• Asian Pacific Journal of Cancer Prevention
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• v.13 no.9
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• pp.4745-4749
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• 2012

The diagnosis of malignant mesothelioma (MM) remains a clinical challenge and the fluorescence in situ hybridization (FISH) assay has been reported to be one promising tool. The present meta-analysis aimed to establish the overall diagnostic accuracy of FISH for diagnosing MM. After a systematic review of English language studies, the sensitivity, specificity and other measures of accuracy of FISH in the diagnosis of MM were pooled using random-effects models. Summary receiver operating characteristic curves were applied to summarize overall test performance. Nine studies met our inclusion criteria, the pooled sensitivity and specificity for FISH for diagnosing MM being 0.72 (95% CI 0.67-0.76) and 1.00 (95% CI 0.98-1.00), respectively. The positive likelihood ratio was 34.5 (95% CI 14.5-82.10), the negative likelihood ratio was 0.24 (95% CI 0.16-0.36), and the diagnostic odds ratio was 204.9 (95% CI 76.8-546.6), the area under the curve being 0.99. Our data suggest that the FISH assay is likely to be a useful diagnostic tool for confirming MM. However, considering the limited studies and patients included, further large scale studies are needed to confirm these findings.

• Korean Journal of Ecology and Environment
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• v.37 no.4 s.109
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• pp.363-367
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• 2004

For comparative analysis of the eubacterial community structure at 8 sampling sites throughout the Nak-Dong River, FISH (fluorescence in situ hybridization) method was employed. The total ratio of each determined eubacterial group such as ${\alpha}\;{\cdot}\;{\beta}\;{\cdot}\;{\gamma}-subclasses$proteobacteria and Cytophaga-Flavobacterium(CF) group to total counts(DAPI) at each site varied 9.3-42.5% with the highest value at uppermost part. And each ratio of determined eubacterial groups reached mostly under 10% except that of CF group (23%) at uppermost part. Furthermore, compared to lower part, upper part represented unexpectedly higher proportions of ${\gamma}-subclass$ proteobacteria comprised almost fast growing bacteria on degradable organics. Also the variations of ammonia-oxidizing bacteria ranged from $2.7{\times}10^4$ to $18.0{\times}10^4$ cells $mL^{-1}$ with the lowest value in lower part and the highest value in mid part whereas those of nitrite-oxidizing bacteria varied 5.2-7.7{\times}10^4$ cells $mL^{-1}$ without noticeable differences throughout the sites. Additionally, the ratio of nitrifying bacteria to total counts ranged from 1.0% to 13.6% with no differences between ammonia-oxidizing bacteria and nitrite-oxidizing bacteria. In conclusion, FISH method introduced in this study for monitoring, normally used for the quantitative analysis of bacteria, provided also good information on their environmental status in the Nak-Dong River.

• Proceedings of the Korean Society of Plant Biotechnology Conference
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• 2005.04a
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• pp.126-126
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• 2005

• Journal of the Optical Society of Korea
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• v.10 no.3
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• pp.130-142
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• 2006

Lab-on-a-chip technology is attracting great interest because the miniaturization of reaction systems offers practical advantages over classical bench-top chemical systems. Rapid mixing of the fluids flowing through a microchannel is very important for various applications of microfluidic systems. In addition, highly sensitive on-chip detection techniques are essential for the in situ monitoring of chemical reactions because the detection volume in a channel is extremely small. Recently, a confocal surface enhanced Raman spectroscopic (SERS) technique, for the highly sensitive biological analysis in a microfluidic sensor, has been developed in our research group. Here, a highly precise quantitative measurement can be obtained if continuous flow and homogeneous mixing condition between analytes and silver nano-colloids are maintained. Recently, we also reported a new analytical method of DNA hybridization involving a PDMS microfluidic sensor using fluorescence energy transfer (FRET). This method overcomes many of the drawbacks of microarray chips, such as long hybridization times and inconvenient immobilization procedures. In this paper, our recent applications of the confocal Raman/fluorescence microscopic technology to a highly sensitive lab-on-a-chip detection will be reviewed.

• Korean Journal of Ecology and Environment
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• v.40 no.4
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• pp.553-559
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• 2007

The vertical distributions of sulfate reducing bacteria (SRB) in sediments of lakes in Korea (Lake Sihwa and Lake Soyang) and China (Lake Aha and Lake Erhai) were investigated by fluorescence in situ hybridization (FISH). SRB from sediment of Lakes of China were located to deeper layer than those in Lakes of Korea. SRB were not detected below 19 cm and 10 cm depth in sediments of Lake Sihwa and Lake Soyang, respectively. SRB numbers were, however, detected at all observed sediments in Lake Aha and Lake Erhai. In case of lakes in Korea, the proportion of SRB ranged from 2.9 to 25.6% (Lake Sihwa) and ranged from 0.6 to 7.1% (Lake Soyang). For lakes in China, the proportions of SRB were from 0.6 to 19.4% and from 2.9 to 11.2% within sediments from Lake Aha and from Lake Erhai, respectively. The high peaks of SRB numbers in sediments of all lakes were appearing at depths between 0 cm and 2 cm.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.8
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• pp.3825-3827
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• 2012

FISH is one of the most sensitive molecular methods to detect genetic abnormalities with DNA probes. When cytogenetic studies are normal or insufficient, FISH may detect cryptic rearrangements, rare or slowly proliferative abnormal populations in non-mitotic cells. We cytogenetically evaluated 70 childhood ALL - 67.1% were found to have an abnormal karyotype. The 23 patients (32.9%) with a normal karyotype were analyzed by FISH applying two probes; TEL/AML1 and MYB which detect cryptic rearrangements of t(12;21)(p13;q22) and deletion of (6q) respectively, associated with a good prognosis. Out of 23 patients, one was positive for t(12;21)(p13;q22) (4.3%). None of our patients were positive for MYB del(6q). Two patients showed an extra signal for MYB on chromosomes other than 6 (8.6 %) indicating amplification or duplication. Findings were compared with the available literature. Our study clearly indicated the integrated FISH screening method to increase the abnormality detection rate in a narrow range. FISH is less useful for diagnostic study of patients with suspected del(6q) but it helps in detecting known cryptic rearrangements as well as identification of new abnormalities(translocation , duplication and amplification) at the gene level.

• Biotechnology and Bioprocess Engineering:BBE
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• v.9 no.6
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• pp.482-489
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• 2004

Bacillus species were observed and quantified by molecular approaches, using the 16S rDNA primers/probes, in a wastewater treatment plant designed for the purpose of stimulating the growth of Bacillus species. The plant has been operating as a test plant since 1997 in the city of Ina, Japan, with excellent treatment performance. Observations by in situ hybridization, using Bacillus-specific probes, indicated that Bacillus strains were inhabited in the plant and their num­bers decreased during the treatment process. Similar results were obtained from a quantitative PCR analysis using a Bacillus-specific primer set, and the amount of DNA originating from various Bacillus species was maximally $1.91%\$ of the total DNA in the wastewater treatment tank. Clone library analysis using the Bacillus-specific primers suggested that, while the population was no­ticeably increased, the phylogenetic diversity of the increasing Bacillus species was very low.

• Journal of the korean academy of Pediatric Dentistry
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• v.31 no.2
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• pp.314-322
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• 2004

The production of a glucan was affected by the concentration of ions and buffer solutions, and nutrients in an oral cavity. In this study, the effects of ions and buffer solutions on the mRNA expression of gtfD gene in Streptococcus mutans, an important causative agent of dental caries, were investigated by Fluorescent in situ hybridization(FISH). At first, ions and buffer solutions had little effect on the multiplication of Streptococcus mutans. The green fluorescence according to the mRNA expression of gtfD gene was detected in the BHI broth containing 1% sucrose. The intensities of the green fluorescence were strong at 0.25mM of $CaCl_2$. Little fluorescence was detected by the addition of KCl, except far 10mM KCl at which fluorescence intensities were similar to those of the control. Fluorescence intensities were weak at each concentration of $MgCl_2$ when compared to the control. As for buffer solutions, fluorescence intensities were similar to those of the control at each concentration of buffer solutions, except that they were little detected at 100mM of potassium phosphate.

• Proceedings of the Botanical Society of Korea Conference
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• 1998.07a
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• pp.61-70
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• 1998

Genome and chromosome analyses in plants using fluorescence in situ hybridization (FISH) and immuno-staining (IMS) methods are reviewed by presenting the recent results obtained by the Chromosome Link, a group of chromosome and genome researchers. FISH is now effective to detect unique nucleotide sequences with 153 bp on the extended DNA fibers. Genomic in situ hybridization (GISH) also allows painting plant chromosomes of different genomes. GISH is quite effective to detect the genomic differentiation in the individual chromosomes within a nucleus. Three dimensional (3D) analyses are now available by confocal microscopy and a deconvolution system. These techniques are invaluable to visualize both the structural and functional dynamics within a nucleus. 3D-FISH revealed the spatial differentiation of different genomees within a nucleus. 3D-FISH also proved structural partition of centromeric and telomeric domains within a barely nucleus. The dynamic acetylation of histone H4 at the specific regions of a genome during a cell cycle is also analyzed using 3D-IMS. It is anticipated that these methods will provide us powerful tools to understand the structural and functional significance of plant chromosomes and genomes.

• Animal Bioscience
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• v.35 no.9
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• pp.1289-1302
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• 2022

The next generation sequencing has significantly contributed to clarify the genome structure of many species of zootechnical interest. However, to date, some portions of the genome, especially those linked to a heterogametic nature such as the Y chromosome, are difficult to assemble and many gaps are still present. It is well known that the fluorescence in situ hybridization (FISH) is an excellent tool for identifying genes unequivocably mapped on chromosomes. Therefore, FISH can contribute to the localization of unplaced genome sequences, as well as to correct assembly errors generated by comparative bioinformatics. To this end, it is necessary to have starting points; therefore, in this study, we reviewed the physically mapped genes on the Y chromosome of cattle, buffalo, sheep, goats, pigs, horses and alpacas. A total of 208 loci were currently mapped by FISH. 89 were located in the male-specific region of the Y chromosome (MSY) and 119 were identified in the pseudoautosomal region (PAR). The loci reported in MSY and PAR were respectively: 18 and 25 in Bos taurus, 5 and 7 in Bubalus bubalis, 5 and 24 in Ovis aries, 5 and 19 in Capra hircus, 10 and 16 in Sus scrofa, 46 and 18 in Equus caballus. While in Vicugna pacos only 10 loci are reported in the PAR region. The correct knowledge and assembly of all genome sequences, including those of genes mapped on the Y chromosome, will help to elucidate their biological processes, as well as to discover and exploit potentially epistasis effects useful for selection breeding programs.