• Journal of Microbiology and Biotechnology
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• 제26권11호
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• pp.1972-1982
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• 2016

Influenza A virus is a single-stranded RNA virus with a genome of negative polarity. Owing to the antigenic diversity and cross concrete shift, an immense number of novel strains have developed astronomically over the years. The present work deals with the codon utilization partialness among five different influenza A viruses isolated from human hosts. All the subtypes showed the homogeneous pattern of nucleotide utilization with a little variation in their utilization frequencies. A lower bias in codon utilization was observed in all the subtypes as reflected by higher magnitudes of an efficacious number of codons. Dinucleotide analysis showed very low CpG utilization and a high predilection of A/T-ending codons. The H5N1 subtype showed noticeable deviation from the rest. Codon pair context analysis showed remarkable depletion of NNC-GNN and NNT-ANN contexts. The findings alluded towards GC-compositional partialness playing a vital role, which is reflected in the consequential positive correlation between the GC contents at different codon positions. Untangling the codon utilization profile would significantly contribute to identifying novel drug targets that will pacify the search for antivirals against this virus.

• Asian Pacific Journal of Cancer Prevention
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• 제13권2호
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• pp.511-516
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• 2012

Background: We investigated the association between polymorphisms in the $p53$ tumor suppressor gene and breast cancer risk in women especially in the Southern part of India. Methods: Genotyping was performed for 50 breast cancer women and 50 controls to determine the status of $p53$ exon 4 codon 72 polymorphism and exon 7 codon 249 mutation and their possible role in breast cancer risk. Results: Frequency of Arg/Arg at codon 72 was 18% in controls and 28% in patients, Arg/Pro frequency was 56% and 66%, Pro/Pro genotype was 8% in controls and 8% in patients. No significance was observed for breast cancer risk with either Arg/Arg or Pro/Pro genotype in codon 72 polymorphism. Similarly, mutation analysis of exon 7 codon 249 revealed that 72% of breast cancer patients have mutation, which is not statistically significant. However, there is a strong association between increase in exon 7 codon 249 mutation and exposure to pollution. Conclusion: The results suggested that there is no risk for exon 4 with Arg/Arg or Pro/Pro polymorphisms in the $p53$ gene and there is no strong correlation between breast cancer patients and mutation in exon 7 codon 249 in South Indian women.

• Asian Pacific Journal of Cancer Prevention
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• 제13권7호
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• pp.3047-3052
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• 2012

The enzyme encoded by the MGMT gene is involved in the repair of alkylated lesions formed in DNA by carcinogenic nitrosamines. Since dietary items consumed by the Kashmiri population contain high concentrations of these agents, it is biologically plausible that MGMT polymorphic variants may be associated with their risk of esophageal cancer. The present study was performed to assess whether non-synonymous SNPS at codon Leu84Phe and codon Ileu143Val of the MGMT gene, close to the active site of the protein, might be linked to predisposition of Kashmiris to esophageal cancer. Genotyping was carried out by polymerase chain reaction-restriction fragment length polymorphism on 92 cases and 77 healthy controls. Codon 84 and codon 143 SNPs of the MGMT gene were not associated with any increase in risk. While the frequency of the Phe allele at codon 84 in cases was (0.16), slightly higher than controls (0.12), the difference was not statistically significant. Similarly, the frequency of Valine allele in cases at codon 143 (0.08) and controls (0.09) was nearly equal. Moreover, no significant association of MGMT genotypes with the clinicopatholgic variables of esophageal cancer patients was observed. In conclusion, MGMT variants at codon 84 and codon143 may not be involved in the susceptibility of the Kashmiri population to esophageal cancer.

• Genomics & Informatics
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• 제15권1호
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• pp.38-47
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• 2017

Research into new methods for identifying highly expressed genes in anonymous genome sequences has been going on for more than 15 years. We presented here an alternative approach based on modified score of relative codon usage bias to identify highly expressed genes in crenarchaeal genomes. The proposed algorithm relies exclusively on sequence features for identifying the highly expressed genes. In this study, a comparative analysis of predicted highly expressed genes in five crenarchaeal genomes was performed using the score of Modified Relative Codon Bias Strength (MRCBS) as a numerical estimator of gene expression level. We found a systematic strong correlation between Codon Adaptation Index and MRCBS. Additionally, MRCBS correlated well with other expression measures. Our study indicates that MRCBS can consistently capture the highly expressed genes.

• Journal of Microbiology and Biotechnology
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• 제13권4호
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• pp.584-590
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• 2003

The xylA gene of Bacillus stearothermophilus No. 236 encoding ${\beta}-xylosidase$, a major xylanolytic enzyme, was previously cloned and sequenced by the present authors. Sequence analysis indicated that translation of the xylA gene was initiated from the noncanonical initiation codon UUG, confirmed by analyzing three different amber (UAG) mutants of the xylA gene. In the present study, the UUG initiation codon was mutated into AUG or GUG, and the effects of the mutations on the XylA synthesis were examined. The AUG initiation codon was found to direct the highest level of ${\beta}-xylosidase$ synthesis; three-fold and fourteen-fold more enzyme activity than the UUG codon in E. coli and B. subtilis cells, respectively. Surprisingly, contrary to other systems reported to date, the UUG start codon was found next to AUG in the relative order of translational efficiency in both organisms. In addition, a greater abundance of the xylA mRNA was detected with the AUG start codon in both of these host cells than with GUG or UUG. Northern blot and Toeprint assays revealed that this was due to enhanced stability of mRNA with the AUG initiation codon. As expected, the ${\beta}-xylosidase$ protein level in the bacterial cells containing mRNA with the AUC start codon was also much higher than the levels with the other two different mRNAs.

• International Journal of Advanced Culture Technology
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• 제5권2호
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• pp.9-18
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• 2017

The purpose of this study is to find out how to use emotional activity rate in sentence. The aim is to estimate the Emotion-Codon status of emotion-DNA wiggling as well as the sequence of codons in which amino acids of human body are spread. It is as if the amino acids are translated from the DNA of the human body, and the emotions that cooperate with each other are diversified and refined. Through these attempts, we anticipate the change of emotions by literary works and present the direction of the synapse working and the direction of the encoding. Therefore, this study analyzed the emotional activity of Rated Emotion-Codon, which works as Rated Sijo. At this time, the emotional change in the human body, in which the sentence is more clearly pronounced, is predicted and detected. This result shows how emotions can activate the human body. This state of activation is an indicator of how much the sentence pushes the physiological action of the human body. It is judged that Codon is constructed precisely for the activation of the rated Sijo additive definition by this index. Our result is evidenced by the fact that three sentences of Rated Sijo show an array with the same rating as the Rated Codon's, The first sentence fuses with the sentiment between the second sentence and the third sentence of Rated Sijo. The emotional symbols between the sentence symbols "A, U, J, L" in the first base of the Codon table and the sentences fusing between the sentences of the first sentence and the third sentence are "A, U, J, L". The emotional symbols between the sentences flowing in the second base of the Codon table and between the sentences of the first sentence and the second sentence are structured in the third base of the Codon table as "A, U, J, L". The Rated Sijo, which is resiliently and precisely assigned to the human body's Rated Emotion-Codon, will require a rich experience in our Rated Life.

• Journal of Microbiology and Biotechnology
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• 제29권2호
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• pp.304-310
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• 2019

Interleukin-21 is a common ${\gamma}$-chain cytokine that controls the immune responses of B cells, T cells, and natural killer cells. Targeting IL-21 to strengthen the immune system is promising for the development of vaccines as well as anti-infection and anti-tumor therapies. However, the practical application of IL-21 is limited by the high production cost. In this study, we improved IL-21 production by codon optimization and selection of appropriate signal peptide in CHO-K1 cells. Codon-optimized or non-optimized human IL-21 was stably transfected into CHO-K1 cells. IL-21 expression was 10-fold higher for codon-optimized than non-optimized IL-21. We fused five different signal peptides to codon-optimized mature IL-21 and evaluated their effect on IL-21 production. The best result (a 3-fold increase) was obtained using a signal peptide derived from human azurocidin. Furthermore, codon-optimized IL-21 containing the azurocidin signal peptide promoted $IFN-{\gamma}$ secretion and STAT3 phosphorylation in NK-92 cells similar to codon-optimized IL-21 containing original signal peptide. Collectively, these results indicate that codon optimization and azurocidin signal peptides provide an efficient approach for the high-level production of IL-21 as a biopharmaceutical.

• Journal of Plant Biotechnology
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• 제49권1호
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• pp.46-60
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• 2022

The genetic variability and population structure of apple mosaic virus (ApMV) have been studied; however, synonymous codon usage patterns influencing the survival rates and fitness of ApMV have not been reported. Based on phylogenetic analyses of 52 ApMV coat protein (CP) sequences obtained from apple, pear, and hazelnut, ApMV isolates were clustered into two groups. High molecular diversity in GII may indicate their recent expansion. A constant and conserved genomic composition of the CP sequences was inferred from the low codon usage bias. Nucleotide composition and relative synonymous codon usage (RSCU) analysis indicated that the ApMV CP gene is AU-rich, but G- and U-ending codons are favored while coding amino acids. This unequal use of nucleotides together with parity rule 2 and the effective number of codon (ENC) plots indicate that mutation pressure together with natural selection drives codon usage patterns in the CP gene. However, in this combination, selection pressure plays a more crucial role. Based on principal component analysis plots, ApMV seems to have originated from apple trees in Europe. However, according to the relative codon deoptimization index and codon adaptation index (CAI) analyses, ApMV exhibited the greatest fitness to hazelnut. As inferred from the results of the similarity index analysis, hazelnut has a major role in shaping ApMV RSCU patterns, which is consistent with the CAI analysis results. This study contributes to the understanding of plant virus evolution, reveals novel information about ApMV evolutionary fitness, and helps find better ApMV management strategies.

• Genomics & Informatics
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• 제20권4호
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• pp.43.1-43.18
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• 2022

Atropa belladonna is a valuable medicinal plant and a commercial source of tropane alkaloids, which are frequently utilized in therapeutic practice. In this study, bioinformatic methodologies were used to examine the pattern of coding sequences and the factors that might influence codon usage bias in the chloroplast genome of Atropa belladonna and other nightshade genomes. The chloroplast engineering being a promising field in modern biotechnology, the characterization of chloroplast genome is very important. The results revealed that the chloroplast genomes of Nicotiana tabacum, Solanum lycopersicum, Capsicum frutescens, Datura stramonium, Lyciumbarbarum, Solanum melongena, and Solanum tuberosum exhibited comparable codon usage patterns. In these chloroplast genomes, we observed a weak codon usage bias. According to the correspondence analysis, the genesis of the codon use bias in these chloroplast genes might be explained by natural selection, directed mutational pressure, and other factors. GC12 and GC3S were shown to have no meaningful relationship. Further research revealed that natural selection primarily shaped the codon usage in A. belladonna and other nightshade genomes for translational efficiency. The sequencing properties of these chloroplast genomes were also investigated by investing the occurrences of palindromes and inverted repeats, which would be useful for future research on medicinal plants.

• Tuberculosis and Respiratory Diseases
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• 제43권1호
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• pp.8-13
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• 1996

연구배경: 결핵균 katG유전자내 463 codon의 돌연변이는 INH 내성과 관련이 있을 것으로 보고되고 있어서 INH 감수성 균주를 대상으로 katG 유전자내 463 codon의 돌연변이 발생빈도를 관찰하여 INH 내성과의 관련성을 밝히고자 하였다. 방법: INH 감수성 균주(MIC${\geq}\;0.2{\mu}g/ml$) 28주를 선정하여 DNA를 추출하여 katG 유전자내 463 codon을 포함하는 지역을 PCR로 증폭 합성하였다. PCR산물을 제한효소인 Msp I으로 처리하여 절단 여부를 관찰하였고 그리고 SSCP로 표준균주와 차이를 관찰하였다. 결과: INH 감수성 균주 28주 중에서 7주(25%)만이 제한효소 Msp I에 의해 절단 되었다. 절단되지 않은 21주(75%)는 SSCP에서도 표준균주와 다른 양상을 나타내었다. 제한 효소로 절단되지 않은 균주의 katG 유전자를 염기서열 분석한 결과 463 codon Arg(CGG)이 Leu(CTG)으로 치환 되어있었다. 결론: INH내성에 영향을 줄 것으로 추정 되고있던 katG 유전자 463 codon 돌연변이는 INH 내성과 무관한 것으로 판명되었다.