Ribosome Profiling Reveals Genome-wide Cellular Translational Regulation upon Heat Stress in Escherichia coli

Heat shock response is a classical stress-induced regulatory system in bacteria, characterized by extensive transcriptional reprogramming. To compare the impact of heat stress on the transcriptome and translatome in Escherichia coli, we conducted ribosome profiling in parallel with RNA-Seq to investigate the alterations in transcription and translation efficiency when E. coli cells were exposed to a mild heat stress (from 30â¯Â°C to 45â¯Â°C). While general changes in ribosome footprints correlate with the changes of mRNA transcripts upon heat stress, a number of genes show differential changes at the transcription and translation levels. Translation efficiency of a few genes that are related to environment stimulus response is up-regulated, and in contrast, some genes functioning in mRNA translation and amino acid biosynthesis are down-regulated at the translation level in response to heat stress. Moreover, our ribosome occupancy data suggest that in general ribosomes accumulate remarkably in the starting regions of ORFs upon heat stress. This study provides additional insights into bacterial gene expression in response to heat stress, and suggests the presence of stress-induced but yet-to-be characterized cellular regulatory mechanisms of gene expression at translation level. Keywords: Ribosome profiling, Translation regulation, RNA-Seq, Heat shock response, Transcription regulatio

Systematic Reconstruction of Molecular Cascades Regulating GP Development Using Single-Cell RNA-Seq

Summary: The growth plate (GP) comprising sequentially differentiated cell layers is a critical structure for bone elongation and regeneration. Although several key regulators in GP development have been identified using genetic perturbation, systematic understanding is still limited. Here, we used single-cell RNA-sequencing (RNA-seq) to determine the gene expression profiles of 217 single cells from GPs and developed a bioinformatics pipeline named Sinova to de novo reconstruct physiological GP development in both temporal and spatial high resolution. Our unsupervised model not only confirmed prior knowledge, but also enabled the systematic discovery of genes, potential signal pathways, and surface markers CD9/CD200 to precisely depict development. Sinova further identified the effective combination of transcriptional factors (TFs) that regulates GP maturation, and the result was validated using an in vitro EGFP-Col10a screening system. Our case systematically reconstructed molecular cascades in GP development through single-cell profiling, and the bioinformatics pipeline is applicable to other developmental processes. Video Abstract: : Li et al. have developed an unsupervised clustering approach called Sinova to analyze single-cell RNA-seq data. By using this pipeline to analyze single-cell RNA-seq data from developing GPs in mice, they have generated a spatial and temporal map of the GP and identified molecular networks involved in GP development

Inhalable Microorganisms in Beijing’s PM_2.5 and PM₁₀ Pollutants during a Severe Smog Event

Particulate matter (PM) air pollution poses a formidable public health threat to the city of Beijing. Among the various hazards of PM pollutants, microorganisms in PM_2.5 and PM₁₀ are thought to be responsible for various allergies and for the spread of respiratory diseases. While the physical and chemical properties of PM pollutants have been extensively studied, much less is known about the inhalable microorganisms. Most existing data on airborne microbial communities using 16S or 18S rRNA gene sequencing to categorize bacteria or fungi into the family or genus levels do not provide information on their allergenic and pathogenic potentials. Here we employed metagenomic methods to analyze the microbial composition of Beijing’s PM pollutants during a severe January smog event. We show that with sufficient sequencing depth, airborne microbes including bacteria, archaea, fungi, and dsDNA viruses can be identified at the species level. Our results suggested that the majority of the inhalable microorganisms were soil-associated and nonpathogenic to human. Nevertheless, the sequences of several respiratory microbial allergens and pathogens were identified and their relative abundance appeared to have increased with increased concentrations of PM pollution. Our findings may serve as an important reference for environmental scientists, health workers, and city planners

Metagenomic Human Repiratory Air in a Hospital Environment

<div><p>Hospital-acquired infection (HAI) or nosocomial infection is an issue that frequent hospital environment. We believe conventional regulated Petri dish method is insufficient to evaluate HAI. To address this problem, metagenomic sequencing was applied to screen airborne microbes in four rooms of Beijing Hospital. With air-in amount of sampler being setup to one person’s respiration quantity, metagenomic sequencing identified huge numbers of species in the rooms which had already qualified widely accepted petridish exposing standard, imposing urgency for new technology. Meanwhile,the comparative culture only got small portion of recovered species and remain blind for even cultivable pathogens reminded us the limitations of old technologies. To the best of our knowledge, the method demonstrated in this study could be broadly applied in hospital indoor environment for various monitoring activities as well as HAI study. It is also potential as a transmissible pathogen real-time modelling system worldwide.</p></div

Results in bacteria comparative culture of parallel hospital samples (Filter paper elution half to metagenomic sequencing and half to conventional Peri dish culture).

<p>(For those not identified to species such as Bacillus, Genus abundance instead of species abundance was used).</p><p>Results in bacteria comparative culture of parallel hospital samples (Filter paper elution half to metagenomic sequencing and half to conventional Peri dish culture).</p

Main routes of transmission for nosocomial infection.

<p>Main routes of transmission for nosocomial infection.</p

Number of metagenomic recovered species for each group of microorganisms.

<p>a) sampling equipment, the soft tube connected to sampling head allows it to be easily fixed at any position, even could be put before the mouth. b) the sampling filter paper at Nov.6,2013. Left: blank; right: after work for 24 hours. c) Numbers of species and d) proportions of species number in each group of microbes in four rooms.</p

Heatmap of metagenomic recoverd species for each group of microorganisms in four rooms.

<p>For bacteria and eukaryote, top 100 abundant species for the heatmap.</p

PCoA analysis for indoor and outdoor air.

<p>Data were normalized between 0 and 1 and compared with PM2.5 and PM10 data set[<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0139044#pone.0139044.ref047" target="_blank">47</a>]. (red: Indoor results; blue: outdoor results).</p