A machine learning approach for genome-wide prediction of morbid and druggable human genes based on systems-level data

Background: The genome-wide identification of both morbid genes, i.e., those genes whose mutations cause hereditary human diseases, and druggable genes, i.e., genes coding for proteins whose modulation by small molecules elicits phenotypic effects, requires experimental approaches that are time-consuming and laborious. Thus, a computational approach which could accurately predict such genes on a genome-wide scale would be invaluable for accelerating the pace of discovery of causal relationships between genes and diseases as well as the determination of druggability of gene products.Results: In this paper we propose a machine learning-based computational approach to predict morbid and druggable genes on a genome-wide scale. For this purpose, we constructed a decision tree-based meta-classifier and trained it on datasets containing, for each morbid and druggable gene, network topological features, tissue expression profile and subcellular localization data as learning attributes. This meta-classifier correctly recovered 65% of known morbid genes with a precision of 66% and correctly recovered 78% of known druggable genes with a precision of 75%. It was than used to assign morbidity and druggability scores to genes not known to be morbid and druggable and we showed a good match between these scores and literature data. Finally, we generated decision trees by training the J48 algorithm on the morbidity and druggability datasets to discover cellular rules for morbidity and druggability and, among the rules, we found that the number of regulating transcription factors and plasma membrane localization are the most important factors to morbidity and druggability, respectively.Conclusions: We were able to demonstrate that network topological features along with tissue expression profile and subcellular localization can reliably predict human morbid and druggable genes on a genome-wide scale. Moreover, by constructing decision trees based on these data, we could discover cellular rules governing morbidity and druggability.

Fat body in some genera of leaf-cutting ants (Hymenoptera : Formicidae). Proteins, lipids and polysaccharides detection

The comparative histochemical analysis of the fat body of workers belonging to the basal species Cyphomyrmex rimosus and Mycetarotes parallelus and to derived species Acromyrmex disciger and Atta laevigata revealed that this tissue is constituted mainly by cells denominated trophocytes and oenocytes. The trophocytes of all species studied here were characterized mainly by the proteins and lipids synthesis and storage, being the derived species the ones who have presented higher quantity of lipids in the trophocytes when compared to the trophocytes of basal species. In workers M. parallelus and A. laevigata, besides proteins and lipids, there has being observed the presence of polysaccharides, however, in C. rimosus and A. disciger these elements were detected in lower quantities. The histochemical studies of the oenocytes of basal and derived species revealed significant presence of proteins as well as lipids in these cells. In the oenocytes of derived species A. disciger and A. laevigata a higher quantity of lipidic inclusions has being observed, when compared to the basal species. (c) 2005 Elsevier Ltd. All rights reserved.

The intramandibular gland of leaf-cutting ants (Atta sexdens rubropilosa Forel 1908)

The eusociality developed in Hymenoptera and Isoptera is driven by an efficient interaction between exocrine glands and jointed appendages, both in close interaction with the environment. In this context, the mandible of ants plays an important role, since, in addition to being the main jointed appendage, it possess glandular functions. As an example we might name the two glands associated with the mandible: the mandibular and the intramandibular glands. The intramandibular gland is found inside the mandible and consists of a hypertrophied secretory epithelium and secretory cells in the mandible's lumen. The secretion of the secretory epithelium is liberated through intracuticular ducts that open at the base of hairs at the mandible's surface. The secretion of the intramandibular gland (epithelium and secretory cells) reacted positively to tests for the detection of polysaccharides and proteins, thus suggesting that it consists of glycoproteins. The ultrastructure of the secretor epithelium presents variations related to the developmental stage of the individual, showing a large number of ribosomes and microvilli close to the cuticle in young individuals, while in the older specimens it was possible to note the formation of ail intracellular reservoir. These variations of secretory epithelium, as also the interaction between the cellular groups inside the mandible, are important information about this gland in leaf-cutting ants. (c) 2005 Elsevier Ltd. All rights reserved.

The functional morphology of the metapleural gland of the leaf-cutting ant Atta laevigata (Formicidae: Attini)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Secretory Profile of Metapleural Gland Cells of the Leaf-Cutting Ant Acromyrmex coronatus (Formicidae: Attini)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Leaf-cutting ant faecal fluid and mandibular gland secretion: effects on microfungi spore germination

The mandibular gland secretion (MGS) and the faecal fluid (FF) of the leaf-cutting ant Atta sexdens rubropilosa Forel affected the spore germination of selected microfungi isolated from nests of this insect. MGS was more effective than the FF, completely inhibiting the spore germination of four out of six microfungi species.

Antagonistic interactions between garden yeasts and microfungal garden pathogens of leaf-cutting ants

We investigate the diversity of yeasts isolated in gardens of the leafcutter ant Atta texana. Repeated sampling of gardens from four nests over a 1-year time period showed that gardens contain a diverse assemblage of yeasts. The yeast community in gardens consisted mostly of yeasts associated with plants or soil, but community composition changed between sampling periods. In order to understand the potential disease-suppressing roles of the garden yeasts, we screened isolates for antagonistic effects against known microfungal garden contaminants. In vitro assays revealed that yeasts inhibited the mycelial growth of two strains of Escovopsis (a specialized attine garden parasite), Syncephalastrum racemosum (a fungus often growing in gardens of leafcutter lab nests), and the insect pathogen Beauveria bassiana. These garden yeasts add to the growing list of disease-suppressing microbes in attine nests that may contribute synergistically, together with actinomycetes and Burkholderia bacteria, to protect the gardens and the ants against diseases. Additionally, we suggest that garden immunity against problem fungi may therefore derive not only from the presence of disease-suppressing Pseudonocardia actinomycetes, but from an enrichment of multiple disease-suppressing microorganisms in the garden matrix.

Yeasts and filamentous fungi carried by the gynes of leaf-cutting ants

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)