Te evolution of virulence and pathogenicity in plant pathogen populations

The term virulence has a conflicting history among plant pathologists. Here we define virulence as the degree of damage caused to a host by parasite infection, assumed to be negatively correlated with host fitness, and pathogenicity the qualitative capacity of a parasite to infect and cause disease on a host. Selection may act on both virulence and pathogenicity, and their change in parasite populations can drive parasite evolution and host– parasite co-evolution. Extensive theoretical analyses of the factors that shape the evolution of pathogenicity and virulence have been reported in last three decades. Experimental work has not followed the path of theoretical analyses. Plant pathologists have shown greater interest in pathogenicity than in virulence, and our understanding of the molecular basis of pathogenicity has increased enormously. However, little is known regarding the molecular basis of virulence. It has been proposed that the mechanisms of recognition of parasites by hosts will have consequences for the evolution of pathogenicity, but much experimental work is still needed to test these hypotheses. Much theoretical work has been based on evidence from cellular plant pathogens. We review here the current experimental and observational evidence on which to test theoretical hypotheses or conjectures. We compare evidence from viruses and cellular pathogens, mostly fungi and oomycetes, which differ widely in genomic complexity and in parasitism. Data on the evolution of pathogenicity and virulence from viruses and fungi show important differences, and their comparison is necessary to establish the generality of hypotheses on pathogenicity and virulence evolution

A quantitative analysis of complementation of deleterious mutants in plant virus populations

Complementation can be defined as the process by which the function affected by a mutation is provided in trans by fully competent genotypes. Complementation can, thus, counter the effects of selection of deleterious mutants. Complementation of mutants defective for replication, movement and transmission has been often described in experiments with viruses and, occasionally, has been reported to occur in their natural populations. However, the role of complementation in virus evolution has been overlooked. Here is provided a quantitative estimate of the efficiency of complementation, defined as the probability that a non-functional mutant accomplishes a function relative to a functional one. For this, the frequency of mutants of Tobacco mosaic virus (TMV) defective for cell to cell movement was estimated in wild type tobacco plants and in transgenic plants expressing the TMV movement protein (MP) from a transgene. Mutants lethal for cell-to-cell movement were complemented by wild-type TMV in the first case, and by the transgene-expressed MP in the second case. Assuming that complementation is fully efficient in the transgenic plants, a value for the efficiency of complementation of 0.34 was obtained. Thus, complementation can efficiently counter selection on lethal mutants, and may have an important role on virus evolution. Complementation may be relevant for management of viral diseases if the complemented deleterious mutation is linked to other functions affecting the pathogenicity or epidemiology of the virus. - La complementación puede definirse como el proceso por el cual una función afectada por una mutación es provista en trans por genotipos competentes para dicha función. La complementación de mutantes defectivos para replicación, movimiento o transmisión se ha descrito con frecuencia en poblaciones experimentales de virus y, ocasionalmente, en poblaciones de campo. Sin embargo, el papel de la complementación en la evolución de los virus no se ha considerado. En este trabajo presentamos una estima de la eficacia de la complementación, definida como la probabilidad de que un mutante no funcional realice la función respecto a un genotipo funcional. Para ello se estimó la frecuencia de mutantes del virus del mosaico del tabaco (TMV) defectivos para el movimiento de célula a célula en plantas silvestres de tabaco y en plantas transgénicas que expresan constitutivamente la proteína del movimiento (MP) de TMV. En el primer caso, los mutantes letales para movimiento serán complementados por genotipos silvestres de TMV, y en el segundo, por la MP transgénica. Suponiendo que la complementación en las plantas transgénicas es totalmente eficaz, se obtuvo un valor de la eficacia de complementación de 0,34. Esto muestra que la complementación puede contrarrestar eficazmente el efecto de la selección sobre mutantes deletéreos y tener un papel importante en la evolución de virus, con importantes implicaciones prácticas si la mutación deletérea complementada está ligada a otras funciones que afecten a la patogenicidad o epidemiología del virus

Hematology and serum biochemistry values of free-ranging Iberian wolves (Canis lupus) trapped by leg-hold snares

Hematology and serum biochemistry are important tools in assessing the health and physiological status of wildlife populations. Nevertheless, studies on free-ranging wolves (Canis lupus) are scarce, and no reference values are available neither for Iberian wolves nor for wolves captured with leghold snares. We report 37 hematology and serum biochemistry variables obtained from 26 free-ranging Iberian wolves captured with leg-hold snares between 2007 and 2014, including variables previously not reported in the literature. The values obtained are similar to the published reference intervals for Scandinavian wolves captured by darting from a helicopter, except for higher values for mean corpuscular hemoglobin concentration (MCHC), red blood cell distribution width (RDW), leukocyte count, creatinine kinase (CK), ?-globulins, and total bilirubin (TBIL) and lower values for alkaline phosphatase (ALP). We propose that differences in leukocyte count, CK, and TBIL are related to the method of capture, while differences in RDW, MCHC, ALP, and ?-globulins could reflect physiological adaptations to environmental conditions, sampling, or pre-analytical artifacts. Lymphocyte count was lower and neutrophil/lymphocyte ratio was significantly higher in older, reproductive females, while ALP and phosphorus were higher in juvenile wolves. For the first time, we describe hematology and serum biochemistry values of free-ranging Iberian wolves captured with leg-hold snares. The data reported here is the first published reference for wolves captured with similar methods and for monitoring Iberian wolves populations’ physiological and health status.We thank Nuria Fandos and Carla Ferreira, rangers from Xunta de Galicia and Parque Nacional de los Picos de Europa, and volunteers who helped during the trapping sessions. The wolves were captured under projects financed by Associacao de Conservacao do Habitat do Lobo Iberico (ACHLI) in Portugal and by Picos de Europa National Park, Ministerio de Agricultura, Alimentacion y Medio Ambiente, and Xunta de Galicia in Spain. Sara Roque benefited from grant SFRH/BD/12291/2003 from Fundacao para a Ciencia e a Tecnologia. Jose V. Lopez-Bao was supported by a postdoctoral contract from the Spanish Ministry of Economy and Competitiveness. This is the paper no. 5 from the Iberian Wolf Research Team

The neotropical reforestation hotspots : a biophysical and socioeconomic typology of contemporary forest expansion

Tropical reforestation is a significant component of global environmental change that is far less understood than tropical deforestation, despite having apparently increased widely in scale during recent decades. The regional contexts defining such reforestation have not been well described. They are likely to differ significantly from the geographical profiles outlined by site-specific observations that predominate in the literature. In response, this article determines the distribution, extent, and defining contexts of apparently spontaneous reforestation. It delineates regional ‘hotspots’ of significant net reforestation across Latin America and the Caribbean and defines a typology of these hotspots with reference to the biophysical and socioeconomic characteristics that unite and distinguish amongst them. Fifteen regional hotspots were identified on the basis of spatial criteria pertaining to the area, distribution, and rate of reforestation 2001–2014, observed using a custom continental MODIS satellite land-cover classification. Collectively, these hotspots cover 11% of Latin America and the Caribbean and they include 167,667.7 km2 of new forests. Comparisons with other remotely sensed estimates of reforestation indicate that these hotspots contain a significant amount of tropical reforestation, continentally and pantropically. The extent of reforestation as a proportion of its hotspot was relatively invariable (3–14%) given large disparities in hotspot areas and contexts. An ordination analysis defined a typology of five clusters, distinguished largely by their topographical roughness and related aspects of agro-ecological marginality, climate, population trends, and degree of urbanization: ‘Urban lowlands’, ‘Mountainous populated areas’, ‘Rural highlands’, ‘Rural humid lands’ and ‘Rural dry lands’. The typology highlights that a range of distinct, even oppositional regional biophysical, demographic, and agricultural contexts have equally given rise to significant, regional net reforestation, urging a concomitant diversification of forest transition science

Natural regeneration and biodiversity: a global meta-analysis and implications for spatial planning

Natural regeneration offers a cheaper alternative to active reforestation and has the potential to become the predominant way of restoring degraded tropical landscapes at large-scale. We conducted a meta-analysis for tropical regions and quantified the relationships between both ecological and socioeconomic factors and biodiversity responses in naturally regenerating areas. Biogeographic realms, past disturbance, and the human development index (HDI) were used as explanatory variables for biodiversity responses. In addition, we present a case study of large-scale natural regeneration in the Brazilian Atlantic Forest and identify areas where different forms of restoration would be most suitable. Using our dataset for tropical regions, we showed that natural regeneration was predominantly reported within: the Neotropical realm; areas that were intensively disturbed; and countries with medium HDI. We also found that biodiversity in regenerating forests was more similar to the values found in old growth forests in: countries with either low, high, or very high HDI; less biodiverse realms; and areas of less intensive past disturbance. Our case study from Brazil showed that the level of forest gain resulting from environmental legislation, in particular the Brazilian Forest Code, has been reduced, but remains substantial. Complementary market incentives and financial mechanisms to promote large-scale natural regeneration in human-modified agricultural landscapes are also needed. Our analysis provides insights into the factors that promote or limit the recovery of biodiversity in naturally regenerating areas, and aids to identify areas with higher potential for natural regeneration

New H-mode regimes with small ELMs and high thermal confinement in the Joint European Torus

New H-mode regimes with high confinement, low core impurity accumulation, and small edge-localized mode perturbations have been obtained in magnetically confined plasmas at the Joint European Torus tokamak. Such regimes are achieved by means of optimized particle fueling conditions at high input power, current, and magnetic field, which lead to a self-organized state with a strong increase in rotation and ion temperature and a decrease in the edge density. An interplay between core and edge plasma regions leads to reduced turbulence levels and outward impurity convection. These results pave the way to an attractive alternative to the standard plasmas considered for fusion energy generation in a tokamak with a metallic wall environment such as the ones expected in ITER.& nbsp;Published under an exclusive license by AIP Publishing

Interpretative and predictive modelling of Joint European Torus collisionality scans

Transport modelling of Joint European Torus (JET) dimensionless collisionality scaling experiments in various operational scenarios is presented. Interpretative simulations at a fixed radial position are combined with predictive JETTO simulations of temperatures and densities, using the TGLF transport model. The model includes electromagnetic effects and collisions as well as □(→┬E ) X □(→┬B ) shear in Miller geometry. Focus is on particle transport and the role of the neutral beam injection (NBI) particle source for the density peaking. The experimental 3-point collisionality scans include L-mode, and H-mode (D and H and higher beta D plasma) plasmas in a total of 12 discharges. Experimental results presented in (Tala et al 2017 44th EPS Conf.) indicate that for the H-mode scans, the NBI particle source plays an important role for the density peaking, whereas for the L-mode scan, the influence of the particle source is small. In general, both the interpretative and predictive transport simulations support the experimental conclusions on the role of the NBI particle source for the 12 JET discharges

Predictive JET current ramp-up modelling using QuaLiKiz-neural-network

This work applies the coupled JINTRAC and QuaLiKiz-neural-network (QLKNN) model on the ohmic current ramp-up phase of a JET D discharge. The chosen scenario exhibits a hollow T-e profile attributed to core impurity accumulation, which is observed to worsen with the increasing fuel ion mass from D to T. A dynamic D simulation was validated, evolving j, n(e), T-e, T-i, n(Be), n(Ni), and n(W) for 7.25 s along with self-consistent equilibrium calculations, and was consequently extended to simulate a pure T plasma in a predict-first exercise. The light impurity (Be) accounted for Z(eff) while the heavy impurities (Ni, W) accounted for Prad. This study reveals the role of transport on the Te hollowing, which originates from the isotope effect on the electron-ion energy exchange affecting T-i. This exercise successfully affirmed isotopic trends from previous H experiments and provided engineering targets used to recreate the D q-profile in T experiments, demonstrating the potential of neural network surrogates for fast routine analysis and discharge design. However, discrepancies were found between the impurity transport behaviour of QuaLiKiz and QLKNN, which lead to notable T-e hollowing differences. Further investigation into the turbulent component of heavy impurity transport is recommended

The role of ETG modes in JET-ILW pedestals with varying levels of power and fuelling

We present the results of GENE gyrokinetic calculations based on a series of JET-ITER-like-wall (ILW) type I ELMy H-mode discharges operating with similar experimental inputs but at different levels of power and gas fuelling. We show that turbulence due to electron-temperature-gradient (ETGs) modes produces a significant amount of heat flux in four JET-ILW discharges, and, when combined with neoclassical simulations, is able to reproduce the experimental heat flux for the two low gas pulses. The simulations plausibly reproduce the high-gas heat fluxes as well, although power balance analysis is complicated by short ELM cycles. By independently varying the normalised temperature gradients (omega(T)(e)) and normalised density gradients (omega(ne )) around their experimental values, we demonstrate that it is the ratio of these two quantities eta(e) = omega(Te)/omega(ne) that determines the location of the peak in the ETG growth rate and heat flux spectra. The heat flux increases rapidly as eta(e) increases above the experimental point, suggesting that ETGs limit the temperature gradient in these pulses. When quantities are normalised using the minor radius, only increases in omega(Te) produce appreciable increases in the ETG growth rates, as well as the largest increases in turbulent heat flux which follow scalings similar to that of critical balance theory. However, when the heat flux is normalised to the electron gyro-Bohm heat flux using the temperature gradient scale length L-Te, it follows a linear trend in correspondence with previous work by different authors