• Applied Biological Chemistry
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• v.36 no.6
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• pp.525-532
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• 1993

To characterize the prolamines in rice cultivars, the complete coding sequences of 17 prolamine genes from the database were analyzed. According to the phylogenic analysis of the sequences, these genes could be classified into 4 groups, Group I to IV. The multiple alignment of the deduced amino acid sequences revealed that the four groups differ from one another in chain length caused by deletion of short internal amino acids or carboxyl terminal fragments. Each group was also found to have different amino acid composition with 1, 4, 10 and 30% of sulfur containing amino acids (methionine and cysteine) in Group I to IV prolamines, respectively. Also the isoelectric points of these groups showed the different values of 9.2, 8.2, 6.7 and 7.4. Finally, from the analysis of codon usage pattern of prolamine genes, the codon usage for arginine, serine, threonine, isoleucine, asparagine, aspartic acid, glutamic acid and cysteine were higly biased. In the analysis of the codon usage pattern, the relation of the fraction of G/C ending codons to effective codon numbers suggests the different translational efficiency in the expression of the prolamine multigenes.

• Microbiology and Biotechnology Letters
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• v.47 no.3
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• pp.449-458
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• 2019

Hepatitis B treatments using immune therapy are gaining interest because of the improvements in dendritic cell performance for antigen presentation, which induces an appropriate immune response and raises patient survival rates. This research aims to produce a significant amount of the HBcAg antigen, which can induce an immune response and have a curative effect on HBV infection. In this study, the HBV subgenotype B3 of the HBcAg gene was used, which is dominant in Indonesia. Further, Lactococcus lactis bacteria was used as the host because of its safety and tightly regulated protein expression. The codon usage for the HBcAg gene was optimized to improve protein expression in L. lactis, which is important because a codon is not random between species. The HBcAg gene is attached to a pNZ8148 plasmid and transformed into the L. lactis NZ3900 expression host. The results confirm that a positive protein band (21 kDa) in two fractions of purified HBcAg was recognized by both western blotting and dot blot hybridization, even if the HBcAg optimized codon has higher GC contents than that suggested for L. lactis expression. Overall, this research strengthens the broad use of L. lactis bacteria for any protein expression, including higher protein expression of codon optimized HBcAg gene compared to non-optimized genes. Furthermore, the improvement in the codon optimization of the HBcAg gene significantly increases the total protein expression by 10-20%, and the expression level of the codon optimized HBcAg increases 1.5 to 3.2-times that of the native HBcAg.

• Parasites, Hosts and Diseases
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• v.55 no.2
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• pp.175-183
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• 2017

Codon usage bias (CUB) is a unique property of genomes and has contributed to the better understanding of the molecular features and the evolution processes of particular gene. In this study, genetic indices associated with CUB, including relative synonymous codon usage and effective numbers of codons, as well as the nucleotide composition, were investigated in the Clonorchis sinensis tyrosinase genes and their platyhelminth orthologs, which play an important role in the eggshell formation. The relative synonymous codon usage patterns substantially differed among tyrosinase genes examined. In a neutrality analysis, the correlation between $GC_{12}$ and $GC_3$ was statistically significant, and the regression line had a relatively gradual slope (0.218). NC-plot, i.e., $GC_3$ vs effective number of codons (ENC), showed that most of the tyrosinase genes were below the expected curve. The codon adaptation index (CAI) values of the platyhelminth tyrosinases had a narrow distribution between 0.685/0.714 and 0.797/0.837, and were negatively correlated with their ENC. Taken together, these results suggested that CUB in the tyrosinase genes seemed to be basically governed by selection pressures rather than mutational bias, although the latter factor provided an additional force in shaping CUB of the C. sinensis and Opisthorchis viverrini genes. It was also apparent that the equilibrium point between selection pressure and mutational bias is much more inclined to selection pressure in highly expressed C. sinensis genes, than in poorly expressed genes.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.8
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• pp.3505-3508
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• 2015

Background: Ras genes are thought to play an important role in human cancer since they have been found to be activated frequently in several types of tumors including breast cancer, where the overall incidence of K-RAS oncogene activation is 0-10%. Evaluation of K-RAS gene not only for mutational frequency but also for mutation types in this downstream signaling gene pathway is necessary to determine the mechanisms of action. The present study was conducted to test the hypothesis that K-RAS activation is involved in breast cancer risk of south Indian population. Materials and Methods: A total of 70 paired pathologically confirmed tumor and non-tumor tissues from the same breast cancer patients were analysed for most common K-RAS mutations of codon 12,13 and 61 by polymerase chain reaction followed by restriction digestion and direct nucleotide sequencing method. Results: We found that a high rate of homozygous and heterozygous mutations of codon 12, but not codon 13 and 61, may influence the invasive ductal carcinoma of breast risk in this study. Conclusions: Our study indicated that only codon 12 may be involved in initiating breast carcinogenesis in India.

• The Journal of the Convergence on Culture Technology
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• v.5 no.1
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• pp.13-20
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• 2019

This study aims to study the codes that can code the Sijo's emotional codes into AI and use them in literature therapy. In this study, we conducted emotional coding of the Sijo Crying Cuckoo at the Empty Mountain. As a result, the Emotion Codon was able to indicate the state of sadness catharsis. This implanting of the Sijo's emotional codes into Emotion Codon is like implanting human emotions into AI. If the basic emotion codes are implanted in the Emotion Codon and induced of AI's self-learning, We think AI can combine various emotions that occur in the human body. AI can then replace human emotions, which can be useful in treating of human emotions. It is believed that continuing this study will induce human emotions to heal the mind and spirit.

• Communications for Statistical Applications and Methods
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• v.22 no.6
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• pp.575-587
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• 2015

The development in data collection techniques results in high dimensional data sets, where discrimination is an important and commonly encountered problem that are crucial to resolve when high dimensional data is heterogeneous (non-common variance covariance structure for classes). An example of this is to classify microbial habitat preferences based on codon/bi-codon usage. Habitat preference is important to study for evolutionary genetic relationships and may help industry produce specific enzymes. Most classification procedures assume homogeneity (common variance covariance structure for all classes), which is not guaranteed in most high dimensional data sets. We have introduced regularized elimination in partial least square coupled with QDA (rePLS-QDA) for the parsimonious variable selection and classification of high dimensional heterogeneous data sets based on recently introduced regularized elimination for variable selection in partial least square (rePLS) and heterogeneous classification procedure quadratic discriminant analysis (QDA). A comparison of proposed and existing methods is conducted over the simulated data set; in addition, the proposed procedure is implemented to classify microbial habitat preferences by their codon/bi-codon usage. Five bacterial habitats (Aquatic, Host Associated, Multiple, Specialized and Terrestrial) are modeled. The classification accuracy of each habitat is satisfactory and ranges from 89.1% to 100% on test data. Interesting codon/bi-codons usage, their mutual interactions influential for respective habitat preference are identified. The proposed method also produced results that concurred with known biological characteristics that will help researchers better understand divergence of species.

• Clinical and Experimental Reproductive Medicine
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• v.29 no.4
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• pp.311-315
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• 2002

Objective: The present study was performed to evaluate the association o f p53 codon 72 polymorphism and endometriosis. Materials and Methods: We investigate 74 women who were operated for endometriosis and 93 women who had no endometriotic lesion proved by operation. Polymerase chain reaction was used to detect p53 codon polymorphisms. Result: We have found no significant difference between endometriosis and control group in the p53 codon polymorphism. The respective proportion of arginine homozygotes, heterozygotes and proline homozygotes in endometriosis group were 18.9%, 62.2% and 18.9%, respectively, and were 12.9%, 75.2% and 11.9%, respective in the group without endometriosis. Conclusion: Endometriosis is not associated with p53 polymorphism in Korean endometriosis patients.

• The Journal of the Institute of Internet, Broadcasting and Communication
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• v.17 no.2
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• pp.95-104
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• 2017

We investigate the God gate olleh of the largest tomb, pyramid, in the world which is scattered in Jeju Island and construct link which is connecting Jeju people's custom to modern science. The three sacred gates and the two tombs are connected to the olegil space. In this space, the principle of complementarity in which coexistence exist between life and death is hidden in Jeju culture. It is a question and wait. Contrarily, the opposite is complementary. (Contraria Sunt Complementa Latin) This refers to the relationship of each other in relation to one another and in a mutually dependent relationship. Seminal vesicles are used as basic logic in DNA codon of human body as well as communication principle.

• Journal of Life Science
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• v.16 no.3 s.76
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• pp.415-419
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• 2006

The epoxide hydrolase (EH) of Rhodotorula glutinis which has a high enantioselectivity against aromatic epoxide substrates was expressed to high levels in Escherichia coli based on codon usage. We analysed the Preference of codon usage between the yeast, R. glutinis, and bacteria, E. coli. E. coli, Rosetta(DE3)pLysS, harbors pRARE plasmid with tRNA genes for rare-codons was employed as a host strain. The recombinant E. coli expressing R. glutinis EH showed an enhanced enantioselective hydrolysis activity toward racemic styrene oxide. Enantiopure (S)-styrene oxide with a high enantiopurity of 99% ee (enantiomeric excess) was obtained from racemic substrates.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.12
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• pp.6055-6057
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• 2012

The mismatch repair system (MMR) is a post-replicative DNA repair mechanism whose defects can lead to cancer. The MSH3 protein is an essential component of the system. We postulated that MSH3 gene polymorphisms might therefore be associated with prostate cancer (PC). We studied MSH3 codon 222 and MSH3 codon 1036 polymorphisms in a group of Iranian sporadic PC patients. A total of 60 controls and 18 patients were assessed using the polymerase chain reaction and single strand conformational polymorphism. For comparing the genotype frequencies of patients and controls the chi-square test was applied. The obtained result indicated that there was significantly association between G/A genotype of MSH3 codon 222 and G/G genotype of MSH3 codon 1036 with an increased PC risk (P=0.012 and P=0.02 respectively). Our results demonstrated that MSH3 codon 222 and MSH3 codon 1036 polymorphisms may be risk factors for sporadic prostate cancer in the Iranian population.