Mutation analysis using the restriction site mutation (RSM) assay

The restriction site mutation RSM assay see Steingrimsdottir et al. H. Steingrimsdottir, D. Beare, J. Cole, J.F.M. Leal, Ž. Ž w T. Kostic, J. Lopez-Barea, G. Dorado, A.R. Lehmann, Development of new molecular procedures for the detection of genetic alteration in man, Mutat. Res. 353 1996 pp. 109–121 for a review has been developed as a genotypic mutation Ž . x . detection system capable of identifying mutations occurring in restriction enzyme sites of genomic DNA. Here we will report the steps taken to overcome some of the initial problems of the assay, namely the lack of quantitative data and limited sensitivity, the aim being to achieve a methodology suitable for the study of low dose chemical exposures. Quantitative data was achieved in the RSM assay by the inclusion of an internal standard molecule in the PCR amplification stage, thus allowing the calculation of both spontaneous and induced mutation frequencies. The sensitivity of the assay was increased through the discovery that intron sequences of genomic DNA accumulated more mutations in vivo compared to the exons, presumably due to differential selective pressure within genes G.J.S. Jenkins, I.deG. Mitchell, J.M. Parry, Enhanced w restriction site mutation RSM analysis of 1,2-dimethylhydrazine-induced mutations, using endogenous Ž . p53 intron sequences, Mutagenesis 12 1997 pp. 117–123 . This increased sensitivity was examined by applying the RSM assay to Ž . x analyse the persistence of N-ethyl-N-nitrosourea ENU -induced mutations in mice testes. Germ line mutations were sought Ž . in testes DNA 3, 10 and 100 days after ENU treatment. Mutations were detected in exons and especially intron regions, the intron mutations were more persistent, still being detected 100 days post-chemical treatment. Assignment of these mutations as ENU induced was complicated in some cases where the spontaneous mutation level was high. This theme of mutation persistence was further investigated by studying the presence of 4-nitroquinoline-1-oxide 4-NQO -induced DNA mutations Ž . in vitro. This study also analysed the relationship between DNA adduct formation and DNA mutation induction by the concurrent RSM analysis and 32P post-labelling analysis of 4-NQO treated human fibroblasts. The results demonstrated that early DNA mutations detected 4 days post-treatment by the RSM assay were probably ex vivo mutations induced by Taq polymerase misincorporation of 4-NQO adducted DNA, due to the maximum levels of 4-NQO adducts being present at this time point. A later mutational peak, after the adduct level had declined, was assumed to be due to DNA sequence changes produced in the fibroblasts by the in vivo processing of DNA adducts

SALT observations of the Chromospheric Activity of Transiting Planet Hosts: Mass Loss and Star Planet Interactions

We measured the chromospheric activity of the four hot Jupiter hosts WASP-43, WASP-51/HAT-P-30, WASP-72 & WASP-103 to search for anomalous values caused by the close-in companions. The Mount Wilson Ca II H&K S-index was calculated for each star using observations taken with the Robert Stobie Spectrograph at the Southern African Large Telescope. The activity level of WASP-43 is anomalously high relative to its age and falls among the highest values of all known main sequence stars. We found marginal evidence that the activity of WASP-103 is also higher than expected from the system age. We suggest that for WASP-43 and WASP-103 star-planet interactions (SPI) may enhance the Ca II H&K core emission. The activity levels of WASP-51/HAT-P-30 and WASP-72 are anomalously low, with the latter falling below the basal envelope for both main sequence and evolved stars. This can be attributed to circumstellar absorption due to planetary mass loss, though absorption in the ISM may contribute. A quarter of known short period planet hosts exhibit anomalously low activity levels, including systems with hot Jupiters and low mass companions. Since SPI can elevate and absorption can suppress the observed chromospheric activity of stars with close-in planets, their Ca II H&K activity levels are an unreliable age indicator. Systems where the activity is depressed by absorption from planetary mass loss are key targets for examining planet compositions through transmission spectroscopy

VIP enhances TRH-stimulated prolactin secretion of pituitary tumours Studies with 31P NMR

AbstractIntravenous thyrotrophin releasing hormone (TRH) caused a 6.5-fold increase in plasma prolactin (PRL) in rats carrying implanted pituitary tumours. Vasoactive intestinal polypeptide (VIP) had no effect, but TRH given after VIP raised TRH stimulated secretion 13-fold above basal. 31P NMR spectroscopy showed that VIP caused a decrease in high energy metabolites (depleted phosphocreatine, elevated inorganic phosphate and lowered intracellular pH). TRH alone caused a similar but smaller effect; given after VIP, it caused no detectable depletion. We suggest that the changes in high energy metabolite cencentrations reflect increased cellular energy consumption consistent with a priming process (stage 1) in PRL secretion, followed by hormone release (stage 2). VIP induces stage 1 whereas RTH induced both stages

Benchmark low-mass objects in Moving Groups

This is an Open Access article distributed under the terms of the Creative Commons Attribution License 2.0, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.In order to compile a sample of ultracool dwarfs that will serve as benchmarks for testing theoretical formation and evolutionary models, we selected low-mass cool (>M7) objects that are potentially members of five known young Moving Groups in the solar neighbourhood. We have studied the kinematics of the sample, finding that 49 targets belong to the young disk area, from which 36 are kinematic member of one of the five moving groups under study. Some of the identified low-mass members have been spectroscopically characterised (T-eff, log g) and confirmed as young members through a detailed study of age indicators

Velocity correlations in dense granular gases

We report the statistical properties of spherical steel particles rolling on an inclined surface being driven by an oscillating wall. Strong dissipation occurs due to collisions between the particles and rolling and can be tuned by changing the number density. The velocities of the particles are observed to be correlated over large distances comparable to the system size. The distribution of velocities deviates strongly from a Gaussian. The degree of the deviation, as measured by the kurtosis of the distribution, is observed to be as much as four times the value corresponding to a Gaussian, signaling a significant breakdown of the assumption of negligible velocity correlations in a granular system.Comment: 4 pages, 4 Figure

Granular clustering in a hydrodynamic simulation

We present a numerical simulation of a granular material using hydrodynamic equations. We show that, in the absence of external forces, such a system phase-separates into high density and low density regions. We show that this separation is dependent on the inelasticity of collisions, and comment on the mechanism for this clustering behavior. Our results are compatible with the granular clustering seen in experiments and molecular dynamic simulations of inelastic hard disks.Comment: 4 pages, 5 figure

Ab-initio density-functional lattice-dynamics studies of ice

We present the results of first-principles computational studies of the dynamical properties of hexagonal ice using both the ab-initio pseudopotential method and the full-potential augmented plane-wave method. Properties obtained using both the generalized gradient approximation (GGA) and the meta-GGA in density-functional theory are compared. The lattice-dynamical properties of the structures are obtained using a finite-difference evaluation of the dynamical matrix and force-constant matrix from atomic forces. Phonon dispersion is evaluated by the direct determination of the force-constant matrix in supercells derived from the primitive molecule unit cells with the assumption that force constants are zero beyond the second molecular nearest neighbors. The k-dependent phonon frequencies are then obtained from the force-constant matrix and dispersion relations, and the Brillouin-zone integrated density of states is evaluated. The importance of phonon dispersion in the various regions of the phonon spectra is then assessed and compared to existing neutron-scattering data. Frozen-phonon calculations are used to compare phonon frequencies evaluated in both the GGA and meta-GGA

Symmetry-breaking instability in a prototypical driven granular gas

Symmetry-breaking instability of a laterally uniform granular cluster (strip state) in a prototypical driven granular gas is investigated. The system consists of smooth hard disks in a two-dimensional box, colliding inelastically with each other and driven, at zero gravity, by a "thermal" wall. The limit of nearly elastic particle collisions is considered, and granular hydrodynamics with the Jenkins-Richman constitutive relations is employed. The hydrodynamic problem is completely described by two scaled parameters and the aspect ratio of the box. Marginal stability analysis predicts a spontaneous symmetry breaking instability of the strip state, similar to that predicted recently for a different set of constitutive relations. If the system is big enough, the marginal stability curve becomes independent of the details of the boundary condition at the driving wall. In this regime, the density perturbation is exponentially localized at the elastic wall opposite to the thermal wall. The short- and long-wavelength asymptotics of the marginal stability curves are obtained analytically in the dilute limit. The physics of the symmetry-breaking instability is discussed.Comment: 11 pages, 14 figure

Contributions from SUSY-FCNC couplings to the interpretation of the HyperCP events for the decay \Sigma^+ \to p \mu^+ \mu^-

The observation of three events for the decay $\Sigma^+ \to p \mu^+ \mu^-$ with a dimuon invariant mass of $214.3\pm0.5$MeV by the HyperCP collaboration imply that a new particle X may be needed to explain the observed dimuon invariant mass distribution. We show that there are regions in the SUSY-FCNC parameter space where the $A^0_1$ in the NMSSM can be used to explain the HyperCP events without contradicting all the existing constraints from the measurements of the kaon decays, and the constraints from the $K^0-\bar{K}^0$ mixing are automatically satisfied once the constraints from kaon decays are satisfied.Comment: 18 pages, 7 figure

Determination of atomic abundances of solar-type stars

We discuss the results of abundance determinations of the solar-type stars HD 1835 and HD 10700 using our new procedure. This procedure has the advantage of automated pipeline usage for large amounts of spectroscopic data, with minimal user input. It is based on the spectral synthesis method, where the best values are found with our own developed minimization technique. We reduce the number of free parameters in minimization space using the fit to the observed atomic iron lines. We calibrated our procedure using fits to the observed solar spectrum. Then we determined abundances in two solar-type stars, namely the metal-deficient star HD 10700 and the metal-rich star HD 1835. We found good agreement with previously published results. Thus, we aim to use this procedure for the abundance determination of solar-type stars, particularly planet hosting stars, where the knowledge of abundances is crucial for our understanding of their evolution and formation processes