• The Journal of Korean Medicine
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• v.25 no.4
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• pp.147-151
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• 2004

Objective : Angelica species are some of the most medicinally important materials in Oriental medicine. This study was performed to determine if Angelica species could be identified by genetic analysis and to verify Pyrosequencing analyses, which were used to assess genetic variation. Methods : The DNAs of Angelica acutiloba, Angelica gigas and Angelica sinensis were extracted. We have investigated the typing of single-base variations of Angelica species in DNA by using Pyrosequencing. Results : Angelica gigas showed a different pattern compared with Angelica acutiloba and Angelica sinensis. The peak of Angelica gigas was very weak in the second C nucleotide base compared with that of the others. The peak of Angelica acutiloba was present in the fourth C nucleotide base compared with that of the others. From these results we verified that our Angelica species-specific sequencing primer was well designed. Conclusion : Pyrosequencing analysis might be able to provide the identification of the Angelica species.

• BMB Reports
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• v.28 no.4
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• pp.359-362
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• 1995

The highly polymorphic variable number of tandem repeat (VNTR) loci in the human genome are informative markers for the genetic characterization of individuals in the paternity test and forensic science as well as for the study of human disease. In this study, VNTR loci D1S80 and D2S123 have been amplified by PCR and the amplified length polymorphic alleles were detected with a discontinuous vertical PAGE system and silver staining. For explicit DNA typing, PCR optimization, in which amplification efficiencies are similar over a wide range of allele sizes, non-specific amplifications are minimal, and new longer alleles have high amplification efficiency, has been performed by changing the PCR reaction buffer composition and thermal cycling conditions. It turned out that adding an appropriate amount of Tween 20 and NP40 to the PCR reaction buffer and raising the annealing temperature to $68^{\circ}C$ in thermal cycling made it possible for optimal VNTR loci amplification. A modified PAGE system for VNTR separation was established. Under these conditions, new longer alleles in the 01580 locus were discovered and 025123 pattern changes in colorectal tumors were observed. These technical tips are valuable for detecting various amplified fragment length polymorphisms.

• Korean Journal of Organic Agriculture
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• v.12 no.2
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• pp.197-207
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• 2004

Identification of animals has been used with an e ar tag with dummy code and blood typing has been used for paternity and individual identification in live animals. Various genetic markers are different for breeds of pig and hence, it is necessary to identity the discrete genetic marker in korean native pig. A total of 240 pigs were used to find korean native pig population specific markers that expressed in population of korean native pigs. To identify the individual traceability, 20 animals were randomly chosen and tested for a whole process from being live to slaughter stages. The candidate genetic marker used in the study were 18 DNA microsatellites which were identified in pig genome. The number of alleles of those DNA microsatellites ranged form a minimum of 3 to maximum of 6. The heterozygote frequency rang6d from 0.44 to 0.69. Effective number of alleles for each DNA microsatellotes were 2 to 4. By choosing 6 candidate genetic markers among all, the traceability of individual identification was estimated as accurate as 99.99%(p>0.0014), nearly.

• 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.

• Pediatric Gastroenterology, Hepatology & Nutrition
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• v.21 no.1
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• pp.72-75
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• 2018

Colorectal carcinoma is a well-known malignancy in adults. However, it is rare in children. Besides, it also has different behaviour in paediatric age-group and usually presents with non-specific symptoms like abdominal pain, weight loss, and anaemia. This usually leads to delay in diagnosis. Adenocarcinoma in children has unfavourable tumour histology (mucinous subtype) and advanced disease stage at presentation which lead to poorer prognosis in children. Family history, genetic typing and sibling screening are essential components of management as this malignancy is frequently seen associated with hereditary syndromes. We describe a case of unusual presentation of rectal carcinoma in a 12-year-old girl.

• Korean Journal of Microbiology
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• v.37 no.1
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• pp.56-60
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• 2001

Molecular typing of Bacillus anthracis has been extremely difficult due to the lack of polymorphic DNA markers. Aiming to develop a DNA marker specific for Bacillus anthracis and to be able to discriminate this species from Bacillus genus, we applied the random amplified polymorphic DNA (RAPD)-PCR. We have identified B. anthracis from various Bacillus species. The analysis performed by RAPD clearly demonstrated substantial genetic variations among Bacillus species. This type of analysis is an easy, quick and highly discriminatory technique that may help in diagnosis of anthrax.

• 보존과학연구
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• s.24
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• pp.153-167
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• 2003

We performed nuclear DNA typing and mitochondrial DNA sequencing analysis based on PCR from an ancient Korean remainsexcavated from Siheung in Korea. 7 bones were collected and partially STR(short tandem repeat) systems, Sex determination Amelogenin kit(Promega co, USA), were used in this study. Mitochondrial DNAs were also amplified and sequenced by ABI 310 DNA sequencer. We know that sample no. 2 and no. 3 were females and also sample no. 2 and no.7 possessed the same maternal inheritance by mitochondrial DNA sequencing results. Throughout this research, the mitochondrial DNA sequencing of human in the middle of Joseon Dynasty in Korea is obtained. In addition, this finding will be an important foundation for the future research.

• Proceedings of the PSK Conference
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• 2003.10b
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• pp.163.2-163.2
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• 2003

The genera Bifidobacterium is a member of the normal intestinal flora in humans, and important in food industry. In order to test the genetic identity of this bacterial genera, four primers originated from rice genome (SRILS Microbial $UniPrimers^{TM}$ kit) were used in molecular typing of 7 Bifidobacterial species and 20 isolates from various source. SRILS Microbial $UniPrimers^{TM}$ kit were effectively applied to genomic fingerprinting of various organism such as plant, animal and microorganism. (omitted)

• Journal of Microbiology and Biotechnology
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• v.26 no.9
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• pp.1643-1649
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• 2016

The aims of this study were to characterize the molecular epidemiological profiles of CTX-M-producing uropathogenic Escherichia coli isolates from a tertiary hospital in Daejeon, Korea, and to investigate the genetic diversity and compare the prevalence of sequence types (STs) in different areas. Extended spectrum β-lactamase-producing E. coli strains isolated from urine were analyzed for CTX-M, integrons, and insertion sequence common regions (ISCRs) by PCR and sequencing. Multilocus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE), phylogenetic analysis, and rep-PCR were also used for molecular typing of the isolates. Of 80 CTX-M producers, 31 and 46 expressed CTX-M-15 and CTX-M-14, respectively. MLST analysis indicated that the most prevalent ST was ST131 (n = 34, 42.5%), followed by ST38 (n = 22, 27.5%), ST405 (n = 8, 10.0%), and ST69 (n = 6, 7.5%). Most CTX-M producers harbored class 1 integrons. ST131 strains belonged to phylogenetic group B2 and showed identical rep-PCR patterns, whereas ST69, ST38, and ST405 strains belonged to phylogenetic group D; the ST38 and ST405 strains displayed the same rep-PCR pattern, respectively. ST131 and ST38 isolates showed 21 and 19 distinct types, respectively, by PFGE. In Daejeon, D-ST38 CTX-M-14 producers were relatively more prevalent than in other countries and Korean cities. Our results indicate that CTX-M-producing E. coli isolates belonged mostly to ST131 or ST38 and were more related to hospital-onset than to community-onset infections and that the bla_CTX-M gene may vary according to the ST.

• Korean Journal of Veterinary Research
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• v.55 no.1
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• pp.31-39
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• 2015

The present study was conducted to determine the full rpoB and eight house-keeping gene sequences of 78 and 35, respectively, avian pathogenic E. coli (APEC) strains. Phylogenetic comparison with 66 E. coli and Shigella strains from GenBank and EMBL was also conducted. Based on the full rpoB sequence, 50 different rpoB sequence types (RSTs) were identified. RST 1 was assigned to a major RST that included 34.7% (50/144) of the analyzed strains. RST 2 to RST 50 were then assigned to other strains with higher nucleotide sequence similarity to RST 1 in order. RST 1, 11, and 23 were mixed with APEC along with human commensal and pathogenic strains while RST 2, 6, 9, 13-15, 22, 24, 25, 33, 34, 36, and 41 were unique to APEC strains. Only five APEC strains grouped into RST 32 and 47, which contained human pathogenic E. coli (HPEC). Thus, most of the APEC strains had genetic backgrounds different from HPEC strains. However, the minor APEC strains similar to HPEC should be considered potential zoonotic risks. The resolution power of multi-locus sequence typing (MLST) was better than RST testing. Nevertheless, phylogenetic analysis of rpoB was simpler and more economic than MLST.