• Korean Journal of Microbiology
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• v.34 no.3
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• pp.169-174
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• 1998

To define the structure and diversity of bacterial communities in the aqutic ecosystem, Lake Soyang, the largest artificial reservoir in Korea, a new method, fluorescent in situ hybridization was applied. This technique relies on the specific hybridization of the nucleic acid probes to the naturally amplified intracellular rRNA. By this method, the bacterial community composition of Lake Soyang and bacterial numbers belong to eubacteria, proteobacteria and Cytophaga-Flavobacterium group were estimated. Total bacterial numbers ranged from $0.3{\times}10^6{\sim}2.0{\times}10^6cells{\cdot}ml^{-1}$, and vertical profile of total bacteria showed the peak at 2 and 5 m depths. The ratio of eubacteria to total bacteria were 22~100% and varied with depth and season. The percentage of Proteobacteria ${\alpha}$-group ranged 2.6~66.7%, ${\beta}$-group 4.5~53.5%, ${\gamma}$-group 4.6~76.7% and Cytophaga-Flavobacterium group 2.1~35.9%. Also, bacteria] community had spatial and temporal characteristics. The dominant groups were ${\beta}$-group in winter, ${\gamma}$-group in spring and early summer and ${\alpha}$-group in summer.

• Restorative Dentistry and Endodontics
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• v.21 no.1
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• pp.1-18
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• 1996

There are many advantages when using IIF and DNA probe methods over anaerobic culture method in that they are time-and effort-saving, more precise and more sensitive. Furthermore, in IIF and DNA probe methods, the detection is possible only with small amount of bacteria, the quantitative analysis is possible, and the cell viability is not necessary. The purpose of this study is to observe the incidence of P.endodontalis by carrying out anaerobic culture, IIF and colony lift using DNA probe method respectively, and to compare these 3 methods in terms of effectiveness and sensitivity in order to identify the most effective detection method. 30 teeth with at least one clinical symptoms, with single canal, and with pulp necrosis were sampled. For sampling bacteria, access cavity was prepared after disinfecting tooth and its surroundings. Then the paper point was inserted up to the periapical area, leave there for a while, and finally it was placed into PRAS Ringer's sol. and PBS sol. In anaerobic culture method, P.endodontalis was identified by biochemical tests after subculturing black and brown colonies which were produced after 7 days of incubation on BAP and Brucella BAP in anaerobic chamber. To identify P.endodontalis in IIF method, species-specific polyclonal rabbit-antisera of P.endodontalis(ATCC 35406) was reacted with sampled PBS sol. dispensed onto glass slide, and then P.endodontalis was examined by phase contrast microscopy after incubating with Goat anti-rabbit lgG conjugated to Fluorescein isothiocyanate. For colony lift using DNA probe method, membranes were laid over colonies on the surface of BAP and were hybridized with cloned DNA probe of P.endodontalis. The existence of P.endodontalis was then identified by the methods of chemiluminescent detection and color metric detection. Black colony was found in 11 teeth out of 30 teeth and P.endodontalis was detected in 6 teeth (20 %) by anaerobic culture method, 16 teeth (53 %) by IIF method, and 7 teeth (23 %) by DNA probe method. IIF method is significantly better in detecting P.endodontalis than DNA probe method and anaerobic culture method. There was no significant differences between DNA probe method and anaerobic culture method. There was significant correlation between the formation of black colony and the existence of P.endodontalis. The probability of detecting P.endodontalis when black colony being present is 2.89 times higher than when not being present. There was significant relationship between the foul odor of clinical symptoms and P.endodontalis. The sensitivity of existing P.endodontalis when foul odor being present was 93.75 %, while the specificity of not existing P.endodontalis when foul odor not being present was 28.57 %. These results suggested that the probes of P.endodontalis will be used to decide the method and prognosis in endodontic treatments.

• Clinical and Experimental Pediatrics
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• v.56 no.6
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• pp.247-253
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• 2013

Purpose: In children with acute leukemia, bone marrow genetic abnormalities (GA) have prognostic significance, and may be the basis for minimal residual disease monitoring. Since April 2007, we have used a multiplex reverse transcriptase-polymerase chain reaction tool (HemaVision) to detect of GA. Methods: In this study, we reviewed the results of HemaVision screening in 270 children with acute leukemia, newly diagnosed at The Catholic University of Korea from April 2007 to December 2011, and compared the results with those of fluorescence in situ hybridization (FISH), and G-band karyotyping. Results: Among the 270 children (153 males, 117 females), 187 acute lymphoblastic leukemia and 74 acute myeloid leukemia patients were identified. Overall, GA was detected in 230 patients (85.2%). HemaVision, FISH, and G-band karyotyping identified GA in 125 (46.3%), 126 (46.7%), and 215 patients (79.6%), respectively. TEL-AML1 (20.9%, 39/187) and AML1-ETO (27%, 20/74) were the most common GA in ALL and AML, respectively. Overall sensitivity of HemaVision was 98.4%, with false-negative results in 2 instances: 1 each for TEL-AML1 and MLL-AF4. An aggregate of diseases-specific FISH showed 100% sensitivity in detection of GA covered by HemaVision for actual probes utilized. G-band karyotype revealed GA other than those covered by HemaVison screening in 133 patients (49.3%). Except for hyperdiplody and hypodiploidy, recurrent GA as defined by the World Health Organizationthat were not screened by HemaVision, were absent in the karyotype. Conclusion: HemaVision, supported by an aggregate of FISH tests for important translocations, may allow for accurate diagnosis of GA in Korean children with acute leukemia.

• Journal of Applied Biological Chemistry
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• v.55 no.4
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• pp.227-234
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• 2012

We observed that oil began to accumulate at 25 seed days after flowering (DAF) and reached the maximum potential at 35 seed DAF of oilseed rape, and the greatest weight of 100 seeds was obtained at 35 seed DAF. To survey a broad analysis of gene expression in developing embryos of Brassica napus, the Bn 300k microarray have been constructed. The Bn 300k Microarrary was designed from 80,696 unigenes clustered from 543,448 ESTs and 780 cDNA at NCBI. These arrays have been hybridized in a series of experiments with probes derived from seeds and leaf of B. napus. Approximately 8.5% of the 7,000 genes were expressed as ratios 2-fold higher in seed (25 DAF) than leaves and 0.4% at ratios 10. Also we observed that storage and cell differentiation-related genes were highly expressed at 10 DAF, whereas energy-related genes including fatty acid metabolism were increased up depending on seed maturation using Microarray, which was confirmed by reverse transcriptase polymerase chain reaction. These results suggest that B. napus arrays provide a very useful data set of seed-specific expression that can be further analyzed by examination of the promoter regions of these genes and help our understanding of the complex regulatory network in developing seeds.

• The Korean Journal of Pharmacology
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• v.24 no.1
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• pp.1-10
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• 1988

To obtain information about the structure of the human phenylethanolamin N-methyltransferase (PNMT) and to further define the extent of the evolutionary relationships among PNMT molecules of several spesies, a full length cDNA clone for bovine adrenal PNMT was used to screen a charon 4A genomic library. One phage was isolated and identified, which included the entire PNMT gene. The length of inserted genomic DNA was 13.1-Kilobase (Kb) containing two internal EcoRI sites. Construction of a restriction map and subsequent Southern and dot blot analysis with 5'-and3'-specific cDNA probes allowed the identification of exon-containing fragments. This is the first report of the cloning of gene for human epinephrine synthesizing enzyme.

• The Korean Journal of Mycology
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• v.26 no.2 s.85
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• pp.173-181
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• 1998

To identify genetic difference of 13 strains in three Pleurotus species, analyses of rDNA, AP-PCR and RFLP were carried out. IGRI and $ITSI{\sim}II$ regions of rDNA amplified by PCR were about 0.9 and 0.7 kb, respectively. These PCR products were digested with six restriction enzymes to analyse polymorphism. Especially, treatment of HaeIII enzyme on $ITSI{\sim}II$ regions showed specific bands in three Pleurotus sajor-caju strains. Genetic differences among three species were classified by similarity analyses based on rDNA polymorphism. Various band patterns of $2,500{\sim}150\;bp$ were showed by AP-PCR. Identification of species and varieties in 13 Pleurotus strains was possible according to primers used in AP-PCR. In order to develop genetic markers, RFLPs using IGRI and $ITSI{\sim}II$ probes derived from ASI 2180 and 2070 were carried out on eight Pleurotus varieties. RFLP patterns using IGRI probe were more various than that of $ITSI{\sim}II$ probe.

• Journal of Life Science
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• v.19 no.10
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• pp.1463-1467
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• 2009

Telomeres, comprised of tandem repeats of TTAGGG sequences, are special nucleoprotein structures that protect and stabilize chromosome ends. These structures form the crux of the telomere concept of aging, senescence and genomic instability. The classic terminal restriction fragment (TRF) analysis to quantify the amount of telomeric DNA is disadvantageous in species containing ultra long telomeres like in mice (100Kb). In this study, we used a more sensitive quantitative fluorescence in situ hybridization (Q FISH) technique to quantify telomeric DNA, and used it as a biological aging marker in mice. 12 litters each of Senescence-Resistant (SAMR1) and -Prone (SAMP1) known as senescence accelerated mouse strains were purchased from Central Lab, Animal Inc. We quantified the amount of telomeric DNA using telomere specific DNA probes on the two strains of male mice at 8 weeks, 18 weeks and 26 weeks of age. The amount of telomeric DNA correlated with aging and age associated changes in body and organ weight between SAMR1 and SAMP1 strains of mice. These data suggest the usefulness of the amount of telomeric DNA as a biological aging marker in human aging studies.

• Journal of Radiation Protection and Research
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• v.29 no.4
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• pp.243-249
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• 2004

The cytokinesis-block micronucleus (CBMN) assay in combination with FISH technique using chromosome-specific centromeric probes for chromosome 1 and 4 was performed in mitogen stimulated human lymphocytes which were exposed to x-radiation to identify different sensitivity of chromosomes to the induction of micronuclei(MN) and aneuploidy by radiation. The frequencies of micronucleated cytokinesis-blocked(MNCB) cells and MN in binucleated lymphocytes(BN) increased with the increase in radiation dose. A significant induction of aneuploidy of chromosome 1 and 4 were found. The frequency of aneuploidy of chromosome 1 and 4 in the control were 9 per 2,000 BN cells and this increased to 47 and 71 following irradiation at a dose of 1 and 2 Gy, respectively. The induction of aneuploidy of chromosome 1 was higher than that of chromosome 4. The frequency of aneuploid BN cells with MN exhibiting positive centromere signal for either chromosome 1 and/or 4 increased in a dose dependent manner, and that for chromosome 1 is higher than that for chromosome 4. Among the total induced MN in irradiated lymphocytes, smaller proportion of MN exhibit centromeric signal of chromosome indicating that radiation-induced MN are mainly originated from chromosomal breakage rather than chromosomal non-disjunction. These results suggest that x-radiation can induce aneuploidy and supports the finding that chromosome vary in their sensitivity to aneuploidy induction by x-irradiation.

• Molecules and Cells
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• v.37 no.6
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• pp.449-456
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• 2014

The use of synovial fluid-derived mesenchymal stem cells (SFMSCs) obtained from patients with degenerative arthropathy may serve as an alternative therapeutic strategy in osteoarthritis (OA) and rheumatoid arthritis (RA). For treatment of OA and RA patients, autologous transplantation of differentiated MSCs has several beneficial effects for cartilage regeneration including immunomodulatory activity. In this study, we induced chondrogenic differentiation of SFMSCs by inhibiting protein kinase A (PKA) with a small molecule and microRNA (miRNA). Chondrogenic differentiation was confirmed by PCR and immunocytochemistry using probes specific for aggrecan, the major cartilaginous proteoglycan gene. Absorbance of alcian blue stain to detect chondrogenic differentiation was increased in H-89 and/or miRNA-23b-transfected cells. Furthermore, expression of matrix metalloproteinase (MMP)-9 and MMP-2 was decreased in treated1 cells. Therefore, differentiation of SFMSCs into chondrocytes through inhibition of PKA signaling may be a therapeutic option for OA or RA patients.

• Journal of Ginseng Research
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• v.41 no.4
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• pp.469-476
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• 2017

Background: Panax ginseng Meyer (Asian ginseng) has a large nuclear genome size of > 3.5 Gbp in haploid genome equivalent of 24 chromosomes. Tandem repeats (TRs) occupy significant portions of the genome in many plants and are often found in specific genomic loci, making them a valuable molecular cytogenetic tool in discriminating chromosomes. In an effort to understand the P. ginseng genome structure, we characterized an ultrahigh copy 167-bp TR (Pg167TR) and explored its chromosomal distribution as well as its utility for chromosome identification. Methods: Polymerase chain reaction amplicons of Pg167TR were labeled, along with 5S and 45S rDNA amplicons, using a direct nick-translation method. Direct fluorescence in situ hybridization (FISH) was used to analyze the chromosomal distribution of Pg167TR. Results: Recently, we reported a method of karyotyping the 24 chromosome pairs of P. ginseng using rDNA and DAPI (4',6-diamidino-2-phenylindole) bands. Here, a unique distribution of Pg167TR in all 24 P. ginseng chromosomes was observed, allowing easy identification of individual homologous chromosomes. Additionally, direct labeling of 5S and 45S rDNA probes allowed the identification of two additional 5S rDNA loci not previously reported, enabling the refinement of the P. ginseng karyotype. Conclusion: Identification of individual P. ginseng chromosomes was achieved using Pg167TR-FISH. Chromosome identification is important in understanding the P. ginseng genome structure, and our method will be useful for future integration of genetic linkage maps and genome scaffold anchoring. Additionally, it is a good tool for comparative studies with related species in efforts to understand the evolution of P. ginseng.