A high-quality genome of Eragrostis curvula grass provides insights into Poaceae evolution and supports new strategies to enhance forage quality.

The Poaceae constitute a taxon of flowering plants (grasses) that cover almost all Earth's inhabitable range and comprises some of the genera most commonly used for human and animal nutrition. Many of these crops have been sequenced, like rice, Brachypodium, maize and, more recently, wheat. Some important members are still considered orphan crops, lacking a sequenced genome, but having important traits that make them attractive for sequencing. Among these traits is apomixis, clonal reproduction by seeds, present in some members of the Poaceae like Eragrostis curvula. A de novo, high-quality genome assembly and annotation for E. curvula have been obtained by sequencing 602 Mb of a diploid genotype using a strategy that combined long-read length sequencing with chromosome conformation capture. The scaffold N50 for this assembly was 43.41 Mb and the annotation yielded 56,469 genes. The availability of this genome assembly has allowed us to identify regions associated with forage quality and to develop strategies to sequence and assemble the complex tetraploid genotypes which harbor the apomixis control region(s). Understanding and subsequently manipulating the genetic drivers underlying apomixis could revolutionize agriculture.

GeRNet: a gene regulatory network tool.

Gene regulatory networks (GRNs) are crucial in every process of life since they govern the majority of the molecular processes. Therefore, the task of assembling these networks is highly important. In particular, the so called model-free approaches have an advantage modeling the complexities of dynamic molecular networks, since most of the gene networks are hard to be mapped with accuracy by any other mathematical model. A highly abstract model-free approach, called rule-based approach, offers several advantages performing data-driven analysis; such as the requirement of the least amount of data. They also have an important ability to perform inferences: its simplicity allows the inference of large size models with a higher speed of analysis. However, regarding these techniques, the reconstruction of the relational structure of the network is partial, hence incomplete, for an effective biological analysis. This situation motivated us to explore the possibility of hybridizing with other approaches, such as biclustering techniques. This led to incorporate a biclustering tool that finds new relations between the nodes of the GRN. In this work we present a new software, called GeRNeT that integrates the algorithms of GRNCOP2 and BiHEA along a set of tools for interactive visualization, statistical analysis and ontological enrichment of the resulting GRNs. In this regard, results associated with Alzheimer disease datasets are presented that show the usefulness of integrating both bioinformatics tools.

S6K1 determines the metabolic requirements for BCR-ABL survival.

In chronic myelogenous leukemia, the constitutive activation of the BCR-ABL kinase transforms cells to an addicted state that requires glucose metabolism for survival. We investigated S6K1, a protein kinase that drives glycolysis in leukemia cells, as a target for counteracting glucose-dependent survival induced by BCR-ABL. BCR-ABL potently activated S6K1-dependent signaling and glycolysis. Although S6K1 knockdown or rapamycin treatment suppressed glycolysis in BCR-ABL-transformed cells, these treatments did not induce cell death. Instead, loss of S6K1 triggered compensatory activation of fatty-acid oxidation, a metabolic program that can support glucose-independent cell survival. Fatty-acid oxidation in response to S6K1 inactivation required the expression of the fatty-acid transporter carnitine palmitoyl transferase 1c, which was recently linked to rapamycin resistance in cancer. Finally, addition of an inhibitor of fatty-acid oxidation significantly enhanced cytotoxicity in response to S6K1 inactivation. These data indicate that S6K1 dictates the metabolic requirements mediating BCR-ABL survival and provide a rationale for combining targeted inhibitors of signal transduction, with strategies to interrupt oncogene-induced metabolism.

HLA antigens in asthmatic children.

The purpose of the present study was to analyze the frequency of HLA-DR and DQ antigens in Brazilian asthmatic children with skin-test and RAST positivity to Dermatophagoides pteronyssinus. The comparison of HLA-DR and DQ antigenic frequencies between patients (n = 30) and controls disclosed a significantly higher HLA-DQ2 frequency in the patients (60% versus 34%, p = 0.013; R. R. = 2.8).