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Abstract Xylella fastidiosais a bacterium that infects crops like grapevines, coffee, almonds, citrus and olives. There is little understanding of the genes that contribute to plant resistance, the genomic architecture of resistance, and the potential role of climate in shaping resistance, in part because major crops like grapevines (Vitis vinifera) are not resistant to the bacterium. Here we study a wild grapevine species,V. arizonica, that segregates for resistance. Using genome-wide association, we identify candidate resistance genes. Resistance-associated kmers are shared with a sister species ofV. arizonicabut not with more distant species, suggesting that resistance evolved more than once. Finally, resistance is climate dependent, because individuals from low ( < 10 °C) temperature locations in the wettest quarter were typically susceptible to infection, likely reflecting a lack of pathogen pressure in colder climates. In fact, climate is as effective a predictor of resistance phenotypes as some genetic markers. We extend our climate observations to additional crops, predicting that increased pathogen pressure is more likely for grapevines and almonds than some other susceptible crops. 

Domesticated grapevines spread to Europe around 3,000 years ago. Previous studies have revealed genomic signals of introgression from wild to cultivated grapes in Europe, but the time, mode, genomic pattern, and biological effects of these introgression events have not been investigated. Here, we studied resequencing data from 345 samples spanning the distributional range of wild (Vitis viniferassp.sylvestris) and cultivated (V. viniferassp.vinifera) grapes. Based on machine learning–based population genetic analyses, we detected evidence for a single domestication of grapevine, followed by continuous gene flow between European wild grapes (EU) and cultivated grapes over the past ~2,000 y, especially from EU to wine grapes. We also inferred that soft-selective sweeps were the dominant signals of artificial selection. Gene pathways associated with the synthesis of aromatic compounds were enriched in regions that were both selected and introgressed, suggesting EU wild grapes were an important resource for improving the flavor of cultivated grapes. Despite the potential benefits of introgression in grape improvement, the introgressed fragments introduced a higher deleterious burden, with most deleterious SNPs and structural variants hidden in a heterozygous state. Cultivated wine grapes have benefited from adaptive introgression with wild grapes, but introgression has also increased the genetic load. In general, our study of beneficial and harmful effects of introgression is critical for genomic breeding of grapevine to take advantage of wild resources. 

ABSTRACT We present the analysis of the absorption troughs of six outflows observed in quasar SDSS J1130 + 0411 ($$z$$ ≈ 3.98) with radial velocities ranging from −2400 to $$-15\, 400$$ km s−1. These spectra were taken with the Very Large Telescope/Ultraviolet and Visual Echelle Spectrograph over the rest-frame wavelength range of 1135–1890 Å. In the main outflow system ($$v$$ ≈ −3200 km s−1), we identify Fe ii and several Fe ii* absorption troughs, as well as Si ii and Si ii* troughs, which we use to determine the electron number density $$\log n_e = 2.6_{-0.7}^{+0.8}$$ cm−3. Using the column densities of these and other ions, we determine a photoionization solution with hydrogen column density $$\log N_H = 21.44_{-0.33}^{+0.24}$$ cm−2 and ionization parameter $$\log U_H = -1.75_{-0.45}^{+0.28}$$. From these values, we derive the distance $$R = 16_{-11}^{+23}$$ kpc, the average mass flow rate $$\dot{M} = 4100_{-2400}^{+6600}$$ M⊙ yr−1, and the kinetic luminosity $$\log \dot{E}_k = 46.13_{-0.37}^{+0.41}$$ erg s−1. This $$\dot{E}_k$$ is $$1.4_{-0.8}^{+2.2}$$ per cent of the quasar’s Eddington luminosity, and therefore contributes significantly to AGN feedback. 

ABSTRACT We analyse the VLT/UVES spectrum of the quasar SDSS J143907.5-010616.7, retrieved from the UVES Spectral Quasar Absorption Database. We identify two outflow systems in the spectrum: a mini broad absorption line (mini-BAL) system and a narrow absorption line (NAL) system. We measure the ionic column densities of the mini-BAL ($$v$$ = −1550 km s−1) outflow, which has excited state absorption troughs of $${\rm Fe\, \rm {\small {ii}}}$$. We determine that the electron number density $$\log {n_e}=3.4^{+0.1}_{-0.1}$$, based on the ratios between the excited and ground state abundances of $${\rm Fe\, \rm {\small {ii}}}$$, and find the kinetic luminosity of the outflow to be $${\lesssim}0.1\,\hbox{per cent}$$ of the quasar’s Eddington luminosity, making it insufficient to contribute to AGN feedback. 

Abstract Earth's core has produced a global magnetic field for at least the last 3.5 Gyrs, presently sustained by inner core (IC) growth. Models of the core with high thermal conductivity suggest potentially insufficient power available for the geodynamo prior to IC formation ∼1 Ga. Precipitation of silicon from the liquid core might offer an alternative power source for the ancient magnetic field, although few estimates of the silicon partition coefficient exist for conditions of the early core. We present the first ab initio determination of the silicon partition coefficient at core‐mantle boundary conditions and use these results to confirm a thermodynamic description of partitioning that is integrated into a model of coupled core‐mantle thermal evolution. We show that models including precipitation of silicon can satisfy constraints of IC size, mantle convective heat flux, mantle temperature and a persistent ancient geodynamo, and favor an oxygen poor initial core composition. 

Abstract Background Introgressive hybridization can reassort genetic variants into beneficial combinations, permitting adaptation to new ecological niches. To evaluate evolutionary patterns and dynamics that contribute to introgression, we investigate six wild Vitis species that are native to the Southwestern United States and useful for breeding grapevine ( V. vinifera ) rootstocks. Results By creating a reference genome assembly from one wild species, V. arizonica , and by resequencing 130 accessions, we focus on identifying putatively introgressed regions (pIRs) between species. We find six species pairs with signals of introgression between them, comprising up to ~ 8% of the extant genome for some pairs. The pIRs tend to be gene poor, located in regions of high recombination and enriched for genes implicated in disease resistance functions. To assess potential pIR function, we explore SNP associations to bioclimatic variables and to bacterial levels after infection with the causative agent of Pierce’s disease ( Xylella fastidiosa ). pIRs are enriched for SNPs associated with both climate and bacterial levels, suggesting that introgression is driven by adaptation to biotic and abiotic stressors. Conclusions Altogether, this study yields insights into the genomic extent of introgression, potential pressures that shape adaptive introgression, and the evolutionary history of economically important wild relatives of a critical crop. 

Microservice Architecture (MSA) is becoming the predominant direction of new cloud-based applications. There are many advantages to using microservices, but also downsides to using a more complex architecture than a typical monolithic enterprise application. Beyond the normal poor coding practices and code smells of a typical application, microservice-specific code smells are difficult to discover within a distributed application setup. There are many static code analysis tools for monolithic applications, but tools to offer code-smell detection for microservice-based applications are lacking. This paper proposes a new approach to detect code smells in distributed applications based on microservices. We develop an MSANose tool to detect up to eleven different microservice specific code smells and share it as open-source. We demonstrate our tool through a case study on two robust benchmark microservice applications and verify its accuracy. Our results show that it is possible to detect code smells within microservice applications using bytecode and/or source code analysis throughout the development process or even before its deployment to production. 

It is important in software development to enforce proper restrictions on protected services and resources. Typically software services can be accessed through REST API endpoints where restrictions can be applied using the Role-Based Access Control (RBAC) model. However, RBAC policies can be inconsistent across services, and they require proper assessment. Currently, developers use penetration testing, which is a costly and cumbersome process for a large number of APIs. In addition, modern applications are split into individual microservices and lack a unified view in order to carry out automated RBAC assessment. Often, the process of constructing a centralized perspective of an application is done using Systematic Architecture Reconstruction (SAR). This article presents a novel approach to automated SAR to construct a centralized perspective for a microservice mesh based on their REST communication pattern. We utilize the generated views from SAR to propose an automated way to find RBAC inconsistencies.