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Review : Why Genes are in Pieces? A Genomics Perspective
Kyong Cheul Park,Soon Jae Kwon,Nam Soo Kim 한국유전학회 2008 Genes & Genomics Vol.30 No.5
Three decades after their discovery, both the biological function and evolutionary origin of introns still remain topics of considerable debate. Sequencing of complete genomes continues to provide key genetic insights into the elusive introns. Although supportive evidence exists both for an `introns-early` as well as an `introns-late` model of origin, neither theory is sufficient to account for the presence of both ancient and new introns in current eukaryotic genes; instead, a synthetic theory merging the two models may be valid. Insights into the biological role of introns are also available from genomics and experimental data sets. Introns regulate gene expression by means of a nonsense-mediated decay of mRNAs. Genome diversity generated by recombination between introns of paralogs, and proteome diversity generated by alternative intron splicing, would have been beneficial for the fitness of organisms. In gene families, intron gain or loss followed by gene duplication would have contributed to gene family divergence, and subsequently to species diversity and differentiation.
<i>Isaac</i>-CACTA transposons: new genetic markers in maize and sorghum
Lee, Ju Kyong,Kwon, Soon-Jae,Park, Kyong-Cheul,Kim, Nam-Soo Canadian Science Publishing 2005 Genome Vol.48 No.3
<P> CACTA is an En/Spm transposon superfamily present in high copy number in plant genomes, and Isaac is a subfamily of the CACTA superfamily. The TIR sequence of the Isaac subfamily was used for the purpose of transposon display (TD) in maize and sorghum. The Isaac TD produced 5080 amplified fragments, depending on the primer combination, and the amplification profile was highly polymorphic among maize inbred lines. Isaac TD-based phylogenetic clustering distinguished the maize inbred lines according to their lineages and was consistent with the results of phylogenetic reports derived from other marker techniques by others researchers. The Isaac TD profile proved to be highly reproducible with different brands of Taq DNA polymerases and thermocyclers. The Isaac TD was also applied to recombinant inbred lines to assess genetic segregation; we observed 4050 recordable segregation markers, depending on the primer combination. These Isaac TD markers segregated mostly as dominant markers, although, in a few cases, non-parental bands were observed in the segregating populations. In addition, the Isaac TD was very successful in the amplification of sorghum accessions. Therefore, the Isaac TD may provide another useful protocol for genetic analysis in maize and sorghum.Key words: CACTA, Isaac, transposon display, maize, sorghum. </P>
Molecular Genetic Distances and Hybrid Performances among Maize lnbreds and Their Hybrids
Lee, Ju Kyong,Min, Hwang-Kee,Park, Jong-Yeol,Huh, Nam-Ki,Park, Ki-Jin,Choi, Jae-Keun,Park, Kyong-Cheul,Kim, Nam-Soo 한국유전학회 2002 Genes & Genomics Vol.24 No.3
Genetic variations and genetic distances of the maize inbred breeding lines were analyzed using SSR (simple sequence repeats) and AFLP (amplified fragment length polymorphisms) techniques in order to assess the agronomic performances in their hybrids. The 25 inbred lines utilized consisted of mainly two groups of Lancaster Sure Crops in BSSS and Reid Yellow Dents except one line. The genetic distances, GDs, between groups were higher than the GDs within groups. The AFLP-based GDs were higher than the SSR-based GDs in all inbreds. While the clustering patterns derived from SSR polymorphisms showed low correlations with the pedigree information, AFLP-based clustering pattern generally matched with the pedigree grouping. In the analysis of correlation of GDs with agronomic performance in the hybrids, the AFLP-GDs showed high correlations with the plant height, ear diameter, hundred seed weight, and grain yield. However, there was a low correlations between the SSR-GDs and the above traits. The possible reasons of this low correlation and ambiguity in clustering pattern using SSR analysis were sought in the discussion. The trait of ear length showed low correlation with GDs from either technique. Therefore, the AFLP analysis might provide an efficient and practical utility in predicting hybrid performance in the yield components except ear length.
Growth of crack-free GaN/Si heteroepitaxy by a patterned Si substrate method
Kyong-Jun Kim,Cheul-Ro Lee,Yoon-Bong Hahn 한국물리학회 2005 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.46 No.4
In this study, we describe a unique approach to the growth of near crack-free GaN single crystals by using periodically striped patterned Si(111). Prior to the growth of the crystals, the patterned Si(111) was fabricated with various patterned terrace sizes ranging from 17 to 120 μm by using a combination of a photolithography patterning technique and an inductively coupled plasma (ICP) etching method. GaN layers were grown on the Si substrates by using metalorganic chemical vapor deposition (MOCVD), and the technique is called the patterned Si substrate technique. We compared the quality of the GaN layer that was grown using patterned Si(111) with that of the layer that was grown using unpatterned Si(111). The crack density in the GaN layer on the patterned Si(111) was shown to be drastically reduced in comparison with that of the GaN layer on the unpatterned Si(111). The full width at half maximum (FWHM) values clearly decreased with decreasing patterned terrace size on the Si substrates. Moreover, the micro photoluminescence intensity at room temperature was found to increase with decreasing pattern size. Consequently, the patterned Si substrate technique is thought to not only improve the quality of the GaN layer but also reduce the tensile stress caused by the thermal and the lattice mismatches.
Distribution of MITE Transposons in a Rice Genetic Map
Kyung Cheul Park,Ju Kyong Lee,Soon Jae Kwon,Ji Hyun Shin,Jeom Ho Lee,Chang In Yang,Nam Soo Kim 한국육종학회 2004 한국육종학회지 Vol.36 No.2
Molecular genetic markers have wide applicability for a various genetic analyses, and genetic mapping with PCR-based markers has identified many loci in the rice genome. This study was conducted to develop a genetic map of rice based on SSR and MITE-AFLP
Hwi-Cheul Lee,Gi-Sun lm.,Hak Jae Chung.,Poong-Yeon Lee,Jin-Ki Park,Won-Kyong Chang,Boh-Suk Yang,Keitaro Yamanouchi,Masugi Nishihara 한국동물생명공학회(구 한국동물번식학회) 2006 Reproductive & developmental biology Vol.30 No.4
Our previous research has identified granulin (grn) and p130 genes as sex steroidinducible genes in the rat hypothalamus, which might be involved in sexual differentiation of the brain. Phthalate esters that are used as plasticizers and also found at low levels in foods such as dairy products are often mentioned as suspected endocrine disrupters. The purpose of the present study is to elucidate whether perinatal exposure to dinbutyl phthalate (DBP), diisononyl phthalate (DINP) and di2ethylhexyl adipate (DEHA) affects hypothalamic sex steroidinducible genes. The present study assessed the effects of perinatal exposure to DBP, DINP and DEHA on sex steroid hormones levels and hypothalamic grn and p130 mRNA expressions at postnatal day (PND) 3 and 7. Pregnant rats were fed a soyfree diet containing 20, 200, 2,000 and 10,000 ppm of DBP, 40, 400, 4,000 and 20,000 ppm of DINP, or 480, 2,400 and 12,000 ppm of DEHA from gestational day (GD) 15 to GD 3 or 7. At PND 3 and 7, perinatal exposure to these chemicals did not substantially affect serum concentrations of testosterone and estradiol. At PND 3, the expression of grn mRNA levels in males was decreased by DEHA, and that of p130 was decreased by DBP, DINP and DEHA, though the effects were not dosedependent. At PND 7, the expression of grn gene in female pups was increased by higher doses of DBP and all the doses, except for 4,000 ppm, of DINP, while that in male pups decreased by 480 and 12,000 ppm of DEHA. Hypothalamic expression of p130 mRNA in males was increased by lower doses of DBP and all the doses of DINP, whereas that of females was decreased by 480 and 2,400 ppm of DEHA. These results suggest that these chemicals may affect the expression of grn and p130 genes by directly acting on the hypothalamus, thus leading to inappropriate expression of these genes.
Hwi-Cheul Lee,Gi-Sun Im,Hak Jae Chung,Poong-Yeon Lee,Jin-Ki Park,Won-Kyong Chang,Boh-Suk Yang,Keitaro Yamanouchi,Masugi Nishihara 사단법인 한국동물생명공학회 2006 Reproductive & developmental biology Vol.30 No.4
Our previous research has identified granulin (grn) and p130 genes as sex steroidinducible genes in the rat hypothalamus, which might be involved in sexual differentiation of the brain. Phthalate esters that are used as plasticizers and also found at low levels in foods such as dairy products are often mentioned as suspected endocrine disrupters. The purpose of the present study is to elucidate whether perinatal exposure to dinbutyl phthalate (DBP), diisononyl phthalate (DINP) and di2ethylhexyl adipate (DEHA) affects hypothalamic sex steroidinducible genes. The present study assessed the effects of perinatal exposure to DBP, DINP and DEHA on sex steroid hormones levels and hypothalamic grn and p130 mRNA expressions at postnatal day (PND) 3 and 7. Pregnant rats were fed a soyfree diet containing 20, 200, 2,000 and 10,000 ppm of DBP, 40, 400, 4,000 and 20,000 ppm of DINP, or 480, 2,400 and 12,000 ppm of DEHA from gestational day (GD) 15 to GD 3 or 7. At PND 3 and 7, perinatal exposure to these chemicals did not substantially affect serum concentrations of testosterone and estradiol. At PND 3, the expression of grn mRNA levels in males was decreased by DEHA, and that of p130 was decreased by DBP, DINP and DEHA, though the effects were not dosedependent. At PND 7, the expression of grn gene in female pups was increased by higher doses of DBP and all the doses, except for 4,000 ppm, of DINP, while that in male pups decreased by 480 and 12,000 ppm of DEHA. Hypothalamic expression of p130 mRNA in males was increased by lower doses of DBP and all the doses of DINP, whereas that of females was decreased by 480 and 2,400 ppm of DEHA. These results suggest that these chemicals may affect the expression of grn and p130 genes by directly acting on the hypothalamus, thus leading to inappropriate expression of these genes.
Lee, Hwi-Cheul,Im, Gi-Sun,Chung, Hak-Jae,Lee, Poong-Yeon,Park, Jin-Ki,Chang, Won-Kyong,Yang, Boh-Suk,Yamanouchi, Keitaro,Nishihara, Masugi The Korean Society of Animal Reproduction 2006 Reproductive & developmental biology Vol.30 No.4
Our previous research has identified granulin (grn) and p130 genes as sex steroid-inducible genes in the rat hypothalamus, which might be involved in sexual differentiation of the brain. Phthalate esters that are used as plasticizers and also found at low levels in foods such as dairy products are often mentioned as suspected endocrine disrupters. The purpose of the present study is to elucidate whether perinatal exposure to di-n-butyl phthalate (DBP), diisononyl phthalate (DINP) and di-2-ethylhexyl adipate (DEHA) affects hypothalamic sex steroid-inducible genes. The present study assessed the effects of perinatal exposure to DBP, DINP and DEHA on sex steroid hormones levels and hypothalamic gm and p130 mRNA expressions at postnatal day (PND) 3 and 7. Pregnant rats were fed a soy-free diet containing 20, 200, 2,000 and 10,000 ppm of DBP, 40, 400, 4,000 and 20,000 ppm of DINP, or 480, 2,400 and 12,000 ppm of DEHA from gestational day (GD) 15 to GD 3 or 7. At PND 3 and 7, perinatal exposure to these chemicals did not substantially affect serum concentrations of testosterone and estradiol. At PND 3, the expression of grn mRNA levels in males was decreased by DEHA, and that of p130 was decreased by DBP, DINP and DEHA, though the effects were not dose-dependent. At PND 7, the expression of gm gene in female pups was increased by higher doses of DBP and all the doses, except for 4,000 ppm, of DINP, while that in male pups decreased by 480 and 12,000 ppm of DEHA. Hypothalamic expression of p130 mRNA in males was increased by lower doses of DBP and all the doses of DINP, whereas that of females was decreased by 480 and 2,400 ppm of DEHA. These results suggest that these chemicals may affect the expression of gm and p130 genes by directly acting on the hypothalamus, thus leading to inappropriate expression of these genes.