• Title/Summary/Keyword: Single strand

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Identification of Mycobacterium avium complex (MAC) Clinical Strains to a Species Level by Sequencing and PCR-SSCP Analysis of rpoB DNA (비결핵항산성균의 rpoB DNA 염기서열과 SSCP pattern 분석에 따른 Mycobacterium avium complex (MAC) 임상분리균주의 동정)

  • Kim, Bum-Joon;Lee, Seung-Hyun;Lee, Kuen-Hwa;Park, Chung-Kyu;Choi, Myung-Sik;Kim, Ik-Sang;Choi, Sung-Bai;Hwang, Eung-Su;Cha, Chang-Yong;Kim, Sang-Jae;Bai, Gill-Han;Kook, Yoon-Hoh
    • The Journal of the Korean Society for Microbiology
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    • v.34 no.5
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    • pp.491-500
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    • 1999
  • A recent study showed that comparative sequence analysis of rpoB DNAs could reveal natural relationships in genus Mycobacterium [J Clin Microbial. 37 (6). 1999]. rpoB DNAs showed interspecies variation and intraspecies conservation. Based on these data, we developed polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) protocols which enable species differentiation in genus Mycobacterium. When this assay was applied to 24 clinical isolates identified as M. avium complex (MAC) by biochemical test, these were successfully differentiated into M. avium and M. intracellulare. These results were concordant with those obtained by 16s rDNA analysis. It is the first report that PCR-SSCP analysis of rpoB DNA could be used for species differentiation of MAC strains.

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Complete Mitochondrial Genome of Haplorchis taichui and Comparative Analysis with Other Trematodes

  • Lee, Dongmin;Choe, Seongjun;Park, Hansol;Jeon, Hyeong-Kyu;Chai, Jong-Yil;Sohn, Woon-Mok;Yong, Tai-Soon;Min, Duk-Young;Rim, Han-Jong;Eom, Keeseon S.
    • Parasites, Hosts and Diseases
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    • v.51 no.6
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    • pp.719-726
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    • 2013
  • Mitochondrial genomes have been extensively studied for phylogenetic purposes and to investigate intra- and interspecific genetic variations. In recent years, numerous groups have undertaken sequencing of platyhelminth mitochondrial genomes. Haplorchis taichui (family Heterophyidae) is a trematode that infects humans and animals mainly in Asia, including the Mekong River basin. We sequenced and determined the organization of the complete mitochondrial genome of H. taichui. The mitochondrial genome is 15,130 bp long, containing 12 protein-coding genes, 2 ribosomal RNAs (rRNAs, a small and a large subunit), and 22 transfer RNAs (tRNAs). Like other trematodes, it does not encode the atp8 gene. All genes are transcribed from the same strand. The ATG initiation codon is used for 9 protein-coding genes, and GTG for the remaining 3 (nad1, nad4, and nad5). The mitochondrial genome of H. taichui has a single long non-coding region between trnE and trnG. H. taichui has evolved as being more closely related to Opisthorchiidae than other trematode groups with maximal support in the phylogenetic analysis. Our results could provide a resource for the comparative mitochondrial genome analysis of trematodes, and may yield genetic markers for molecular epidemiological investigations into intestinal flukes.

Development of SNP markers for the identification of apple flesh color based on RNA-Seq data (RNA-Seq data를 이용한 사과 과육색 판별 SNP 분자표지 개발)

  • Kim, Se Hee;Park, Seo Jun;Cho, Kang Hee;Lee, Han Chan;Lee, Jung Woo;Choi, In Myung
    • Journal of Plant Biotechnology
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    • v.44 no.4
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    • pp.372-378
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    • 2017
  • For comparison of the transcription profiles in apple (Malus domestica L.) cultivars differing in flesh color expression, two cDNA libraries were constructed. Differences in gene expression between red flesh apple cultivar, 'Redfield' and white flesh apple cultivar, 'Granny Smith' were investigated by next-generation sequencing (NGS). Expressed sequence tag (EST) of clones from the red flesh apple cultivar and white flesh apple cultivar were selected for nucleotide sequence determination and homology searches. High resolution melting (HRM) technique measures temperature induced strand separation of short PCR amplicons, and is able to detect variation as small as one base difference between red flesh apple cultivars and white flesh apple cultivars. We applied high resolution melting (HRM) analysis to discover single nucleotide polymorphisms (SNP) based on the predicted SNP information derived from the apple EST database. All 103 pairs of SNPs were discriminated, and the HRM profiles of amplicons were established. Putative SNPs were screened from the apple EST contigs by HRM analysis displayed specific difference between 10 red flesh apple cultivars and 11 white flesh apple cultivars. In this study, we report an efficient method to develop SNP markers from an EST database with HRM analysis in apple. These SNP markers could be useful for apple marker assisted breeding and provide a good reference for relevant research on molecular mechanisms of color variation in apple cultivars.

THE EFFECT OF GENETIC VARIATION IN THE DNA BASE REPAIR GENES ON THE RISK OF HEAD AND NECK CANCER (DNA 염기손상 치유유전자의 변이와 두경부암 발생 위험성)

  • Oh, Jung-Hwan;Yoon, Byung-Wook;Choi, Byung-Jun
    • Journal of the Korean Association of Oral and Maxillofacial Surgeons
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    • v.34 no.5
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    • pp.509-517
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    • 2008
  • DNA damage accumulates in cells as a result of exposure to exogenous agents such as benzopyrene, cigarette smoke, ultraviolet light, X-ray, and endogenous chemicals including reactive oxygen species produced from normal metabolic byproducts. DNA damage can also occur during aberrant DNA processing reactions such as DNA replication, recombination, and repair. The major of DNA damage affects the primary structure of the double helix; that is, the bases are chemically modified. These modification can disrupt the molecules'regular helical structure by introducing non-native chemical bonds or bulky adducts that do not fit in the standard double helix. DNA repair genes and proteins scan the global genome to detect and remove DNA damage and damage to single nucleotides. Direct reversal of DNA damage, base excision repair, double strand break. DNA repair are known relevant DNA repair mechanisms. Four different mechanisms are distinguished within excision repair: direct reversal, base excision repair, nucleotide excision repair, and mismatch repair. Genetic variation in DNA repair genes can modulate DNA repair capacity and alter cancer risk. The instability of a cell to properly regulate its proliferation in the presence of DNA damage increase risk of gene mutation and carcinogenesis. This article aimed to review mechanism of excision repair and to understand the relationship between genetic variation of excision repair genes and head and neck cancer.

Characterization of Single Stranded DNA-Dependent ATPase Activities of Deinococcus radiodurans RecA Protein (Deinococcus radiodurans RecA 단백질의 외가닥 DNA-의존성 ATPase 활성 분석)

  • Kim, Jong-Il
    • Korean Journal of Microbiology
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    • v.43 no.4
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    • pp.250-255
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    • 2007
  • The RecA protein of Deinococcus radiodurans is essential for the extreme radiation resistance of this organism. The central steps involved in recombinational DNA repair require DNA-dependent ATP hydrolysis by recA protein. Key feature of RecA protein-mediated activities is the interactions with ssDNA and dsDNA. The ssDNA is the site where RecA protein filament formation nucleates and where initiation of DNA strand exchange takes place. The effect of sequence heterogeneity of ssDNA was examined in this experiment. The rate of homopolymeric synthetic ssDNA-dependent ATP hydrolysis was constant or nearly so over a broader range of pHs. For poly(dT)-dependent ATP or dATP hydrolysis, rates were generally faster, with a broader optimum between pH 7.0 and 8.0. Activities of RecA protein were affected by the ionic environment. The ATPase activity was shown to have different sensitivity to anionic species. The presence of glutamate seemed to slimulate the hydrolytic activity. Dr RecA protein was shown to require $Mg^{2+}$ ion greater than 2 mM for binding to etheno ssDNA and the binding stoichiometry of 3 nucleotide for RecA protein monomer.

온라인 증권거래 서비스의 고객만족 요인에 대한 실증적 연구

  • Choe, Don-Hwang;Hong, Jae-Beom;Yang, Jeong-Sik
    • Proceedings of the Korea Association of Information Systems Conference
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    • 2005.05a
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    • pp.161-175
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    • 2005
  • 본 연구에서는 온라인 증권거래 서비스 품질과 고객만족 나아가 고객행동을 분석한 연구이다. 이를 위해 설문조사를 실시하였으며 조사원이 직접 증권사 객장을 방문하여 운라인 증권거래경험이 있는 고객을 대상으로 설문조사를 실시하였다. 이를 위해 40개 증권사, 420여개설문이 회수되었다. 분석결과, 첫째, 온라인 증권거래를 이용하는 고객층을 분석하면, 여성보다는 남성이 온라인 증권거래를 활발히 이용하고 있으며 연령별로는 40대, 50대, 30대 순으로 나타났으며 직업은 대부분 근로생활자가 많이 활용하고 있는 것으로 나타났으며 전체 50%이상이 매일 접속하고 거래하는 것으로 나타났으며 운영 규모는 1천만원이하가 다수로 나타났다. 둘째, 온라인 증권거래 서비스 품질요인으로 지각된 신뢰성, 지각된 편의성, 지각된 유형성, 지각된 응답성 순으로 고객만족에 영향을 미치는 것으로 나타났다. 지각된 신뢰성은 약속된 서비스를 정확하게 수행하는 능력에 대한 지각으로 나타내며, 지각된 편의성은 온라인증권거래를 이용하기에 얼마나 용이한 지에 대한 지각을 나타낸다. 지각된 유형성은 물적 시설, 장비, 사람, 의사소통 도구의 외형과 같은 부분에 대한 지각을 나타내는 것이다 지각된 응답성은고객을 돕고 즉각적인 서비스를 제공하려는 의지에 대한 지각을 나타낸다. 마지막으로 고객만족은 재이용이나 구전의도에 긍정적인 효과를 미치는 것으로 나타났다. 이러한 결과는 고객지향적인 온라인 증권거래 서비스 시스템 구축 및 운영이 이용확대에 중요한 요인임을 제시한다. 본 연구는 온라인 증권거래에 대한 고객만족의 탐색적인 연구로써 보다 심도 있는 연구를 위한 기초를 제공하였다는 점과 온라인 증권거래 성과측정요소로써 고객만족에 영향을 미치는 요인을 제시했다는 점에서 의미를 지닌다.에 의해 유도된 single-strand 절단을 억제하였다. 이상과 같이 간세포 일차배양에서 양파추출물은 t-BHP에 의해 유발된 간독성, 간세포 생존율 감소, 지질과산화를 농도 의존적으로 억제시켰고 또한 t-BHP에 의해 억제된 GSH-Px, GSH-Rd 및 catalase의 활성을 증가시켰다. 이와 같이 양파추출물의 간보호 및 항산화 효과는 항산화 효소, 특히 catalase의 활성 증가와 hydroxyl radical에 의해 유도된 산화억제 및 이에 따른 지질과산화 억제에 기인하는 것으로 사료된다.chno-economic paradigm)의 시각에서 제시하는 한국경제의 성장 ${\cdot}$ 고용 ${\cdot}$ 분배를 위한 정책방향은 다음과 같은 동태적발전과정으로 요약할 수 있다 : 기초과학연구능력 확충 ${\rightarrow}$ 소화 ${\cdot}$ 흡수 ${\cdot}$ 개량 ${\rightarrow}$ 토착화 능력의 배양 ${\rightarrow}$ 자체기술개발, 선진기술 도입, 산업간 및 산업내 기술확산, 국제기술협력 ${\rightarrow}$ 기술혁신의 촉진 ${\rightarrow}$ 총요소생산성과 기업경쟁력(자원 및 역량, 프로세스 경쟁력, 품질경쟁력, 시장경쟁력, 고객성과, 시장성과, 재무성과)의 제고 ${\rightarrow}$ 가격경쟁력(임금, 금리, 물류비용, 환율 등)과 비(非)가격경쟁력(디자인, 에프터서비스, 품질, 운송 등)의 제고 ${\rightarrow}$ 국가경쟁력의 제고 ${

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The Relationship between Isoniazid Resistance and 463 CodonMutation of katG Gne in Mycobacterium Tuberculosis (결핵균 katG 유전자내 463 Codon 돌연변이와 Isoniazid내성 관계)

  • Park, Young-Kil;Shim, Myung-Sup;Cho, Sang-Hyun;Bai, Gill-Han;Kim, Sang-Jae
    • Tuberculosis and Respiratory Diseases
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    • v.43 no.1
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    • pp.8-13
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    • 1996
  • Background: The 463 codon mutation of katG gene has been reported as an useful marker for the detection of isoniazid(INH) resistant strains of M. tuberculosis. This study aimed to elucidate relationship between 463 mutation in katG gene and INH resistance in M. tuberculosis. Method: DNA was extracted from 28 INH susceptible strains(MIC$\geq\;0.2{\mu}g/ml$ on the L$\ddot{o}$wenstein Jensen media) and used for amplification of 189bp fragment containing 463 codon by PCR. Amplified fragments were digested by restriction enzyme Msp I, analyzed by single strand conformation polymorphism(SSCP) in the MDE gel and sequenced to prove mutation. Result: Only 7(25%) out of 28 were digestible by restriction enzyme Msp I. The SSCP pattern of 21 strains were distinctly different from that of M. tuberculosis H37Rv. Msp I undigestible PCR fragment was substituted at 463 codon from Arg(CGG) to Leu(CTG). Conclusion: This finding clearly indicate no relationship between 463 codon mutation of the katG gene and INH resistance.

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Prenatal diagnosis of the spinal muscular atrophy type I using genetic information from archival slides and paraffin-embedded tissues

  • Choi, Soo-Kyung;Cho, Eun-Hee;Kim, Jin-Woo;Park, So-Yeon;Kim, Young-Mi;Ryu, Hyun-Mee;Kang, Inn-Soo;Jun, Jung-Young;Chi, Je-G.
    • Journal of Genetic Medicine
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    • v.2 no.2
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    • pp.53-57
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    • 1998
  • Spinal muscular atrophy (SMA) type I is a common severe autosomal recessive inherited neuromuscular disorder that has been mapped to chromosome 5q11.2-13.3. The survival motor neuron (SMN) gene, a candidate gene, is known to be deleted in 96% of patients with SMA type I. Presently, PCR and single strand conformation polymorphism (PCR-SSCP) analyses have been made possible for application to both archival slides and paraffin-embedded tissues. Archival materials represent valuable DNA resources for genetic diagnosis. We applied these methods for the identification of SMN gene of SMA type I in archival specimens for the prenatal diagnosis. In this study, we performed the prenatal diagnosis with chorionic villus sampling (CVS) cells on two women who had experienced neonatal death of SMA type I. DNA extraction was done from archival slide and tissue materials and PEP-PCR was performed using CVS cells. In order to identify common deletion region of SMN and neuronal apoptosis-inhibitory protein (NAIP) genes, cold PCR-SSCP and PCR-restriction site assay were carried out. Case 1 had deletions of the exons 7 and 8, and case 2 had exon 7 only on the telomeric SMN gene. Both cases were found to be normal on NAIP gene. These results were the same for both CVS and archival biopsied specimens. In both cases, the fetuses were, therefore, predicted to be at very high risk of being affected and the pregnancy were terminated. These data clearly demonstrate that archival slide and paraffin-embedded tissues can be a valuable source of DNA when the prenatal genetic diagnosis is needed in case any source for genetic analysis is not readily available due to previous death of the fetus or neonate.

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Genetic Variants of NBS1 Predict Clinical Outcome of Platinum-based Chemotherapy in Advanced Non-small Cell Lung Cancer in Chinese

  • Xu, Jia-Li;Hu, Ling-Min;Huang, Ming-De;Zhao, Wan;Yin, Yong-Mei;Hu, Zhi-Bin;Ma, Hong-Xia;Shen, Hong-Bing;Shu, Yong-Qian
    • Asian Pacific Journal of Cancer Prevention
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    • v.13 no.3
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    • pp.851-856
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    • 2012
  • Objective: NBS1 plays a key role in the repair of DNA double-strand break (DSB). We conducted this study to investigate the effect of two critical polymorphisms (rs1805794 and rs13312840) in NBS1 on treatment response and prognosis of advanced non-small cell lung cancer (NSCLC) patients with platinum-based chemotherapy. Methods: Using TaqMan methods, we genotyped the two polymorphisms in 147 NSCLC patients. Odds ratios (ORs) and their 95% confidential intervals (CIs) were calculated as a measure of difference in the response rate of platinum-based chemotherapy using logistic regression analysis. The Kaplan-Meier and log-rank tests were used to assess the differences in progression-free survival (PFS) and overall survival (OS). Cox proportional hazards model was applied to assess the hazard ratios (HRs) for PFS and OS. Results: Neither of the two polymorphisms was significantly associated with treatment response of platinum-based chemotherapy. However, patients carrying the rs1805794 CC variant genotype had a significantly improved PFS compared to those with GG genotype (16.0 vs. 8.0 months, P = 0.040). Multivariable cox regression analysis further showed that rs1805974 was a significantly favorable prognostic factor for PFS [CC/CG vs. GG: Adjusted HR = 0.62, 95% CI: 0.39-0.99; CC vs. CG/GG: Adjusted HR = 0.56, 95% CI: 0.32-0.97). Similarly, rs13312840 with a small sample size also showed a significant association with PFS (CC vs. CT/TT: Adjusted HR = 25.62, 95% CI: 1.53-428.39). Conclusions: Our findings suggest that NBS1 polymorphisms may be genetic biomarkers for NSCLC prognosis especially PFS with platinum-based chemotherapy in the Chinese population.

The Effects of Stress Related Genes on Carcass Traits and Meat Quality in Pigs

  • Jin, H.J.;Park, B.Y.;Park, J.C.;Hwang, I.H.;Lee, S.S.;Yeon, S.H.;Kim, C.D.;Cho, C.Y.;Kim, Y.K.;Min, K.S.;Feng, S.T.;Li, Z.D.;Park, C.K.;Kim, C.I.
    • Asian-Australasian Journal of Animal Sciences
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    • v.19 no.2
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    • pp.280-285
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    • 2006
  • The current study was conducted to investigate the relationship between stress related gene and meat quality in pigs. A total number of 212 three-way cross bred (Landrace-$Yorkshire{\times}Duroc$) and 38 Duroc were sampled from the Korean pig industry to determine genotype frequency of porcine stress syndrome (PSS) and heat shock protein 70 kDa (HSP70) genes and their relationship with carcass traits and longissimus meat quality. Screen of HSP70 was performed by the single strand conformation polymorphism (SSCP) technique. Based on the analysis of restriction fragment length polymorphism (RFLP) in ryanodine receptor 1 (RYR1) gene, genetic disorder of PSS was related to a mutation at $18,168^{th}$ (C to T) of exon 17. There was no significant difference in ultimate meat pH and backfat thickness between HSP70 K1-AA type and -BB type in pure Duroc breed. In Landrace-$Yorkshire{\times}Duroc$ (L-$Y{\times}D$) cross bred pig, our results indicated that HSP70 derivate type in Duroc had a limited effect on backfat thickness, but L-$Y{\times}D$ type had a noticeable linkage with HSP70 K1-AA and K3-AB. This tendency was also observed in hot carcass weight where HSP70 K1-AA and K3-AB resulted in heavier weight with 86.3 kg compared to HSP70 K1-AB and K3-BB of 74.3 kg. Results imply that stress related HSP70 genotype has a potential association with backfat thickness and carcass weight.