obaDIA: one-step biological analysis pipeline for data-independent acquisition and other quantitative proteomics data.

MOTIVATION: Data mining and data quality evaluation are indispensable constituents of quantitative proteomics, but few integrated tools available. RESULTS: We introduced obaDIA, a one-step pipeline to generate visualizable and comprehensive results for quantitative proteomics data. obaDIA supports fragment-level, peptide-level and protein-level abundance matrices from DIA technique, as well as protein-level abundance matrices from other quantitative proteomic techniques. The result contains abundance matrix statistics, differential expression analysis, protein functional annotation and enrichment analysis. Additionally, enrichment strategies which use total proteins or expressed proteins as background are optional, and HTML based interactive visualization for differentially expressed proteins in the KEGG pathway is offered, which helps biological significance mining. In short, obaDIA is an automatic tool for bioinformatics analysis for quantitative proteomics. AVAILABILITY AND IMPLEMENTATION: obaDIA is freely available from https://github.com/yjthu/obaDIA.git. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Dynamic and persistent effects of ethanol exposure on development: an in vivo analysis during and after embryonic ethanol exposure in Caenorhabditis elegans.

BACKGROUND: Defects caused by ethanol (EtOH) exposure during development can be different depending on the time of observation. To investigate this temporal component of developmental delay, we use the fast-developing nematode model Caenorhabditis elegans. We first defined the longitudinal effects of EtOH on development using age-appropriate markers and then closely followed embryonic development before, during, and after EtOH exposure. METHODS: C. elegans embryos were bathed in 0 to 20% EtOH (w/w in ddH(2)O) for 8 hours or were left untreated during embryonic development. Development was followed longitudinally and scored as embryonic stage at the end of the exposure, hatch time, hatching probability (mortality), body length, postembryonic stage, and egg-laying pattern. The rate of in vivo embryonic development was observed hourly for 24 hours covering times before, during, and after EtOH exposure. RESULTS: After exposure to 10% EtOH, embryos were at younger embryonic stages, hatched later, and had higher mortality compared to unexposed controls. Embryos exposed to 5% EtOH were at normal embryonic stages, showed no change in mortality, but hatched later than controls. Both EtOH groups showed shorter mean body lengths and slower postembryonic development; however, the 5% group recovered to control levels faster than the 10% group. The pattern of egg laying was delayed in the 10% group, but not in the 5% group. Hourly in vivo observations revealed that a developmental delay was first visible a few hours into 10% EtOH exposure and that the delay increased after the removal of EtOH exposure. CONCLUSIONS: Developmental delays occurred during and immediately after exposure and were not uniform but rather dynamic. This article highlights the importance of investigating EtOH-induced defects using different markers and at multiple time points. Attention to temporal effects during and immediately after EtOH exposure can provide understanding of these sensitive time points for observation and treatment.