Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes.

BackgroundGeneral translational cis-elements are present in the mRNAs of all genes and affect the recruitment, assembly, and progress of preinitiation complexes and the ribosome under many physiological states. These elements include mRNA folding, upstream open reading frames, specific nucleotides flanking the initiating AUG codon, protein coding sequence length, and codon usage. The quantitative contributions of these sequence features and how and why they coordinate to control translation rates are not well understood.ResultsHere, we show that these sequence features specify 42-81% of the variance in translation rates in Saccharomyces cerevisiae, Schizosaccharomyces pombe, Arabidopsis thaliana, Mus musculus, and Homo sapiens. We establish that control by RNA secondary structure is chiefly mediated by highly folded 25-60 nucleotide segments within mRNA 5' regions, that changes in tri-nucleotide frequencies between highly and poorly translated 5' regions are correlated between all species, and that control by distinct biochemical processes is extensively correlated as is regulation by a single process acting in different parts of the same mRNA.ConclusionsOur work shows that general features control a much larger fraction of the variance in translation rates than previously realized. We provide a more detailed and accurate understanding of the aspects of RNA structure that directs translation in diverse eukaryotes. In addition, we note that the strongly correlated regulation between and within cis-control features will cause more even densities of translational complexes along each mRNA and therefore more efficient use of the translation machinery by the cell

Micro ion beam analysis for the erosion of beryllium marker tiles in a tokamak limiter

Beryllium limiter marker tiles were exposed to plasma in the Joint European Torus to diagnose the erosion of main chamber wall materials. A limiter marker tile consists of a beryllium coating layer (7-9 mu m) on the top of bulk beryllium, with a nickel interlayer (2-3 mu m) between them. The thickness variation of the beryllium coating layer, after exposure to plasma, could indicate the erosion measured by ion beam analysis with backscattering spectrometry. However, interpretations from broad beam backscattering spectra were limited by the non-uniform surface structures. Therefore, micro-ion beam analysis (mu-IBA) with 3 MeV proton beam for Elastic back scattering spectrometry (EBS) and PIXE was used to scan samples. The spot size was in the range of 3-10 mu m. Scanned areas were analysed with scanning electron microscopy (SEM) as well. Combining results from mu-IBA and SEM, we obtained local spectra from carefully chosen areas on which the surface structures were relatively uniform. Local spectra suggested that the scanned area (approximate to 600 mu m x 1200 mu m) contained regions with serious erosion with only 2-3 mu m coating beryllium left, regions with intact marker tile, and droplets with 90% beryllium. The nonuniform erosion, droplets mainly formed by beryllium, and the possible mixture of beryllium and nickel were the major reasons that confused interpretation from broad beam EBS

Approximate analytic expressions using Stokes model for tokamak polarimetry and their range of validity

The analysis of the polarimetry measurements has the aim of validating models (De Marco and Segre 1972 Plasma Phys. 14 245), with a careful attention to the clarification of their limits of application. In this paper a new approximation method is introduced, the so-called special constant Omega direction (SCOD), which gives an analytical solution to the polarimetry exact Stokes model equations. The available approximate solutions (including SCOD) of the polarimetry propagation equations are presented, compared and their application limits determined, using a reference tokamak configuration, which is a simplified equilibrium for a circular tokamak. The SCOD approximation is compared successfully to the Stokes model in the context also of equilibria evaluated for two JET discharges. The approximation methods are analytical or very simple mathematical expressions which can also be used in equilibrium codes for their optimization

Modelling of the effect of ELMs on fuel retention at the bulk W divertor of JET

Effect of ELMs on fuel retention at the bulk W target of JET ITER-Like Wall was studied with multi-scale calculations. Plasma input parameters were taken from ELMy H-mode plasma experiment. The energetic intra-ELM fuel particles get implanted and create near-surface defects up to depths of few tens of nm, which act as the main fuel trapping sites during ELMs. Clustering of implantation-induced vacancies were found to take place. The incoming flux of inter-ELM plasma particles increases the different filling levels of trapped fuel in defects. The temperature increase of the W target during the pulse increases the fuel detrapping rate. The inter-ELM fuel particle flux refills the partially emptied trapping sites and fills new sites. This leads to a competing effect on the retention and release rates of the implanted particles. At high temperatures the main retention appeared in larger vacancy clusters due to increased clustering rate

Overview of the JET results

Since the last IAEA Conference JET has been in operation for one year with a programmatic focus on the qualification of ITER operating scenarios, the consolidation of ITER design choices and preparation for plasma operation with the ITER-like wall presently being installed in JET. Good progress has been achieved, including stationary ELMy H-mode operation at 4.5 MA. The high confinement hybrid scenario has been extended to high triangularity, lower ρ*and to pulse lengths comparable to the resistive time. The steady-state scenario has also been extended to lower ρ*and ν*and optimized to simultaneously achieve, under stationary conditions, ITER-like values of all other relevant normalized parameters. A dedicated helium campaign has allowed key aspects of plasma control and H-mode operation for the ITER non-activated phase to be evaluated. Effective sawtooth control by fast ions has been demonstrated with3He minority ICRH, a scenario with negligible minority current drive. Edge localized mode (ELM) control studies using external n = 1 and n = 2 perturbation fields have found a resonance effect in ELM frequency for specific q95values. Complete ELM suppression has, however, not been observed, even with an edge Chirikov parameter larger than 1. Pellet ELM pacing has been demonstrated and the minimum pellet size needed to trigger an ELM has been estimated. For both natural and mitigated ELMs a broadening of the divertor ELM-wetted area with increasing ELM size has been found. In disruption studies with massive gas injection up to 50% of the thermal energy could be radiated before, and 20% during, the thermal quench. Halo currents could be reduced by 60% and, using argon/deuterium and neon/deuterium gas mixtures, runaway electron generation could be avoided. Most objectives of the ITER-like ICRH antenna have been demonstrated; matching with closely packed straps, ELM resilience, scattering matrix arc detection and operation at high power density (6.2 MW m-2) and antenna strap voltages (42 kV). Coupling measurements are in very good agreement with TOPICA modelling. \ua9 2011 IAEA, Vienna

A new mechanism for increasing density peaking in tokamaks: improvement of the inward particle pinch with edge E x B shearing

Developing successful tokamak operation scenarios, as well as confident extrapolation of present-day knowledge requires a rigorous understanding of plasma turbulence, which largely determines the quality of the confinement. In particular, accurate particle transport predictions are essential due to the strong dependence of fusion power or bootstrap current on the particle density details. Here, gyrokinetic turbulence simulations are performed with physics inputs taken from a JET power scan, for which a relatively weak degradation of energy confinement and a significant density peaking is obtained with increasing input power. This way physics parameters that lead to such increase in the density peaking shall be elucidated. While well-known candidates, such as the collisionality, previously found in other studies are also recovered in this study, it is furthermore found that edge E x B shearing may adopt a crucial role by enhancing the inward pinch. These results may indicate that a plasma with rotational shear could develop a stronger density peaking as compared to a non-rotating one, because its inward convection is increased compared to the outward diffusive particle flux as long as this rotation has a significant on E x B flow shear stabilization. The possibly significant implications for future devices, which will exhibit much less torque compared to present day experiments, are discussed

Overview of the JET results

Since the last IAEA Conference JET has been in operation for one year with a programmatic focus on the qualification of ITER operating scenarios, the consolidation of ITER design choices and preparation for plasma operation with the ITER-like wall presently being installed in JET. Good progress has been achieved, including stationary ELMy H-mode operation at 4.5 MA. The high confinement hybrid scenario has been extended to high triangularity, lower ρ*and to pulse lengths comparable to the resistive time. The steady-state scenario has also been extended to lower ρ*and ν*and optimized to simultaneously achieve, under stationary conditions, ITER-like values of all other relevant normalized parameters. A dedicated helium campaign has allowed key aspects of plasma control and H-mode operation for the ITER non-activated phase to be evaluated. Effective sawtooth control by fast ions has been demonstrated with3He minority ICRH, a scenario with negligible minority current drive. Edge localized mode (ELM) control studies using external n = 1 and n = 2 perturbation fields have found a resonance effect in ELM frequency for specific q95values. Complete ELM suppression has, however, not been observed, even with an edge Chirikov parameter larger than 1. Pellet ELM pacing has been demonstrated and the minimum pellet size needed to trigger an ELM has been estimated. For both natural and mitigated ELMs a broadening of the divertor ELM-wetted area with increasing ELM size has been found. In disruption studies with massive gas injection up to 50% of the thermal energy could be radiated before, and 20% during, the thermal quench. Halo currents could be reduced by 60% and, using argon/deuterium and neon/deuterium gas mixtures, runaway electron generation could be avoided. Most objectives of the ITER-like ICRH antenna have been demonstrated; matching with closely packed straps, ELM resilience, scattering matrix arc detection and operation at high power density (6.2 MW m-2) and antenna strap voltages (42 kV). Coupling measurements are in very good agreement with TOPICA modelling. \ua9 2011 IAEA, Vienna

EDGE2D-EIRENE simulations of the influence of isotope effects and anomalous transport coefficients on near scrape-off layer radial electric field

EDGE2D-EIRENE (the 'code') simulations show that radial electric field, Er, in the near scrape-off layer (SOL) of tokamaks can have large variations leading to a strong local E x B shear greatly exceeding that in the core region. This was pointed out in simulations of JET plasmas with varying divertor geometry, where the magnetic configuration with larger predicted near SOL E-r was found to have lower H-mode power threshold, suggesting that turbulence suppression in the SOL by local E. x. B shear can be a player in the L-H transition physics (Delabie et al 2015 42nd EPS Conf. on Plasma Physics (Lisbon, Portugal, 22-26 June 2015) paper O3.113 (http://ocs.ciemat.es/EPS2015PAP/pdf/O3.113.pdf), Chankin et al 2017 Nucl. Mater. Energy 12 273). Further code modeling of JET plasmas by changing hydrogen isotopes (H-D-T) showed that the magnitude of the near SOL E-r is lower in H cases in which the H-mode threshold power is higher (Chankin et al 2017 Plasma Phys. Control. Fusion 59 045012). From the experiment it is also known that hydrogen plasmas have poorer particle and energy confinement than deuterium plasmas, consistent with the code simulation results showing larger particle diffusion coefficients at the plasma edge, including SOL, in hydrogen plasmas (Maggi et al 2018 Plasma Phys. Control. Fusion 60 014045). All these experimental observations and code results support the hypothesis that the near SOL E x B shear can have an impact on the plasma confinement. The present work analyzes neutral ionization patterns of JET plasmas with different hydrogen isotopes in L-mode cases with fixed input power and gas puffing rate, and its impact on target electron temperature, T-e, and SOL E-r. The possibility of a self-feeding mechanism for the increase in the SOL E-r via the interplay between poloidal E x B drift and target T-e is discussed. It is also shown that reducing anomalous turbulent transport coefficients, particle diffusion and electron and ion heat conductivities, leads to higher peak target T-e and larger E-r, suggesting the possibility of a positive feedback loop, under an implicitly made assumption that the E x B shear in the SOL is capable of suppressing turbulence

A power-balance model of the density limit in fusion plasmas: application to the L-mode tokamak

A power-balance model, with radiation losses from impurities and neutrals, gives a unified description of the density limit (DL) of the stellarator, the L-mode tokamak, and the reversed field pinch (RFP). The model predicts a Sudo-like scaling for the stellarator, a Greenwald- like scaling, alpha I-p(8/9), for the RFP and the ohmic tokamak, a mixed scaling, alpha (PIp4/9)-I-4/9, for the additionally heated L-mode tokamak. In a previous paper (Zanca et al 2017 Nucl. Fusion 57 056010) the model was compared with ohmic tokamak, RFP and stellarator experiments. Here, we address the issue of the DL dependence on heating power in the L-mode tokamak. Experimental data from high-density disrupted L-mode discharges performed at JET, as well as in other machines, arc taken as a term of comparison. The model fits the observed maximum densities better than the pure Greenwald limit