• Applied Microscopy
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• v.51
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• pp.4.1-4.12
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• 2021

Fluorescence in situ hybridization (FISH) is a technique to visualize specific DNA/RNA sequences within the cell nuclei and provide the presence, location and structural integrity of genes on chromosomes. A confocal Whole Slide Imaging (WSI) scanner technology has superior depth resolution compared to wide-field fluorescence imaging. Confocal WSI has the ability to perform serial optical sections with specimen imaging, which is critical for 3D tissue reconstruction for volumetric spatial analysis. The standard clinical manual scoring for FISH is labor-intensive, time-consuming and subjective. Application of multi-gene FISH analysis alongside 3D imaging, significantly increase the level of complexity required for an accurate 3D analysis. Therefore, the purpose of this study is to establish automated 3D FISH scoring for z-stack images from confocal WSI scanner. The algorithm and the application we developed, SHIMARIS PAFQ, successfully employs 3D calculations for clear individual cell nuclei segmentation, gene signals detection and distribution of break-apart probes signal patterns, including standard break-apart, and variant patterns due to truncation, and deletion, etc. The analysis was accurate and precise when compared with ground truth clinical manual counting and scoring reported in ten lymphoma and solid tumors cases. The algorithm and the application we developed, SHIMARIS PAFQ, is objective and more efficient than the conventional procedure. It enables the automated counting of more nuclei, precisely detecting additional abnormal signal variations in nuclei patterns and analyzes gigabyte multi-layer stacking imaging data of tissue samples from patients. Currently, we are developing a deep learning algorithm for automated tumor area detection to be integrated with SHIMARIS PAFQ.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.147-150
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• 2005

Proper PCR primer design determines the success or failure of Polymerase Chain Reaction (PCR) reactions. In this project, we develop GENE-PRIMER, a genomes specific PCR primer design program that is amenable to a genome-wide scale. To achieve this, we incorporated various parameters with biological significance into our program, namely, primer length, melting temperature of primers Tm, guanine/cytosine (GC) content of primer, homopolymeric runs in primer and self-hybridization tendency of primer. In addition, BLAST algorithm is utilized for the purpose of primer specificity check. In summary, selected primers adhered to both physico-chemical criteria and also display specificity to intended binding site in the genome.

• Mycobiology
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• v.34 no.2
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• pp.104-107
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• 2006

Flammulina velutipes was transformed efficiently by Agrobacterium-mediated transformation system. The transformation frequency was about 16% with the gill tissues of the fungal fruiting body. Southern hybridization and genetic analysis suggest that the introduced DNA was inserted onto different locations of the fungal genome, and inherited stably to the next generation via basidiospores. Transformation or gene tagging with Agrobacterium T-DNA based vector should be useful for wide ranges of genetic or molecular biological studies of the mushroom.

• Proceedings of the Korean Society of Crop Science Conference
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• 2020.11a
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• pp.143-143
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• 2020

• Journal of Life Science
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• v.11 no.1
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• pp.1-7
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• 2001

The caffeine intake cause a local or wide ranges of convulsion and it is associated with release of dopamine (DA) receptors into the brain striatum. However, the effect of caffeine addiction on expression of DA receptors gene in the rat caudate-putamen (CPu), nucleus accumbens (NAc), and olfactory tubercle (OTu) has not been elucidated. In this study, we examined the influence of caffeine addiction on DA D $_1$and D$_2$receptor mRNAs after the treatment of caffeine for four weeks. Using the specific antisense ribo-probes for DA D$_1$and D$_2$receptor cDNAs, in situ hybridization was performed on the CPu, NAc, and OTu of the adult male Sprague Dawely rats. In caffeine-treated group, DA D$_1$and D$_2$receptor mRNAs were highly increased in CPu, NAc, and OTu. The expression density of DA D$_1$receptor mRNAs were 2.52${\pm}$1.40 (CPu), 2.78${\pm}$1.69 (NAc), and 3.91${\pm}$1.28 (OTu) in control group and 7.76${\pm}$2.09 (CPu), 4.2 ${\pm}$1.85 (NAc), and 8.21${\pm}$1.72 (OTu) in caffeine-treated group. The expression density of DA D$_2$receptor mRNA was 2.32${\pm}$1.52 (CPu), 2.63${\pm}$2.11 (NAc), and 3.61${\pm}$1.43 (OTu) in control group, and 6.41${\pm}$1.82 (CPu), 6.89${\pm}$1.32 (NAc), and 6.82${\pm}$1.18 (OTu) in caffeine-treated group. DA D$_1$receptor mRNA was higher expressed than DA D$_2$ receptor mRNA in CPu and NAc. These results suggest that caffeine reacts as a upregulator of the expression of DA D$_1$and D$_2$receptor mRNA among the neurotransmitters.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2022.09a
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• pp.37-37
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• 2022

밀은 세계 3대 작물로 국내 1인당 소비량은 지속적으로 증가하고 있다. 하지만 국내 밀의 유전적 배경 확대와 기후변화 신속 대응을 위한 국내 밀 유전자 풀의 확장은 밀의 질적 향상을 위해 매우 중요한 목표이다. 국내 자생 갯그령(Leymus mollis)은 해안가에서 번식하는 영년생 식물로 뿌리줄기를 이용한 왕성한 번식력을 가지고 있다. 또한, 해안가의 뜨겁고 염에 대한 적응성과 저항성을 가지고 있다. 이러한 특성은 밀 유전자 풀의 확장에 매우 유용할 것이다. 국내 밀 재배지 한계 극복을 위한 간척지 재배가 가능한 내염성 강화 밀 자원 개발을 위하여 모본인 보통 밀(Triticum aestivum L., Chinese Spring)과 부본인 갯그령을 원연교배하였다. 갯그령과 보통 밀의 원연 교배를 통한 종자 형성은 매우 어려우나 불가능한 것은 아니며, 최종적으로 10개의 교배 종자를 얻어 F₁ 식물체로 생장하는 과정에서 5 식물체는 고사하였고, 나머지 5 식물체는 영년생 특성인 뿌리줄기에 의해 새로운 줄기가 출현하는 것을 확인하였다. 또한, 갯그령의 DNA를 이용한 genomic in situ hybridization 방법으로 F₁ 식물체에서 갯그령의 염색체가 밀의 유전적 배경에 이입된 것을 확인하였다. F₂ 식물체는 모본인 보통 밀보다 긴 수장과 간장을 나타내고 이삭 수는 많았지만, 출수기는 보통 밀보다 3주 이상 늦어지는 것을 확인하였다. 내염성 평가를 위하여 F₂ 종자를 2% 소금물에서 발아시켜 생육이 좋은 식물체를 선발하여 50 cm 투명 아크릴 원통에 이식하고 2% 소금물을 지속적으로 관개하였다. 내염성 강화 F₂ 식물체는 염에 감수성을 보인 식물체에 비하여 상대적으로 긴 이삭과 종자 형성을 보였으며, 감수성 식물체는 종자 형성이 이루어지지 않았다. 또한, 내염성 강화 F₂ 식물체는 감수성 식물체에 비하여 좋은 뿌리의 신장과 천근성을 보였다. 이러한 갯그령의 식물학적 특성이 이입된 계통은 기후변화 대응, 환경 적응성 강화, 및 근권 강화에 좋은 작물 소재로 이용할 수 있다고 생각한다.

• Journal of Life Science
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• v.19 no.4
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• pp.449-456
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• 2009

Murine Neuro-2a (N2a) cells have been widely used for the investigation of neuronal differentiation, trophic interaction and neurotoxic effects of various compounds and their associated mechanisms. N2a cells have many genomic variations such as gains or losses in DNA copy number, similar to other neuroblastoma cells, and no systematic or high-resolution studies of their genome-wide chromosomal aberrations have been reported. Presently, we conducted a systematic genome-wide determination of chromosomal aberrations in N2a cells using a high-throughput, oligonucleotide array-based comparative genomic hybridization (oaCGH) technique. A hidden Markov Model was employed to assign each genomic oligonucleotide to a DNA copy number state: double loss, single loss, normal, gain, double gain and amplification. Unlike most neuroblastoma cells, Mycn amplification was not observed in N2a cells. In addition, these cells showed gain only in the neuron-derived neurotrophic factor (NF), while other neurotrophic factors such as glial line-derived NF and brain-derived NF presented normal copy numbers. Chromosomes 4, 8, 10, 11 and 15 displayed more than 1000 aberrational oligonucleotides, while chromosomes 3, 17, 18 and 19 displayed less than 20. The largest region of gain was located on chromosome 8 and its size was no less than 26.7 Mb (Chr8:8427841-35162415), while chromosome 4 had the longest region of single deletion, with a size of 15.1 Mb (Chr4:73265785-88374165).

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2001.10a
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• pp.61-86
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• 2001

All cancers are caused by abnormalities in DNA sequence. Throughout life, the DNA in human cells is exposed to mutagens and suffers mistakes in replication, resulting in progressive, subtle changes in the DNA sequence in each cell. Since the development of conventional and molecular cytogenetic methods to the analysis of chromosomal aberrations in cancers, more than 1,800 recurring chromosomal breakpoints have been identified. These breakpoints and regions of nonrandom copy number changes typically point to the location of genes involved in cancer initiation and progression. With the introduction of molecular cytogenetic methodologies based on fluorescence in situ hybridization (FISH), namely, comparative genomic hybridization (CGH) and multicolor FISH (m-FISH) in carcinomas become susceptible to analysis. Conventional CGH has been widely applied for the detection of genomic imbalances in tumor cells, and used normal metaphase chromosomes as targets for the mapping of copy number changes. However, this limits the mapping of such imbalances to the resolution limit of metaphase chromosomes (usually 10 to 20 Mb). Efforts to increase this resolution have led to the "new"concept of genomic DNA chip (1 to 2 Mb), whereby the chromosomal target is replaced with cloned DNA immobilized on such as glass slides. The resulting resolution then depends on the size of the immobilized DNA fragments. We have completed the first draft of its Korean Genome Project. The project proceeded by end sequencing inserts from a library of 96,768 bacterial artificial chromosomes (BACs) containing genomic DNA fragments from Korean ethnicity. The sequenced BAC ends were then compared to the Human Genome Project′s publicly available sequence database and aligned according to known cancer gene sequences. These BAC clones were biotinylated by nick translation, hybridized to cytogenetic preparations of metaphase cells, and detected with fluorescein-conjugated avidin. Only locations of unique or low-copy Portions of the clone are identified, because high-copy interspersed repetitive sequences in the probe were suppressed by the addition of unlabelled Cotl DNA. Banding patterns were produced using DAPI. By this means, every BAC fragment has been matched to its appropriate chromosomal location. We have placed 86 (156 BAC clones) cytogenetically defined landmarks to help with the characterization of known cancer genes. Microarray techniques would be applied in CGH by replacement of metaphase chromosome to arrayed BAC confirming in oncogene and tumor suppressor gene: and an array BAC clones from the collection is used to perform a genome-wide scan for segmental aneuploidy by array-CGH. Therefore, the genomic DNA chip (arrayed BAC) will be undoubtedly provide accurate diagnosis of deletions, duplication, insertions and rearrangements of genomic material related to various human phenotypes, including neoplasias. And our tumor markers based on genetic abnormalities of cancer would be identified and contribute to the screening of the stage of cancers and/or hereditary diseases

• Journal of Microbiology and Biotechnology
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• v.15 no.6
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• pp.1240-1249
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• 2005

Saccharomyces cerevisiae KNU5377 has potential as an industrial strain that can ferment wasted paper for fuel ethanol at $40^{\circ}C$ [15, 16]. To understand the characteristics of the strain, genome-wide expression was performed using DNA microarray technology. We compared the homology of the DNA microarray between genomic DNAs of S. cerevisiae KNU5377 and a control strain, S. cerevisiae S288C. Approximately $97\%$ of the genes in S. cerevisiae KNU5377 were identified with those of the reference strain. YHR053c (CUP1), YLR155c (ASP3), and YDR038c (ENA5) showed lower homology than those of S. cerevisiae S288C. In particular, the differences in the regions of YHR053c and YLR155c were confirmed by Southern hybridization, but did not with that of the region of YDR038c. The expression level of mRNA in S. cerevisiae KNU5377 and S288C was also compared: the 550 ORFs of S. cerevisiae KNU5377 showed more than two-fold higher intensity than those of S. cerevisiae S288C. Among the 550 ORFs, 59 ORFs belonged to the groups of ribosomal proteins and mitochondrial ribosomal proteins, and 200 ORFs belonged to the group of cellular organization. DIP5 and GAP1 were the most highly expressed genes. These results suggest that upregulated DIP5 and GAP 1 might take the place of ASP3 and, additionally, the sensitivity against copper might be contributable to the lowest expression level of copper-binding metallothioneins encoded by CUP 1a (YHR053c) and CUP1b (YHR055c) in S. cerevisiae KNU5377.

• International Journal of Industrial Entomology and Biomaterials
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• v.47 no.1
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• pp.1-11
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• 2023

The Indian golden muga silkworm, Antheraea assamensis Helfer is an economically important wild silkworm endemic to Northeastern part of India. In recent years, climate change has posed a threat to muga silk production due to the requirement that larvae be reared outdoors. Since the muga silkworm larvae are exposed to the vagaries of nature, the changing climate has increased the incidence of microbial diseases in the rearing fields. Accurate diagnosis of the disease causing pathogens and its associated epidemiology are prerequisites to manage the diseases in the rearing field. Although conventional microbial culturing methods are widely used to identify pathogenic bacteria, they would not provide meaningful information on a wide variety of silkworm pathogens. The information on use of molecular diagnostic tools in detection of microbial pathogens of wild silk moths is very limited. A wide range of molecular and immunodiagnostic techniques including denaturing gradient gel electrophoresis (DGGE), random amplified polymorphism (RAPD), 16S rRNA/ITSA gene sequencing, multiplex polymerase chain reaction (M-PCR), fluorescence in situ hybridization (FISH), immunofluorescence, and repetitive-element PCR (Rep-PCR), have been used for detecting and characterizing the pathogens of insects with economic significance. Nevertheless, the application of these molecular tools for detecting and typing entomopathogens in surveillance studies of muga silkworm rearing is very limited. Here, we discuss the possible application of these molecular techniques, their advantages and major limitations. These methods show promise in better management of diseases in muga ecosystem.