• Pediatric Infection and Vaccine
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• v.16 no.2
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• pp.199-204
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• 2009

Purpose : Various proteins encoded in the early region 3 (E3) of adenoviruses protect cells from being killed by cytotoxic T cells and death-inducing cytokines. We sought to find out whether the genetic heterogeneity of the E3 gene might contribute to the molecular diversity of adenoviruses. Methods : Sequences in the E3 region were analyzed for 14 adenovirus type 3 (Ad3) strains that were isolated from children with lower respiratory tract infections in the Seoul National University Children's Hospital during the period 1991-2000. Full-length adenoviral DNA was purified from the infected A549 cell lysates using a modified Hirt procedure. Results : There was 98% homology between 14 Korean Ad3 strains with a reference strain (M15952). Homology within the Korean Ad3 strains was 98.7%. Variation was found in the region of transcripts 20.1 kDa, 20.6 kDa, truncated 7.7 kDa, 10.3 kDa, 14.9 kDa, and 15.3 kDa. In particular, all 14 Korean strains showed a missense single point mutation at the start codon of the truncated 7.7 kDa. In addition, a deletion was found in the truncated 7.7 kDa region by 58 base pairs in 10 strains and 94 base pairs in 4 strains. Variations in amino acids were observed in the receptor internalization and degradation complex (10.3 kDa/14.9 kDa) which stimulates the clearance from the cell surface and subsequent degradation of the receptors for the Fas ligand and TRAIL, while no variations were observed in another immunoregulatory transcript, 19 kDa. Conclusion : Sequence analysis of the immunoregulatory region of adenovirus E3 shows that genetic heterogeneities are related to genome type patterns.

• Research in Plant Disease
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• v.11 no.2
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• pp.140-145
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• 2005

A collection of 12 Erwinia carotovora strains from blackleg diseased potato in Jeju island was characterized genetic diversity by 5. cayotovora subsp. atposeptica (Eca)-specific PCR, PCR-RFLP of the two genes (16S rRNA and pel) and repetitive sequence PCR (ERIC-PCR). The results were compared with those of the other E. carotovora representative strains. None of the blackleg strains produced PCR amplicons with Eca-specific primers in contrast to the single 690 bp amplicon obtained with Eca strains. In addition, on the basis of pel gene RFLP with Sau3AI, the blackleg strains belonged to the pattern 2 whereas Eca strains belonged to the other one (pattern 3). By analysis of 16S rDNA RELP generated with HinfI, the most strains including the E. carotovera subsp. carotovora (Ecc) representative strains used in this study belonged to the pattern 1 whereas the blackleg strains belonged to the pattern 2 except for one strain. Moreover, ERIC-PCR analysis showed that the blackleg strains were closely related to each other and had an unique DNA band. Based on these molecular approaches, we have confirmed that the blackleg disease of potato is caused by a different E. carotovora from Eca and Ecc in Jeju island.

• Journal of Life Science
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• v.21 no.11
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• pp.1619-1624
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• 2011

Endophytic fungal strains were isolated from the roots of six species plants in the Dokdo islands. Native plant samples, such as Artemisia japonica, Chenopodium album and Solanum nigrum were isolated from Dongdo, and those such as Cyrtomium falcatum, Dianthus longicalyx and Tetragonia tetragonoides were isolated from Seodo. In total, thirty two fungal strains were isolated from these native plants. To identify the fungal strains, polymerase chain reaction (PCR) amplification of internal transcribed spacer (ITS: containing ITS1, 5.8s and ITS2 region) regions was done with universal primers ITS1 and ITS4. Endophytic fungi of four species were isolated from A. japonica, eight species from C. album, three species from S. nigrum, three species from C. falcatum, three species from D. longicalyx and eleven species from T. tetragonoides. Culture filtrates (CF) of isolated endophytic fungi were used to treatwaito-c rice seedlings to test plant growth-promoting activity. As a result of bioassay, Ca-5-2-2 strain isolated from C. album expressed highest plant growth-promotion activity. Of all the endophytic fungi isolated, Penicillium sp., Fusarium sp. and Aspergillus sp. were the most abundantly distributed fungal strains in the six plants used in this study.

• Biomedical Science Letters
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• v.16 no.2
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• pp.75-82
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• 2010

The molecular epidemiological characteristics of methicillin-resistant Staphylococcus aureus (MRSA) isolates have demonstrated their genetic diversity and evolution. A total of 137 strains of MRSA clinical isolates was collected from Korean healthcare facility in 2007. The MRSA clinical isolates were analyzed by molecular typings (SCCmec element and agr locus typing), virule nce factor gene detections {(Panton-Valentine leukocidin (PVL), enterotoxin, exfoliative toxin and toxic shock syndrome toxin-1), and amplified fragment length polymorphism (AFLP)}. The MRSA clinical isolates were classified as SCCmec type II-agr type 1 (2 strains), type II-agr type 2 (79 strains), type III-agr type 1 (24 strains), type III-agr type 2 (2 strains), type IV-agr type 1 (27 strains), type IV-agr type 2 (2 strains), and non-typable (1 strain, agr type 3). Based on SCCmec types, SCCmec type II (95.1%) and III (88.5%) indicated higher multidrug resistance rate than SCCmec type IV (10.3%) (P<0.001). The most common enterotoxin genes were seg (83.8%), sei (83.1%), and sec (80.2%). The tst gene was present in 86 out of 137 (62.8%) MRSA isolates. All MRSA isolates were negative for PVL and exfoliative toxin genes. The combinations of toxin genes were observed in particular SCCmec types; 97.6% of SCCmec type II strains carried sec, seg, sei and tst genes, 73.0% of SCCmec type III strains carried sea gene, and 89.7% of SCCmec type IV strains carried sec, seg and sei genes. Each of the SCCmec types of MRSA isolates had distinct AFLP profile. In conclusion, SCCmec type II, agr type 1 and 2 have demonstrated to be the most common types in Korea, and the results indicated that the virulence factors are closely associated with their molecular types (SCCmec and agr types).

• Korean Journal of Food Science and Technology
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• v.46 no.4
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• pp.438-445
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• 2014

We examined biogenic amine (BA) production as well as the diversity of bacterial flora in 11 types of commercial makgeolli stored at 4 and $20^{\circ}C$. Moreover, we studied the BA-producing activity of three L. plantarum strains isolated from makgeolli. At $20^{\circ}C$, the BA content was highly increased and the denatured DNA bands were more variable in non-sterilized makgeolli compared to sterilized makgeolli. The major BAs produced in commercial makgeolli were histamine and putrescine. Histamine, tyramine, putrescine, and cadaverine were produced in excess by inoculation of the three L. plantarum isolates to makgeolli stored at $20^{\circ}C$ for 21 days. These results suggest that some L. plantarum strains in makgeolli can produce different types of BAs, depending on the extent of degradation of makgeolli.

• Korean Journal of Microbiology
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• v.54 no.1
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• pp.31-37
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• 2018

Campylobacter jejuni is an important food-borne pathogen causing gastroenteritis in human. We isolated 208 strains of Campylobacter jejuni from 430 diarrhea patients and food employees with 17 food-poisoning outbreaks between 2014 and 2016 in Gyeonggi area. The strains were tested for genetic relationship and the genotype distribution using PFGE and multiplex-PCR typing. Among the 47 Penner-serotypes known for C. jejuni, it was identified as a genotype consisting of 35 genotypes by multiplex-PCR typing and represented 7 genotypes (HS2, HS4A, HS8, HS15, HS29, HS41, and HS53) in the selected strain. From the PFGE analysis of 11 food-poisoning outbreaks, 5 group of PFGE profile were obtained, and genetic similarity in these clusters ranged from 61.8 to 66.6%. This study examines the genetic diversity of C. jejuni that have been separated in the Gyeonggi area through various genetic analysis methods and identifies the correlation between strains in patients who have been infected with the disease in the future.

• Food Science of Animal Resources
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• v.29 no.6
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• pp.695-701
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• 2009

This study was performed to evaluate the effectiveness of biological critical control points using the genetic profile of Escherichia coli isolates from pork cutting plants. Samples were collected from carcasses, equipment (knife, table, glove, transport belt, boning and skinning machine), the environment (wall and floor), and meat cuts during the cutting process from two plants. Pulsed-field gel electrophoresis (PFGE) was used to characterize the E. coli isolates. An identical genotype was detected from the carcasses, equipment, environment, and final meat cuts, and showed that the incoming carcasses, which were contaminated during transportation from slaughterhouses, were a major source of E. coli that was spread throughout processing. Also, consistent cross-contamination due to improper cleaning and disinfection procedures was another possibility. As a result, incoming carcasses and cleaning procedures should be considered critical control points in pork cutting plants, since a heating step is not used to inactivate microorganisms. Furthermore, the high rate (59.6%) of E. coli isolation indicates E. coli can be a good indicator in livestock processing plants even though it has genetic diversity.

• Korean Journal of Microbiology
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• v.55 no.1
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• pp.74-76
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• 2019

Gram-positive anaerobic bacilli Actinomyces spp. commonly reside on mucosal surfaces of the oropharynx, gastrointestinal tract, and urogenital tract. Here, we first report the draft genome sequence of Actinomyces georgiae KHUD_A1, isolated from dental plaque of a Korean elderly woman. The genome is 2,652,059 bp in length and has a GC content of 68.06%. The genome includes 2,242 protein-coding genes, 9 rRNAs, and 64 tRNA. We identified 157 KHUD_A1 strain-specific genes, including genes encoding CPBP family intramembrane metalloprotease, bile acid: sodium symporter family protein, Txe/YoeB family addiction module toxin and Phd/YefM family antitoxin. The sequence information of A. georgiae KHUD_A1 will help understand the general characteristics of the bacterial species and the genome diversity of the genus Actinomyces.

• Journal of Life Science
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• v.31 no.1
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• pp.73-82
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• 2021

Throughout history, barley was the typical crop of the soils of Jeju Island due to its topographical features. People in Jeju eat Shindari or Dansul. Shindari or Dansul is a fermented drink of Jeju, made from the leftovers of cooked barely and nuruk of short fermentation periods. Although Makgeolli and Shindari share a similar fermentation period and materials, research on Shindari or Dansul is still in its early stages. In this study, we examined major bacterial species of Shindari or Dansul. In addition, we confirmed the antibacterial activities of an isolated strain against fish and human-harmful bacteria. Among the isolates, Firmicutes consisted of 73% and the Proteobacteria of 27%, indicating that the Firmicutes phylum was the dominant one. In addition, the Pediococcus genus and the Bacillus genus were the most prevalent consisting of 25%, followed by the Cronobacter genus (25%), the Enterococcus genus (16%), the Aneurinibacillus genus (5%), the Klebsiella genus (4%), and the Paenibacillus genus (2%). We conclude that the Lactobacillus genus predominated in Makgeolli, but the Pediococcus genus predominated in Shindari. In a study of the antibacterial activity, growth inhibition was observed for all bacteria, except for the fish disease bacterium Photobacterium damselae subsp. piscicida and the human-harmful bacterium Streptococcus mutans.

• The Korean Journal of Mycology
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• v.48 no.4
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• pp.389-396
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• 2020

Lentinula edodes is one of the most widely consumed edible mushrooms in Korea. Mating in L. edodes is regulated by a tetrapolar system, and two unlinked genetic loci, A and B, are known to be major determinants of the mating types, as reported in other heterothallic basidiomycetes. The A locus of L. edodes encodes a pair of homeodomain (HD) transcription factors. The highly variable N-termini of these HD transcription factors contribute to the diversity among the A mating types. In this study, we developed a cleaved amplified polymorphic sequence (CAPS) marker to discriminate 11 different A mating type alleles predominant among both cultivated and wild strains. Amplification of the variable region of the A locus followed by digestion with HaeIII and EcoRI restriction enzymes enabled successful discrimination among the 11 A mating type alleles. We also evaluated the applicability of this method in the identification of two A mating types of a dikaryotic strain.