• Journal of Gastric Cancer
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• 제16권4호
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• pp.221-229
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• 2016

Purpose: Dysregulated microRNAs (miRNAs) can contribute to cancer development by leading to abnormal proliferation of cells, apoptosis, and differentiation. Although several miRNAs that are related to gastric cancer have been identified, the reported results have been inconsistent. The aim of this study was to determine miRNA expression profiles and validate miRNAs up- and down-regulated in gastric cancer. Materials and Methods: We evaluated 34 primary gastric cancer tissues and paired adjacent nontumorous gastric tissues. Total RNA was extracted, and low-molecular-weight RNAs (<200 nucleotides) were isolated for further analysis. Two pairs of tissues were processed for GeneChip microarray analysis, and the identified up- and down-regulated miRNAs were validated by real-time quantitative polymerase chain reaction (qPCR). Results: In the set of differentially expressed miRNAs, 5 were overexpressed by more than 2 fold, and 5 were reduced by 2 fold or less in gastric cancer tissues compared with normal gastric tissues. Four of these miRNAs (miR-196b-5p, miR-375, miR-483-5p, and miR-486-5p) were then validated by qPCR, and the relative expression levels of 2 miRNAs (miR-196b-5p and miR-375) were significantly different between cancer and normal tissues. Conclusions: Our results revealed that the expression of miR-196b-5p and miR-375 significantly correlates with gastric cancer. These miRNAs could therefore serve as diagnostic biomarkers of gastric cancer.

• Fisheries and Aquatic Sciences
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• 제12권3호
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• pp.171-178
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• 2009

The Perciformes include approximately 40% of all bony fishes and are the largest order of vertebrates. This order includes some of the most economically relevant marine fishes, particularly the red seabream, black seabream and rock bream. A 409 bp fragment of the cytochrome b (cyt b) gene and 403 bp and 518 bp fragments of ribosomal RNA (12S and 16S rRNA, respectively) were sequenced from five populations of natural and cultured red seabreams, natural black seabream, and natural and cultured rock breams. The mitochondrial DNA sequences were utilized for the genetic identification and population structural analyses of these three species. Phylogenetic relationships of intra- and inter-species were elucidated using three types of molecular genetic markers from three species of the order Perciformes in Korea. We noted no significant differences in the intra-specific variation of the cyt b and rRNA genes in each population however, inter-specific divergences were greater than intra-specific variation. Inter-specific variation was induced more by transition than transversion type in the cyt b and rRNA genes. The cyt b gene and rRNA genes make it possible to determine the inter-species divergence. The rRNA genes have more conserved sequences than the cyt b gene. Therefore, these genes are expected to prove useful among species belonging to the different genera or families.

• 미생물학회지
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• 제34권3호
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• pp.132-136
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• 1998

자연환경의 미생물군집을 분자생태학적 방법으로 분석하기 위해서는 오염되지 않은 순수한 핵산의 분리가 필요하다. 해양퇴적물에서 핵산을 추출할 때 같이 추출되는 부식물질(humic substances)은 핵산중폭반응을 저해하기 때문에, 이를 제거하기 위한 네 가지의 방법, 아가로즈젤 전기영동후 용출, Sephadex G-75 젤, Hydroxyapatite 젤, 그리고 PVPP(poluvinylpolypyrrolidone) microspin column 방법에 대해 그 효율성을 비교하였다. 조산된 방법 중에서 PVPP microspin column을 이용하면 건조 퇴적물 1g당 $4.8{\mu}g$의 순수한 DNA를 신속하고 간편하게 얻을 수 있었고, 이 방법으로 분리된 DNA를 PCR의 주형으로 사용한 결과 16S rRNA 유전자의 거의 전 범위에 해당하는 1.5 kb 크기의 PCR 산물을 얻을 수 있었다.

• 한국식품저장유통학회지
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• 제17권2호
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• pp.301-306
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• 2010

본 연구에서는 계육 창상부위의 원인이 되는 세균을 동정하였다. 계육의 등과 다리 창상 부위로부터 무작위 선별법을 통해 총 10주의 균주를 분리하였다. 순수 분리 배양된 균주의 세포막 지방산 조성 분석 결과, 5 균주가 높은 유효성을 지녔으며, Shigella sonnei, Proteus mirabilis, Escherichia coli로 동정되었다. 또한 16S rRNA sequence를 실시한 결과, 동정된 균주는 Shigella sonnei(99%), Proteus mirabilis(99%) 그리고 Escherichia coli(99%)와 높은 염기서열 상동성을 나타냈다. 따라서 본 연구에서 조사된 계육의 등과 다리 부위 주요 창상 원인균은 Shigella sonnei, Proteus mirabilis, Escherichia coli인 것으로 밝혀졌다.

• Journal of Periodontal and Implant Science
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• 제34권2호
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• pp.255-268
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• 2004

The purpose of the research is to compare the distribution of Black-pigmented Bacteroides between Chronic Periodontitis and Aggressive Periodontitis. P. gingivalis, P. intermedia and P. nigrescens were examined in order to evaluate their distribution in patients with Chronic Periodontitis(CP) and Aggressive Periodontitis(AP). PCR and dot-blots hybridization of 16s rRNA gene were used to compare bacterial distribution of two groups - CP group and AP group, which were divided into two subgroups. Subgingival plaque taken from the diseased sites(pocket $depth{\geq}6$ mm) and healthy sites(pocket $depth{\leq}3$ mm) were grouped into the experimental group and the control group. The result are as follows ; 1. The distribution of P. gingivalis was 98.33% for chronic Periodotitis(CP), 94.17% for Aggressive Periodontitis(AP), the distribution of P. intermedia was 77.50% for CP, 64.17% for AP, and the distribution of P. nigrescens was 35.00%, 29.17%. In all 3 types of bacteria, CP group showed higher distribution compared to AP group, but only P. intermedia showed statistically significant difference. 2. In the case of CP, every type of bacteria showed higher distribution in the experimental group with statistically significant difference. 3. In the case of AP, every type of bacteria also showed higher distribution in the experimental group, but P. gingivalis and p..intermedia showed the result with statistically significant difference, and the other did not 4. In 3 all bacteria type, N-AP showed higher distribution than N-CP without statistically significant difference These results suggest that the comparison of the distribution of Bacteroides between Chronic Periodontitis and Aggressive Periodontitis has no statistically significant difference, except P. intermedia.

• 미생물학회지
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• 제50권1호
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• pp.67-72
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• 2014

담배식물과 담배재배 토양으로부터 최소배지에 유일 탄소원으로 니코틴을 첨가한 배지(MB/N)를 이용하여 니코틴을 분해하는 새로운 균주의 분리를 시도하였다. 16S rRNA 유전자의 염기서열 분석과 표현형 시험 및 형태학적 시험으로 분리균주들은 Micrococcaceae 과의 Arthrobacter 속에 포함되는 균주로 판명되었다. NU15는 Arthrobacter nicotinovorans와 99.8%의 상동성을 보였고, NU11는 Arthrobacter equi와 98.2%의 상동성을 보여 신주일 가능성이 있었다. 두 균주 모두 양성의 간구균이며, catalase 양성, oxidase 음성이었다. 신주일 가능성이 있는 NU11균주의 니코틴 분해를 확인하기 위하여 MB/N 액체배지에서 배양하면서 니코틴 특이적으로 나타내는 260 nm에서의 흡광도가 감소를 측정한 결과, 니코틴이 균주에 의해 특이적으로 분해되는 것을 확인 할 수 있었으며, 분해균들은 니코틴 오염을 복원하는데 사용될 수 있을 것으로 생각된다.

• Journal of Microbiology and Biotechnology
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• 제22권3호
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• pp.301-310
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• 2012

Prosopis juliflora and Parthenium hysterophorus are the two arid, exotic weeds of India that are characterized by distinct, profuse growth even in nutritionally poor soils and environmentally stressed conditions. Owing to the exceptional growth nature of these two plants, they are believed to harbor some novel bacterial communities with wide adaptability in their rhizosphere. Hence, in the present study, the bacterial communities associated with the rhizosphere of Prosopis and Parthenium were characterized by clonal 16S rRNA gene sequence analysis. The culturable microbial counts in the rhizosphere of these two plants were higher than bulk soils, possibly influenced by the root exudates of these two plants. The phylogenetic analysis of V1_V2 domains of the 16S rRNA gene indicated a wider range of bacterial communities present in the rhizosphere of these two plants than in bulk soils and the predominant genera included Acidobacteria, Gammaproteobacteria, and Bacteriodetes in the rhizosphere of Prosopis, and Acidobacteria, Betaproteobacteria, and Nitrospirae in the Parthenium rhizosphere. The diversity of bacterial communities was more pronounced in the Parthenium rhizosphere than in the Prosopis rhizosphere. This culture-independent bacterial analysis offered extensive possibilities of unraveling novel microbes in the rhizospheres of Prosopis and Parthenium with genes for diverse functions, which could be exploited for nutrient transformation and stress tolerance in cultivated crops.

• Journal of Species Research
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• 제8권2호
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• pp.176-190
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• 2019

A total of 38 bacterial strains within the classes Bacilli and Deinococci were isolated from various sources in Korea. Samples were collected from animal intestine, urine, soil, tidal flat mud, and kimchi. In the sequence comparison and phylogenetic analysis of 16S rRNA sequences, the 38 isolates were assigned to the classes Bacilli and Deinococci with sequence similarities more than 98.7%. Twenty-four strains and 13 strains were classified the order Bacillales and Lactobacillales in the class Bacilli, respectively. In the order Bacillales, there were nine species in the genus Bacillus, seven species in the genus Paenibacillus, and the remaining eight species in the genera Domibacillus, Halobacillus, Virgibacillus, Lysinibacillus, Paenisporosarcina, Planococcus, Savagea, and Staphylococcus. In the order Lactobacillales, there were four species in the genus Lactobacillus, three species in the genus Leuconostoc, three species in the genus Lactococcus, and the remaining three species in the genera Aerococcus, Enterococcus, and Streptococcus. One species was related to the genus Deinococcus of the order Deinococcales. Most of the isolated strains were Gram-stain-positive, but some were Gram-stain-variable or Gram-stain-negative. Cells were rod or cocci-shaped. Based on the results of 16S rRNA analysis, we report 38 strains as previously unrecorded species to Korea, and the basic characteristics of strains are described herein.

• Journal of Species Research
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• 제10권2호
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• pp.117-133
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• 2021

In 2019, 43 bacterial strains were isolated from food, soil, marine environments, human, and animals related sources from the Republic of Korea. Based on the analysis of 16S rRNA gene sequence, these isolates were allocated to the phyla Bacteroidetes and Firmicutes as unrecorded species in Korea. The 10 Bacteroidetes strains were classified into the families Bacteroidaceae, Chitinophagaceae, Cytophagaceae, Flavobacteriaceae, and Prolixibacteraceae (of the orders Bacteroidales, Chitinophagales, Cytophagales, Flavobacteriales, and Marinilabiliales, respectively). The 33 Firmicutes strains belonged to the families Bacillaceae, Paenibacillaceae, Planococcaceae, Staphylococcaceae, Clostridiaceae, Lachnospiraceae, Peptostreptococcaceae, Enterococcaceae, Lactobacillaceae, Leuconostocaceae, and Streptococcaceae (of the orders Bacillales, Clostridiales, and Lactobacillales). These unrecorded bacteria were determined based on taxonomic criterion (>98.7%; 16S rRNA gene sequence similarity). In addition, their phylogenetic affiliation, as well as cell and colony morphologies, staining reactions, and physiological and biochemical properties were investigated. Therefore, we report 43 isolates as unrecorded species, and described basic features, isolation source, and locations of these strains.

• Journal of Species Research
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• 제12권4호
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• pp.374-414
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• 2023

As part of a comprehensive investigation of indigenous prokaryotic species in Republic of Korea in 2022, 156 bacterial strains were isolated from diverse environmental habitats. These strains were assigned to six phyla, namely Acidobacteriota, Deinococcota, Actinomycetota, Bacillota, Bacteroidota, and Pseudomonadota. Each strain was identified based on 16S rRNA gene sequence similarity (>98.7%) and the formation of robust phylogenetic clades with their closest reported species. Among isolates, there is one species belonging to the phylum Acidobacteriota, one species belonging to the phylum Deinococcota, 28 species belonging to the phylum Actinomycetota, 19 species belonging to the phylum Bacillota, 19 species belonging to the phylum Bacteroidota, and 88 species belonging to the phylum Pseudomonadota (comprising 34 species of the class Alphaproteobacteria, 20 species of the class Betaproteobacteria, and 34 species of the class Gammaproteobacteria). Based on 16S rRNA gene sequence analysis, each strain was assigned to independent and predefined bacterial species. Since there were no published or official reports regarding these 156 isolates in Republic of Korea, they are reported as unrecorded species in Republic of Korea. The Gram stain, colony and cell morphology, basic biochemical characteristic, isolation source, and strain ID of each species are described in the species descriptions.