A conserved fungal glycosyltransferase facilitates pathogenesis of plants by enabling hyphal growth on solid surfaces

Article Authors Metrics Comments Related Content Abstract Author summary Introduction Results and discussion Conclusions Methods Supporting information Acknowledgments References Reader Comments (0) Media Coverage (0) Figures Abstract Pathogenic fungi must extend filamentous hyphae across solid surfaces to cause diseases of plants. However, the full inventory of genes which support this is incomplete and many may be currently concealed due to their essentiality for the hyphal growth form. During a random T-DNA mutagenesis screen performed on the pleomorphic wheat (Triticum aestivum) pathogen Zymoseptoria tritici, we acquired a mutant unable to extend hyphae specifically when on solid surfaces. In contrast “yeast-like” growth, and all other growth forms, were unaffected. The inability to extend surface hyphae resulted in a complete loss of virulence on plants. The affected gene encoded a predicted type 2 glycosyltransferase (ZtGT2). Analysis of >800 genomes from taxonomically diverse fungi highlighted a generally widespread, but discontinuous, distribution of ZtGT2 orthologues, and a complete absence of any similar proteins in non-filamentous ascomycete yeasts. Deletion mutants of the ZtGT2 orthologue in the taxonomically un-related fungus Fusarium graminearum were also severely impaired in hyphal growth and non-pathogenic on wheat ears. ZtGT2 expression increased during filamentous growth and electron microscopy on deletion mutants (ΔZtGT2) suggested the protein functions to maintain the outermost surface of the fungal cell wall. Despite this, adhesion to leaf surfaces was unaffected in ΔZtGT2 mutants and global RNAseq-based gene expression profiling highlighted that surface-sensing and protein secretion was also largely unaffected. However, ΔZtGT2 mutants constitutively overexpressed several transmembrane and secreted proteins, including an important LysM-domain chitin-binding virulence effector, Zt3LysM. ZtGT2 likely functions in the synthesis of a currently unknown, potentially minor but widespread, extracellular or outer cell wall polysaccharide which plays a key role in facilitating many interactions between plants and fungi by enabling hyphal growth on solid matrices

Genome-Wide Association Study in BRCA1 Mutation Carriers Identifies Novel Loci Associated with Breast and Ovarian Cancer Risk

BRCA1-associated breast and ovarian cancer risks can be modified by common genetic variants. To identify further cancer risk-modifying loci, we performed a multi-stage GWAS of 11,705 BRCA1 carriers (of whom 5,920 were diagnosed with breast and 1,839 were diagnosed with ovarian cancer), with a further replication in an additional sample of 2,646 BRCA1 carriers. We identified a novel breast cancer risk modifier locus at 1q32 for BRCA1 carriers (rs2290854, P = 2.7×10-8, HR = 1.14, 95% CI: 1.09-1.20). In addition, we identified two novel ovarian cancer risk modifier loci: 17q21.31 (rs17631303, P = 1.4×10-8, HR = 1.27, 95% CI: 1.17-1.38) and 4q32.3 (rs4691139, P = 3.4×10-8, HR = 1.20, 95% CI: 1.17-1.38). The 4q32.3 locus was not associated with ovarian cancer risk in the general population or BRCA2 carriers, suggesting a BRCA1-specific associat

Expression of the Chlamydia trachomatis major outer membrane protein-encoding gene in Escherichia coli: role of the 3′ end in mRNA stability

The major outer membrane protein (MOMP)-encoding gene (ompl) of Chlamydia trachomatis has been cloned into Escherichia coli and partially sequenced. This recombinant gene expresses a full-length 40-kDa product, which is recognized by a monoclonal antibody directed against the species-specific epitope of MOMP. The recombinant ompl is expressed in either insertion orientation, indicating that it utilizes its own promoter system. The endogenous ompl promoter possesses a relatively low activity despite the high level of MOMP expression. Deletion of a 520-bp fragment at the 3′ end encoding 39 amino acids (aa) at the C terminus and the remainder of the noncoding region leads to a significant decrease in mRNA stability and loss of protein synthesis. When the MOMP-encoding plasmid was introduced into E. coli minicells, it expressed 40- and 43-kDa proteins; however, inhibition of post-translational processing by ethanol revealed only a 43-kDa protein. These data indicate that the unprocessed ompl gene product contains a 22-aa leader sequence which is cleaved during translocation to the outer membrane, to yield a processed 40-kDa protein. The recombinant MOMP was localized to the outer membrane E. coli fraction, comparable to the location of the native C. trachomatis protein

Identification and mitigation of narrow spectral artifacts that degrade searches for persistent gravitational waves in the first two observing runs of Advanced LIGO

International audienceSearches are under way in Advanced LIGO and Virgo data for persistent gravitational waves from continuous sources, e.g. rapidly rotating galactic neutron stars, and stochastic sources, e.g. relic gravitational waves from the Big Bang or superposition of distant astrophysical events such as mergers of black holes or neutron stars. These searches can be degraded by the presence of narrow spectral artifacts (lines) due to instrumental or environmental disturbances. We describe a variety of methods used for finding, identifying and mitigating these artifacts, illustrated with particular examples. Results are provided in the form of lists of line artifacts that can safely be treated as non-astrophysical. Such lists are used to improve the efficiencies and sensitivities of continuous and stochastic gravitational wave searches by allowing vetoes of false outliers and permitting data cleaning

Euclid preparation. The impact of relativistic redshift-space distortions on two-point clustering statistics from the Euclid wide spectroscopic survey

International audienceMeasurements of galaxy clustering are affected by RSD. Peculiar velocities, gravitational lensing, and other light-cone projection effects modify the observed redshifts, fluxes, and sky positions of distant light sources. We determine which of these effects leave a detectable imprint on several 2-point clustering statistics extracted from the EWSS on large scales. We generate 140 mock galaxy catalogues with the survey geometry and selection function of the EWSS and make use of the LIGER method to account for a variable number of relativistic RSD to linear order in the cosmological perturbations. We estimate different 2-point clustering statistics from the mocks and use the likelihood-ratio test to calculate the statistical significance with which the EWSS could reject the null hypothesis that certain relativistic projection effects can be neglected in the theoretical models. We find that the combined effects of lensing magnification and convergence imprint characteristic signatures on several clustering observables. Their S/N ranges between 2.5 and 6 (depending on the adopted summary statistic) for the highest-redshift galaxies in the EWSS. The corresponding feature due to the peculiar velocity of the Sun is measured with a S/N of order one or two. The $P_{\ell}(k)$ from the catalogues that include all relativistic effects reject the null hypothesis that RSD are only generated by the variation of the peculiar velocity along the line of sight with a significance of 2.9 standard deviations. As a byproduct of our study, we demonstrate that the mixing-matrix formalism to model finite-volume effects in the $P_{\ell}(k)$ can be robustly applied to surveys made of several disconnected patches. Our results indicate that relativistic RSD, the contribution from weak gravitational lensing in particular, cannot be disregarded when modelling 2-point clustering statistics extracted from the EWSS

Euclid preparation: Determining the weak lensing mass accuracy and precision for galaxy clusters

International audienceWe investigate the level of accuracy and precision of cluster weak-lensing (WL) masses measured with the \Euclid data processing pipeline. We use the DEMNUni-Cov $N$-body simulations to assess how well the WL mass probes the true halo mass, and, then, how well WL masses can be recovered in the presence of measurement uncertainties. We consider different halo mass density models, priors, and mass point estimates. WL mass differs from true mass due to, e.g., the intrinsic ellipticity of sources, correlated or uncorrelated matter and large-scale structure, halo triaxiality and orientation, and merging or irregular morphology. In an ideal scenario without observational or measurement errors, the maximum likelihood estimator is the most accurate, with WL masses biased low by $\langle b_M \rangle = -14.6 \pm 1.7 \, \%$ on average over the full range $M_\text{200c} > 5 \times 10^{13} \, M_\odot$ and $z < 1$. Due to the stabilising effect of the prior, the biweight, mean, and median estimates are more precise. The scatter decreases with increasing mass and informative priors significantly reduce the scatter. Halo mass density profiles with a truncation provide better fits to the lensing signal, while the accuracy and precision are not significantly affected. We further investigate the impact of additional sources of systematic uncertainty on the WL mass, namely the impact of photometric redshift uncertainties and source selection, the expected performance of \Euclid cluster detection algorithms, and the presence of masks. Taken in isolation, we find that the largest effect is induced by non-conservative source selection. This effect can be mostly removed with a robust selection. As a final \Euclid-like test, we combine systematic effects in a realistic observational setting and find results similar to the ideal case, $\langle b_M \rangle = - 15.5 \pm 2.4 \, \%$, under a robust selection

Euclid preparation. Simulations and nonlinearities beyond Λ\LambdaCDM. 4. Constraints on f(R)f(R) models from the photometric primary probes

International audienceWe study the constraint on $f(R)$ gravity that can be obtained by photometric primary probes of the Euclid mission. Our focus is the dependence of the constraint on the theoretical modelling of the nonlinear matter power spectrum. In the Hu-Sawicki $f(R)$ gravity model, we consider four different predictions for the ratio between the power spectrum in $f(R)$ and that in $\Lambda$CDM: a fitting formula, the halo model reaction approach, ReACT and two emulators based on dark matter only $N$-body simulations, FORGE and e-Mantis. These predictions are added to the MontePython implementation to predict the angular power spectra for weak lensing (WL), photometric galaxy clustering and their cross-correlation. By running Markov Chain Monte Carlo, we compare constraints on parameters and investigate the bias of the recovered $f(R)$ parameter if the data are created by a different model. For the pessimistic setting of WL, one dimensional bias for the $f(R)$ parameter, $\log_{10}|f_{R0}|$, is found to be $0.5 \sigma$ when FORGE is used to create the synthetic data with $\log_{10}|f_{R0}| =-5.301$ and fitted by e-Mantis. The impact of baryonic physics on WL is studied by using a baryonification emulator BCemu. For the optimistic setting, the $f(R)$ parameter and two main baryon parameters are well constrained despite the degeneracies among these parameters. However, the difference in the nonlinear dark matter prediction can be compensated by the adjustment of baryon parameters, and the one-dimensional marginalised constraint on $\log_{10}|f_{R0}|$ is biased. This bias can be avoided in the pessimistic setting at the expense of weaker constraints. For the pessimistic setting, using the $\Lambda$CDM synthetic data for WL, we obtain the prior-independent upper limit of $\log_{10}|f_{R0}|< -5.6$. Finally, we implement a method to include theoretical errors to avoid the bias

Euclid preparation: Determining the weak lensing mass accuracy and precision for galaxy clusters

International audienceWe investigate the level of accuracy and precision of cluster weak-lensing (WL) masses measured with the \Euclid data processing pipeline. We use the DEMNUni-Cov $N$-body simulations to assess how well the WL mass probes the true halo mass, and, then, how well WL masses can be recovered in the presence of measurement uncertainties. We consider different halo mass density models, priors, and mass point estimates. WL mass differs from true mass due to, e.g., the intrinsic ellipticity of sources, correlated or uncorrelated matter and large-scale structure, halo triaxiality and orientation, and merging or irregular morphology. In an ideal scenario without observational or measurement errors, the maximum likelihood estimator is the most accurate, with WL masses biased low by $\langle b_M \rangle = -14.6 \pm 1.7 \, \%$ on average over the full range $M_\text{200c} > 5 \times 10^{13} \, M_\odot$ and $z < 1$. Due to the stabilising effect of the prior, the biweight, mean, and median estimates are more precise. The scatter decreases with increasing mass and informative priors significantly reduce the scatter. Halo mass density profiles with a truncation provide better fits to the lensing signal, while the accuracy and precision are not significantly affected. We further investigate the impact of additional sources of systematic uncertainty on the WL mass, namely the impact of photometric redshift uncertainties and source selection, the expected performance of \Euclid cluster detection algorithms, and the presence of masks. Taken in isolation, we find that the largest effect is induced by non-conservative source selection. This effect can be mostly removed with a robust selection. As a final \Euclid-like test, we combine systematic effects in a realistic observational setting and find results similar to the ideal case, $\langle b_M \rangle = - 15.5 \pm 2.4 \, \%$, under a robust selection

Euclid. V. The Flagship galaxy mock catalogue: a comprehensive simulation for the Euclid mission

International audienceWe present the Flagship galaxy mock, a simulated catalogue of billions of galaxies designed to support the scientific exploitation of the Euclid mission. Euclid is a medium-class mission of the European Space Agency optimised to determine the properties of dark matter and dark energy on the largest scales of the Universe. It probes structure formation over more than 10 billion years primarily from the combination of weak gravitational lensing and galaxy clustering data. The breath of Euclid's data will also foster a wide variety of scientific analyses. The Flagship simulation was developed to provide a realistic approximation to the galaxies that will be observed by Euclid and used in its scientific analyses. We ran a state-of-the-art N-body simulation with four trillion particles, producing a lightcone on the fly. From the dark matter particles, we produced a catalogue of 16 billion haloes in one octant of the sky in the lightcone up to redshift z=3. We then populated these haloes with mock galaxies using a halo occupation distribution and abundance matching approach, calibrating the free parameters of the galaxy mock against observed correlations and other basic galaxy properties. Modelled galaxy properties include luminosity and flux in several bands, redshifts, positions and velocities, spectral energy distributions, shapes and sizes, stellar masses, star formation rates, metallicities, emission line fluxes, and lensing properties. We selected a final sample of 3.4 billion galaxies with a magnitude cut of H_E<26, where we are complete. We have performed a comprehensive set of validation tests to check the similarity to observational data and theoretical models. In particular, our catalogue is able to closely reproduce the main characteristics of the weak lensing and galaxy clustering samples to be used in the mission's main cosmological analysis. (abridged