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.

Study of the thermal decomposition of petrochemical sludge in a pilot plant reactor

The pyrolysis of a sludge produced in the waste water treatment plant of an oil refinery was studied in a pilot plant reactor provided with a system for condensation of semivolatile matter. The study comprises experiments at 350, 400, 470 and 530 °C in nitrogen atmosphere. Analysis of all the products obtained (gases, liquids and chars) are presented, with a thermogravimetric study of the char produced and analysis of main components of the liquid. In the temperature range studied, the composition of the gas fraction does not appreciably vary. In the liquids, the light hidrocarbon yield increases with increasing temperature, whereas the aromatic compounds diminish. The decomposition of the solid fraction has been analysed, finding a material that reacts rapidly with oxygen regardless of the conditions it is formed.

Enrichment of the Phenotypic and Genotypic Data Warehouse analysis using Question Answering systems to facilitate the decision making process in cereal breeding programs

Currently there are an overwhelming number of scientific publications in Life Sciences, especially in Genetics and Biotechnology. This huge amount of information is structured in corporate Data Warehouses (DW) or in Biological Databases (e.g. UniProt, RCSB Protein Data Bank, CEREALAB or GenBank), whose main drawback is its cost of updating that makes it obsolete easily. However, these Databases are the main tool for enterprises when they want to update their internal information, for example when a plant breeder enterprise needs to enrich its genetic information (internal structured Database) with recently discovered genes related to specific phenotypic traits (external unstructured data) in order to choose the desired parentals for breeding programs. In this paper, we propose to complement the internal information with external data from the Web using Question Answering (QA) techniques. We go a step further by providing a complete framework for integrating unstructured and structured information by combining traditional Databases and DW architectures with QA systems. The great advantage of our framework is that decision makers can compare instantaneously internal data with external data from competitors, thereby allowing taking quick strategic decisions based on richer data.

Drought and grazing combined: Contrasting shifts in plant interactions at species pair and community level

The combined effects of drought stress and grazing pressure on shaping plant–plant interactions are still poorly understood, while this combination is common in arid ecosystems. In this study we assessed the relative effect of grazing pressure and slope aspect (drought stress) on vegetation cover and soil functioning in semi-arid Mediterranean grassland–shrublands in southeastern Spain. Moreover, we linked these two stress factors to plant co-occurrence patterns at species-pair and community levels, by performing C-score analyses. Vegetation cover and soil functioning decreased with higher grazing pressure and more south-facing (drier) slopes. At the community level, plants at south-facing slopes were negatively associated at no grazing but positively associated at low grazing pressure and randomly associated at high grazing pressure. At north-facing slopes, grazing did not result in a shift in the direction of the association. In contrast, analysis of pairwise species co-occurrence patterns showed that the dominant species Stipa tenacissima and Anthyllis cytisoides shifted from excluding each other to co-occurring with increasing grazing pressure at north-facing slopes. Our findings highlight that for improved understanding of plant interactions along stress gradients, interactions between species pairs and interactions at the community level should be assessed, as these may reveal contrasting results.

Endophytic colonization of barley (Hordeum vulgare) roots by the nematophagous fungus Pochonia chlamydosporia reveals plant growth promotion and a general defense and stress transcriptomic response

Plant crop yields are negatively conditioned by a large set of biotic and abiotic factors. An alternative to mitigate these adverse effects is the use of fungal biological control agents and endophytes. The egg-parasitic fungus Pochonia chlamydosporia has been traditionally studied because of its potential as a biological control agent of plant-parasitic nematodes. This fungus can also act as an endophyte in monocot and dicot plants, and has been shown to promote plant growth in different agronomic crops. An Affymetrix 22K Barley GeneChip was used in this work to analyze the barley root transcriptomic response to P. chlamydosporia root colonization. Functional gene ontology (GO) and gene set enrichment analyses showed that genes involved in stress response were enriched in the barley transcriptome under endophytism. An 87.5 % of the probesets identified within the abiotic stress response group encoded heat shock proteins. Additionally, we found in our transcriptomic analysis an up-regulation of genes implicated in the biosynthesis of plant hormones, such as auxin, ethylene and jasmonic acid. Along with these, we detected induction of brassinosteroid insensitive 1-associated receptor kinase 1 (BR1) and other genes related to effector-triggered immunity (ETI) and pattern-triggered immunity (PTI). Our study supports at the molecular level the growth-promoting effect observed in plants endophytically colonized by P. chlamydosporia, which opens the door to further studies addressing the capacity of this fungus to mitigate the negative effects of biotic and abiotic factors on plant crops.

An ethnopharmacological and historical analysis of “Dictamnus”, a European traditional herbal medicine

Ethnopharmacological relevance and background: “Dictamnus” was a popular name for a group of medicinal herbaceous plant species of the Rutaceae and Lamiaceae, which since the 4th century have been used for gynaecological problems and other illnesses BCE and still appear in numerous ethnobotanical records. Aims: This research has as four overarching aims: Determining the historical evolution of medical preparations labelled “Dictamnus” and the different factors affecting this long-standing herbal tradition. Deciphering and differentiating those medicinal uses of “Dictamnus” which strictly correspond to Dictamnus (Rutaceae), from those of Origanum dictamnus and other Lamiaceae species. Quantitatively assessing the dependence from herbal books, and pharmaceutical tradition, of modern Dictamnus ethnobotanical records. Determining whether differences between Western and Eastern Europe exist with regards to the Dictamnus albus uses in ethnopharmacology and ethnomedicine. Methods: An exhaustive review of herbals, classical pharmacopoeias, ethnobotanical and ethnopharmacological literature was conducted. Systematic analysis of uses reported which were standardized according to International Classification of Diseases – 10 and multivariate analysis using factorial, hierarchical and neighbour joining methods was undertaken. Results and discussion: The popular concept “Dictamnus” includes Origanum dictamnus L., Ballota pseudodictamnus (L.) Benth. and B. acetabulosa (L.) Benth. (Lamiaceae), as well as Dictamnus albus L. and D. hispanicus Webb ex Willk. (Rutaceae), with 86 different types of uses. Between 1000 and 1700 CE numerous complex preparations with “Dictamnus” were used in the treatment of 35 different pathologies. On biogeographical grounds the widespread D. albus is a far more likely prototypical “Dictamnus” than the Cretan endemic Origanum dictamnus. However both form integral parts of the “Dictamnus” complex. Evidence exists for a sufficiently long and coherent tradition for D. albus and D. hispanicus, use to treat 47 different categories of diseases. Conclusions: This approach is a model for understanding the cultural history of plants and their role as resources for health care. “Dictamnus” shows how transmission of traditional knowledge about materia medica, over 26 centuries, represents remarkable levels of development and innovation. All this lead us to call attention to D. albus and D. hispanicus which are highly promising as potential herbal drug leads. The next steps of research should be to systematically analyse phytochemical, pharmacological and clinical evidence and to develop safety, pharmacology and toxicology profiles of the traditional preparations.

Where Is My Food? Brazilian Flower Fly Steals Prey from Carnivorous Sundews in a Newly Discovered Plant-Animal Interaction

A new interaction between insects and carnivorous plants is reported from Brazil. Larvae of the predatory flower fly Toxomerus basalis (Diptera: Syrphidae: Syrphinae) have been found scavenging on the sticky leaves of several carnivorous sundew species (Drosera, Droseraceae) in Minas Gerais and São Paulo states, SE Brazil. This syrphid apparently spends its whole larval stage feeding on prey trapped by Drosera leaves. The nature of this plant-animal relationship is discussed, as well as the Drosera species involved, and locations where T. basalis was observed. 180 years after the discovery of this flower fly species, its biology now has been revealed. This is (1) the first record of kleptoparasitism in the Syrphidae, (2) a new larval feeding mode for this family, and (3) the first report of a dipteran that shows a kleptoparasitic relationship with a carnivorous plant with adhesive flypaper traps. The first descriptions of the third instar larva and puparium of T. basalis based on Scanning Electron Microscope analysis are provided.

Structural Analysis with ANSYS on Stone Constructions in the Historical Spanish Heritage

According to the importance of rehabilitation and recovery of Architectural Heritage in the live of people, this paper is aimed to strengthen the traditional methods of stone vaults calculation taking advantage of the technological characteristics of the powerful program ANSYS Workbench. As an example of this, it could find out the possible pathologies that could arise during the construction history of the building. To limit this research, the upper vault of the main chapel of the Santiago parish church in Orihuela -Alicante- is selected as a reference which is a Jeronimo Quijano´s important building work in the XVI century in the Renaissance. Moreover, it is an innovative stone masonry vault that consists of 8 double intercrossed arches with each other and braced by severies. During the seventeenth century there was a lantern in the central cap and it is unknown why it was removed. Its construction could justify the original constructive solution with intercrossed arches that freed the center to create a more enlightened and comfortable presbytery. By similarity with other Quijano’s works, it is considered a small lantern drilling the central spherical cap. It is proposed to carry out a comparative study of it with different architectural solutions from the same period and based on several common parameters such as: a vault of square plant with spherical surround, intercrossed arches, a possible lantern, the dimension of the permitted space, similar states of loads and compact limestone masonry. The three solutions are mainly differentiated by their size and the type of lantern and its comparison lets us know which one is the most resistant and stable. The other two building works maintain some connection with the Quijano's professional scope. It has selected the particular case of the Communion chapel of the Basilica in Elche (a large prismatic lantern with a large cylindrical drum that starts from the own arches and an upper hemispherical dome), for its conservation, its proximity to Orihuela and its implementation during the century XVIII. Finally, a significant Dome Spanish Renaissance complete the selection: a cross vault of the Benavides Chapel of the Saint Francisco Convent in Baeza - Jaén-, designed by Andres of Vandelvira in the sixteenth century (a large hemispherical dome that starts from the own arcs). To simplify the calculation and standardize the work that have to be contrasted, all of them were considered with some similar characteristics: 30 cm constant thickness, the intercrossed arches were specifically analyzed and had identical loads, Young's modulus and Poisson's ratio. Regarding the calculation solutions, in general terms, the compressive stresses predominate, influencing on it the joint collaboration of the filling material on the vault, the vault itself, the thick side walls, the buttresses and the top cover weight . In addition, the three solutions are suitable, being the Orihuela one the safest and the Baeza one the riskiest for its large dimensions. Thus, the idea of intercrossed arches with suitable thickness would allow carry out the heaviest lantern and this would confirm it as a Renaissance architectural typology built in stone.

Large scale optimization of a sour water stripping plant using surrogate models

In this work, we propose a new methodology for the large scale optimization and process integration of complex chemical processes that have been simulated using modular chemical process simulators. Units with significant numerical noise or large CPU times are substituted by surrogate models based on Kriging interpolation. Using a degree of freedom analysis, some of those units can be aggregated into a single unit to reduce the complexity of the resulting model. As a result, we solve a hybrid simulation-optimization model formed by units in the original flowsheet, Kriging models, and explicit equations. We present a case study of the optimization of a sour water stripping plant in which we simultaneously consider economics, heat integration and environmental impact using the ReCiPe indicator, which incorporates the recent advances made in Life Cycle Assessment (LCA). The optimization strategy guarantees the convergence to a local optimum inside the tolerance of the numerical noise.