Nanog but reduced PCP signaling components Wnt9a, Prickle1, and Fzd2 and lowered ß-catenin activity. Depletion of Wnt9a/Prickle1/Fzd2 from wild-type ESCs or overexpression of Nanog largely phenocopies these cellular defects. Co-culture of Jarid2(-/-) with wild-type ESCs restores variable Nanog expression and ß-catenin activity and can partially rescue the differentiation block of mutant cells. In addition, we show that ESCs lacking Jarid2 or Wnt9a/Prickle1/Fzd2 or overexpressing Nanog induce multiple ICM formation when injected into normal E3.5 blastocysts. These data describe a previously unrecognized role for Jarid2 in regulating a core pluripotency and Wnt/PCP signaling circuit that is important for ESC differentiation and for pre-implantation development.

Graphene metascreen for designing compact infrared absorbers with enhanced bandwidth.

We propose a compact, wideband terahertz and infrared absorber, comprising a patterned graphene sheet on a thin metal-backed dielectric slab. This graphene-based nanostructure can achieve a low or negative effective permeability, necessary for realizing the perfect absorption. The dual-reactive property found in both the plasmonic graphene sheet and the grounded high-permittivity slab introduces extra poles into the equivalent circuit model of the system, thereby resulting in a dual-band or broadband magnetic resonance that enhances the absorption bandwidth. More interestingly, the two-dimensional patterned graphene sheet significantly simplifies the design and fabrication processes for achieving resonant magnetic response, and allows the frequency-reconfigurable operation via electrostatic gating.

A nonlinear plasmonic resonator for three-state all-optical switching.

A nonlinear plasmonic resonator design is proposed for three-state all-optical switching at frequencies including near infrared and lower red parts of the spectrum. The tri-stable response required for three-state operation is obtained by enhancing nonlinearities of a Kerr medium through multiple (higher order) plasmons excited on resonator's metallic surfaces. Indeed, simulations demonstrate that exploitation of multiple plasmons equips the proposed resonator with a multi-band tri-stable response, which cannot be obtained using existing nonlinear plasmonic devices that make use of single mode Lorentzian resonances. Multi-band three-state optical switching that can be realized using the proposed resonator has potential applications in optical communications and computing.

Behavior of obliquely incident vector Bessel beams at planar interfaces.

We investigate the behavior of full-vector electromagnetic Bessel beams obliquely incident at an interface between two electrically different media. We employ a Fourier transform domain representation of Bessel beams to determine their behavior upon reflection and transmission. This transform, which is geometric in nature, consists of elliptical support curves with complex weighting associated with them. The behavior of the scattered field at an interface is highly complex, owing to its full-vector nature; nevertheless, this behavior has a straightforward representation in the transform domain geometry. The analysis shows that the reflected field forms a different vector Bessel beam, but in general, the transmitted field cannot be represented as a Bessel beam. Nevertheless, using this approach, we demonstrate a method to propagate a Bessel beam in the refractive medium by launching a non-Bessel beam at the interface. Several interesting phenomena related to the behavior of Bessel beams are illustrated, such as polarized reflection at Brewster's angle incidence, and the Goos-Hänchen and Imbert-Federov shifts in the case of total reflection.

Atypical heterochromatin organization and replication are rapidly acquired by somatic cells following fusion-mediated reprogramming by mouse ESCs.

We recently reported that mouse embryonic stem cells (ESCs) in S/G 2 are more efficient at reprogramming somatic cells than ESCs at other stages of the cell cycle. We also provided evidence that DNA replication is induced in the nuclei of somatic partners upon fusion with ESC partners, and showed that this was critical for their conversion toward a pluripotent state. (1) Here we have used counterflow centrifugal elutriation to enrich for ESCs at different cell cycle phases, so as to examine in detail the properties of S/G 2 phase cells. This revealed that the replication and organization of DAPI-intense heterochromatin in ESCs is unusual in two respects. First, replication of heterochromatin occurred earlier during S phase and was associated with precocious H3S10 phosphorylation. Second, heterochromatin protein 1 α (HP1α), which invariably marks DAPI-intense and H3K9me3-enriched pericentromeric domains in mouse somatic cells, (2) was not necessarily associated with these H3K9me3-enriched domains in undifferentiated ESCs. These data, which complement recent replication timing (3) and electron spectroscopic imaging (ESI) analyses, (4) suggest that heterochromatin is atypical in ESCs. Interestingly, as these unusual features were rapidly acquired by somatic nuclei upon ESC fusion-mediated reprogramming, our results suggest that fundamental changes in cell cycle structure and heterochromatin dynamics may be important for conferring pluripotency.

DNA demethylation in pluripotency and reprogramming: the role of tet proteins and cell division.

Cytosine methylation is found in the genomes of many plants and animals and has been associated with transcriptional silencing in mammals. At critical stages in embryo development, when cellular potential is reset, DNA methylation is lost in a series of "sequential waves." The mechanism underlying this is controversial and complex. Several new reports now suggest that TET enzymes and cell division are important for these in vivo transitions as well as for experimentally induced reprogramming.

A 3D tunable and multi-frequency graphene plasmonic cloak.

We demonstrate the possibility of cloaking three-dimensional objects at multi-frequencies in the far-infrared part of the spectrum. The proposed cloaking mechanism exploits graphene layers wrapped around the object to be concealed. Graphene layers are doped via a variable external voltage difference permitting continuous tuning of the cloaking frequencies. Particularly, two configurations are investigated: (i) Only one graphene layer is used to suppress the scattering from a dielectric sphere. (ii) Several of these layers biased at different gate voltages are used to achieve a multi-frequency cloak. These frequencies can be set independently. The proposed cloak's functionality is verified by near- and far-field computations. By considering geometry and material parameters that are realizable by practical experiments, we contribute to the development of graphene based plasmonic applications that may find use in disruptive photonic technologies.

Different roles for Tet1 and Tet2 proteins in reprogramming-mediated erasure of imprints induced by EGC fusion.

Genomic imprinting directs the allele-specific marking and expression of loci according to their parental origin. Differential DNA methylation at imprinted control regions (ICRs) is established in gametes and, although largely preserved through development, can be experimentally reset by fusing somatic cells with embryonic germ cell (EGC) lines. Here, we show that the Ten-Eleven Translocation proteins Tet1 and Tet2 participate in the efficient erasure of imprints in this model system. The fusion of B cells with EGCs initiates pluripotent reprogramming, in which rapid re-expression of Oct4 is accompanied by an accumulation of 5-hydroxymethylcytosine (5hmC) at several ICRs. Tet2 was required for the efficient reprogramming capacity of EGCs, whereas Tet1 was necessary to induce 5-methylcytosine oxidation specifically at ICRs. These data show that the Tet1 and Tet2 proteins have discrete roles in cell-fusion-mediated pluripotent reprogramming and imprint erasure in somatic cells.