Single-cell Transcriptomes Reveal Characteristics of MicroRNAs in Gene Expression Noise Reduction / 基因组蛋白质组与生物信息学报·英文版

Isogenic cells growing in identical environments show cell-to-cell variations because of the stochasticity in gene expression. High levels of variation or noise can disrupt robust gene expression and result in tremendous consequences for cell behaviors. In this work, we showed evidence from single-cell RNA sequencing data analysis that microRNAs (miRNAs) can reduce gene expression noise at the mRNA level in mouse cells. We identified that the miRNA expression level, number of targets, target pool abundance, and miRNA-target interaction strength are the key features contributing to noise repression. miRNAs tend to work together in cooperative subnetworks to repress target noise synergistically in a cell type-specific manner. By building a physical model of post-transcriptional regulation and observing in synthetic gene circuits, we demonstrated that accelerated degradation with elevated transcriptional activation of the miRNA target provides resistance to extrinsic fluctuations. Together, through the integrated analysis of single-cell RNA and miRNA expression profiles, we demonstrated that miRNAs are important post-transcriptional regulators for reducing gene expression noise and conferring robustness to biological processes.

Tongue coating microbiome as a potential biomarker for gastritis including precancerous cascade

The development of gastritis is associated with an increased risk of gastric cancer. Current invasive gastritis diagnostic methods are not suitable for monitoring progress. In this work based on 78 gastritis patients and 50 healthy individuals, we observed that the variation of tongue-coating microbiota was associated with the occurrence and development of gastritis. Twenty-one microbial species were identified for differentiating tongue-coating microbiomes of gastritis and healthy individuals. Pathways such as microbial metabolism in diverse environments, biosynthesis of antibiotics and bacterial chemotaxis were up-regulated in gastritis patients. The abundance of Campylobacter concisus was found associated with the gastric precancerous cascade. Furthermore, Campylobacter concisus could be detected in tongue coating and gastric fluid in a validation cohort containing 38 gastritis patients. These observations provided biological evidence of tongue diagnosis in traditional Chinese medicine, and indicated that tongue-coating microbiome could be a potential non-invasive biomarker, which might be suitable for long-term monitoring of gastritis.

Progress of Bioinformatics Study in DNA Methylation / 生物化学与生物物理进展

DNA methylation is an important epigenetic system. It plays many crucial roles in the gene regulation. With the development of the high-throughput detection techniques, the bioinformatics study has been an active hot topic in the research of DNA methylation. The major achievements and progress on the prediction of DNA methylation status, the mechanism that the majority of CpG islands are resistant to DNA methylation, the relationship between DNA methylation and other epigenetics, as well as the association between aberrant DNA methylation and the tumorigenesis were reviewed in this article.

Laparoscopic-assisted small incision operation for the treatment of common bile duct stones / 中国微创外科杂志

Objective To investigate the feasibility of laparoscopic-assisted small incision exploration and stone extraction for the treatment of common bile duct stones. Methods Following the laparoscopic cholecystectomy, the location of the common bile duct was determined under laparoscope. A small abdominal incision was made at the corresponding site and the exploration of common bile duct and extraction of stones were conducted via the incision. Results Among a total of 17 cases, the operation was successfully accomplished in 16 cases and a conversion to open surgery was required in 1 case. The operative time was 90～160 min (mean, 120 min). The number of extracted stones per case was 1～4, with the maximum size of 2.5 cm. All the stones were removed on one session. Postoperative cholangiography 3～4 weeks after the surgery indicated no residual stones. Follow-up for 8～36 months (mean, 14 months) showed no residual stones or occurrence of cholangitis. Conclusions Laparoscopic-assisted small incision exploration and stone extraction for common bile duct stones is feasible, being readily to popularize in basic hospitals.