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

Critical points and supersymmetric vacua, III: String/M models

A fundamental problem in contemporary string/M theory is to count the number of inequivalent vacua satisfying constraints in a string theory model. This article contains the first rigorous results on the number and distribution of supersymmetric vacua of type IIb string theories compactified on a Calabi-Yau 3-fold $X$ with flux. In particular, complete proofs of the counting formulas in Ashok-Douglas and Denef-Douglas are given, together with van der Corput style remainder estimates. We also give evidence that the number of vacua satisfying the tadpole constraint in regions of bounded curvature in moduli space is of exponential growth in $b_3(X)$.Comment: Final revision for publication in Commun. Math. Phys. Minor corrections and editorial change

Greener One-pot Synthesis of Chromeno Oxazin and Oxazin Quinoline Derivatives and their Antibacterial Activity

An efficient green method for the synthesis of oxazino quinoline-2-amine derivatives, oxazino quinoline derivatives and chromeno oxazin-5-one derivatives have been synthesized through cyclization of aromatic aldehyde, ammonium acetate, substituted amides and 8-hydroxy-quinoline or 4-hydroxy coumarin by one-pot condensation method is described. The synthesized compounds are characterized by FT-IR, 1H NMR and MASS spectral techniques and are screened further for biological activities against Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus and Bacillus subtilis using cup plate method and disc diffusion method

Incoherent Pair Tunneling as a Probe of the Cuprate Pseudogap

We argue that incoherent pair tunneling in a cuprate superconductor junction with an optimally doped superconducting and an underdoped normal lead can be used to detect the presence of pairing correlations in the pseudogap phase of the underdoped lead. We estimate that the junction characteristics most suitable for studying the pair tunneling current are close to recently manufactured cuprate tunneling devices.Comment: ReVTeX 3.1; 4 pages, 2 EPS figures (included

Synthesis of Carboxamides Tranylcypromine Analogues as LSD1 (KDM1A) Inhibitors for AML

Lysine-specific demethylase 1 (LSD1/KDM1A) oxidatively removes methyl groups from histone proteins and its aberrant activity has been correlated with cancers including acute myeloid leukemia (AML). We report a novel series of tranylcypromine analogues containing a carboxamide at the 4-position of the aryl ring and novel carbamates. These compounds were potent submicromolar LSD1 inhibitors in enzyme assays and were anti-proliferative against a panel of AML cell lines. LSD1 target engagement in cells was demonstrated through the effects on H3K4me2 protein expression, CD86, CD11b and CD14 levels

Strong CH+ J=1-0 emission and absorption in DR21

We report the first detection of the ground-state rotational transition of the methylidyne cation CH+ towards the massive star-forming region DR21 with the HIFI instrument onboard the Herschel satellite. The line profile exhibits a broad emission line, in addition to two deep and broad absorption features associated with the DR21 molecular ridge and foreground gas. These observations allow us to determine a CH+ J=1-0 line frequency of 835137 +/- 3 MHz, in good agreement with a recent experimental determination. We estimate the CH+ column density to be a few 1e13 cm^-2 in the gas seen in emission, and > 1e14 cm^-2 in the components responsible for the absorption, which is indicative of a high line of sight average abundance [CH+]/[H] > 1.2x10^-8. We show that the CH+ column densities agree well with the predictions of state-of-the-art C-shock models in dense UV-illuminated gas for the emission line, and with those of turbulent dissipation models in diffuse gas for the absorption lines.Comment: Accepted for publication in A&

Technical aspects of CT imaging of the spine

This review article discusses technical aspects of computed tomography (CT) imaging of the spine. Patient positioning, and its influence on image quality and movement artefact, is discussed. Particular emphasis is placed on the choice of scan parameters and their relation to image quality and radiation burden to the patient. Strategies to reduce radiation burden and artefact from metal implants are outlined. Data acquisition, processing, image display and steps to reduce artefact are reviewed. CT imaging of the spine is put into context with other imaging modalities for specific clinical indications or problems. This review aims to review underlying principles for image acquisition and to provide a rough guide for clinical problems without being prescriptive. Individual practice will always vary and reflect differences in local experience, technical provisions and clinical requirements