Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

A Comprehensive Appraisal of Meta-Analyses of Exercise-Based Stroke Rehabilitation with Trial Sequential Analysis

Meta-analysis is a common technique used to synthesise the results of multiple studies through the combination of effect size estimates and testing statistics. Numerous meta-analyses have investigated the efficacy of exercise programmes for stroke rehabilitation. However, meta-analyses may also report false-positive results because of insufficient information or random errors. Trial sequential analysis (TSA) is an advanced technique for calculating the required information size (RIS) and more restrictive statistical significance levels for the precise assessment of any specific treatment. This study used TSA to examine whether published meta-analyses in the field of stroke rehabilitation reached the RIS and whether their overall effect sizes were sufficient. A comprehensive search of six electronic databases for articles published before May 2022 was conducted. The intervention methods were divided into four primary groups, namely aerobic or resistance exercise, machine-assisted exercise, task-oriented exercise, and theory-based exercise. The primary outcome measure was gait speed and the secondary outcome measure was balance function. The data were obtained either from the meta-analyses or as raw data from the original cited texts. All data analysis was performed in TSA software. In total, 38 articles with 46 analysable results were included in the TSA. Only 17 results (37.0%) reached the RIS. In conclusion, meta-analysis interpretation is challenging. Clinicians must consider the RIS of meta-analyses before applying the results in real-world situations. TSA can provide accurate evaluations of treatment effects, which is crucial to the development of evidence-based medicine

Evolution of genes and genomes on the Drosophila phylogeny

Affiliations des auteurs : cf page 216 de l'articleInternational audienceComparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species

Evolution of genes and genomes on the Drosophila phylogeny

Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species