• Journal of Genetic Medicine
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• v.10 no.1
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• pp.33-37
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• 2013

Purpose: Myotonic dystrophy 1 (DM1, OMIM 160900) is an autosomal-dominant muscular disorder caused by an expansion of CTG repeats in the 3' UTR of the DMPK gene. Variable expansions of CTG repeats preclude the accurate determination of repeat size. We tried to show the clinical and analytical validity of the application of Southern blotting after long-range PCR was demonstrated in Korean DM1 patients. Materials and Methods: The Southern blotting of long-range PCR was applied to 1,231 cases with clinical suspicion of DM1, between 2000 and 2011. PCR was performed using genomic DNA with forward 5'-CAGTTCACAACCGCTCCGAGC-3' and reverse 5'-CGTGGAGGATGGAACACGGAC-3' primers. Subsequently, the PCR fragments were subjected to gel electrophoresis, capillary transfer to a nylon membrane, hybridization with a labeled (CAG)10 probe. The correlation between clinical manifestations and the CTG repeat expansions were analyzed. Results: Among a total of 1,231 tested cases, 642 individuals were diagnosed with DM1 and the range of the detected expansion was 50 to 2,500 repeats; fourteen cases with mild DM1 ($75{\pm}14$ repeats), 602 cases with classical DM1 ($314{\pm}143$ repeats), and 26 cases with congenital DM1 ($1,219{\pm}402$ repeats). The positive and negative predictive values were 100%. The age at test requested and the CTG repeat numbers were inversely correlated (R=-0.444, P<0.01). Conclusion: This study indicates that Southern blotting after long-range PCR is a reliable diagnostic method DM1.

• Nuclear Engineering and Technology
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• v.45 no.5
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• pp.573-580
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• 2013

The combined effects of reactivity coefficients, along with other core nuclear characteristics, determine reactor core behavior in normal operation and accident conditions. The Power Coefficient of Reactivity (PCR) is an aggregate indicator representing the change in reactor core reactivity per unit change in reactor power. It is an integral quantity which captures the contributions of the fuel temperature, coolant void, and coolant temperature reactivity feedbacks. All nuclear reactor designs provide a balance between their inherent nuclear characteristics and the engineered reactivity control features, to ensure that changes in reactivity under all operating conditions are maintained within a safe range. The $CANDU^{(R)}$ reactor design takes advantage of its inherent nuclear characteristics, namely a small magnitude of reactivity coefficients, minimal excess reactivity, and very long prompt neutron lifetime, to mitigate the demand on the engineered systems for controlling reactivity and responding to accidents. In particular, CANDU reactors have always taken advantage of the small value of the PCR associated with their design characteristics, such that the overall design and safety characteristics of the reactor are not sensitive to the value of the PCR. For other reactor design concepts a PCR which is both large and negative is an important aspect in the design of their engineered systems for controlling reactivity. It will be demonstrated that during Loss of Regulation Control (LORC) and Large Break Loss of Coolant Accident (LBLOCA) events, the impact of variations in power coefficient, including a hypothesized larger than estimated PCR, has no safety-significance for CANDU reactor design. Since the CANDU 6 PCR is small, variations in the range of values for PCR on the performance or safety of the reactor are not significant.

• Journal of Microbiology and Biotechnology
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• v.24 no.6
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• pp.812-822
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• 2014

Metagenomic analysis of the human intestinal microbiota has extended our understanding of the role of these bacteria in improving human intestinal health; however, a number of reports have shown that current total fecal DNA extraction methods and 16S rRNA universal primer sets could affect the species coverage and resolution of these analyses. Here, we improved the extraction method for total DNA from human fecal samples by optimization of the lysis buffer, boiling time (10 min), and bead-beating time (0 min). In addition, we developed a new long-range 16S rRNA universal PCR primer set targeting the V6 to V9 regions with a 580 bp DNA product length. This new 16S rRNA primer set was evaluated by comparison with two previously developed 16S rRNA universal primer sets and showed high species coverage and resolution. The optimized total fecal DNA extraction method and newly designed long-range 16S rRNA universal primer set will be useful for the highly accurate metagenomic analysis of adult and infant intestinal microbiota with minimization of any bias.

• Journal of Fisheries and Marine Sciences Education
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• v.29 no.3
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• pp.834-846
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• 2017

Aquaculture practices to ensure greater production, such as high density breeding and excessive feeding, are become stressors that raise the prevalence of diseases. Accordingly, increasingly large volumes of antibiotics are used more frequently each year. Long term use antibiotics can generate resistant bacteria, which interrupt treatments and cause a potential transfer to human bodies. Thus, antibiotic resistance is of importance in public health. Tetracycline (Tc) is one of the typical medicines used in the aquaculture drugs, which has a wide range of application including gram-positive and gram-negative bacteria. In the examination of 153 strains isolated from olive flounder (Paralichthys olivaceus) farms located in Jeju in 2016, it turned out that a total of 84 strains were resistant to Tc or oxytetracycline (OTC). The extent to which the strains are resistant to Tc and OTC was confirmed through MIC test, mostly within the range of 25 to $100{\mu}g/m{\ell}$. Twelve different types of tet genes were detected using single and multiplex PCR in the 84 Tc-resistant strains. The PCR was used to find tet(K), tet(M), tet(O), and tet(S), which are known to exist primarily in gram positive strains. According to the results, - tet(S) is the most dominant gene in 49 strains of Streptococcus parauberis, accounting for 63.2%. And there were two strains that have two different types of resistant genes. The multiplex PCR was used to detect tet(A), tet(B), tet(C), tet(D), tet(E), and tet(G), which are commonly found in gram-negative strains. Each of tet(B), tet(D), and tet(B)&(M) was found in a strain presumed to be Vibrio sp., and only tet(D) was found in 10 Edwardsiella tarda strains.

• Journal of Food Hygiene and Safety
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• v.33 no.4
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• pp.280-288
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• 2018

In this study, an approach for the analysis of the five cephalopod species (octopus, long-arm octopus, squid, wet-foot octopus, beka squid) consumed in the Republic of Korea is developed. The samples were collected from the Southeast Asian countries Thailand, Indonesia, Vietnam, and China. The SYBR-green-based real-time qPCR method, based on the mitochondrial DNA genome of the five cephalopods was developed and validated. The intergroup variations in the mitochondrial DNA are evident in the bioinformatic analysis of the mitochondrial genomic DNA sequences of the five groups. Some of the highly-conserved and slightly-variated regions are identified in the mitochondrial cytochrome-c-oxidase subunit I (COI) gene, 16s ribosomal RNA (16s rRNA) gene, and 12s ribosomal RNA (12s rRNA) gene of these groups. To specify each five cephalopod groups, specific primer sets were designed from the COI, 16s rRNA and 12s rRNA regions. The specific primer sets amplified the DNA using the SYBR-green-based real-time PCR system and 11 commercially secured animal tissues: Octopus vulgaris, Octopus minor, Todarodes pacificus, Dosidicus gigas, Sepia esculenta, Amphioctopus fangsiao, Amphioctopus aegina, Amphioctopus marginatus, Loliolus beka, Loligo edulis, and Loligo chinensis. The results confirmed by a conveient way to calculate relative amplification levels between different samples in that it directly uses the threshold cycles (Ct)-value range generated by the qPCR system from these samples. This genomic DNA-based molecular technique provides a quick, accurate, and reliable method for the taxonomic classification of the animal tissues using the real-time qPCR.

• BLOOD RESEARCH
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• v.53 no.4
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• pp.320-324
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• 2018

Background Recent studies have devoted much attention to non-protein-coding transcripts in relation to a wide range of malignancies. MALAT1, a long non-coding RNA, has been reported to be associated with cancer progression and prognosis. Thus, we here determined MALAT1 gene expression in chronic lymphocytic leukemia (CLL), a genetically heterogeneous disease, and explored its possible relationships with cytogenetic abnormalities. Methods MALAT1 expression level was evaluated using real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) on blood mononuclear cells from 30 non-treated CLL patients and 30 matched healthy controls. Cytogenetic abnormalities were determined in patients by fluorescence in situ hybridization (FISH). Results MALAT1 expression level was up-regulated in the CLL group compared to healthy controls (P=0.008). Del13q14, followed by Del11q22, were the most prevalent cytogenetic abnormalities. We found no association between the FISH results and MALAT1 expression in patients. Conclusion Altered expression of MALAT1 is associated with CLL development. Further investigations are required to assess the relationship between this long non-coding RNA and CLL patient survival and prognosis.

• Research in Plant Disease
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• v.8 no.4
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• pp.207-214
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• 2002

Tobacco rattle virus(TRV) was detected from Gladiolus hybridus, Crocus spp. and Narcissus spp. leaves show-ing notched or stripe on the leaf and malformation symptoms collected from Daegu and Kyungbuk province by electron microscopy (EM), immunosorbent electron microscopy (ISEM) and host range study. Direct negative staining method by EM showed rigid rod long particles 170~200$\times$22 nm and rigid rod short particles 40~114$\times$22 m. TRV-K isolated from G. hybridus propagated with Nicotiana tabacum. TRV coat protein(CP) gene was amplified using specific oligonucleotide primer by RT-PCR. Sequence analysis of amplified CP gene showed 99.5％ nucleotide similarity to TRV-ORY.

• Herbal Formula Science
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• v.19 no.2
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• pp.83-92
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• 2011

Objectives : This study was carried out to moniter microbial flora on freeze-dried herbal powder and identify isolated bacteria. Methods : We measured the total number of bacteria and fungi in 29 herbal powder which had made according to the guideline of KFDA. For the identification, we observed microscopic properties and carried out polymerase chain reaction(PCR). The purified DNA was analyzed by DNA sequencer. Results : Among the 29 herbal powders, the fungi were detected only one sample as unacceptable range of total aerobic bacteria. Isolated bacteria were identified as Bacillus cereus, B. subtilis, B. megaterium, B. licheniformis, Erwinia tasmaniensis, E. amylovora, and Pantoea agglomerans by 16S rDNA analysis. E. tasmaniensis was observed 20 herbal samples. Conclusions : According to above results, further studies for the effective sterilization of low herbal materials should be needed.

• Journal of Nutrition and Health
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• v.48 no.5
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• pp.390-397
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• 2015

Purpose: In this study, we investigated the effects of chronic alcohol and excessive iron intake on mitochondrial DNA (mtDNA) damage and the progression of alcoholic liver injury in rats. Methods: Twenty-four Sprague-Dawley male rats were divided into four groups (Control, EtOH, Fe, and EtOH + Fe), and fed either control or ethanol (36% of total calories) liquid diet with or without 0.6% carbonyl iron for eight weeks. Serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST) activities, liver malondialdehyde concentrations were measured by colorimetric assays. Liver histopathology was examined by Hematoxylin-eosin staining of the fixed liver tissues. The integrity of the hepatic mtDNA and nuclear DNA was measured by long-range PCR. The gene expression levels of cytochrome c oxidase subunit 1 (Cox1) and NADH dehydrogenase subunit 4 (Nd4) were examined by real-time PCR. Results: Serum ALT and AST activities were significantly higher in the EtOH+Fe group, as compared to the Control group. Similarly, among four groups, liver histology showed the most severe lipid accumulation, inflammation, and necrosis in the EtOH + Fe group. PCR amplification of near-full-length (15.9 kb) mtDNA showed more than 50% loss of full-length product in the liver of the EtOH + Fe group, whereas amounts of PCR products of a nuclear DNA were unaffected. In addition, the changes in the mtDNA integrity showed correlation with reductions in the mRNA levels of mitochondrial gene Cox1 and Nd4. Conclusion: Our data suggested that the liver injury associated with excessive iron and alcohol intake involved mtDNA damage and corresponding mitochondrial dysfunction.

• Microbiology and Biotechnology Letters
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• v.26 no.1
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• pp.23-33
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• 1998

The entire sequence of a 4,214,810 bp genome of the Bacillus subtilis 168 has been determined by an international project, and the completion has been announced on July 19, 1997. For the sequencing project an international consortium was established and 25 European, 7 Japanese laboratories, 2 biotechnology companies, and our laboratory participated in the project. Within this framework we determined the complete nucleotide sequence of a 53,289 bp fragment upstream of the odhA gene (181 $^{\circ}$) of the B. subtilis 168 chromosome. On the basis of the published DNA sequences of the B. subtilis sspC and odhA genes, we obtained genomic fragments by plasmid rescue and long-range PCR. The sequenced fragment contains 56 putative open reading frames (designated yojA-yolI and 9 known genes (sspC, cge cluster, orfE5, orfRMl and odhA), in which we found many interesting features. In addition, the entire nucleotide sequence of a 53,289 bp region enabled us to revise the current genetic map of this region.