1,388 research outputs found
Adaptive genomic structural variation in the grape powdery mildew pathogen, Erysiphe necator.
BackgroundPowdery mildew, caused by the obligate biotrophic fungus Erysiphe necator, is an economically important disease of grapevines worldwide. Large quantities of fungicides are used for its control, accelerating the incidence of fungicide-resistance. Copy number variations (CNVs) are unbalanced changes in the structure of the genome that have been associated with complex traits. In addition to providing the first description of the large and highly repetitive genome of E. necator, this study describes the impact of genomic structural variation on fungicide resistance in Erysiphe necator.ResultsA shotgun approach was applied to sequence and assemble the genome of five E. necator isolates, and RNA-seq and comparative genomics were used to predict and annotate protein-coding genes. Our results show that the E. necator genome is exceptionally large and repetitive and suggest that transposable elements are responsible for genome expansion. Frequent structural variations were found between isolates and included copy number variation in EnCYP51, the target of the commonly used sterol demethylase inhibitor (DMI) fungicides. A panel of 89 additional E. necator isolates collected from diverse vineyard sites was screened for copy number variation in the EnCYP51 gene and for presence/absence of a point mutation (Y136F) known to result in higher fungicide tolerance. We show that an increase in EnCYP51 copy number is significantly more likely to be detected in isolates collected from fungicide-treated vineyards. Increased EnCYP51 copy numbers were detected with the Y136F allele, suggesting that an increase in copy number becomes advantageous only after the fungicide-tolerant allele is acquired. We also show that EnCYP51 copy number influences expression in a gene-dose dependent manner and correlates with fungal growth in the presence of a DMI fungicide.ConclusionsTaken together our results show that CNV can be adaptive in the development of resistance to fungicides by providing increasing quantitative protection in a gene-dosage dependent manner. The results of this work not only demonstrate the effectiveness of using genomics to dissect complex traits in organisms with very limited molecular information, but also may have broader implications for understanding genomic dynamics in response to strong selective pressure in other pathogens with similar genome architectures
Travelling on Graphs with Small Highway Dimension
We study the Travelling Salesperson (TSP) and the Steiner Tree problem (STP)
in graphs of low highway dimension. This graph parameter was introduced by
Abraham et al. [SODA 2010] as a model for transportation networks, on which TSP
and STP naturally occur for various applications in logistics. It was
previously shown [Feldmann et al. ICALP 2015] that these problems admit a
quasi-polynomial time approximation scheme (QPTAS) on graphs of constant
highway dimension. We demonstrate that a significant improvement is possible in
the special case when the highway dimension is 1, for which we present a
fully-polynomial time approximation scheme (FPTAS). We also prove that STP is
weakly NP-hard for these restricted graphs. For TSP we show NP-hardness for
graphs of highway dimension 6, which answers an open problem posed in [Feldmann
et al. ICALP 2015]
The structure of invariant tori in a 3D galactic potential
We study in detail the structure of phase space in the neighborhood of stable
periodic orbits in a rotating 3D potential of galactic type. We have used the
color and rotation method to investigate the properties of the invariant tori
in the 4D spaces of section. We compare our results with those of previous
works and we describe the morphology of the rotational, as well as of the tube
tori in the 4D space. We find sticky chaotic orbits in the immediate
neighborhood of sets of invariant tori surrounding 3D stable periodic orbits.
Particularly useful for galactic dynamics is the behavior of chaotic orbits
trapped for long time between 4D invariant tori. We find that they support
during this time the same structure as the quasi-periodic orbits around the
stable periodic orbits, contributing however to a local increase of the
dispersion of velocities. Finally we find that the tube tori do not appear in
the 3D projections of the spaces of section in the axisymmetric Hamiltonian we
examined.Comment: 26 pages, 34 figures, accepted for publication in the International
Journal of Bifurcation and Chao
Geometry of dynamics, Lyapunov exponents and phase transitions
The Hamiltonian dynamics of classical planar Heisenberg model is numerically
investigated in two and three dimensions. By considering the dynamics as a
geodesic flow on a suitable Riemannian manifold, it is possible to analytically
estimate the largest Lyapunov exponent in terms of some curvature fluctuations.
The agreement between numerical and analytical values for Lyapunov exponents is
very good in a wide range of temperatures. Moreover, in the three dimensional
case, in correspondence with the second order phase transition, the curvature
fluctuations exibit a singular behaviour which is reproduced in an abstract
geometric model suggesting that the phase transition might correspond to a
change in the topology of the manifold whose geodesics are the motions of the
system.Comment: REVTeX, 10 pages, 5 PostScript figures, published versio
Conservation of energy and momenta in nonholonomic systems with affine constraints
We characterize the conditions for the conservation of the energy and of the
components of the momentum maps of lifted actions, and of their `gauge-like'
generalizations, in time-independent nonholonomic mechanical systems with
affine constraints. These conditions involve geometrical and mechanical
properties of the system, and are codified in the so-called
reaction-annihilator distribution
Space-time evolution of electron cascades in diamond
Here we describe model calculations to follow the spatio-temporal evolution
of secondary electron cascades in diamond. The band structure of the insulator
has been explicitly incorporated into the calculations as it affects
ionizations from the valence band. A Monte-Carlo model was constructed to
describe the path of electrons following the impact of a single electron of
energy E 250 eV. The results show the evolution of the secondary electron
cascades in terms of the number of electrons liberated, the spatial
distribution of these electrons, and the energy distribution among the
electrons as a function of time. The predicted ionization rates (5-13 electrons
in 100 fs) lie within the limits given by experiments and phenomenological
models. Calculation of the local electron density and the corresponding Debye
length shows that the latter is systematically larger than the radius of the
electron cloud. This means that the electron gas generated does not represent a
plasma in a single impact cascade triggered by an electron of E 250 eV energy.
This is important as it justifies the independent-electron approximation used
in the model. At 1 fs, the (average) spatial distribution of secondary
electrons is anisotropic with the electron cloud elongated in the direction of
the primary impact. The maximal radius of the cascade is about 50 A at this
time. As the system cools, energy is distributed more equally, and the spatial
distribution of the electron cloud becomes isotropic. At 90 fs maximal radius
is about 150 A. The Monte-Carlo model described here could be adopted for the
investigation of radiation damage in other insulators and has implications for
planned experiments with intense femtosecond X-ray sources.Comment: 26 pages, latex, 13 figure
Relativistic effects and quasipotential equations
We compare the scattering amplitude resulting from the several quasipotential
equations for scalar particles. We consider the Blankenbecler-Sugar, Spectator,
Thompson, Erkelenz-Holinde and Equal-Time equations, which were solved
numerically without decomposition into partial waves. We analyze both
negative-energy state components of the propagators and retardation effects. We
found that the scattering solutions of the Spectator and the Equal-Time
equations are very close to the nonrelativistic solution even at high energies.
The overall relativistic effect increases with the energy. The width of the
band for the relative uncertainty in the real part of the scattering
matrix, due to different dynamical equations, is largest for
backward-scattering angles where it can be as large as 40%.Comment: Accepted for publication in Phys. Rev.
Lowering IceCube's energy threshold for point source searches in the Southern Sky
Observation of a point source of astrophysical neutrinos would be a "smoking gun" signature of a cosmic-ray accelerator. While IceCube has recently discovered a diffuse flux of astrophysical neutrinos, no localized point source has been observed. Previous IceCube searches for point sources in the southern sky were restricted by either an energy threshold above a few hundred TeV or poor neutrino angular resolution. Here we present a search for southern sky point sources with greatly improved sensitivities to neutrinos with energies below 100 TeV. By selecting charged-current Îœ ÎŒ interacting inside the detector, we reduce the atmospheric background while retaining efficiency for astrophysical neutrino-induced events reconstructed with sub-degree angular resolution. The new event sample covers three years of detector data and leads to a factor of 10 improvement in sensitivity to point sources emitting below 100 TeV in the southern sky. No statistically significant evidence of point sources was found, and upper limits are set on neutrino emission from individual sources. A posteriori analysis of the highest-energy (~100 TeV) starting event in the sample found that this event alone represents a 2.8Ï deviation from the hypothesis that the data consists only of atmospheric background.Fil: Aartsen, M. G.. University of Adelaide; AustraliaFil: Abraham, K.. Technische UniversitĂ€t MĂŒnchen; AlemaniaFil: Ackermann, M.. Deutsches Elektronen-Synchrotron; AlemaniaFil: Adams, J.. University Of Canterbury; Nueva ZelandaFil: Aguilar, J. A.. UniversitĂ© Libre de Bruxelles; BĂ©lgicaFil: Golup, Geraldina Tamara. ComisiĂłn Nacional de EnergĂa AtĂłmica. Gerencia del Ărea de EnergĂa Nuclear. Instituto Balseiro; Argentina. Consejo Nacional de Investigaciones CientĂficas y TĂ©cnicas. Centro CientĂfico TecnolĂłgico Conicet - Patagonia Norte; ArgentinaFil: Wallace, A.. University of Adelaide; AustraliaFil: Wallraff, M.. Rwth Aachen University; AlemaniaFil: Wandkowsky, N.. University of Wisconsin; Estados UnidosFil: Weaver, Ch.. University of Alberta; CanadĂĄFil: Wendt, C.. University of Wisconsin; Estados UnidosFil: Westerhoff, S.. University of Wisconsin; Estados UnidosFil: Whelan, B. J.. University of Adelaide; AustraliaFil: Whitehorn, N.. University of California at Berkeley; Estados UnidosFil: Wickmann, S.. Rwth Aachen University; AlemaniaFil: Wiebe, K.. Johannes Gutenberg Universitat Mainz; AlemaniaFil: Wiebusch, C. H.. Rwth Aachen University; AlemaniaFil: Wille, L.. University of Wisconsin; Estados UnidosFil: Williams, D. R.. University of Alabama at Birmingahm; Estados UnidosFil: Wills, L.. Drexel University; Estados UnidosFil: Wissing, H.. University of Maryland; Estados UnidosFil: Wolf, M.. Stockholms Universitet; SueciaFil: Wood, T. R.. University of Alberta; CanadĂĄFil: Woschnagg, K.. University of California at Berkeley; Estados UnidosFil: Xu, D. L.. University of Wisconsin; Estados UnidosFil: Xu, X. W.. Southern University; Estados UnidosFil: Xu, Y.. Stony Brook University; Estados UnidosFil: Yanez, J. P.. Deutsches Elektronen-Synchrotron; AlemaniaFil: Yodh, G.. University of California at Irvine; Estados UnidosFil: Yoshida, S.. Chiba University; JapĂłnFil: Zoll, M.. Stockholms Universitet; Sueci
Increasing condom use in heterosexual men: development of a theory-based interactive digital intervention
Increasing condom use to prevent sexually transmitted infections is a key public health goal. Interventions are more likely to be effective if they are theory- and evidence-based. The Behaviour Change Wheel (BCW) provides a framework for intervention development. To provide an example of how the BCW was used to develop an intervention to increase condom use in heterosexual men (the MenSS website), the steps of the BCW intervention development process were followed, incorporating evidence from the research literature and views of experts and the target population. Capability (e.g. knowledge) and motivation (e.g. beliefs about pleasure) were identified as important targets of the intervention. We devised ways to address each intervention target, including selecting interactive features and behaviour change techniques. The BCW provides a useful framework for integrating sources of evidence to inform intervention content and deciding which influences on behaviour to target
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