• Journal of Plant Biotechnology
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• v.43 no.2
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• pp.157-163
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• 2016

This study was conducted to investigate the potential use of New Zealand spinach (Tetragonia tetragonioides) as a new vegetable crop which will be cultivated in salt-affected soils such as reclaimed areas. New Zealand spinach ecotypes native to Korea were collected across the Southern, Western and Eastern seashore regions of the Korean peninsula, among which fifty-five accessions were later further propagated and evaluated genetically by using an AFLP (amplified fragment length polymorphism) marker. Based on the AFLP analysis performed to uncover the genetic diversity of the collected ecotypes, enzymatic cleavage of the extracted DNA was implemented based on 12 EcoRI and MseI combinations. A total of 1,279 alleles (107 alleles per EcoRI and MseI enzyme combination) were successfully amplified, among which 62 alleles per enzyme combination were polymorphic (58%). The AFLP analysis indicated that the rate of genetic dissimilarity was 29% among the New Zealand spinach collections, which were clustered into the 7 genetic diversity group. This is the first report on the genetic variation in the genus Tetragonia, and the basic information can be applied to select parental lines for enhancing the segregation spectrum of the new halophytic vegetable plant grown in salt-affected areas.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.5
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• pp.2311-2314
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• 2012

Genetic polymorphisms of uridine diphosphate-glucuronosyltransferases 1A6 (UGT1A6) and 1A7 (UGT1A7) may lead to genetic instability and colorectal cancer carcinogenesis. Our objective was to measure the interaction between polymorphisms of these repair genes and tobacco smoking in colorectal cancer (CRC). A total of 68 individuals with CRC and 112 non-cancer controls were divided into non-smoker and smoker groups according to pack-years of smoking. Genetic polymorphisms of UGT1A6 and UGT1A7 were examined using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). We found a weak association of UGT1A6 polymorphisms with CRC risk (crude odds ratio [OR], 1.65;95% confidence interval [95% CI], 0.9-3.1, P=0.107; adjusted OR 1.95%, 95% CI 1.0-3.8, P=0.051). The ORs for the UGT1A7 polymorphisms were statistically significant (crude OR: 26.40, 95% CI: 3.5-198.4, P=0.001; adjusted OR: 21.52, 95% CI: 2.8-164.1, P=0.003). The joint effect of tobacco exposure and UGTIA6 polymorphisms was significantly associated with colorectal cancer risk in non-smokers (crude OR, 2.11; 95% CI, 0.9-5.0, P=0.092; adjusted OR 2.63, 95% CI, 1.0-6.7, P=0.042). In conclusion, our findings suggest that UGT1A6 and UGT1A7 gene polymorphisms are associated with CRC risk in the Japanese population. In particualr, UGT1A6 polymorphisms may strongly increase CRC risk through the formation of carcinogens not associated with smoking.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.2
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• pp.1047-1055
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• 2014

Background: MicroRNAs (miRNAs) are an abundant class of endogenous small non-coding RNAs of 20-25 nucleotides in length that function as negative gene regulators. MiRNAs play roles in most biological processes, as well as diverse human diseases including cancer. Recently, many studies investigated the association between SNPs in miR-146a rs2910164, miR-196a2 rs11614913, miR-149 rs229283, miR-499 rs3746444 and colorectal cancer (CRC), which results have been inconclusive. Methodology/Principal Findings: PubMed, EMBASE, CNKI databases were searched with the last search updated on November 5, 2013. For miR-196a2 rs11614913, a significantly decreased risk of CRC development was observed under three genetic models (dominant model: OR = 0.848, 95%CI: 0.735-0.979, P = 0.025; recessive model: OR = 0.838, 95%CI: 0.721-0.974, P = 0.021; homozygous model: OR = 0.754, 95%CI: 0.627-0.907, P = 0.003). In the subgroup analyses, miR-$196a2^*T$ variant was associated with a significantly decreased susceptibility of CRC (allele model: OR = 0.839, 95%CI: 0.749-0.940, P = 0.000; dominant model: OR = 0.770, 95%CI: 0.653-0.980, P = 0.002; recessive model: OR = 0.802, 95%CI: 0.685-0.939, P = 0.006; homozygous model: OR = 0.695, 95%CI: 0.570-0.847, P = 0.000). As for miR-149 rs2292832, the two genetic models (recessive model: OR = 1.199, 95% CI 1.028-1.398, P = 0.021; heterozygous model: OR = 1.226, 95% CI 1.039-1.447, P = 0.013) demonstrated increased susceptibility to CRC. On subgroup analysis, significantly increased susceptibility of CRC was found in the genetic models (recessive model: OR = 1.180, 95% CI 1.008-1.382, P = 0.040; heterozygous model: OR = 1.202, 95% CI 1.013-1.425, P = 0.013) in the Asian group. Conclusions: These findings supported that the miR-196a2 rs11614913 and miR-149 rs2292832 polymorphisms may contribute to susceptibility to CRC.

• Biomedical Science Letters
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• v.9 no.3
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• pp.139-144
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• 2003

Since water borne infection causes acute diseases and results in spread of diseases by secondary infection, the prevention is very important. Therefore, it is necessary to have a method that is rapid and effective to monitor pathogenic bacteria in drinking water. In this study, we employed a systematic method, Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) analysis, to develop an effective monitoring system for possible bacterial contaminants in drinking water. For this purpose, PCR primers were derived from 992 bp region of the 16s rRNA gene that is highly conserved through the different species of prokaryotes. To test whether the PCR primers designed are indeed useful for detecting all the possible microbial contaminants in the water, the primers were used to amplify 16s rRNA regions of different microbial water-borne pathogens such as E. coli, Salmonella, Yersinia, Listeria, and Staphylococcus. As expected, all of tested microorganisms amplified expected size of PCR products indicating designed PCR primers for 16s rRNA indeed can be useful to amplify all different microbial water-borne pathogens in the water. Furthermore, to test whether these 16s rRNA based PCR primers can detect bacterial populations present in the water, water samples taken from diverse sources, such as river, tap, and sewage, were used for amplification. PCR products were for then subjected for cloning into a T-vector to generate a library containing 16s rRNA sequences from various bacteria. With cloned PCR products, RFLP analysis was done using PCR products digested with restriction enzyme such as Hae III to obtain species-specific RFLP profiles. After PCR-RFLP, the bacterial clones which showed the same RFLP profiles were regarded as the same ones, and the clones which showed distinctive RFLP profiles were subsequently subjected for sequence analysis for species identification. By this PCR-RFLP analysis, we were able to reveal diverse populations of bacteria living in water. In brief, in unsterilized natural river water, over 60 different species of bacteria were found. On the other hand, no PCR products were detected in drinking tap-water. The results from this study clearly indicate that the PCR-RFLP-sequence analysis can be a useful method for monitoring diverse, perhaps pathogenic bacteria contaminated in water in a rapid fashion.

• Korean Journal of Microbiology
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• v.45 no.1
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• pp.17-25
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• 2009

We studied soil components, methane production, the number of methanogens, and T-RFLP patterns dependent on agricultural methods with the change of seasons. There is no regular increase or decrease tendency of the most soil components followed by sampling period. And the water content in soil was higher in October than May. Also a lot of methanogens existed in soil, and acetotrophs were relatively of smaller number than hydogenotrophs and formate utilizing methanogens using MPN (most probable number) enumeration. In the experiment using the formate, it was used from the first week, and only a minute amount was detecte after four weeks. However in the acetate, it was increased until the third week, and after that was consumed. And there was higher methane production for all soil samples which administered with the hydrogen spike. The activity of methanogens was higher in the organic and low-agrichemical agricultural method samples, and the organic agricultural method had high methanogen activity among the other samples. A result of T-RFLP pattern of mcrA gene digested with Sau96I, methanogen community have a little relation with agricultural methods and seasons. This results also agreed to no critical difference the soil components dependent on agricultural methods, but some analytical data have a positive relationship with a agricultural methods. Therefor we could concluded that the comparison study of community for soil bacteria sufficiently could be useful for the microbiological indicator.

• The Journal of Internal Korean Medicine
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• v.25 no.4
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• pp.18-24
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• 2004

연구배경 : 플라스미노겐 활성 억제인자-1 (plasminogen activator inhibitor-1; PAI-1)은 허혈성 뇌경색의 발생의 원인이 되는 섬유소 용해작용의 저하를 매개하는 인자로서, PAI-1의 작용이 촉진되면 섬유소 용해기능이 저하되어 관상동맥 및 뇌혈관질환의 발생을 증가시키게 된다. PAI-1 유전자의 촉진자(promoter) 영역에는 -675 4G/5G (4G/5G)와A -844G (A/G)의 두 개의 유전자 다형성이 존재하며, 이는 PAI-1의 유전자 전사과정에 영향을 미쳐 혈청 PAI-1의 농도를 증가시키고 결과적으로 허혈성 뇌경색의 발생확률을 높이는 작용을 하게 된다. 연구방법 : 허혈성 뇌경색으로 진단 받은 167명의 환자와 173명의 건강인의 말초혈액에서 DNA를 분리한 후 PAI-1의 4G/5G와 A/G 유전자 다형성에 대한 연쇄중합반응 및 제한효소 절편길이 다형성 (polymerase chain reaction-restriction fragment length polymorphism; PCR-RFLP) 방법을 이용하여 허혈성 뇌경색 발생과 유전자 다형성과의 관계를 비교 분석하였다. 결과 : 허혈성 뇌경색 환자에서의 4G/4G의 유전자형의 빈도는 15.0%으로 정상 대조군의 33.5%에 비해 현저하게 낮게 나타났다 (P < 0.0001). 각각의 유전자형과 허혈성 뇌경색의 발생 위험도 (odd ratio ; OR)와의 관계를 분석했을 때 4G/4G 유전자형을 가질 경우 위험도는 0.35배로 현저하게 낮아졌으며, (P < 0.0001), 5G/5G 유전자형을 가질 경우 위험도는 4.49배 로 현저하게 높아졌다 (P < 0.0001). 그러나, A/G 유전자 다형성과 허혈성 뇌경색의 발생과는 유의한 연관성을 발견하지 못하였다. 결론 : 이상의 결과로 볼 때 PAI-1 유전자의 4G/4G 유전자형은 허혈성 뇌경색의 발생 비율을 감소시키는 작용을 하는 것으로 여겨진다.

• Horticultural Science & Technology
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• v.35 no.3
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• pp.333-343
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• 2017

Bloomless cucumber fruits are commercially produced by grafting onto the pumpkin stocks (Cucurbita moschata) to restricted silicon ($SiO_2$) absorption. Inhibition of silicon absorption in bloomless stocks is conferred by a mutant allele of the CmLsi1 homologous to Lsi1 in rice. In this study, we characterized the Lsi1 homologs in pumpkin (C. moschata) and its cold-tolerant wild relative C. ficifolia ('Heukjong') in order to develop a DNA marker for selecting a bloomless trait and to establish the molecular basis for breeding bloomless stock cultivars of C. ficifolia. A Cleaved amplified polymorphic sequence (CAPS) marker (CM1-CAPS) was designed based on a non-sysnonymous single nucleotide polymorphism (SNP, C>T) of the CmLsi1 mutant-type allele, and its applicability for Marker-assisted selection (MAS) was confirmed by evaluating three bloom and five bloomless pumpkin stock cultivars. Quantitative RT-PCR of the CmLsi1 for these stock cultivers implied that expression level of the CmLsi1 gene does not appear to be associated with the bloom/bloomless trait and may differ depending on plant species and tissues. A full length cDNA of the Lsi1 homolog [named CfLsi1($B^+$)] of 'Heukjong' (C. ficifolia), was cloned and sequence comparison between CmLsi1($B^+$) and CfLsi1($B^+$) revealed that there exists total 24 SNPs, of which three were non-synonymous. Phylogenetic analysis of CfLsi1($B^+$) and Lsi1 homologs further revealed that CfLsi1($B^+$) is closesly related to Nodulin 26-like intrinsic proteins (NIPs) and most similar to CpNIP1 of C. pepo than C. moschata.

• Korean Journal of Microbiology
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• v.39 no.4
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• pp.272-276
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• 2003

Sapgyo Lake is an artificial freshwater reservoir which is located to the midwest of Korea and is the main water reservoir for industry and agriculture of the region. In this study we investigated environmental factors and the change of bacterial community with the influence of surrounding inflow water and the seasonal variation using the molecular ecological approach. Water samples were collected at front of the dike in May and August, 2001. Bacterial genomic DNAs were extracted directly and purified for the amplification of bacterial 16S rDNA. Clone libraries of the 16S rDNA were constructed using pGEM-T easy vector and RFLP analysis was performed to make a group as OTUs with 4 base recognizing enzymes (MspI and HaeIII). The estimated values of richness in August sample was higher than in May. Thirty-three of 153 clones in May and thirty-eight of 131 clones in August were sequenced from forward region of bacterial 16S rDNA for about 600~800 bp. Proteobacteria, Cytophaga, gram positive bacteria and Verrucomicrobia were observed both months. Especially, Planctomyces, cyanobacteria and chloroplast appeared in August when algal bloom occurred. On the whole investigation, Sapgyo lake showed a typical community structure of estuarine and was influenced by heterochthonous organic matters from the surrounding stream.

• Journal of Microbiology and Biotechnology
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• v.15 no.2
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• pp.287-295
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• 2005

In order to compare bacteria] community structure and diversity in activated sludges, terminal restriction fragment length polymorphism (T-RFLP) of PCR-amplified 16s rDNAs was analyzed for 31 domestic and industrial wastewater treatment plants (WTPs). Regardless of the characteristics of the wastewaters, the bacteria] community structures of activated sludges appeared diverse and complex. In particular, activated sludges in domestic WTPs contained higher bacterial diversity than those in industrial WTPs. It was also found that terminal restriction fragment (T-RF) profiles derived from domestic WTPs were very similar with each other, although activated sludges were collected from different plants at different locations. Interestingly, activated sludges of a WTP where restaurant and toilet sewages of a company were managed showed a bacterial community structure similar to that of domestic WTPs. Activated sludges in leather industria] WTPs also showed a high similarity. However, other wastewaters possessed different bacterial communities, so that overall similarity was as low as about $30\%$. Since activated sludges from WTPs for domestic wastewaters and a company sewage appeared to hold similar bacterial communities, it was necessary to confirm if similar wastewaters induce a similar bacterial community. To answer this question, analysis of T-RFs for activated sludges, taken from another 12 domestic WTPs, was conducted by using a 6­FAM$^{TM}$-Iabeled primer and an automated DNA sequencer for higher sensitivity. Among 12 samples, it was again found that T-RF profiles of activated sludges from Yongin, Sungnam, Suwon, and Tancheon domestic WTPs in Kyonggi-do were very similar with each other. On the other hand, T-RF profiles of activated sludges from Shihwa and Ansan WTPs were quite different from each other. It was thought that this deviation was caused by wastewaters, since Ansan and Shihwa WTPs receive both domestic and industrial wastewaters. From these results, it was tentatively concluded that similar bacterial communities might be developed in activated sludges, if WTPs treat similar wastewaters.

• Tuberculosis and Respiratory Diseases
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• v.48 no.3
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• pp.308-314
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• 2000

Background : DNA fingerprinting of Mycobacterium tuberculosis with RFLP is a very useful tool for deciphering the molecular epidemiology of tuberculosis. An international comparison of the RFLP pattern became possible with the proposal to standardize RFLP methodology using Pvu-II restricted IS-6110, and the comparison has noted some predominance of RFLP pattern in East Asia. The RFLP patterns of tuberculosis strains collected at SNUH was studied and was compared with other strains from East Asia. Method : Fifty strains of M. tuberculosis were isolated from patients who visited 'or were admitted to the SNUH in 1998. Some isolates belonging to the Beijing family were also received. After the extraction of DNA from M. tuberculosis isolates, the chromosomal DNAs were digested with Pvu-II and analyzed by the Southern blot method with DNA probe to IS6110. Result : Six strains belonged to the Beijing family. The RFLP patterns of other 9 strains were similar to each other. No statistically significant endobronchial tuberculosis, presence of underlying disease. and the province of residence were found. Conclusion : Few groups of M. tuberculosis strains from SNUH showed similar RFLP patterns, but their clinical implications are not yet clear.