• Journal of Aquaculture
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• v.20 no.2
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• pp.140-143
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• 2007

Cytogenetic analyses of an endemic species, Coreoleuciscus splendidus (Cyprinidae) was performed including erythrocyte measurement, chromosome count and karyotyping, nucleolar organizing region (NOR) banding and flow cytometric analysis of genome size. C. splendidus had the same modal chromosome number of 2n = 48 between sexes, however, displayed a sex-related dimorphism in their chromosome karyotypes. Males represented a pair of heteromorphic chromosomes which couldn‘t be seen in any female individuals, indicating that the sex determination mechanism of this species should be a typical XX-XY based male heterogamety (female=10M+6SM+8A+XX vs male=10M+6SM+8A+XY). Other cytogenetic features such as Ag-NORs located in a pair of acrocentric chromosomes, estimated nuclear volume ($28{\mu}m^3$) and cellular DNA content (2.4 pg/cell) suggest that genetic recombination might be the main driving force responsible for the evolution of this species rather than the polyploidy-based evolutionary process as in many other Cyprinidae species.

• Journal of Genetic Medicine
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• v.5 no.2
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• pp.145-149
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• 2008

46,XX male is a rare sex constitution characterized by the development of bilateral testis in persons who lack a Y chromosome. Manifestations of 46,XX males are usually hypogonadism, gynecomastia, azoospermia, and hyalinations of seminiferous tubules. The incidence of XX male reversal is approximately 1 in 20,000 male neonates. The SRYgene is located at the short arm of the Y chromosome(Yp11.31) and codes for testis determining factor in humans. Here, the patient, who presented with a normal male phenotype, was referred for azoospermia. Conventional cytogenetic analysis showed a 46,XX karyotype. Quantitative fluorescent polymerase chain reaction(QF-PCR) and Multiplex PCR studies identified SRY gene. And, Fluorescence In Situ Hybridization(FISH) confirmed the SRY gene on the distal short arm of chromosome X. We identified the SRY gene on the distal short arm of chromosome X by molecular cytogenetic and molecular analyses. Therefore, molecular-cytogenetics and molecular studies were proved to be clinically useful adjunctive tool to conventional prenatal cytogenetic analysis.

• Journal of Genetic Medicine
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• v.5 no.1
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• pp.41-46
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• 2008

Purpose : Fragile X syndrome (FXS) is the most common heritable cause of cognitive impairment. FXS is caused by hyperexpansion and hypermethylation of a polymorphic CGG trinucleotide repeat in the 5' untranslated region of the fragile X mental retadation-1(FMR1) gene. Combination of Southern blotting and simple polymerase chain reaction(PCR) amplification of the FMR1 repeat region is commonly used for diagnosis in females. To give a definite diagnosis in a female child suspected of having FXS, we carried out the molecular diagnostic test for FXS using the recently developed Abbott Molecular Fragile X PCR Kit. Methods : The PCR amplification of the FMR1 repeat region was performed using the Abbott Mdecular Fragile X PCR Kit. The amplified products were analyzed by size-separate analysis on 1.5% agarose gels and by DNA fragment analysis using Gene scan. Results : Agarose gel and Gene scan analyses of PCR products of the FMR1 repeat region showed that the patient had two heterozygous alleles with a normal 30 repeats and full mutation of >200 repeats whereas her mother had two heterozygous alleles with the normal 30 repeats and premutation of 108 repeats, suggesting that the premutation of 108 repeats in her mother may have led to the full mutation of >200 repeats in the patient. Conclusion : We diagnosed FXS in a female patient using a simplified molecular diagnostic test. This commercially available diagnostic test for FXS, based on PCR, may be a suitable alternative or complement method to Southern blot analysis and PCR analysis and/or methylation specific(MS)-PCR analysis for the molecular diagnosis of FXS in both males and females.

• Molecules and Cells
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• v.24 no.1
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• pp.83-94
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• 2007

During monocarpic senescence in higher plants, functional stay-green delays leaf yellowing, maintaining photosynthetic competence, whereas nonfunctional stay-green retains leaf greenness without sustaining photosynthetic activity. Thus, functional stay-green is considered a beneficial trait that can increase grain yield in cereal crops. A stay-green japonica rice 'SNU-SG1' had a good seed-setting rate and grain yield, indicating the presence of a functional stay-green genotype. SNU-SG1 was crossed with two regular cultivars to determine the inheritance mode and identify major QTLs conferring stay-green in SNU-SG1. For QTL analysis, linkage maps with 100 and 116 DNA marker loci were constructed using selective genotyping with $F_2$ and RIL (recombinant inbred line) populations, respectively. Molecular marker-based QTL analyses with both populations revealed that the functional stay-green phenotype of SNU-SG1 is regulated by several major QTLs accounting for a large portion of the genetic variation. Three main-effect QTLs located on chromosomes 7 and 9 were detected in both populations and a number of epistatic-effect QTLs were also found. The amount of variation explained by several digenic interactions was larger than that explained by main-effect QTLs. Two main-effect QTLs on chromosome 9 can be considered the target loci that most influence the functional stay-green in SNU-SG1. The functional stay-green QTLs may help develop low-input high-yielding rice cultivars by QTL-marker-assisted breeding with SNU-SG1.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.11
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• pp.6673-6680
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• 2013

Objective: Insulin resistance (IR) is an established risk factor for colorectal cancer (CRC). Given that CRC and IR physiologically overlap and the calpain-10 gene (CAPN10) is a candidate for IR, we explored the association between CAPN10 and CRC risk. Methods: Blood samples of 400 case-control pairs were genotyped, and the lifestyle and dietary habits of these pairs were recorded and collected. Unconditional logistic regression (LR) was used to assess the effects of CAPN10 SNP43 and SNP19, and environmental factors. Both generalized multifactor dimensionality reduction (GMDR) and the classification and regression tree (CART) were used to test gene-environment interactions for CRC risk. Results: The GA+AA genotype of SNP43 and the Del/Ins+Ins/Ins genotype of SNP19 were marginally related to CRC risk (GA+AA: OR = 1.35, 95% CI = 0.92-1.99; Del/Ins+Ins/Ins: OR = 1.31, 95% CI = 0.84-2.04). Notably, a high-order interaction was consistently identified by GMDR and CART analyses. In GMDR, the four-factor interaction model of SNP43, SNP19, red meat consumption, and smoked meat consumption was the best model, with a maximum cross-validation consistency of 10/10 and testing balance accuracy of 0.61 (P < 0.01). In LR, subjects with high red and smoked meat consumption and two risk genotypes had a 6.17-fold CRC risk (95% CI = 2.44-15.6) relative to that of subjects with low red and smoked meat consumption and null risk genotypes. In CART, individuals with high smoked and red meat consumption, SNP19 Del/Ins+Ins/Ins, and SNP43 GA+AA had higher CRC risk (OR = 4.56, 95%CI = 1.94-10.75) than those with low smoked and red meat consumption. Conclusions: Though the single loci of CAPN10 SNP43 and SNP19 are not enough to significantly increase the CRC susceptibility, the combination of SNP43, SNP19, red meat consumption, and smoked meat consumption is associated with elevated risk.

• Journal of Ginseng Research
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• v.33 no.3
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• pp.234-239
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• 2009

This study aims to establish the directions for the optimal nutrient contents determined by soil and leaf analyses. The study is to be used as a source for basic information in investigating the effects of nutritional environment on ginseng growth at the fields of Ansung region in Gyeonggi province. The physical property of soil porosity is closely related to ginseng growth, with more than 50% of good growth in the field. The optimal range of chemical properties in soil was analyzed as 0.20-0.28% T-N, 500-900 mg/kg Av.P$_2$O$_5$, and 2.3-3.5 cmol$^+$/kg Exch.Ca. The optimal range of inorganic nutrient contents in leaves was also analyzed. P value was less than 0.25%, and Mg was more than 0.22%. Other elements were not found clearly. The ratios of N/P, N/Mg, K/Mg, and Ca/P of leaves with good growth in the field showed 10<, 10-13, <14, 1<, respectively. In addition, the Ca:Mg:K ratio of the Exch.cation (cmol$^+$/kg) may be useful as an indicator in the assessment of plant growth in ginseng.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.238-238
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• 2017

Salt stress is one of the deteriorating abiotic stresses due to the climate change, which causes over-accumulation of $Na^+$ and $Cl^-$ ions in plants and inhibits the growth and yield of rice especially in coastal Southeastern Asia. The yield components of rice plant (panicle number, spikelet number per panicle, 1000-grain weight, % of ripened grains) that are majorly affected by salt stress vary with growth stages at which the plant is subjected to the stress. In addition, the salt sensitivity of each yield component differs among rice varieties even when the salt-affected growth stage was same, which indicates that the physiological mechanism to maintain each yield component is different from each other. Therefore, we hypothesized that rice plant has different genes/QTLs that contribute to the maintenance of each yield component. Using a Japanese leading rice cultivar, Koshihikari, and salt-tolerant Nona bokra's chromosome segment substitution lines (CSSLs) with the genetic background of Koshihikari (44 lines in total) (Takai et al. 2007), we screened higher yielding CSSLs under salinity in comparison to Koshihikari and identified the yield components that were improved by the introgression of chromosome segment(s) of Nona bokra. The experiment was conducted in a salinized paddy field. One-month-old seedlings were transplanted into a paddy field without salinity. These were allowed to establish for one month, and then the field was salinized by introducing saline water to maintain the surface water at 0.4% salinity until harvest. The experiments were done twice in 2015 and 2016. Although all the CSSLs and Koshihikari decreased their yield under salinity, some CSSLs showed relatively higher yield compared with Koshihikari. In Koshihikari, all the yield components except panicle number were decreased by salinity and % of ripened grains was mostly reduced, followed by spikelet number per panicle and 1000-grain weight. When compared with Koshihikari, keeping a higher % of ripened grains under salinity attributed to the significantly greater yield in one CSSL. This indicated that the % of ripened grains is the most sensitive to salt stress among the yield components of Koshihikari and that the Nona bokra chromosome segments that maintained it contributed to increased yield under salt stress. In addition, growth analyses showed that maintaining relative growth rate in the late grain filling stage led to the increased yield under salt stress but not in earlier stages.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.20-20
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• 2017

Plant genomes include heterochromatic loci that consist of repetitive sequences and transposable elements. LTR retrotransposon is the major class of transposons in advanced plants in terms of proportion in plant genome. The elements contribute not only to genome size but also to genome stability and gene expression. A number of cases have been reported transposon insertions near genic regions affect crop traits such as fruit pigments, stress tolerance, and yields. Functional LTR retrotransposons produce extrachromosomal DNA from genomic RNA by reverse transcription that takes place within virus-like-particles (VLPs). DECREASED DNA METHYLATION 1 (DDM1) plays important roles in maintaining DNA methylation of heterochromatin affecting all sequence contexts, CG, CHG, and CHH. Previous studies showed that ddm1 mutant exhibits massive transcription of retrotransposons in Arabidopsis, but only few of them were able to create new insertions into the genome. RNA-dependent RNA POLYMERASE 6 (RDR6) is known to function in restricting accumulation of transposon RNA by processing the transcripts into 21-22 nt epigenetically activated small interfering RNA (easiRNA). We purified VLPs and sequence cDNA to identify functional LTR retrotransposons in Arabidopsis ddm1 and ddm1rdr6 plants. Over 20 LTR copia and gypsy families were detected in ddm1 and ddm1rdr6 sequencing libraries and most of them were not reported for mobility. In ddm1rdr6, short fragments of ATHILA gypsy elements were detected. It suggests easiRNAs might regulate reverse transcription steps. The highest enriched element among transposon loci was previously characterized EVADE element. It has been reported that active EVADE element is more efficiently silenced through female germline than male germline. By genetic analyses, we found ddm1 and rdr6 mutation affect maternal silencing of active EVADE elements. DDM1-GFP protein accumulated in megaspore mother cell but was not found in mature egg cell. The fusion protein was also found in early embryo and maternal DDM1-GFP allele was more dominantly expressed in the embryo. We observed localization of DDM1-GFP in Arabidopsis and DDM1-YFP in maize and found the proteins accumulated in dividing zone of root tips. Currently we are looking at cell cycle dependency of DDM1 expression using maize system. Among 10 AGO proteins in Arabidopsis, AGO9 is specifically expressed in egg cell and shoot meristematic cells. In addition, mutation of AGO9 and RDR6 caused failure in maternal silencing, implying 21-22 nt easiRNA pathway is important for retrotransposon silencing in female gametophyte or/and early embryo. On the other hand, canonical 24 nt sRNA-directed DNA methylation (RdDM) pathways did not contribute to maternal silencing as confirmed by this study. Heat-activated LTR retrotransposon, ONSEN, was not silenced by DDM1 but the silencing mechanisms require RdDM pathways in somatic cells. We will propose distinct mechanisms of LTR retrotransposons in germline and somatic stages.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.97-97
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• 2017

Plant genomes include heterochromatic loci that consist of repetitive sequences and transposable elements. LTR retrotransposon is the major class of transposons in advanced plants in terms of proportion in plant genome. The elements contribute not only to genome size but also to genome stability and gene expression. A number of cases have been reported transposon insertions near genic regions affect crop traits such as fruit pigments, stress tolerance, and yields. Functional LTR retrotransposons produce extrachromosomal DNA from genomic RNA by reverse transcription that takes place within virus-like-particles (VLPs). DECREASED DNA METHYLATION 1 (DDM1) plays important roles in maintaining DNA methylation of heterochromatin affecting all sequence contexts, CG, CHG, and CHH. Previous studies showed that ddm1 mutant exhibits massive transcription of retrotransposons in Arabidopsis, but only few of them were able to create new insertions into the genome. RNA-dependent RNA POLYMERASE 6 (RDR6) is known to function in restricting accumulation of transposon RNA by processing the transcripts into 21-22 nt epigenetically activated small interfering RNA (easiRNA). We purified VLPs and sequence cDNA to identify functional LTR retrotransposons in Arabidopsis ddm1 and ddm1rdr6 plants. Over 20 LTR copia and gypsy families were detected in ddm1 and ddm1rdr6 sequencing libraries and most of them were not reported for mobility. In ddm1rdr6, short fragments of ATHILA gypsy elements were detected. It suggests easiRNAs might regulate reverse transcription steps. The highest enriched element among transposon loci was previously characterized EVADE element. It has been reported that active EVADE element is more efficiently silenced through female germline than male germline. By genetic analyses, we found ddm1 and rdr6 mutation affect maternal silencing of active EVADE elements. DDM1-GFP protein accumulated in megaspore mother cell but was not found in mature egg cell. The fusion protein was also found in early embryo and maternal DDM1-GFP allele was more dominantly expressed in the embryo. We observed localization of DDM1-GFP in Arabidopsis and DDM1-YFP in maize and found the proteins accumulated in dividing zone of root tips. Currently we are looking at cell cycle dependency of DDM1 expression using maize system. Among 10 AGO proteins in Arabidopsis, AGO9 is specifically expressed in egg cell and shoot meristematic cells. In addition, mutation of AGO9 and RDR6 caused failure in maternal silencing, implying 21-22 nt easiRNA pathway is important for retrotransposon silencing in female gametophyte or/and early embryo. On the other hand, canonical 24 nt sRNA-directed DNA methylation (RdDM) pathways did not contribute to maternal silencing as confirmed by this study. Heat-activated LTR retrotransposon, ONSEN, was not silenced by DDM1 but the silencing mechanisms require RdDM pathways in somatic cells. We will propose distinct mechanisms of LTR retrotransposons in germline and somatic stages.

• Journal of Educational Research in Mathematics
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• v.11 no.2
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• pp.363-384
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• 2001

The purpose of this thesis is, through analysing the characteristics of the definitions in Korean school mathematics textbooks, to explore the levels of them and to make suggestions for definition - teaching as a mathematising activity, Definitions used in academic mathematics are rigorous. But they should be transformed into various types, which are presented in school mathematics textbooks, with didactical purposes. In this thesis we investigated such types of transformation. With the result of this investigation we tried to identify the levels of the definitions in school mathematics textbooks. And in school mathematics textbooks there are definitions which carry out special functions in mathematical contexts or situations. We can say that we understand those definitions, only if we also understand the functions of definitions in those contexts or situations. In this thesis we investigated the cases in school mathematics textbooks, when such functions of definition are accompanied. With the result of this investigation we tried to make suggestions for definition-teaching as an intellectual activity. To begin with we considered definition from two aspects, methods of definition and functions of definition. We tried to construct, with consideration about methods of definition, frame for analysing the types of the definitions in school mathematics and search for a method for definition-teaching through mathematization. Methods of definition are classified as connotative method, denotative method, and synonymous method. Especially we identified that connotative method contains logical definition, genetic definition, relational definition, operational definition, and axiomatic definition. Functions of definition are classified as, description-function, stipulation-function, discrimination-function, analysis-function, demonstration-function, improvement-function. With these analyses we made a frame for investigating the characteristics of the definitions in school mathematics textbooks. With this frame we identified concrete types of transformations of methods of definition. We tried to analyse this result with van Hieles' theory about levels of geometry learning and the mathematical language levels described by Freudenthal, and identify the levels of definitions in school mathematics. We showed the levels of definitions in the geometry area of the Korean school mathematics. And as a result of analysing functions of definition we found that functions of definition appear more often in geometry than in algebra or analysis and that improvement-function, demonstration-function appear regularly after demonstrative geometry while other functions appear before demonstrative geometry. Also, we found that generally speaking, the functions of definition are not explained adequately in school mathematics textbooks. So it is required that the textbook authors should be careful not to miss an opportunity for the functional understanding. And the mathematics teachers should be aware of the functions of definitions. As mentioned above, in this thesis we analysed definitions in school mathematics, identified various types of didactical transformations of definitions, and presented a basis for future researches on definition teaching in school mathematics.