• Genomics & Informatics
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• v.1 no.1
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• pp.50-54
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• 2003

Genome of an extreme thermophile, Thermus caldophilus GK24 has been analyzed to construct the genomic map. The genomic DNAs encapsulated in agarose gel were digested with SspI, EcoRI, SpeI, and HpaI restriction endonucleases, and then the resulting genomic DNA fragments were analyzed by pulsed-field gel electrophoresis. Its restriction map has been constructed by analyzing sizes of the restriction fragments obtained from both complete and partial digestions. The circular form of its genome was composed of about 1.98 Mbp and a megaplasmid. The genomic loci for the genes of xylose isomerase, thioredoxin, tRNA-16S rRNA, 23S rRNA, L5 ribosomal protein, ADP-glucose pyrophosphorylase, DNA-ligase, and Tca DNA polymerase were determined by both Southern hybridization and PCR.

• Journal of Microbiology and Biotechnology
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• v.30 no.8
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• pp.1195-1206
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• 2020

Beringraja pulchra, Cham-hong-eo in Korean, is a mottled skate which is belonging to the cartilaginous fish. Although this species is economically valuable in South Korea as an alkaline-fermented food, there are few microbial studies on such fermentation. Here, we analyzed microbial changes and pH before, during, and after fermentation and examined the effect of inoculation by a skin microbiota mixture on the skate fermentation (control vs. treatment). To analyze microbial community, the V4 regions of bacterial 16S rRNA genes from the skates were amplified, sequenced and analyzed. During the skate fermentation, pH and total number of marine bacteria increased in both groups, while microbial diversity decreased after fermentation. Pseudomonas, which was predominant in the initial skate, declined by fermentation (Day 0: 11.39 ± 5.52%; Day 20: 0.61 ± 0.9%), while the abundance of Pseudoalteromonas increased dramatically (Day 0: 1.42 ± 0.41%; Day 20: 64.92 ± 24.15%). From our co-occurrence analysis, the Pseudoalteromonas was positively correlated with Aerococcaceae (r = 0.638) and Moraxella (r = 0.474), which also increased with fermentation, and negatively correlated with Pseudomonas (r = -0.847) during fermentation. There are no critically significant differences between control and treatment. These results revealed that the alkaline fermentation of skates dramatically changed the microbiota, but the initial inoculation by a skin microbiota mixture didn't show critical changes in the final microbial community. Our results extended understanding of microbial interactions and provided the new insights of microbial changes during alkaline fermentation.

• Korean Journal of Microbiology
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• v.26 no.4
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• pp.305-311
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• 1988

The spectinomycin resistant strain of slow growing R. japonicum R-168 was selected to be participated in conjugation with E. coli WA803/pGS9. Tn5 was introduced from suicide vector pGS9 into R. japonicum R-168 $spr^{r}$ chromosome at the frequency of $1.0\times 10^{-5}-5.0\times 10^{-7}$ and the transconjugante were selected on the yeast extract-mannitol plate containing kanamycin ($50{\mu}$g/ml) and spectinomycin ($100{\mu}$g/ml) after 8-9 days incubation. All transconjugants we tested were found to contain Tn 5 DNA on their genome, which was confirmed by Southern hybridization experiments. R. japonicum RNa75, which had been selected through plant test, was found to be defective in symbiotic nitrogen fixing ability and the production of leghemoglobin in soybean nodules formed by the inoculation of this mutant. In addition, this mutant strain hardly developed nitrogenase activity asymbiotically in contrast with the wild type strain, indicating that some nitrogen fixing gene might be blocked in this strain and the production of leghemoglobin could be decreased by the interference in nitrogen fixing genes.

• Journal of Animal Science and Technology
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• v.46 no.6
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• pp.917-924
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• 2004

Using PCR-RFLP haplotyping for the mitochondrial DNA(mtDNA) fragment containing the NADH dehydrogenase 2 gene(ND2) and three tRNA genes(tRNA-Met, tRNA-Trp and tRNA-Ala), we characterized the genetic diversity of five pig breeds including Jeju native pigs. mtDNA polymorphisms showing distinct cleavage patterns were found in the pig breeds. Two digestion patterns were detected when HaeIII- and Hinfl-RFLP, and four in the Tsp5091-RFLP analyses. Combining the three restriction enzyme digestion patterns found in five different pig breeds, four mtDNA haplotypes were observed and the haplotype frequencies were significantly different by the pig breeds. A monomorphic haplotype, mtWB, was observed in both Korean wild boars and Large White pigs. Both Duroc and Landrace pigs contained two haplotypes suggesting their multiple maternal lineages. Jeju native pig has two haplotypes(mtJN and mtJD). Of these, mtJN is identified as a Jeju native pig specific haplotype. This study suggested that more than two progenitor populations have been taken part in the domestication process of the Jeju native pig population, and/or probably subsequent crossing with other pig breeds from near east Asia. Unlike with our prediction, there was no direct evidence under molecular levels on the maternal introgression of Korean wild boar in the domestication of Jeju native pigs. In conclusion, specificity of mtDNA haplotypes related to pig breeds win be useful for identifying the maternal lineage as wen as constructing the genealogical pedigree in pigs.

• Asian-Australasian Journal of Animal Sciences
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• v.30 no.8
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• pp.1198-1205
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• 2017

Objective: An experiment was conducted to isolate and identify new methanogens in Korea from an anaerobic digester that uses pig slurry. Methods: An anaerobic digestate sample was collected from an anaerobic digester using pig slurry. Pre-reduced media were used for the growth and isolation of methanogens. Growth temperature range, pH range, NaCl concentration range, substrate utilization, and antibiotic tolerance were investigated to determine the physiological characteristics of isolated methanogens. The isolates were also examined microscopically for their morphology and Gram-stained. Polymerase chain reaction of 16S rRNA and mcrA gene-based amplicons was used for identification purpose. Results: Four strains, designated KOR-3, -4, -5, and -6, were isolated and were non-motile, irregular coccoid, and 0.5 to $1.5{\mu}m$ in diameter. Moreover, the cell walls of isolated strains were Gram-negative. KOR-3 and KOR-4 strains used acetate for methane production but did not use $H_2+CO_2$, formate, or methanol as a growth substrate KOR-5 and KOR-6 strains utilized acetate, methanol, and trimethylamine for methanogenesis but did not use $H_2+CO_2$ or formate as a growth substrate. The optimum temperature and pH for growth of four strains were $39^{\circ}C$ and 6.8 to 7.2, respectively. The optimum concentration of NaCl for growth of KOR-3, KOR-5, and KOR-6 were 1.0% (w/v). The optimum NaCl concentration for KOR-4 was 0.5% (w/v). All of the strains tolerated ampicillin, penicillin G, kanamycin, streptomycin, and tetracycline; however, chloramphenicol inhibited cell growth. Phylogenetic analysis of 16S rRNA and mcrA genes demonstrated that strains KOR-3, -4, -5, and -6 are related to Methanosarcina mazei (M. mazei, 99% sequence similarity). Conclusion: On the basis of physiological and phylogenetic characteristics, strains KOR-3, -4, -5, and -6 are proposed to be new strains within the genus Methanosarcina, named M. mazei KOR-3, -4, -5, and -6.

• Tuberculosis and Respiratory Diseases
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• v.67 no.5
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• pp.413-421
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• 2009

Background: MicroRNAs (miRNAs) play an important role in the regulation of cell proliferation, apoptosis, development and differentiation. Several studies have shown that aberrant expression of miRNAs is involved in cancer development and progression by regulating the expression of proto-oncogenes or tumor suppressor genes. In this study, we investigated miRNA expression profiles in Korean patients with non-small cell lung cancer (NSCLC). Methods: We performed miRNA microarray analysis containing 60~65 bp oligonucleotide probes representing human 318 miRNAs and validated the results of the microarray with Northern blot analysis or quantitative RT-PCR. Next, we examined the correlation between miRNA expression and the target gene transcriptional profile using a human whole-genome-expression microarray. Results: We showed that 35 miRNAs were expressed differentially in the NSCLCs and corresponding non-malignant lung tissues. We showed that 35 miRNAs were expressed differentially in the NSCLCs and corresponding nonmalignant lung tissues. Thirteen of the 35 differentially expressed miRNAs were newly identified in the present study. Of the 35 miRNAs, 2 (miR-371 and miR-210) were over-expressed in lung cancers, and 33 miRNAs, including miR-145, were under-expressed in lung cancers. miR-99b expression consistently showed a negative correlation with FGFR3 expression. Conclusion: Albeit a small number of patients were examined, these results suggest that miRNA expression profiles in Korean lung cancers may be somewhat different from the expression profiles reported on lung cancers in Western populations. The findings suggest that miR-99b might be a tumor suppressor through its up-regulation of FGFR3.

• Korean Journal of Microbiology
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• v.22 no.4
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• pp.235-242
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• 1984

Sep gene, which is one of the cell division genes coding for penicillin binding protein 3 was subcloned from ${\lambda}607sep^{+2}$ to plasmid pBR322. which has a strong promotor such as lac UV5(lacP). It was confirmed that the sep gene cloned to pLJ3 was in the proper orientation for expressionfrom lactose promotor. To analyze the expression efficiency of sep gene within the plasmids newly constructed, sep mRNA was assated by using ${\lambda$\mid$\;607sep^{+2}$ DNA as a probe. Sep mRNA level was increased 25 times in the cells carrying sep gene cloned to pBR322 compared to E. coli C600 which has wild type sep gene within the chromosome instead of plasmed. Furthermore, the cells carrying sep gene cloned to pLJ3 derected the synthesis of about 50 times as much sep mRNA as did cells carrying sep gene cloned to pBR 322, representing that the sep gene was successfully cloned to pLJ3.

• Journal of Microbiology and Biotechnology
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• v.18 no.1
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• pp.5-14
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• 2008

The deep subseafloor rock in oil reservoirs represents a unique environment in which a high oil contamination and a very low biomass can be observed. Sampling this environment has been a challenge owing to the techniques used for drilling and coring. In this study, the facilities developed by the Brazilian oil company PETROBRAS for accessing deep subsurface oil reservoirs were used to obtain rock samples at 2,822-2,828 m below the ocean floor surface from a virgin field located in the Atlantic Ocean, Rio de Janeiro. To address the bacterial diversity of these rock samples, PCR amplicons were obtained using the DNA from four core sections and universal primers for 16S rRNA and for APS reductase (aps) genes. Clone libraries were generated from these PCR fragments and 87 clones were sequenced. The phylogenetic analyses of the 16S rDNA clone libraries showed a wide distribution of types in the domain bacteria in the four core samples, and the majority of the clones were identified as belonging to Betaproteobacteria. The sulfate-reducing bacteria community could only be amplified by PCR in one sample, and all clones were identified as belonging to Gammaproteobacteria. For the first time, the bacterial community was assessed in such a deep subsurface environment.

• The Plant Pathology Journal
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• v.32 no.6
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• pp.584-588
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• 2016

Several Bacillus species were isolated from rice field soils, and 16S rRNA gene sequence analysis showed that Bacillus cereus was the most abundant. A strain named BC1 showed antifungal activity against Rhizoctonia solani. Bacteriophages infecting strain BC1 were isolated from the same soil sample. The isolated phage PK16 had an icosahedral head of $100{\pm}5nm$ and tail of $200{\pm}5nm$, indicating that it belonged to the family Myoviridae. Analysis of the complete linear dsDNA genome revealed a 158,127-bp genome with G + C content of 39.9% comprising 235 open reading frames as well as 19 tRNA genes (including 1 pseudogene). Blastp analysis showed that the proteins encoded by the PK16 genome had the closest hits to proteins of seven different bacteriophages. A neighbor-joining phylogenetic tree based on the major capsid protein showed a robust clustering of phage PK16 with phage JBP901 and BCP8-2 isolated from Korean fermented food.

• Parasites, Hosts and Diseases
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• v.54 no.1
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• pp.87-91
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• 2016

Deer serve as reservoirs of tick-borne pathogens that impact on medical and veterinary health worldwide. In the Republic of Korea, the population of Korean water deer (KWD, Hydropotes inermis argyropus) has greatly increased from 1982 to 2011, in part, as a result of reforestation programs established following the Korean War when much of the land was barren of trees. Eighty seven Haemaphysalis flava, 228 Haemaphysalis longicornis, 8 Ixodes nipponensis, and 40 Ixodes persulcatus (21 larvae, 114 nymphs, and 228 adults) were collected from 27 out of 70 KWD. A total of 89/363 ticks (266 pools, 24.5% minimum infection rate) and 5 (1.4%) fed ticks were positive for Anaplasma phagocytophilum using nested PCR targeting the 16S rRNA and groEL genes, respectively. The 16S rRNA gene fragment sequences of 88/89 (98.9%) of positive samples for A. phagocytophilum corresponded to previously described gene sequences from KWD spleen tissues. The 16S rRNA gene fragment sequences of 20/363 (5.5%) of the ticks were positive for A. bovis and were identical to previously reported sequences. Using the ITS specific nested PCR, 11/363 (3.0%) of the ticks were positive for Bartonella spp. This is the first report of Anaplasma and Bartonella spp. detected in ticks collected from KWD, suggesting that ticks are vectors of Anaplasma and Bartonella spp. between reservoir hosts in natural surroundings.