• KSBB Journal
• /
• v.24 no.4
• /
• pp.410-414
• /
• 2009

Single-nucleotide polymorphisms (SNPs) are the DNA sequences difference among the same species in the level of nucleic acids and are widely applied in clinical fields such as personalized medicine. The routine and labor-intensive methods to determine SNPs are performing the sequence homology search by using BLAST and navigating the trace of chromatogram files generated by high-throughput DNA sequencing machine by using Chromas program. In this paper, we developed SNPchaser, a web-based program for detecting SNPs substitution and heterozygosity existence, to improve the labor-intensive method in determining SNPs. SNPchaser performed sequence alignment and visualized the suspected region of SNPs by using user's reference sequence, AB1 files, and positional information of SNPs. It simultaneously provided the results of sequences alignment and chromatogram of relevant area of SNPs to user. In addition, SNPchaser can easily determine existence of heterozygosity in SNPs area. SNPchaser is freely accessible via the web site http://www.bioinformatics.ac.kr/SNPchaser and the source codes are available for academic research purpose.

• Pediatric Gastroenterology, Hepatology & Nutrition
• /
• v.5 no.1
• /
• pp.39-50
• /
• 2002

Hepatitis B viral infection which affect about 10% of Korean population manifests asymptomatic carrier, chronic hepatitis and liver cirrhosis and even associates with hepatocellular carcinoma. Clinical manifestations induced by hepatitis B virus vary depending on the degree of immune response by cytotoxic T cells against viral epitope-presenting liver cells. Since hepatitis B virus presents high rate of mutaton that might change the presented epitope and eventually alter immune response, viral mutations, especially in promoters and enhancers, have an important implication in hepatic inflammation and viral replication. To identify mutations related to the hepatic inflammation, we investigated sequence variations of hepatitis B viral promotor regions in the presence or absence of symptoms in hepatitis B carriers. For this, sera from persistently hepatitis B virus-infected mother-child pairs were collected. After PCR amplifiation of all hepatitis B viral promoters (C promoter, S1 promoter, S2/S promoter, X promoter) using serum DNA from each pair, viral promotors were sequenced by automatic sequencer and then sequence data were analyzed by ClustalW. In most cases, the dominant type of maternal virus was transmitted to the child. However, in some children, some new host specific viral variants could be observed in Cp, S1p and S2/Sp. The mutations in C promoter did not seem to be vertically transmitted but arose in new host independently after the wild type had been transmitted. Enhancer I containing X promoter revealed high host specific variations as has been reported before. Two S promoters, S1p and S2/Sp, have shown some point mutations in children, but no deletion mutations were detected as in chronic hepatitis patients in whom deletion mutations are frequently found. In conclusion, the children with the vertically transmitted hepatitis B virus mostly retain the dominant type virus that had been transmitted. However, host specific variants tended to accumulate over time, possibly as clinical symptoms develop.

• The Journal of the Acoustical Society of Korea
• /
• v.40 no.5
• /
• pp.523-529
• /
• 2021

In this paper, we designed and developed an Emotional Speech Synthesis Markup Language (SSML) processor. Multi-speaker emotional speech synthesis technology that can express multiple voice colors and emotional expressions have been developed, and we designed Emotional SSML by extending SSML for multiple voice colors and emotional expressions. The Emotional SSML processor has a graphic user interface and consists of following four components. First, a multi-speaker emotional text editor that can easily mark specific voice colors and emotions on desired positions. Second, an Emotional SSML document generator that creates an Emotional SSML document automatically from the result of the multi-speaker emotional text editor. Third, an Emotional SSML parser that parses the Emotional SSML document. Last, a sequencer to control a multi-speaker and emotional Text-to-Speech (TTS) engine based on the result of the Emotional SSML parser. Based on SSML which is a programming language and platform independent open standard, the Emotional SSML processor can easily integrate with various speech synthesis engines and facilitates the development of multi-speaker emotional text-to-speech applications.

• Proceedings of the Plant Resources Society of Korea Conference
• /
• 2019.10a
• /
• pp.73-73
• /
• 2019

Angelica gigas Nakai (Korean danggui), a member of the Umbelliferae family, is a Korean traditional medicinal plant whose roots have been used for treating gynecological diseases. Transcriptomics is the study of the transcriptome, which is the complete set of RNA transcripts that are produced by the genome, using high-throughput methods, such as microarray analysis. In this study, transcriptome analysis of A.gigas Nakai was carried out. Transcriptome sequencing and assembly was carried out by using Illumina Hiseq 2500, Velvet and Oases. A total of 109,591,555 clean reads of A. gigas Nakai was obtained after trimming adaptors. The obtained reads were assembled with an average length of 1,154 bp, a maximum length of 13,166 bp, a minimum length of 200 pb, and N50 of 1,635 bp. Functional annotation and classification was performed using NCBI NR, InterprotScan, KOG, KEGG and GO. Candidate genes for phenylpropanoid biosynthesis were obtanied from A.gigas transcriptome and the genes and its proteins were confirmed through the NCBI homology BLAST searches, revealing high identity with other othologous genes and proteins from various plants pecies. In RNA sequencing analysis using an Illumina Next-Seq2500 sequencer, we identified a total 94,930 transcripts and annotated 71,281 transcripts, which provide basic information for further research in A.gigas Nakai. Our transcriptome data reveal that several differentially expressed genes related to flower color in A.gigas Nakai. The results of this research provide comprehensive information on the A.gigas Nakai genome and enhance our understanding of the flower color related gene pathways in this plant.

• KOREAN JOURNAL OF CROP SCIENCE
• /
• v.52 no.1
• /
• pp.81-88
• /
• 2007

The evaluation of soybean germplasm has mainly been carried out by morphological characters at Genetic Resources Division, Rural Development Administration (RDA). However, this information has been limited serving a diverse information for user and effectively managing the soybean germplasm. To resolve this problem, soybean collection conserved at RDA gene bank was profiled using nine soybean SSR (Simple Sequence Repeat) markers. Soybean SSR allele was confirmed using genescan and genotyper softwares of automatic sequencer for accurate genotyping of each accession and continuous accumulation of data. SSR profiling of soybean germplasm has been carried out from 2,855 (Satt458) to 4,368 (Satt197) accessions by locus. The number of allele revealed 267 with an average of 29.6 in total accession, and varied from a low of 21 (Satt532 and Satt141) to a high of 58 (Sat_074). Although the number of accessions of wild soybean is less than that of soybean landraces, Korean wild soybean is more variable than other soybean landraces populations in total number of alleles. However, Korean soybean landraces were more variable than Korean wild soybeans in 5 loci. In the allele frequency, wild soybean accessions showed an even distribution in all alleles and higher distribution in low ladder than in high ladder. Also, Korean soybean landraces revealed a high condensed frequency in Satt286 (202 bp, 232 bp), Chinese soybean landraces in Satt197 (171 bp) and Satt458 (173 bp), and Japanese soybean landraces in Sat_074 (244 bp) and Satt458 (170 bp). These SSR profile information will be provided as indications of redundancies or omissions of accessions and can aid in managing soybean collection held at RDA gene bank. The information on diversity analysis could help to enlarge the genetic diversity of materials in breeding program, and could be used to develop a core collection of soybean germplasm.

• Korean journal of applied entomology
• /
• v.45 no.3 s.144
• /
• pp.293-299
• /
• 2006

A survey was conducted to find out the major plant parasitic nematode in Chrysanthemum morifolium fields in Korea from May to June in 2005. A genus of Pratylenchus was determined as the most important plant parasitic nematode based on analysis of total 50 samples from 8 cities of chrysanthemum field. Pratylenchus showed 86% occurrence rate and average numbered 1,095 per 200cc soils and 1g root. Five Pratylenchus isolates, 'Muan', 'Masan', 'Tean', 'Gumi', 'Jeongup', were selected for the molecular identification of the species of Pratylenchus, and ITS and D3-28S ribosomal DNA were amplified by PCR. For the ITS, only 'Muan' isolate was differentiated by total 1 kb PCR amplification, which was 200 bp larger than all the other isolates. There was no size variation in amplified D3-28S rDNA and all isolate represented approximately 320 bp of PCR product. Sequence data of D3-28S rDNA were analysed by MegAlign program in DNASTAR software and phylogenetic tree was constructed. Sequence homology was 100% between 'Gumi' isolate and 'Tean' isolate and 'Jeongup' isolate was also close to these isolates by 99.7% sequence homology. 'Gumi', 'Tean' group and 'Jeongup' isolate were determined to be closely related to Pratylenchus vulnus by 96.7% and 96.3% similarity in respectively. D3 sequence of 'Masan' isolate was 100% identical to P. penetrans, and 'Muan' isolate showed 99.7% similarity to P. brachyurus. This result was congruent with the branch divergence pattern shown in phylogenetic tree.

• Journal of Life Science
• /
• v.17 no.2 s.82
• /
• pp.279-285
• /
• 2007

Detection of Mycoplasma DNA from the 30 cases of cancer tissues and the normal tissues surrounding the cancer tissues obtained from the patients with gastric cancer and the other 30 cases of cancer tissues and the normal tissues surrounding the cancer tissues obtained from the patients with colon cancer were evaluated by polymerase chain reaction(PCR). The PCR products were sequenced using an ABI 377 automatic DNA sequencer, and these sequences were confirmed by comparing sequences with the database of the National Center for Biotechnology Information BLAST network server. Mycoplasmas DNA were defected in 18 (60%) cases of normal tissues which were around gastric cancer and were 13 (43.3%) cases of gastric cancer tissues. Mycoplasmas DNA were detected in 15(50%) cases of normal tissues which were around colon cancer and 12 (40%) cases of colon cancer tissues. The M. faucium, M. subdolum, M. salivarium, M. auris, M. hyosynoviae, and M. conjunctivae were detected from the gastric cancer tissues. The M. faucium, M. subdolum,, M. salivarium, M. auris, M. hyosynoviae, M. bovigenitalium and M. pulmonis were detected from the normal tissues around gastric cancer. The M. faucium, M. subdolum, M. salivarium, M. auris, M. hyosynoviae, M. synoviae M. bovigenitalium, M. gallinarum, and M. moatsii were detected from the colon cancer. The M. faucium, M. subdolum, M. salivarium, M. auris, M. hyosynoviae, M. bovis, M. opalescens, M. bovigenitalium, M. gallinarum, and M. moatsii were detected from the normal tissues around the colon cancer. These results suggest that Mycoplasmas infection may not correlate with gastric cancer and colon cancer, because of the detection rate of Mycoplasmas DNA were not significantly differences between normal and cancer tissues from the patients.

• Journal of the Korean Society of International Agriculture
• /
• v.23 no.5
• /
• pp.546-551
• /
• 2011

Chrysanthemums, often called mums or chrysanths, belong to the genus Chrysanthemum, which includes about 30 species of perennial flowering plants in the family Asteraceae. We extracted DNA from Dendranthema grandiflorum ('Smileball') to construct a simple sequence repeat (SSR)-enriched library, using a modified biotin-streptavidin capture method. GS FLX (Genome Sequencer FLX System which provides the flexibility to perform the broad range of applications) sequencing (at the 1/8 run specification) resulted in 18.83 mega base pairs (Mbp) with an average read length of 280.06 bp. Sequence analyses of all SSR-containing clones revealed a predominance of di-nucleotide motifs (16,375, 61.5%) followed by tri-nucleotide motifs (6,616, 24.8%), tetra-nucleotide motifs (1,674, 6.3%), penta-nucleotide motifs (1,283, 4.8%), and hexa-nucleotide motifs (693, 2.6%). Among the di-nucleotide motifs, the AC/CA class was the most frequently identified (93.5% of all di-nucleotide types), followed by the GA/AG class (6.1%), the AT/TA class (0.4%), and the CG/GC class (0.03%). When we analyzed the distribution of different repeat motifs and their respective numbers of repeats, regardless of the motif class, of 100 SSR markers, we found a higher number of di-nucleotide motifs with 70 to 80 repeats; we also found two di-nucleotide motifs with 83 and 89 repeats, respectively, but their product lengths were within optimum size (297 and 300 bp). In future work, we will screen for polymorphisms of possible primer pairs. The results will provide a useful tool for assessing molecular diversity and investigating the population structure among and within Chrysanthemum species.