• Journal of Genetic Medicine
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• v.20 no.1
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• pp.1-5
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• 2023

Until now, rare disease studies have mainly been carried out by detecting simple variants such as single nucleotide substitutions and short insertions and deletions in protein-coding regions of disease-associated gene panels using diagnostic next-generation sequencing in association with patient phenotypes. However, several recent studies reported that the detection rate hardly exceeds 50% even when whole-exome sequencing is applied. Therefore, the necessity of introducing whole-genome sequencing is emerging to discover more diverse genomic variants and examine their association with rare diseases. When no diagnosis is provided by whole-genome sequencing, additional omics techniques such as RNA-seq also can be considered to further interrogate causal variants. This paper will introduce a description of these multi-omics techniques and their applications in rare disease studies.

• Korean Journal of Plant Taxonomy
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• v.43 no.1
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• pp.63-68
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• 2013

ITS DNA sequences of two variants of Pinus spp. having single fasciculate leaf or two to three fasciculate leaves within an individual were analysed in order to determine their origin. Also, the same DNA locus of P. densiflora, P. rigida and P. koraiensis, distributed at the same region together with the OTUs having leaf variations, were analysed to compare with each other. Aligned sequences including ITS1, 5.8S and ITS2 were 580~584 bp in length. The 5.8S region was well conserved among all the OTUs we tested except for P. koraiensis, which has two nucleotide substitutions. The partial ITS1 region upstream of the 5.8S region showed relatively high sequence diversity compare to the ITS2 and has 181~185 bp in length. In this region, the sequences of the two variants were identical to that of P. densiflora. The ITS2 has identical for all OTUs in length and the two variants also have same sequences compare to that of P. densiflora. These two variants and samples of P. densiflora were grouped together in the UPGMA tree with 100% similarity level. The result strongly suggest that these two variants were originated from P. densiflora.

• Biomolecules & Therapeutics
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• v.23 no.2
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• pp.189-194
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• 2015

P450 1A2 is responsible for the metabolism of clinically important drugs and the metabolic activation of environmental chemicals. Genetic variations of P450 1A2 can influence its ability to perform these functions, and thus, this study aimed to characterize the functional significance of three P450 1A2 allelic variants containing nonsynonymous single nucleotide polymorphisms (P450 $1A2^*8$, R456H; $^*15$, P42R; $^*16$, R377Q). Variants containing these SNPs were constructed and the recombinant enzymes were expressed and purified in Escherichia coli. Only the P42R variant displayed the typical CO-binding spectrum indicating a P450 holoenzyme with an expression level of ~ 170 nmol per liter culture, but no P450 spectra were observed for the two other variants. Western blot analysis revealed that the level of expression for the P42R variant was lower than that of the wild type, however the expression of variants R456H and R377Q was not detected. Enzyme kinetic analyses indicated that the P42R mutation in P450 1A2 resulted in significant changes in catalytic activities. The P42R variant displayed an increased catalytic turnover numbers ($k_{cat}$) in both of methoxyresorufin O-demethylation and phenacetin O-deethylation. In the case of phenacetin O-deethylation analysis, the overall catalytic efficiency ($k_{cat}/K_m$) increased up to 2.5 fold with a slight increase of its $K_m$ value. This study indicated that the substitution P42R in the N-terminal proline-rich region of P450 contributed to the improvement of catalytic activity albeit the reduction of P450 structural stability or the decrease of substrate affinity. Characterization of these polymorphisms should be carefully examined in terms of the metabolism of many clinical drugs and environmental chemicals.

• Journal of Plant Biotechnology
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• v.30 no.1
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• pp.19-25
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• 2003

Radiation technique in agriculture was initiated to develop mutant rice. Seeds of Daechungbyeo rice were irradiated with 250 Gy gamma ray for the purpose of inducing and selecting rice variants. Some quantitative traits of the variants in M$_{8}$ generation were evaluated and RAPD analysis was carried out. Variants showed a wider range of agronomic characteristics in both a positive and a negative direction compared with their original variety. The new mutants were characterized by an increased or decreased in plant height, lodging resistance and shorter panicle. RAPD analysis showed that polymorphic bands were presented in most of the primers. In comparison with the original variety, variants were classified into four groups through UPGMA analysis. Among mutants no. 91, 139, 140 and 141 was ranked as salt tolerance and the proline content of these mutants was more increased than that of original variety. The lines of 139, 140 and 141 had the highest genetic distance as compared to original variety in the dendrogram. It is expected that such variants will be useful not only for studying molecular genetics but also for breeding research and genetic analysis.s.

• Proceedings of the Korean Society of Toxicology Conference
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• 2006.11a
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• pp.32-33
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• 2006

There is compelling evidence that chronic inflammation predisposes to biliary tract cancer. Previously we found that aspirin use and variants in the PTGS2 gene, both of which are closely linked to inflammation, were associated with biliary tract cancer risk in a population-based study in China. To test the inflammation hypothesis further, we examined the associations of variants in 20 genes involved in the inflammation pathway with risk of biliary tract cancer and stones in a large population-based case-control study in Shanghai, China. We genotyped 56 single nucleotide polymorphisms (SNPs)from 20 inflammation genes in 411 biliary tract cancer cases (237 gallbladder cancers, 127 extrahepatic bile duct cancers, and 47 ampullary cancers), 895 subjects with biliary stones, and 786 population controls. Unconditional logistic regression was used to calculate odds ratios (ORs) and 95% confidence intervals (Cls) for the association of individual SNPs and haplotypes with biliary stones and biliary tract cancer risk. Of the 56 SNPs examined, 20 showed some associations with biliary cancer and stones. Specifically, variants of the IL8, IL8RB, RNASEL, TGF-beta, and TNF-alpha genes were associated with gallstone risk, while variants in the IL1A, IL10, VEGF, and RNASEL genes were associated with gallbladder cancer risk. Adjustment for multiple comparisons did not materially change these results. Of the 10 genes with multiple SNPs, we inferred halotypes; only one haplotype in the IL8RBgene was associated with gallstones. The haplotype frequency was significantly different between bile dict cancer cases and control (p=0.007). A haplotype comprising 3 SNPs in the IL8RB gene (rs2230054, rs1126579, rs1126580) was associated with a 54% increased risk of bile duct stones (95% CI 1.14-2.07, p=0.02), relative to the most frequent haplotype. In summary, common variants in immune-related genes influencing inflammatory responeses were associated with gallstones and biliary tract cancer, lending further support to the role of inflammation in the pathogenesis of biliary stones and biliary tract cancer. Future larger studies with more complete gene coverage are needed to confirm these results.

• FLOWER RESEARCH JOURNAL
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• v.16 no.2
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• pp.128-133
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• 2008

This study was conducted to select new variants with different characteristics in plant height, leaf color, and petal color of plantain lily (Hosta plantaginea) and Japanese farfugium (Farfugium japonicum). After 10-30Gy ${\gamma}-ray$ irradiation to seeds of both species, seed germination, variant induction, growth of variants, and survival ratios were estimated. Days required for seed germination were lengthened and % seed germination decreased as the dosage of ${\gamma}-ray$ increased over 20Gy. Lethal dose ($LD_{50}$) for plantain lily and Japanese farfugium were 30Gy and 25Gy, respectively. Plantain lily and Japanese farfugium treated by more than 20Gy ${\gamma}-ray$ showed dwarf characteristics in growth, and variations in leaf and petal colors. Total 166 variants in plantain lily were induced by ${\gamma}-ray$ irradiation in a $M_1$ generation, among which 12 promising variants were selected in a $M_2$ generation. Total 57 variants of Japanese farfugium were induced by ${\gamma}-ray$ irradiation in a $M_1$ generation, among which nine promising variants were selected in a $M_2$ generation.

• Journal of Korean Society for Quality Management
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• v.29 no.2
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• pp.104-119
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• 2001

Brainstorming is one of the most well-known and frequently-used creativity techniques. Although the original brainstorming has several merits, it also has some drawbacks in its applications. Thus, lots of its variants have been introduced. Reverse Brainstorming, Cordon Method, Phillips 66, Brainwriting, 6-3-5 Brainwriting, Crawford Slip Writing, Nominal Group Technique, KJ Method are some examples. These techniques are classified into some categories, and their main characteristics are examined in this paper. Guidelines for applying the techniques are also provided.

• Journal of applied mathematics & informatics
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• v.27 no.5_6
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• pp.1195-1209
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• 2009

In this paper, we point out some errors in a recent paper by Cordero and Torregrosa [7]. We prove the convergence of the variants of Newton's method for solving the system of nonlinear equations using two different approaches. Several examples are given, which illustrate the cubic convergence of these methods and verify the theoretical results.

• Proceedings of the IEEK Conference
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• 2000.07a
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• pp.294-297
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• 2000

Among the multi-dimensional query types, ranking query is needed if we want the object one by one until we satisfy for the result. In multi-dimensional indexing structures like R-tree or its variants, not many methods are introduced in this area. In this paper, we introduce new ranking query processing algorithm which use the filtering mechanism in the R-tree variants.

• Kyungpook Mathematical Journal
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• v.56 no.2
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• pp.409-418
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• 2016

In this paper, we define two kinds variants of the super Catalan matrix as well as their q-analoques. We give explicit expressions for LU-decompositions of these matrices and their inverses.