• International journal of advanced smart convergence
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• 제5권3호
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• pp.8-15
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• 2016

In recent years, one of deep learning models called Deep Belief Network (DBN) which formed by stacking restricted Boltzman machine in a greedy fashion has beed widely used for classification and recognition. With an ability to extracting features of high-level abstraction and deal with higher dimensional data structure, this model has ouperformed outstanding result on image and speech recognition. In this research, we assess the applicability of deep learning in dna classification level. Since the training phase of DBN is costly expensive, specially if deals with DNA sequence with thousand of variables, we introduce a new encoding method, using decimal-binary vector to represent the sequence as input to the model, thereafter compare with one-hot-vector encoding in two datasets. We evaluated our proposed model with different contrastive algorithms which achieved significant improvement for the training speed with comparable classification result. This result has shown a potential of using decimal-binary vector on DBN for DNA sequence to solve other sequence problem in bioinformatics.

• International Journal of Fuzzy Logic and Intelligent Systems
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• 제4권2호
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• pp.231-235
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• 2004

According to revealing the DNA sequence of human and living things, it increases that a demand on a new computational processing method which utilizes DNA sequence information. In this paper we propose a classification algorithm based on negative selection of the immune system to classify DNA patterns. Negative selection is the process to determine an antigenic receptor that recognize antigens, nonself cells. The immune cells use this antigen receptor to judge whether a self or not. If one composes n group of antigenic receptor for n different patterns, they can classify into n patterns. In this paper we propose a pattern classification algorithm based on negative selection in nucleotide base level and amino acid level.

• 대한수의학회지
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• 제41권3호
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• pp.357-365
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• 2001

This study was performed to detect the Salmonella genus-specific DNA marker for comparing of polymophisms between S pullorum and S gallinarum by using PCR amplified techniques. A total of ten primers were used to detect DNA polymorphisms from S pullorum and S gallinarum. The number of DAF bands detected per each primer varied from 26 to 45, with an average of 32.7 using 10 primers. A total of 327 DAF bands were generated and among them 123 bands were polymorphic(37.6%). These DNA amplified fingerprinting(DAF) specific bands for S pullorum and S gallinarum were observed from all primers. For S pullorum, GEN 60-04, GEN 70-04 and GEN 70-03 primers showed a high level of polymorphism with 0.79, 0.70 and 0.57, respectively. But GEN 60-05 primer did not show a level of polymorphism. For S gallinarum, GEN 70-03, 60-04, 60-07, 70-05 and 70-04 primers showed a higher a low level of polymorphism from 0.16 to 0.28. Each five strains of S pullorum and S gallinarum were isolated from chickens showed typical clinical signs related with infection of pullorum disease or fowl typhoid at commercial chicken farms. DNA markers of these strains produced by GEN 70-04, GEN 70-05 and GEN 70-08 showed significant difference of band patterns between S pullorum and S gallinarum. These DNA markers could be used for comparison of DNA marker polymorphism between S pullorum and S gallinarum as well as rapid diagnosis of fowl typhoid and pullorum disease of domestic fowls.

• International Journal of Oral Biology
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• 제38권1호
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• pp.21-27
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• 2013

Anginosus group streptococci (AGS) were classified based on the nucleotide sequences of the 16S rRNA gene (16S rDNA) and comprised Streptococcus anginosus, Streptococcus intermedius, and Streptococcus constellatus. It is known that AGS is a causative factor of oral and systematic diseases. The purpose of this study was to discriminate the 56 clinical strains of AGS isolated from Korean oral cavities using phylogenetic analysis of 16S rDNA and species-specific PCR at the species-level. The 16S rDNA of clinical strains of AGS was sequenced using the dideoxy chain termination method and analyzed using MEGA version 5 software. PCR was performed to identify the clinical strains using species-specific primers described in previous studies and S. intermedius-specific PCR primers developed in our laboratory. The resulting phylogenetic data showed that the 16S rDNA sequences can delineate the S. anginosus, S. intermedius, and S. constellatus strains even though the 16S rDNA sequence similarity between S. intermedius and S. constellatus is above 98%. The PCR data showed that each species-specific PCR primer pair could discriminate between clinical strains at the species-level through phylogenetic analysis of 16S rDNA nucleotide sequences. These results suggest that phylogenetic analysis of 16S rDNA and PCR are useful tools for discriminating between AGS strains at the species-level.

• International Journal of Oral Biology
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• 제38권1호
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• pp.29-36
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• 2013

Mitis group streptococci (MGS) were classified based on the nucleotide sequences 16S rRNA gene (16S rDNA) and comprised 13 Streptococcus species. However, 16S rDNA homogeneity among MGS was too high to discriminate between clinical strains at the species level, notably between Streptococcus mitis, Streptococcus oralis, Streptococcus pneumoniae, and Streptococcus pseudopneumoniae. The purpose of this study was to discriminate between 37 strains of MGS isolated from Korean oral cavities using phylogenetic analysis of the DNA-dependant RNA polymerase beta-subunit gene (rpoB). 16S rDNA and rpoB from clinical strains of MGS were sequenced using the dideoxy chain termination method and analyzed using MEGA version 5 software. The resulting phylogenetic data showed that the rpoB sequences could delineate clinical strains of MGS at the species level. Phylogenetic analysis of rpoB is therefore a useful approach for identifying MGS at the species level.

• Journal of Plant Biology
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• 제39권4호
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• pp.279-286
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• 1996

To know the changes of rbcL mRNA level by illumination, Northern hybridization analysis was performed with maize (Zea mays L.cv. Golden X Bantam). The average level of rbcL. mRNA in the light-grown shoots was 3.1 times higher than that of the dark-grown shoots after 6 to 10 growth days. The maximum difference of rbcL mRNA level between the dark-grown and the light-grown shoots was 5.1 folds. These results indicate that accumulation of rbcL mRNAin maize shoots is induced by light. Since the transcriptional DNA binding proteins and their cognate promoter elements, we carried out gel-retardation assays to elucidate the specific binding proteins on the rbcL promoter. It was found that plastid proteins of light-grown shoots bound to the R2 DNA fragment (-33 to -229) and R3 DNA fragment (-230 to -418 from ATG) of the rbcL promoter. From the results of competitive binding assays and heat or protease treatments, it was demonstrated that the bindings were sequence-specific DNA-protein interactions. Therefore, it could be concluded that the rbcL promoter region has at least two specific recognition sites for plastid proteins.

• 한국환경성돌연변이발암원학회지
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• 제17권2호
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• pp.71-77
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• 1997

The single cell gel electrophoressis(SCGE) assay, also known as the comet assay, is a rapid, simple, visual and sensitive technique for measuring and analysing DNA breakage in mammalian cells. The SCGE or comet assay is a promising test for the detection of DNA damage and repair in individnal cells. It has widespread potential applications in DNA damage and repair studies, genotoxicity testing and biomonitoring. In this microgel electrophoresis technique, cells are embedded in agarose gel on microscope slides, iysed and electrophoresed under alkaline conditions. Cells with increased DNA damage display increased migration of DNA from the nucleus towards the anode. The length of DNA migration indicates the amount of DNA breakage in the cell. The comet assay is also capable of identifying apoptotic cells which contain highly fragmented DNA. Here we review the development of the SCGE assay, existing protocols for the detection and analysis of comets, the relevant underlying principles determining the behaviour of DNA and the potential applications of the technique.

• 생명과학회지
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• 제23권1호
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• pp.31-37
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• 2013

본 연구는 줄날도래(Hydropsyche kozhantschikovi) 에탄올 추출물이 산화적 스트레스에 미치는 영향을 알아보기 위해 활성산소에 의한 세포와 DNA의 손상 억제력을 조사하였다. 줄날도래 에탄올 추출물의 DPPH 유리 라디칼과 수산화 라디칼 제거능은 대조군에 비해 각각 60.4%, 60.0%로 나타났으며, $Fe^{2+}$-chelating 효과는 37.5%로 조사되었다. 줄날도래 추출물이 활성산소에 의해 유도되는 세포손상에 미치는 억제 효과를 조사하기 위해 지질과산화의 상대적 수준과 p21 단백질의 발현율을 해보면 줄날도래 추출물은 라디칼 처리군에 비해 지질과산화를 거의 완벽하게 억제하고 있으며, p21 단백질의 발현은 대조군의 92.2%로 회복되는 것으로 조사되었다. 또한 줄날도래 추출물의 DNA 분절화 억제 활성은 대조군에 비해 74.1%로 나타나 산화적 스트레스에 의해 유발되는 DNA 분절화를 효율적으로 억제하고 있으며, H2AX 단백질의 인산화비는 라디칼 처리군의 16.7%에 해당하는 수준으로 조사되어 줄날도래 추출물은 히스톤 단백질의 인산화를 83.3% 억제하는 것으로 확인되었다. 이러한 결과로 보아 줄날도래 추출물은 활성산소에 대한 항산화 효과 뿐만 아니라 세포와 DNA의 손상을 억제하는데 효과적인 것으로 사료된다.

• Journal of Genetic Medicine
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• 제2권1호
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• pp.31-34
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• 1998

The N-methylpurine-DNA glycosylase (MPG), a ubiquitous DNA repair enzyme, removes N-methylpurine and other damaged purines induced in DNA. Tissue-specific mRNA levels of the N-methylpurine-DNA glycosylase (MPG) were investigated in Balb/c mice of four different growing stages; newborn, 1, 4 and 8-weeks postpartum. MPG expressions in the newborn and the 8-week-old mice were the highest in thymus and testis, respectively. The tested tissues of the newborn mice had consistently higher MPG mRNA level than 8-week-old adults except in testis and thymus. The MPG mRNA level in testis was the lowest in the newborn mice, but it attained the highest in the 8-week-old mice. The levels of MPG mRNA among the different tissues in the newborn and the 8-week-old mice were more than 9.0 and 19.0-fold respectively. These results suggest that the of MPG expression was dependent on the growing stage and had tissue-specificity.

• Toxicological Research
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• 제8권2호
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• pp.331-342
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• 1992

The chicken major histocompatibility complex (MHC), the B complex, is beginning to be analyzed at the DNA level. Inbred lines of chickens have been reported to possess 3~5 MHC class II genes. To further analyzed the molecular structure of the chicken MHC class II genes, cDNA clones coding for chicken MHC class II (B-L) ${\beta}$ chain molecules were isolated from chicken spleen and liver. Tissue-specific transcription of B-L ${\beta}$genes was studied by Northern blot analysis. A high level of expression was detected for spleen poly(A)$^+$ RNA whereas a faint signal was detected for liver poly(A)$^+$ RNA. Twenty-nine cDNA clones were isolated from the spleen and eight cDNA clones were isolated from the liver. Based on restriction maps, most clones could be clustered into one family of genes. Four cDNA clones were sequenced (S7, S10 and S19 from the spleen and L1, which was identical to S19, from the liver). Complete amino acid sequences of B-L ${\beta}$ chain molecules were predicated from the nucleotide sequences of the cDNA clones. Although both the nature and the location of the conserved residues were similar in chicken and mammalian sequences, some species-specific differences were found, suggesting that the structures of the B-L molecules are similar, but not identical to their mammalian counterparts.