• Genomics & Informatics
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• 제19권2호
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• pp.15.1-15.7
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• 2021

The direction of evolution can estimate based on the variation among nonsynonymous to synonymous substitution. The simulative study investigated the nucleotide sequence of closely related strains of respiratory syndrome viruses, codon-by-codon with maximum likelihood analysis, z selection, and the divergence time. The simulated results, dN/dS > 1 signify that an entire substitution model tends towards the hypothesis's positive evolution. The effect of transition/transversion proportion, Z-test of selection, and the evolution associated with these respiratory syndromes, are also analyzed. Z-test of selection for neutral and positive evolution indicates lower to positive values of dN-dS (0.012, 0.019) due to multiple substitutions in a short span. Modified Nei-Gojobori (P) statistical technique results also favor multiple substitutions with the transition/transversion rate from 1 to 7. The divergence time analysis also supports the result of dN/dS and imparts substantiating proof of evolution. Results conclude that a positive evolution model, higher dN-dS, and transition/transversion ratio significantly analyzes the evolution trend of severe acute respiratory syndrome coronavirus 2, severe acute respiratory syndrome coronavirus, and Middle East respiratory syndrome coronavirus.

• 동의생리병리학회지
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• 제24권3호
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• pp.504-511
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• 2010

Diabetes is a disease that contains a high concentration of glucose in blood and due to defects in either insulin secretion or insulin action. Although the distinctive causes and factors of diabetes have not been clarified, the genetic factors are suggested as a main susceptibility until now. SNP (Single Nucleotide Polymorphism), as the most common genetic variation, has an influence on personal susceptibility for diseases. A nonsynonymous SNP, which changes the amino acid of the protein and its function, is especially important. Therefore, this study hypothesized that there are associations between specific SNPs of the targeted genes. Transcription factor 7-like 2 (TCF7L2) and fat mass and obesity associated (FTO) genes were selected as target genes from the results of genome-wide association and other related research studies. Second, four nonsynonymous SNPs (three in TCF7L2 and one in FTO gene) were selected as target SNPs by using public database of NCBI (National Center for Biotechnology Information). The recruited personnel was classified into three subgroups of diabetes, impaired fasting glucose (IFG) and normal groups. The individual genotypes of each group were analyzed by resequencing. None of genetic variations at four targeted SNP sites was revealed in all samples of this study. However, this study found two new SNPs that were not reported in TCF7L2 gene. One is synonymous SNP, which is heterozygous of C/T and no amino acid change of asparagine/asparagines, was located at c1641 and found in one normal person. Another is nonsynonymous SNP, which is heterozygous of G/A, was located at c1501 and found in two samples. This new discovered nonsynonymous SNP induce the amino acid change from alanine to threonine. Moreover, this new nonsynonymous SNP was found among two persons, one of whom was a diabetes patient and the other one was a person at boundary between IFG and normal, suggesting that this variant might be associated with IFG or diabetes. Even if there is a limitation of sample number for statistical power, this study has an importance due to the discovery of new SNPs. In the future study, a large sample number of diabetes cohort will be needed to investigate the frequency and association with new discovered SNP.

• Journal of Microbiology
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• 제45권1호
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• pp.75-78
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• 2007

Nucleotide and amino acid substitution pattern in vif gene of the Korean clade of HIV-1 isolated from Koreans were analyzed using consensus sequences. At nucleotide level, transition/transversion substitution ratio was 1.88, and nonsynonymous/synonymous substitution ratio was 2.67, suggesting a divergent evolution in the Korean clade. At amino acid level, there were 17 substitutions and $G{\rightarrow}E$ substitution at position 37 may be responsible for change in predicted secondary structure.