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Summary: Plastids and mitochondria are endosymbiotic organelles that store genetic information. The genomes of these organelles generally exhibit contrasting patterns regarding genome architecture and genetic content. However, they have similar genetic features in Selaginellaceae, and little is known about what causes parallel evolution. Here, we document the multipartite plastid genomes (plastomes) and the highly divergent mitochondrial genomes (mitogenomes) from spikemoss obtained by combining short‐ and long‐reads. The 188‐kb multipartite plastome has three ribosomal operon copies in the master genomic conformation, creating the alternative subgenomic conformation composed of 110‐ and 78‐kb subgenomes. The long‐read data indicated that the two different genomic conformations were present in almost equal proportions in the plastomes of Selaginella nipponica. The mitogenome of S. nipponica was assembled into 27 contigs with a total size of 110 kb. All contigs contained directly arranged repeats at both ends, which introduced multiple conformations. Our results showed that plastomes and mitogenomes share high tRNA losses, GC‐biased nucleotides, elevated substitution rates and complicated organization. The exploration of nuclear‐encoded organelle DNA replication, recombination and repair proteins indicated that, several single‐targeted proteins, particularly plastid‐targeted recombinase A1, have been lost in Selaginellaceae; conversely, the dual‐targeted proteins remain intact. According to the reported function of recombinase A1, we propose that the plastomes of spikemoss often fail to pair homologous sequences during recombination, and the dual‐targeted proteins play a key role in the convergent genetic features of plastomes and mitogenomes. Our results provide a distinctive evolutionary pattern of the organelle genomes in Selaginellaceae and evidence of their convergent evolution. Significance Statement: Plastid and mitochondrial genomes usually exhibit contrasting patterns of conserved plastid genomes and diverged mitochondrial genomes. Here, we document that both the organelle genomes in Selaginellaceae exhibit parallel genetic features. In addition, we explore which factor is likely responsible for the unconventional features of plastid genomes, and convergent evolution of the two organelle genomes. This study helps explain the distinctive evolutionary patterns of organelle genomes in Selaginellaceae, and advance our current understanding of organelle genomics. [ABSTRACT FROM AUTHOR]

Severe fever with thrombocytopenia syndrome (SFTS) was firstly identified in mainland China in 2009 and the geographic distribution has expanded in recent years. In this study, we constructed ecological niche models (ENM) of SFTS with meteorological factors, environmental factor, and density of domestic animals using MaxEnt. We found four significant associated factors including altitude, yearly average temperature, yearly accumulated precipitation, and yearly average relative humidity which accounted for 94.1% percent contribution. SFTS occurrence probability was high when altitude was between −100 m and 100 m, and the probability was nearly 0 when altitude was beyond 3000 m. Response curves of SFTS to the yearly average temperature, yearly accumulated precipitation, and yearly average relative humidity were all reversed V-shape. SFTS occurrence probability was high where the yearly average temperature, yearly accumulated precipitation, and yearly relative humidity were 12.5–17.5 °C, 700–2250 mm and 63–82%, respectively. ENMs predicted that the potential high-risk areas were mainly distributed in eastern areas and central areas of China. But there were some predicted potential high-risk areas where no SFTS case was reported up to date. More researches should be done to make clear whether SFTS case had occurred in these areas. Unlabelled Image • We firstly constructed ENMs based on national SFTS data of China using MaxEnt. • Altitude, temperature, and precipitation contributed greatly to SFTS spatial distribution. • SFTS occurrence probability was high when these factors were 12.5–17.5 °C, 700–2250 mm and 63–82%. • In contrast to ENMs prediction, some predicted high-risk areas have no SFTS cases reported yet. [ABSTRACT FROM AUTHOR]

Circular RNAs (circRNAs) are potential biomarkers and therapeutic targets of coronary artery disease due to their high stability, covalently closed structure. And implied roles in gene regulation. The aim of this study was to identify and characterize circRNAs from human coronary arteries. Epicardial coronary arteries were removed during the autopsy of an 81-year-old man who died from heart attack. The natural history and histological classification of atherosclerotic lesions in coronary artery segments were analyzed by hematoxylin and eosin staining, and their circRNA expression profiles were characterized by RNA sequencing. RNA sequencing identified 1259 annotated and 381 novel circRNAs. Combined with the results of histologic examination, intersection analysis identified 54 upregulated and 12 downregulated circRNAs, representing 4.0% of the total number. Coronary artery segments with or without severe atherosclerosis showed distinctly different circRNA profiles on the basis of hierarchical clustering. Our results suggest that these 66 circRNAs contribute to the pathology underlying coronary artery atherosclerosis and may serve as diagnostic or therapeutic targets in coronary artery disease., Competing Interests: None., (AJTR Copyright © 2019.)

Aim: Anaplastic thyroid carcinoma (ATC) is the most lethal thyroid malignancy. Identification of novel drug targets is urgently needed., Materials & Methods: We re-analyzed several GEO datasets by systematic retrieval and data merging. Differentially expressed genes (DEGs) were filtered out. We also performed pathway enrichment analysis to interpret the data. We predicted key genes based on protein-protein interaction networks, weighted gene co-expression network analysis and genes' cancer/testis expression pattern. We also further characterized these genes using data from the Cancer Genome Atlas (TCGA) project and gene ontology annotation., Results: Cell cycle-related pathways were significantly enriched in upregulated genes in ATC. We identified TRIP13 , DLGAP5 , HJURP , CDKN3 , NEK2 , KIF15 , TTK , KIF2C , AURKA and TPX2 as cell cycle-related key genes with cancer/testis expression pattern. We further uncovered that most of these putative key genes were critical components during chromosome segregation., Conclusion: We predicted several key genes harboring potential therapeutic value in ATC. Cell cycle-related processes, especially chromosome segregation, may be the key to tumorigenesis and treatment of ATC., Competing Interests: The authors declare there are no competing interests.

Aim: To explore the relationship of clinicopathological features and the proteins of C-met expression in the prognosis of cholangiocarcinoma., Methods: Clinical data and the completed follow-up information of patients with cholangiocarcinoma who underwent cholangiocarcinoma operation from January 2004 to December 2010 were analyzed retrospectively. The relationship of clinicopathological features and C-met in the prognosis of the patients was analyzed., Results: Patients with high expression of C-met had significantly shorter overall survival than those with low expression of C-met, the difference being statistically significant (P = .003). Patients with high C-met expression had significantly shorter disease-free survival time than those with low expression of C-met, the difference being statistically significant (P = .009). By COX multivariate analysis, high C-met expression in tumor tissues was an independent risk factor in predicting overall survival and disease-free survival for patients with cholangiocarcinoma (P = .038, .048, relative risk = 1.390, 1.427)., Conclusion: Patients with high C-met expression in cancer tissues had shorter disease-free survival and overall survival. High expression of C-met is an independent risk factor for overall survival and disease-free survival., (© The Author(s) 2015.)

Background: Cholangiocarcinoma is one of the most common malignancies in China. Surgical resection is the only treatment option; however, diagnosis at advanced stage precludes surgery. Comprehensive knowledge of prognostic markers is missing. Hence, the aim of this study was to determine clinicopathological indexes that would be indicative of prognosis in post-operative cases of cholangiocarcinoma., Material and Methods: A retrospective analysis of 293 cases of cholangiocarcinoma patients attending the 301 Military Hospital in Beijing, China between January 2004 and December 2010 were included in the study. The patients had follow-up history until August 2012. Cox proportional hazards model analysis was performed to identify indexes of prognosis. All indicators were analyzed by univariate and multivariate analysis., Results: The median follow-up time was 55.90 months, with recurrence and metastasis in 162 cases (55.3%) and death in 223 cases (76.1%). The 1-year, 3-year, and 5-year survival rates were 71.7%, 38.2%, and 10.6%, respectively. The independent risk factors of overall survival were degree of tumor differentiation, TNM stage, surgical margin, intraoperative blood transfusion, tumor location, alkaline phosphatase levels in blood, and relapse., Conclusions: Good prognosis in cholangiocarcinoma patients is indicated by highly differentiated tumor, early stages of TNM staging, no resection margin invaded, no intraoperative blood transfusion, intrahepatic tumor, normal alkaline phosphatase levels, and no relapse.

Aim: To explore the relationship of clinicopathological features and the distribution of neutrophils in the tumor microenvironment with the prognosis of cholangiocarcinoma., Methods: Two hundred and fifty-four formalin-fixed and paraffin embedded tissue blocks were analyzed, including tissues from cholangiocarcinoma (n = 254), and tumor adjacent tissues (n = 238). Tissue sections were stained for CD15 using immunohistochemical staining. CD15 expression was detected to identify the distribution of neutrophils in the local tumor microenvironment. The neutrophil density of the tumor tissues and the adjacent tumor tissues was detected to reflect their inflammatory status. Clinical data and follow-up information of cholangiocarcinoma patients who underwent surgery from January 2004 to December 2010 were analyzed retrospectively. The relationship between clinicopathological features and the distribution of neutrophils with prognosis of the patients were analyzed., Results: The positive expression level of CD15 was only significantly related to the TNM stage. CD15 expression was higher in tumor tissues than in adjacent tissues (73.6% vs 54.6%), with significant differences. Patients with high expression of CD15 had significantly shorter overall survival (OS) than those with low expression of CD15 (median overall survival time 39.77 mo vs 16.87 mo, P = 0.008). Patients with high CD15 expression had significantly shorter disease free survival time (DFS) than those with low expression of CD15 (median DFS 38.27 mo vs 16.83 mo, P = 0.029). COX multivariate analysis indicated that high CD15 expression in tumor tissues was an independent risk factor for predicting OS for patients with cholangiocarcinoma [P = 0.012, relative risk (RR) = 1.601], but it was not an independent risk factor for predicting DFS (P = 0.073, RR = 1.462)., Conclusion: Patients with high CD15 expression in cancer tissues had shorter DFS and OS. High expression of CD15 is an independent risk factor for OS.