eRNA binding produces tailored CBP activity profiles to regulate gene expression

Enhancers are cis- regulatory genetic elements crucial for controlling temporal and cell-type specific patterns of gene expression. Active enhancers generate bi-directional non-coding RNA transcripts called enhancer RNAs (eRNAs). eRNAs are important for stimulating gene expression, but precise mechanisms for this ability remain unclear. Here we highlight recent findings that demonstrate a direct interaction between RNAs and the transcriptional co-activator Creb-binding protein (CBP). Notably, RNA binding could stimulate the core histone acetyltransferase activity of the enzyme, observable in cells as a link between eRNA production, CBP-dependent histone acetylation and expression of genes regulated by specific enhancers. Although RNA binding was independent of RNA sequence, specificity arises in a locus-specific manner at transcribed sites where CBP was bound to chromatin. The results suggest a functional role for eRNAs as regulatory molecules that are able to stimulate the activity of a key epigenetic regulatory enzyme, thereby promoting gene expression. Furthermore, they suggest an intriguing role for eRNAs: by modulating the activity of chromatin modifying enzymes, they could directly impact transcription by altering the chromatin environment

The Singularity Threshold of the Nonlinear Sigma Model Using 3D Adaptive Mesh Refinement

Numerical solutions to the nonlinear sigma model (NLSM), a wave map from 3+1 Minkowski space to S^3, are computed in three spatial dimensions (3D) using adaptive mesh refinement (AMR). For initial data with compact support the model is known to have two regimes, one in which regular initial data forms a singularity and another in which the energy is dispersed to infinity. The transition between these regimes has been shown in spherical symmetry to demonstrate threshold behavior similar to that between black hole formation and dispersal in gravitating theories. Here, I generalize the result by removing the assumption of spherical symmetry. The evolutions suggest that the spherically symmetric critical solution remains an intermediate attractor separating the two end states.Comment: 5 pages, 5 figures, 1 table; To be published in Phys. Rev. D.; Added discussion of initial data; Added figure and reference

A time series transcriptome analysis of cassava (Manihot esculenta Crantz) varieties challenged with Ugandan cassava brown streak virus

Open Access Journal; Published online: 29 August 2017A time-course transcriptome analysis of two cassava varieties that are either resistant or susceptible to cassava brown streak disease (CBSD) was conducted using RNASeq, after graft inoculation with Ugandan cassava brown streak virus (UCBSV). From approximately 1.92 billion short reads, the largest number of differentially expressed genes (DEGs) was obtained in the resistant (Namikonga) variety at 2 days after grafting (dag) (3887 DEGs) and 5 dag (4911 DEGs). At the same time points, several defense response genes (encoding LRR-containing, NBARC-containing, pathogenesis-related, late embryogenesis abundant, selected transcription factors, chaperones, and heat shock proteins) were highly expressed in Namikonga. Also, defense-related GO terms of ‘translational elongation’, ‘translation factor activity’, ‘ribosomal subunit’ and ‘phosphorelay signal transduction’, were overrepresented in Namikonga at these time points. More reads corresponding to UCBSV sequences were recovered from the susceptible variety (Albert) (733 and 1660 read counts per million (cpm)) at 45 dag and 54 dag compared to Namikonga (10 and 117 cpm respectively). These findings suggest that Namikonga’s resistance involves restriction of multiplication of UCBSV within the host. These findings can be used with other sources of evidence to identify candidate genes and biomarkers that would contribute substantially to knowledge-based resistance breeding

Chiral Symmetry and Diffractive Neutral Pion Photo- and Electroproduction

We show that diffractive production of a single neutral pion in photon-induced reactions at high energy is dynamically suppressed due to the approximate chiral symmetry of QCD. These reactions have been proposed as a test of the odderon exchange mechanism. We show that the odderon contribution to the amplitude for such reactions vanishes exactly in the chiral limit. This result is obtained in a nonperturbative framework and by using PCAC relations between the amplitudes for neutral pion and axial vector current production.Comment: 22 pages, 7 figure

Signals that stop the rot : regulation of secondary metabolite defences in cereals

Plants accumulate a vast arsenal of chemically diverse secondary metabolites for defence against pathogens. This review will focus on the signal transduction and regulation of defence secondary metabolite production in five food security cereal crops: maize, rice, wheat, sorghum and oats. Recent research advances in this field have revealed novel processes and chemistry in these monocots that make this a rich field for future research.The National Research Foundation (NRF) and the Genomics Research Institute at the University of Pretoria (UP), South Africa.http://www.elsevier.com/locate/pmpp2017-04-30hb2016Forestry and Agricultural Biotechnology Institute (FABI)Plant Scienc

No-horizon theorem for vacuum gravity with spacelike G1 isometry groups

We show that (3+1) vacuum spacetimes admitting a global, spacelike, one-parameter Lie group of isometries of translational type cannot contain apparent horizons. The only assumption made is that of the existence of a global spacelike Killing vector field with infinite open orbits; the four-dimensional vacuum spacetime metric is otherwise arbitrary. This result may thus be viewed as a hoop conjecture theorem for vacuum gravity with one spacelike translational Killing symmetry.Comment: 6 pages, revtex4; published in Phys. Rev. D Rapid Com

Adaptive Mesh Refinement for Characteristic Grids

I consider techniques for Berger-Oliger adaptive mesh refinement (AMR) when numerically solving partial differential equations with wave-like solutions, using characteristic (double-null) grids. Such AMR algorithms are naturally recursive, and the best-known past Berger-Oliger characteristic AMR algorithm, that of Pretorius & Lehner (J. Comp. Phys. 198 (2004), 10), recurses on individual "diamond" characteristic grid cells. This leads to the use of fine-grained memory management, with individual grid cells kept in 2-dimensional linked lists at each refinement level. This complicates the implementation and adds overhead in both space and time. Here I describe a Berger-Oliger characteristic AMR algorithm which instead recurses on null \emph{slices}. This algorithm is very similar to the usual Cauchy Berger-Oliger algorithm, and uses relatively coarse-grained memory management, allowing entire null slices to be stored in contiguous arrays in memory. The algorithm is very efficient in both space and time. I describe discretizations yielding both 2nd and 4th order global accuracy. My code implementing the algorithm described here is included in the electronic supplementary materials accompanying this paper, and is freely available to other researchers under the terms of the GNU general public license.Comment: 37 pages, 15 figures (40 eps figure files, 8 of them color; all are viewable ok in black-and-white), 1 mpeg movie, uses Springer-Verlag svjour3 document class, includes C++ source code. Changes from v1: revised in response to referee comments: many references added, new figure added to better explain the algorithm, other small changes, C++ code updated to latest versio

Critical Collapse of the Massless Scalar Field in Axisymmetry

We present results from a numerical study of critical gravitational collapse of axisymmetric distributions of massless scalar field energy. We find threshold behavior that can be described by the spherically symmetric critical solution with axisymmetric perturbations. However, we see indications of a growing, non-spherical mode about the spherically symmetric critical solution. The effect of this instability is that the small asymmetry present in what would otherwise be a spherically symmetric self-similar solution grows. This growth continues until a bifurcation occurs and two distinct regions form on the axis, each resembling the spherically symmetric self-similar solution. The existence of a non-spherical unstable mode is in conflict with previous perturbative results, and we therefore discuss whether such a mode exists in the continuum limit, or whether we are instead seeing a marginally stable mode that is rendered unstable by numerical approximation.Comment: 11 pages, 8 figure

Crackling Noise, Power Spectra and Disorder Induced Critical Scaling

Crackling noise is observed in many disordered non-equilibrium systems in response to slowly changing external conditions. Examples range from Barkhausen noise in magnets to acoustic emission in martensites to earthquakes. Using the non-equilibrium random field Ising model, we derive universal scaling predictions for the dependence of the associated power spectra on the disorder and field sweep rate, near an underlying disorder-induced non-equilibrium critical point. Our theory applies to certain systems in which the crackling noise results from avalanche-like response to a (slowly) increasing external driving force, and is characterized by a broad power law scaling regime of the power spectra. We compute the critical exponents and discuss the relevance of the results to experiments.Comment: 27 Latex Pages, 14 eps figure

Type IIA Orientifold Limit of M-Theory on Compact Joyce 8-Manifold of Spin(7)-Holonomy

We show that M-theory compactified on a compact Joyce 8-manifold of $Spin(7)$-holonomy, which yields an effective theory in $D = 3$ with $\N$ = 1 supersymmetry, admits at some special points in it moduli space a description in terms of type IIA theory on an orientifold of compact Joyce 7-manifold of $G_2$-holonomy. We find the evidence in favour of this duality by computing the massless spectra on both M-thory side and type IIA side. For the latter, we compute the massless spectra by going to the orbifold limit of the Joyce 7-manifold.Comment: 26 pages, 2 eps figures, Latex file, two references and one footnote added, corrected some typo