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.

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.

Trypsin inhibitor 결여 大豆品種의 탐색 및 그의 遺傳育種學的 硏究 : I. Trypsin inhibitors의 전기영동 감정방법에 의한 대두 품종별 비교 및 DEAE-cellulose에 의한 분리 I. Soybean trypsin inhibitors: electrophoretic differences among varieties and their fractionation on DEAE-cellulose

金秀一,李錫河,李弘石,文亢植,羅志英 서울大學校 農科大學 1985 서울대농학연구지 Vol.10 No.1

대두의 단백추출액을 polyacrylamide gel 전기영동에 의하여 분류하고 trypsin inhibitor (T.I) band를 동정하였다. T.I. band는 전기영동한 gel을 trypsin으로 가수분해하거나 추출액에 trypsin을 처리한 후 전기영동하거나 발색기질을 이용하여 gel을 착색시키거나 또는 gel slice의 T.I.activity를 측정하는 등 네 가지 방법을 사용하여 검정하였다. 이중 추출액을 trypsin으로 처리한 후 전기영동하는 방법과 gel slice의 T.I.activity를 측정하는 방법이 가장 적합하였으며 두 방법의 결과를 비교하여 T.I.band를 검정하는 것이 보다 확실하였다. Sephadex G-75 Chromatography 에서 물로 추출한 대두 단백질은 3 fraction으로 분리하였고 T.I.activity는 제 2 fraction 에만 나타났다. Kunitz 및 Bowman-Birk형 inhibitor는 DEAE-cellulose column chromatography로 분리하였다. Kunitz형은 5개의 fraction으로, Bowman-birk형은 4개의 fraction으로 분리되었다. 단백질 추출액과 DEAE-cellulose chormatography에서 분리된 Kuniz 및 Bowman-Birk T.I.의 polyacryamide gel 전기영동 pattern을 비교하여 본 결과, 확실하게 동정된 T.I.band는 band3과 band4로서 각각 Orf등이 발표한 Ti¹과 Ti2에 해당하였으며, 그 외에 band 6과 band 10이 T.I.로 추정되었고 band 1,2,5,7,8,9는 T.I.가 아닌 것으로 판명되었다. trypsin inhibitor 함유량은 총 trypsin units inhibited 값(T.U.I)으로 볼 때 42품종에서 25에서 76까지 품종 간에 차이가 현저하였으며 시비 및 파종기의 영향은 나타나지 않았다. Ti¹ inhibitor 를 보유하고 있는 것은 37품종이었고, Ti²를 보유하는 것은 7품종이었으며, Ti¹과 Ti²를 같이 가지고 있는 품종은 발견되지 않았다. 이러한 품종의 Ti¹,Ti² 보유 pattern은 재배조건에 의해 변화되지 않았다. 2조합의 pattern은 재배조건에 의해 변화되지 않았다. 2조합의 정역교배에서 얻은 F₁ 종자의 전기영동 pattern을 비교해 본 결과, Ti¹품종끼리의 교배종자에서는 정역교배에 상관없이 Ti¹ inhibitor 만 나타났고 Ti¹품종과 Ti²품종의 교배종자에서는 Ti²를 모본으로 한 종자에서는 Ti¹과 Ti² 두 inhibitor가 검출되었으나 여교배에서는 모본의 Ti¹ inhibitor만 검출되었다. 여교배에서 Ti¹만 나타난 것은 분석시료 종자가 적었고 교배의 여부를 확인할 수 없어 모본의 세포질적 영향에 의한 것인지 또는 자가수정에 의한 것인지 분명치 않았다. The protein extracts from soybean seeds were examined by polyacrylamide gel electrophoresis and the trypsin inhibitor (T.I) bands were detected. The water-extractable protein was fractionated into three fractions by Sephadex G-75 gel filtration. The T.I activity was found only in the second fraction. Kunitz and Bowman-Birk inhibitors were fractionated by DEAE-cellulose chromatography into seven and six fractions, respectively. In kunitz inhibitor, 5 fractions were found to have T.I activity and 4 fractions in Bowman-Birk inhibitor. From the and patterns of the protein extracts and those of DEAE-cellulose chromatographic fractions, it was found that band 3 and 4 were T.I. band, corresponding to Ti¹ and Ti² band, respectively. In addition, band 6 and 10 were presumed to be T.I. band. Of the 42 varieties sampled, 35 revealed only Ti¹ band and 7 only Ti² band. The T.I. band patterns were not changed by the culture condition. The T.I. content, when expressed as the number of trypsin units inhibited (T.U.I), showed remarkable differences from 25 to 76 between varieties. The seedtime and fertilization condition had no effect on the T.I. content. Judged from the results of F ₁seeds analysis, we assumed that Ti¹ and Ti²band were controlled by codominant allele at a single locus.

Cytogenetic assessment of <i>Lilium longiflorum × L. hansonii</i> revealed by genomic in situ hybridization (GISH)

Mazharul, I.M.,Reshma, Y.,Jung, J.M.,Mohammad, D.D.,Lim, K.B. International Society for Horticultural Science 2019 Acta Horticulturae Vol.1237 No.-

<P> Martagon (<I>Lilium hansonii;</I> MM) and <I>Longiflorum</I> (LL) are two major groups under the family <I>Liliaceae</I>, used for modern breeding to introduce new inter-genomic lily cultivars. Interspecific F<SUB>1</SUB> hybrids (LM) introduced through cut-style method between two diploid <I>Lilium longiflorum (2n=2x=24)</I> and <I>Lilium hansonii (2n=2x=24)</I> were evaluated cytogenetically by genomic in situ hybridization (GISH) technique. However, GISH analysis of F<SUB>1</SUB> interspecific (LM) hybrids showed equal chromosomal contribution from both female <I>Lilium longiflorum</I> (LL) and male <I>Lilium hansonii</I> (MM). Each of the parent contributed 12 chromosomes except three crosses i.e., two of <I>L. longiflorum</I> 'White Tower' × <I>L. hansonii;</I> (2x-1) and one of <I>L. longiflorum</I> 'Bright Tower' × <I>L. hansonii;</I> (2x-1). Among 11 inter-genomic crosses, 3 crosses failed (False hybrid) and 8 crosses (True hybrids) showed different ploidy level i.e., 2n=2x=24, 2n=2x-1=23 and 2n=2x-1=23 respectively. Recombinant chromosome usually not found in F<SUB>1</SUB> interspecific lily hybrids. Most often, genomic recombination occurred in the cross between two genetically different parents. Chromosome pairing and crossing over normally occurred during meiosis in backcross progenies. However, in this study, genome analysis (GISH) of F<SUB>1</SUB> hybrids (<I>L. longiflorum</I> 'White Tower' × <I>L. hansonii</I>) showed four recombinant sites including two M/L and two L/M recombinant chromosomes that denotes high genetic relationship between <I>L. longiflorum</I> and <I>L. hansonii.</I> </P>

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>

Diagnostic usefulness of a T cell-based assay for latent tuberculosis infection in kidney transplant candidates before transplantation

Kim, S.-H.,Lee, S.-O.,Park, I.-A.,Park, S.J.,Choi, S.-H.,Kim, Y.S.,Woo, J.H.,Park, S.-K.,Park, J.S.,Kim, S.C.,Han, D.J. Blackwell Publishing Inc 2010 Transplant infectious disease Vol.12 No.2

<P>S.-H. Kim, S.-O. Lee, I.-A. Park, S.J. Park, S.-H. Choi, Y.S. Kim, J.H. Woo, S.-K. Park, J.S. Park, S.C. Kim, D.J. Han. Diagnostic usefulness of a T cell-based assay for latent tuberculosis infection in kidney transplant candidates before transplantation.Transpl Infect Dis 2010: <B>12:</B> 113–119. All rights reserved</P><P>Background</P><P>The presence of latent tuberculosis (TB) infection (LTBI) should be evaluated before kidney transplantation. Although a new T cell-based assay for diagnosing LTBI gave promising results, this assay has not yet been compared with the tuberculin skin test (TST) for diagnosing LTBI in renal transplant candidates before transplantation.</P><P>Patients and methods</P><P>All adult patients admitted to a single institute for renal transplantation over a 1-year period were prospectively enrolled. A clinically predictive risk of LTBI was defined as: (i) recent close contact with a person with pulmonary TB; (ii) abnormal chest radiography; (iii) a history of untreated or inadequately treated TB; or (iv) a new infection (i.e., a recent conversion of TST).</P><P>Results</P><P>Of 209 renal recipients, 47 (22%) had a positive TST≥5 mm, 21 (10%) had a positive TST≥10 mm, 65 (30%) had a positive T-SPOT.<I>TB</I> test, and 25 (12%) had an indeterminate T-SPOT.<I>TB</I> test. The induration size of TST was significantly associated with a high positivity rate on T-SPOT.<I>TB</I> (<I>P</I><0.001). Agreement between T-SPOT.<I>TB</I> test and TST≥10 mm was fair (<I>k</I>=0.24, 95% confidence interval 0.11–0.36). However, neither univariate nor multivariate analysis showed any association between the clinical risk for LTBI and positivity on T-SPOT.<I>TB</I> or TST.</P><P>Conclusion</P><P>T-SPOT.<I>TB</I> test was more frequently positive than TST in renal transplant candidates. However, further longitudinal studies are awaited to determine whether the ability of T-SPOT.<I>TB</I> assay to detect LTBI in renal transplant recipients can better predict the development of TB than can TST after transplantation.</P>

Reproduction and population dynamics of <i>Leptochela gracilis</i> (Decapoda: Pasiphaeidae) on the western coast of Korea, Yellow Sea

Oh, C.W.,Kim, J.Y.,Jeong, I.J.,Suh, H.L.,Cho, Y.K. Cambridge University Press 2006 Journal of the Marine Biological Association of th Vol.86 No.1

<P>Investigations were made on reproduction and population dynamics of <I>Leptochela gracilis</I> on the western coast of Korea, Yellow Sea, between May 2000 and October 2001. The egg volume was significantly larger at later egg stage than at early egg stage. Brood loss did not occur during the incubation period. Based on dry weight, the reproductive output (mass of incubating eggs/mass of female) averaged 0.18. The mature females first appeared in May, reached a peak in July and August, and then did not appear after September. The main breeding season was summer, although slightly different between the two years. A similar pattern could be found in monthly changes of gonadosomatic index (GSI), showing relatively higher GSI during the annual breeding season. A significant difference in ovarian dry weight between females with non-eyed eggs and eyed eggs indicates that ovarian maturation occurred during the embryonic development, suggesting that females were potentially consecutive breeders, capable of multiple spawning within a reproductive season. The size at which 50% of females were mature (CL50) was estimated as 7.63 mm carapace length. Females grew faster and reached a larger size at age than males (<I>L</I>∞=12.43 mm CL and <I>K</I>=0.90 y<SUP>−1</SUP> for females, and <I>L</I>∞=12.22 mm CL and <I>K</I>=0.58 y<SUP>−1</SUP> for males).</P>

Two NF-κB inhibitor-alpha (IκBα) genes from rock bream (Oplegnathus fasciatus): Molecular characterization, genomic organization and mRNA expression analysis after immune stimulation

Lee, Y.,Umasuthan, N.,Whang, I.,Revathy, K.S.,Lee, S.,De Zoysa, M.,Oh, C.,Kang, D.H.,Noh, J.K.,Lee, J. Academic Press 2014 FISH AND SHELLFISH IMMUNOLOGY Vol.41 No.2

IκBα is a member of IκB family, which sequesters NF-κB in an inactivate form in the cytoplasm and blocks the translocation of NF-κB to nucleus. The IκBα paralogs of rock bream (OfIκBα-A and OfIκBα-B) encoded IκBα proteins with typical features including, highly conserved IκB degradation motif, six ankyrin repeats and a PEST sequence. However, their amino acid identity and similarity were only 55.6 and 69.7%, respectively suggesting that these two genes could be the two different isoforms of IκBα. The number and size of the exons of OfIκBα-A and OfIκBα-B were conserved well with all the compared vertebrate species, although they have significantly different genomic sizes. Phylogenetic analysis revealed that OfIκBα-A and OfIκBα-B proteins cluster with IκBα family members; however, they were grouped with different subclades in IκBα family. Tissue specific expression of OfIκBα mRNA was constitutively detected in all the tested tissues, and they showed the higher transcription level in heart, liver, gill and peripheral blood cells, respectively. The injection of flagellin stimulated the mRNA expression of OfIκBα paralogs in head kidney and intestine. Moreover, the OfIκBα mRNA expression in gill and liver was significantly up-regulated by LPS, poly I:C and Edwardsiella tarda challenges. The transcription of OfIκBα was up-regulated in early-phase of injection and then rapidly restored. These results suggest that the OfIκBα paralogs might be involved in rapid immune responsive reactions in rock bream against bacterial and viral pathogens.

이산시간 I-PD형 제어기의 설계에 관한 연구

염만오,윤일로,김영민 경남대학교 공업기술연구소 2000 硏究論文集 Vol.18 No.-

본 연구에서는 Exact 모델매칭법에 기초한 이산시간 I-PD형 제어기를 설계한다. 보통의 모델 매칭은 이산시간 I-PD형 제어계와 경우 시스템의 지연시간 때문에 참조모델에 있어서 중요한 저차항의 매칭이 행해지지 않는 문제점이 발생된다. 따라서 임의의 참조모델에 대하여 모델매칭을 행하는 것이 불가능하다. 이것을 해결하기 위해 제어대상에 전치보상기를 새롭게 투입하고 확대계에 대하여 모델매칭을 행하는 방법에 관하여 고찰한다. 다음으로 위의 방법에 기초하여 제어기에 포함되는 PID 게인을 자동 조정한 적응 게인 조정법에 의한 I-PD형 제어기를 설계한다. 적응 게인 조정법을 사용한 오토튜닝 PID 제어계와 셀프튜닝 PID 제어계에 관한 연구가 보고되고 있지만 제어계 설계가 복잡했고 실제 장치화가 어려운 경우가 있었다. 본 연구에서 설계하는 적응 게인 조정법은 이산시간계에서의 설계방법이고 간단한 제어 알고리즘으로 구성되어 있어 실제로 제어계를 구현하는 것이 쉽다. Discrete-timeler based on exact model matching method is designed in this study. Usual discrete-time I-PD type controller leads to a matter of output errors which are due to time-delay element of the system. So it is impossible that model matching about spontaneous reference model. To settle this problem, a new I-PD type controller inserted a pre-compensator is used. According to this method, adaptive gain adjustment law is developed. Though Previous studies about auto-tuning and self-tuning PID controller by using adaptive gain adjustment method were published, they were complicated to design of controller and apply to actual plants. Adaptive gain adjustment law proposed in this paper is a method of design in discrete-time domain and it consists of simple control algorithm. Furthermore control system implementation is easy. In this study, discrete-time I-PD type controllers by model matching method and adaptive gain adjustment law are designed and simulated.