• 한국지능시스템학회:학술대회논문집
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• 한국퍼지및지능시스템학회 2004년도 춘계학술대회 학술발표 논문집 제14권 제1호
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• pp.97-100
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• 2004

The identification of the DNA structure as a double-stranded helix consting of two nucleotide chain molecules was a milestone in modern molecular biology. The DNA chip technology is based on reverse hybridization that follows the principle of complementary binding of double-stranded DNA. DNA chip can be described as the deposition of defined nucleic acid sequences, probes, on a solid substrate to form a regular array of elements that are available for hybridization to complementary nucleic acids, targets. DNA chips based on cDNA clons, oligonucleotides and genomic clons have been developed for gene expression studies, genetic variation analysis and genomic changes associated with disease including cancers and genetic diseases. DNA chips for gene expression profiling can be used for functional analysis in human eel Is and animal models, disease-related gene studies, assessment of gene therapy, assessment of genetically modified food, and research for drug discovery. DNA chips for genetic variation detection can be used for the detection of mutations or chromosomal abnormalities in cnacers, drug resistances in cancer cells or pathogenic microbes, histocompatibility analysis for transplantation, individual identification for forensic medicine, and detection and discrimination of pathogenic microbes. The DNA chip will be generalized as a useful tool in clinical diagnostics in near future. Lab-on-a chip and informatics will facilitate the development of a variety of DNA chips for diagnostic purpose.

• Fisheries and Aquatic Sciences
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• 제16권4호
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• pp.291-301
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• 2013

The genomic organization, tissue distribution, and developmental expression of two paralogous GAPDH isoforms were characterized in the mud loach Misgurnus mizolepis (Cypriniformes). The mud loach gapdh isoform genes (mlgapdh-1 and mlgapdh-2) had different exon-intron organizations: 12 exons in mlgapdh-1 (spanning to 4.88 kb) and 11 in mlgapdh-2 (11.78 kb), including a non-translated exon 1 in each isoform. Southern blot hybridization suggested that the mud loach might possess the two copies of mlgapdh-1 and a single copy of mlgapdh-2. The mlgapdh-1 transcript levels are high in tissues requiring high energy flow, such as skeletal muscle and heart, whereas mlgapdh-2 is expressed abundantly in the brain. Both isoforms are differentially regulated during embryonic and larval development, during which their expression is upregulated with the progress of development. Lipopolysaccharide challenge preferentially induced mlgapdh-2 transcripts in the liver. Therefore, the two isoforms have diversified functionally; mlgapdh-1 is associated more closely with energy metabolism, while mlgapdh-2 is related more to stress/immune responses, in the mud loach.

• The Plant Pathology Journal
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• 제17권3호
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• pp.115-122
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• 2001

Potato virus X (PVX) is a flexuous rod-shaped virus containing a single plus-strand RNA. Viral RNA synthesis is precisely regulated by regulatory viral sequences and by viral and/or host proteins. RNA sequence element as well as stable RNA stem-loop structure in the 5' end of the genome affect accumulation of genomic RNA and subgenomic RNA (sgRNA). The putative sgRNA promoter regions upstream of the PVX triple gene block (TB) and coat protein (CP) gene were critical for both TB and CP sgRNA accumulation. Mutations that disrupted complementarity between a region at the 5' end of the genomic RNA and the sequences located upstream of each sgRNA initiation site is important for PVX RNA accumulation. Compensatory mutations that restore complementarity restored sgRNA accumulation levels. However, the extent of reductions in RNA levels did not directly correlate with the degree of complementarity, suggesting that the sequences of these elements are also important. Gel-retardation assays showed that the 5' end of the positive-strand RNA formed an RNA-protein complex with cellular proteins, suggesting possible involvement of cellular proteins for PVX replication. Future studies on cellular protein binding to the PVX RNA and their role in virus replication will bring a fresh understanding of PVX RNA replication.

• 한국가금학회:학술대회논문집
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• 한국가금학회 2000년도 제17차 정기총회 및 학술발표
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• pp.78-80
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• 2000

A new murine TGF-$\beta$ family member, myostatin(growth/differentiation factor-8) is expressed specifically in developing and adult skeletal muscle and may be a negative regulator of skeletal muscle development. This study aims at characterization and identification of genomic organization of chicken myostatin gene. In thi study, we identified the genomic organization and sequence of chicken myostatin gene. Results of RT-PCR and Northern blots from various tissues showed different mRNA expression levels in developmental stages of chick embryos and demonstrated strong expression of myostatin mRNA in skeletal muscle. These facts suggest that chicken myostatin gene would play an important role not only in skeletal muscle cell but also in other tissues.

• Genomics & Informatics
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• 제11권4호
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• pp.164-173
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• 2013

Genomic instability, which occurs through both genetic mechanisms (underlying inheritable phenotypic variations caused by DNA sequence-dependent alterations, such as mutation, deletion, insertion, inversion, translocation, and chromosomal aneuploidy) and epigenomic aberrations (underlying inheritable phenotypic variations caused by DNA sequence-independent alterations caused by a change of chromatin structure, such as DNA methylation and histone modifications), is known to promote tumorigenesis and tumor progression. Mechanisms involve both genomic instability and epigenomic aberrations that lose or gain the function of genes that impinge on tumor suppression/prevention or oncogenesis. Growing evidence points to an epigenome-wide disruption that involves large-scale DNA hypomethylation but specific hyper-methylation of tumor suppressor genes, large blocks of aberrant histone modifications, and abnormal miRNA expression profile. Emerging molecular details regarding the modulation of these epigenetic events in cancer are used to illustrate the alterations of epigenetic molecules, and their consequent malfunctions could contribute to cancer biology. More recently, intriguing evidence supporting that genetic and epigenetic mechanisms are not separate events in cancer has been emerging; they intertwine and take advantage of each other during tumorigenesis. In addition, we discuss the collusion between epigenetics and genetics mediated by heterochromatin protein 1, a major component of heterochromatin, in order to maintain genome integrity.

• Ocean and Polar Research
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• 제43권4호
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• pp.371-374
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• 2021

Triglopsis quadricornis Linnaeus, 1758 (Cottidae) is distributed in the Atlantic and Arctic and has four unique bony protuberances on its head. Here, we report the complete, circular, and annotated mitochondrial genome of T. quadricornis. The complete T. quadricornis mitochondrion was sequenced by high-throughput Illumina HiSeq platform. The sequences are 16,736 bp in size and contains 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, a control region, and large and small ribosomal subunits. The overall genomic structure of T. quadricornis mitochondrion was conserved with the gene arrangement of Megalocottus and Myoxocephalus species, and phylogenetic analysis supports their sister relationships. Most PCGs consist of TAA or TAG as a termination codon, whereas COII, ND4, and CYTB have T-- as a stop codon. This complete mitochondrial DNA information of T. quadricornis will provide an essential genomic resource to elucidate the phylogenetic relationship and evolutionary history of the family Cottidae.

• Mycobiology
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• 제46권4호
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• pp.361-369
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• 2018

The rice blast fungus, Magnaporthe oryzae, is an important pathogen of rice plants. It is well known that genes encoded in the genome have different evolutionary histories that are related to their functions. Phylostratigraphy is a method that correlates the evolutionary origin of genes with evolutionary transitions. Here we applied phylostratigraphy to partition total gene content of M. oryzae into distinct classes (phylostrata), which we designated PS1 to PS7, based on estimation of their emergence time. Genes in individual phylostrata did not show significant biases in their global distribution among seven chromosomes, but at the local level, clustering of genes belonging to the same phylostratum was observed. Our phylostrata-wide analysis of genes revealed that genes in the same phylostratum tend to be similar in many physical and functional characteristics such as gene length and structure, GC contents, codon adaptation index, and level of transcription, which correlates with biological functions in evolutionary context. We also found that a significant proportion of genes in the genome are orphans, for which no orthologs can be detected in the database. Among them, we narrowed down to seven orphan genes having transcriptional and translational evidences, and showed that one of them is implicated in asexual reproduction and virulence, suggesting ongoing evolution in this fungus through lineage-specific genes. Our results provide genomic basis for linking functions of pathogenicity factors and gene emergence time.

• 한국환경과학회지
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• 제33권4호
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• pp.235-247
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• 2024

A total of 64 individuals of Acanthogobius flavimanus, which inhabit the coast of Korea, were collected from 8 regions from July to August 2023. A haplotype network and a phylogenetic tree were created. The genomic DNA of the target fish species was compared and analyzed with the genomic DNA of four regions in Japan downloaded from the National Center for Biotechnology Information (NCBI). In the haplotype network of Acanthogoboius flavimanus, Eocheong-do (EC) and Goseong (MAJ) exhibited low genetic similarity with other regions in Korea and Japan. The Phylogenetic tree showed that the population of MAJ exhibited differences in genetic structure compared to populations in other regions of Korea and Japan, indicating a distant relationship. Most marine organisms are known to migrate and spread via ocean currents, which is the most crucial factor promoting gene flow through larvae between populations. The haplotype of Acanthogobius flavimanus in MAJ differs from the haplotypes in Korea and Japan. The population in MAJ is believed to have limited genetic exchange due to the North Korea Cold Currents. We identified haplotype patterns based on the geographical distribution of Acanthogobius flavimanus off the coast of Korea and inferred that ocean currents have some influence on genetic distances.

• BMB Reports
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• 제49권10호
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• pp.560-565
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• 2016

Granzyme A (GzmA) was first identified as a cytotoxic T lymphocyte protease protein with limited tissue expression. A number of cellular proteins are known to be cleaved by GzmA, and its function is to induce apoptosis. Histones H1, H2B, and H3 were identified as GzmA substrates during apoptotic cell death. Here, we demonstrated that histone H4 was cleaved by GzmA during staurosporine-induced cell death; however, in the presence of caspase inhibitors, staurosporine-treated Raji cells underwent necroptosis instead of apoptosis. Furthermore, histone H4 cleavage was blocked by the GzmA inhibitor nafamostat mesylate and by GzmA knockdown using siRNA. These results suggest that histone H4 is a novel substrate for GzmA in staurosporine-induced cells.

• International Journal of Industrial Entomology and Biomaterials
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• 제7권2호
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• pp.181-189
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• 2003

We describe here the complete nucleotide sequence and the exon-intron structure of the luciferase gene of the firefly, Pyrocoelia rufa. The luciferase gene of the P. rufa firefly consisted of six introns and seven exons coding for 548 amino acid residues. From the translational start site to the end of last exon, however, the genomic DNA length of the P. rufa luciferase gene from the Korean and Chinese samples spans 1,968 bp and 1983 bp, respectively, and 3 amino acid residues were different to each other. Additionally, we also analyzed mitochondrial cytochrome oxidase I(COI) gene of the Chinese P. rufa fireflies. Analysis of DNA sequences from the mitochondrial COI protein-coding gene revealed 4 mitochondrial DNA sequence-based haplotypes with a maximum divergence of 0.7％. With the 20 P. rufa haplotypes found in Korea, phylogenetic analyses using PAUP and PHYLIP subdivided the P. rufa into three clades, termed clades A and B for the Korean sample, and clade C for the Chinese sample.