• Parasites, Hosts and Diseases
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• v.53 no.6
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• pp.689-697
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• 2015

The tapeworm Taenia solium is an important human zoonotic parasite that causes great economic loss and also endangers public health. At present, an effective vaccine that will prevent infection and chemotherapy without any side effect remains to be developed. In this study, codon usage patterns in the T. solium genome were examined through 8,484 protein-coding genes. Neutrality analysis showed that T. solium had a narrow GC distribution, and a significant correlation was observed between GC12 and GC3. Examination of an NC (ENC vs GC3s)-plot showed a few genes on or close to the expected curve, but the majority of points with low-ENC (the effective number of codons) values were detected below the expected curve, suggesting that mutational bias plays a major role in shaping codon usage. The Parity Rule 2 plot (PR2) analysis showed that GC and AT were not used proportionally. We also identified 26 optimal codons in the T. solium genome, all of which ended with either a G or C residue. These optimal codons in the T. solium genome are likely consistent with tRNAs that are highly expressed in the cell, suggesting that mutational and translational selection forces are probably driving factors of codon usage bias in the T. solium genome.

• Korean Journal of Microbiology
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• v.38 no.4
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• pp.260-266
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• 2002

In this study, chromosomal DNA fragment related to the regulation of phenol metabolism in Ralstonia eutropha JMP 134 was cloned and sequenced. The result has shown that two open reading frames (ORF1 and ORF2) exist on this regulatory region. ORF1, which initiates from 454 bp downstream of the stop codon of the phenol hydroxylase genes, was found to be composed of 501 amino acids. ORF2, whose start codon is overlapped with the stop codon of ORFl, was found to contain 232 amino acids. The comparison of amino acid sequences with other proteins has revealed that ORF1 belongs to the family of NtrC transcriptional activator, whereas ORF2 shares high homology with the family of GntR protein, which is known to be a negative regulator. ORF1 and ORF2 were designated as a putative positive regulator, phlR2 and a negative regulator phlA, respectively. Possible regulatory mechanisms of phenol metabolism in this strain was discussed.

• The Plant Pathology Journal
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• v.21 no.4
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• pp.334-342
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• 2005

The prototype Chlorella virus PBCV-l encodes 11 tRNA genes and over 350 protein-encoding genes in its 330 kbp genome. Initial attempts to overexpress the recombinant A189/192R protein, a putative virus attachment protein, in E. coli strain BL21(DE3) SI were unsuccessful, and multiple protein bands were detected on Western blots. However, the full-length A189/192R recombinant protein or fragments derived from it were detected when they were expressed in E. coli BL21 CodonPlus (DE3) RIL, which contains extra tRNAs. Codon usage analysis of the a189/192r gene showed highly biased usage of the AGA and AVA codons compared to genes encoded by E. coli and Chlorella. In addition, there were biases of XXA/U($56\%$) and XXG/ C($44\%$) in the codons recognized by the viral tRNAs, which correspond to the codon usage bias in the PBCV-1 genome of XXA/U ($63\%$) over those ending in XXC/G ($37\%$). Analysis of the codon usage in the major capsid protein and DNA polymerase showed preferential usage of codons that can be recognized by the viral tRNAs. The Asn (AAC) and Lys (AAG) codons whose corresponding tRNA genes are duplicated in the tRNA gene cluster were the most abundant (i.e., preferred) codons in these two proteins. The tRNA genes encoded in the PBCV-l genome seem to play a very important role during the synthesis of viral proteins through supplementing the tRNAs that are frequently used in viral proteins, but are rare in the host cells. In addition, these tRNAs would help the virus to adapt to a wide range of hosts by providing tRNAs that are rare in the host cells.

• Korean Journal of Clinical Laboratory Science
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• v.38 no.3
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• pp.196-202
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• 2006

Treatment of hepatitis B virus (HBV) with lamivudine is effective in suppressing virus replication and results in reduced inflammatory activity. However the most troublesome problem of lamivudine treatment is the emergence of lamivudine-resistant strains with amino acid substitution in the YMDD motif of DNA polymerase gene during the treatment. The aim of this study was to determine the mutation of YMDD motif (codon 552) and codon 528 in chronic HBV patients with lamivudine therapy using PCR-direct sequencing and to investigate the relationship between lamivudine mediated HBV mutation and HBeAg. HBV DNA was extracted from serum samples of HBV patients and amplified by nested PCR with two sets of primer pairs selected in HBV DNA polymerase gene. Amplified PCR product was analyzed by 2% agarose gel electrophoresis and direct sequencing. HBV mutation was detected in 124 out of 207 samples (60%). Single mutation was 50.8% for M552I, 43.5% for M552V, 5.7% for M552I/V and the L528M mutation was 67.0%. Double mutation was 43.6% for M552V/L528M, 33.1% for M552I/L528(wild type), 17.7% for M552I/L528M and 5.6% for M552I/V/L528M. Serine mutation at YMDD motif (M552S) was not found and the L528M mutation frequently accompanied M552V type. In this study, the typical difference of frequencies for HBV mutation depending on HBeAg was not found. Moreover, the PCR-direct sequencing method used in this study might be a powerful tool for the mutation study in clinical reference laboratories with high volume.

• Genomics & Informatics
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• v.14 no.4
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• pp.234-240
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• 2016

Different mechanisms, including transcriptional and post transcriptional processes, regulate tissue specific expression of genes. In this study, we report differences in gene/protein compositional features between apoptosis involved genes selectively expressed in human tissues. We found some correlations between codon/amino acid usage and tissue specific expression level of genes. The findings can be significant for understanding the translational selection on these features. The selection may play an important role in the differentiation of human tissues and can be considered for future studies in diagnosis of some diseases such as cancer.

• Proceedings of the Korean Statistical Society Conference
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• 2004.11a
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• pp.79-84
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• 2004

We use principal component analysis (PCA) to identify exons of a gene and further analyze their internal structures. The PCA is conducted on the short-time Fourier transform (STFT) based on the 64 codon sequences and the 4 nucleotide sequences. By comparing to independent component analysis (ICA), we can differentiate between the exon and intron regions, and how they are correlated in terms of the square magnitudes of STFTs. The experiment is done on the gene F56F11.4 in the chromosome III of C. elegans. For this data, the nucleotide based PCA identifies the exon and intron regions clearly. The codon based PCA reveals a weak internal structure in some exon regions, but not the others. The result of ICA shows that the nucleotides thymine (T) and guanine (G) have almost all the information of the exon and intron regions for this data. We hypothesize the existence of complex exon structures that deserve more detailed analysis.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.18
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• pp.8239-8245
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• 2016

The p53 gene is inactivated by the human papillomavirus (HPV) E6 protein in the majority of cervical cancers. Treatment of HeLa S3 cells with siRNA for HPV E6 permitted adenovirus-mediated transduction of a p53 gene linked to an upstream estrogen response element (ERE). Our previous study in non-siRNA treated HHUA cells, which are derived from an endometrial cancer and express estrogen receptor ${\beta}$, showed enhancing effects of an upstream ERE on adenovirus-mediated p53 gene transduction. In HeLa S3 cells treated with siRNA for HPV E6, adenovirus-mediated transduction was enhanced by an upstream ERE linked to a p53 gene carrying a proline variant at codon 72, but not for a p53 gene with arginine variant at codon 72. Expression levels of p53 mRNA and Coxsackie/adenovirus receptor (CAR) mRNA after adenovirus-mediated transfer of an ERE-linked p53 gene (proline variant at codon 72) were higher compared with those after non-ERE-linked p53 gene transfer in siRNA-treated HeLa S3 cells. Western blot analysis showed lower ${\beta}$-tubulin levels and comparatively higher p53/${\beta}$-tubulin or CAR/${\beta}$-tubulin ratios in siRNA-treated HeLa S3 cells after adenovirus-mediated ERE-linked p53 gene (proline variant at codon 72) transfer compared with those in non-siRNA-treated cells. Apoptosis, as measured by annexin V binding, was higher after adenovirus-mediated ERE-linked p53 gene (proline variant at codon 72) transfer compared with that after non-ERE-linked p53 gene transfer in siRNA-treated cells.

• Pediatric Infection and Vaccine
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• v.15 no.2
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• pp.195-201
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• 2008

Purpose : We hypothesized that the mannose binding lectin gene (MBL2), a key molecule of innate immunity may contribute to the development of Kawasaki disease (KD) in early childhood. This study was performed to investigate the polymorphisms of MBL2 and the risk of developing KD in Korean children. Methods : The study subjects were 112 children with KD who were admitted to the Seoul National University Bundang Hospital between October 2003 and March 2005. The control subjects consisted of 224 anonymous, healthy Korean blood donors. Extracted genomic DNA was amplified for codon 54 of MBL2 exon 1 and alleles (a and b) were assigned via sequencing analysis. The frequency of the alleles of the MBL2 exon 1 was compared between the case and control groups. Results : The median age of patients was 27 months (range, 3 months-7 years), 45.5% were <24 months of age and 54.5% were ${\geq}2$ years. The genotype distribution reached Hardy-Weinberg equilibrium in both cases and control subjects. In the cases with KD, the genotypic frequencies of codon 54 polymorphisms were 67.9% for aa, 29.5% for ab, and 2.6% for bb. There were no significant differences in the overall distribution of the polymorphisms between the cases and the control subjects. In addition, the genotype distribution was not different according to age. Conclusions : Our findings indicate that the codon 54 polymorphism of the MBL2 gene is not likely to contribute to the risk of developing KD in Korean children. Further studies on the development of coronary artery lesions with regard to MBL2 genotypes are warranted.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.2
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• pp.717-723
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• 2014

Background: This study was carried out to investigate the interaction of p53 codon 72 polymorphism, dietary and tobacco habits with reference to risk of stomach cancer in Mizoram, India. A total of 105 histologically confirmed stomach cancer cases and 210 age, sex and ethnicity matched healthy population controls were included in this study. Materials and Methods: The p53 codon 72 polymorphism was detected by PCR-RFLP and sequencing. H. pylori infection status was determined by ELISA. Information on various dietary and tobacco related habits was recorded with a standard questionnaire. Results: This study revealed that overall, the Pro/Pro genotype was significantly associated with a higher risk of stomach cancer (OR, 2.54; 95%CI, 1.01-6.40) as compared to the Arg/Arg genotype. In gender stratified analysis, the Pro/Pro genotype showed higher risk (OR, 7.50; 95%CI, 1.20-47.0) than the Arg/Arg genotype among females. Similarly, the Pro/Pro genotype demonstrated higher risk of stomach cancer (OR, 6.30; 95%CI, 1.41-28.2) among older people (>60 years). However, no such associations were observed in males and in individuals <60 years of age. Smoke dried fish and preserved meat (smoke dried/sun dried) consumers were at increased risk of stomach cancer (OR, 4.85; 95%CI, 1.91-12.3 and OR, 4.22; 95%CI, 1.46-12.2 respectively) as compared to non-consumers. Significant gene-environment interactions exist in terms of p53 codon 72 polymorphism and stomach cancer in Mizoram. Tobacco smokers with Pro/Pro and Arg/Pro genotypes were at higher risk of stomach cancer (OR, 16.2; 95%CI, 1.72-153.4 and OR, 9.45; 95%CI, 1.09-81.7 respectively) than the non-smokers Arg/Arg genotype carriers. The combination of tuibur user and Arg/Pro genotype also demonstrated an elevated risk association (OR, 4.76; 95%CI, 1.40-16.21). Conclusions: In conclusion, this study revealed that p53 codon 72 polymorphism and dietary and tobacco habit interactions influence stomach cancer development in Mizoram, India.

• Korean Journal of Microbiology
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• v.50 no.3
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• pp.185-190
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• 2014

The aim of this study was to investigate the prevalence of quinolone resistant E. coli from raw bulk milk and to characterize the resistance determinants. In this study, the gyrA, gyrB, parC, and parE quinolone resistance determining regions (QRDR) were sequenced from quinolone resistant E. coli isolates. Also, the presence of plasmid-mediated quinolone resistance (PMQR) and the expression of efflux pump genes based on quantitative real-time PCR (qRT-PCR) were investigated. Of the 487 coliform bacteria, 9 strains showed nalidixic acid resistance, and 6 of the 9 nalidixic acid resistant isolates were also ciprofloxacin resistant. These 9 strains had a single mutation at codon 83 (S83L) in gyrA, 2 of them had double mutations at codon 83 and 87 (S83L and D87N) in gyrA and 3 of the 9 isolates had single mutations at codon 80 (S80I) in parC. None of the 9 isolates harbored PMQR determinants. Compared with wild-type E. coli ATCC 25922, an over-expression of the acrB gene (2.15-5.74 fold), encoding the pump component of the AcrAB-TolC efflux pump was observed in 4 of 6 ciprofloxacin resistant isolates. This study identified the quinolone resistance mechanism of E. coli isolated from raw milk samples in Gyeonggi-do.