Ty1 integrase overexpression leads to integration of non-Ty1 DNA fragments into the genome of Saccharomyces cerevisiae

The integrase of the Saccharomyces cerevisiae retrotransposon Ty1 integrates Ty1 cDNA into genomic DNA likely via a transesterification reaction. Little is known about the mechanisms ensuring that integrase does not integrate non-Ty DNA fragments. In an effort to elucidate the conditions under which Ty1 integrase accepts non-Ty DNA as substrate, PCR fragments encompassing a selectable marker gene were transformed into yeast strains overexpressing Ty1 integrase. These fragments do not exhibit similarity to Ty1 cDNA except for the presence of the conserved terminal dinucleotide 5′-TG-CA-3′. The frequency of fragment insertion events increased upon integrase overexpression. Characterization of insertion events by genomic sequencing revealed that most insertion events exhibited clear hallmarks of integrase-mediated reactions, such as 5 bp target site duplication and target site preferences. Alteration of the terminal dinucleotide abolished the suitability of the PCR fragments to serve as substrates. We hypothesize that substrate specificity under normal conditions is mainly due to compartmentalization of integrase and Ty cDNA, which meet in virus-like particles. In contrast, recombinant integrase, which is not confined to virus-like particles, is able to accept non-Ty DNA, provided that it terminates in the proper dinucleotide sequence

Determination of isotope ratio in the divertor of JET-ILW by high-resolution H alpha spectroscopy: H-D experiment and implications for D-T experiment

The data of the H alpha high-resolution spectroscopy, collected on the multiple lines of sight, which cover the entire divertor space in poloidal cross-section, during the recent hydrogen-deuterium experiments in JET-ILW (ITER-like wall), are processed. A strong spatial inhomogeneity of the hydrogen concentration, H/(H + D), in divertor is found in many pulses. Namely, the H/(H + D) ratio may be lower in the inner divertor than that in the outer divertor by the values of 0.15-0.35, depending on the conditions of gas puffing and plasma heating. This effect suggests the necessity of spatially-resolved measurements of isotope ratio in the divertor in the upcoming deuterium-tritium experiments. Also, separation of the overlapped T alpha and D alpha spectral lines is shown to be a challenging task especially when the local Doppler-broadened (Gaussian) line shapes are noticeably distorted by the net inward flux of fast non-Maxwellian neutral atoms. We use the respective, formerly developed model of an asymmetric spectral line shape, while analysing the data of the first deuterium-tritium experiment in JET-C (carbon wall), and test the model via comparing the isotope ratio results with another diagnostic's measurements. This model is shown to increase the accuracy of tritium concentration measurements in the divertor

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

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

Fast ion synergistic effects in JET high performance pulses

Fast ion synergistic effects were studied by predictive modelling of JET best performing pulses for various levels of neutral beam injection (NBI) and radio frequency (RF) power. Calculated DD neutron yields were analysed with the intention of separating the impact of RF synergistic effects due to changes in fast ion (FT) distribution function (DF) from secondary effects accompanying the application of RF power, namely changes in T-e and T-i . A novel approach in analysing the efficiency of fast ions in fusion reactions based on evaluation of the cumulative reaction rates is outlined and used in the study. Conclusions on the impact of fast ion synergistic effects on fusion performance are based on comparisons of beam-target (BT) and thermal (Th) DD reaction rates. It was found that changes in auxiliary heating power, NBI and RF, by 4 MW will affect DD fusion performance and neutron rates significantly. Simulations of the best performing JET pulses show that for H minority RF heating scheme with available RF power the impact of RF synergistic effects is somewhat lesser than the secondary effects related to changes in T-e and T-i . In conditions of much higher RF power the modification in fast ion distribution function (FI DF) and the impact of the fast ions on BT DD fusion becomes significant. The impact of the RF and NBI power on the BT reactivities was found to be of similar order; however, the NAT power has greater impact on reaction rates due to its larger effect on fast ion density