Key Pathways and Genes of and Roots under Cadmium Stress Responses: Differences and Similarities.

Cadmium (Cd) is among the world's major health concerns, as it renders soils unsuitable and unsafe for food and feed production. Phytoremediation has the potential to remediate Cd-polluted soils, but efforts are still needed to develop a deep understanding of the processes underlying it. In this study, we performed a comprehensive analysis of the root response to Cd stress in , which can phytostabilize Cd, and in , which is a Cd hyperaccumulator.

Network-Based Analysis to Identify Hub Genes Involved in Spatial Root Response to Mechanical Constrains.

Previous studies report that the asymmetric response, observed along the main poplar woody bent root axis, was strongly related to both the type of mechanical forces (compression or tension) and the intensity of force displacement. Despite a large number of targets that have been proposed to trigger this asymmetry, an understanding of the comprehensive and synergistic effect of the antistress spatially related pathways is still lacking. Recent progress in the bioinformatics area has the potential to fill these gaps through the use of in silico studies, able to investigate biological functions and pathway overlaps, and to identify promising targets in plant responses.

Root and shoot biology of Arabidopsis halleri dissected by WGCNA: an insight into the organ pivotal pathways and genes of an hyperaccumulator.

Arabidopsis halleri is a hyperaccumulating pseudo-metallophyte and an emerging model to explore molecular basis of metal tolerance and hyperaccumulation. In this regard, understanding of interacting genes can be a crucial aspect as these interactions regulate several biological functions at molecular level in response to multiple signals. In this current study, we applied a weighted gene co-expression network analysis (WGCNA) on root and shoot RNA-seq data of A.

PANEV: an R package for a pathway-based network visualization.

Background: During the last decade, with the aim to solve the challenge of post-genomic and transcriptomic data mining, a plethora of tools have been developed to create, edit and analyze metabolic pathways. In particular, when a complex phenomenon is considered, the creation of a network of multiple interconnected pathways of interest could be useful to investigate the underlying biology and ultimately identify functional candidate genes affecting the trait under investigation.

Results: PANEV (PAthway NEtwork Visualizer) is an R package set for gene/pathway-based network visualization.

Formation of Annual Ring Eccentricity in Coarse Roots within the Root Cage of Growing on Slopes.

The coarse roots of included in the cage are the ones most involved in tree stability. This study explored the variations in traits, such as volume, cross-sectional area, and radius length of cage roots, and used those data to develop a mathematical model to better understand the type of forces occurring for each shallow lateral root segment belonging to different quadrants of the three-dimensional (3D) root system architecture. The pattern and intensity of these forces were modelled along the root segment from the branching point to the cage edge.

Phylo_dCor: distance correlation as a novel metric for phylogenetic profiling.

Background: Elaboration of powerful methods to predict functional and/or physical protein-protein interactions from genome sequence is one of the main tasks in the post-genomic era. Phylogenetic profiling allows the prediction of protein-protein interactions at a whole genome level in both Prokaryotes and Eukaryotes. For this reason it is considered one of the most promising methods.

An Integrated Approach to Explore Composition and Dynamics of Cholesterol-rich Membrane Microdomains in Sexual Stages of Malaria Parasite.

Membrane microdomains that include lipid rafts, are involved in key physiological and pathological processes and participate in the entry of endocellular pathogens. These assemblies, enriched in cholesterol and sphingolipids, form highly dynamic, liquid-ordered phases that can be separated from the bulk membranes thanks to their resistance to solubilization by nonionic detergents. To characterize complexity and dynamics of detergent-resistant membranes of sexual stages of the rodent malaria parasite , here we propose an integrated study of raft components based on proteomics, lipid analysis and bioinformatics.

The FAD-dependent glycerol-3-phosphate dehydrogenase of Giardia duodenalis: an unconventional enzyme that interacts with the g14-3-3 and it is a target of the antitumoral compound NBDHEX.

The flagellated protozoan Giardia duodenalis is a worldwide parasite causing giardiasis, an acute and chronic diarrheal disease. Metabolism in G. duodenalis has a limited complexity thus making metabolic enzymes ideal targets for drug development.