Gene family encoding the major toxins of lethal \u3ci\u3eAmanita\u3c/i\u3e mushrooms

Amatoxins, the lethal constituents of poisonous mushrooms in the genus Amanita, are bicyclic octapeptides. Two genes in A. bisporigera, AMA1 and PHA1, directly encode α-amanitin, an amatoxin, and the related bicyclic heptapeptide phallacidin, a phallotoxin, indicating that these compounds are synthesized on ribosomes and not by nonribosomal peptide synthetases. α-Amanitin and phallacidin are synthesized as proproteins of 35 and 34 amino acids, respectively, from which they are predicted to be cleaved by a prolyl oligopeptidase. AMA1 and PHA1 are present in other toxic species of Amanita section Phalloidae but are absent from nontoxic species in other sections. The genomes of A. bisporigera and A. phalloides contain multiple sequences related to AMA1 and PHA1. The predicted protein products of this family of genes are characterized by a hypervariable ‘‘toxin’’ region capable of encoding a wide variety of peptides of 7–10 amino acids flanked by conserved sequences. Our results suggest that these fungi have a broad capacity to synthesize cyclic peptides on ribosomes

Critical Currents and Vortex States at Fractional Matching Fields in Superconductors with Periodic Pinning

We study vortex states and dynamics in 2D superconductors with periodic pinning at fractional sub-matching fields using numerical simulations. For square pinning arrays we show that ordered states form at 1/1, 1/2, and 1/4 filling fractions while only partially ordered states form at other filling fractions, such as 1/3 and 1/5, in agreement with recent imaging experiments. For triangular pinning arrays we observe matching effects at filling fractions of 1/1, 6/7, 2/3, 1/3, 1/4, 1/6, and 1/7. For both square and triangular pinning arrays we also find that, for certian sub-matching fillings, vortex configurations depend on pinning strength. For weak pinning, ordering in which a portion of the vortices are positioned between pinning sites can occur. Depinning of the vortices at the matching fields, where the vortices are ordered, is elastic while at the incommensurate fields the motion is plastic. At the incommensurate fields, as the applied driving force is increased, there can be a transition to elastic flow where the vortices move along the pinning sites in 1D channels and a reordering transition to a triangular or distorted triangular lattice. We also discuss the current-voltage curves and how they relate to the vortex ordering at commensurate and incommensurate fields.Comment: 14 figure

Melting and transverse depinning of driven vortex lattices in the periodic pinning of Josephson junction arrays

We study the non-equilibrium dynamical regimes of a moving vortex lattice in the periodic pinning of a Josephson junction array (JJA) for {\it finite temperatures} in the case of a fractional or submatching field. We obtain a phase diagram for the current driven JJA as a function of the driving current I and temperature T. We find that when the vortex lattice is driven by a current, the depinning transition at $T_p(I)$ and the melting transition at $T_M(I)$ become separated even for a field for which they coincide in equilibrium. We also distinguish between the depinning of the vortex lattice in the direction of the current drive, and the {\it transverse depinning} in the direction perpendicular to the drive. The transverse depinning corresponds to the onset of transverse resistance in a moving vortex lattice at a given temperature $T_{tr}$. For driving currents above the critical current we find that the moving vortex lattice has first a transverse depinning transition at low T, and later a melting transition at a higher temperature, $T_{M}>T_{tr}$.Comment: 17 pages, 19 figure

The interplay of intrinsic and extrinsic bounded noises in genetic networks

After being considered as a nuisance to be filtered out, it became recently clear that biochemical noise plays a complex role, often fully functional, for a genetic network. The influence of intrinsic and extrinsic noises on genetic networks has intensively been investigated in last ten years, though contributions on the co-presence of both are sparse. Extrinsic noise is usually modeled as an unbounded white or colored gaussian stochastic process, even though realistic stochastic perturbations are clearly bounded. In this paper we consider Gillespie-like stochastic models of nonlinear networks, i.e. the intrinsic noise, where the model jump rates are affected by colored bounded extrinsic noises synthesized by a suitable biochemical state-dependent Langevin system. These systems are described by a master equation, and a simulation algorithm to analyze them is derived. This new modeling paradigm should enlarge the class of systems amenable at modeling. We investigated the influence of both amplitude and autocorrelation time of a extrinsic Sine-Wiener noise on: $(i)$ the Michaelis-Menten approximation of noisy enzymatic reactions, which we show to be applicable also in co-presence of both intrinsic and extrinsic noise, $(ii)$ a model of enzymatic futile cycle and $(iii)$ a genetic toggle switch. In $(ii)$ and $(iii)$ we show that the presence of a bounded extrinsic noise induces qualitative modifications in the probability densities of the involved chemicals, where new modes emerge, thus suggesting the possibile functional role of bounded noises

Spatio-temporal dynamics and plastic flow of vortices in superconductors with periodic arrays of pinning sites

We present simulations of flux-gradient-driven superconducting rigid vortices interacting with square and triangular arrays of columnar pinning sites in an increasing external magnetic field. These simulations allow us to quantitatively relate spatio-temporal microscopic information of the vortex lattice with typically measured macroscopic quantities, such as the magnetization $M(H)$. The flux lattice does not become completely commensurate with the pinning sites throughout the sample at the magnetization matching peaks, but forms a commensurate lattice in a region close to the edge of the sample. Matching fields related to unstable vortex configurations do not produce peaks in $M(H)$. We observe a variety of evolving complex flux profiles, including flat terraces or plateaus separated by winding current-carrying strings and, near the peaks in $M(H)$, plateaus only in certain regions, which move through the sample as the field increases

Search for non-relativistic Magnetic Monopoles with IceCube

The IceCube Neutrino Observatory is a large Cherenkov detector instrumenting $1\,\mathrm{km}^3$ of Antarctic ice. The detector can be used to search for signatures of particle physics beyond the Standard Model. Here, we describe the search for non-relativistic, magnetic monopoles as remnants of the GUT (Grand Unified Theory) era shortly after the Big Bang. These monopoles may catalyze the decay of nucleons via the Rubakov-Callan effect with a cross section suggested to be in the range of $10^{-27}\,\mathrm{cm^2}$ to $10^{-21}\,\mathrm{cm^2}$. In IceCube, the Cherenkov light from nucleon decays along the monopole trajectory would produce a characteristic hit pattern. This paper presents the results of an analysis of first data taken from May 2011 until May 2012 with a dedicated slow-particle trigger for DeepCore, a subdetector of IceCube. A second analysis provides better sensitivity for the brightest non-relativistic monopoles using data taken from May 2009 until May 2010. In both analyses no monopole signal was observed. For catalysis cross sections of $10^{-22}\,(10^{-24})\,\mathrm{cm^2}$ the flux of non-relativistic GUT monopoles is constrained up to a level of $\Phi_{90} \le 10^{-18}\,(10^{-17})\,\mathrm{cm^{-2}s^{-1}sr^{-1}}$ at a 90% confidence level, which is three orders of magnitude below the Parker bound. The limits assume a dominant decay of the proton into a positron and a neutral pion. These results improve the current best experimental limits by one to two orders of magnitude, for a wide range of assumed speeds and catalysis cross sections.Comment: 20 pages, 20 figure

The IceCube Neutrino Observatory Part VI: Ice Properties, Reconstruction and Future Developments

Papers on ice properties, reconstruction and future developments submitted to the 33nd International Cosmic Ray Conference (Rio de Janeiro 2013) by the IceCube Collaboration.Comment: 28 pages, 38 figures; Papers submitted to the 33nd International Cosmic Ray Conference, Rio de Janeiro 2013; version 2 corrects errors in the author lis

Determining neutrino oscillation parameters from atmospheric muon neutrino disappearance with three years of IceCube DeepCore data

We present a measurement of neutrino oscillations via atmospheric muon neutrino disappearance with three years of data of the completed IceCube neutrino detector. DeepCore, a region of denser instrumentation, enables the detection and reconstruction of atmospheric muon neutrinos between 10 GeV and 100 GeV, where a strong disappearance signal is expected. The detector volume surrounding DeepCore is used as a veto region to suppress the atmospheric muon background. Neutrino events are selected where the detected Cherenkov photons of the secondary particles minimally scatter, and the neutrino energy and arrival direction are reconstructed. Both variables are used to obtain the neutrino oscillation parameters from the data, with the best fit given by $\Delta m^2_{32}=2.72^{+0.19}_{-0.20}\times 10^{-3}\,\mathrm{eV}^2$ and $\sin^2\theta_{23} = 0.53^{+0.09}_{-0.12}$ (normal mass hierarchy assumed). The results are compatible and comparable in precision to those of dedicated oscillation experiments.Comment: 10 pages, 7 figure