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.

Both H4K20 mono-methylation and H3K56 acetylation mark transcription-dependent histone turnover in fission yeast

Yang, H.,Kwon, C.S.,Choi, Y.,Lee, D. Academic Press 2016 Biochemical and biophysical research communication Vol. No.

Nucleosome dynamics facilitated by histone turnover is required for transcription as well as DNA replication and repair. Histone turnover is often associated with various histone modifications such as H3K56 acetylation (H3K56Ac), H3K36 methylation (H3K36me), and H4K20 methylation (H4K20me). In order to correlate histone modifications and transcription-dependent histone turnover, we performed genome wide analyses for euchromatic regions in G2/M-arrested fission yeast. The results show that transcription-dependent histone turnover at 5' promoter and 3' termination regions is directly correlated with the occurrence of H3K56Ac and H4K20 mono-methylation (H4K20me1) in actively transcribed genes. Furthermore, the increase of H3K56Ac and H4K20me1 and antisense RNA production was observed in the absence of the histone H3K36 methyltransferase Set2 and histone deacetylase complex (HDAC) that are involved in the suppression of histone turnover within the coding regions. These results together indicate that H4K20me1 as well as H3K56Ac are bona fide marks for transcription-dependent histone turnover in fission yeast.

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.

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.

H. pylori성 위염에서 위축진행과 Myeloperoxidase(MPO) 유전자 다형성(genetic polymorphism)의 관련성

이만용 ( M. Y. Lee ),노임환 ( I. H. Roe ),양미라 ( M. R. Yang ),남승우 ( S. W. Nam ),허재형 ( J. H. Heo ),임창영 ( C. Y. Lim ),송일한 ( I. H. Song ),김정원 ( J. W. Kim ),신지현 ( J. H. Shin ) 대한소화기학회 2002 대한소화기학회 춘계학술대회 Vol.2002 No.-

<목적> H. pylori는 위 점막에서 많은 중성구들의 침윤이 특징적으로 관찰되는 활동성 위염을 일으키며 중성구들에서 나오는 많은 산소라디칼 등은 상피세포의 손상과 apoptosis을 유도하고 위축성 변화로 진전하는데 주도적인 역할을 한다. 특히 중성구의 myeloperioxidase(MPO)는 산소라디칼의 공격적인 산화적 잠재력을 중폭시키고 monochloramine을 생성하여 위세포의 손상과 위축성 변화를 야기한다고 이해되고 있다. 그러나 위축성위

H. pylori 제균 실패율과 clarithromycin 내성률의 일치성

허재형 ( J. H. Heo ),남승우 ( S. W. Nam ),노임환 ( I. H. Roe ),양미라 ( M. R. Yang ),김정택 ( J. T. Kim ),송일환 ( I. H. Song ),임창영 ( C. Y. Lim ),김정원 ( J. W. Kim ),신지현 ( J. H. Shin ) 대한소화기학회 2002 대한소화기학회 춘계학술대회 Vol.2002 No.-

<목적> H. pylori 제균 치료성적을 좌우하는 요소에는 약제와 대상 환자군의 선정, 균검사방법의 차이, 항생제 저항성 등이 중요시되고 있다. 이 중에서도 항생제 저항성은 나라간의 H. pylori 제균 성적을 다르게 하는 대표적인 원인이다. 우리나라는 제균률이 외국보다 저조하여 85%내외로 보고되고 있다. 본 연구의 목적은 H. pylori 제균 실패율과 clarithromycin 내성률을 조사하여 제균 실패 원인으로서의 clarithromycin

발화합성용액의 pH 가 Y1Ba2Cu3O7-x 초전도상 생성 속도에 미치는 영향

박정식,김영순,양석우,김춘영,신형식 ( J . S . Park,Y . S . Kim,S . W . Yang,C . Y . Kim,H . S,Shin ) 한국공업화학회 1998 공업화학 Vol.9 No.2

Y₂O₃(99.9%)와 BaCO₃(99.9%) 및 CuO(99.9%)를 사용하여 Y₁Ba₂Cu₃O_(7-x)(123) 분말을 발화합성법에 의해 제조하였다. 발화전 용액을 여러 가지 pH로 변화시켜 제조하였으며, 이 분말을 성형하여 열처리 온도와 시간 변화에 따른 상형성과 반응특성을 조사하였다. 시료의 조성과 조직의 특성은 ICP와 SEM을 이용하여 측정하였고, Y-Ba-Cu-O계의 상형성과 전화율을 결정하기 위해 X선 회절분석을 하였다. 발화합성법을 이용하여 pH 7(±0.3)에서 제조된 123 분말이 순도와 균일성 및 반응특성에서 가장 좋은 결과를 보였다. pH 7(±0.3)에서 제조된 분말을 이용한 123 상생성에 따른 활성화에너지(ΔE_n)는 191 kJ/mol으로서 고상반응법의 230 kJ/mol에 약 13% 정도 더 낮았다. The Y₁Ba₂Cu₃O_(7-x)(123) superconductor powders were prepared by pyrophoric synthesis method(PSM) using Y₂O₃(99.9%), BaCO₃(99.9%), and CuO(99.9%) powders. The phase formation and reaction kinetics of 123 superconductor manufactured with powders prepared in various pHs of pyrophoric synthetic solution have been studied through the experiments at various heat treatment temperatures and times. Inductively coupled plasma(ICP) spectroscopy and scanning electron microscopy(SEM) measurements were performed to examine the composition and morphology of the sample. X-ray diffraction(XRD) analysis was done to determine phase formation and conversion ratio of Y-Ba-Cu-O systems. The 123 powder prepared at pH 7(±0.3) yields the best result in terms of purity, homogeneity, and reactivity. The activation energies(ΔE_n) of 123 phase formation were found to be 191 kJ/mol and 230 kJ/mol in solid state reaction method and pyrophoric synthesis method, respectively.

Effects of Exogenous Enzymes on Ruminal Fermentation and Degradability of Alfalfa Hay and Rice Straw

Yang, H.E.,Son, Y.S.,Beauchemin, K.A. Asian Australasian Association of Animal Productio 2011 Animal Bioscience Vol.24 No.1

This study was conducted to evaluate the use of exogenous enzymes as a potential means of improving the ruminal digestion (i.e., degradability) of alfalfa hay and rice straw. Twenty six enzyme-additives were examined in terms of protein concentration and enzymic activities on model substrates. The exogenous enzymes contained ranges of endoglucanase, xylanase, ${\beta}$-glucanase, ${\alpha}$-amylase, and protease activities. Six of the enzyme additives were chosen for further investigation. The enzyme additives and a control without enzyme were applied to mature quality alfalfa hay substrate and subsequently incubated in rumen batch cultures. Five of the enzyme additives (CE2, CE13, CE14, CE19, and CE24) increased total gas production (GP) at 48 h of incubation compared to the control (p<0.05). The two additives (CE14 and CE24) having the greatest positive effects on alfalfa hay dry matter, neutral detergent fibre (NDF) and acid detergent fibre (ADF) degradability were further characterized for their ability to enhance degradation of low quality forages. The treatments CE14, CE24, a 50:50 combination of CE14 and CE24 (CE14+24), and control (no enzyme) were applied to mature alfalfa hay and rice straw. For alfalfa hay, application of the two enzyme additives, alone and in combination, increased GP compared to the control at 48 h fermentation (p<0.05), whereas only CE14 and CE14+24 treatments improved GP from rice straw (p<0.05). Rumen fluid volatile fatty acid concentrations throughout the incubation of rice straw were analyzed. Acetate concentration was slightly lower (p<0.05) for CE14${\times}$CE24 compared to the control, although individually, CE14 and CE24 acetate concentrations were not different from the control. Increases (p<0.05) in alfalfa hay NDF degradability measured at 12 and 48 h of incubation occurred only for CE14 (at 12 h) and for CE14+24 (at 12 and 48 h). Similarly, ADF degradability increased (p<0.05) with CE14 and CE14+24. As for rice straw, increased DM degradability was observed at 12 and 48 h of incubation for all enzyme treatments with an exception for CE14 at 12 h. The degradability of NDF was improved by all the enzyme treatments at either incubation time, while ADF degradability was only enhanced at 48 h. Overall, the enzymes led to enhanced digestion of mature alfalfa and there was evidence of improved digestibility of rice straw, an even lower quality forage.

발화합성용액의 pH가 Y₁Ba₂Cu₃O_7-x 초전도상 생성 속도에 미치는 영향

박정식,김영순,양석우,김춘영,신형식,Park, J.S.,Kim, Y.S.,Yang, S.W.,Kim, C.Y.,Shin, H.S. 한국공업화학회 1998 공업화학 Vol.9 No.2

$Y_2O_3$(99.9%)와 $BaCO_3$(99.9%) 및 CuO(99.9%)를 사용하여 $Y_1Ba_2Cu_3O_{7-x}$(123) 분말을 발화합성법에 의해 제조하였다. 발화전 용액을 여러 가지 pH로 변화시켜 제조하였으며, 이 분말을 성형하여 열처리 온도와 시간 변화에 따른 상형성과 반응특성을 조사하였다. 시료의 조성과 조직의 특성은 ICP와 SEM을 이용하여 측정하였고, Y-Ba-Cu-O계의 상형성과 전화율을 결정하기 위해 X선 회절분석을 하였다. 발화합성법을 이용하여 pH 7(${\pm}0.3$)에서 제조된 123 분말이 순도와 균일성 및 반응특성에서 가장 좋은 결과를 보였다. pH 7(${\pm}0.3$)에서 제조된 분말을 이용한 123 상생성에 따른 활성화에너지(${\Delta}E_a$)는 191kJ/mol으로서 고상반응법의 230kJ/mol에 약 13% 정도 더 낮았다. The $Y_1Ba_2Cu_3O_{7-x}$(123) superconductor powders were prepared by pyrophoric synthesis method(PSM) using $Y_2O_3$(99.9%), $BaCO_3$(99.9%), and CuO(99.9%) powders. The phase formation and reaction kinetics of 123 superconductor manufactured with powders prepared in various pHs of pyrophoric synthetic solution have been studied through the experiments at various heat treatment temperatures and times. Inductively coupled plasma(ICP) spectroscopy and scanning electron microscopy(SEM) measurements were performed to examine the composition and morphology of the sample. X-ray diffraction(XRD) analysis was done to determine phase formation and conversion ratio of Y-Ba-Cu-O systems. The 123 powder prepared at pH 7(${\pm}0.3$) yields the best result in terms of purity, homogeneity, and reactivity. The activation energies(${\Delta}E_a$) of 123 phase formation were found to be 191 kJ/mol and 230kJ/mol in solid state reaction method and pyrophoric synthesis method, respectively.

In vitro Fertilization and Development of Pig Oocytes Inseminated with Boar Sperm by Different Sperm Washing Media after Thawing of the Frozen Straws

Yi, Y.J.,Ko, H.J.,Lee, S.H.,Yang, C.B.,Son, D.S.,Kim, H.K.,Park, C.S. 충남대학교 형질전환복제돼지연구센터 2004 논문집 Vol. No.8

This study was carried out to investigate in vitro fertilization and development of in vitro matured pig oocytes inseminated with the Duroc boar sperm by different sperm washing media after thawing of the 5 ml frozen straws. Immature follicular oocytes (30-40) were transferred into each well of a Nunc 4-well multidish containing 500㎕ mTCM 199 maturation medium. The sperm rich portion of ejaculates was collected into a 250 ml insulated vacuum bottle and gradually cooled 22 to 24℃ over a 2 h period. Semen was centrifuged at 800g for 10 min and the seminal Plasma discarded. Sperm were resuspended in a lactose-egg yolk and N-acetyl-D-glucosamine (LEN) diluent to contain 1×10^9 sperm/ml and cooled to 5℃ over a 2 h period. Immediately before freezing, semen was rediluted with an equal volume of LEN+4% glycerol and packed Into 5 ml straws. After thawing of the 5 ml straw, the 5 ml semen was diluted with 20 ml Beltsville thawing solution (BTS) at room temperature. Oocγtes were inseminated with untreated (unwashed and nonpreincubated) or treated sperm (washed two times in BTS, mTLP-PVA and mTBM media, respectively and nonpreincubated) with 2×10^7 sperm concentration. Oocytes were coincubated for 6 h in 500㎕ mTBM fertilization. At 6 h after IVF, oocytes were transferred Into 500㎕ NCSU-23 culture medium for further culture of 6 h. Sperm penetration, polyspermy and male pronuclear formation of oocytes at 12 h after IVF and developmental ability of oocytes at 48 h after IVF were evaluated. Sperm penetration rate, male pronuclear formation and rate of cleaved embryos were higher in the BTS, mTLP-PVA and mTBM treatments than the unwashed treatment (p<0.05). The rate of blastocysts from the cleaved oocytes (2-4 cell stage) were higher in the mTLP-PVA treatment than in the unwashed, BTS and mTBM treatments. In conclusion, we recommend the washing of frozen-thawed sperm with mTLP-PYA medium before in vitro fertilization of oocytes in mTBM medium.