• Biomedical Science Letters
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• v.10 no.4
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• pp.473-477
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• 2004

Methicillin-Resistant Staphylococcus aureus (MRSA) strains are resistant to a wide range of antibiotics and are a major cause of nosocomial infections. Accurate and rapid typing of MRSA is needed to implement effective infection control measures. Arbitrarily Primed PCR (AP-PCR) is a very useful method in rapid typing. AP-PCR is not necessary information about target DNA sequence because this is basically DNA amplification and could be useful in epidemiological typing by classified band pattern. In this study, MRSA were isolated and identified from ICU, Neu, IM and Ped environments and investigated molecular typing by AP-PCR. Ped, the MRSA pattern determines the la, IIa type, 1M is Ib type, Neu is IIa type and ICU determines the IIa, lIb types. All MRSA in this study were typeable by AP-PCR, which was easy to perform and reproduce with evidence of MRSA for purposes of nosocomial infection control.

• Journal of Microbiology and Biotechnology
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• v.25 no.9
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• pp.1410-1416
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• 2015

Wolbachia is an obligate symbiotic bacteria that is ubiquitous in arthropods, with 25-70% of insect species estimated to be infected. Wolbachia species can interact with their insect hosts in a mutualistic or parasitic manner. Sequence types (ST) of Wolbachia are determined by multilocus sequence typing (MLST) of housekeeping genes. However, there are some limitations to MLST with respect to the generation of clone libraries and the Sanger sequencing method when a host is infected with multiple STs of Wolbachia. To assess the feasibility of massive parallel sequencing, also known as next-generation sequencing, we used pyrosequencing for sequence typing of Wolbachia in butterflies. We collected three species of butterflies (Eurema hecabe, Eurema laeta, and Tongeia fischeri) common to Korea and screened them for Wolbachia STs. We found that T. fischeri was infected with a single ST of Wolbachia, ST41. In contrast, E. hecabe and E. laeta were each infected with two STs of Wolbachia, ST41 and ST40. Our results clearly demonstrate that pyrosequencing-based MLST has a higher sensitivity than cloning and Sanger sequencing methods for the detection of minor alleles. Considering the high prevalence of infection with multiple Wolbachia STs, next-generation sequencing with improved analysis would assist with scaling up approaches to Wolbachia MLST.

• Journal of Animal Science and Technology
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• v.63 no.2
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• pp.248-261
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• 2021

Attributable to their major function in pathogen recognition, the use of bovine leukocyte antigens (BoLA) as disease markers in immunological traits in cattle is well established. However, limited report exists on polymorphism of the BoLA gene in zebu cattle breeds by high resolution typing methods. Thus, we used a polymerase chain reaction sequence-based typing (PCR-SBT) method to sequence exon 2 of the BoLA class II DRB3 gene from 100 animals (Boran, n = 13; Sheko, n = 20; Fogera, n = 16; Horro, n = 19), Hanwoo cattle (n = 18) and Bangladesh Red Chittagong zebu (n = 14). Out of the 59 detected alleles, 43 were already deposited under the Immuno Polymorphism Database for major histocompatibility complex (IPD-MHC) while 16 were unique to this study. Assessment of the level of genetic variability at the population and sequence levels with genetic distance in the breeds considered in this study showed that Zebu breeds had a gene diversity score greater than 0.752, nucleotide diversity score greater than 0.152, and mean number of pairwise differences higher than 14, being very comparable to those investigated for other cattle breeds. Regarding neutrality tests analyzed, we investigated that all the breeds except Hanwoo had an excess number of alleles and could be expected from a recent population expansion or genetic hitchhiking. Howbeit, the observed heterozygosity was not significantly (p < 0.05) higher than the expected heterozygosity. The Hardy Weinberg equilibrium (HWE) analysis revealed non-significant excess of heterozygote animals, indicative of plausible over-dominant selection. The pairwise FST values suggested a low genetic variation among all the breeds (FST = 0.056; p < 0.05), besides the rooting from the evolutionary or domestication history of the cattle. No detached clade was observed in the evolutionary divergence study of the BoLA-DRB3 gene, inferred from the phylogenetic tree based on the maximum likelihood model. The investigation herein indicated the clear differences in BoLA-DRB3 gene variability between African and Asian cattle breeds.

• Fisheries and Aquatic Sciences
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• v.9 no.2
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• pp.70-74
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• 2006

DNA sequence-based typing is considered a robust tool for the discrimination of dinoflagellate species because of the availability of extensive rDNA sequences. Here, we present a rapid, cost-effective DNA-sequencing technique for various PCR products. This sequencing strategy relies on 'nested' or 'tailed' primer labeled with near-infrared dye, and uses a minimal volume of unpurified PCR product (ca. $5{\mu}L$) as the DNA template for sequencing reactions. Reliable and accurate base identification was obtained for several hundred PCR fragments of rRNA genes. This quick, inexpensive technique is widely applicable to sequence-based typing in clinical applications, as well as to large-scale DNA sequencing of the same genomic regions from related species for studies of molecular evolution.

• Journal of Microbiology
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• v.44 no.4
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• pp.457-460
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• 2006

A suspicious meningococcal meningitis death case was reported to the Beijing CDC. The blood specimen was analyzed via multi-PCR and MLST. 6 isolates from close contacts were analyzed via PFGE and MLST. According to the results of the above analyses, the cause of this case was identified as a serogroup A Neisseria meningitidis, which, in terms of sequence typing, belonged the ST7 group.

• Mycobiology
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• v.43 no.3
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• pp.360-365
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• 2015

Multilocus sequence typing analysis was applied to determine the genotypes of 147 (137 clinical and 10 environmental) Cryptococcus neoformans and three clinical Cryptococcus gattii isolates from 1993 to 2014 in Korea. Among the 137 clinical isolates of C. neoformans, the most prevalent genotype was ST5 (n = 131), followed by ST31 (n = 5) and ST127 (n = 1). Three C. gattii strains were identified as ST57, ST7, and ST113. All environmental isolates were identified as C. neoformans with two genotypes, ST5 (n = 7) and ST31 (n = 3). Our results show that C. neoformans isolates in Korea are genetically homogeneous, and represent a close genetic relationship between clinical and environmental isolates.

• Proceedings of the Zoological Society Korea Conference
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• 1996.10a
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• pp.254.1-254
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• 1996

No Abstract, See Full Text

• BMB Reports
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• v.30 no.1
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• pp.26-32
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• 1997

Of all HLA class I molecules, HLA-C gene products are most poorly understood because they express at a low level on the cell surface compared to HLA-A and -B. In order to identify serologically detectable and undetectable HLA-C antigens, we have established a DNA-based tissue typing method for the HLA-C locus by PCR-SSP (polymerase chain reaction-sequence specific primers). Genomic DNA prepared from Iymphoblastoid 21 B-cell lines and 120 Korean individuals by proteinase K digestion and pheno/chloroform extractions have been typed by PCR-SSP (23 primer mixes were used). The PCR-SSP results of control cell lines were discrepant from serology in 1 case among 21 cases: Cw6 which was negative by serology but positive by PCR-SSP (cell line: MANIKA). Twenty four HLA-Cw "blank" antigens among fifty Korean individuals were completely determined by PCR-SSP DNA typing. HLA-Cw*0101 (15.3%), Cw*1401 (12.3%) and Cw*0701 (11.7%) alleles were frequently found in 120 Korean individual samples. In conclusion. the high level of discrimination for HLA-C alleles may prove useful and informative in the study of transplant survival, and identify the importance of allelic differences, not readily detectable by serology, on host and donor compatibility.

• Asian-Australasian Journal of Animal Sciences
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• v.20 no.12
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• pp.1791-1797
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• 2007

A study was conducted with 70 Hanwoo (Korean cattle) for genotyping bovine leukocyte antigen (BoLA)-DRB3.2 gene by using the polymerase chain reaction (PCR) and sequence based typing (SBT). Two-step PCR was carried out for amplifying a 284 bp fragment of the target gene and the PCR products were digested with three restriction enzymes namely RsaI, BstYI and HaeIII. Seventeen alleles were detected with frequencies ranging from 1.43 to 18.57% and one (x'aa) of these alleles was identified as a new allele that has not been reported before. The frequency of the new x'aa allele identified in this breed was 12.86%. In addition, the seven most frequently observed alleles (DRB3.2 *10, *15, *16, *26, *27, *54 and x'aa) accounted for 74.28% of the alleles in this population. The phylogenetic tree showed that the BoLA-DRB3.2 allele sequences of Hanwoo were shared with other Bos taurus breeds and no specific clade for Hanwoo was identified. It indicates high heterogeneity of the BoLA-DRB3 gene in this population and may give some ideas for breeding animals having better disease resistance.

• Korean Journal of Veterinary Research
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• v.58 no.1
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• pp.51-55
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• 2018

Bovine mastitis (BM) has resulted in enormous economic loss in the dairy industry and coagulase-negative staphylococci (CNS) have caused subclinical BM. Although VITEK 2 GP ID card (VITEK 2) has been used for CNS identification, the probability of identification varies. The rpoB sequence typing (RSTing) method has been used for molecular diagnosis and epidemiology of bacterial infections. In this study, we undertook RSTing of CNS and compared the results with those of VITEK2 and 16S rRNA gene sequencing. As compared VITEK2, the molecular-based methods were more reliable for species identification; moreover, RSTing provided more molecular epidemiological information than that from 16S rRNA gene sequencing.