Infectivity decline of an RNA plant virus by increased mutagenesis supports the lethal defection model in vivo

Lethal mutagenesis is a new antiviral therapy based on increasing the mutation rate by using mutagenic base and nucleoside analogues whose molecular mechanisms are not fully understood. Most of the research has been conducted on animal RNA viruses in cell culture and, to a lesser extent, in vivo. There is experimental evidence supporting the model of lethal defection for lethal mutagenesis of RNA viruses. In this model, viral genomes with a low degree of mutation and low specific infectivity, termed "defectors", exert an interfering activity leading to virus loss. Lethal mutagenesis of plant viruses has not been addressed yet despite being excellent in vivo model systems that develop systemic infections, undergo rapid bottlenecks and pose no ethical issues. Here, we address lethal mutagenesis in vivo of Tobacco mosaic virus (TMV), a single-stranded positive RNA virus of 6.4 Kb. Nicotiana tabacum plants cultured in vitro were treated with 25, 50 and 100 µg/ml of the base analogue 5-fluorouracil (FU) and 24 h later were inoculated with 50 lesion forming units (lfu) of TMV. We analyzed the infectivity, viral load and mutant spectra of viral populations after 5 and 10 days of treatment, as well as of populations that went 10 days of treatment followed by 21 days of ex vitro growth in the absence of FU. The results show that TMV infectivity decreases when treated with 50 and 100 µg/ml FU for 10 days. TMV mutagenized populations grown without FU reach infectivity values higher than untreated populations. Predominant mutations in FU-treated populations with decreased infectivity at 10 dpi are U→C, A→G and G→A transitions, which are expected due to the action of FU. TMV replication is not affected by FU at any dose and there are no imbalances of ribonucleotide triphosphate pools measured by HPLC. No differences in mutation frequencies and Shannon Entropies between control and FU-treated populations with declined infectivity were found. However, we did found a dose-dependent decrease of specific infectivity in FU-treated populations, but not in untreated samples, as well as dominance of molecules with a low degree of mutation. Specific infectivity recovered to control levels after 21 days of growth without the analogue. Altogether, our results suggest that TMV defector molecules mediate the decrease in TMV infectivity. This is the first report that addresses the molecular basis of lethal defection in vivo using an RNA plant virus.Junta de Andalucía (P09-CVI-5428 y P10-CVI-6561), Plan Nacional I+D+i (BFU2007-65080 BMC) y Universidad de Málaga (Plan propio

Bohr's stopping-power formula derived for a classical free-electron gas

Bohr's centenary stopping-power formula is rederived for a free electron gas (FEG) system within the framework of nonrelativistic classical mechanics. A simple and more concise expression for the stopping power of charged particles in FEG is demonstrated on classical grounds. Using semiclassical arguments and the Euler-Maclaurin well-known mathematical formula, Bloch's correction that links Bethe's quantum theory to Bohr's classical model is also recovered. The proposed semiclassical stopping-power formula contains the main physical ingredients for a general stopping formula applicable for different systems and energies and facilitates computational calculations

Alternative treatment for the energy-transfer and transport cross section in dressed electron-ion binary collisions

A formula for determining the electronic stopping power and the transport cross section in electron-ion binary collisions is derived from the induced density for spherically symmetric potentials using the partial-wave expansion. In contrast to the previous one found in many textbooks, the present formula converges to the Bethe and Bloch stopping-power formulas at high ion velocities and agrees rather well with experimental stopping-power data, as shown here for Al, C, and H2O targets. It can be employed in plasma physics and particularly in any application that requires electronic stopping-power values of quasifree electrons with high accuracy

Protection of Electrical Power Systems with Full Penetration of Converter-Interface Generation

Mención Internacional en el título de doctorSince the advent of generation with converter-interface, mainly wind and solar photovoltaic (PV), power system operators have deal with some problems to maintain system stability and security. However, due to its low penetration in the system, it had barely any consequences and its study lack of interest. But over the years the generation scheme has changed, and converter-interface generators have been increasing their presence due to their low energy costs and policies against climate change. When the penetration rate is 100 %, protection systems have detection problems in the overcurrent scheme and pick-up problems in the distance scheme, jeopardising the safety of the electrical power system. This thesis proposes to use the Wavelet transform analysis method to solve these problems in full penetration scenarios of converter-interface generation. It can detect high and low frequency variations in voltage and current signals, and classify them in time and magnitude when they occur. In order to be able to propose a satisfactory solution, this thesis has carried out a study of the main key factors to be considered for fault detection. Analysing the differences between synchronous generators and generators with converter-interface, and the consequences of each of them for the protection systems. Describing the main converter control architectures and defining the equivalent model of converter short-circuit. Introducing the different types of faults in power systems. And describing the fundamental criteria for protection, and the most common protection schemes. The model used to obtain the results and check the feasibility of the proposal is the IEEE nine-bus system in a ring layout. It has been modelled including all power system elements (transmission lines, transformers, and loads) and both generation technologies (synchronous generators and converter-interface generators). In addition, the converter control strategy and its current limiting have also been considered. The results show a correct and immediate fault detection.Desde la aparición de los sistemas de generación de energía eléctrica con interfaz de convertidor electrónico, mayoritariamente eólica y solar fotovoltaica, los operadores de red han tenido que lidiar con los diferentes problemas que estos provocan para mantener la estabilidad y la seguridad del sistema. Aunque debido a su baja penetración en el sistema apenas tenía consecuencias y su estudio carecía de interés. Pero con el paso de los años ha ido cambiando el esquema de generación y los generadores con interfaz de convertidor electrónico han ido incrementando su presencia debido a sus bajos costes de la energía y a las políticas de lucha contra el cambio climático. Cuando se alcanzan niveles de penetración del 100 %, los sistemas de protección tienen problemas de detección en el esquema de sobrecorriente y de arranque en el esquema de distancia, poniendo en riesgo la seguridad del sistema eléctrico. Esta tesis propone utilizar el método de análisis de la transformada de Wavelet para solventar estos problemas en escenarios con máxima penetración de generación con interfaz de convertidor. El cual permite detectar variaciones de alta y baja frecuencia en las señales de tensión y de corriente, y clasificarlas tanto en tiempo como en tamaño cuando se producen. Para poder presentar una solución con garantías de ser satisfactoria, en esta tesis se ha realizado un estudio de los principales factores clave para tener en cuenta para la detección de faltas. Analizando las diferencias entre generadores síncronos y generadores con interfaz de convertidor electrónico, y qué consecuencias tiene cada uno de ellos para los sistemas de protección. Describiendo las principales arquitecturas de control de convertidores y definiendo los modelos equivalentes de cortocircuito del convertidor. Presentando los diferentes tipos de faltas en los sistemas eléctricos. Y describiendo los criterios fundamentales de las protecciones y los esquemas de protección más comunes. El modelo utilizado para la obtención de los resultados y comprobar la viabilidad de la propuesta es el sistema de nueve nudos del IEEE dispuesto en anillo. El cual ha sido modelado incluyendo todos los elementos del sistema (líneas de transmisión, transformadores y cargas) y ambas tecnologías de generación (generadores síncronos y generadores con interfaz de convertidor electrónico). Además, también se ha tenido en cuenta la estrategia de control del convertidor y su limitación de corriente. Los resultados muestran una correcta e inmediata detección de la falta.Programa de Doctorado en Ingeniería Eléctrica, Electrónica y Automática por la Universidad Carlos III de MadridPresidenta: Mónica Chinchilla Sánchez.- Secretario: Joaquín Eloy-García Carrasco.- Vocal: Roberto Lorenzo Alves Baraciart

Exploring the Barkas effect with keV-electron scattering

The energy loss of fast ions at close collision is mainly due to electron-ion collisions. The electrons are approximately stationary and they collidewith a fast-moving ion. Herewe study the same collision experimentally, in a reference system where the ions (or atoms) are stationary and interacting with keV electrons. Scattering cross sections under these conditions deviate from Rutherford, and we link these deviations, at higher energies, to the Z3 contributions to the electronic stopping and the related Barkas effect and, at lower energies, also to quantum interference. The present measurements are well described by partial-wave calculations of the elastic cross section of electrons scattering from atoms. Encouraged by this agreement we use these calculations to estimate the Barkas factor for all elements and many energies. A universal curve for the Barkas factor due to close collisions is obtained for neutral projectiles and similar curves with smaller magnitude are found for ions

Analysis of hypervariable DNA sequences by NGS technologies: QuasiFlow

The development of Next Generation Sequencing (NGS) technologies has allowed deep characterization of highly variable sequences such as viral or mitochondrial genomes. With respect to RNA and ssDNA viruses, their low replication fidelity generates viral populations consisting of complex mutant spectra termed viral quasispecies. Their study is of special interest as they can be considered a phenotypic reservoir1. Similarly, heteroplasmy of human mitochondrial genomes, in which different sequences are found within a single individual, might have important clinical consequences. For the analysis of the mutant spectrum of such hypervariable sequences from NGS data, we have developed QuasiFlow, a workflow designed in AutoFlow2 that uses Illumina reads. QuasiFlow provides information about DNA variability, such as SNPs, indels and recombination events (Figure 1). Furthermore, it allows haplotype reconstruction of viral quasispecies and characterization of its diversity through normalized Shannon index, nucleotide diversity and mutation networks. Quasiflow performs also a comparative study among samples, based on correlation, ANOVA and PCA analysis, in order to determine which parameters are affected by the experiment and how the samples behave according to their biological origin. In this work, we have applied QuasiFlow to analyze the population structure of the begomovirus Tomato yellow leaf curl virus (TYLCV) infectious clone inoculated in Arabidopsis thaliana plants, using HiSeq or MiSeq reads. Their analysis allowed detection of minor quasispecies variants with a frequency of 10-4 to 10-5 and reconstructed the haplotypes present in the sample. In addition, QuasiFlow was used to discover variants and recombinants in mixed infections of tomato plants. These results show the fast generation of recombinant genomes in geminivirus mixed infections and demonstrate the potential of QuasiFlow for the analysis of mutant spectra using Illumina MiSeq sequencing data. We have extended the use of QuasiFlow to the analysis of highly variable sequences such as the mitochondrial DNA. For that, we have analyzed DNA Illumina Miseq reads from 47 human mitochondrial samples from different cell lines obtained from the NCBI SRA database. Quasiflow generated automatically SNPs, SNP frequencies, indels and analyzed up to 23 variables using PCA analysis and performed an hierarchical clustering of the samples. Our analysis was able to detect pathological variants presented in a frequency lower than 1%.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech. This research was funded by Junta de Andalucía and EU through the ERDF 2014-2020, Projects P10-CVI-6075 to M. G.C. and P10-CVI-6561 to A.G-P

Nonlinear ion-stopping calculations for a classical free-electron gas at high projectile energies

In this work, we solved the classical equations of motion and Poisson equation self-consistently, equivalent to the nonlinear Vlasov-Poisson equation, for a projectile moving in a static free-electron gas to calculate the full noncentral self-consistent electron-ion potential, and thus the ion stopping power. We investigated the origin of the Barkas effect, namely, the first nonlinear effect for projectiles at high velocities responsible for the difference between the energy-loss results for positively and negatively charged ions traversing the same target. This effect is strongly enhanced by the multipolar part of the electron-ion potential as first suggested by Lindhard [J. Lindhard, Nucl. Instr. and Meth. 132, 1438 (1976)]. Moreover, this effect is partially related to the nonconservation of the angular momentum in electron-ion collisions. These nonlinear calculations are applied to understanding the stopping of protons and antiprotons in Al at high projectile energie

Wavelet Analysis to Detect Ground Faults in Electrical Power Systems with Full Penetration of Converter Interface Generation

The requirements for the increased penetration of renewable energy sources in electrical power systems have led to a dominance of power electronic interfaces. As a result, short-circuit currents have been reduced by the thermal limitations of power electronics, leading to problems associated with the sensitivity, selectivity, and reliability of protective relays. Although many solutions can be found in the literature, these depend on communications and are not reliable in all grid topologies or under different types of electrical fault. Hence, in this paper, the analysis of ground fault currents and voltages using a wavelet transform in combination with a new algorithm not only detects such ground faults but also allows them to be cleared quickly and selectively in scenarios with low fault current contribution due to a full penetration converter-interface-based generation. To verify and validate the proposed protection system, different ground faults are simulated using an arc ground fault model in a grid scheme based on the IEEE nine-bus standard test system, with only grid-forming power converters as generation sources. The test system is modelled in the MATLAB/Simulink environment. Therefore, the protection relays that verify all the steps established in the new algorithm can detect and clear any ground defect. Simulations are also presented involving different fault locations to demonstrate the effectiveness of the proposed ground fault protection method.This work was supported by the Autonomous Community of Madrid under the PROMINT-CM project (S2018/EMT-4366)

Infectivity decline of an RNA plant virus by increased mutagenesis in vivo

According to the lethal defection model, during lethal mutagenesis viral genomes with a low degree of mutation and low specific infectivity exert an interfering activity that leads to virus loss. Lethal mutagenesis of plant viruses has not been reported to date. We address lethal defection in vivo of Tobacco mosaic virus (TMV), a single-stranded positive RNA virus. Nicotiana tabacum plants cultured in vitro were treated with 25, 50 and 100 µg/ml of the base analogue 5-fluorouracil (FU) and 24h later were inoculated with 50 lesion forming units of TMV. Results show that TMV infectivity decreases when treated with 50 and 100 µg/ml FU for 10 days. TMV mutagenized populations grown without FU reach infectivity values higher than untreated populations. Predominant mutations in FU-treated populations with decreased infectivity at 10 dpi are transitions which are expected due to the action of FU. Viral load is not affected by FU at any dose and there are no imbalances of ribonucleotide triphosphate pools measured by HPLC. No differences in mutation frequencies and Shannon Entropies between control and FU-treated populations were found. However, we found a dose-dependent decrease of specific infectivity in FU-treated populations, but not in untreated samples, as well as dominance of molecules with a low degree of mutation. Specific infectivity recovered to control levels after 21 days of growth without the analogue. Altogether, our results suggest that TMV defector molecules mediate the decrease in TMV infectivity. This is the first report that addresses the molecular basis of lethal defection in vivo using an RNA plant virus.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Effect of agroecosystems on seroprevalence of St. Louis encephalitis and West Nile viruses in birds, La Pampa, Argentina, 2017–2019

In Argentina, the La Pampa ecoregion has been almost completely transformed into agroecosystems. To evaluate the environmental (agricultural area, tree coverage, distance to the nearest water body and urban site) and biological (dove, cowbird, and sparrow abundance) effects on free-ranging bird exposure to St. Louis encephalitis virus (SLEV) and West Nile virus (WNV), we used generalized linear mixed models. For 1,019 birds sampled during 2017–2019, neutralizing antibodies were found against SLEV in samples from 60 (5.8%) birds and against WNV for 21 (2.1%). The best variable for explaining SLEV seroprevalence was agricultural area, which had a positive effect; however, for WNV, no model was conclusive. Our results suggest that agroecosystems in the La Pampa ecoregion increase the exposure of avian hosts to SLEV, thus potentially increasing virus activity.Fil: Mansilla, Ana Paula. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Ciencias de la Tierra y Ambientales de La Pampa. Universidad Nacional de La Pampa. Facultad de Ciencias Exactas y Naturales. Instituto de Ciencias de la Tierra y Ambientales de La Pampa; ArgentinaFil: Grande, Juan Manuel. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Ciencias de la Tierra y Ambientales de La Pampa. Universidad Nacional de La Pampa. Facultad de Ciencias Exactas y Naturales. Instituto de Ciencias de la Tierra y Ambientales de La Pampa; ArgentinaFil: Diaz, Luis Adrian. Universidad Nacional de Córdoba. Facultad de Medicina. Instituto de Virología Dr. J. M. Vanella; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; Argentin