Conversational OLAP in Action

The democratization of data access and the adoption of OLAP in scenarios requiring hand-free interfaces push towards the creation of smart OLAP interfaces. In this demonstration we present COOL, a tool supporting natural language COnversational OLap sessions. COOL interprets and translates a natural language dialogue into an OLAP session that starts with a GPSJ (Generalized Projection, Selection and Join) query. The interpretation relies on a formal grammar and a knowledge base storing metadata from a multidimensional cube. COOL is portable, robust, and requires minimal user intervention. It adopts an n-gram based model and a string similarity function to match known entities in the natural language description. In case of incomplete text description, COOL can obtain the correct query either through automatic inference or through interactions with the user to disambiguate the text. The goal of the demonstration is to let the audience evaluate the usability of COOL and its capabilities in assisting query formulation and ambiguity/error resolution

Evaluating the impact of drought stress in Nure and Tremois barleys (Hordeum vulgare) treated with plant growth promoting rhizobacteria (PGPR) at seedling phase

Barley is the fifth cultivated herbaceous crop in the world, and its important is due to its economic and nutritional value. Climate change is posing a new challenge to barley production. While drought stress was traditionally associated with the flowering and caryopsis filling stages in barley plants, a new form of drought is now emerging in seedling stage. To mitigate the impact of environmental stresses, plant growth promoting rhizobacteria (PGPR) have been proposed to promote nutrient absorption and plant growth with the production of a range of beneficial substances, such as phytohormones, organic acids, and enzymes. The aim of this study was to evaluate the genotype response and the impact of PGPR treatment on two cultivars of barley, Nure (Italian feeding barley, winter habitus) and Tremois (French malting barley, spring habitus) in seedling phase under drought stress. At sowing, the soil was treated with PGPR and after two weeks of control condition two different water regimes were applied on seedlings (control at 25% and stressed at 12% of soil moisture). The results showed that both genotypes exhibited analogous stress response, however the PGPR treatment showed different effects on the two cultivars. Specifically, PGPR treatment increased root dry weight in stress conditions in Nure seedlings (by 36.6%) and increased dry weight in control conditions in Tremois seedlings (by 31.1%). Furthermore, the treatment increased the photosynthesis efficiency (PhiPS2) in Tremois seedlings (by 6.2%) and generally in both cultivars (by 7.6%) under drought stress. These findings suggest that the use of PGPR could be a useful tool for protecting barley seedlings against drought stress in early stages of development. However, further research is needed to fully understand the mechanisms of action to determine the optimal conditions for using this approach in the field

Effect of the nud gene on grain yield in barley

Naked barleys are less yielding than the hulled ones while the reason for this difference has not beendefinitely clarified. To investigate the effect of the nud gene on yield, a barley doubled haploid (DH, Proctor 7Nudinka) population was initially tested in three environments and a QTL study was run on the entire populationas well as on two nud/NUD DH subpopulations. Among the agronomic traits studied, a QTL effect was found atnud locus on chromosome 7H only for yield and thousand grain weight (TGW), while a second QTL was found on6H, although contributed by the naked parent. Other QTLs for TGW were identified on 2H, 3H and 5H. Most QTLsfound in the entire population were confirmed by the study on the two groups. No interaction was observed betweenQTLs. To provide a more accurate evaluation of the effects of the nud gene upon grain yield, its components andother agronomic traits, sixteen naked advanced backcross (AB) BC5F2 lines in the hulled background of cultivarArda were prepared and evaluated in a replicated yield trial for two years. The only differences found betweenAB lines and Arda in grain yield and TGW were due to hull weight (11.97% of kernel weight). No differences wereobserved in other traits such as grains/m2, grains per spike, plant height, heading date and mildew resistance. Inconclusion, we think to have clarified that the effect of the nud gene on yield is due to hulls, and we did not findany pleiotropic effect of nud on other traits. This suggests, together with the finding of a QTL contributed by thenaked parent, that there is a great potential to improve naked barley up to the yield levels of hulled barley

In Silico Identification of MYB and bHLH Families Reveals Candidate Transcription Factors for Secondary Metabolic Pathways in Cannabis sativa L

Plant secondary metabolic pathways are finely regulated by the activity of transcription factors, among which members of the bHLH and MYB subfamilies play a main role. Cannabis sativa L. is a unique officinal plant species with over 600 synthesized phytochemicals having diverse scale-up industrial and pharmaceutical usage. Despite comprehensive knowledge of cannabinoids\u2019 metabolic pathways, very little is known about their regulation, while the literature on flavonoids\u2019 metabolic pathways is still scarce. In this study, we provide the first genome-wide analysis of bHLH and MYB families in C. sativa reference cultivar CBDRx and identification of candidate coding sequences for these transcription factors. Cannabis sativa bHLHs and MYBs were then classified into functional subfamilies through comparative phylogenetic analysis with A. thaliana transcription factors. Analyses of gene structure and motif distribution confirmed that CsbHLHs and CsMYBs belonging to the same evolutionary clade share common features at both gene and amino acidic level. Candidate regulatory genes for key metabolic pathways leading to flavonoid and cannabinoid synthesis in Cannabis were also retrieved. Furthermore, a candidate gene approach was used to identify structural enzyme-coding genes for flavonoid and cannabinoid synthesis. Taken as a whole, this work represents a valuable resource of candidate genes for further investigation of the C. sativa cannabinoid and flavonoid metabolic pathways for genomic studies and breeding programs

Copy number variation at the HvCBF4–HvCBF2 genomic segment is a major component of frost resistance in barley

A family of CBF transcription factors plays a major role in reconfiguring the plant transcriptome in response to low-freezing temperature in temperate cereals. In barley, more than 13 HvCBF genes map coincident with the major QTL FR-H2 suggesting them as candidates to explain the function of the locus. Variation in copy number (CNV) of specific HvCBFs was assayed in a panel of 41 barley genotypes using RT-qPCR. Taking advantage of an accurate phenotyping that combined Fv/Fm and field survival, resistance-associated variants within FR-H2 were identified. Genotypes with an increased copy number of HvCBF4 and HvCBF2 (at least ten and eight copies, respectively) showed greater frost resistance. A CAPS marker able to distinguish the CBF2A, CBF2B and CBF2A/B forms was developed and showed that all the higher-ranking genotypes in term of resistance harbour only CBF2A, while other resistant winter genotypes harbour also CBF2B, although at a lower CNV. In addition to the major involvement of the HvCBF4-HvCBF2 genomic segment in the proximal cluster of CBF elements, a negative role of HvCBF3 in the distal cluster was identified. Multiple linear regression models taking into account allelic variation at FR-H1/VRN-H1 explained 0.434 and 0.550 (both at p < 0.001) of the phenotypic variation for Fv/Fm and field survival respectively, while no interaction effect between CNV at the HvCBFs and FR-H1/VRN-H1 was found. Altogether our data suggest a major involvement of the CBF genes located in the proximal cluster, with no apparent involvement of the central cluster contrary to what was reported for wheat

Physiological responses of processing tomato in organic and conventional Mediterranean cropping systems

Processing tomato is a globally important horticultural crop. It is generally grown in high-input conventional systems, and there is little knowledge regarding its physiological responses in organic cultivation. Therefore, the aim of this work was to determine the influence of organic management on the physiological behavior of cultivars of processing tomato usually cultivated in conventional management in a Mediterranean area. The study was performed by means of: (1) field testing of a set of commercial cultivars for 2 years, in two systems, in one location in Southern Italy, and (2) crop physiological investigations during the growth cycle of processing tomato. Results of the two-year trials indicate that, under the organic cropping system, processing tomato showed, as 2 years average, higher intercellular CO2 concentration (Ci) (+10.3%), transpiration (E) (+15.5%) and stomatal conductance (gs) (+16.5%). Average net assimilation (A) was similar in the two systems and differences were only observed depending on years. In contrast, average leaf area index (LAI) and water use efficiency (WUE) were lower in the organic cropping system ( 1242% and 1217.8%), as were average fruit (FDW) and total (TDW) dry weight ( 1237.5% and 1229%). In our conditions, LAI at the end of the cultivation was highly correlated with total and fruit dry weight. As differences in fruit and total dry weight of processing tomato cannot be explained by differences in net assimilation per leaf area unit, other reasons may be linked to the effects of the organic management on the crop as weeds and pathogens

Epigenetic chromatin modifiers in barley: IV. The study of barley Polycomb group (PcG) genes during seed development and in response to external ABA

<p>Abstract</p> <p>Background</p> <p>Epigenetic phenomena have been associated with the regulation of active and silent chromatin states achieved by modifications of chromatin structure through DNA methylation, and histone post-translational modifications. The latter is accomplished, in part, through the action of PcG (Polycomb group) protein complexes which methylate nucleosomal histone tails at specific sites, ultimately leading to chromatin compaction and gene silencing. Different PcG complex variants operating during different developmental stages have been described in plants. In particular, the so-called FIE/MEA/FIS2 complex governs the expression of genes important in embryo and endosperm development in <it>Arabidopsis</it>. In our effort to understand the epigenetic mechanisms regulating seed development in barley (<it>Hordeum vulgare</it>), an agronomically important monocot plant cultivated for its endosperm, we set out to characterize the genes encoding barley PcG proteins.</p> <p>Results</p> <p>Four barley <it>PcG </it>gene homologues, named <it>HvFIE</it>, <it>HvE(Z), HvSu(z)12a</it>, and <it>HvSu(z)12b </it>were identified and structurally and phylogenetically characterized. The corresponding genes <it>HvFIE</it>, <it>HvE(Z), HvSu(z)12a</it>, and <it>HvSu(z)12b </it>were mapped onto barley chromosomes 7H, 4H, 2H and 5H, respectively. Expression analysis of the <it>PcG </it>genes revealed significant differences in gene expression among tissues and seed developmental stages and between barley cultivars with varying seed size. Furthermore, <it>HvFIE </it>and <it>HvE(Z) </it>gene expression was responsive to the abiotic stress-related hormone abscisic acid (ABA) known to be involved in seed maturation, dormancy and germination.</p> <p>Conclusion</p> <p>This study reports the first characterization of the <it>PcG </it>homologues, <it>HvFIE, HvE(Z)</it>, <it>HvSu(z)12a </it>and <it>HvSu(z)12b </it>in barley. All genes co-localized with known chromosomal regions responsible for malting quality related traits, suggesting that they might be used for developing molecular markers to be applied in marker assisted selection. The <it>PcG </it>differential expression pattern in different tissues and seed developmental stages as well as in two barley cultivars with different seed size is suggestive of a role for these genes in barley seed development. <it>HvFIE </it>and <it>HvE(Z) </it>were also found to be induced by the plant hormone ABA implying an association with ABA-mediated processes during seed development, germination and stress response.</p

Nitrogen Fertilizers Shape the Composition and Predicted Functions of the Microbiota of Field-Grown Tomato Plants

The microbial communities thriving at the root_soil interface have the potential to improve plant growth and sustainable crop production. Yet, how agricultural practices, such as the application of either mineral or organic nitrogen fertilizers, impact on the composition and functions of these communities remains to be fully elucidated. By deploying a two-pronged 16S rRNA gene sequencing and predictive metagenomics approach, we demonstrated that the bacterial microbiota of field-grown tomato (Solanum lycopersicum) plants is the product of a selective process that progressively differentiates between rhizosphere and root microhabitats. This process initiates as early as plants are in a nursery stage and it is then more marked at late developmental stages, in particular at harvest. This selection acts on both the bacterial relative abundances and phylogenetic assignments, with a bias for the enrichment of members of the phylum Actinobacteria in the root compartment. Digestate-based and mineral-based nitrogen fertilizers trigger a distinct bacterial enrichment in both rhizosphere and root microhabitats. This compositional diversification mirrors a predicted functional diversification of the root-inhabiting communities, manifested predominantly by the differential enrichment of genes associated to ABC transporters and the two-component system. Together, our data suggest that the microbiota thriving at the tomato root_soil interface is modulated by and in responses to the type of nitrogen fertilizer applied to the field