• Proceedings of the Plant Resources Society of Korea Conference
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• 2010.10a
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• pp.11-11
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• 2010

The Korean ginseng, Panax ginseng C. A. Meyer is a popular medicinal herb in Araliaceae. Genetic map in crops provides valuable information for breeding, genetic and genomic researches. However, little information is available for construction of genetic map in ginseng. Up to now, we have produced large amounts of expressed sequence tags (ESTs) from four ginseng cultivars (37Mb, 49Mb, 39Mb, 47Mb from Gopoong, Gumpoong, Chunpoong and Yunpoong respectively using pyrosequencing technique and 5Mb from normalized full-length cDNA library of Chunpoong) to obtain comprehensive information of gene expression, and constructed EST database including ESTs from public database. Till now, we designed 261 SSR primer sets using EST sequences and identified 106 intergenic polymorphic markers. And 44 of the 106 showed polymorphisms among panax ginseng cultivars. Among 44 markers, 27 SSR polymorphic markers were inspected to 51 $F_2$ population from Yunpoong x Chunpoong, which showed good at the fitness of Mendellian segregation ratio 1:2:1. To enrich the number of markers, and thus construct high resolution genetic map which can be used as frame map for further genome sequencing. we are planning to develop large scale EST-derived SNP markers which are available in the F2 population. This study provides genetic information as well as foundation for ginseng researches such as genetics, genomics, breeding, and the final goal for whole genome sequencing. This study was supported by Technology Development Program for Agriculture and Forestry, Ministry for Food, Agriculture, Forestry and Fisheries, Republic of Korea (Grant No. 609001-051SB210).

• Genomics & Informatics
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• v.17 no.4
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• pp.39.1-39.20
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• 2019

Analyzing patterns in data points embedded in linear and non-linear feature spaces is considered as one of the common research problems among different research areas, for example: data mining, machine learning, pattern recognition, and multivariate analysis. In this paper, data points are heterogeneous sets of biosequences (composite data points). A composite data point is a set of ordinary data points (e.g., set of feature vectors). We theoretically extend the derivation of the largest generalized eigenvalue-based distance metric D_ij(γ₁) in any linear and non-linear feature spaces. We prove that D_ij(γ₁) is a metric under any linear and non-linear feature transformation function. We show the sufficiency and efficiency of using the decision rule $\bar{{\delta}}_{{\Xi}i}$(i.e., mean of D_ij(γ₁)) in classification of heterogeneous sets of biosequences compared with the decision rules min_𝚵iand median_𝚵i. We analyze the impact of linear and non-linear transformation functions on classifying/clustering collections of heterogeneous sets of biosequences. The impact of the length of a sequence in a heterogeneous sequence-set generated by simulation on the classification and clustering results in linear and non-linear feature spaces is empirically shown in this paper. We propose a new concept: the limiting dispersion map of the existing clusters in heterogeneous sets of biosequences embedded in linear and nonlinear feature spaces, which is based on the limiting distribution of nucleotide compositions estimated from real data sets. Finally, the empirical conclusions and the scientific evidences are deduced from the experiments to support the theoretical side stated in this paper.

• Communications of the Korean Mathematical Society
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• v.37 no.1
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• pp.259-267
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• 2022

We use L_∞ models to compute the rational homotopy type of the mapping space of the component of the natural inclusion i_n,k : ℂPⁿ ↪ ℂP^n+k between complex projective spaces and show that it has the rational homotopy type of a product of odd dimensional spheres and a complex projective space. We also characterize the mapping aut₁ ℂPⁿ → map(ℂPⁿ, ℂP^n+k; i_n,k) and the resulting G-sequence.

• Journal of Life Science
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• v.30 no.10
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• pp.844-850
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• 2020

Disaster-related extreme weather is rapidly increasing due to climate change. In Korea, typhoons accompanied by rainfall usually approach in August and September, causing great damage. The purpose of this study is to find a gene that regulates the heading date of rice in order to avoid loss of harvest from climate change and typhoons. Cheongcheong/Nagdong doubled haploid (CNDH) was used as the plant material to investigate the location of heading-related genes using QTL and sequence analysis by cloning the gene. In the distribution chart, the heading dates, culm lengths, panicle lengths, numbers of panicles, and 1,000-grain weights all have normal distributions. QTL analysis found 13 contigs on chromosome 8. One QTL, named qHd8, was detected on chromosome 8. The range at qHd8 was approximately 7.7 cM, with RM72 and RM404 markers near the peak. There were 13 contigs and 1 ORF. Protein sequence analysis showed that rice was similar to Os08g0341700, AtSFH13, and AtSFH7 proteins. Os08g0341700, which is involved in signal transduction, is similar to phosphatidylinositol transfer-like protein II, and complete information is not available, but it is believed to play a role in the phosphatidylinositol-specific signaling pathway related to Sec14P.

• Journal of Microbiology
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• v.34 no.4
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• pp.355-362
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• 1996

Complementation cloning of the argC, E, B, D, F, and G genes in Corynebacterium glutamicum was done by transforming the genomic DNA library into the corresponding arginine auxotrophs fo Escherichia coli. Recombinant plasmids containing 6.7 kb and 4.8kb fragments complementing the E. coli argB mutant were also able to complement the E. coli argC, E, A, D, and F mutants, indicating the clustered organization of the arginine biosynthetic genes within the cloned DNA fragments. The insert DNA fragments in the recombinant plasmids, named pRB1 AND pRB2, were physically mapped with several restriction enzymes. By further subcloning the entire DNA fragment containing the functions and by complementation analysis, we located the arg genes in the order of ACEBDF on the restriction map. We also determined the DNA nucleotide sequence of the fragment and report here the sequence of the argB gene. When compared to that with the mutant strain, higher enzyme activity of N-acetylglutamate kinase was detected in the extract of the mutant carrying the plasmid containing the putative argB gene, indicating that the plasmid contains a functional argB gene. Deduced amino acid sequence of the argB gene shows 45%, 38%, and 25% identity to that from Bacillus strearothermophilus, Bacillus substilus, and E. coli respectively. Our long term goal is genetically engineering C. glutamicum which produces more arginine than a wild type strain does.

• Journal of Biomedical Engineering Research
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• v.32 no.3
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• pp.245-250
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• 2011

Parallel imaging technique can provide several advantages for a multitude of MRI applications. Especially, in SENSE technique, sensitivity maps were always required in order to determine the reconstruction matrix, therefore, a number of difference approaches using sensitivity information from coils have been demonstrated to improve of image quality. Moreover, many filtering methods were proposed such as adaptive matched filter and nonlinear diffusion technique to optimize the suppression of background noise and to improve of image quality. In this study, we performed SENSE reconstruction using computer simulations to confirm the most suitable method for the feasibility of filtering effect and according to changing order of polynomial fit that were applied on variation of spatial resolution of sensitivity map. The image was obtained at 0.32T(Magfinder II, Genpia, Korea) MRI system using spin-echo pulse sequence(TR/TE = 500/20 ms, FOV = 300 mm, matrix = $128{\times}128$, thickness = 8 mm). For the simulation, obtained image was multiplied with four linear-array coil sensitivities which were formed of 2D-gaussian distribution and the image was complex white gaussian noise was added. Image processing was separated to apply two methods which were polynomial fitting and filtering according to spatial resolution of sensitivity map and each coil image was subsampled corresponding to reduction factor(r-factor) of 2 and 4. The results were compared to mean value of geomety factor(g-factor) and artifact power(AP) according to r-factor 2 and 4. Our results were represented while changing of spatial resolution of sensitivity map and r-factor, polynomial fit methods were represented the better results compared with general filtering methods. Although our result had limitation of computer simulation study instead of applying to experiment and coil geometric array such as linear, our method may be useful for determination of optimal sensitivity map in a linear coil array.

• Journal of Intelligence and Information Systems
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• v.15 no.2
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• pp.33-48
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• 2009

Capsule endoscopy is one of the most remarkable inventions in last ten years. Causing less pain for patients, diagnosis for entire digestive system has been considered as a most convenience method over a normal endoscope. However, it is known that the diagnosis process typically requires very long inspection time for clinical experts because of considerably many duplicate images of same areas in human digestive system due to uncontrollable movement of a capsule endoscope. In this paper, we propose a method for clinical diagnosticians to get highly valuable information from capsule-endoscopy video. Our software system consists of three global maps, such as movement map, characteristic map, and brightness map, in temporal domain for entire sequence of the input video. The movement map can be used for effectively removing duplicated adjacent images. The characteristic and brightness maps provide frame content analyses that can be quickly used for segmenting regions or locating some features(such as blood) in the stream. Our experiments show the results of four patients having different health conditions. The result maps clearly capture the movements and characteristics from the image frames. Our method may help the diagnosticians quickly search the locations of lesion, bleeding, or some other interesting areas.

• BMB Reports
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• v.33 no.1
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• pp.92-95
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• 2000

The HIV-1 p24(202-221) sequence ETINNEEEWDRVHPV HAGP contains a B-cell epitope with the earliest immune response and the highest antibody titer against anti-mouse sera obtained by immunization with p24 antigens. A novel mouse monoclonal antibody (mAb) was generated against the immunodominant B-cell epitope of the HIV-1 p24 capsid protein, p24(202-221). BALB/c mice were immunized with the four branched multiple antigenic peptide (MAP) containing the HIV-1p24(202-221) sequence, and antibody-secreting hybridoma were produced by fusion of mouse splenocytes with P3X63Ag8.653, mouse myeloma cells. One clone which produced the antigen-specific mAb named KI-24 (Isotype IgG1, light chain: ${\kappa}$) was identified. mAb KI-24 was highly specific for both the p24(202-221) and p24 proteins when analyzed by ELISA and Western blotting. Since p24(202-221) also contains a cytotoxic T-lymphocyte epitope, this specfic peptide epitope and the monoclonal antibody with specific reactivity against the p24 protein and p24(202-221) can be used in peptide vaccine development and p24 antigen detection from HIV patients.

• BMB Reports
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• v.31 no.1
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• pp.58-63
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• 1998

In this study, a mouse monoclonal antibody (mAb) against gp41(584-618), the immunodominant epitope protein, was generated. For this purpose, BALB/c mice were immunized with double branched multiple antigenic peptides derived from the HIV-1 gp41(584-618) sequence, and antibody-secreting hybridoma were produced by fusion of mice splenocytes with SP2/0 myeloma cells. One clone producing an antigen specific mAb, termed KI-41(isotype IgG1) was identified, whose specific reactivity against gp41(584-618) could be confirmed by ELISA and Western blot analysis. Epitope mapping revealed the recognition site of the mAb KI-41 to be located around the sequence RILAVERYLKDQQLLG, which comprises the N-terminal region within the immunized gp41(584-618) peptied. Since this mAb recognizes this specific epitope within the HIV-1 gp41 without any cross-reactivity to other immunodominant regions in the HIV-2 gp35, KI-41 will provide some alternative possibilities in further applications such as the development of indirect or competitive ELISA for specific antibody detection in HIV-1 infection or for other basic researches regarding the role and function of HIV-1 gp41.

• Mycobiology
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• v.45 no.2
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• pp.105-109
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• 2017

Sixteen genomic DNA simple sequence repeat (SSR) markers of Lentinula edodes were developed from 205 SSR motifs present in 46.1-Mb long L. edodes genome sequences. The number of alleles ranged from 3-14 and the major allele frequency was distributed from 0.17-0.96. The values of observed and expected heterozygosity ranged from 0.00-0.76 and 0.07-0.90, respectively. The polymorphic information content value ranged from 0.07-0.89. A dendrogram, based on 16 SSR markers clustered by the paired hierarchical clustering' method, showed that 33 shiitake cultivars could be divided into three major groups and successfully identified. These SSR markers will contribute to the efficient breeding of this species by providing diversity in shiitake varieties. Furthermore, the genomic information covered by the markers can provide a valuable resource for genetic linkage map construction, molecular mapping, and marker-assisted selection in the shiitake mushroom.