Bacteria from natural populations transfer plasmids mostly towards their kin

This is the final version. Available on open access from the Royal Society via the DOI in this recordData accessibility: The datasets supporting this article are available from the Dryad Digital Repository at https://doi.org/10.5061/dryad.ff045t7 [52].Plasmids play a key role in microbial ecology and evolution, yet the determinants of plasmid transfer rates are poorly understood. Particularly, interactions between donor hosts and potential recipients are understudied. Here, we investigate the importance of genetic similarity between naturally co-occurring Escherichia coli isolates in plasmid transfer. We uncover extensive variability, spanning over five orders of magnitude, in the ability of isolates to donate and receive two different plasmids, R1 and RP4. Overall, transfer is strongly biased towards clone-mates, but not correlated to genetic distance when donors and recipients are not clone-mates. Transfer is limited by the presence of a functional restriction-modification system in recipients, suggesting sharing of strain-specific defence systems contributes to bias towards kin. Such restriction of transfer to kin sets the stage for longer-term coevolutionary interactions leading to mutualism between plasmids and bacterial hosts in natural communities.Medical Research Council (MRC

Bacteria from natural populations transfer plasmids mostly towards their kin

This is the final version. Available on open access from the Royal Society via the DOI in this recordData accessibility: The datasets supporting this article are available from the Dryad Digital Repository at https://doi.org/10.5061/dryad.ff045t7 [52].Plasmids play a key role in microbial ecology and evolution, yet the determinants of plasmid transfer rates are poorly understood. Particularly, interactions between donor hosts and potential recipients are understudied. Here, we investigate the importance of genetic similarity between naturally co-occurring Escherichia coli isolates in plasmid transfer. We uncover extensive variability, spanning over five orders of magnitude, in the ability of isolates to donate and receive two different plasmids, R1 and RP4. Overall, transfer is strongly biased towards clone-mates, but not correlated to genetic distance when donors and recipients are not clone-mates. Transfer is limited by the presence of a functional restriction-modification system in recipients, suggesting sharing of strain-specific defence systems contributes to bias towards kin. Such restriction of transfer to kin sets the stage for longer-term coevolutionary interactions leading to mutualism between plasmids and bacterial hosts in natural communities.Medical Research Council (MRC

Spin orientation and magnetostriction of Tb1−xDyxFe2 from first principles

The optimal amount of dysprosium in the highly magnetostrictive rare-earth compounds Tb1−xDyxFe2 for room-temperature applications has long been known to be x=0.73 (Terfenol-D). Here, we derive this value from first principles by calculating the easy magnetization direction and magnetostriction as a function of composition and temperature. We use crystal-field coefficients obtained within density-functional theory to construct phenomenological anisotropy and magnetoelastic constants. The temperature dependence of these constants is obtained from disordered-local-moment calculations of the rare-earth magnetic order parameter. Our calculations find the critical Dy concentration required to switch the magnetization direction at room temperature to be xc=0.78, with magnetostrictions λ111=2700 and λ100=−430 ppm, close to the Terfenol-D values

Nested sampling of materials’ potential energy surfaces : case study of Zirconium

The nested sampling (NS) method was originally proposed by John Skilling to calculate the evidence in Bayesian inference. The method has since been utilised in various research fields, and here we focus on how NS has been adapted to sample the Potential Energy Surface (PES) of atomistic systems, enabling the straightforward estimation of the partition function. Using two interatomic potential models of zirconium, we demonstrate the workflow and advantages of using nested sampling to calculate pressure-temperature phase diagrams. Without any prior knowledge of the stable phases or the phase transitions, we are able to identify the melting line, as well as the transition between the body-centred-cubic and hexagonal-close-packed structures

Spatial variation of trace elements in the peri-urban soil of Madrid

Purpose The peri-urban region to the south east of Madrid contains a mixture of housing, manufacturing industry and farming, some of which disperse metals, in particular cadmium, copper, lead, and zinc, into the soil. We have mapped the concentrations of these elements and identified the major influences on their distributions. Material and methods We sampled the topsoil at 125 sites across 1,050 km2 of peri-urban land to the south east of the city on two grids, one nested inside the other. At each site, we measured the current contents of the four trace elements in the soil. We used robust geostatistical methods to model the complex spatial distributions of the data as mixtures of fixed and random effects. The empirical best linear unbiased predictor was used to map the elements. Site descriptors (lithology, land cover, cultivation, relief, erosion, and stoniness) were then included as covariates to identify significant effects on trace element concentrations. Results and discussion The complex spatial distributions of the elements seem to arise from several sources. The concentrations generally increase from southeast to northwest, i.e.;with increasing proximity to Madrid itself, the main potential source of pollution. This pattern is clear for lead and similar for copper and zinc, though with "hot spots" at or near industrial sites. The spatial pattern of cadmium is more complex and depends on varied lithology, industry, and land use such as irrigation and cultivation. In general, the concentrations of the four elements appear to decrease with increases in stoniness and erosion, and to be largest on the valley floors. Conclusions Robust geostatistical methods enabled us to analyze and map the complex patterns of spatial variation of trace elements in a peri-urban region of Madrid. They show that distance to the city center, lithology, manufacturing industry, and cultivation all play their parts in loading the soil with lead, copper, zinc, and cadmium. In the event, none of the metals has yet exceeded the legislative thresholds, but some concentrations are already substantially greater than would arise from natural sources, especially closest to Madrid itself. © 2013 The Author(s)

Modules for Experiments in Stellar Astrophysics (MESA): Convective Boundaries, Element Diffusion, and Massive Star Explosions

We update the capabilities of the software instrument Modules for Experiments in Stellar Astrophysics (MESA) and enhance its ease of use and availability. Our new approach to locating convective boundaries is consistent with the physics of convection, and yields reliable values of the convective core mass during both hydrogen and helium burning phases. Stars with $M<8\,{\rm M_\odot}$ become white dwarfs and cool to the point where the electrons are degenerate and the ions are strongly coupled, a realm now available to study with MESA due to improved treatments of element diffusion, latent heat release, and blending of equations of state. Studies of the final fates of massive stars are extended in MESA by our addition of an approximate Riemann solver that captures shocks and conserves energy to high accuracy during dynamic epochs. We also introduce a 1D capability for modeling the effects of Rayleigh-Taylor instabilities that, in combination with the coupling to a public version of the STELLA radiation transfer instrument, creates new avenues for exploring Type II supernovae properties. These capabilities are exhibited with exploratory models of pair-instability supernova, pulsational pair-instability supernova, and the formation of stellar mass black holes. The applicability of MESA is now widened by the capability of importing multi-dimensional hydrodynamic models into MESA. We close by introducing software modules for handling floating point exceptions and stellar model optimization, and four new software tools -- MESAWeb, MESA-Docker, pyMESA, and mesastar.org -- to enhance MESA's education and research impact.Comment: 64 pages, 61 figures; Accepted to AAS Journal

Approximate techniques for dispersive shock waves in nonlinear media

Many optical and other nonlinear media are governed by dispersive, or diffractive, wave equations, for which initial jump discontinuities are resolved into a dispersive shock wave. The dispersive shock wave smooths the initial discontinuity and is a modulated wavetrain consisting of solitary waves at its leading edge and linear waves at its trailing edge. For integrable equations the dispersive shock wave solution can be found using Whitham modulation theory. For nonlinear wave equations which are hyperbolic outside the dispersive shock region, the amplitudes of the solitary waves at the leading edge and the linear waves at the trailing edge of the dispersive shock can be determined. In this paper an approximate method is presented for calculating the amplitude of the lead solitary waves of a dispersive shock for general nonlinear wave equations, even if these equations are not hyperbolic in the dispersionless limit. The approximate method is validated using known dispersive shock solutions and then applied to calculate approximate dispersive shock solutions for equations governing nonlinear optical media, such as nematic liquid crystals, thermal glasses and colloids. These approximate solutions are compared with numerical results and excellent comparisons are obtained

A simple, versatile laser system for the creation of ultracold ground state molecules

Paper Part of Focus on New Frontiers of Cold Molecules Research A narrow-linewidth, dual-wavelength laser system is vital for the creation of ultracold ground state molecules via stimulated Raman adiabatic passage (STIRAP) from a weakly bound Feshbach state. Here we describe how a relatively simple apparatus consisting of a single fixed-length optical cavity can be used to narrow the linewidth of the two different wavelength lasers required for STIRAP simultaneously. The frequency of each of these lasers is referenced to the cavity and is continuously tunable away from the cavity modes through the use of non-resonant electro-optic modulators. Self-heterodyne measurements suggest the laser linewidths are reduced to several 100 Hz. In the context of 87Rb133Cs molecules produced via magnetoassociation on a Feshbach resonance, we demonstrate the performance of the laser system through one- and two-photon molecular spectroscopy. Finally, we demonstrate transfer of the molecules to the rovibrational ground state using STIRAP

Working with Children with Learning Disabilities and/or who Communicate Non-verbally: Research experiences and their implications for social work education, increased participation and social inclusion

Social exclusion, although much debated in the UK, frequently focuses on children as a key 'at risk' group. However, some groups, such as disabled children, receive less consideration. Similarly, despite both UK and international policy and guidance encouraging the involvement of disabled children and their right to participate in decision-making arenas, they are frequently denied this right. UK based evidence suggests that disabled children's participation lags behind that of their non-disabled peers, often due to social work practitioners' lack of skills, expertise and knowledge on how to facilitate participation. The exclusion of disabled children from decision-making in social care processes echoes their exclusion from participation in society. This paper seeks to begin to address this situation, and to provide some examples of tools that social work educators can introduce into pre- and post-qualifying training programmes, as well as in-service training. The paper draws on the experiences of researchers using non-traditional qualitative research methods, especially non-verbal methods, and describes two research projects, focusing on the methods employed to communicate with and involve disabled children, the barriers encountered and lessons learnt. Some of the ways in which these methods of communication can inform social work education are explored alongside wider issues of how and if increased communication can facilitate greater social inclusion

Wave nucleation rate in excitable systems in the low noise limit

Motivated by recent experiments on intracellular calcium dynamics, we study the general issue of fluctuation-induced nucleation of waves in excitable media. We utilize a stochastic Fitzhugh-Nagumo model for this study, a spatially-extended non-potential pair of equations driven by thermal (i.e. white) noise. The nucleation rate is determined by finding the most probable escape path via minimization of an action related to the deviation of the fields from their deterministic trajectories. Our results pave the way both for studies of more realistic models of calcium dynamics as well as of nucleation phenomena in other non-equilibrium pattern-forming processes