3D RNA-seq: a powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists.

RNA-sequencing (RNA-seq) analysis of gene expression and alternative splicing should be routine and robust but is often a bottleneck for biologists because of different and complex analysis programs and reliance on specialized bioinformatics skills. We have developed the '3D RNA-seq' App, an R shiny App and web-based pipeline for the comprehensive analysis of RNA-seq data from any organism. It represents an easy-to-use, flexible and powerful tool for analysis of both gene and transcript-level gene expression to identify differential gene/transcript expression, differential alternative splicing and differential transcript usage (3D) as well as isoform switching from RNA-seq data. 3D RNA-seq integrates state-of-the-art differential expression analysis tools and adopts best practice for RNA-seq analysis. The program is designed to be run by biologists with minimal bioinformatics experience (or by bioinformaticians) allowing lab scientists to analyse their RNA-seq data. It achieves this by operating through a user-friendly graphical interface which automates the data flow through the programs in the pipeline. The comprehensive analysis performed by 3D RNA-seq is extremely rapid and accurate, can handle complex experimental designs, allows user setting of statistical parameters, visualizes the results through graphics and tables, and generates publication quality figures such as heat-maps, expression profiles and GO enrichment plots. The utility of 3D RNA-seq is illustrated by analysis of data from a time-series of cold-treated Arabidopsis plants and from dexamethasone-treated male and female mouse cortex and hypothalamus data identifying dexamethasone-induced sex- and brain region-specific differential gene expression and alternative splicing.

Three poisonous plants (Oenanthe, Cicuta and Anamirta) that antagonise the effect of γ-aminobutyric acid in human brain.

Although we are familiar with common British plants that are poisonous, such as Atropa belladonna (deadly nightshade) and Aconitum napellus (monkshood), the two most poisonous plants in the British Flora are Oenanthe crocata (dead man's fingers) and Cicuta virosa (cowbane). In recent years their poisons have been shown to be polyacetylenes (n-C2H2). The plants closely resemble two of the most common plants in the family Apiaceae (Umbelliferae), celery and parsley. Unwittingly, they are ingested by naive foragers and death occurs very rapidly. The third plant Anamirta derives from South-East Asia and contains a powerful convulsant, picrotoxin, which has been used from time immemorial to catch fish, and more recently to poison Birds of Paradise. All three poisons have been shown to block the γ-aminobutyric acid (GABA) system in the human brain that normally has a powerful inhibitory neuronal action. It has also been established that two groups of sedative drugs, barbiturates and benzodiazepines, exert their inhibitory action by stimulating the GABA system. These drugs are the treatments of choice for poisoning by the three vicious plants.