Sequencing and functional analysis of the genome of a nematode egg-parasitic fungus, Pochonia chlamydosporia

Pochonia chlamydosporia is a worldwide-distributed soil fungus with a great capacity to infect and destroy the eggs and kill females of plant-parasitic nematodes. Additionally, it has the ability to colonize endophytically roots of economically-important crop plants, thereby promoting their growth and eliciting plant defenses. This multitrophic behavior makes P. chlamydosporia a potentially useful tool for sustainable agriculture approaches. We sequenced and assembled ∼41 Mb of P. chlamydosporia genomic DNA and predicted 12,122 gene models, of which many were homologous to genes of fungal pathogens of invertebrates and fungal plant pathogens. Predicted genes (65%) were functionally annotated according to Gene Ontology, and 16% of them found to share homology with genes in the Pathogen Host Interactions (PHI) database. The genome of this fungus is highly enriched in genes encoding hydrolytic enzymes, such as proteases, glycoside hydrolases and carbohydrate esterases. We used RNA-Seq technology in order to identify the genes expressed during endophytic behavior of P. chlamydosporia when colonizing barley roots. Functional annotation of these genes showed that hydrolytic enzymes and transporters are expressed during endophytism. This structural and functional analysis of the P. chlamydosporia genome provides a starting point for understanding the molecular mechanisms involved in the multitrophic lifestyle of this fungus. The genomic information provided here should also prove useful for enhancing the capabilities of this fungus as a biocontrol agent of plant-parasitic nematodes and as a plant growth-promoting organism.

A new algorithm to accelerate harmonic analysis of time series

The Lomb periodogram has been traditionally a tool that allows us to elucidate if a frequency turns out to be important for explaining the behaviour of a given time series. Many linear and nonlinear reiterative harmonic processes that are used for studying the spectral content of a time series take into account this periodogram in order to avoid including spurious frequencies in their models due to the leakage problem of energy from one frequency to others. However, the estimation of the periodogram requires long computation time that makes the harmonic analysis slower when we deal with certain time series. Here we propose an algorithm that accelerates the extraction of the most remarkable frequencies from the periodogram, avoiding its whole estimation of the harmonic process at each iteration. This algorithm allows the user to perform a specific analysis of a given scalar time series. As a result, we obtain a functional model made of (1) a trend component, (2) a linear combination of Fourier terms, and (3) the so-called mixed secular terms by reducing the computation time of the estimation of the periodogram.

Nonlinear dynamics in discretionary accruals: An analysis of bank loan-loss provisions

Several studies have analyzed discretionary accruals to address earnings-smoothing behaviors in the banking industry. We argue that the characteristic link between accruals and earnings may be nonlinear, since both the incentives to manipulate income and the practical way to do so depend partially on the relative size of earnings. Given a sample of 15,268 US banks over the period 1996–2011, the main results in this paper suggest that, depending on the size of earnings, bank managers tend to engage in earnings-decreasing strategies when earnings are negative (“big-bath”), use earnings-increasing strategies when earnings are positive, and use provisions as a smoothing device when earnings are positive and substantial (“cookie-jar” accounting). This evidence, which cannot be explained by the earnings-smoothing hypothesis, is consistent with the compensation theory. Neglecting nonlinear patterns in the econometric modeling of these accruals may lead to misleading conclusions regarding the characteristic strategies used in earnings management.

Efficient split eld FDTD analysis of third-order nonlinear materials in two-dimensionally periodic media

In this work the split-field finite-difference time-domain method (SF-FDTD) has been extended for the analysis of two-dimensionally periodic structures with third-order nonlinear media. The accuracy of the method is verified by comparisons with the nonlinear Fourier Modal Method (FMM). Once the formalism has been validated, examples of one- and two-dimensional nonlinear gratings are analysed. Regarding the 2D case, the shifting in resonant waveguides is corroborated. Here, not only the scalar Kerr effect is considered, the tensorial nature of the third-order nonlinear susceptibility is also included. The consideration of nonlinear materials in this kind of devices permits to design tunable devices such as variable band filters. However, the third-order nonlinear susceptibility is usually small and high intensities are needed in order to trigger the nonlinear effect. Here, a one-dimensional CBG is analysed in both linear and nonlinear regime and the shifting of the resonance peaks in both TE and TM are achieved numerically. The application of a numerical method based on the finite- difference time-domain method permits to analyse this issue from the time domain, thus bistability curves are also computed by means of the numerical method. These curves show how the nonlinear effect modifies the properties of the structure as a function of variable input pump field. When taking the nonlinear behaviour into account, the estimation of the electric field components becomes more challenging. In this paper, we present a set of acceleration strategies based on parallel software and hardware solutions.

Biological significance of dead biomass retention trait in Mediterranean Basin species: an analysis between different successional niches and regeneration strategies as functional groups

Standing dead biomass retention is considered one of the most relevant fuel structural traits to affect plant flammability. However, very little is known about the biological significance of this trait and its distribution between different functional groups. Our aim was to analyse how the proportion of dead biomass produced in Mediterranean species is related to the successional niche of species (early-, mid- and late-successional stages) and the regeneration strategy of species (seeders and resprouters). We evaluated biomass distribution by size classes and standing dead biomass retention in nine dominant species from the Mediterranean Basin in different development stages (5, 9, 14 and 26 years since the last fire). The results revealed significant differences in the standing dead biomass retention of species that presented a distinct successional niche or regeneration strategy. These differences were restricted to the oldest ages studied (>9 years). Tree and small tree resprouters, typical in late-successional stages, presented slight variations with age and a less marked trend to retain dead biomass, while seeder shrubs and dwarf shrubs, characteristic of early-successional stages, showed high dead biomass loads. Our results suggest that the species that tend to retain more dead branches are colonising species that may promote fire in early-successional stages.