A web application prototype for the multiscale modelling of seismic input

A web application prototype is described, aimed at the generation of synthetic seismograms for user-defined earthquake models. The web application graphical user interface hides the complexity of the underlying computational engine, which is the outcome of the continuous evolution of sophisticated computer codes, some of which saw the light back in the middle '80s. With the web application, even the non-experts can produce ground shaking scenarios at the local or regional scale in very short times, depending on the complexity of the adopted source and medium models, without the need of a deep knowledge of the physics of the earthquake phenomenon. Actually, it may even allow neophytes to get some basic education in the field of seismology and seismic engineering, due to the simplified intuitive experimental approach to the matter. One of the most powerful features made available to the users is indeed the capability of executing quick parametric tests in near real-time, to explore the relations between each model's parameter and the resulting ground motion scenario. The synthetic seismograms generated through the web application can be used by civil engineers for the design of new seismo-resistant structures, or to analyse the performance of the existing ones under seismic load.Comment: 23 pages, 13 figure

Distinctive expansion of gene families associated with plant cell wall degradation, secondary metabolism, and nutrient uptake in the genomes of grapevine trunk pathogens

BackgroundTrunk diseases threaten the longevity and productivity of grapevines in all viticulture production systems. They are caused by distantly-related fungi that form chronic wood infections. Variation in wood-decay abilities and production of phytotoxic compounds are thought to contribute to their unique disease symptoms. We recently released the draft sequences of Eutypa lata, Neofusicoccum parvum and Togninia minima, causal agents of Eutypa dieback, Botryosphaeria dieback and Esca, respectively. In this work, we first expanded genomic resources to three important trunk pathogens, Diaporthe ampelina, Diplodia seriata, and Phaeomoniella chlamydospora, causal agents of Phomopsis dieback, Botryosphaeria dieback, and Esca, respectively. Then we integrated all currently-available information into a genome-wide comparative study to identify gene families potentially associated with host colonization and disease development.ResultsThe integration of RNA-seq, comparative and ab initio approaches improved the protein-coding gene prediction in T. minima, whereas shotgun sequencing yielded nearly complete genome drafts of Dia. ampelina, Dip. seriata, and P. chlamydospora. The predicted proteomes of all sequenced trunk pathogens were annotated with a focus on functions likely associated with pathogenesis and virulence, namely (i) wood degradation, (ii) nutrient uptake, and (iii) toxin production. Specific patterns of gene family expansion were described using Computational Analysis of gene Family Evolution, which revealed lineage-specific evolution of distinct mechanisms of virulence, such as specific cell wall oxidative functions and secondary metabolic pathways in N. parvum, Dia. ampelina, and E. lata. Phylogenetically-informed principal component analysis revealed more similar repertoires of expanded functions among species that cause similar symptoms, which in some cases did not reflect phylogenetic relationships, thereby suggesting patterns of convergent evolution.ConclusionsThis study describes the repertoires of putative virulence functions in the genomes of ubiquitous grapevine trunk pathogens. Gene families with significantly faster rates of gene gain can now provide a basis for further studies of in planta gene expression, diversity by genome re-sequencing, and targeted reverse genetic approaches. The functional validation of potential virulence factors will lead to a more comprehensive understanding of the mechanisms of pathogenesis and virulence, which ultimately will enable the development of accurate diagnostic tools and effective disease management

The seismicity of Ghana

Although West Africa is generally an area of very low seismicity, an exception is a concentration of activity in Southern Ghana, especially near to the capital, Accra, which was heavily damaged by earthquakes in 1862 and 1939. Modern instrumental seismicity is poorly understood due to the limitations of seismic monitoring in the country. In this study, all available data are brought together to provide an earthquake catalogue for Ghana, and a new interpretation of the data for the 1862 earthquake is made. It is tentatively suggested that much of the recorded seismicity around Accra is in fact a very protracted aftershock sequence of the 1862 event

Dispersal of conidia of Fusicladium eriobotryae and spatial patterns of scab in loquat orchards in Spain.

Dispersal of conidia of Fusicladium eriobotryae, the causal agent of loquat scab, was investigated in two loquat orchards in Spain from 2010 to 2012. A volumetric spore sampler, horizontally and vertically orientated microscope slides, and rain collectors were placed in loquat fields to trap conidia of F. eriobotryae. No conidia were collected in the volumetric sampler, and highly variable numbers of conidia were collected in the rain gatherers. Large numbers of conidia were collected by microscope slides, particularly by those held in a horizontal orientation compared with those held in a vertical orientation. Approximately 90%of the F. eriobotryae conidia were collected during rainy periods. Based on ROC and Bayesian analysis, using 65 0.2 mm rainfall as a cut-off value resulted in a high probability of correctly predicting actual conidial dispersal, and had a low probability of failing to predict actual conidial dispersal. Based on the index of dispersion and the binary power law, the incidence of loquat scab on fruit was highly aggregated in space between and within trees, and aggregation was influenced by disease incidence. Our results demonstrate, for the first time, that F. eriobotryae is dispersed mainly in rain splash. The results will be integrated into a mechanistic, weather-driven, disease prediction model that should help growers to minimize fungicide application for the management of loquat scab