Retrotransposition creates sloping shores: a graded influence of hypomethylated CpG islands on flanking CpG sites

Long interspersed elements (LINEs), through both self-mobilization and trans-mobilization of short interspersed elements and processed pseudogenes, have made an indelible impact on the structure and function of the human genome. One consequence is the creation of new CpG islands (CGIs). In fact, more than half of all CGIs in the genome are associated with repetitive DNA, three-quarters of which are derived from retrotransposons. However, little is known about the epigenetic impact of newly inserted CGIs. We utilized a transgenic LINE-1 mouse model and tracked DNA methylation dynamics of individual germline insertions during mouse development. The retrotransposed GFP marker sequence, a strong CGI, is hypomethylated in male germ cells but hypermethylated in somatic tissues, regardless of genomic location. The GFP marker is similarly methylated when delivered into the genome via the Sleeping Beauty DNA transposon, suggesting that the observed methylation pattern may be independent of the mode of insertion. Comparative analyses between insertion- and non-insertion-containing alleles further reveal a graded influence of the retrotransposed CGI on flanking CpG sites, a phenomenon that we described as "sloping shores." Computational analyses of human and mouse methylomic data at single-base resolution confirm that sloping shores are universal for hypomethylated CGIs in sperm and somatic tissues. Additionally, the slope of a hypomethylated CGI can be affected by closely positioned CGI neighbors. Finally, by tracing sloping shore dynamics through embryonic and germ cell reprogramming, we found evidence of bookmarking, a mechanism that likely determines which CGIs will be eventually hyper- or hypomethylated

Recent Advances in Understanding Particle Acceleration Processes in Solar Flares

We review basic theoretical concepts in particle acceleration, with particular emphasis on processes likely to occur in regions of magnetic reconnection. Several new developments are discussed, including detailed studies of reconnection in three-dimensional magnetic field configurations (e.g., current sheets, collapsing traps, separatrix regions) and stochastic acceleration in a turbulent environment. Fluid, test-particle, and particle-in-cell approaches are used and results compared. While these studies show considerable promise in accounting for the various observational manifestations of solar flares, they are limited by a number of factors, mostly relating to available computational power. Not the least of these issues is the need to explicitly incorporate the electrodynamic feedback of the accelerated particles themselves on the environment in which they are accelerated. A brief prognosis for future advancement is offered.Comment: This is a chapter in a monograph on the physics of solar flares, inspired by RHESSI observations. The individual articles are to appear in Space Science Reviews (2011

Fast variability from black-hole binaries

Currently available information on fast variability of the X-ray emission from accreting collapsed objects constitutes a complex phenomenology which is difficult to interpret. We review the current observational standpoint for black-hole binaries and survey models that have been proposed to interpret it. Despite the complex structure of the accretion flow, key observational diagnostics have been identified which can provide direct access to the dynamics of matter motions in the close vicinity of black holes and thus to the some of fundamental properties of curved spacetimes, where strong-field general relativistic effects can be observed.Comment: 20 pages, 11 figures. Accepted for publication in Space Science Reviews. Also to appear in hard cover in the Space Sciences Series of ISSI "The Physics of Accretion onto Black Holes" (Springer Publisher

High-Accuracy X-Ray Diffraction Analysis of Phase Evolution Sequence During Devitrification of Cu50Zr50 Metallic Glass

Real-time high-energy X-ray diffraction (HEXRD) was used to investigate the crystallization kinetics and phase selection sequence for constant-heating-rate devitrification of fully amorphous Cu50Zr50, using heating rates from 10 K/min to 60 K/min (10 °C/min to 60 °C/min). In situ HEXRD patterns were obtained by the constant-rate heating of melt-spun ribbons under synchrotron radiation. High-accuracy phase identification and quantitative assessment of phase fraction evolution though the duration of the observed transformations were performed using a Rietveld refinement method. Results for 10 K/min (10 °C/min) heating show the apparent simultaneous formation of three phases, orthorhombic Cu10Zr7, tetragonal CuZr2 (C11b), and cubic CuZr (B2), at 706 K (433 °C), followed immediately by the dissolution of the CuZr (B2) phase upon continued heating to 789 K (516 °C). Continued heating results in reprecipitation of the CuZr (B2) phase at 1002 K (729 °C), with the material transforming completely to CuZr (B2) by 1045 K (772 °C). The Cu5Zr8 phase, previously reported to be a devitrification product in C50Zr50, was not observed in the present study

Stochastic Acceleration by Turbulence

The subject of this paper is stochastic acceleration by plasma turbulence, a process akin to the original model proposed by Fermi. We review the relative merits of different acceleration models, in particular the so called first order Fermi acceleration by shocks and second order Fermi by stochastic processes, and point out that plasma waves or turbulence play an important role in all mechanisms of acceleration. Thus, stochastic acceleration by turbulence is active in most situations. We also show that it is the most efficient mechanism of acceleration of relatively cool non relativistic thermal background plasma particles. In addition, it can preferentially accelerate electrons relative to protons as is needed in many astrophysical radiating sources, where usually there are no indications of presence of shocks. We also point out that a hybrid acceleration mechanism consisting of initial acceleration by turbulence of background particles followed by a second stage acceleration by a shock has many attractive features. It is demonstrated that the above scenarios can account for many signatures of the accelerated electrons, protons and other ions, in particular $^3$He and $^4$He, seen directly as Solar Energetic Particles and through the radiation they produce in solar flares.Comment: 29 pages 7 figures for proceedings of ISSI-Bern workshop on Particle Acceleration 201

The Origin, Early Evolution and Predictability of Solar Eruptions

Coronal mass ejections (CMEs) were discovered in the early 1970s when space-borne coronagraphs revealed that eruptions of plasma are ejected from the Sun. Today, it is known that the Sun produces eruptive flares, filament eruptions, coronal mass ejections and failed eruptions; all thought to be due to a release of energy stored in the coronal magnetic field during its drastic reconfiguration. This review discusses the observations and physical mechanisms behind this eruptive activity, with a view to making an assessment of the current capability of forecasting these events for space weather risk and impact mitigation. Whilst a wealth of observations exist, and detailed models have been developed, there still exists a need to draw these approaches together. In particular more realistic models are encouraged in order to asses the full range of complexity of the solar atmosphere and the criteria for which an eruption is formed. From the observational side, a more detailed understanding of the role of photospheric flows and reconnection is needed in order to identify the evolutionary path that ultimately means a magnetic structure will erupt

Study of Z → llγ decays at √s = 8 TeV with the ATLAS detector

This paper presents a study of Z → llγ decays with the ATLAS detector at the Large Hadron Collider. The analysis uses a proton–proton data sample corresponding to an integrated luminosity of 20.2 fb−1 collected at a centre-ofmass energy √s = 8 TeV. Integrated fiducial cross-sections together with normalised differential fiducial cross-sections, sensitive to the kinematics of final-state QED radiation, are obtained. The results are found to be in agreement with stateof-the-art predictions for final-state QED radiation. First measurements of Z → llγ γ decays are also reported

Search for leptoquark pair production decaying into te−te¯ + or tμ−t¯μ+ in multi-lepton final states in pp collisions at √s = 13 TeV with the ATLAS detector

A search for leptoquark pair production decaying into te−te¯ + or tμ−t¯μ+ in final states with multiple leptons is presented. The search is based on a dataset of pp collisions at √s = 13 TeV recorded with the ATLAS detector during Run 2 of the Large Hadron Collider, corresponding to an integrated luminosity of 139 fb−1. Four signal regions, with the requirement of at least three light leptons (electron or muon) and at least two jets out of which at least one jet is identified as coming from a b-hadron, are considered based on the number of leptons of a given flavour. The main background processes are estimated using dedicated control regions in a simultaneous fit with the signal regions to data. No excess above the Standard Model background prediction is observed and 95% confidence level limits on the production cross section times branching ratio are derived as a function of the leptoquark mass. Under the assumption of exclusive decays into te− (tμ−), the corresponding lower limit on the scalar mixed-generation leptoquark mass mLQd mix is at 1.58 (1.59) TeV and on the vector leptoquark mass mU˜1 at 1.67 (1.67) TeV in the minimal coupling scenario and at 1.95 (1.95) TeV in the Yang–Mills scenario