• Parasites, Hosts and Diseases
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• v.31 no.3
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• pp.285-292
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• 1993

C. sinensis total RMh was containing large amount of 185 rRNA but little 285 rRNA. The size of the double-stranded cDNA synthesized from poly $(A)^{+}$ mRNA was 0.4-4.2 kb long with tapering unto 9.5 kb. Degenerated oligonucleotides (as 2 sense and 3 antisense Primers) were designed on the conserved regions of the known tropomyosin amino acid sequences. From one out of the PCR amplifications using total CDNA and matrix of primers, a specific gene product, 580 bp in size, was produced. Upon Southern hybridization of the PCR products with Schistosomn mnnsoni tropomyosin (SMTM) CDNA, only one signal appeared at the band of 580 bp product. This 580 bp product was considered to encode C. sinensis tropomyosin (CSTM) and cloned in pGEM-3Zf(-) for DNA sequencing. CSTM cDNA was 575 bp containing one open reading frame of 191 predicted amino acids, which revealed 86.3% homology with SMTM and 51.1% with rrichostronsylur coeubnlormis tropomyosin. CSTM cDNA obtained will serve as a probe in the studies of molecular cloning of CSTM.

• The Journal of the Korea Contents Association
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• v.13 no.8
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• pp.466-473
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• 2013

Gene expression is regulated by a wide range of mechanisms at the DNA sequence level. In addition, gene expression is also regulated by epigenetic mechanisms through DNA methylation, histone modification, and ncRNA. To understand the regulation of gene expression at the epigenetic level, we constructed aging related gene database and analyzed epigenetic properties that are focused on DNA methylation. The DNA methylation of promoter or upstream region of the genes induces to repress the gene expression. We compared and analyzed distribution between whole human genes and aging related genes in the epigenetic properties such as CGI distribution, methylation motif pattern, and TFBS (transcription factor binding site) distribution. In contrast to methylation motif pattern, CGI and TFBS distributions are positively correlated with epigenetic regulation of aging related gene expression. In this study, the epigenetic data about DNA methylation of the aging genes will provide us to understand phenomena of the aging and epigenetic mechanism for regulation of aging related genes.

• Journal of Life Science
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• v.14 no.4
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• pp.627-635
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• 2004

In order to distinguish the genetic polymorphism among the olive flounder (Paralichthys olivaceus) obtained from East sea of Jumunjin, aquaculture of Tongyoung and Geoje, and East sea of North Korea, the ND-4 and cytochrome b genes of olive flounder were divided into 5 regions. Each region was analyzed by degenerating gel electrophoresis scanning (DGES), and by subsequent DNA sequencing. The DGES disclosed characteristic DNA polymorphisms in ND-4-2 and ND-4-3 regions of olive flounder, which were also confirmed by the DNA sequencing. The olive flounders obtained from the different marine areas showed DNA mutations in ND-4-2 region (G390A, C402T, and A411G； GenBank： AB028664), and also showed frequent DNA mutations in ND-4-3 region (C515G, C537T, C538T, A567G, G714A, C736T, G756A, A759T, T817C, and T829G), white the cytochrome b gene showed no DNA mutation both in the DGES and DNA sequencing. These data suggest that the ND-4-2 and ND-4-3 regions are candidate loci to distinguish the origin of olive flounder, and that the DGES used in this study provided fast and reliable informations for the genetic polymorphism.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2001.10a
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• pp.87-96
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• 2001

삼성종합기술원에서는 인간의 genomic DNA의 이상을 발견하여 이와 연관된 질병을 진단하는 DNA chip을 개발하고 있다. 이를 위하여 특정한 염기서열의 변화에 따라 민감하게 hybridization strength가 변화하는 oligomer를 선택해야 한다. 따라서, specificity가 가장 큰 probe를 골라내야 한다. 여기에는 열역학적인 고려와 여러가지 물리화학적인 approximation이 사용되며, DNA chip 생산 공정에 의존하는 요소도 포함되어 있다 모든 생산용 data와 결과의 분석은 database를 기반으로 이루어지며, 자동화된 통계적 분석법과 최적화 방법이 함께 사용된다.

• Proceedings of the Korean Society of Grassland Science Conference
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• 1999.06a
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• pp.71.2-72
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• 1999

고등식물에 있어서 엽록체에 존재하는 저 분자량 heat shock protein (smHSP)은 식물의 내열성 획득에 있어서 필수유전자임이 mutant를 이용한 유전학적인 연구에 의해 보고된 바 있다. 고온내성이 강한 작물인 벼로부터 엽록체 smHSP cDNA를 분리하고자 벼의 잎에서 분리한 mRNA로 작성한 cDNA library로부터 screening하였다. 선발된 smHSP cDNA는 1,026 bp의 염기로 구성되어 있었으며, 239개의 아미노산으로 구성되는 예상분자량 26.6 kDa의 단백질을 code하고 있었다. 또한 다른 식물로부터(중략)

• Korean Journal of Microbiology
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• v.45 no.4
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• pp.430-434
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• 2009

Bacterial 16S rRNA gene sequences have been widely used for the studies on molecular phylogeny, evolutional history, and molecular detections. Bacterial genomes have multiple rRNA operons, of which gene sequences sometimes are variable. In the present study, heterogeneity of the Vibrio 16S rRNA gene sequences were investigated. Vibrio 16S rRNA sequences were obtained from GenBank databases, considering the completion of gene annotation of Vibrio genome sequences. These included V. cholerae, V. harveyi, V. parahaemolyticus, V. splendidus, and V. vulnificus. Chromosome 1 of the studied Vibrio had 7~10 copies of the 16S rRNA gene, and their intragenomic variations were less than 0.9% dissimilarity (more than 99.1% DNA similarity). Chromosome 2 had none or single 16S rRNA gene. Intragenomic 16S rRNA genotypes were detected at least 5 types (V. vulnificus #CMCP6) to 8 types (V. parahaemolyticus #RIMD 2210633, V. harveyi #ATCC BAA-1116). These suggest that Vibrio has high heterogeneity of the 16S rRNA gene sequences.

• Korean Journal of Microbiology
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• v.42 no.1
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• pp.77-81
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• 2006

Degenerate primers corresponding to the sequences of the N-terminal regions of Mn-peroxidase isozymes were used to isolate the genomic fragments encoding the isozymes of Mn-peroxidase, CVMP1, CVMP2, CVMP3 and CVMP5 from the white-rot fungus Trametes versicolor KN9522. Three isozymes except one gave the expected PCR products (cmp1, cmp2 and cmp5) of about 900 base pairs, respectively. DNA sequence data obtained from each PCR products were used to analyze the BLAST program search on the National Center for Biotechnology Information. cmp1, cmp2 and cmp5 were similar to MPG-I (GenBank accession number Z30668) and PGV-II (GenBank accession number, Z54279) gene T. versicolor PRL572. PCR products of cmp1 and cmp2 showed 77%, 95% base sequence similarities to MPG-I gene and cmp5 showed about 88% similarity to PGV-II gene from T. versicolor PRL572. From this experiment, we could isolate genomic DNA fragments with degenerate primers designed from the N-terminal amino acid sequences of Mn-peroxidase isozyme family.

• Korean Journal of Plant Taxonomy
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• v.36 no.1
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• pp.21-40
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• 2006

We examined nrDNA ITS sequences from 16 taxa of Polygonum sect. Persicaria(Polygonaceae) in Korea to infer relationships among the taxa within the section. A neighbor-joining tree obtained from the analysis of the ITS sequences suggest that the ITS region was useful inferring the phylogenetic relationships among the taxa. The neighbor-joining tree indicates that P.amphibium is clearly separated from the other Korean taxa. The tree also reveals the presence of five major groups in the Korean taxa of the section; 1) P. lapathifolium var. lapathifolium, 2) P. persicaria and P. viscoferum, 3) P. orientale and P. viscosum, 4) P. japonicum and 5) a group including the remaining taxa. these relationships depicted on the ITS tree are largely congruent with those inferred from morphological and anatomical characters.

• Journal of Life Science
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• v.31 no.4
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• pp.410-417
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• 2021

Next-generation sequencing (NGS) is a high-throughput technique for sequencing large numbers of DNA fragments that are prepared from a genome. This sequencing technique has been used to elucidate whole genome sequences of living organisms and to analyze complementary DNA (cDNA) or chromatin immunoprecipitated DNA (ChIPed DNA) at the genome level. After NGS, the use of proper tools is important for processing and analyzing data with reasonable parameters. However, handling large-scale sequencing data and programing for data analysis can be difficult. The Galaxy platform, a public web service system, provides many different tools for NGS data analysis, and it allows researchers to analyze their data on a web browser with no deep knowledge about bioinformatics and/or programing. In this study, we explain the procedure for preparing chromatin immunoprecipitation-sequencing (ChIP-seq) libraries and steps for analyzing ChIP-seq data using the Galaxy platform. The data analysis steps include the NGS data upload to Galaxy, quality check of the NGS data, premapping processes, read mapping, the post-mapping process, peak-calling and visualization by window view, heatmaps, average profile, and correlation analysis. Analysis of our histone H3K4me1 ChIP-seq data in K562 cells shows that it correlates with public data. Thus, NGS data analysis using the Galaxy platform can provide an easy approach to bioinformatics.

• Journal of Food Hygiene and Safety
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• v.36 no.4
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• pp.331-341
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• 2021

DNA barcode sequences of commercial seafood products, which are difficult to morphologically discriminate, were analyzed to determine cases of food fraud. The gene sequences were analyzed by amplifying the COX I (cytochrome C oxidase subunit I) gene region of mitochondrial DNA, which is mainly used for species identification. The DNA barcode sequences were compared with the gene sequence of each fish registered in the US National Center for Biotechnology. A total of 46 processed seafood products (12 Pagrus majo, 4 Oplegnathus fasciatus, 7 Dentex tumifrons, 2 Acanthopagrus schlegelii, 7 Oreochromis niloticus, 6 Branchiostegus japonicus, 8 Branchiostegus albus) were investigated. Having DNA sequence identity of more than 97% was judged as the same species. As a result of this study, no cases of forgery and alteration were detected. However, some disparities in the commercial names used in local markets and the standard names given in the Korea Food Code were found, which may cause confusion for consumers. It is therefore suggested that the standard name or scientific name be displayed on seafood product labels.