A multiplex PCR system for 13 RM Y-STRs with separate amplification of two different repeat motif structures in DYF403S1a

Lee, E.Y.,Lee, H.Y.,Kwon, S.Y.,Oh, Y.N.,Yang, W.I.,Shin, K.J. ELSEVIER SCIENCE B V AMSTERDAM 2017 FORENSIC SCIENCE INTERNATIONAL GENETICS Vol.26 No.-

<P>In forensic science and human genetics, Y-chromosomal short tandem repeats (Y-STRs) have been used as very useful markers. Recently, more Y-STR markers have been analyzed to enhance the resolution power in haplotype analysis, and 13 rapidly mutating (RM) Y-STRs have been suggested as revolutionary tools that can widen Y-chromosomal application from paternal lineage differentiation to male individualization. We have constructed two multiplex PCR sets for the amplification of 13 RM Y-STRs, which yield small-sized amplicons (<400 bp) and a more balanced PCR efficiency with minimum PCR cycling. In particular, with the developed multiplex PCR system, we could separate three copies of DYF403S1a into two copies of DYF403S1a and one of DYF403S1b1. This is because DYF403S1b1 possesses distinguishable sequences from DYF403S1a at both the front and rear flanking regions of the repeat motif; therefore, the locus could be separately amplified using sequence-specific primers. In addition, the other copy, defined as DYF403S1b by Ballantyne et al., was renamed DYF403S1b2 because of its similar flanking region sequence to DYF403S1b1. By redefining DYF403S1 with the developed multiplex system, all genotypes of four copies could be successfully typed and more diverse haplotypes were obtained. We analyzed haplotype distributions in 705 Korean males based on four different Y-STR subsets: Yfiler, PowerPlex Y23, Yfiler Plus, and RM Y-STRs. All haplotypes obtained from RM Y-STRs were the most diverse and showed strong discriminatory power in Korean population. (C) 2016 Elsevier Ireland Ltd. All rights reserved.</P>

Investigation into the sequence structure of 23 Y chromosomal STR loci using massively parallel sequencing

Kwon, S.Y.,Lee, H.Y.,Kim, E.H.,Lee, E.Y.,Shin, K.J. Elsevier Science 2016 FORENSIC SCIENCE INTERNATIONAL GENETICS Vol.25 No.-

Next-generation sequencing (NGS) can produce massively parallel sequencing (MPS) data for many targeted regions with a high depth of coverage, suggesting its successful application to the amplicons of forensic genetic markers. In the present study, we evaluated the practical utility of MPS in Y-chromosome short tandem repeat (Y-STR) analysis using a multiplex polymerase chain reaction (PCR) system. The multiplex PCR system simultaneously amplified 24 Y-chromosomal markers, including the PowerPlex<SUP>®</SUP> Y23 loci (DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS481, DYS533, DYS549, DYS570, DYS576, DYS635, DYS643, and YGATAH4) and the M175 marker with the small-sized amplicons ranging from 85 to 253bp. The barcoded libraries for the amplicons of the 24 Y-chromosomal markers were produced using a simplified PCR-based library preparation method and successfully sequenced using MPS on a MiSeq<SUP>®</SUP> System with samples from 250 unrelated Korean males. The genotyping concordance between MPS and the capillary electrophoresis (CE) method, as well as the sequence structure of the 23 Y-STRs, were investigated. Three samples exhibited discordance between the MPS and CE results at DYS385, DYS439, and DYS576. There were 12 Y-STR loci that showed sequence variations in the alleles by a fragment size determination, and the most varied alleles occurred in DYS389II with a different sequence structure in the repeat region. The largest increase in gene diversity between the CE and MPS results was in DYS437 at +34.41%. Single nucleotide polymorphisms (SNPs), insertions, and deletions (indels) were observed in the flanking regions of DYS481, DYS576, and DYS385, respectively. Stutter and noise ratios of the 23 Y-STRs using the developed MPS system were also investigated. Based on these results, the MPS analysis system used in this study could facilitate the investigation into the sequences of the 23 Y-STRs in forensic genetics laboratories.

Runx3 is required for the differentiation of lung epithelial cells and suppression of lung cancer

Lee, K-S,Lee, Y-S,Lee, J-M,Ito, K,Cinghu, S,Kim, J-H,Jang, J-W,Li, Y-H,Goh, Y-M,Chi, X-Z,Wee, H,Lee, H-W,Hosoya, A,Chung, J-H,Jang, J-J,Kundu, J K,Surh, Y-J,Kim, W-J,Ito, Y,Jung, H-S,Bae, S-C Macmillan Publishers Limited 2010 Oncogene Vol.29 No.23

Human lung adenocarcinoma, the most prevalent form of lung cancer, is characterized by many molecular abnormalities. K-ras mutations are associated with the initiation of lung adenocarcinomas, but K-ras-independent mechanisms may also initiate lung tumors. Here, we find that the runt-related transcription factor Runx3 is essential for normal murine lung development and is a tumor suppressor that prevents lung adenocarcinoma. Runx3−/− mice, which die soon after birth, exhibit alveolar hyperplasia. Importantly, Runx3−/− bronchioli exhibit impaired differentiation, as evidenced by the accumulation of epithelial cells containing specific markers for both alveolar (that is SP-B) and bronchiolar (that is CC10) lineages. Runx3−/− epithelial cells also express Bmi1, which supports self-renewal of stem cells. Lung adenomas spontaneously develop in aging Runx3+/− mice (∼18 months after birth) and invariably exhibit reduced levels of Runx3. As K-ras mutations are very rare in these adenomas, Runx3+/− mice provide an animal model for lung tumorigenesis that recapitulates the preneoplastic stage of human lung adenocarcinoma development, which is independent of K-Ras mutation. We conclude that Runx3 is essential for lung epithelial cell differentiation, and that downregulation of Runx3 is causally linked to the preneoplastic stage of lung adenocarcinoma.

Analysis of 22 Y chromosomal STR haplotypes and Y haplogroup distribution in Pathans of Pakistan

Lee, E.Y.,Shin, K.J.,Rakha, A.,Sim, J.E.,Park, M.J.,Kim, N.Y.,Yang, W.I.,Lee, H.Y. Elsevier Science 2014 FORENSIC SCIENCE INTERNATIONAL GENETICS Vol.11 No.-

We analyzed haplotypes for 22 Y chromosomal STRs (Y-STRs), including 17 Yfiler loci (DYS19, DYS385a/b, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DY438, DYS439, DYS448, DYS456, DYS458, DYS635 and Y-GATA-H4) and five additional STRs (DYS388, DYS446, DYS447, DYS449 and DYS464), and Y chromosomal haplogroup distribution in 270 unrelated individuals from the Pathans residing in the Federally Administered Tribal Areas and the North-West Frontier Province of Pakistan using in-house multiplex PCR systems. Each Y-STR showed diversities ranging from 0.2506 to 0.8538, and the discriminatory capacity (DC) was 73.7% with 199 observed haplotypes using 17 Yfiler loci. By the addition of 5 Y-STRs to the Yfiler system, the DC was increased to 85.2% while showing 230 observed haplotypes. Among the additional 5 Y-STRs, DYS446, DYS447 and DYS449 were major contributors to enhancing discrimination. In the analysis of molecular variance, the Pathans of this study showed significant differences from other Pathan populations as well as neighboring population sets. In Y-SNP analysis, a total of 12 Y chromosomal haplogroups were observed and the most frequent haplogroup was R1a1a with 49.3% frequency. To obtain insights on the origin of Pathans, the network analysis was performed for the haplogroups G and Q observed from the Pathans and the Jewish population groups including Ashkenazim and Sephardim, but little support for a Jewish origin could be found. In the present study, we report Y-STR population data in Pathans of Pakistan, and we emphasize the need for adding additional markers to the commonly used 17 Yfiler loci to achieve more improved discriminatory capacity in a population with low genetic diversity.

Haplotype and mutation analysis for newly suggested Y-STRs in Korean father-son pairs

Oh, Y.N.,Lee, H.Y.,Lee, E.Y.,Kim, E.H.,Yang, W.I.,Shin, K.J. Elsevier Science 2015 FORENSIC SCIENCE INTERNATIONAL GENETICS Vol.15 No.-

In this study, 363 Korean father-son haplotype transfers in 351 families were analyzed using an in-house multiplex PCR system for 14 Y-STRs (DYS385a/b, DYF387S1, DYS391, DYS449, DYS460, DYS481, DYS518, DYS533, DYS549, DYS570, DYS576, DYS627 and DYS643), that included 11 loci newly added to the PowerPlex Y23 system or the Yfiler Plus system. The Y-STRs showed gene diversity values ranging from 0.2499 to 0.9612; the multicopy Y-STR loci DYS385 and DYF387S1 had high gene diversity of 0.9612 and 0.9457, respectively. In addition, DYF387S1, which has two copies, showed three alleles in seven individuals, and micro-variant alleles were observed in 14 individuals at four loci (DYS448, DYS518, DYS570 and DYS627). Among 351 haplotypes for the 11 newly added Y-STRs, 350 different haplotypes were observed, with an overall haplotype diversity of 0.9999 and discrimination capacity of 99.72%. In 363 haplotype transfers from 351 pedigrees, 29 single-step mutations were observed at 11 Y-STRs. Locus-specific mutation rate estimates varied from 0.0 to 1.93x10<SUP>-2</SUP>, with an average estimated mutation rate of 6.66x10<SUP>-3</SUP>. Two father-son pairs had mutations at two different loci in 11 Y-STRs. The number of pairs with mutations at multiple loci increased to five when the mutation event was investigated for haplotype transfer at 28 Y-STRs including 17 Yfiler loci and 11 Y-STRs examined in this study: four father-son pairs had mutations at two loci, and one pair had mutations at three loci. Overall, mutations were frequently observed at DYS449, DYS576 and DYS627 loci, which are known to be rapidly mutating Y-STRs. Mutation rate estimates at most loci were not significantly different from rates in other populations, but estimates for DYF387S1, DYS518 and DYS570 were considerably lower in the Korean population than in other populations.

K₂WO₄ flux 에 의한 K₂Oㆍ6TiO₂ whisker 의 합성

이진식 ( J. S. Lee ),이상문 ( S. M. Lee ),이철태 ( C. T. Lee ),권긍택 ( K. T. Kohn ),김영명 ( Y. M. Kim ) 한국공업화학회 1993 한국공업화학회 연구논문 초록집 Vol.1993 No.0

K₂Oㆍ6TiO₂ whisker는 구조적인 특성 때문에 물리ㆍ화학적으로 매우 안정하며 보강재, 마찰재, 단열재 등의 많은 용도를 갖게된다. 특히 최근에는 석면이 발암물질로 인한 자동차 브레이크 마찰재료의 사용이 금지됨에 따라 K₂Oㆍ6TiO₂ whisker는 이의 대체 섬유로서 주목을 받고 있다. 이러한 K₂Oㆍ6TiO₂ whisker의 합성방법으로는 TiO₂와 K₂CO₃의 화학양론적 조성의 혼합들을 설정온도에서 소성(calcination method)시키는 방법을 비롯하여 응용법(melting method), 수열법(hydrothermal method), 융제법(flux) 및 KDC법(kneading-drying-calcination method) 등의 방법이 있다. 그러나 수열법의 경우 양질의 whisker를 얻을 수 있으나 고압합성 이므로 위험하고 가격이 비싼 결점이 있으며 공업상 제조에 필요한 조건이 복잡하고 연속조작이 어려워 비현실적인 방법이다. 또한 서냉소성법의 경우 공정이 단순하며 공업화가 쉬우나 비교적 장섬유가 얻어지게 된다. 따라서 본 연구에서는 융제법을 이용하여 K₂Oㆍ6TiO₂ whisker를 합성하였으며. 과거에 용제로 사용된 KC1-KF계. K₂O-Na₂O-B₂O₃계 등의 높은 volatility와 viscosity 그리고 낮은 solubility에 대한 문제점을 개선하기 위해 K₂WO₄를 flux로 선정하여 K₂Oㆍ6TiO₂ whisker를 합성하였다.

Confirmation of Y haplogroup tree topologies with newly suggested Y-SNPs for the C2, O2b and O3a subhaplogroups

Kwon, S.Y.,Lee, H.Y.,Lee, E.Y.,Yang, W.I.,Shin, K.J. Elsevier Science 2015 FORENSIC SCIENCE INTERNATIONAL GENETICS Vol.19 No.-

Y chromosome single nucleotide polymorphisms (Y-SNPs) are useful markers for reconstructing male lineages through hierarchically arranged allelic sets known as haplogroups, and are thereby widely used in the fields such as human evolution, anthropology and forensic genetics. The Y haplogroup tree was recently revised with newly suggested Y-SNP markers for designation of several subgroups of haplogroups C2, O2b and O3a, which are predominant in Koreans. Therefore, herein we analyzed these newly suggested Y-SNPs in 545 unrelated Korean males who belong to the haplogroups C2, O2b or O3a, and investigated the reconstructed topology of the Y haplogroup tree. We were able to confirm that markers L1373, Z1338/JST002613-27, Z1300, CTS2657, Z8440 and F845 define the C2 subhaplogroups, C2b, C2e, C2e1, C2e1a, C2e1b and C2e2, respectively, and that markers F3356, L682, F11, F238/F449 and F444 define the O subhaplogroups O2b1, O2b1b, O3a1c1, O3a1c2 and O3a2c1c, respectively. Among six C2 subhaplogroups (C2b, C2e, C2e1*, C2e1a, C2e1b and C2e2), the C2e haplogroup and its subhaplogroups were found to be predominant, and among the four O2b subhaplogroups (O2b*, O2b1*, O2b1a and O2b1b), O2b1b was most frequently observed. Among the O3a subhaplogroups, O3a2c1 was predominant and it was further divided into the subhaplogroups O3a2c1a and O3a2c1c with a newly suggested marker. However, the JST002613-27 marker, which had been known to define the haplogroup C2f, was found to be an ancestral marker of the C2e haplogroup, as is the Z1338 marker. Also, the M312 marker for the O2b1 haplogroup designation was replaced by F3356, because all of the O2b1 haplotypes showed a nucleotide change at F3356, but not at M312. In addition, the F238 marker was always observed to be phylogenetically equivalent to F449, while both of the markers were assigned to the O3a1c2 haplogroup. The confirmed phylogenetic tree of this study with the newly suggested Y-SNPs could be valuable for anthropological and forensic investigations of East Asians including Koreans.

Urea와 K₂SO₄ 처리에 의한 복숭아 '미백도'에서 수확 시 과실의 무기성분 농도 및 과피색 변화

문병우,윤익구,문영지,남기웅,이영철,Moon, B.W.,Yoon, I.K.,Moon, Y.J.,Nam, K.W.,Lee, Y.C. 국립한국농수산대학교 교육개발센터 2013 현장농업연구지 = Journal of practical agricultural resear Vol.15 No.1

This study has been conducted to investigate the effect of Urea and K₂SO₄ treatment at stone hardening stage and 20 days before harvest on soil chemical properties, mineral nutrient concentration and quality of 'Mibaekdo' fruit peach. K concentration after Urea and K₂SO₄ treatment in soil was increased significantly by Urea 162g+K₂SO₄ 188g/tree(standard amount) treatment at stone hardening stage, K₂SO₄ 1.0% tree-spray, Urea 81g+K₂SO₄ 94g/tree(half amount), Urea 162g+K₂SO₄ 188g/tree and Urea 324g+K₂SO₄ 376g/tree(double amount) soil treatment before harvest 20 days compared to control. T-N, K and Ca concentration in leaf was increased significantly by all treatment. but Na concentration in leaf was increased by Urea 0.5% and K₂SO₄ 1.0% tree-spray treatment before harvest 20 days. T-N concentration in fruit skin was increased significantly by standard amount soil treatment, which decreased by K₂SO₄ 1.0% tree-spray and half amount soil treatment. T-N, K and Ca concentration in fruit flesh(1~10mm depth flesh from peel) were increased markedly by all treatment excepted Urea 0.5% tree-spray. The leaf weight at harvest was increased markedly by Urea 0.5% tree-spray, standard amount and double amount treatment before harvest 20 days. Fruit weight was increased significantly by standard amount compared to all treatment. Red fruit skin(Hunter a value) progress was effective by K₂SO₄ tree-spray, half amount and double amount treatment before harvest 20 days. Fruit SSC was increased significantly by Urea 0.5% and K₂SO₄ tree-spray before harvest 20 days, standard amount treatment at stone hardening stage compared to control.

Cellulase-amyloglucosidase와 효모의 가스생성법에 의한 사료의 에너지가 측정에 관한 연구

김영길,이광목,김욱 東亞大學校生命資源科學大學附設 農業資源硏究所 1993 農業生命資援硏究 Vol.2 No.2

粗飼料와 濃厚飼料를 混合한 飼料의 營養價를 Cellulase와 Amyloglucosidase, 酵母를 利用한 가스 生成法에 의하여 消化率과 TDN을 測定할 수 있는 方法을 確立하고자 本 硏究를 實施한 實驗 結果는 다음과 같다. 1. Cellulose 加水分解 酵素인 Trichoderma viride cellulase의 最適 活性 pH는 4.5-4.8이었으며 pH가 5.0보다 높을 때에는 活性이 急激히 저하하였다. 2. Cellulose 加水分解시 Trichoderma viride celulase의 溫度의 의한 影響은 50℃에서 最大 活性을 나타내었으며, 40℃에서는 活性이 92%정도로 나타났다. 3. Trichoderma viride-aspergillus niger 混合, cellulase 使用時의 가스 生成量은 Trichoderma viride cellulase 使用時 가스 生成量 보다 20-30% 높게 나타났으므로 cellulose 加水分解時 Trichoderma viride-aspergillus niger 混合 cellulase를 使用하는 것이 더욱 效果的일 것으로 思料된다. 4. 포도당(X)과 가스 生成量(Y)과의 關係는 Y=6.82+165X의 回歸式과 相關係數는 0.92로서 高度의 有意性(P<0.01)이 있었다. 5. Trichoderma viride cellulase 使用時 가스 生成量(X)과 乾物 消化率(Y)과의 關係는 Y=29.9+1.13X(r=78**)의 回歸式을 나타내었고, Trichoderma viride-aspergillus niger 混合 vellulase 使用時 가스 生成量(X)과 乾物 消化率(Y)과의 關係는 Y=28.9+0.88X(r=0.82**)의 回歸式을 나타내었다. Trichoderma viride cellulase 使用時 보다 Trichoderma viride-aspergillus niger 혼합 cellulase 사용시 相關係數가 더 높았다. 6. 가스 生成量(X)과 TDN(Y)과의 關係는 Y=35.8+0.585X의 回歸式과 相關係數 0.93으로서 高度의 有意性을 나타내었고, TDN(X)과 가스 生成量(Y)과의 關係는 Y=1.68X-59.6의 回歸式을 나타내었다. The experiment was conducted to establish the gas production method by cellulase, amyloglucosidase and yeast to determine the digestibility and energy value(TDN) of feedstuffs. The results obtained were summarized as follows; 1. The highest activity of Trichoderma viride cellulase was shown at pH 4.8 and the activity of the cellulase decreased rapidly at higher pH than 5.0. 2. The highest activity of Trichoderma virie cellulase was shown at 50℃ and the activity at 40℃ was approximately 92% compared with that at 50℃. 3. The mixed celllulases of Trichoderma viride and Aspergillus nigher produced more gas than Trichoderma viride cellulase when incubated with feedstuffs and were identified to be more effectively used for gas production method. 4. The regression equation of gas production(Y) on glucose production (X) was Y=6.82+165X with significant correlation coefficient of 0.92. 5. The regression equation of DMD(Y) on gas production(X) was Y=29.9+1.13X(r=0.78) with Trichoderma viride cellulase and Y=28.9+0.88X (r=0.82) with both Trichoderma viride and Aspergillus niger cellulase. 6. The regression equation of TDN(Y) on gas production(X) was Y=35.8+0.58X with significant correlation coefficients of 0.93 and in conclusion energy value of feedstuffs can be estimated by gas production method.

Proposed mechanism in the change of cellular composition in the outer medullary collecting duct during potassium homeostasis.

Park, E-Y,Kim, W-Y,Kim, Y-M,Lee, J-H,Han, K-H,Weiner, I D,Kim, J Gutenberg 2012 HISTOLOGY AND HISTOPATHOLOGY Vol.27 No.12

<P>Potassium depletion (K?-D) induces hypertrophy and hyperplasia of collecting duct cells, and potassium repletion (K?-R) induces regression of these changes. The purpose of this study was to examine the time courses of the changes in cellular composition, the origin of intercalated cells (ICs) and the mechanism responsible for these changes. SD rats received K?-depleted diets for 1, 7, or 14 days. After K?-D for 14 days some of the rats received normal diets for 1, 3, 5, or 7 days. In the inner stripe of the outer medulla, K?-D increased significantly the number and proportion of H?-ATPase-positive ICs, but decreased the proportion of H?-ATPase-negative principal cells (PCs). However, proliferation was limited to H?-ATPase-negative PCs. During K?-R, the cellular composition was recovered to control level. Apoptosis increased during K?-R and exclusively limited in H?-ATPase-negative PCs. Double immunolabeling with antibodies to PC and IC markers identified both cells negative or positive for all markers during both K?-D and K?-R. Electron microscopic observation showed that ultrastructure of AE1-positive some cells were similar to AE1-negative some cells during K?-R. LC3 protein expression increased significantly and autophagic vacuoles appeared particularly in PCs on days 14 of K?-D and in ICs on days 3 of K?-R. These results suggest that PCs and ICs may interconvert in response to changes in dietary K+ availability and that autophagic pathways may be involved in the interconversion.</P>