• Genomics & Informatics
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• v.14 no.1
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• pp.34-40
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• 2016

Due to advances in omics technologies, numerous genome-wide studies on human samples have been published, and most of the omics data with the associated clinical information are available in public repositories, such as Gene Expression Omnibus and ArrayExpress. While analyzing several public datasets, we observed that errors in gender information occur quite often in public datasets. When we analyzed the gender description and the methylation patterns of gender-specific probes (glucose-6-phosphate dehydrogenase [G6PD], ephrin-B1 [EFNB1], and testis specific protein, Y-linked 2 [TSPY2]) in 5,611 samples produced using Infinium 450K HumanMethylation arrays, we found that 19 samples from 7 datasets were erroneously described. We also analyzed 1,819 samples produced using the Affymetrix U133Plus2 array using several gender-specific genes (X (inactive)-specific transcript [XIST], eukaryotic translation initiation factor 1A, Y-linked [EIF1AY], and DEAD [Asp-Glu-Ala-Asp] box polypeptide 3, Y-linked [DDDX3Y]) and found that 40 samples from 3 datasets were erroneously described. We suggest that the users of public datasets should not expect that the data are error-free and, whenever possible, that they should check the consistency of the data.

• Food Science and Biotechnology
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• v.18 no.5
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• pp.1118-1123
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• 2009

Event-specific real-time polymerase chain reaction (PCR) detection method for genetically modified (GM) maize MIR604 was developed based on integration junction sequences between the host plant genome and the integrated transgene. In this study, 2 primer pairs and probes were designed for specific amplification of 100 and 111 bp DNA fragments from the zSSIIb gene (the maize endogenous reference gene) and MIR604. The quantitative method was validated using 3 certified reference materials (CRMs) with levels of 0.1, 1, and 10% MIR604. The method was also assayed with 14 different plants and other GM maize. No amplification signal was observed in real-time PCR assays with any of the species tested other than MIR604 maize. As a result, the bias from the true value and the relative deviation for MIR604 was within the range from 0 to 9%. Precision, expressed as relative standard deviation (RSD), varied from 2.7 to 10% for MIR604. Limits of detections (LODs) of qualitative and quantitative methods were all 0.1%. These results indicated that the event-specific quantitative PCR detection system for MIR604 is accurate and useful.

• Journal of the Korean Society for Precision Engineering
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• v.23 no.3 s.180
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• pp.179-186
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• 2006

Single-walled carbon nanotubes (SWNT) exhibit strong Raman signals as well as fluorescence emissions in the near infrared regions where most biomolecules are transparent. Such signals do not blink or photobleach under prolonged excitation. which is advantageous to optical nano-bio marker applications. In this paper, single walled carbon nanotubes are conjugated with specific types of single-stranded DNA in order to detect oligonucleotides of corresponding complimentary sequences. Dot blotting experiments and comparative Raman spectroscopy observations demonstrated excellent sensitivity and specificity of carbon nanotube-DNA probes. The results show the possibility of using SWNT as generic nano-bio markers for the precise detection of specific kinds of genes.

• Bulletin of the Korean Chemical Society
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• v.26 no.3
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• pp.379-383
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• 2005

This research aims to develop DNA chip array without an indicator. We fabricated microelectrode array by photolithography technology. Several DNA probes were immobilized on an electrode. Then, indicator-free target DNA was hybridized by an electrical force and measured electrochemically. Cyclic-voltammograms (CVs) showed a difference between DNA probe and mismatched DNA in an anodic peak. Immobilization of probe DNA and hybridization of target DNA could be confirmed by fluorescent. This indicator-free DNA chip microarray resulted in the sequence-specific detection of the target DNA quantitatively ranging from $10^{-18}\;M\;to\;10^{-5}$ M in the buffer solution. This indicator-free DNA chip resulted in a sequence-specific detection of the target DNA.

• 한국균학회소식:학술대회논문집
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• 2014.10a
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• pp.42-42
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• 2014

Mating of tetrapolar mushrooms is regulated by to chromosomal loci, A and B. A locus contains A gene that expresses a homeodomain protein whereas B locus contains multiple pheromones and receptor genes. In order to characterize the mating loci in Korean cultivated strains of Lentinula edodes, one hundred monokaryotic myclelia were isolated from the basidiospores of cultivated strains, including Cham-A-Ram, Sanjo701, and Sanjo707. Both mating loci were amplified using primer sets targeting conserved sequence regions for homeodomain (HD), pheromone, and receptor genes. Subsequent sequence analysis revealed that the Korean strains contained significant variations in the homeodomain of A locus, even within the same A1 or A2 mating type. Similarly, B locus was also highly diversified in the sequences of pheromones and receptors as well as gene organization. These results enabled us to design mating type-specific probes which can distinguish mating type of each strain. The specificity was confirmed by between intra- and inter-strain mating experiment.

• Journal of the Korean Chemical Society
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• v.65 no.2
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• pp.121-124
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• 2021

RNA molecules which bind to the G-rich sequence in the 5'-UTR RNA which plays an important role in expression of N-ras, were selected. The secondary structures of five selected RNA aptamers including primer sequence were found by the CLC RNA workbench ver. 4.2 program (www.clcbio.com) and investigated with RNA structural probes such as RNase T1 which has specificity for a G in single-stranded region, RNase V1 specific for double strand and nuclease S1 specific for single strand. The generalized secondary structure model was proposed and characterized. It was composed of a central long double strand region flanked by single strand region at both end sides. The double strand region had an internal single-strand region and bulges. The single strand loop in the right side was composed of four or five nucleotides.

• Journal of Radiation Protection and Research
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• v.26 no.2
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• pp.101-111
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• 2001

To study the relationship between the DNA content of human chromosomes and their involvement in radiation-induced structural chromosome aberrations, the frequencies of translocations and dicentrics induced in human lymphocytes after in vitro exposure to 2Gy of x-tay were analysed by fluorescence in situ hybridization(FISH). Single whole chromosome probes(WCP), specific for chromosomes 1, 2, 4, 7, 8, 9, and 21 and triple combination of probes tot chromosome 1, 2 & 4 were used separately. A significant deviation of the frequency of symmetrical translocation and dicentrics from a DNA-proportional distribution was observed. Chromosomes 2, 7, 8, 9 and 21 were less frequently involved in the formation of symmetrical translocations and dicentrics than expected, whereas chromosomes 1 and 4 were more frequently involved. Chromosome 2 and 4 showed a higher frequency of acentric fragments. When triple combination probe for chromosome 1, 2 & 4 was used, no differences were found between the observed and expected frequency of exchange type aberrations. The results showed that the frequency of radiation-induced chromosome aberrations was not proportional to DNA contents, suggesting the difference in the susceptibility to specific aberrations among individual chromosomes. The results also indicated that the FISH technique with combination of probes for chromosome 1, 2 & 4 was useful for radiation biodosimetry.

• Journal of Radiopharmaceuticals and Molecular Probes
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• v.9 no.1
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• pp.17-21
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• 2023

In this study, we evaluated the targeting of prostate cancer (PCa) using [¹⁸F]Florastamin in non-clinical study, for the purpose of therapeutic monitoring of [¹⁷⁷Lu]Ludotadipep, a therapeutic radiopharmaceutical for PCa, [¹⁸F]Florastamin/[¹⁷⁷Lu]Ludotadipep was co-administered to a single-individual prostate tumor bearing mouse model, mimicking clinical condition. Considering the difference in half-life of the two isotopes (¹⁸F or ¹⁷⁷Lu), image scan of whole-body autoradiography was performed at 24 or 48 h after preparation of frozen section, respectively. Then, it was confirmed whether they showed the same targeting efficiency for the area of tumor. A tumor xenograft model was prepared using PSMA-overexpressing PC3-PIP prostate cancer cells. [¹⁸F]Florastamin [111 MBq (3 mCi) in 100 µL]/¹⁷⁷Lu]Ludotadipep [3.7 MBq (100 µCi) in 100 µL] was co-administered through the tail vein, and 2 hours after administration, the mice were frozen, and after freezing for 24 hours, whole-body cryosection was performed at 24 h after freezing. Image scanning using cryosection was performed after 24 or 48 hours after freezing, respectively. In the scan image after 24 hours, tumor uptake of [¹⁸F] Florastamin/[¹⁷⁷Lu]Ludotadipep were simultaneously observed specific uptake in the tumor. In the scan image after 48 hours in the same section, signal of ¹⁸F was lost by decay of radioisotope, and specific uptake image for [¹⁷⁷Lu]Ludotadipep was observed in the tumor. Uptake of [¹⁷⁷Lu]Ludotadipep was specific to the same tumor region where [¹⁸F]Florastamin/[¹⁷⁷Lu]Ludotadipep was uptake. These results suggested that [¹⁸F]Florastamin showed the same tumor uptake efficiency to PCa as [¹⁷⁷Lu]Ludotadipep, and effective therapeutic monitoring is expected to be enable using [¹⁸F]Florastamin during [¹⁷⁷Lu]Ludotadipep therapy for PCa.

• Environmental Mutagens and Carcinogens
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• v.22 no.2
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• pp.90-96
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• 2002

Benzene is a widespread human carcinogen, inducing leukemia and hematotoxicity. Exposure to benzene metabolites has been shown to cause genetic damage, including aneusomy and chromosome aberrations. Fluorescence in situ hybridization(FISH) procedure was used to determine if the benzene metabolite, 1, 2, 4-benzenetriol(BT), hydroquinone(HQ) and trans, trans-muconic acid(t,t-MA) induced specific chromosomal change in HL-60 cells. Treatment with BT, HQ and t,t-MA resulted in the induction of monosomy 8 and 21 in HL-60 cells in a dose-dependent manner. All of these metabolites also induced trisomy 8 and 21, but no correlation between frequencies of trisomy and concentration was found. Translocations between chromosome 8 and another unidentified chromosome ［t(8:\ulcorner)］, and between chromosome 21 and another unidentified chromosome ［t(8:21)］ were found. However, translocation between chromosome 8 and 21 ［t(8:21)］ was not found. Results indicate that the benzene metabolites, BT, HQ and t,t-MA, induce chromosome specific numerical and structural aberrations, and the fluorescence in situ hybridization (FISH) approach may be a useful and powerful technique for detection of aneuploidy.

• Animal cells and systems
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• v.2 no.4
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• pp.529-538
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• 1998

In order to analyze the intracellu1ar localization of specific RNA components of ribonucleoproteins (RNP) in Xenopus oocytes, a modified protocol of whole-mount in situ Hybridization is presented in this paper, Mitochondria specific 12S rRNA probe was used to detect the amplification and distribution of mitochondria in various stages of the oocyte life cycle, and the results were found to be consistent with previously known distribution of mitochondria. The results with other specific probes (U1 and U3 small nuclear RNAs, and 5S RNA) also indicate that this procedure is generally effective in localizing RNAs in RNP complexes even inside organelles. In addition, the RNA component of RNase MRP, the RNP with endoribo-nuclease activity, localize to the nucleus in various stages of the oocyte life cycle. Some of MRP RNA, however, were found to be localized to the special population of mitochondria near the nucleus, especially in the active stage of mitochondrial amplification. It suggests dual localization of RNase MRP in the nucleus and mitochondria, which is consistent with the proposed roles of RNase MRP in mitochondrial DNA replication and in rRNA processing in the nucleolus.