• The Plant Pathology Journal
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• v.20 no.4
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• pp.283-288
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• 2004

Four Erwinia carotovora strains isolated from potatoes showing blackleg symptoms and rotted Chinese cabbage were analysed by biochemical tests and sequence analysis of 16S rDNA and 16S-23S rRNA intergenic spacer (IGS) regions, and the data were compared to related E. carotovora strains. Based on the results of the biochemical tests and sequence analysis, 2 of the 4 strains were identified as E. carotovora subsp. carotovora (Ecc), whereas the rest strains were distinct from Ecc. The last two strains, HCC3 and JEJU, were biochemically similar to E, carotovora subsp. atroseptica (Eca). However, the results of sequence analysis and Eca-specific PCR assays showed that the strains were distinct from Eca. On the basis of 16S rDNA sequence analysis, HCC3 and JEJU strains were placed in E. carotovora subsp. odorifera and E. carotovora subsp. wasabiae, respectively. The results of sequence analysis and specific PCR assay for Eca indicated that Asian Eca strains were distinct from European Eca strains, although they were phenotycally homogeneous.

• Journal of Life Science
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• v.19 no.2
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• pp.277-283
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• 2009

Biogenic amines are generally formed through the decarboxylation of specific free amino acids by exogenous decarboxylases released by microbial species associated with the fish products and fermented feeds. This study was conducted to investigate the properties of e tuna waste regarding the control of degradation of biogenic amines (histamine, tyramine, tryptamine, putrescine, and cadaverine) that might be related with the anti-nutritional factor of the tuna waste that is used for manufacturing domestic fish meal. The values of pH and the salt content were 6.51, 3.35% in tuna waste and 5.58 and 5.83% in tuna fish meal, respectively. The strains and dominant bacteria tested in the tuna waste sample were 9.20, 9.29, 5.67, 7.82 and 7.58 log CFU/g of total bacteria, aerobic plate count (APC), total coliform (TC), Lactobacillus spp. and Bacillus spp., respectively. The main histamine forming-bacteria (HFB) in tuna waste were detected by silica gel thin-layer chromatography (TLC) and 7 histamine-forming bacterial species were isolated among microbes grown in selective medium. The histamine concentration was determined by detection of fluorescence of ο-phthaldialdehyde (OPA) derivatives using HPLC and the date were used to reconfirm the identities of the amine-producing bacteria. The 15 histamine- forming bacteria strains grown in trypicase soy broth (TSB) supplemented with 1% L-histidine (TSBH) were identified as Lactococcus(L.) lactis subsp. lactis, Klebsiella pneummonlae, L. garvieae 36, Vibrio olivaceus, Hafnia alvei and L. garvieae which were main dominant amine - producing strains, and Morganella morganii identified by 16S ribosomal RNA (rRNA) sequencing with PCR amplification. A Phylogenetic tree generated from the 16S rRNA sequencing data showed different phyletic lines that could be readily classified as biogenic amine forming gram-positive and negative bacteria.

• Journal of Animal Science and Technology
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• v.46 no.6
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• pp.937-946
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• 2004

Duroc is widely used to improve the meat quality and productivity. To elucidate the phylogenetic relation and the sequence specificity for the maternal property, the complete sequence of mitochondrial genome was determined and the population diversity of Duroc was investigated in this study. The length of mtDNA tested is 16,584-bp. There are several insertion/deletion mutations in the control region and coding regions for tRNA and rRNA, respectively, but not in peptide-coding regions. Four peptide-coding genes(COⅡ, COⅢ, ND3 and ND4) showed incomplete termination codon sequences such as T--, and two(ND2 and ND4L) did alternative initiation codons(AIC), respectively. Especially, the initiation codon sequences of ND2 gene were polymorphic in this population. Polymorphisms were detected in 11-bp duplication motif within control region as well as ND2 and CYTB. Variation patterns observed from the tests on three mtDNA regions were linked completely and then two haplotypes obtained from combining the data dividing this population. Duroc mtDNA is observed at the European pig cluster in the phylogenetic tree, however, the results from the population analyses supported previous opinions. This study suggests that the breed Duroc was mainly originated from the European pig lineage, and Asian lineage was also used to form the pig breed Duroc as maternal progenitors.

• Journal of Food Hygiene and Safety
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• v.28 no.2
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• pp.188-193
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• 2013

Anatoxin-a, saxitoxin and neosaxitoxin are produced by Aphanizomenon flos-aquae that is a sort of the cyanobacteria phylum. Therefore, it is not permitted for food materials in Korea. Traditionally, the classification of cyanobacteria has been based on morphological characters such as trichome width, cell size, division planes, shape, and the presence of character such as gas vacuole. But, some diagnostic features, such as gas vacuole or akinetes, can show variation with different environmental or growth conditions and even be lost during cultivation. Therefore, we developed detection method for functional foods containing Aph. flos-aquae by PCR. To design the primer, 16S rRNA region of Aph. flos-aquae, Spirulina laxissima, and Spirulina spp. registered in the GeneBank (www.ncbi.nlm.nih.gov) have been used and for comparative analysis, BioEdit ver. 7.0.9.0. was used. As a result, we was design AFA-F1/AFA-R1 (363 bp) primer for the differentiation Aph. flos-aquae from chlorella, spirulina, green tea, and spinach. Also, it could be distinguished chlorella and spirulina products those are made to contain 1% Aph. flos-aquae.

• Korean Journal of Microbiology
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• v.54 no.4
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• pp.428-435
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• 2018

In this study, we isolated and identified bacteria from freshwater and soil collected from Osang reservoir, to screen antimicrobial bacteria against various pathogenic bacteria. 38 strains were isolated and assigned to the class Proteobacteria (22 strains), Actinobacteria (7 strains), Bacteroidets (6 strains), and Firmicutes (3 strains) based on 16S rRNA gene sequence analysis. Among them, strain OS17 showed a good growth inhibition against 5 methicillin-resistant Staphylococcus aureus subsp. aureus strains and Bacillus cereus, Bacillus subtilis, Filobasidium neoformans. As a result of the 16S rRNA gene sequence analysis, strain OS17 show the high similarity with Burkholderia ambifaria $AMMD^T$, B. diffusa $AM747629^T$, B. tettitorii $LK023503^T$ 99.8%, 99.7%, 99.6%, respectively. We investigated cell growth and antimicrobial activity according to commercial culture medium, temperature, pH for culture optimization of strain OS17. Optimal conditions for growth and antimicrobial activity in strain OS17 were found to be: YPD medium, $35^{\circ}C$ and pH 6.5. When the strain was cultured in LB, NB, TSB, R2A media at $20^{\circ}C$ and $25^{\circ}C$, the antimicrobial activity did not show. Culture filtrate of strain OS17 showed antimicrobial activity against 5 MRSA strains, Bacillus cereus, Bacillus subtilis, and Filobasidium neoformans with inhibition zones from 2 to 8 mm. Optimal reaction time was 48 h in YPD medium, 100 rpm and 0.3 vvm in 2 L-scale fed-batch fermentation process for antimicrobial activity. Culture optimization of strain OS17 can be improved on antimicrobial activity. Therefore, the antimicrobial activity of Burkholderia sp. OS17 had potential as antibiotics for pathogens including MRSA.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.5
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• pp.1839-1843
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• 2015

Background: MicroRNAs are a class of noncoding RNAs which regulate multiple cellular processes during tumor development. The purpose of this report is to investigate the clinicopathological and prognostic significance of miR-218 in human gliomas. Materials and Methods: Quantitative RT-PCR (qRT-PCR) was conducted to detect the expression of miR-218 in primary normal human astrocytes, three glioma cell lines and 98 paired glioma and adjacent normal brain tissues.Associations of miR-218 with clinicopathological variables of glioma patients were statistically analyzed. Finally, a survival analysis was performed using the Kaplan-Meier method and Cox's proportional hazards model. Results: The expression level of miR-218 in primary normal human astrocytes was significantly higher than that in glioma cell lines (p<0.01). Also, the expression level of miR-218 in glioma tissues was significantly downregulated in comparison with that in the adjacent normal brain tissues (p<0.001). Statistical analyses demonstrated that low miR-218 expression was closely associated with advanced WHO grade (p=0.002) and low Karnofsky performance score (p=0.010) of glioma patients. Kaplan-Meier analysis with the log-rank test showed that patients with low-miR-218 expression had poorer disease-free survival and overall survival (p=0.0045 and 0.0124, respectively). Multivariate analysis revealed that miR-218 expression was independently associated with the disease-free survival (p=0.009) and overall survival (p=0.004) of glioma patients. Conclusions: Our results indicate that miR-218 is downregulated in gliomas and that its status might be a potential valuable biomarker for glioma patients.

• Asian-Australasian Journal of Animal Sciences
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• v.29 no.9
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• pp.1345-1352
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• 2016

The hindgut of horses is an anaerobic fermentative chamber for a complex and dynamic microbial population, which plays a critical role in health and energy requirements. Research on the gut microbiota of Mongolian horses has not been reported until now as far as we know. Mongolian horse is a major local breed in China. We performed high-throughput sequencing of the 16S rRNA genes V4 hypervariable regions from gut fecal material to characterize the gut microbiota of Mongolian horses and compare them to the microbiota in Thoroughbred horses. Fourteen Mongolian and 19 Thoroughbred horses were used in the study. A total of 593,678 sequence reads were obtained from 33 samples analyzed, which were found to belong to 16 phyla and 75 genera. The bacterial community compositions were similar for the two breeds. Firmicutes (56% in Mongolian horses and 53% in Thoroughbred horses) and Bacteroidetes (33% and 32% respectively) were the most abundant and predominant phyla followed by Spirochaete, Verrucomicrobia, Proteobacteria, and Fibrobacteres. Of these 16 phyla, five (Synergistetes, Planctomycetes, Proteobacteria, TM7, and Chloroflexi) were significantly different (p<0.05) between the two breeds. At the genus level, Treponema was the most abundant genus (43% in Mongolian horses vs 29% in Thoroughbred horses), followed by Ruminococcus, Roseburia, Pseudobutyrivibrio, and Anaeroplasma, which were detected in higher distribution proportion in Mongolian horses than in Thoroughbred horses. In contrast, Oscillibacter, Fibrobacter, Methanocorpusculum, and Succinivibrio levels were lower in Mongolian horses. Among 75 genera, 30 genera were significantly different (p<0.05) between the two breeds. We found that the environment was one of very important factors that influenced horse gut microbiota. These findings provide novel information about the gut microbiota of Mongolian horses and a foundation for future investigations of gut bacterial factors that may influence the development and progression of gastrointestinal disease in horses.

• Korean Journal of Environmental Biology
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• v.29 no.3
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• pp.126-137
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• 2011

Although Sumunmulbangdui wetland at the Halla Mountain in Jeju Island, a kind of montane wetlands, has been considered to bear high biodiversity, no study has been reported on the bacterial diversity. In this study, soil and water samples were collected from the wetland in order to isolate novel bacterial species. Bacterial strains belonging to the phyla Bacteroidetes, Firmicutes, and Actinobacteria were isolated after spreading soil and water samples onto solid agar media. The 16S rRNA gene sequences of the strains assigned to the three phyla were compared to those of type strains of the species in the phyla. The strains that showed less than 98.7% 16S rRNA gene sequence similarity to the validly published species were considered to be novel species candidates. A total of 32 strains were regarded as novel species candidates in the phyla Bacteroidetes, Firmicutes, and Actinobacteria. Diversity of novel species candidates was very low; the candidates were confined to only few genera. In the Bacteroidetes, 13 novel candidate species were affiliated with the genera Mucilaginibacter, Sphingobacterium, Pedobacter, Flavobacterium, and Chryseobacterium. A total of 13 novel candidate species that assigned to the genera Paenibacillus Lysinibacillus, and Bacillus were identified in the phylum Firmicutes. Only two candidate species that belonged to the genera Mycobacterium and Nocardia were excavated in the Actinobacteria. Cultural, physiological, and chemotaxonomic characteristics have been determined for the novel species candidates, and the characteristics are described in this study.

• Korean Journal of Ecology and Environment
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• v.50 no.1
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• pp.137-147
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• 2017

The identity of toxin producers remains only hypothesis unless there were identified by strain isolation and analytical confirmation of both the cyanotoxin production and the genetic identity of the monoculture. The purposes of this study were to identify a morphologic and phylogenetic classification in Aphanizomenon flos-aquae strains isolated from the Nakdong River and to investigate the potential ability of the strains to produce toxins such as saxitoxin and cylindrospermopsin using target genes. The 16S rRNA and sxtA, sxtI, cyrA, cyrJ genes were analyzed on two strains (DGUC001, DGUC003) isolated from the Nakdong River. Morphological features of the strains were observed a shape of aggregated trichomes in parallel fascicles which can reach up to macroscopic size and a hyaline terminal cell without aerotope. In addition, the 16S rRNA phylogenetic analyses showed that the strains were identified as the same species with high genetic similarity of 98.4% and grouped within a monospecific andsupported cluster I of Aphanizomenon flos-aquae selected from GenBank of the NCBI. The cyrA and cyrJ genes encoding for the cylindrospermopsin-biosynthesis were not detected in the present study. The sxtA gene was in detected both the two strains, whereas the sxtI gene which had been suggested as a suitable molecular marker to detect saxitoxin-producing cyanobacteria was not found both the strains. Thus, the two strains isolated from Nakdong River were identified as the same species of Aphanizomenon flos-aquae Ralfs ex Bornet et Flahault 1888, the two strains were confirmed as potential non-producing strains of the saxitoxin and cylindrospermopsin.

• Journal of Oriental Neuropsychiatry
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• v.16 no.1
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• pp.81-96
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• 2005

This experiment was designed to investigate the effect of Dichroa febrifuga(DIF) on the Alzheimer’s disease. The effects of DIF extract on $IL-1{\beta}$, IL-6, $TNF-{\alpha}$ mRNA of THP-1 cell treated by $A{\beta}$ plus LPS and amyloid precursor proteins(APP), acetylcholinesterase(AChE), glial fibrillary acidic protein(GFAP) mRNA of PC-12 cell treated by $A{\beta}$ plus $rIL-1{\beta}$ and AChE activity of PC-12 cell lysate treated by $A{\beta}$ plus $rIL-1{\beta}$ and behavior of memory deficit mice induced by scopolamine and mice glucose, uric acid, AChE activity of memory deficit rats induced by scopolamine were investigated, respectively. The results were summarized as follows ; 1. DIF extract suppressed APP, AChE, GFAP mRNA in PC-12 cell treated by $A{\beta}$. 2. DIF extract suppressed $IL-1{\beta}$, IL-6, $TNF-{\alpha}$ mRNA in THP-1 cell treated by LPS. 3. DIF extract suppressed AChE activity in cell lysate of PC-12 cell treated by $A{\beta}$. 4. DIF extract increased glucose, decreased uric acid and AChE significantly in the serum of the memory deficit rats induced by scopolamine. 5. DIF extract group showed significantly inhibitory effect on the memory deficit of mice induced by scopolamine in the experiment of Morris water maze. According to the above results, it is suggested that DIF extract might be usefully applied for prevention and treatment of Alzheimer’s disease and memory deficit.