The genome sequence and effector complement of the flax rust pathogen Melampsora lini

Rust fungi cause serious yield reductions on crops, including wheat, barley, soybean, coffee, and represent real threats to global food security. Of these fungi, the flax rust pathogen Melampsora lini has been developed most extensively over the past 80 years as a model to understand the molecular mechanisms that underpin pathogenesis. During infection, M. lini secretes virulence effectors to promote disease. The number of these effectors, their function and their degree of conservation across rust fungal species is unknown. To assess this, we sequenced and assembled de novo the genome of M. lini isolate CH5 into 21,130 scaffolds spanning 189 Mbp (scaffold N50 of 31 kbp). Global analysis of the DNA sequence revealed that repetitive elements, primarily retrotransposons, make up at least 45% of the genome. Using ab initio predictions, transcriptome data and homology searches, we identified 16,271 putative protein-coding genes. An analysis pipeline was then implemented to predict the effector complement of M. lini and compare it to that of the poplar rust, wheat stem rust and wheat stripe rust pathogens to identify conserved and species-specific effector candidates. Previous knowledge of four cloned M. lini avirulence effector proteins and two basidiomycete effectors was used to optimize parameters of the effector prediction pipeline. Markov clustering based on sequence similarity was performed to group effector candidates from all four rust pathogens. Clusters containing at least one member from M. lini were further analyzed and prioritized based on features including expression in isolated haustoria and infected leaf tissue and conservation across rust species. Herein, we describe 200 of 940 clusters that ranked highest on our priority list, representing 725 flax rust candidate effectors. Our findings on this important model rust species provide insight into how effectors of rust fungi are conserved across species and how they may act to promote infection on their hosts.This work was funded by a grant from the CSIRO Transformational Biology Capability Platform to Adnane Nemri. Claire Anderson was supported by an ARC Discovery Grant (DP120104044) awarded to David A. Jones and Peter N. Dodds

Piecewise Conserved Quantities

We review the treatment of conservation laws in spacetimes that are glued together in various ways, thus adding a boundary term to the usual conservation laws. Several examples of such spacetimes will be described, including the joining of Schwarzschild spacetimes of different masses, and the possibility of joining regions of different signatures. The opportunity will also be taken to explore some of the less obvious properties of Lorentzian vector calculus.Comment: To appear in Gravity and the Quantum, Springer 2017 (http://www.springer.com/in/book/9783319516998

Crystallization, X-ray diffraction analysis and preliminary structure determination of the TIR domain from the flax resistance protein L6

The Toll/interleukin-1 receptor (TIR) domain is a protein-protein interaction domain that is found in both animal and plant immune receptors. In animal Toll-like receptor signalling, both homotypic TIR-domain interactions between two receptor molecules and heterotypic interactions between receptors and TIR-domain-containing adaptors are required for initiation of an innate immune response. The TIR domains in cytoplasmic nucleotide-binding/leucine-rich repeat (NB-LRR) plant disease-resistance proteins are not as well characterized, but recent studies have suggested a role in defence signalling. In this study, the crystallization, X-ray diffraction analysis and preliminary structure determination of the TIR domain from the flax resistance protein L6 (L6TIR) are reported. Plate-like crystals of L6TIR were obtained using PEG 200 as a precipitant and diffracted X-rays to 2.3 angstrom resolution. Pseudo-translation complicated the initial assignment of the crystal symmetry, which was ultimately found to correspond to space group P2(1)2(1)2 with two molecules per asymmetric unit. The structure of L6TIR was solved by molecular replacement using the structure of the TIR-domain-containing protein AT1G72930 from Arabidopsis as a template

Abrupt vessel closure complicating coronary angioplasty: Clinical, angiographic and therapeutic profile

AbstractTo assess the clinical, angiographic and procedural correlates of outcome after abrupt vessel closure during coronary angioplasty, results were analyzed of 109 patients (8.3%) who had abrupt vessel closure during 1,319 consecutive coronary angioplasty procedures performed between July 1, 1988 and June 30, 1990. These 109 patients had a mean age of 59 ± 11 years; 63% were male, 57% had had a prior myocardial infarction and 61% had multivessel disease. Coronary angioplasty was performed in the settings of acute myocardial infarction (14%), recent myocardial infarction (36%), unstable angina (34%) and stable ischemia (29%).Abrupt vessel closure occurred at a median of 27 min (range 0 min to 5 days) from the first balloon inflation. By angiographic criteria, thrombus or coronary dissection was identified in 20% and 28% of cases, respectively; both thrombus and dissection were present in 7% of closures, and 45% were due to indeterminate mechanisms. Successful reversal of abrupt vessel closure, defined as restoration of normal Thrombolysis In Myocardial Infarction (TIMI) grade 3 flow without resultant Q wave myocardial infarction, emergency bypass surgery or death, was achieved in 47 patients (43%). By hierarchal analysis, the incidence of death, emergency coronary bypass surgery, Q wave and non-Q wave myocardial infarction was 8%, 20%, 9% and 11%, respectively.Univariate analysis using 23 clinical, morphologic and procedural variables demonstrated that successful outcome after abrupt closure was associated with prolonged balloon inflations (>120 s) (odds ratio = 6.87, p < 0.001), unstable angina (odds ratio = 2.37, p = 0.034) and placement of an intracoronary stent (odds ratio = 5.33, p = 0.062). By multivariate analysis, independent correlates of successful outcome were prolonged balloon inflations (odds ratio = 5.11, p = 0.001) and intracoronary stenting (odds ratio = 4.37, p = 0.049).Thus, although prolonged balloon inflations and intracoronary stents may improve outcome after abrupt vessel closure, the cumulative risk of morbidity or mortality remains significant and mandates investigation into improved strategies for its prevention and treatment

Comparative genomics of Australian isolates of the wheat stem rust pathogen Puccinia graminis f. sp. tritici reveals extensive polymorphism in candidate effector genes

The wheat stem rust fungus Puccinia graminis f. sp. tritici (Pgt) is one of the most destructive pathogens of wheat. In this study, a draft genome was built for a founder Australian Pgt isolate of pathotype (pt.) 21-0 (collected in 1954) by next generation DNA sequencing. A combination of reference-based assembly using the genome of the previously sequenced American Pgt isolate CDL 75-36-700-3 (p7a) and de novo assembly were performed resulting in a 92 Mbp reference genome for Pgt isolate 21-0. Approximately 13 Mbp of de novo assembled sequence in this genome is not present in the p7a reference assembly. This novel sequence is not specific to 21-0 as it is also present in three other Pgt rust isolates of independent origin. The new reference genome was subsequently used to build a pan-genome based on five Australian Pgt isolates. Transcriptomes from germinated urediniospores and haustoria were separately assembled for pt. 21-0 and comparison of gene expression profiles showed differential expression in ∼10% of the genes each in germinated spores and haustoria. A total of 1,924 secreted proteins were predicted from the 21-0 transcriptome, of which 520 were classified as haustorial secreted proteins (HSPs). Comparison of 21-0 with two presumed clonal field derivatives of this lineage (collected in 1982 and 1984) that had evolved virulence on four additional resistance genes (Sr5, Sr11, Sr27, SrSatu) identified mutations in 25 HSP effector candidates. Some of these mutations could explain their novel virulence phenotypes.Authors wish to thank the Two Blades Foundation for financial support. Part of this work was supported through access to facilities managed by Bioplatforms Australia and funded by the Australian Government National Collaborative Research Infrastructure Strategy and Education Investment Fund Super Science Initiative

The Assembly History of Field Spheroidals: Evolution of Mass-to-light Ratios and Signatures of Recent Star Formation

We present a comprehensive catalog of high signal-to-noise spectra obtained with the DEIMOS spectrograph on the Keck II telescope for a sample of F850LP<22.43 (AB) field spheroidal (E+S0s; 163) and bulge dominated disk (61) galaxies in the redshift range 0.2<z<1.2. We examine the zero point, tilt and scatter of the Fundamental Plane (FP) as a function of redshift and morphological properties, carefully accounting for luminosity-dependent biases via Montecarlo simulations. The evolution of the overall FP can be represented by a mean change in effective mass-to-light ratio given by <d \log (M/L_{\rm B})/dz>=-0.72^{+0.07}_{-0.05}\pm0.04. However, this evolution depends significantly on the dynamical mass, being slower for larger masses as reported in a previous letter. In addition, we separately show the intrinsic scatter of the FP increases with redshift as d(rms(M/L_{\rm B}))/dz=0.040\pm0.015. Although these trends are consistent with single burst populations which formed at $z_f>2$ for high mass spheroidals and z_{f}~1.2 for lower mass systems, a more realistic picture is that most of the stellar mass formed in all systems at z>2 with subsequent activity continuing to lower redshifts (z<1.2). The fraction of stellar mass formed at recent times depend strongly on galactic mass, ranging from <1% for masses above 10^{11.5} M_{\odot} to 20-40% below 10^{11} M_{\odot}. Independent support for recent activity is provided by spectroscopic ([\ion{O}{2}] emission, H\delta) and photometric (blue cores and broad-band colors) diagnostics. Via the analysis of a large sample with many independent diagnostics, we are able to reconcile previously disparate interpretations of the assembly history of field spheroidals. [Abridged]Comment: 26 pages including 24 figures, submitted to ApJ. Complete and compact version with full resolution images available at http://www.astro.ucla.edu/~ttreu/ms.pd

Paclitaxel-Eluting Coronary Stents in Patients With Diabetes Mellitus Pooled Analysis From 5 Randomized Trials

ObjectivesWe sought to examine the safety and efficacy of paclitaxel-eluting stents (PES) in patients with diabetes mellitus (DM).BackgroundCompared with patients without DM, patients with DM undergoing percutaneous coronary intervention are at increased risk for mortality and restenosis. The safety of drug-eluting stents in diabetic patients has recently been called into question by a published meta-analysis of randomized trials.MethodsPatient-level data were pooled from 5 prospective, double-blind, randomized trials of PES versus bare-metal stents (BMS) (n = 3,513). Safety and efficacy outcomes through 4 years of follow-up were assessed among the 827 randomized patients (23.6%) with DM.ResultsPatients treated with PES and BMS has similar baseline characteristics among both the diabetic and nondiabetic cohorts within these trials. At 4-year follow-up, there were no significant differences between PES and BMS among diabetic patients in the rates of death (8.4% vs. 10.3%, respectively, p = 0.61), myocardial infarction (6.9% vs. 8.9%, p = 0.17), or stent thrombosis (1.4% vs. 1.2%, p = 0.92). Treatment of diabetic patients with PES compared with treatment with BMS was associated with a significant and durable reduction in target lesion revascularization over the 4-year follow-up period (12.4% vs. 24.7%, p < 0.0001). The relative safety and efficacy of PES compared with the relative safety and efficacy of BMS in diabetic patients extended to both those requiring and not requiring insulin.ConclusionsIn these 5 randomized trials in which patients with single, primarily noncomplex lesions were enrolled, treatment with PES compared with treatment with BMS was safe and effective, resulting in markedly lower rates of target lesion revascularization at 4 years, with similar rates of death, myocardial infarction, and stent thrombosis