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

P2Y Receptors Sensitize Mouse and Human Colonic Nociceptors

Activation of visceral nociceptors by inflammatory mediators contributes to visceral hypersensitivity and abdominal pain associated with many gastrointestinal disorders. Purine and pyrimidine nucleotides (e.g., ATP and UTP) are strongly implicated in this process following their release from epithelial cells during mechanical stimulation of the gut, and from immune cells during inflammation. Actions of ATP are mediated through both ionotropic P2X receptors and metabotropic P2Y receptors. P2X receptor activation causes excitation of visceral afferents; however, the impact of P2Y receptor activation on visceral afferents innervating the gut is unclear. Here we investigate the effects of stimulating P2Y receptors in isolated mouse colonic sensory neurons, and visceral nociceptor fibers in mouse and human nerve-gut preparations. Additionally, we investigate the role of Na(v)1.9 in mediating murine responses. The application of UTP (P2Y(2) and P2Y(4) agonist) sensitized colonic sensory neurons by increasing action potential firing to current injection and depolarizing the membrane potential. The application of ADP (P2Y(1), P2Y(12), and P2Y(13) agonist) also increased action potential firing, an effect blocked by the selective P2Y(1) receptor antagonist MRS2500. UTP or ADP stimulated afferents, including mouse and human visceral nociceptors, in nerve-gut preparations. P2Y(1) and P2Y(2) transcripts were detected in 80% and 56% of retrogradely labeled colonic neurons, respectively. Na(v)1.9 transcripts colocalized in 86% of P2Y(1)-positive and 100% of P2Y(2)-positive colonic neurons, consistent with reduced afferent fiber responses to UTP and ADP in Na(v)1.9(−/−) mice. These data demonstrate that P2Y receptor activation stimulates mouse and human visceral nociceptors, highlighting P2Y-dependent mechanisms in the generation of visceral pain during gastrointestinal disease. SIGNIFICANCE STATEMENT Chronic visceral pain is a debilitating symptom of many gastrointestinal disorders. The activation of pain-sensing nerves located in the bowel wall and their sensitization to physiological stimuli, including bowel movements, underpins the development of such pain, and is associated with mediators released during disease. This work addresses the unstudied role of purine and pyrimidine nucleotides in modulating colonic nociceptors via P2Y receptors using a combination of electrophysiological recordings from human ex vivo samples and a detailed functional study in the mouse. This is the first report to identify colonic purinergic signaling as a function of P2Y receptor activation, in addition to established P2X receptor activity, and the results contribute to our understanding of the development of visceral pain during gastrointestinal disease

Electrical detection of magnetic skyrmions by non-collinear magnetoresistance

Magnetic skyrmions are localised non-collinear spin textures with high potential for future spintronic applications. Skyrmion phases have been discovered in a number of materials and a focus of current research is the preparation, detection, and manipulation of individual skyrmions for an implementation in devices. Local experimental characterization of skyrmions has been performed by, e.g., Lorentz microscopy or atomic-scale tunnel magnetoresistance measurements using spin-polarised scanning tunneling microscopy. Here, we report on a drastic change of the differential tunnel conductance for magnetic skyrmions arising from their non-collinearity: mixing between the spin channels locally alters the electronic structure, making a skyrmion electronically distinct from its ferromagnetic environment. We propose this non-collinear magnetoresistance (NCMR) as a reliable all-electrical detection scheme for skyrmions with an easy implementation into device architectures

Qualitative thematic analysis of consent forms used in cancer genome sequencing

<p>Abstract</p> <p>Background</p> <p>Large-scale whole genome sequencing (WGS) studies promise to revolutionize cancer research by identifying targets for therapy and by discovering molecular biomarkers to aid early diagnosis, to better determine prognosis and to improve treatment response prediction. Such projects raise a number of ethical, legal, and social (ELS) issues that should be considered. In this study, we set out to discover how these issues are being handled across different jurisdictions.</p> <p>Methods</p> <p>We examined informed consent (IC) forms from 30 cancer genome sequencing studies to assess (1) stated purpose of sample collection, (2) scope of consent requested, (3) data sharing protocols (4) privacy protection measures, (5) described risks of participation, (6) subject re-contacting, and (7) protocol for withdrawal.</p> <p>Results</p> <p>There is a high degree of similarity in how cancer researchers engaged in WGS are protecting participant privacy. We observed a strong trend towards both using samples for additional, unspecified research and sharing data with other investigators. IC forms were varied in terms of how they discussed re-contacting participants, returning results and facilitating participant withdrawal. Contrary to expectation, there were no consistent trends that emerged over the eight year period from which forms were collected.</p> <p>Conclusion</p> <p>Examining IC forms from WGS studies elucidates how investigators are handling ELS challenges posed by this research. This information is important for ensuring that while the public benefits of research are maximized, the rights of participants are also being appropriately respected.</p

Sum rules and electrodynamics of high-Tc cuprates in the pseudogap state

We explore connections between the electronic density of states (DOS) in a conducting system and the frequency dependence of the scattering rate $1/\tau(\omega)$ inferred from infrared spectroscopy. We show that changes in the DOS upon the development of energy gaps can be reliably tracked through the examination of the $1/\tau(\omega)$ spectra using the sum rules discussed in the text. Applying this analysis to the charge dynamics in high-$T_c$ cuprates we found radically different trends in the evolution of the DOS in the pseudogap state and in the superconducting state.Comment: 4 pages, 3 figure

Gap structure in the electron-doped Iron-Arsenide Superconductor Ba(Fe0.92Co0.08)2As2: low-temperature specific heat study

We report the field and temperature dependence of the low-temperature specific heat down to 400 mK and in magnetic fields up to 9 T of the electron-doped Ba(Fe0.92Co0.08)2As2 superconductor. Using the phonon specific heat obtained from pure BaFe2As2 we find the normal state Sommerfeld coefficient to be 18 mJ/mol.K^2 and a condensation energy of 1.27 J/mol. The temperature dependence of the electronic specific heat clearly indicate the presence of the low-energy excitations in the system. The magnetic field variation of field-induced specific heat cannot be described by single clean s- or d-wave models. Rather, the data require an anisotropic gap scenario which may or may not have nodes. We discuss the implications of these results.Comment: New Journal of Physics in press, 10 pages, 5 figure

Muon spin rotation study of magnetism and superconductivity in BaFe2-xCoxAs2 and Pr1-xSrxFeAsO

We present a muon spin rotation (\muSR) study of the magnetic and superconducting properties of single crystals of electron-doped BaFe2-xCoxAs2 with x=0.08, 0.20, and 0.25 (Tc=9, 25 and 20K) and of polycrystalline hole-doped Pr1-xSrxFeAsO with x=0 and 0.2 (Tc=15 K). In the former series we observe some interesting parallels with the electron doped SmFeAsO1-xFx 1111-type system [A.J. Drew et al., to appear in Nature Materials 2009 and arXiv:0807.4876]. In particular, we obtain evidence that strongly disordered static magnetism coexists with superconductivity on a microscopic scale in underdoped samples and even at optimum doping there is a slowing down (or enhancement) of dynamic magnetic correlations below Tc\approx25K. To the contrary, for the hole-doped Pr1-xSrxFeAsO samples we obtain evidence for a mesoscopic phase segregation into regions with nearly unperturbed AF order and others that are non magnetic and most likely superconducting. The observed trend resembles the one that was previously reported for hole-doped Ba1-xKxFe2As2 [A.A. Aczel et al., Phys. Rev. B 78, 214503 (2008); J.T. Park et al., arXiv:0811.2224] and thus seems to be fairly common in these hole doped systems.Comment: 17 pages, 6 figure