Search

Salt stress negatively affects plant growth and crop productivity. As an ideal model pathway of salt tolerance in glycophyte. To better understand the molecular mechanisms of salt-response in glycophyte, 466 of 15,768 Arabidopsis thaliana proteins with the GO term of biological with known genetic background, Arabidopsis thaliana has been widely applied to disclose the process 'response to salt stress' were retrieved from UniPort and analyzed by bioinformatics tools of PANTHER, DAVID, KEGG, Cytoscape and STRING. Our results not only indicated the involvement of salt-responsive proteins in various pathways and interaction networks, but also demonstrated the more complicated cross-tolerances to both abiotic stresses (osmosis, water deprivation, abscisic acid, cold, heat, light and wounding) and biotic stresses (bacterium and fungus) and multiple subcellular locations of these salt-responsive proteins. Furthermore, protein activities of superoxide dismutase (SOD) and peroxidase (POD) in Arabidopsis thaliana were determined under salt, cold and osmotic stresses, which validated the hypothesis of cross-tolerance to multiple stresses. Our work will greatly improve the current knowledge of salt tolerance mechanism in glycophytes and provide potential salt-responsive candidates for promoting plant growth and increasing crop output. [ABSTRACT FROM AUTHOR]

Rationale: Extrachromosomal circular DNA is a hallmark of cancer, but its role in shaping the genome heterogeneity of urothelial bladder carcinoma (UBC) remains poorly understood. Here, we comprehensively analyzed the features of extrachromosomal circular DNA in 80 UBC patients. Methods: We performed whole-genome/exome sequencing (WGS/WES), Circle-Seq, single-molecule real-time (SMRT) long-read sequencing of circular DNA, and RNA sequencing (RNA-Seq) on 80 pairs of tumor and AT samples. We used our newly developed circular DNA analysis software, Circle-Map ++ to detect small extrachromosomal circular DNA from Circle-Seq data. Results: We observed a high load and significant heterogeneity of extrachromosomal circular DNAs in UBC, including numerous single-locus and complex chimeric circular DNAs originating from different chromosomes. This includes highly chimeric circular DNAs carrying seven oncogenes and circles from nine chromosomes. We also found that large tumor-specific extrachromosomal circular DNAs could influence genome-wide gene expression, and are detectable in time-matched urinary sediments. Additionally, we found that the extrachromosomal circular DNA correlates with hypermutation, copy number variation, oncogene amplification, and clinical outcome. Conclusions: Overall, our study provides a comprehensive extrachromosomal circular DNA map of UBC, along with valuable data resources and bioinformatics tools for future cancer and extrachromosomal circular DNA research., Competing Interests: Competing Interests: The authors have declared that no competing interest exists., (© The author(s).)