Useful ‘junk': Alu RNAs in the human transcriptome

Abstract.: Alu elements are the most abundant repetitive elements in the human genome; they have amplified by retrotransposition to reach the present number of more than one million copies. Alu elements can be transcribed in two different ways, by two independent polymerases. ‘Free Alu RNAs' are transcribed by Pol III from their own promoter, while ‘embedded Alu RNAs' are transcribed by Pol II as part of protein- and non-protein-coding RNAs. Recent studies have demonstrated that both free and embedded Alu RNAs play a major role in post transcriptional regulation of gene expression, for example by affecting protein translation, alternative splicing and mRNA stability. These discoveries illustrate how a part of the ‘junk DNA' content of the human genome has been recruited to important functions in regulation of gene expressio

Polarization Observables in eta and pi Production Using a Polarized Target with the Crystal Ball/TAPS at MAMI

Recent experiments using the Crystal Ball/TAPS setup at the MAMI accelerator in Mainz, Germany, continue to study the properties and the excitation spectrum of the nucleon with meson photoproduction. Electromagnetic excitations of the proton and neutron are essential for understanding their isospin decomposition. The electromagnetic coupling of photons to protons is different than that to neutrons in certain states. Hence, a complete partial wave analysis (PWA) can assist in yielding more information about any reaction, but requires the determination of polarization observables. Polarization observables play a crucial role as they are essential in disentangling the contributing resonant and non-resonant amplitudes, whereas cross section data alone is not sufficient for separating broad overlapping resonances. Preliminary results of polarization observables of η, single, and double π production off a polarized neutron (dButanol) target will be shown with comparison to predictions of recent multipole analyses. These results will greatly increase the world database on pseudoscalar meson production on neutrons

Northern Galápagos corals reveal twentieth century warming in the eastern tropical Pacific

Models and observations disagree regarding sea surface temperature (SST) trends in the eastern tropical Pacific. We present a new Sr/Ca‐SST record that spans 1940–2010 from two Wolf Island corals (northern Galápagos). Trend analysis of the Wolf record shows significant warming on multiple timescales, which is also present in several other records and gridded instrumental products. Together, these data sets suggest that most of the eastern tropical Pacific has warmed over the twentieth century. In contrast, recent decades have been characterized by warming during boreal spring and summer (especially north of the equator), and subtropical cooling during boreal fall and winter (especially south of the equator). These SST trends are consistent with the effects of radiative forcing, mitigated by cooling due to wind forcing during boreal winter, as well as intensified upwelling and a strengthened Equatorial Undercurrent.Key PointsA new coral Sr/Ca record from Wolf Island, Galápagos, indicates SST warming on decadal to multidecadal timescalesTrend analysis of multiple data sets confirms long‐term warming throughout the eastern tropical Pacific, consistent with radiative forcingEastern Pacific warming since 1982 is overprinted by seasonally variable cooling from wind forcing and the ocean dynamical thermostatPeer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/142987/1/grl56975_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142987/2/grl56975-sup-0001-2017GL075323-S01.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142987/3/grl56975.pd

Altimeter-derived variability of surface velocities in the California Current System : 1. Evaluation of TOPEX altimeter velocity resolution

In this paper, we evaluate the temporal and horizontal resolution of geostrophic surface velocities calculated from TOPEX satellite altimeter heights. Moored velocities (from vector-averaging current meters and an acoustic Doppler current profiler) at depths below the Ekman layer are used to estimate the temporal evolution and accuracy of altimeter geostrophic surface velocities at a point. Surface temperature gradients from satellite fields are used to determine the altimeter's horizontal resolution of features in the velocity field. The results indicate that the altimeter resolves horizontal scales of 50-80 km in the along-track direction. The rms differences between the altimeter and current meters are 7-8 cm s⁻¹, much of which comes from small-scale variability in the oceanic currents. We estimate the error in the altimeter velocities to have an rms magnitude of 3-5 cm s⁻¹ or less. Uncertainties in the eddy momentum fluxes at crossovers are more difficult to evaluate and may be affected by aliasing of fluctuations with frequencies higher than the altimeter's Nyquist frequency of 0.05 cycles d⁻¹, as indicated by spectra from subsampled current meter data. The eddy statistics that are in best agreement are the velocity variances, eddy kinetic energy and the major axis of the variance ellipses. Spatial averaging of the current meter velocities produces greater agreement with all altimeter statistics and increases our confidence that the altimeter's momentum fluxes and the orientation of its variance ellipses (the statistics differing the most with single moorings) represent well the statistics of spatially averaged currents (scales of 50-100 km) in the ocean. Besides evaluating altimeter performance, the study reveals several properties of the circulation in the California Current System: (1) velocity components are not isotropic but are polarized, strongly so at some locations, (2) there are instances of strong and persistent small-scale variability in the velocity, and (3) the energetic region of the California Current is isolated and surrounded by a region of lower energy starting 500-700 km offshore. This suggests that the source of the high eddy energy within 500 km of the coast is the seasonal jet that develops each spring and moves offshore to the central region of the California Current, rather than a deep-ocean eddy field approaching the coast from farther offshore

Nucleic Acids Res

Type II topoisomerases are essential enzymes that regulate DNA topology through a strand-passage mechanism. Some type II topoisomerases relax supercoils, unknot and decatenate DNA to below thermodynamic equilibrium. Several models of this non-equilibrium topology simplification phenomenon have been proposed. The kinetic proofreading (KPR) model postulates that strand passage requires a DNA-bound topoisomerase to collide twice in rapid succession with a second DNA segment, implying a quadratic relationship between DNA collision frequency and relaxation rate. To test this model, we used a single-molecule assay to measure the unlinking rate as a function of DNA collision frequency for Escherichia coli topoisomerase IV (topo IV) that displays efficient non-equilibrium topology simplification activity, and for E. coli topoisomerase III (topo III), a type IA topoisomerase that unlinks and unknots DNA to equilibrium levels. Contrary to the predictions of the KPR model, topo IV and topo III unlinking rates were linearly related to the DNA collision frequency. Furthermore, topo III exhibited decatenation activity comparable with that of topo IV, supporting proposed roles for topo III in DNA segregation. This study enables us to rule out the KPR model for non-equilibrium topology simplification. More generally, we establish an experimental approach to systematically control DNA collision frequency

Photoproduction of π0\pi^0-pairs off protons and off neutrons

Total cross sections, angular distributions, and invariant-mass distributions have been measured for the photoproduction of $\pi^0\pi^0$ pairs off free protons and off nucleons bound in the deuteron. The experiments were performed at the MAMI accelerator facility in Mainz using the Glasgow photon tagging spectrometer and the Crystal Ball/TAPS detector. The accelerator delivered electron beams of 1508 and 1557~MeV, which produced bremsstrahlung in thin radiator foils. The tagged photon beam covered energies up to 1400~MeV. The data from the free proton target are in good agreement with previous measurements and were only used to test the analysis procedures. The results for differential cross sections (angular distributions and invariant-mass distributions) for free and quasi-free protons are almost identical in shape, but differ in absolute magnitude up to 15\%. Thus, moderate final-state interaction effects are present. The data for quasi-free neutrons are similar to the proton data in the second resonance region (final state invariant masses up to $\approx$1550~MeV), where both reactions are dominated by the $N(1520)3/2^-\rightarrow \Delta(1232)3/2^+\pi$ decay. At higher energies, angular and invariant-mass distributions are different. A simple analysis of the shapes of the invariant-mass distributions in the third resonance region is consistent with strong contributions of an $N^{\star}\rightarrow N\sigma$ decay for the proton, while the reaction is dominated by a sequential decay via a $\Delta\pi$ intermediate state for the neutron. The data are compared to predictions from the Two-Pion-MAID model and the Bonn-Gatchina coupled channel analysis.Comment: accepted for publication in Eur. Phys. J.

Photoproduction of π0-pairs off protons and off neutrons

Total cross sections, angular distributions, and invariant-mass distributions have been measured for the photoproduction of π0π0 pairs off free protons and off nucleons bound in the deuteron. The experiments were performed at the MAMI accelerator facility in Mainz using the Glasgow photon tagging spectrometer and the Crystal Ball/TAPS detector. The accelerator delivered electron beams of 1508 and 1557MeV, which produced bremsstrahlung in thin radiator foils. The tagged photon beam covered energies up to 1400MeV. The data from the free proton target are in good agreement with previous measurements and were only used to test the analysis procedures. The results for differential cross sections (angular distributions and invariant-mass distributions) for free and quasi-free protons are almost identical in shape, but differ in absolute magnitude up to 15%. Thus, moderate final-state interaction effects are present. The data for quasi-free neutrons are similar to the proton data in the second resonance region (final-state invariant masses up to ≈1550 MeV), where both reactions are dominated by the N(1520)3/2−→Δ(1232)3/2+π decay. At higher energies, angular and invariant-mass distributions are different. A simple analysis of the shapes of the invariant-mass distributions in the third resonance region is consistent with strong contributions of an N⋆→Nσ decay for the proton, while the reaction is dominated by a sequential decay via a Δπ intermediate state for the neutron. The data are compared to predictions from the Two-Pion-MAID model and the Bonn-Gatchina coupled-channel analysis

Measurement of the transverse target and beam-target asymmetries in η\eta meson photoproduction at MAMI

We present new data for the transverse target asymmetry T and the very first data for the beam-target asymmetry F in the $\vec \gamma \vec p\to\eta p$ reaction up to a center-of-mass energy of W=1.9 GeV. The data were obtained with the Crystal-Ball/TAPS detector setup at the Glasgow tagged photon facility of the Mainz Microtron MAMI. All existing model predictions fail to reproduce the new data indicating a significant impact on our understanding of the underlying dynamics of $\eta$ meson photoproduction. The peculiar nodal structure observed in existing T data close to threshold is not confirmed.Comment: 5 pages, 3 figures, accepted for publication in PR

An operational analysis of Lake Surface Water Temperature

Operational analyses of Lake Surface Water Temperature (LSWT) have many potential uses including improvement of numerical weather prediction (NWP) models on regional scales. In November 2011, LSWT was included in the Met Office Operational Sea Surface Temperature and Ice Analysis (OSTIA) product, for 248 lakes globally. The OSTIA analysis procedure, which has been optimised for oceans, has also been used for the lakes in this first version of the product. Infra-red satellite observations of lakes and in situ measurements are assimilated. The satellite observations are based on retrievals optimised for Sea Surface Temperature (SST) which, although they may introduce inaccuracies into the LSWT data, are currently the only near-real-time information available. The LSWT analysis has a global root mean square difference of 1.31 K and a mean difference of 0.65 K (including a cool skin effect of 0.2 K) compared to independent data from the ESA ARC-Lake project for a 3-month period (June to August 2009). It is demonstrated that the OSTIA LSWT is an improvement over the use of climatology to capture the day-to-day variation in global lake surface temperatures