• Genomics & Informatics
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• 제7권2호
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• pp.65-84
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• 2009

Sequences from the clones of full-length enriched cDNA libraries serve as valuable resources for functional genomics related studies, genome annotation and SNP discovery. We analyzed 7,392 high-quality chromatograms (Phred value ${\geq}$30) obtained from sequencing the 5' ends of clones derived from full-length enriched cDNA libraries of Korean native pigs including brainstem, liver, cerebellum, neocortex and spleen libraries. In addition, 50,000 EST sequence trace files obtained from GenBank were combined with our sequences to identify cSNPs in silico. The process generated 11,324 contigs, of which 2,895 contigs contained at least one SNP and among them 610 contigs had a minimum of one sequence from Korean native pigs. Of 610 contigs, we randomly selected 262 contigs and performed in silico analysis for the identification of cSNPs. From the results, we identified 1,531 putative coding single nucleotide polymorphisms (cSNPs) and the SNP detection frequency was one SNP per 465 bp. A large-scale sequencing result of clones from full-length enriched cDNA libraries and identified cSNPs will serve as a useful resource to functional genomics related projects such as a pig HapMap project in the near future.

• Speech Sciences
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• 제5권1호
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• pp.49-62
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• 1999

This study is concerned with the educational program Visual Analysis Tool (VAT) for sound development for foreign intonation using personal computer. The VAT can run on IBM-PC 386 compatible or higher. It shows the spectrogram, waveform, intensity and the pitch contour. The system can work freely on either waveform zoom in-out or the documentation of measured value. In this paper, intensity and pitch contour information were used. Twelve French sentences were recorded from a French conversational tape. And three Korean participated in this study. They spoke out twelve sentences repeatly and trid to make the same pitch contour - by visually matching their pitcgh contour to the native speaker's. A sentences were recorded again when the participants themselves became familiar with intonation, intensity and pauses. The difference of pitch contour(rising or falling), pitch value, energy, total duration of sentences and the boundary of rhythmic group between native speaker's and theirs before and after training were compared. The results were as following: 1) In a declarative sentence: a native speaker's general pitch contour falls at the end of sentences. But the participant's pitch contours were flat before training. 2) In an interrogative: the native speaker made his pitch contours it rise at the end of sentences with the exception of wh-questions (qu'est-ce que) and a pitch value varied a greath. In the interrogative 'S + V' form sentences, we found the pitch contour rose higher in comparison to other sentences and it varied a great deal. 3) In an exclamatory sentence: the pitch contour looked like a shape of a mountain. But the participants could not make it fall before or after training.

• Journal of Life Science
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• 제18권8호
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• pp.1090-1095
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• 2008

Marbling (intramuscular fat) is an important factor in determining meat quality in Korean beef market. A grain based finishing system for improving marbling leads to inefficient meat production due to an excessive fat production. Identification of intramuscular fat-specific gene might be achieved more targeted meat production through alternative genetic improvement program such as marker assisted selection (MAS). We carried out ddRT-PCR in 12 and 27 month old Hanwoo steers and detected 300 bp PCR product of the inducible cAMP early repressor (ICER) gene, showing highly gene expression in 27 months old. A 1.5 kb sequence was re-sequenced using primer designed base on the Hanwoo EST sequence. We then predicted the open reading frame (ORF) of ICER gene in ORF finder web program. Tissue distribution of ICER gene expression was analysed in eight Hanwoo tissue using realtime PCR analysis. The highest ICER gene expression showed in Small intestine followed by Longissimus dorsi. Interestingly, the ICER gene expressed 2.5 time higher in longissimus dorsi than in same muscle type, Rump. For gene expression analysis in high- and low marbled individuals, we selected 4 and 3 animal based on the muscle crude fat contents (high is 17-32%, low is 6-7% of crude fat contents). The ICER gene expression was analysed using ANOVA model. Marbling (muscle crude fat contents) was affected by ICER gene (P=0.012). Particularly, the ICER gene expression was 4 times higher in high group (n=4) than low group (n=3). Therefore, ICER gene might be a functional candidate gene related to marbling in Hanwoo.

• Journal of Plant Biotechnology
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• 제38권2호
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• pp.176-185
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• 2011

Rice is one of the most important crop in the world, in particular for food resources. With its small genome size of 383 Mb, the Oryza sativa is a model plant for genome research. Indeed, it's grain provides human with a source of carbohydrates and proteins. Rice grain has relatively low protein contents (around 8%) compared to other legume seeds (around 40%). Osborne classified seed proteins into water soluble albumin, salt soluble globulin, alcohol soluble prolamin and acidic/alkaline solution soluble glutelin. Glutelin and prolamin are the major storage proteins in rice. For the gene expression study of seed storage proteins, we analyzed 33,192 EST clones at immature stages in a rice cultivar (Oryza sativa L. cv. 'Ilpum'). Based on the expression analysis, we cloned 11 glutelin genes and figured out the 8 genes are located on Chromosome 2. The expression of glutelin genes appears to be about 28.2% of total level in immature seeds. Interestingly, glu-04 is duplicated as inverted sequences on the same chromosomes as far 4.5 kb. Our results indicate that glutelin genes, evolutionarily, were replicated on the chromosome and thus expressed as specific manners. In a whole protein composition analysis, glu05 (type B7) contains the highest lysin contents (4.51%) among the 11 rice glutelin genes. It will be an interesting future work to increase lysin contents by the gene overexpressor strategy with the aim of improved diet nutritionally fortified.

• Journal of the Korea Society of Computer and Information
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• 제10권6호
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• pp.47-54
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• 2005

In the most of speaker recognition system, speaker's characteristics is extracted from acoustic parameter by speech analysis and we make speaker's reference pattern. Parameters used in speaker recognition system are desirable expressing speaker's characteristics fully and being a few difference whenever it is spoken. Therefore we su99est following to solve this problem. This paper is proposed to use strong spectrum characteristic in non-noise circumstance and prosodic information in noise circumstance. In a stage of making code book, we make the number of data we need to combine spectrum characteristic and Prosodic information. We decide acceptance or rejection comparing test pattern and each model distance. As a result, we obtained more improved recognition rate than we use spectrum and prosodic information especially we obtained stational recognition rate in noise circumstance.

• Molecular & Cellular Toxicology
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• 제1권1호
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• pp.17-25
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• 2005

There are some critical drawbacks in the use of biomarkers for a global assessment of the toxicological impacts many chemicals and environmental pollutants have, primarily due to an individual biomarker's specificity for an explicit chemical or toxicant. In other words, the biomarker-based assessment methodology used to analyze toxicological effects lacks a high-throughput capability. Therefore, eco-toxicogenomics, or the study of toxicogenomics with organisms present within a given environmental locale, has recently been introduced with the advent of the so-called "-omics" era, which began with the creation of microarray technologies. Fish are comparable with humans in their toxicological responses and thus data from toxicogenomic studies performed with fish could be applied, with appropriate tools and implementation protocols, to the evaluation of environments where human or animal health is of concern. At present, there have been very active research streams for developing expression sequence tag (EST) databases (DBs) for zebra fish and rainbow trout. Even though few reports involve toxicogenomic studies with fish, a few groups have successfully fabricated and used cDNA microarrays or oligo DNA chips when studying the toxicological impacts of hypoxia or some toxicants with fish. Furthermore, it is strongly believed that this technology can also be implemented with non-model fish. With the standardization of DNA microarray technologies and ample progress in bioinformatics and proteomic technologies, data obtained from DNA microarray technologies offer not only multiple biomarker assays or an analysis of gene expression profiles, but also a means of elucidating gene networking, gene-gene relations, chemical-gene interactions, and chemical-chemical relationships. Accordingly, the ultimate target of eco-toxicogenomics should be to predict and map the pathways of stress propagation within an organism and to analyze stress networking.

• KIISE Transactions on Computing Practices
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• 제23권4호
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• pp.250-255
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• 2017

Given the explosion of genomic data and expansion of applications such as precision medicine, the importance of efficient genome-database management continues to grow. Traditional compression techniques may be effective in reducing the size of a database, but a new challenge follows in terms of performing operations such as comparison and searches on the compressed database. Based on that many genome databases typically have numerous duplicated or similar sequences, and that the runtime of genome analyses is normally proportional to the number of sequences in a database, we propose a technique that can compress a genome database by eliminating similar entries from the database. Through our experiments, we show that we can remove approximately 84% of sequences with 1% similarity threshold, accelerating the downstream classification tasks by approximately 10 times. We also confirm that our compression method does not significantly affect the accuracy of taxonomy diversity assessments or classification.

• The Plant Pathology Journal
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• 제24권4호
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• pp.478-481
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• 2008

The cDNA clone of Brassica rapa WRKY7 (BrWRKY7) was obtained from EST collection in Brassica genomics team and its DNA sequence was determined. The cDNA clone is 1,037 bp long in nucleotides and encodes an open reading frame of 307 amino acids. Based on a phylogenetic tree, BrWRKY7 belongs to group IId. BrWRKY7 was induced by wound and SA. It was also induced by pathogen attack such as Xanthomonas campestris pv. campestris (Xcc), suggesting that this BrWRKY may play an essential role in defense response of chinese cabbages.

• Asian-Australasian Journal of Animal Sciences
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• 제21권12호
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• pp.1703-1709
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• 2008

As genetic markers, single nucleotide polymorphisms (SNP) are very appropriate for the development of genetic tests for economic traits in livestock. Several microsatellite markers have been identified as useful markers for the genetic improvement of Hanwoo. Among those markers, ILSTS035 was recently mapped at a similar position with four SNPs (AH1_11, AH1_9, 31465_446, and 12273_165) in a linkage map of EST-based SNP in BAT6. Among the four SNPs, two SNPs (31465_446 and 12273_165) were analyzed using BLAST at the NCBI web site. The sequences including the 12273_165 SNP were identified at the intron region within the LOC534614 gene on the gene sequence map (Bos taurus NCBI Map view, build 3.1). The LOC534614 gene represents a protein similar to myosin heavy chain, fat skeletal muscle, embryonic isoform 1 in the dog, and myosin_1 (Myosin heavy chain D) in Macaca mulatta. In cattle, the myosin heavy chain was associated with muscle development. The phenotypic data for growth and carcass traits in the 415 animals were analyzed by the mixed ANCOVA (analysis of covariance) linear model using PROC GLM module in SAS v9.1. By the genotyping of Hanwoo individuals (n = 415) to evaluate the association of SNP with growth and carcass traits, it was shown that the 12273_165 SNP region within LOC534614 may be a candidate marker for growth. The results of the statistical analyses suggested that the genotype of the 12273_165 SNP significantly affected birth weight, weight of the cattle at 24 months of age, average daily gain and carcass cold weight (p<0.05). Consequently, the 12273_165 SNP polymorphisms at the LOC534614 gene may be associated with growth in Hanwoo, and functional validation of polymorphisms in LOC534614 should be performed in the future.

• Animal cells and systems
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• 제9권2호
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• pp.87-94
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• 2005

Spindle position checkpoint monitors the orientation of mitotic spindle for proper segregation of replicated chromosomes into mother cell and the daughter, and prohibits mitotic exit when mitotic spindle is misaligned. BUB2 forms one of the key upstream element of spindle position checkpoint in budding yeast, but its functional homologues have not been identified in higher eukaryotes. Here, we analyzed the functions of two putative BUB2 homologues of C. elegans in the spindle orientation checkpoint. From the C. elegans genome database, we found that two open reading frames (ORFs), F35H12_2 and C33F10_2, showed high sequence homology with BUB2. We obtained the expressed sequence tag (EST) clones for F35H12_2 (yk221d4) and C33F10_2 (yk14e10) and verified the full cDNA for each ORF by sequencing and 5' RACE with SL1 primer. The functional complementation assays of yk221d4 and yk14e10 in ${\Delta}bub2$ of S. cerevisiae revealed that these putative BUB2 homologues of C. elegans could not replace the function of BUB2 in spindle position checkpoint and mitotic exit. Our attempt to document the component of spindle position checkpoint in metazoans using sequence homology was not successful. This suggests that structural information about its components might be required to identify functional homologues of the spindle position checkpoint in higher eukaryotes.