• Journal of Microbiology and Biotechnology
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• v.22 no.4
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• pp.462-469
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• 2012

A metagenomic fosmid library was constructed from genomic DNA isolated from the microbial community residing in hindguts of a wood-feeding higher termite (Microcerotermes sp.) collected in Thailand. The library was screened for clones expressing lignocellulolytic activities. Fourteen independent active clones (2 cellulases and 12 xylanases) were obtained by functional screening at pH 10.0. Analysis of shotgun-cloning and pyrosequencing data revealed six ORFs, which shared less than 59% identity and 73% similarity of their amino acid sequences with known cellulases and xylanases. Conserved domain analysis of these ORFs revealed a cellulase belonging to the glycoside hydrolase family 5, whereas the other five xylanases showed significant identity to diverse families including families 8, 10, and 11. Interestingly, one fosmid clone was isolated carrying three contiguous xylanase genes that may comprise a xylanosome operon. The enzymes with the highest activities at alkaline pH from the initial activity screening were characterized biochemically. These enzymes showed a broad range of enzyme activities from pH 5.0 to 10.0, with pH optimal of 8.0 retaining more than 70% of their respective activities at pH 9.0. The optimal temperatures of these enzymes ranged from $50^{\circ}C$ to $55^{\circ}C$. This study provides evidence for the diversity and function of lignocellulose-degrading enzymes in the termite gut microbial community, which could be of potential use for industrial processes such as pulp biobleaching and denim biostoning.

• Proceedings of the KIEE Conference
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• 2005.05a
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• pp.9-11
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• 2005

We propose a optimal identification of information granulation(IG)-based fuzzy model to carry out the model identification of complex and nonlinear systems. To optimally identity we use genetic algorithm (GAs) sand Hard C-Means (HCM) clustering. An initial structure of fuzzy model is identified by determining the number of input, the selected input variables, the number of membership function, and the conclusion inference type by means of GAs. Granulation of information data with the aid of Hard C-Means(HCM) clustering algorithm help determine the initial parameters of fuzzy model such as the initial apexes of the membership functions and the initial values of polynomial functions being used in the premise and consequence part of the fuzzy rules. And the initial parameters are tuned effectively with the aid of the genetic algorithms(GAs) and the least square method. Numerical example is included to evaluate the performance of the proposed model.

• Korean Journal of Plant Taxonomy
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• v.41 no.3
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• pp.209-214
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• 2011

The taxonomy of the umbelliferous species Angelica amurensis and its allies was reviewed on the basis of molecular phylogenies derived from sequences of nuclear ribosomal DNA internal transcribed spacer (ITS) regions. Strict consensus of six minimal length 119-step trees derived from equally weighted maximum parsimony analysis of combined nuclear rDNA ITS1 and ITS2 sequences from 29 accessions of Angelica and outgroups indicated that Angelica purpuraefolia, known to be endemic to Korea, is the same species as A. amurensis. Comparisons of sequence pairs across both spacer regions revealed identity or 1-2 bp differences between A. purpuraefolia and A. amurensis. These results indicated that the two taxa are not distinguished taxonomically. Also, nuclear rDNA ITS regions are discussed as potential barcoding loci for identifying Korean Angelica.

• International Journal of Fuzzy Logic and Intelligent Systems
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• v.4 no.3
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• pp.283-287
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• 2004

In this paper, a method of designing the efficient batch blind equalization with low complexity using a micro genetic algorithm (GA), is presented. In general, the blind equalization techniques that are focused on the complexity reduction might be carried out with minor effect on the performance. Among the advanced various subjects in the field of GAs, a micro genetic algorithm is employed to identity the unknown channel impulse response in order to reduce the search space effectively. A new cost function with respect to the constant modulus criterion is suggested considering its relation to the Wiener criterion. We provide simulation results to show the superiority of the proposed techniques compared to other existing techniques.

• Journal of Microbiology and Biotechnology
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• v.32 no.10
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• pp.1307-1314
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• 2022

In this study, we sought to investigate the various characteristics of Salmonella spp. isolated from raw chicken meats available in Korean markets. The data collected, such as food source of isolation, sampling information, serotype, virulence, and genetic profile including sequence type, were registered in the database for further comparative analysis of the strains isolated from the traceback investigation samples. To characterize serotype, virulence and gene sequences, we examined 113 domestically distributed chicken meat samples for contamination with Salmonella spp. Phylogenetic analysis was conducted on 24 strains (21.2%) of Salmonella isolated from 113 commercially available chicken meats and by-products, using pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Serotyping of the isolated Salmonella spp. revealed S. Enteritidis in 11 strains (45.8%), S. Virchow in 6 strains (25%), S. Montevideo in 2 strains (8.3%), S. Bsilla in 2 strains (8.3%), S. Bareilly in 1 strain (4.2%), S. Dessau in 1 strain (4.2%), and S. Albany in 1 strain (4.2%). The genetic correlation indicated that 24 isolated strains were classified into 18 clusters with a genetic similarity of 64.4-100% between them. Eleven isolated S. Enteritidis strains were classified into 9 genotypes with a sequence identity of 74.4%, whereas the most distantly related S. Virchow was divided into five genotypes with 85.9% identity. Here, the MLST analysis indicated that the major Sequence Type (ST) of the Salmonella spp. isolated from domestic chicken sold in Chungcheong Province belongs to the ST 11 and 16, which differs from the genotype of Salmonella isolated from imported chicken. The differential sequence characteristics can be a genetic marker for identifying causative bacteria for epidemiological investigations of food poisoning.

• Proceedings of the National Institute of Ecology of the Republic of Korea
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• v.3 no.4
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• pp.191-198
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• 2022

Natural habitats of the Korean long-tailed goral (Naemorhedus caudatus) have been fragmented by anthropogenic activities in South Korea in the last decades. Here, the individual identity, genetic variation, and population differentiation of the endangered species were examined via the multiple-tube approach using a non-invasive genotyping method. The average number of alleles was 3.16 alleles/locus for the total population. The Yanggu population (1.66) showed relatively lower average number of alleles than the Inje population (3.67). Of the total 19 alleles, only seven (36.8%) alleles were shared by the two populations. Using five polymorphic out of six loci, four and six different goral individuals from the captive Yanggu (n=24) and the wild Inje (n=28) population were identified, respectively. The allele distribution was not identical between the two populations (Fisher's exact test: P<0.01). A considerably low migration rate was detected between the two populations (no. of migrants after correction for size=0.294). Additionally, the F statistics results indicated significant population differentiation between them, however, quite low (F_ST=0.327, P<0.01). The posterior probabilities indicated that the two populations originated from a single panmictic population (P=0.959) and the assignment test results designated all individuals to both populations with nearly equal likelihood. These could be resulted from moderate population differentiation between the populations. No significant evidence supported recent population bottleneck in the total Korean goral population. This study could provide us with useful population genetic information for conservation and management of the endangered species.

• Asian-Australasian Journal of Animal Sciences
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• v.20 no.1
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• pp.25-30
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• 2007

The capability of microsatellite markers for individual identification and their potential for breed assignment of individuals was evaluated in two Indian horse breeds. The strength of these individual assignment methods was also evaluated by increasing the number of loci in increments of five. The probability of identity of two random horses from the two breeds at all twenty five studied loci was as low as $1.08{\times}10^{-32}$ showing their suitability to distinguish between individual horses and their products. In the phylogenetic approach for individual assignment using Nei's genetic distances, 10.81% of horses associated with breed other than the major cluster of the source breed horses when all twenty five microsatellite loci were implemented. Similar results were obtained when the maximum likelihood approach for individual assignment was used. Based on these results it is proposed that, although microsatellite markers may prove very useful for individual identification, their utility for breed assignment of horses needs further evaluation.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.10
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• pp.1491-1500
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• 2019

Objective: European pigs have been imported to improve the economically important traits of Thai pigs by crossbreeding and was finally completely replaced. Currently Thai indigenous pigs are particularly kept in a small population. Therefore, indigenous pigs risk losing their genetic diversity and identity. Thus, this study was conducted to perform large-scale genetic diversity and phylogenetic analyses on the many pig breeds available in Thailand. Methods: Genetic diversity and phylogenetics analyses of 222 pigs belonging to Thai native pigs (TNP), Thai wild boars (TWB), European commercial pigs, commercial crossbred pigs, and Chinese indigenous pigs were investigated by genotyping using 26 microsatellite markers. Results: The results showed that Thai pig populations had a high genetic diversity with mean total and effective ($N_e$) number of alleles of 14.59 and 3.71, respectively, and expected heterozygosity ($H_e$) across loci (0.710). The polymorphic information content per locus ranged between 0.651 and 0.914 leading to an average value above all loci of 0.789, and private alleles were found in six populations. The higher $H_e$ compared to observed heterozygosity ($H_o$) in TNP, TWB, and the commercial pigs indicated some inbreeding within a population. The Nei's genetic distance, mean $F_{ST}$ estimates, neighbour-joining tree of populations and individual, as well as multidimensional analysis indicated close genetic relationship between Thai indigenous pigs and some Chinese pigs, and they are distinctly different from European pigs. Conclusion: Our study reveals a close genetic relationship between TNP and Chinese pigs. The genetic introgression from European breeds is found in some TNP populations, and signs of genetic erosion are shown. Private alleles found in this study should be taken into consideration for the breeding program. The genetic information from this study will be a benefit for both conservation and utilization of Thai pig genetic resources.

• The Korean Journal of Legal Medicine
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• v.41 no.2
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• pp.41-45
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• 2017

Fetal DNA (fDNA) detection in maternal serum is a challenge due to low copy number and the smaller size of fDNA fragments compared to DNA fragments derived from the mother. Massively parallel sequencing (MPS) is a useful technique for fetal genetic analysis that is able to detect and quantify small amounts of DNA. In this study, seven clinical samples of maternal serum potentially containing fDNA were analyzed with a commercial single nucleotide polymorphism (SNP) panel, the HID-Ion $AmpliSeq^{TM}$ Identity Panel, and the results were compared to those from previous studies. Reference profiles for mothers and fetuses were not available, but multiple Y chromosomal SNPs were detected in two samples, indicating that fDNA was present in the serum and thereby validating observations of autosomal SNPs. This suggests that SNP-based MPS can be valuable for fDNA detection, thereby offering an insight into fetal genetic status. This technology could also be used to detect small amounts of DNA in mixed DNA samples for forensic applications.

• Korean Journal of Plant Resources
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• v.28 no.4
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• pp.411-418
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• 2015

Lonicera caerulea var. edulis is a rare species found in some alpine region of Korea. Genetic variation in L. caerulea var. edulis has been investigated by examining 161 individuals from six natural populations: Mt. Seorak 1, Mt. Seorak 2, Mt. Jeombong, Mt. Bangtae, Mt. Gyebang, Mt. Halla. The mean genetic diversity for all the six populations was 0.25 (S.I.). The highest genetic diversity was found in Mt. Seorak (S.I.=0.3158) and the lowest was in Mt. Gyebang (S.I.=0.1047). Comparatively low level of genetic diversity was observed (Ae=1.25, P= 64.6%, S.I.=0.25), which is a typical pattern for rare tree species. AMOVA showed exceptionally large proportion of genetic variations both for among populations (34.69%) and within populations (65.31%). Excluding Mt. Gyebang, the genetic variation among and within population was 18.71% and 81.29% respectively. The UPGMA dendrogram based on genetic distance is not suitable for geographic relationship. Genetic distance of Mt. Gyebang was most distant from the other populations. Excluding Mt. Gyebang, the genetic identities among the five populations were 0.95 to 0.97, which is very high similarity level of genetic identity. This low level of genetic variations and the lack of site in nature indicates that Lonicera caerulea var. edulis demanded a serious conservation.