• Pediatric Infection and Vaccine
• /
• v.12 no.2
• /
• pp.166-177
• /
• 2005

Purpose : The purpose of this study was to examine the molecular epidemiology and genetic variability of adenovirus(Ad) serotypes Ad1, Ad2, and Ad5 over 14 years in Korea. Methods : A total of 382 adenoviral strains isolated from the nasopharyngeal aspirates of children with lower respiratory tract infections in Seoul, Korea from November 1990 to February 2003 were serotyped by neutralization assay with type-specific antisera. Viral DNAs were extracted from infected cell lysates by the modified Hirt procedure. Genome type(GT) was determined by DNA restriction analysis with 12 restriction enzymess(BamHI, BclI, BglI, BglII, BstEII, EcoRI, HindIII, HpaI, SalI, SmaI, XbaI, and XhoI). To evaluate the genetic relatedness, pairwise comigrating restriction fragments(PCRF) analysis was performed. Results : Of 382 strains, 33 strains(9%) were Ad1, 45 strains(12%) were Ad2, and 24 strains(6%) were Ad5. Eighteen GTs(Ad1p1-Ad1p7, Ad1a, Ad1b, Ad1b1-Ad1b3, Ad1c, Ad1d, Ad1e, Ad1e1, Ad1e2, Ad1f) among Ad1, 24(Ad2p1-Ad2p11, Ad2a, Ad2a1-Ad2a6, Ad2b, Ad2c, Ad2d, Ad2e, Ad2e1-Ad2e3) among Ad2, and 10(Ad5p1, Ad5p2, Ad5a, Ad5a1-Ad5a7) among Ad5 strains were identified. One or two strains of the vast majority of GTs were isolated during the study period while a few GTs were identified sporadically with more than 2 strains. It is notable that some GTs such as Ad1p5 and Ad5a1 appeared in cluster during a short period. In analysis of genetic relatedness, the degree of PCRFs(pairwise comigrating restriction fragments) for Ad1 varied from 79 to 99%, for Ad2, 82 to 99%, and for Ad5, 85 to 99%. Conclusion : This study established the comprehensive nomenclature systems of Ad1, Ad2, and Ad5. Diverse GTs identified in this study have crucial implications in the genomic diversity and epidemiological characteristics of Ad1, Ad2, and Ad5.

• The Korean Journal of Ecology
• /
• v.16 no.4
• /
• pp.515-526
• /
• 1993

In order to study the ecotypic variation of Rohinia pseudo-acacia L. distributed in southern area of Korean peninsula, 15 local populations(Daejin, Sokcho, Kangneung, Mt. Surak, Hongcheon, Kwangneung, Namhansanseong, Chungju, Yesan, Andong, Jeonju, Dalseong, Changweon, Mokpo and Wando), located from $34^{\circ}18'N\;to\;38^{\circ}36'N$, were selected based on the latitudes and geographical distances. Seeds of these populations were collected and protein contents of seeds and their band patterns were investigated. The seed proteins of all populations were electrophoresed on SDS-polyacrylamide gel. Total number of protein bands were 35, whose molecular weights ranged from 17, 258 daltons to 142, 232 daltons. The number of bands of seed proteins was 23 in Dalseong and Hongcheon and was 32 in Daejin and Sokcho, showing an increasing tendency in the number of bands as the latitude goes high. The local populations were classified into 3 local types based on protein analysis: the middle north east coastal type(Daejin, Sokcho. Kangneung), the central type (Mt. Surak, Hongcheon, Kwangneung, Namhansanseong, Chungju) and the southern type(Yesan, Andong, Jeonju, Dalseong, Changweon, Mokpo, Wando). According to the results of cluster analysis by UPGMA based on the similarity index(c0efficient of Jaccard) of the patterns, 3 local types were subdivided further into 6 types: the middle north east coastal type(Sokcho, Kangneung), the north central type I (Mt. Surak, Hongcheon), the north central type II (Narnhansanseong, Chungju, Daejin), the north central type III (Kwangneung), the south central type (Yesan, Dalseong, Jeonju) and the southern type(Andong, Changweon, Mokpo, Dalseong, Wando). The No. 12 band of the separated seed proteins showed the highest colored density in the preparations from all the populations. The No. 11~13 and No. 23~28 bands also showed high densities. As a whole, southern type populations (Changweon, Mokpo, Wando) showed high protein contents and high colored density. Total protein contents of the seeds in each population were variable from 9. 68mg / g (Mt. Surak) to 17.30mg/g (Jeonju), showing an increasing trends toward low latitudes.

• Journal of the Korean Vacuum Society
• /
• v.22 no.2
• /
• pp.86-91
• /
• 2013

The optical properties of InAs quantum dots (QDs) grown on GaAs substrates grown by molecular beam epitaxy have been studied using photoluminescence (PL) and time-resolved PL measurements. InAs QDs were grown using an arsenic interruption growth (AIG) technique, in which the As flux was periodically interrupted by a closed As shutter during InAs QDs growth. In this study, the shutter of As source was periodically opened and closed for 1 (S1), 2 (S2), or 3 s (S3). For comparison, an InAs QD sample (S0) without As interruption was grown in a pure GaAs matrix for 20 s. The PL intensity of InAs QD samples grown by AIG technique is stronger than that of the reference sample (S0). While the PL peaks of S1 and S2 are redshifted compared to that of S0, the PL peak of S3 is blueshifted from that of S0. The increase of the PL intensity for the InAs QDs grown by AIG technique can be explained by the reduced InAs clusters, the increased QD density, the improved QD uniformity, and the improved aspect ratio (height/length). The redshift (blueshift) of the PL peak for S1 (S3) compared with that for S0 is attributed to the increase (decrease) in the QD average length compared to the average length of S0. The PL intensity, PL peak position, and PL decay time have been investigated as functions of temperature and emission wavelength. S2 shows no InAs clusters, the increased InAs QD density, the improved QD uniformity, and the improved QD aspect ratio. S2 also shows the strongest PL intensity and the longest PL decay time. These results indicate that the size (shape), density, and uniformity of InAs QDs can be controlled by using AIG technique. Therefore the emission wavelength and luminescence properties of InAs/GaAs QDs can also be controlled.

• Journal of the Mineralogical Society of Korea
• /
• v.24 no.4
• /
• pp.289-300
• /
• 2011

Atomistic origins of carbon solubility into silicates are essential to understand the effect of carbon on the properties of silicates and evolution of the Earth system through igneous and volcanic processes. Here, we investigate the atomic structure and NMR properties of dissolved carbon in enstatite using Raman spectroscopy and quantum chemical calculations. Raman spectrum for enstatite synthesized with 2.4. wt% of amorphous carbon at 1.5 GPa and $1,400^{\circ}C$ shows vibrational modes of enstatite, but does not show any vibrational modes of $CO_2$ or ${CO_3}^{2-}$. The result indicates low solubility of carbon into enstatite at a given pressure and temperature conditions. Because $^{13}C$ NMR chemical shift is sensitive to local atomic structure around carbon and we calculated $^{13}C$ NMR chemical shielding tensors for C substituted enstatite cluster as well as molecular $CO_2$ using quantum chemical calculations to give insights into $^{13}C$ NMR chemical shifts of carbon in enstatite. The result shows that $^{13}C$ NMR chemical shift of $CO_2$ is 125 ppm, consistent with previous studies. Calculated $^{13}C$ NMR chemical shift of C is ~254 ppm. The current calculation will alllow us to assign potential $^{13}C$ NMR spectra for the enstatite dissolved with carbon and thus may be useful in exploring the atomic environment of carbon.

• Journal of Embryo Transfer
• /
• v.31 no.3
• /
• pp.235-242
• /
• 2016

This study tested the association between genotypes of the single nucleotide polymorphism (SNP) marker, rs81437607 and capric acid (FA_C10_0) compositions in longissimus dorsi muscle in pigs. Eighteen fatty acid (FA) compositions were measured in a total of 974 $F_2$ animals among 1,106 $F_2$ progeny produced between Landrace and Jeju Black Pig (JBP). Among FA compositions tested, we identified a cluster of highly significant SNPs for capric acid compositions on 58 Mb position of Sus scrofa chromosome 12 (SSC12) using genome-wide association study (GWAS) with $F_2$ genotypes from SNP panel analysis. GWAS results showed that the rs81437607 was the highest trait-related SNP marker with capric acid levels. Three genotypes (C/C, C/T and T/T) of rs81437607 marker were found in $F_2$ population by further pyrosequencing. Association analysis results showed the significant differences between rs81437607 genotypes and capric acid compositions (P<0.05). The $F_2$ pigs harboring rs81437607 C/C ($0.119{\pm}0.002%$) and C/T ($0.116{\pm}0.002%$) genotypes showed additively higher levels of capric acid content than those of T/T homozygotes ($0.109{\pm}0.002%$) ($P=1.30{\times}10^{-12}$). These results suggested that the genetic variations of rs81437607 may be helpful to find causative variants and assist as molecular genetic markers for improving the capric acid contents in longissimus dorsi muscle in pigs.

• Proceedings of the Korean Society for Bioinformatics Conference
• /
• 2003.10a
• /
• pp.26-51
• /
• 2003

Large scale protein interaction maps provide a new, global perspective with which to analyse protein function. PSIMAP, the Protein Structural Interactome Map, is a database of all the structurally observed interactions between superfamilies of protein domains with known three-dimensional structure in thePDB. PSIMAP incorporates both functional and evolutionary information into a single network. It makes it possible to age protein domains in terms of taxonomic diversity, interaction and function. One consequence of it is to predict the most important protein domain structure in evolution. We present a global analysis of PSIMAP using several distinct network measures relating to centrality, interactivity, fault-tolerance, and taxonomic diversity. We found the following results: ${\bullet}$ Centrality: we show that the center and barycenter of PSIMAP do not coincide, and that the superfamilies forming the barycenter relate to very general functions, while those constituting the center relate to enzymatic activity. ${\bullet}$ Interactivity: we identify the P-loop and immunoglobulin superfamilies as the most highly interactive. We successfully use connectivity and cluster index, which characterise the connectivity of a superfamily's neighbourhood, to discover superfamilies of complex I and II. This is particularly significant as the structure of complex I is not yet solved. ${\bullet}$ Taxonomic diversity: we found that highly interactive superfamilies are in general taxonomically very diverse and are thus amongst the oldest. This led to the prediction of the oldest and most important protein domain in evolution of lift. ${\bullet}$ Fault-tolerance: we found that the network is very robust as for the majority of superfamilies removal from the network will not break up the network. Overall, we can single out the P-loop containing nucleotide triphosphate hydrolases superfamily as it is the most highly connected and has the highest taxonomic diversity. In addition, this superfamily has the highest interaction rank, is the barycenter of the network (it has the shortest average path to every other superfamily in the network), and is an articulation vertex, whose removal will disconnect the network. More generally, we conclude that the graph-theoretic and taxonomic analysis of PSIMAP is an important step towards the understanding of protein function and could be an important tool for tracing the evolution of life at the molecular level.

• KOREAN JOURNAL OF CROP SCIENCE
• /
• v.51 no.3
• /
• pp.259-268
• /
• 2006

Miniature inverted transposable elements (MITEs) are abundant genomic components in plant including rice. MITE-transposon display (MITE-TD) is an Amplified Fragment Length Polymorphism (AFLP)-related technique based on MITE sequence. In this study, we used the MITE-AFLP for the analysis of diversity and relation-ship of the 114 japonica accessions. Of the several MITEs, the mPing family was applied to detect polymorphisms based on PCR amplification. The BfaI adaptor primer and the specific primer derived from mPing terminal inverted repeat (TIR) region were used to PCR amplification of 114 accessions. Nine primer pairs produced a total of 160 polymorphic bands. PIC values of the polymorphic bands generated by nine primer pairs ranged from 0.269 (BfaI + ACT) to 0.426 (BfaI + T). Each accession revealed a distinct fingerprint with two primer combinations, BfaI + G and BfaI + C. Cluster analysis using marker-based genetic similarity classified 114 accessions into five groups. MITE-AFLP markers were genetically mapped using a population of 80 BILs (BC1F7) derived from a cross between the rice accessions, Milyang 23 and Hapcheonaengmi 3. Eight of the markers produced with the primer pair BfaI + 0 were mapped on chromosomes 1, 2, 4, 5, 7, and 9. Considering that one MITE-AFLP marker on chromosome 7 was tightly linked to the Rc gene, the MITE-AFLP markers will be useful for gene tagging and molecular cloning.

• Journal of Microbiology and Biotechnology
• /
• v.23 no.11
• /
• pp.1500-1508
• /
• 2013

Ebosin, a novel exopolysaccharide produced by Streptomyces sp. 139, has obvious antirheumatic arthritis activity in vivo, and its biosynthesis gene cluster (ste), consisting of 27 open reading frames, has been identified. This paper reports our study of the gene functionality of ste8, the predicted protein product of which is homologous to some bacterial chain length determinant Wzz proteins. For characterization of Ste8, ste8 was cloned and expressed in the mutant strain E. coli 086:H2 (${\Delta}wzz$). The functional complementation of wzz by ste8 was demonstrated by the restoration of wild-type lipopolysaccharide biosynthesis and increased levels of serum resistance of E. coli 086:H2 (${\Delta}wzz$) (pET30a-ste8). To examine the function of ste8 in ebosin biosynthesis, the gene was knocked out with a double crossover via homologous recombination. The molecular weight of the ebosin derivative EPS-8m produced by the mutant Streptomyces sp. 139 ($ste8^-$) was much lower than that of ebosin, and the binding activity of EPS-8m for IL-1R decreased significantly compared with ebosin. These results demonstrate that ste8 encodes a chain length determinant (Wzz) that functions in ebosin biosynthesis.

• Journal of Sericultural and Entomological Science
• /
• v.38 no.2
• /
• pp.81-92
• /
• 1996

This study was conducted to characterize mulberry varieties by the analysis of morphological characters as well as biochemical and molecular biological markers. As for the budding stage Geumsang, Chosang i and Yeongbyeonchuwoo were early, but Dangsang 6, Hwangchuwoo were late. The lowest varietiy in rate of death atop was Dangsang 8(0.0%). Suncheonppong was the highest leaf yields in spring and autumn rearing season. In biochemical isozyme analysis, peroxidase gave good zymogram patterns in isoelectric focusing electrophoresis. There were high variations in RAPD analysis among the mulberry trees. From the obtained peroxidase and RAPD variations, cluster phylogenetic analysis was carried out using NT-SYS PC program. There were no clear grouping patterns between native varieties and leading varieties. The highest similarity was observed between Suwonsang 1 and Suwonsang 2 at about 90% similarity level.

• Molecules and Cells
• /
• v.26 no.6
• /
• pp.566-575
• /
• 2008

Twenty-five chipmunk species occur in the world, of which only the Siberian chipmunk, Tamias sibiricus, inhabits Asia. To investigate mitochondrial cytochrome b sequence variations and population structure of the Siberian chipmunk in northeastern Asia, we examined mitochondrial cytochrome b sequences (1140 bp) from 3 countries. Analyses of 41 individuals from South Korea and 33 individuals from Russia and northeast China resulted in 37 haplotypes and 27 haplotypes, respectively. There were no shared haplotypes between South Korea and Russia - northeast China. Phylogenetic trees and network analysis showed 2 major maternal lineages for haplotypes, referred to as the S and R lineages. Haplotype grouping in each cluster was nearly coincident with its geographic affinity. In particular, 3 distinct groups were found that mostly clustered in the northern, central and southern parts of South Korea. Nucleotide diversity of the S lineage was twice that of lineage R. The divergence between S and R lineages was estimated to be 2.98-0.98 Myr. During the ice age, there may have been at least 2 refuges in South Korea and Russia - northeast China. The sequence variation between the S and R lineages was 11.3% (K2P), which is indicative of specific recognition in rodents. These results suggest that T. sibiricus from South Korea could be considered a separate species. However, additional information, such as details of distribution, nuclear genes data or morphology, is required to strengthen this hypothesis.