A bright FIT-PNA hybridization probe for the hybridization state specific analysis of a C → U RNA edit via FRET in a binary system

Oligonucleotide probes that show enhanced fluorescence upon nucleic acid hybridization enable the detection and visualization of specific mRNA molecules, in vitro and in cellulo. A challenging problem is the analysis of single nucleotide alterations that occur, for example, when cellular mRNA is subject to C → U editing. Given the length required for uniqueness of the targeted segment, the commonly used probes do not provide the level of sequence specificity needed to discriminate single base mismatched hybridization. Herein we introduce a binary probe system based on fluorescence resonance energy transfer (FRET) that distinguishes three possible states i.e. (i) absence of target, (ii) presence of edited (matched) and (iii) unedited (single base mismatched) target. To address the shortcomings of read-out via FRET, we designed donor probes that avoid bleed through into the acceptor channel and nevertheless provide a high intensity of FRET signaling. We show the combined use of thiazole orange (TO) and an oxazolopyridine analogue (JO), linked as base surrogates in modified PNA FIT-probes that serve as FRET donor for a second, near-infrared (NIR)-labeled strand. In absence of target, donor emission is low and FRET cannot occur in lieu of the lacking co-alignment of probes. Hybridization of the TO/JO-PNA FIT-probe with the (unedited RNA) target leads to high brightness of emission at 540 nm. Co-alignment of the NIR-acceptor strand ensues from recognition of edited RNA inducing emission at 690 nm. We show imaging of mRNA in fixed and live cells and discuss the homogeneous detection and intracellular imaging of a single nucleotide mRNA edit used by nature to post-transcriptionally modify the function of the Glycine Receptor (GlyR)

Search for Invisible Decays of η\eta and η′\eta^\prime in J/ψ→ϕηJ/\psi \to \phi\eta and ϕη′\phi \eta^\prime

Using a data sample of $58\times 10^6$ $J/\psi$ decays collected with the BES II detector at the BEPC, searches for invisible decays of $\eta$ and $\eta^\prime$ in $J/\psi$ to $\phi\eta$ and $\phi\eta^\prime$ are performed. The $\phi$ signals, which are reconstructed in $K^+K^-$ final states, are used to tag the $\eta$ and $\eta^\prime$ decays. No signals are found for the invisible decays of either $\eta$ or $\eta^\prime$, and upper limits at the 90% confidence level are determined to be $1.65 \times 10^{-3}$ for the ratio $\frac{B(\eta\to \text{invisible})}{B(\eta\to\gamma\gamma)}$ and $6.69\times 10^{-2}$ for $\frac{B(\eta^\prime\to \text{invisible})}{B(\eta^\prime\to\gamma\gamma)}$. These are the first searches for $\eta$ and $\eta^\prime$ decays into invisible final states.Comment: 5 pages, 4 figures; Added references, Corrected typo

Observation of Two New N* Peaks in J/psi -> ppi−nˉp pi^- \bar n and pˉπ+n\bar p\pi^+n Decays

The $\pi N$ system in decays of $J/\psi\to\bar NN\pi$ is limited to be isospin 1/2 by isospin conservation. This provides a big advantage in studying $N^*\to \pi N$ compared with $\pi N$ and $\gamma N$ experiments which mix isospin 1/2 and 3/2 for the $\pi N$ system. Using 58 million $J/\psi$ decays collected with the Beijing Electron Positron Collider, more than 100 thousand $J/\psi \to p \pi^- \bar n + c.c.$ events are obtained. Besides two well known $N^*$ peaks at 1500 MeV and 1670 MeV, there are two new, clear $N^*$ peaks in the $p\pi$ invariant mass spectrum around 1360 MeV and 2030 MeV. They are the first direct observation of the $N^*(1440)$ peak and a long-sought "missing" $N^*$ peak above 2 GeV in the $\pi N$ invariant mass spectrum. A simple Breit-Wigner fit gives the mass and width for the $N^*(1440)$ peak as $1358\pm 6 \pm 16$ MeV and $179\pm 26\pm 50$ MeV, and for the new $N^*$ peak above 2 GeV as $2068\pm 3^{+15}_{-40}$ MeV and $165\pm 14\pm 40$ MeV, respectively

Modeling of complex oxide materials from the first principles: systematic applications to vanadates RVO3 with distorted perovskite structure

"Realistic modeling" is a new direction of electronic structure calculations, where the main emphasis is made on the construction of some effective low-energy model entirely within a first-principle framework. Ideally, it is a model in form, but with all the parameters derived rigorously, on the basis of first-principles electronic structure calculations. The method is especially suit for transition-metal oxides and other strongly correlated systems, whose electronic and magnetic properties are predetermined by the behavior of some limited number of states located near the Fermi level. After reviewing general ideas of realistic modeling, we will illustrate abilities of this approach on the wide series of vanadates RVO3 (R= La, Ce, Pr, Nd, Sm, Gd, Tb, Yb, and Y) with distorted perovskite structure. Particular attention will be paid to computational tools, which can be used for microscopic analysis of different spin and orbital states in the partially filled t2g-band. We will explicitly show how the lifting of the orbital degeneracy by the monoclinic distortion stabilizes C-type antiferromagnetic (AFM) state, which can be further transformed to the G-type AFM state by changing the crystal distortion from monoclinic to orthorhombic one. Two microscopic mechanisms of such a stabilization, associated with the one-electron crystal field and electron correlation interactions, are discussed. The flexibility of the orbital degrees of freedom is analyzed in terms of the magnetic-state dependence of interatomic magnetic interactions.Comment: 23 pages, 13 figure

One-neutron removal reactions on neutron-rich psd-shell nuclei

A systematic study of high energy, one-neutron removal reactions on 23 neutron-rich, psd--shell nuclei (Z=5-9, A=12-25) has been carried out. The longitudinal momentum distributions of the core fragments and corresponding single-neutron removal cross sections are reported for reactions on a carbon target. Extended Glauber model calculations, weighted by the spectroscopic factors obtained from shell model calculations, are compared to the experimental results. Conclusions are drawn regarding the use of such reactions as a spectroscopic tool and spin-parity assignments are proposed for 15B, 17C, 19-21N, 21,23O, 23-25F. The nature of the weakly bound systems 14B and 15,17C is discussed.Comment: 11 pages + 2 figure

Equilibration processes in the Warm-Hot Intergalactic Medium

The Warm-Hot Intergalactic Medium (WHIM) is thought to contribute about 40-50 % to the baryonic budget at the present evolution stage of the universe. The observed large scale structure is likely to be due to gravitational growth of density fluctuations in the post-inflation era. The evolving cosmic web is governed by non-linear gravitational growth of the initially weak density fluctuations in the dark energy dominated cosmology. Non-linear structure formation, accretion and merging processes, star forming and AGN activity produce gas shocks in the WHIM. Shock waves are converting a fraction of the gravitation power to thermal and non-thermal emission of baryonic/leptonic matter. They provide the most likely way to power the luminous matter in the WHIM. The plasma shocks in the WHIM are expected to be collisionless. Collisionless shocks produce a highly non-equilibrium state with anisotropic temperatures and a large differences in ion and electron temperatures. We discuss the ion and electron heating by the collisionless shocks and then review the plasma processes responsible for the Coulomb equilibration and collisional ionisation equilibrium of oxygen ions in the WHIM. MHD-turbulence produced by the strong collisionless shocks could provide a sizeable non-thermal contribution to the observed Doppler parameter of the UV line spectra of the WHIM.Comment: 13 pages, 4 figures, accepted for publication in Space Science Reviews, special issue "Clusters of galaxies: beyond the thermal view", Editor J.S. Kaastra, Chapter 8; work done by an international team at the International Space Science Institute (ISSI), Bern, organised by J.S. Kaastra, A.M. Bykov, S. Schindler & J.A.M. Bleeke

New Insights into White-Light Flare Emission from Radiative-Hydrodynamic Modeling of a Chromospheric Condensation

(abridged) The heating mechanism at high densities during M dwarf flares is poorly understood. Spectra of M dwarf flares in the optical and near-ultraviolet wavelength regimes have revealed three continuum components during the impulsive phase: 1) an energetically dominant blackbody component with a color temperature of T $\sim$ 10,000 K in the blue-optical, 2) a smaller amount of Balmer continuum emission in the near-ultraviolet at lambda $<$ 3646 Angstroms and 3) an apparent pseudo-continuum of blended high-order Balmer lines. These properties are not reproduced by models that employ a typical "solar-type" flare heating level in nonthermal electrons, and therefore our understanding of these spectra is limited to a phenomenological interpretation. We present a new 1D radiative-hydrodynamic model of an M dwarf flare from precipitating nonthermal electrons with a large energy flux of $10^{13}$ erg cm$^{-2}$ s$^{-1}$. The simulation produces bright continuum emission from a dense, hot chromospheric condensation. For the first time, the observed color temperature and Balmer jump ratio are produced self-consistently in a radiative-hydrodynamic flare model. We find that a T $\sim$ 10,000 K blackbody-like continuum component and a small Balmer jump ratio result from optically thick Balmer and Paschen recombination radiation, and thus the properties of the flux spectrum are caused by blue light escaping over a larger physical depth range compared to red and near-ultraviolet light. To model the near-ultraviolet pseudo-continuum previously attributed to overlapping Balmer lines, we include the extra Balmer continuum opacity from Landau-Zener transitions that result from merged, high order energy levels of hydrogen in a dense, partially ionized atmosphere. This reveals a new diagnostic of ambient charge density in the densest regions of the atmosphere that are heated during dMe and solar flares.Comment: 50 pages, 2 tables, 13 figures. Accepted for publication in the Solar Physics Topical Issue, "Solar and Stellar Flares". Version 2 (June 22, 2015): updated to include comments by Guest Editor. The final publication is available at Springer via http://dx.doi.org/10.1007/s11207-015-0708-

Excluded Volume Effects in the Quark Meson Coupling Model

Excluded volume effects are incorporated in the quark meson coupling model to take into account in a phenomenological way the hard core repulsion of the nuclear force. The formalism employed is thermodynamically consistent and does not violate causality. The effects of the excluded volume on in-medium nucleon properties and the nuclear matter equation of state are investigated as a function of the size of the hard core. It is found that in-medium nucleon properties are not altered significantly by the excluded volume, even for large hard core radii, and the equation of state becomes stiffer as the size of the hard core increases.Comment: 14 pages, revtex, 6 figure

Measurements of J/psi Decays into 2(pi+pi-)eta and 3(pi+pi-)eta

Based on a sample of 5.8X 10^7 J/psi events taken with the BESII detector, the branching fractions of J/psi--> 2(pi+pi-)eta and J/psi-->3(pi+pi-)eta are measured for the first time to be (2.26+-0.08+-0.27)X10^{-3} and (7.24+-0.96+-1.11)X10^{-4}, respectively.Comment: 11 pages, 6 figure

Measurements of the Mass and Full-Width of the ηc\eta_c Meson

In a sample of 58 million $J/\psi$ events collected with the BES II detector, the process J/$\psi\to\gamma\eta_c$ is observed in five different decay channels: $\gamma K^+K^-\pi^+\pi^-$, $\gamma\pi^+\pi^-\pi^+\pi^-$, $\gamma K^\pm K^0_S \pi^\mp$ (with $K^0_S\to\pi^+\pi^-$), $\gamma \phi\phi$ (with $\phi\to K^+K^-$) and $\gamma p\bar{p}$. From a combined fit of all five channels, we determine the mass and full-width of $\eta_c$ to be $m_{\eta_c}=2977.5\pm1.0 ({stat.})\pm1.2 ({syst.})$ MeV/$c^2$ and $\Gamma_{\eta_c} = 17.0\pm3.7 ({stat.})\pm7.4 ({syst.})$ MeV/$c^2$.Comment: 9 pages, 2 figures and 4 table. Submitted to Phys. Lett.