• Genomics & Informatics
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• 제10권1호
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• pp.51-57
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• 2012

Mining interesting patterns from DNA sequences is one of the most challenging tasks in bioinformatics and computational biology. Maximal contiguous frequent patterns are preferable for expressing the function and structure of DNA sequences and hence can capture the common data characteristics among related sequences. Biologists are interested in finding frequent orderly arrangements of motifs that are responsible for similar expression of a group of genes. In order to reduce mining time and complexity, however, most existing sequence mining algorithms either focus on finding short DNA sequences or require explicit specification of sequence lengths in advance. The challenge is to find longer sequences without specifying sequence lengths in advance. In this paper, we propose an efficient approach to mining maximal contiguous frequent patterns from large DNA sequence datasets. The experimental results show that our proposed approach is memory-efficient and mines maximal contiguous frequent patterns within a reasonable time.

• Biomolecules & Therapeutics
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• 제11권2호
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• pp.139-144
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• 2003

Ganoderma lucidum is commonly known as medically potent mushroom, which has been widely used in China and other oriental countries for the treatment of various diseases, including cancer. In this report, we investigated the anti-oxidant and protective effect of Ganodema lucidum extract (GLE) against the DNA damage induced by free radical and U.V. In the assay of cell growth inhibition, the inhibitory cell growth rate induced by hydroxyl radical was dose-dependently decreased by GLE. This results support that GLE has a detoxifying activity against cytotoxicity of hydroxyl radical in E. coli cell. GLE also protected ColE1 plasmid DNA damage in the concentration of 200$\mu\textrm{g}$ per reaction on the DNA fragmentation assay. The nuclear tailing by hydrogen peroxide in single cell gel electrophoresis(SCGE) was decreased by GLE in the concentration of 50$\mu\textrm{g}$/ml. These data indicate that Ganoderma lucidum has an anti-oxidative activity to hydrogen peroxide. The mutation rate after irradiation of U.V. was reduced by 50$\mu\textrm{g}$/ml GLE and total number of Rif (Rifampicin) resistant mutants was decreased in a concentration dependent manner when added the GLE exogenously in a culture media. According to the results, it is likely that GLE has not only an anti-oxidative activity to hydroxyl radical but also an anti-mutagenic activity to U.V. mutagenesis.

• Journal of Ecology and Environment
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• 제34권3호
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• pp.323-331
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• 2011

Biodiversity and the community composition of micro-eukaryotic organisms were investigated in the Upo wetland in Korea using molecular analysis. Molecular identification was performed using cytochrome oxidase I (COI) and small subunit ribosomal DNA (SSU rDNA). The genomic DNA was isolated directly from soil samples. The COI and SSU rDNA regions were amplified using universal primers and then sequenced after cloning. In a similarity search of the obtained sequences with BLAST in the Genbank database, the closely related sequences from NCBI were used to identify the amplified sequences. A total of six eukaryotic groups (Annelida, Arthropoda, Rotifera, Chlorophyta, Bacillariophyta, and Stramenopiles) with COI and six groups (Annelida, Arthropoda, Rotifera, Alveolata, Fungi, and Apicomplexa) with SSU rDNA genes were determined in the Upo wetland. Among 38 taxa in 20 genera, which are closely related to the amplified sequences, 10 genera (50%) were newly reported in Korea and five genera (25%) were shown to be distributed in the Upo wetland. This approach is applicable to the development of an efficient method for monitoring biodiversity without traditional taxonomic processes and is expected to produce more accurate results in depositing molecular barcode data in the near future.

• 대한의생명과학회지
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• 제12권4호
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• pp.349-354
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• 2006

Induction of apoptosis allows the organism to get rid of abnormal cells and also of tumor cells. Understanding the mechanism involved in Ultraviolet radiation (UV) induced apoptosis may improve its therapeutic efficacy. In this study, we present expression of poly (ADP-ribose) polymerase (PARP) during apoptosis induced by UV in HeLa $S_3$ cells. Four different assays were performed in this study: morphological assessment of apoptotic cells and cell viability, DNA fragmentation analysis by agarose gel electrophoresis, quantitative assay of fragmented DNA, and expression of PARP by the western blot analysis. The percentages of apoptotic HeLa $S_3$ cells irradiated with $75J/m^2$ UV was increased continuously from 3 hrs incubation. DNA ladder pattern was appeared at 6 hrs. The amount of nucleosomal DNA fragments in cells treated UV increased from 3 to 12 hrs incubation and gradually decreased. The cleavage of PARP in HeLa $S_3$ cells irradiated with UV was induced, and the cleavage of PARP was more delayed in the cells pretreated with $5J/m^2$ UV and subsequently irradiated with $75J/m^2$ UV. than that in the cells only irradiated with $75J/m^2$ UV. Thus these data suggest that the cleavage of PARP relates with DNA fragmentation associated with apoptosis.

• Mycobiology
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• 제28권1호
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• pp.11-16
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• 2000

The nucleotide sequences of the internal transcribed spacer (ITS) regions of the ribosomal DNA including the 5.8S ribosomal RNA gene (rDNA) have been determined for 11 species in order to analyze their intrageneric relationships. The total length of these sequences ranged from 530 nucleotides for Trichoderma reesei KCTC 1286 to 553 nucleotide for Trichoderma koningii IAM 12534. Generally speaking, the length of ITS1 region was about 30 nucleotides longer than that of the ITS2 region. Also, the sequences of 5.8S rDNA were more conserved in length and variation than those of ITS regions. Although the variable ITS sequences were often ambiguously aligned, the conserved sites were also found. Thus, a neighbor-joining tree was constructed using the full sequence data of the ITS regions and the 5.8S rDNA. The Trichoderma genus used to be grouped on the basis of the morphological features and especially the shape of phialides needs to be reexamined. The phylogenetic tree displayed the presence of monophylogeny in the species of Trichoderma. Therefore, it was difficult to distinguish the intrageneric relationships in the Trichoderma genus.

• Journal of Species Research
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• 제9권4호
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• pp.413-426
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• 2020

The Euphorbiaceae family features some of the most economically important plants that are sources of foods, oils, waxes, and medicines. The accurate identification of Euphorbiaceae species is critical in sustainable utilization of plant resources. We examined 234 sequences of nrDNA ITS, cpDNA rbcL and matK loci from 20 species in Euphorbiaceae in Korea and three outgroup taxa to develop efficient DNA barcodes. The three barcode loci were successfully amplified and sequenced for all Euphorbiaceae species. nrDNA ITS locus showed the highest mean interspecific K2P distance (0.3034), followed by cpDNA matK (0.0830), and rbcL (0.0352) locus. The degree of species resolution for individual barcode loci ranged from 75% (rbcL and matK) to 80% (ITS). The degree of species resolution was not enhanced with the different combinations of three barcode loci. The combined data set of the three loci(ITS+rbcL+matK) provided 80% of species resolution. These results confirm that ITS locus, as a single barcode, is the best option for barcoding of the Euphorbiaceae in Korea.

• 대한전기학회논문지:전기물성ㆍ응용부문C
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• 제51권6호
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• pp.265-270
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• 2002

The determination of DNA hybridization reaction can apply the molecular biology research, clinic diagnostics, bioengineering, environment monitoring, food science and application area. So, the improvement of DNA hybridization detection method is very important for the determination of this hybridization reaction. Several molecular biological techniques require accurate predictions of matched versus mismatched hybridization thermodynamics, such as PCR, sequencing by hybridization, gene diagnostics and antisense oligonucleotide probes. In addition, recent developments of oligonucleotide chip arrays as means for biochemical assays and DNA sequencing requires accurate knowledge of hybridization thermodynamics and population ratios at matched and mismatched target sites. In this study, we report the characteristics of the probe and matched, mismatched target oligonucleotide hybridization reaction using thermodynamic method. Thermodynamic of 5 oligonucleotides with central and terminal mismatch sequences were obtained by measured UV-absorbance as a function of temperature. The data show that the nearest-neighbor base-pair model is adequate for predicting thermodynamics of oligonucleotides with average deviations for $\Delta$H$^{0}$ , $\Delta$S$^{0}$ , $\Delta$G$_{37}$ $^{0}$ and T$_{m}$, respectively.>$^{0}$ and T$_{m}$, respectively.

• Bulletin of the Korean Chemical Society
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• 제15권5호
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• pp.364-368
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• 1994

Growth inhibition potency of the anthraquinones, anthraquinone-1,5-disulfonic acid and carminic acid, for Sarcoma 180 and L1210 leukemia cells in vivo and in vitro, was induced by the divalent transition metal ion, $Cu^{2+}$. On the other hand spectroscopic titration data show that the anthraquinone drugs form $Cu2^+$ chelate complexes (carminic acid : $Cu^{2+}$ = 1 : 6; anthraquinone-1,5-disulfonic acid : $Cu^{2+}$ = 1 : 3). Furthermore the $Cu^{2+}$-drug complexes associate with DNA to form the $Cu^{2+}$-anthraquinone-DNA ternary complexes. The formation of the complexes was further supported by the $H_2O_2-dependent$ DNA degradation, which can be inhibited by ethidium bromide, caused by the $Cu^{2+}$-drug complexes. It is likely that the $Cu^{2+}$-mediated cytotoxicity of the anthraquinone drugs is related with the $Cu^{2+}-mediated$ binding of the anthraquinone drugs to DNA and DNA degradation.

• Molecules and Cells
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• 제45권8호
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• pp.522-530
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• 2022

Transposable elements (TEs) account for approximately 45% of the human genome. TEs have proliferated randomly and integrated into functional genes during hominoid radiation. They appear as right-handed B-DNA double helices and slightly elongated left-handed Z-DNAs. Human endogenous retrovirus (HERV) families are widely distributed in human chromosomes at a ratio of 8%. They contain a 5'-long terminal repeat (LTR)-gag-pol-env-3'-LTR structure. LTRs contain the U3 enhancer and promoter region, transcribed R region, and U5 region. LTRs can influence host gene expression by acting as regulatory elements. In this review, we describe the alternative promoters derived from LTR elements that overlap Z-DNA by comparing Z-hunt and DeepZ data for human functional genes. We also present evidence showing the regulatory activity of LTR elements containing Z-DNA in GSDML. Taken together, the regulatory activity of LTR elements with Z-DNA allows us to understand gene function in relation to various human diseases.

• Journal of Nutrition and Health
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• 제48권5호
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• pp.390-397
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• 2015

본 연구에서는 Sprague-Dawley 종 랫트 수컷을 대조군, EtOH군, Fe군, EtOH + Fe군으로 나누어, 알코올과 철분을 액상 사료로 8주간 공급한 후, 간 조직과 간 세포 mtDNA의 손상 정도를 알아보았다. EtOH + Fe군은 대조군, EtOH군, Fe군의 다른 세 군에 비해 혈청 ALT와 혈청 AST 수치가 가장 유의적으로 높았으며, 간 조직 검사의 결과에서도 다수의 지방구, 염증성 세포 침입 및 조직의 괴사가 관찰되는 등 가장 심한 간 손상이 확인되었다. DNA 손상 여부를 긴 영역 PCR을 사용하여 분석한 결과, 만성적인 알코올과 철분에 의한 노출은 간 세포의 mtDNA 손상을 유발하는 것으로 나타났으며, 핵 DNA에는 영향을 미치지 않았다. 또한 미토콘드리아의 호흡에 관여하는 Cox1과 Nd4 유전자 발현 정도를 real-time PCR으로 분석한 결과, 알코올 또는 철분은 간 세포의 Cox1 mRNA와 Nd4 mRNA 수준을 유의적으로 낮추는 것으로 나타났다. 이상의 결과는 만성 알코올 또는 과잉의 철분에 의한 간 손상에 mtDNA 손상 및 미토콘드리아 기능 저하가 관여함을 제시한다.