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Nucleotide composition and synonymous codon usage of open reading frames in Norovirus GII.4 variants
Wei Dan Yan Jin Zizhong Tang Yongmin Li 《Journal of biomolecular structure & dynamics》2020,38(16):4764-4773
AbstractNorovirus GII.4 variants, a genotype in genogroup II belonging to the genus Norovirus, is a single-strand positive sense RNA containing three open reading frames (ORF1, ORF2 and ORF3) and is the most important pathogen causing nonbacterial gastroenteritis outbreaks. By using bioinformatic softwares such as Codon W, SPSS and so on, a total of 292 strains of the viruses isolated from 1974 to 2016 were analyzed for nucleotide composition and synonymous codon usage in each ORF. The result shows that it is enriched for A over the other bases in nucleotide composition, G behind the other bases in the 3rd site of all synonymous codons in the three ORFs. The patterns of nucleotide composition and codon bias of ORF2 are similar to those of ORF3 and different from those of ORF1. There are generally UpA motif and CpG motif in the codons with the lowest proportion. Correspondence analysis indicates that the codon usage may be changing over a certain time period for ORF1 in 2006 and 2012, ORF2 in 2012, and ORF3 in 2013. ENC (effective number of codons) plot and other analyses indicate that both natural selection and mutational pressure play partly roles in the ORFs, but natural selection is more important for ORF2 and ORF3. Besides, we also found all optimal codons in the ORFs. The study provides a basic understanding of the mechanism for norovirus GII.4 codon usage bias. Abbreviations ORF Open Reading Frame ENC Effective Number of Codons COA correspondence analysis RSCU Relative Synonymous Codon Usage CAI Codon Adaptation Index CBI Codon Bias Index Fop frequency of optimal codons L_sym number of synonymous codons L_aa length amino acids GRAVY grand average of hydropathicity Aroma aromaticity Communicated by Ramaswamy H. Sarma 相似文献
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Kamal Osama M. Shah Sayyed Hamad Ahmad Li Yan Hou Xilin Li Ying 《Molecular biology reports》2020,47(9):6887-6897
Molecular Biology Reports - The objective of the present work was the selection of cultivar, suitable medium and explant type for callus, root production, ascorbic acid, total ascorbic acid,... 相似文献
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Li Wanting Ye Anqi Ao Luyao Zhou Lin Yan Yunyi Hu Yahui Fang Weirong Li Yunman 《Neurochemical research》2020,45(10):2258-2277
Neurochemical Research - Stroke is the fifth leading cause of death worldwide and is a main cause of disability in adults. Neither currently marketed drugs nor commonly used treatments can promote... 相似文献
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Tang Xiangming Yan Kunning Wang Yingge Wang Yaping Chen Hongmei Xu Jiang Lu Yaoyao Wang Xiaohong Liang Jingyan Zhang Xinjiang 《Neurochemical research》2020,45(4):837-850
Neurochemical Research - Brain injury has been proposed as the major cause of the poor outcomes associated with intracerebral hemorrhage (ICH). Emerging evidence indicates that the nuclear... 相似文献
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Qiuxia Cui Jianing Tang Dan Zhang Deguang Kong Xing Liao Jiangbo Ren Yan Gong Conghua Xie Gaosong Wu 《Journal of cellular biochemistry》2020,121(8-9):3923-3934
Breast cancer is a popularly diagnosed malignant tumor. Genomic profiling studies suggest that breast cancer is a disease with heterogeneity. Chemotherapy is one of the chief means to treat breast cancer, while its responses and clinical outcomes vary largely due to the conventional clinicopathological factors and inherent chemosensitivity of breast cancer. Using the least absolute shrinkage and selection operator (LASSO) Cox regression model, our study established a multi-mRNA-based signature model and constructed a relative nomogram in predicting distant-recurrence-free survival for patients receiving surgery and following chemotherapy. We constructed a signature of eight mRNAs (IPCEF1, SYNDIG1, TIGIT, SPESP1, C2CD4A, CLCA2, RLN2, and CCL19) with the LASSO model, which was employed to separate subjects into groups with high- and low-risk scores. Obvious differences of distant-recurrence-free survival were found between these two groups. This eight-mRNA-based signature was independently associated with the prognosis and had better prognostic value than classical clinicopathologic factors according to multivariate Cox regression results. Receiver operating characteristic results demonstrated excellent performance in diagnosing 3-year distant-recurrence by the eight-mRNA signature. A nomogram that combined both the eight-mRNA-based signature and clinicopathological risk factors was constructed. Comparing with an ideal model, the nomograms worked well both in the training and validation sets. Through the results that the eight-mRNA signature effectively classified patients into low- and high-risk of distant recurrence, we concluded that this eight-mRNA-based signature played a promising predictive role in prognosis and could be clinically applied in breast cancer patients receiving adjuvant chemotherapy. 相似文献
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