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.

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.

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.

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>

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.

Effects of calcium doping on the superconducting properties of top-seeded melt growth processed Y_1.5Ba_2-xCa_xCu₃O_y superconductors

Park, S.D.,Kim, H.J.,Park, B.J.,Han, Y.H.,Jun, B.H.,Lee, J.S.,Kim, C.J. North-Holland 2011 Physica. C, Superconductivity Vol.471 No.21

The effect of calcium doping on the superconducting properties of top seeded melt growth (TSMG) processed Y<SUB>1.5</SUB>Ba<SUB>2-x</SUB>Ca<SUB>x</SUB>Cu<SUB>3</SUB>O<SUB>y</SUB> superconductors was studied in terms of calcium content (X<SUB>ca</SUB>). YBa<SUB>2-x</SUB>Ca<SUB>x</SUB>Cu<SUB>3</SUB>O<SUB>7-δ</SUB> (X<SUB>ca</SUB>=0, 0.005, 0.01, 0.02, 0.04, 0.1, 0.3) powders were synthesized by the powder calcination method. YBa<SUB>2-x</SUB>Ca<SUB>x</SUB>Cu<SUB>3</SUB>O<SUB>7-δ</SUB> powders were mixed with 0.25mole Y<SUB>2</SUB>O<SUB>3</SUB> powder and 1wt.% CeO<SUB>2</SUB> as Y<SUB>2</SUB>BaCuO<SUB>5</SUB> (Y211) refiner, and finally made into Y<SUB>1</SUB>.<SUB>5</SUB>Ba<SUB>2-x</SUB>Ca<SUB>x</SUB>Cu<SUB>3</SUB>O<SUB>y</SUB> (Y1.5)+1wt.% CeO<SUB>2</SUB> composition. The single Y123 growth on the top surface was observed up to X<SUB>ca</SUB>=0.1, while the multiple Y123 growth was observed at X<SUB>ca</SUB>≥0.1. The superconducting transition temperature (T<SUB>c</SUB>) and critical current density (J<SUB>c</SUB>) of TSMG processed Y1.5 samples were inversely proportional to X<SUB>ca</SUB>. The Y211 size increased with increasing X<SUB>ca</SUB> due to the enhancement of Y211 coarsening by calcium doping. No Y211 refining effect by CeO<SUB>2</SUB> was observed in the calcium doped samples. The T<SUB>c</SUB> and J<SUB>c</SUB> decrease by calcium doping are likely to be due to the calcium incorporation with the Y123 lattice and formation of coarse Y211 particles.

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.

딥러닝 기법을 이용한 전해가공의 홀가공 특성 분석

최승건(S. G. Choi),김준영(J. Y. Kim),이은상(E. S. Lee) 한국생산제조학회 2019 한국생산제조시스템학회 학술발표대회 논문집 Vol.2019 No.5

음이온 치환을 이용한 Li_1-xFeO_2-yF_y-Li_xMnO₂ (Mn/(Mn + Fe) = 0.8, 0≤y≤0.15) 양극 활물질의 합성 및 전기화학적 특성

허정배,박금재,이윤성,Heo, J.B.,Park, G.J.,Lee, Y.S. 한국전기화학회 2007 한국전기화학회지 Vol.10 No.4

산소자리에 치환된 불소가 $Li_{1-x}FeO_2Li_xMnO_2$ (Mn/(Mn + Fe) = 0.8) 양극 활물질에 미치는 영향을 고찰하기 위해 다양한 양의 불소를 치환시킨 $Li_{1-x}FeO_{2-y}F_y-Li_xMnO_2$ (Mn/(Mn + Fe) = 0.8, $0.05{\le}y{\le}0.15$) 양극 활물질을 고상법을 이용하여 합성하였다. 불소 미치환 시료 및 치환양이 0.05와 0.1의 시료의 경우, $1-1.5\;{\mu}m$ 크기의 막대 형상 분말 형태에 50-100 nm정도의 작은 구형 입자들이 주위에 분포되어 있는 형태이었다. 반면, 불소 치환양이 0.15인 시료의 경우, 그 모양이 구형으로 변화되어지며 입자가 급격하게 성장하였다. 합성된 시료를 이용하여 제작된 셀들의 충 방전 수행 결과, $Li/Li_{1-x}FeO_{1.9}F_{0.1}-Li_xMnO_2$ 셀이 163 mAh/g의 가장 높은 초기용량을 보였으며 50 싸이클 후에도 95%의 높은 가역 특성을 보였다. 특히, 활물질내의 불소 치환양이 증가할수록 초기 방전용량도 같이 증가하였으나, 불소이온의 치환양이 일정량을 (y>0.1) 넘는 경우에는 산소 자리에 불소이온이 완전하게 치환되지 못하고 불순물로 존재함으로써 전지의 가역특성을 현저하게 저하시키는 요인으로 작용함을 확인하였다. In order to investigate the effect of fluorine ion in the $Li_{1-x}FeO_2Li_xMnO_2$ (Mn/(Mn + Fe) = 0.8) cathode material, it was synthesized $Li_{1-x}FeO_{2-y}F_y-Li_xMnO_2$ (Mn/(Mn + Fe) = 0.8, $0.05{\le}y{\le}0.15$) cathode materials at $350^{\circ}C$ for 10hrs using solid-state method. $Li_{1-x}FeO_{2-y}F_y-Li_xMnO_2$ (Mn/(Mn + Fe) = 0.8, $0.0{\le}y{\le}0.1$ was composed many large needle-like particles of about $1-1.5\;{\mu}m$ and small particles of about 50-100 nm, which were distributed among the larger particles. However, $Li_{1-x}FeO_{1.85}F_{0.15}-Li_xMnO_2$ material showed slightly different particle morphology. The particles of $Li_{1-x}FeO_{1.85}F_{0.15}-Li_xMnO_2$ were suddenly increased and started to be a spherical type of particle shape. $Li/Li_{1-x}FeO_{1.9}F_{0.1}-Li_xMnO_2$ cell showed a high initial discharge capacity of 163 mAh/g and a high cycle retention rate of 95% after 50 cycles. The initial discharge capacity of $Li/Li_{1-x}FeO_{2-y}F_y-Li_xMnO_2$ ($0.05{\le}y{\le}0.15$) cells increased according to the increase of F content. However, the cycleability of this cell was very rapidly decreased when the substituted fluorine content is over 0.1. We suggested that too large amount of F ion fail to substitute into the $Li_{1-x}FeO_2-Li_xMnO_2$ structure, which resulted in the severe decline of battery performance.

수도의 유묘기 냉해에 관한 연구 II. 주요 신품종들의 제 3 엽기 내냉한계

권용웅,김주헌,오윤진,이문희,Kwon, Y.W.,Kim, J.H.,Oh, Y.J.,Lee, M.H. 한국작물학회 1979 한국작물학회지 Vol.24 No.2

Indica \times Japonica 교잡에 의해 육성된 수도신품종들의 유묘기 내냉한계와 내냉발현특성을 Janica품종들과 비교 고찰하고자 10개 품종을 유묘기 내냉성이 제일 약한 제 3 엽기에 주간 11\circ C야간 5\circ C의 저온조건에 0, 3, 4, 5, 8, 10일 처리한 결과는 다음과 같다. 1. 저온처리 전후에 주야 26\circ C / 18\circ C에서 생장한 파종 후 35일묘의 건물중이 무처리묘의 90% 이상이 되는 최장저온처리기간은 신품종들의 경우 0.8~2.8일 간으로써 특히 조생통일이 짧고 밀야 2003가 길었으며, Japonica 품종들의 경우 4.0~5.2일간으로써 신품종들보다 가역적 내냉한계기간이 배정도 길었다. 2. 저온처리에 따른 냉해발현 종료후 묘생존율이 90%이상되는 최장저온처리기간은 신품종들의 경우 3.0~5.6 일간으로써 수원 258호가 제일 짧고 수원 25001가 제일 길었으며, Japonica 품종들은 공시품종 모두 10일간 이상으로 신품종들보다 비가역적 내냉한계기간이 2~3배 이상 길었다. 3. 저온처리중 엽신변색고사율(y_1) 및 묘고사율(y_2), 저온처리 후 발현된 모신변색고사율(y_3), 묘고사율(y_4), 냉해를 받은 35일묘의 초장(y$_{5}$)과 건물중(y$_{6}$)은 모두 저온처리기간(x)과 고도로 유의한 상관성을 보였는데 특히 y_1, y_3, y$_{6}$와 높은 상관성을 보였으며, y_1~y$_{6}$들 상호간에도 모두 고도로 유의한 상관성을 보였으나 특히 y_1과 y_3, y_3와 y$_{6}$의 상관성이 컸다. 4. 냉해징상들의 발현순서와 상태들간의 상관성 분석결과로부터 가역적 및 비가역적, 직접적 및 간접적 냉해의 발생과 그들의 복합현상으로써 결과되는 관찰되는 냉해징상의 발현과정 모식도를 작성하여 그림 5에 제시하였다. 5. 수도유묘의 내냉성 평가에 있어서 가역적 피해와 비가역적 피해를 종합적으로, 그리고 정량적으로 나타내며 일반적으로 냉해를 나타내는 조사형질들 중 냉해에 가장 예민한 반응을 보이는 건물중율을 1차요인으로 취급할 것으로 제의한다. Comparative tolerance of the new rice varieties from Indicax Japonica cross to elastic and plastic chilling injuries was examined at the 3rd leaf-stage, the most sensitive stage to chilling during nursery, using a chilling chamber set 11\circ C, 13hrs. 20K lux day/5$^{\circ}C$ night. Seedlings were reared until 35 days after seeding in a 26\circ C, 13hrs. day / 18\circ C night chamber except the period of chilling treatment for 0, 3, 4, 6, 8 or 10 days. The new varieties were approximately twice susceptible to elastic injuries, and thrice susceptible to plastic injuries than the Japonica varieties in the term of chilling duration. Among the variables indicating apparant chilling injuries the reduction in dry matter responded most sensitively and differentiated well the varietal difference in chilling resistance even with shorter chilling period. Sequential aspects of the cause and effect relations involved in the development of the apparant chilling injuries are discussed and a schematic diagram is presented as Fig. 5 in the text.