Diseases of plants due to fungi

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Epigenetic modifications affect the rate of spontaneous mutations in a pathogenic fungus

Mutations are the source of genetic variation and the substrate for evolution. Genome-widemutation rates appear to be affected by selection and are probably adaptive. Mutation ratesare also known to vary along genomes, possibly in response to epigenetic modifications, butcausality is only assumed. In this study we determine the direct impact of epigenetic mod-ifications and temperature stress on mitotic mutation rates in a fungal pathogen using amutation accumulation approach. Deletion mutants lacking epigenetic modifications confirmthat histone mark H3K27me3 increases whereas H3K9me3 decreases the mutation rate.Furthermore, cytosine methylation in transposable elements (TE) increases the mutation rate15-fold resulting in significantly less TE mobilization. Also accessory chromosomes havesignificantly higher mutation rates. Finally, wefind that temperature stress substantiallyelevates the mutation rate. Taken together, wefind that epigenetic modifications andenvironmental conditions modify the rate and the location of spontaneous mutations in thegenome and alter its evolutionary trajectory

Greenberger-Horne-Zeilinger state protocols for fully connected qubit networks

We generalize the recently proposed Greenberger-Horne-Zeilinger (GHZ) tripartite protocol [A. Galiautdinov, J. M. Martinis, Phys. Rev. A 78, 010305(R) (2008)] to fully connected networks of weakly coupled qubits interacting by way of anisotropic Heisenberg exchange g(XX+YY)+g1*ZZ. Our model adopted here differs from the more familiar Ising-Heisenberg chain in that here every qubit interacts with every other qubit in the circuit. The assumption of identical couplings on all qubit pairs allows an elegant proof of the protocol for arbitrary N. In order to further make contact with experiment, we study fidelity degradation due to coupling imperfections by numerically simulating the N=3 and N=4 cases. Our simulations indicate that the best fidelity at unequal couplings is achieved when (a) the system is initially prepared in the uniform superposition state (similarly to how it is done in the ideal case), and (b) the entangling time and the final rotations on each of the qubits are appropriately adjusted.Comment: 11 pages, 1 figur

Dynamics of transposable elements in recently diverged fungal pathogens: lineage-specific transposable element content and efficiency of genome defences

Transposable elements (TEs) impact genome plasticity, architecture and evolution in fungal plant pathogens. The wide range of TE content observed in fungal genomes reflects diverse efficacy of host-genome defence mechanisms that can counter-balance TE expansion and spread. Closely related species can harbour drastically different TE repertoires, suggesting variation in the efficacy of genome defences. The evolution of fungal effectors, which are crucial determinants of pathogenicity, has been linked to the activity of TEs in pathogen genomes. Here we describe how TEs have shaped genome evolution of the fungal wheat pathogen Zymoseptoria tritici and four closely related species. We compared de novo TE annotations and Repeat-Induced Point mutation signatures in thirteen genomes from the Zymoseptoria species-complex. Then, we assessed the relative insertion ages of TEs using a comparative genomics approach. Finally, we explored the impact of TE insertions on genome architecture and plasticity. The thirteen genomes of Zymoseptoria species reflect different TE dynamics with a majority of recent insertions. TEs associate with distinct genome compartments in all Zymoseptoria species, including chromosomal rearrangements, genes showing presence/absence variation and effectors. European Z. tritici isolates have reduced signatures of Repeat-Induced Point mutations compared to Iranian isolates and closely related species. Our study supports the hypothesis that ongoing but moderate TE mobility in Zymoseptoria species shapes pathogen genome evolution.Competing Interest StatementThe authors have declared no competing interest

Vertex similarity in networks

We consider methods for quantifying the similarity of vertices in networks. We propose a measure of similarity based on the concept that two vertices are similar if their immediate neighbors in the network are themselves similar. This leads to a self-consistent matrix formulation of similarity that can be evaluated iteratively using only a knowledge of the adjacency matrix of the network. We test our similarity measure on computer-generated networks for which the expected results are known, and on a number of real-world networks

Towards a biosensor based on Anti Resonant Reflecting Optical Waveguide fabricated from porous silicon.

International audienceRecently, we demonstrated that Anti Resonant Reflecting Optical Waveguide (ARROW) based on porous silicon (PS) material can be used as a transducer for the development of a new optical biosensor. Compared to a conventional biosensor waveguide based on evanescent waves, the ARROW structure is designed to allow a better overlap between the propagated optical field and the molecules infiltrated in the porous core layer and so to provide better molecular interactions sensitivity. The aim of this work is to investigate the operating mode of an optical biosensor using the ARROW structure. We reported here an extensive study where the antiresonance conditions were adjusted just before the grafting of the studied molecules for a given refractive index range. The interesting feature of the studied ARROW structure is that it is elaborated from the same material which is the porous silicon obtained via a single electrochemical anodization process. After oxidation and preparation of the inner surface of porous silicon by a chemical functionalization process, bovine serum albumin (BSA) molecules, were attached essentially in the upper layer. Simulation study indicates that the proposed sensor works at the refractive index values ranging from 1.3560 to 1.3655. The experimental optical detection of the biomolecules was obtained through the modification of the propagated optical field and losses. The results indicated that the optical attenuation decreases after biomolecules attachment, corresponding to a refractive index change Δnc of the core. This reduction was of about 2 dB/cm and 3 dB/cm for Transverse Electric (TE) and Transverse Magnetic (TM) polarizations respectively. Moreover, at the detection step, the optical field was almost located inside the core layer. This result was in good agreement with the simulated near field profiles

A Precision Angle Sensor using an Optical Lever inside a Sagnac Interferometer

We built an ultra low noise angle sensor by combining a folded optical lever and a Sagnac interferometer. The instrument has a measured noise floor of 1.3 prad / Hz^(1/2) at 2.4 kHz. We achieve this record angle sensitivity using a proof-of-concept apparatus with a conservative N=11 bounces in the optical lever. This technique could be extended to reach sub-picoradian / Hz^(1/2) sensitivities with an optimized design.Comment: 3 pages, 4 figure

Derivation of the Lorentz Force Law, the Magnetic Field Concept and the Faraday-Lenz Law using an Invariant Formulation of the Lorentz Transformation

It is demonstrated how the right hand sides of the Lorentz Transformation equations may be written, in a Lorentz invariant manner, as 4--vector scalar products. This implies the existence of invariant length intervals analogous to invariant proper time intervals. This formalism, making essential use of the 4-vector electromagnetic potential concept, provides a short derivation of the Lorentz force law of classical electrodynamics, the conventional definition of the magnetic field, in terms of spatial derivatives of the 4--vector potential and the Faraday-Lenz Law. An important distinction between the physical meanings of the space-time and energy-momentum 4--vectors is pointed out.Comment: 15 pages, no tables 1 figure. Revised and extended version of physics/0307133 Some typos removed and minor text improvements in this versio

Electromagnetic force density in dissipative isotropic media

We derive an expression for the macroscopic force density that a narrow-band electromagnetic field imposes on a dissipative isotropic medium. The result is obtained by averaging the microscopic form for Lorentz force density. The derived expression allows us to calculate realistic electromagnetic forces in a wide range of materials that are described by complex-valued electric permittivity and magnetic permeability. The three-dimensional energy-momentum tensor in our expression reduces for lossless media to the so-called Helmholtz tensor that has not been contradicted in any experiment so far. The momentum density of the field does not coincide with any well-known expression, but for non-magnetic materials it matches the Abraham expression

Link Prediction Based on Local Random Walk

The problem of missing link prediction in complex networks has attracted much attention recently. Two difficulties in link prediction are the sparsity and huge size of the target networks. Therefore, the design of an efficient and effective method is of both theoretical interests and practical significance. In this Letter, we proposed a method based on local random walk, which can give competitively good prediction or even better prediction than other random-walk-based methods while has a lower computational complexity.Comment: 6 pages, 2 figure