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.

Association and functional relevance of E237G, a polymorphism of the high-affinity immunoglobulin E-receptor β chain gene, to airway hyper-responsiveness

Kim, Y.-K.,Park, H.-W.,Yang, J.-S.,Oh, S.-Y.,Chang, Y.-S.,Shin, E.-S.,Lee, J.-E.,Kim, S.,Gho, Y. S.,Cho, S.-H.,Min, K.-U.,Kim, Y.-Y. Blackwell Scientific Publications 2007 Clinical and experimental allergy Vol.37 No.4

<P>Summary</P><P>Background</P><P>The hyper-sensitivity reaction of IgE, with its high-affinity receptors (FcϵRI), is central to the phenomenon of atopic diseases.</P><P>Objective</P><P>To evaluate the genetic effects of non-synonymous single-nucleotide polymorphisms (SNPs) of FcϵRI on intermediate phenotypes of asthma, i.e. atopy and airway hyper-responsiveness (AHR), in the Korean general population.</P><P>Subjects and methods</P><P>Atopy and AHR were evaluated in a cohort of 2055 subjects, aged 10–18 years, using skin prick tests (SPTs) for common aeroallergens and total serum IgE and methacholine bronchial provocation tests. All FcϵRI-α, FcϵRI-β, and FcϵRI-γ gene exons of 24 healthy subjects were sequenced to locate informative non-synonymous SNPs (minor allele frequency >2%). Informative SNPs were then scored, using the high-throughput single base extension method. Relative risk (RR) was determined by multiple logistic regression analysis, after adjusting for confounding factors. The functional relevance of non-synonymous SNPs was analysed using the sorting intolerant from tolerant (SIFT) program.</P><P>Results</P><P>The SNP search found only one informative non-synonymous SNP in FcϵRI-β: E237G (minor allele frequency=0.21). The positive rate of AHR was lower among subjects with the 237<SUP>*</SUP>E allele than among those with 237<SUP>*</SUP>G [RR (95% confidence interval)=0.41 (0.19–0.89); <I>P</I>=0.01]. However, the E237G substitution was not associated with either a positive SPT response or total serum IgE levels. Sequence evolution analysis predicted that the E237G variation is an intolerant amino acid substitution, with functional importance.</P><P>Conclusion</P><P>In the Korean general population, AHR is significantly associated with the E237G polymorphism of FcϵRI-β, which results in an intolerant amino acid substitution.</P>

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.

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

소 모색관련 유전자 MC1R 의 RCR - RFLP Marker 를 이용한 한우육 판별

정의룡,김우태,김연수,한상기 한국동물자원과학회 2000 한국축산학회지 Vol.42 No.4

The melanocortin 1 receptor(MClR) plays a central role in regulation of eumelanin(black/brown) and phaeomelanin(red/yellow) pigment synthesis within the mammalian melanocytes. Mutations within the gene encoding MC1R have been shown to explain coat colour variations within several species including cattle. This study was performed to develop the identification technique of Hanwoo meat using MC1R gene associated with the coat colors of cattle. Alleles of the MC1R locus were detected by PCR-RFLP analysis and genotype frequency and DNA sequences of MC1R gene were compared among cattle breeds. Genomic DNA was extracted from meat or blood samples of five breeds including Hanwoo(n=200), Holstein(n=100), Angus(n=20), Hereford(n=20) and Charolais(n=20). The MC1R gene was used to amplify 739bp and 173bp of the bovine E-locus corresponding to positions 228-966 and 318-490, respectively, using the two specific primers. The amplified products were digested with Bse118 I or Msp I and Aci I enzymes, and DNA fragments were separated by gel electrophoresis for RFLP genotype analysis. Six genotypes, E^D/E^D E^D/E^+, E^D/e, E^+/E^+,E^+/e and e/e, controlled by three alleles E^D, E^+ and e were observed in MC1 locus. When the amplified DNA product(739bp) was digested with Bse118 I enzyme, Hanwoo meat showed a single band of 739bp, whereas two fragments of 531bp and 208bp were detected in Holstein meat and Angus breed, respectively. Also, in the RFLP patterns using Msp I enzyme, Hanwoo meat produced two fragments of 535bp and 174bp, while three fragments of 328bp, 207bp and 174bp were observed in Holstein meat and Angus breeds, respectively. Therefore, breed-specific RFLP markers showing distinct differences between these breeds were found by PCR-RFLP analysis. When the amplified DNA product(173bp) was digested with Aci I enzyme to classify subtype of E allele, the E^D allele produced three fragments of 97, 68 and 8bp, while the E^+ and d alleles produced two fragments of 173 and 8bp according to the Aci I recognition sequence. Among the six genotypes, two genotypes of E^+/e and e/e were observed in Hanwoo and their frequencies were 0.07 and 0.93, respectively. However, the E^D/ED and E^D/e genotypes were present in Holstein and E^D/E^D, E^D/E^+ and E^D/e genotypes in Angus breeds. Therefore, the E^+/e and e/e genotypes observed in Hanwoo and E^D/E^D, E^D/E^+ and E^D/e genotypes detected only in Holstein and Angus breeds may be useful as breed-specific DNA markers for distinguishing between Hanwoo meat and Holstein and Angus meats. When comparing MC1R sequences among Hanwoo, Holstein and Angus, a Gly → Val amino acid change due to a single base(G) deletion at colon 104 was found in Hanwoo. Consequently, breed specific RFLP genotypes of MC1R gene related to bovine coat colors could be used as DNA markers for identification of Hanwoo meat from Holstein and Angus meats.

The antimicrobial peptide human cationic antimicrobial protein-18/cathelicidin LL-37 as a putative growth factor for malignant melanoma

Kim, J.E.;Kim, H.J.;choi, J.M.;Lee, K.H.;Kim, T.Y.;Cho, B.K.;Jung, j.Y.;Chung, K.Y.;Cho, D.;Park, H.J. Sookmyung Women's University Research Institute of 2011 여성과 건강 Vol.6 No.2

Background Recent evidence suggests cathelicidin LL-37 to be a growth factor for various human cancers such as lung cancer, ovarian cancer and breast cancer. However, the effect of LL-37 against malignant skin cancer has not been reported. Objectives To investigate whether the human cathelicidin LL-37 is involved in the carcinogenesis of various skin tumours. Methods Human cationic antimicrobial protein-18 (hCAP-18)/LL-37 production in several cell lines including HaCaT, a chronic myelogenous leukaemia (CML) cell line and various melanoma cell lines was examined using reverse transcription polymerase chain reaction and enzyme-linked immunosorbent assay. Immunohistochemical analysis of melanoma, nonmelanoma skin cancer and precancerous and benign skin lesions was performed. After adding LL-37 to a melanoma cell line, tumour cell proliferation, migration and invasion were investigated. Results Human malignant melanoma cell lines overexpressed hCAP-18/LL-37 mRNA and peptide compared with HaCaT and CML cell lines. Immuno- histochemistry showed that the peptide was strongly expressed in malignant melanoma and moderately expressed in squamous cell carcinoma, whereas basal cell carcinoma, precancerous lesions and seborrhoeic keratosis showed no or weak expression. LL-37 also stimulated melanoma cell proliferation, migration and invasion in vitro. Conclusions Cathelicidin LL-37 was primarily expressed in human malignant skin cancer. LL-37 promoted melanoma cell proliferation, migration and invasion in vitro. We report that an increase in the level of LL-37 is associated with malignant skin tumours such as malignant melanoma. These results highlight the importance of LL-37 in the malignant tendency of skin tumours.

Detailed analysis of the density change on chest CT of COPD using non-rigid registration of inspiration/expiration CT scans

Kim, E. Y.,Seo, J. B.,Lee, H. J.,Kim, N.,Lee, E.,Lee, S. M.,Oh, S. Y.,Hwang, H. J.,Oh, Y. M.,Lee, S. D. Springer Science + Business Media 2015 EUROPEAN RADIOLOGY Vol.25 No.2

<P>Objectives One objective was to evaluate the air trapping index (ATI), measured by inspiration/expiration CT, in COPD patients and nonsmokers. Another objective was to assess the association between the pulmonary function test (PFT) and CT parameters such as ATI or other indices, separately in the whole lung, in emphysema, and in hyperinflated and normal lung areas. Methods One hundred and thirty-eight COPD patients and 29 nonsmokers were included in our study. The ATI, the emphysema index (EI), the gas trapping index (Exp -856) and expiration/inspiration ratio of mean lung density (E/Iratio of MLD) were measured on CT. The values of the whole lung, of emphysema, and of hyperinflated and normal lung areas were compared and then correlated with various PFT parameters. Results Compared with nonsmokers, COPD patients showed a higher ATI in the whole lung and in each lung lesion (all P<0.05). The ATI showed a higher correlation than EI with FEF25-75%, RVand RV/TLC, and was comparable to Exp -856 and the E/I ratio of MLD. The ATI of emphysema and hyperinflated areas on CT showed better correlation than the normal lung area with PFT parameters. Conclusions Detailed analysis of density change at inspiration and expiration CT of COPD can provide new insights into pulmonary functional impairment in each lung area.</P>

Effects of Estradiol on the Paracrine Regulator Expression of In Vitro Maturated Murine Ovarian Follicles

Kim, Y. J.,Park, K. E.,Kim, Y. Y.,Kim, H.,Ku, S. Y.,Suh, C. S.,Kim, S. H.,Choi, Y. M. 한국조직공학과 재생의학회 2017 조직공학과 재생의학 Vol.13 No.6

<P>The preservation of female germ cells is important in the individuals with ovarian dysfunction and failure. For this purpose, ovarian follicle in vitro maturation (OFIVM) is an important technology for the retrieval of mature oocytes. In the in vivo follicular development, paracrine factors such as angiotensin (AT) and anti-Mullerian hormone (AMH) play important roles. We attempted to add estrogen during the OFIVM and to assess their expression on the follicular cells. The ovaries and pre-antral follicles were collected from 13-day C57BL/6 mice and cultured in vitro with estradiol (E-2) treatment for up to two weeks. In the whole ovaries, the expression of AT II was decreased and the expression of AMH was similar between control and E-2-treated ovaries after in vitro culture. Although there was no difference in the survival, ovulation, maturation and fertilization rates between control and E-2-treated groups, the expression of AT II in the follicular cells was down-regulated after E-2 treatment at mRNA level, and AMH showed similar expression. In conclusion, adding E-2 in OFIVM may regulate paracrine factors and their receptors that are related to follicular development. Further investigations are necessary to elucidate the roles of various sex hormones in the regulation of AT and AMH expression during the OFIVM.</P>

가족공동체를 떠난 간호대학생들의 대학생활체험

김고은,김유은,김희진,조유진,안주영,허다연,홍서우,차지영,박송이 이화여자대학교 간호학회 2018 이화간호학회지 Vol.- No.52

Purpose: The purpose of this study was to understand and explain the experiences of college life among junior nursing students who live apart from their families. Methods: 14 junior nursing students living apart from their families for at least one semester were recruited through snowballing and convenience sampling. Participants were interviewed individually using open ended questions. Data were collected from July to October in 2017 until data saturation. Interviews were transcribed verbatim and analyzed by using hermeneutic phenomenological method proposed by van Manen. Results: Five essential theme clusters emerged: (1) faced with diverse problems while living apart from family, (2) depend on family when stressed, (3) adapt to college life by being independent and forming self-initiative lifestyle, (4) confront with difficulties once again when adapting to academic curriculum restructured by practicum, (5) pave the way to nursing career and feel proud of overcoming the difficulties independently. Conclusion: Although most participants faced diverse problems in college life, they tried to adapt independently by forming self-initiative lifestyle and overturn the difficulties to positive experiences. In conclusion, the process of living apart from families transformed participants into proactive individuals. Adopting counseling programs could support starting their junior years successfully.