Exploring the Requirements of the Mycobacterium Phage Brujita Integrase

Temperate phages establish lysogeny and immunity to superinfection upon phage integration. Brujita Integrase (Int) is a model for a recently discovered subclass of tyrosine integrases, which lack traditional N-terminal arm-binding domains and contain additional C-terminal degradation tags. Typically, the arm-binding domain recognizes binding sites in the phage attachment DNA (attP) and serves to control the directionality in integration and excision. The absence of this domain raises the question of how Brujita Int binds attachment site substrates to control site selectivity and directionality. In this work, we describe the DNA and protein requirements for Brujita Int function, how it implements site selection, directionality control, and higher order complex formation. We show that Brujita Int is a simple recombinase, which resembles Cre, FLP, and XerC/D more closely than it does the tyrosine phage integrases. In contrast to Lambda Int, Brujita Int uses small DNA substrates, does not discriminate between attP and attB sites, and lacks directional control. It also shows unusual binding to its attachment sites. Binding to attB occurs at two half sites, B and B’ in a cooperative manner, such that binding at B’ is required for binding at B. Binding to attP is also unusual. The attP site is comprised of three half sites, P, P’, and an additional site to the left of P, P1. However, binding is not detected at P, although this site is required for recombination. Additionally, P1 is required for recombination, presumably to stabilize binding at P. Finally, we have solved the crystal structure of the Brujita Int and have found residues responsible for higher order complex formation. In total, our results indicate that Brujita Int may represent an evolutionary precursor to the canonical tyrosine integrases. Moreover, given its relative simplicity, Brujita Int presents a useful tool for the creation of synthetic genetic circuits as well as genome manipulation

3D simulations of gas puff effects on edge density and ICRF coupling in ASDEX Upgrade

In recent experiments, a local gas puff was found to be an effective way to tailor the scrape-off layer (SOL) density and improve the ion cyclotron range of frequency (ICRF) power coupling in tokamaks. In order to quantitatively reproduce these experiments, to understand the corresponding physics and to optimize the gas valve positions and rates, simulations were carried out with the 3D edge plasma transport code EMC3-EIRENE in ASDEX Upgrade. An inter-ELM phase of an H-mode discharge with a moderate gas puff rate (1.2 x 10(22) electrons s(-1)) is used in our simulations. We simulated cases with gas puff in the lower divertor, the outer mid-plane and the top of the machine while keeping other conditions the same. Compared with the lower divertor gas puff, the outer mid-plane gas puff can increase the local density in front of the antennas most effectively, while a toroidally uniform but significantly smaller enhancement is found for the top gas puff. Good agreement between our simulations and experiments is obtained. With further simulations, the mechanisms of SOL density tailoring via local gas puffing and the strategies of gas puff optimization are discussed in the paper

The Evolution of Tyrosine-Recombinase Elements in Nematoda

Transposable elements can be categorised into DNA and RNA elements based on their mechanism of transposition. Tyrosine recombinase elements (YREs) are relatively rare and poorly understood, despite sharing characteristics with both DNA and RNA elements. Previously, the Nematoda have been reported to have a substantially different diversity of YREs compared to other animal phyla: the Dirs1-like YRE retrotransposon was encountered in most animal phyla but not in Nematoda, and a unique Pat1-like YRE retrotransposon has only been recorded from Nematoda. We explored the diversity of YREs in Nematoda by sampling broadly across the phylum and including 34 genomes representing the three classes within Nematoda. We developed a method to isolate and classify YREs based on both feature organization and phylogenetic relationships in an open and reproducible workflow. We also ensured that our phylogenetic approach to YRE classification identified truncated and degenerate elements, informatively increasing the number of elements sampled. We identified Dirs1-like elements (thought to be absent from Nematoda) in the nematode classes Enoplia and Dorylaimia indicating that nematode model species do not adequately represent the diversity of transposable elements in the phylum. Nematode Pat1-like elements were found to be a derived form of another Pat1-like element that is present more widely in animals. Several sequence features used widely for the classification of YREs were found to be homoplasious, highlighting the need for a phylogenetically-based classification scheme. Nematode model species do not represent the diversity of transposable elements in the phylum

The value-added of primary schools: what is it really measuring?

This paper compares the official value-added scores in 2005 for all primary schools in three adjacent LEAs in England with the raw-score Key Stage 2 results for the same schools. The correlation coefficient for the raw- and value-added scores of these 457 schools is around +0.75. Scatterplots show that there are no low attaining schools with average or higher value-added, and no high attaining schools with below average value-added. At least some of the remaining scatter is explained by the small size of some schools. Although some relationship between these measures is to be expected – so that schools adding considerable value would tend to have high examination outcome scores – the relationship shown is too strong for this explanation to be considered sufficient. Value-added analysis is intended to remove the link between a schools’ intake scores and their raw-score outcomes at KS2. It should lead to an estimate of the differential progress made by pupils, assessed between schools. In fact, however, the relationship between value-added and raw scores is of the same size as the original relationship between intake scores and raw-scores that the value-added is intended to overcome. Therefore, however appealing the calculation of value-added figures is, their development is still at the stage where they are not ready to move from being a research tool to an instrument of judgement on schools. Such figures may mislead parents, governors and teachers and, even more importantly, they are being used in England by OFSTED to pre-determine the results of school inspections

Modelling of the ICRF induced E x B convection in the scrape-off-layer of ASDEX Upgrade

In magnetic controlled fusion devices, plasma heating with radio-frequency (RF) waves in the ion cyclotron (IC) range of frequency relies on the electric field of the fast wave to heat the plasma. However, the slow wave can be generated parasitically. The electric field of the slow wave can induce large biased plasma potential (DC potential) through sheath rectification. The rapid variation of the rectified potential across the equilibrium magnetic field can cause significant convective transport (E x B drifts) in the scrape-off layer (SOL). In order to understand this phenomenon and reproduce the experiments, 3D realistic simulations are carried out with the 3D edge plasma fluid and kinetic neutral code EMC3-Eirene in ASDEX Upgrade. For this, we have added the prescribed drift terms to the EMC3 equations and verified the 3D code results against the analytical ones in cylindrical geometry. The edge plasma potential derived from the experiments is used to calculate the drift velocities, which are then treated as input fields in the code to obtain the final density distributions. Our simulation results are in good agreement with the experiments

Temperature Tunable Air-Gap Etalon Filter

We report on experimental measurements of a temperature tuned air-gap etalon filter. The filter exhibits temperature dependent wavelength tuning of 54 pm/C. It has a nominal center wavelength of 532 nm. The etalon filter has a 27 pm optical bandpass and 600 pm free spectral range (finesse approximately 22). The experimental results are in close agreement with etalon theory

Estimation of trace gas fluxes with objectively determined basis functions using reversible-jump Markov chain Monte Carlo

Atmospheric trace gas inversions often attempt to attribute fluxes to a high-dimensional grid using observations. To make this problem computationally feasible, and to reduce the degree of under-determination, some form of dimension reduction is usually performed. Here, we present an objective method for reducing the spatial dimension of the parameter space in atmospheric trace gas inversions. In addition to solving for a set of unknowns that govern emissions of a trace gas, we set out a framework that considers the number of unknowns to itself be an unknown. We rely on the well-established reversible-jump Markov chain Monte Carlo algorithm to use the data to determine the dimension of the parameter space. This framework provides a single-step process that solves for both the resolution of the inversion grid, as well as the magnitude of fluxes from this grid. Therefore, the uncertainty that surrounds the choice of aggregation is accounted for in the posterior parameter distribution. The posterior distribution of this transdimensional Markov chain provides a naturally smoothed solution, formed from an ensemble of coarser partitions of the spatial domain. We describe the form of the reversible-jump algorithm and how it may be applied to trace gas inversions. We build the system into a hierarchical Bayesian framework in which other unknown factors, such as the magnitude of the model uncertainty, can also be explored. A pseudo-data example is used to show the usefulness of this approach when compared to a subjectively chosen partitioning of a spatial domain. An inversion using real data is also shown to illustrate the scales at which the data allow for methane emissions over north-west Europe to be resolved