• Archives of Pharmacal Research
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• 제29권12호
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• pp.1154-1157
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• 2006

The ermK gene from Bacillus lichenformis encodes an inducible rRNA methylase that confers resistance to the macrolide-lincosamide-streptogramin B antibiotics. The ermK mRNA leader sequence has a total length of 357 nucleotides and encodes a 14-amino acid leader peptide together with its ribosome binding site. The secondary structure of ermK leader mRNA and a leader peptide sequence have been reported as the elements that control expression. In this study, the contribution of specific leader peptide amino acid residues to induction of ermK was studied using the PCR-based megaprimer mutation method. ermK methylases with altered leader peptide codons were translationally fused to E. coli ${\beta}-galactosidase$ reporter gene. The deletion of the codons for Thr-2 through Ser-4 reduced inducibility by erythromycin, whereas that for Thr-2 and His-3 was not. The replacement of the individual codons for Ser-4, Met-5 and Arg-6 with termination codon led to loss of inducibility, but stop mutation of codon Phe-9 restored inducibility by erythromycin. Collectively, these findings suggest that the codons for residue 4, 5 and 6 comprise the critical region for induction. The stop mutation at Leu-7 expressed constitutively ermK gene. Thus, ribosome stalling at codon 7 appears to be important for ermK induction.

• 생태와환경
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• 제38권4호통권114호
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• pp.510-517
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• 2005

선형의 남조류 아나베나는 광합성과 질소고정 능이 있으며, 이는 아마도 이 남조류가 각종 육수 환경에 잘 적응하는데 큰 역할을 했다고 볼 수 있다. 작은 patS라는 유전자는 질소 고정세포의 형성을 막으며 결과적으로 질소원이 부족한 환경에서 아나베나의 죽음을 가져온다. 본 연구는 patS 유전자 주변의 DNA 염기 서열을 분석하여 codon 활용도를 알아 본 결과 patS를 제외한 다른 유전자가 존재하지 않음을 밝혔다. patS를 포함하는 세 개의 겹치는 cosmid를 찾아서 기존의 알려진 이형세포 발달 유전자를 탐색하였으나 나타나지 않았다. 질소원의 결핍에 반응하는 patS 유전자의 발현을 Northern blot 분석과 lacZ reporter 유전자 합성 실험을 통하여 각각 전사와 번역의 단계에서 알아보았다. patS 유전자의 발현은 배지로부터 질소원이 제거된 후 12시간 내에 급격히 증가하는 것으로 나타났다.

• 한국인터넷방송통신학회논문지
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• 제16권3호
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• pp.203-211
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• 2016

유전자 코드는 바이오 정보 처리에 키 포인트로 인체의 유기적인 조직체이다. 현대 과학에서는 유전자 코드 분자구조의 신비스러운 특성을 체계적으로 설명하고 이해하는데 연구가 집중되고 있다. 본 논문에서는 유전자 시스템을 대칭적으로 해석하는데 중점을 두었고, Jacket 행렬로 무잡음 RNA 유전자 코드를 가장 단순하게 해석했다. 이유는 Jacket 행렬과 RNA는 그 역행렬이 Element (Block)-wise Inverse로 그 역(Inverse)도 자신이란 점과 대칭적 성질, 그리고 Kronecker곱을 갖기 때문이다. 제안된 방법이 유전자 RNA 코돈(Codon : 괘(卦))의 견지에서 Jacket 행렬의 분해를 통해 간단하고 명료함을 보인다.

• Asian-Australasian Journal of Animal Sciences
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• 제17권11호
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• pp.1491-1495
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• 2004

Small Tail Han Sheep has significant characteristics of high prolificacy and non-seasonal ovulatory activity and is an excellent local sheep breed in P. R. China. Recently a novel member of the transforming growth factor $\beta$ (TGF$\beta$) superfamily termed bone morphogenetic protein 15 (BMP15) was shown to be specifically expressed in oocytes and to be essential for female fertility. Therefore, BMP15 is a candidate gene for reproductive performance of Small Tail Han Sheep. The whole genomic nucleotide sequence of BMP15 gene in Small Tail Han Sheep was searched for polymorphisms by PCR-SSCP and direct sequencing, and only one polymorphism was found. The polymorphism was a result of a 3 base pair deletion, which eliminated a single Leu codon (CTT). The allelic frequencies for A (without deletion) and B (with a codon deletion) are 0.73 and 0.27 respectively. The effects of BMP15 genotype on litter size were evaluated using the least squares model. This indicated that there was a significant association between litter size of Small Tail Han Sheep and a deletion in BMP15 gene (p=0.02<0.05). Small Tail Han Sheep ewes with AA and AB genotype produce on average 0.5 and 0.3 more lambs per litter than those ewes with BB genotype.

• Asian Pacific Journal of Cancer Prevention
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• 제16권14호
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• pp.5663-5667
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• 2015

Background: Earlier studies on the association between p53 codon 72 Arg>Pro polymorphism and cancer risk were inconclusive and conflicting for the Saudi population. Therefore, we performed a meta-analysis to investigate the relationship between the codon 72 Arg>Pro polymorphism and overall cancer risk in Saudi Arabia. Materials and Methods: We searched all eligible published studies and data were pooled together to perform the meta-analysis. Pooled odds ratios (ORs) and 95% confidence intervals (95% CIs) were calculated for homozygous, heterozygous, dominant and recessive genetic models. Results: A total of five eligible published studies covering 502 cancer cases and 784 healthy controls were included in the meta-analysis. No publication bias was detected in this study. The results suggested that the variant (Pro vs Arg: p=0.960; OR=1.004, 95% CI=0.852-1.183), homozygous (Pro.Pro vs Arg.Arg: p=0.970; OR=1.006, 95% CI=0.729-1.390), heterozygous (Arg.Pro vs Arg.Arg: p=0.473; OR=0.783, 95% CI=0.402-1.527) carriers were not associated with overall cancer risk. Similarly, dominant (Pro.Pro+Pro.Arg vs Arg.Arg: p=0.632; OR=0.886, 95% CI=0.540-1.454) and recessive (Pro.Pro vs Pro.Arg+Arg.Arg: p=0.269; OR=1.163, 95%CI=0.890-1.521) models also did not indicate increased risk of cancer. Conclusions: The current meta-analysis suggests that the codon 72 Arg>Pro polymorphism of the p53 gene might not contribute to cancer susceptibility in Saudi population. Future well designed large case control studies are needed to validate our findings.

• Asian Pacific Journal of Cancer Prevention
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• 제13권10호
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• pp.4909-4914
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• 2012

Objective: The aim of this Human Genome Epidemiology (HuGE) review and meta-analysis was to derive a more precise estimation of the association between p53 codon 72 polymorphism (Arg72Pro, rs1042522 G>C) and cervical cancer risk among Asians. Methods: A literature search of Pubmed, Embase, Web of Science and CBM databases from inception through June 2012 was conducted. The meta-analysis was performed using STATA 12.0 software. Crude odds ratios (ORs) with 95% confidence intervals (CIs) were used to assess the strength of any association. Twenty-eight case-control studies were included with a total of 3,580 cervical cancer cases and 3,827 healthy controls. When all the eligible studies were pooled into the meta-analysis, the results showed that the Pro/Pro genotype was associated with increased risk of cervical cancer under the heterozygous model (Pro/Pro vs. Arg/Pro: OR = 1.25, 95%CI: 1.02-1.53, P= 0.005). However, no statistically significant associations were found under four other genetic models (Pro vs. Arg: OR = 0.97, 95%CI: 0.85-1.10, P= 0.624; Pro/Pro + Arg/Pro vs. Arg/Arg: OR = 0.84, 95%CI: 0.70-1.01, P= 0.058; Pro/Pro vs. Arg/Arg + Arg/Pro: OR = 1.13, 95%CI: 0.92-1.39, P= 0.242; Pro/Pro vs. Arg/Arg: OR = 0.97, 95%CI: 0.76-1.22, P= 0.765; respectively). In the subgroup analysis based on country, the Pro/Pro genotype and Pro carrier showed significant associations with increased risk of cervical cancer among Indian populations, but not among Chinese, Japanese and Korean populations. Conclusion: Results from the current meta-analysis suggests that p53 codon 72 polymorphism might be associated with increased risk of cervical cancer, especially among Indians.

• Asian Pacific Journal of Cancer Prevention
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• 제15권24호
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• pp.10647-10652
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• 2015

Background: The aim of our study was to establish COLD-PCR combined with an unlabeled-probe HRM approach for detecting KRAS codon 12 and 13 mutations in plasma-circulating DNA of pancreatic adenocarcinoma (PA) cases as a novel and effective diagnostic technique. Materials and Methods: We tested the sensitivity and specificity of this approach with dilutions of known mutated cell lines. We screened 36 plasma-circulating DNA samples, 24 from the disease control group and 25 of a healthy group, to be subsequently sequenced to confirm mutations. Simultaneously, we tested the specimens using conventional PCR followed by HRM and then used target-DNA cloning and sequencing for verification. The ROC and respective AUC were calculated for KRAS mutations and/or serum CA 19-9. Results: It was found that the sensitivity of Sanger reached 0.5% with COLD-PCR, whereas that obtained after conventional PCR did 20%; that of COLD-PCR based on unlabeled-probe HRM, 0.1%. KRAS mutations were identified in 26 of 36 PA cases (72.2%), while none were detected in the disease control and/or healthy group. KRAS mutations were identified both in 26 PA tissues and plasma samples. The AUC of COLD-PCR based unlabeled probe HRM turned out to be 0.861, which when combined with CA 19-9 increased to 0.934. Conclusions: It was concluded that COLD-PCR with unlabeled-probe HRM can be a sensitive and accurate screening technique to detect KRAS codon 12 and 13 mutations in plasma-circulating DNA for diagnosing and treating PA.

• Journal of Life Science
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• 제9권1호
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• pp.84-89
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• 1999

To determine phylogenetic relatedness of four silk-producing silkmoths (B. mori, B. mandarina, A. yamamai and A. pernyi), internal coding region of arylphorin which is a storage protein in hemolymph protein of insects were amplified by polymerase chain reaction and then sequenced and compared each other. The nucleotide composition was biased toward adenine and thymine(59% A+T) and a strong bias for use of C in the third position of codons was found for Phe and Tyr. Together TTC(Phe) and TAC(Tyr) account for about 16.8% (10 for TTC and 8 for TAC) of all codon usage. The nucleotide similarity of arylphorin gene from B. mori showed 99%, 98% and 97% homology with those of B. mandarina, A. yamamai and A. pernyi, respectively. Also, the nucleotide sequence of arylphorin gene from B. mandarina showed 98% and 97% homology with those of A. yamamai and A.pernyi, respectively. Between A. yamamai and A. pernyi, the sequence homology was 97%. The deduced amino acid sequences in B. mori, B. mandarina and A. yamamai showed almost 99% homology. Although the aryphorin gene provided insufficient variability among the four insect species, A UPGMA tree is generated that supported the monophyly of silk-producing insects, with M. sexta placed basal to it. It is suggest that silk-producing insects have a close relationship and a homogeneous genetic background from comparison with those of other insects.

• Animal cells and systems
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• 제13권4호
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• pp.447-452
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• 2009

We cloned the complete complementary DNA (cDNA) of a Pacific oyster (Crassostrea gigas) cytochrome P450 (CYP450)-related protein using rapid amplification of cDNA ends (RACE). The cDNA included a 1470 bp open reading frame that began with the first ATG codon at position 103 bp and ended with a TAG stop codon at position 1573 bp (GenBank accession EF451959). The sequence had all major functional domains and characteristics of previously characterized CYP450 molecules, including the heme-binding region (FGVGRRRCVG) and putative arginine codon (R) integral to enzymatic function. An NCBI/GenBank database comparison to other CYP450 genes revealed that the deduced C. gigas CYP450 amino acid sequence is similar to that of mouse (Mus musculus) CYP450 2D/II (28%, accession AK078880), rabbit (Oryctolagus cuniculus) CYP450 2D/II (28%, AB008785), and white-tufted-ear marmoset (Callithrix jacchus) CYP450 2D (28%, AY082602). Thus, although the C. gigas CYP450 we cloned appears to belong to the 2D type of the CYP450 group, it has low similarity to this type. CYP450 mRNA expression increased over 6 h in C. gigas gills at $30^{\circ}C$ and $10^{\circ}C$, and then decreased, indicating that CYP450 plays an important role in C. gigas exposed to water temperature changes. This finding can be used as a physiological index for Pacific oysters exposed to changing water temperatures.

• Journal of Microbiology and Biotechnology
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• 제22권3호
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• pp.316-325
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• 2012

Xylanase has been used extensively in the industrial and agricultural fields. However, the low-yield production of xylanase from native species cannot meet the increasing demand of the market. Therefore, improving the heterologous expression of xylanase through basic gene optimization may help to overcome the shortage. In this study, we synthesized a high-GC-content native sequence of the thermostable xylanase gene xynB from Streptomyces olivaceoviridis A1 and, also designed a slightly AT-biased sequence with codons completely optimized to be favorable to Pichia pastoris. The comparison of the sequences' expression efficiencies in P. pastoris X33 was determined through the detection of single-copy-number integrants, which were quantified using qPCR. Surprisingly, the high GC content did not appear to be detrimental to the heterologous expression of xynB in yeast, whereas the optimized sequence, with its extremely skewed codon usage, exhibited more abundant accumulation of synthesized recombinant proteins in the yeast cell, but an approximately 30% reduction of the secretion level, deduced from the enzymatic activity assay. In this study, we developed a more accurate method for comparing the expression levels of individual yeast transformants. Moreover, our results provide a practical example for further investigation of what constitutes a rational design strategy for a heterologously expressed and secreted protein.