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RISS 인기검색어
- 검색키워드
- 저자 : Myeongji Cho (검색결과 8 건)
- 무료
- 기관 내 무료
- 유료
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Construction of a Genetic Information Database for Analysis of Oncolytic Viruses
Myeongji Cho,Hyeon Seok Son,Hayeon Kim 한국인터넷방송통신학회 2020 Journal of Advanced Smart Convergence Vol.9 No.1
Oncolytic viruses are characterized by their ability to selectively kill cancer cells, and thus they have potential for application as novel anticancer agents. Despite an increase in the number of studies on methodologies involving oncolytic viruses, bioinformatic studies generating useful data are lacking. We constructed a database for oncolytic virus research (the oncolytic virus database, OVDB) by integrating scattered genetic information on oncolytic viruses and proposed a systematic means of using the biological data in the database. Our database provides data on 14 oncolytic viral strains and other types of viruses for comparative analysis. We constructed the OVDB using the basic local alignment search tool, and therefore can provides genetic information on highly homologous oncolytic viruses. This study contributes to facilitate systematic bioinformatics research, providing valuable data for development of oncolytic virus-based anticancer therapies.
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Construction of a Genetic Information Database for Analysis of Oncolytic Viruses
Cho, Myeongji,Son, Hyeon Seok,Kim, Hayeon The Institute of Internet 2020 International journal of advanced smart convergenc Vol.9 No.1
Oncolytic viruses are characterized by their ability to selectively kill cancer cells, and thus they have potential for application as novel anticancer agents. Despite an increase in the number of studies on methodologies involving oncolytic viruses, bioinformatic studies generating useful data are lacking. We constructed a database for oncolytic virus research (the oncolytic virus database, OVDB) by integrating scattered genetic information on oncolytic viruses and proposed a systematic means of using the biological data in the database. Our database provides data on 14 oncolytic viral strains and other types of viruses for comparative analysis. We constructed the OVDB using the basic local alignment search tool, and therefore can provides genetic information on highly homologous oncolytic viruses. This study contributes to facilitate systematic bioinformatics research, providing valuable data for development of oncolytic virus-based anticancer therapies.
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Analysis of evolutionary and genetic patterns in structural genes of primate lentiviruses
Cho Myeongji,Min Xianglan,Son Hyeon S. 한국유전학회 2022 Genes & Genomics Vol.44 No.7
Background: Primate lentiviruses (HIV1, HIV2, and Simian immunodeficiency virus [SIV]) cause immune deficiency, encephalitis, and infectious anemia in mammals such as cattle, cat, goat, sheep, horse, and puma. Objective: This study was designed and conducted with the main purpose of confirming the overall codon usage pattern of primate lentiviruses and exploring the evolutionary and genetic characteristics commonly or specifically expressed in HIV1, HIV2, and SIV. Methods: The gag, pol, and env gene sequences of HIV1, HIV2, and SIV were analyzed to determine their evolutionary relationships, nucleotide compositions, codon usage patterns, neutrality, selection pressure (influence of mutational pressure and natural selection), and viral adaptation to human codon usage. Results: A strong 'A' bias was confirmed in all three structural genes, consistent with previous findings regarding HIV. Notably, the ENC-GC3s plot and neutral evolution analysis showed that all primate lentiviruses were more affected by selection pressure than by mutation caused by the GC composition of the gene, consistent with prior reports regarding HIV1. The overall codon usage bias of pol was highest among the structural genes, while the codon usage bias of env was lowest. The virus groups showing high codon bias in all three genes were HIV1 and SIVcolobus. The codon adaptation index (CAI) and similarity D(A, B) values indicated that although there was a high degree of similarity to human codon usage in all three structural genes of HIV, this similarity was not caused by translation pressure. In addition, compared with HIV1, the codon usage of HIV2 is more similar to the human codon usage, but the overall codon usage bias is lower. Conclusion: The origin viruses of HIV (SIVcpz_gor and SIVsmm) exhibit greater similarity to human codon usage in the gag gene, confirming their robust adaptability to human codon usage. Therefore, HIV1 and HIV2 may have evolved to avoid human codon usage by selection pressure in the gag gene after interspecies transmission from SIV hosts to humans. By overcoming safety and stability issues, information from codon usage analysis will be useful for attenuated HIV1 vaccine development. A recoded HIV1 variant can be used as a vaccine vector or in immunotherapy to induce specific innate immune responses. Further research regarding HIV1 dinucleotide usage and codon pair usage will facilitate new approaches to the treatment of AIDS.
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Myeongji Cho,Hayeon Kim,손현석 한국유전학회 2021 Genes & Genomics Vol.43 No.4
Background The large tumor antigen (LT-Ag) and major capsid protein VP1 are known to play important roles in determining the host-specifc infection properties of polyomaviruses (PyVs). Objective The objective of this study was to investigate the physicochemical properties of amino acids of LT-Ag and VP1 that have important efects on host specifcity, as well as classifcation techniques used to predict PyV hosts. Methods We collected and used reference sequences of 86 viral species for analysis. Based on the clustering pattern of the reconstructed phylogenetic tree, the dataset was divided into three groups: mammalian, avian, and fsh. We then used random forest (RF), naïve Bayes (NB), and k-nearest neighbors (kNN) algorithms for host classifcation. Results Among the three algorithms, classifcation accuracy using kNN was highest in both LT-Ag (ACC=98.83) and VP1 (ACC=96.51). The amino acid physicochemical property most strongly correlated with host classifcation was charge, followed by solvent accessibility, polarity, and hydrophobicity in LT-Ag. However, in VP1, amino acid composition showed the highest correlation with host classifcation, followed by charge, normalized van der Waals volume, and solvent accessibility. Conclusions The results of the present study suggest the possibility of determining or predicting the host range and infection properties of PyVs at the molecular level by identifying the host species of active and emerging PyVs that exhibit diferent infection properties among diverse host species. Structural and biochemical diferences of LT-Ag and VP1 proteins in host species that refect these amino acid properties can be considered primary factors that determine the host specifcity of PyV.
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