• Journal of Microbiology
• /
• v.42 no.1
• /
• pp.9-13
• /
• 2004

Culture-independent approaches, based on 16S rDNA sequences, are extensively used in modern microbial ecology. Sequencing of the clone library generated from environmental DNA has advantages over fingerprint-based methods, such as denaturing gradient gel electrophoresis, as it provides precise identification and quantification of the phylotypes present in samples. However, to date, no method exists for comparing multiple bacterial community structures using clone library sequences. In this study, an automated method to achieve this has been developed, by applying pair wise alignment, hierarchical clustering and principle component analysis. The method has been demonstrated to be successful in comparing samples from various environments. The program, named CommCluster, was written in JAVA, and is now freely available, at http://chunlab.snu.ac.kr/commcluster/.

• Journal of Applied Biological Chemistry
• /
• v.62 no.2
• /
• pp.195-202
• /
• 2019

Rhus javanica L. is Anacardiaceae plant distributed in East Asia. We evaluated the antioxidant activity and antiinflammatory effect of leaf, branch, root of ethyl acetate fraction from R. javanica. To confirm effective each extraction, The antioxidant activity was evaluated using 1,1-Diphenyl-2-picryl-hydrazyl and 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) scavenging activity assays, and the anti-inflammatory activity was evaluated based on inhibitory activities on the protein and mRNA expression of iNOS and COX-2 in LPS-induced RAW264.7 cells. The phenolic compounds content of each extract was analyzed with Folin reagents and HPLC/PDA method. The gallic acids were identified and quantified. The roots of R. javanica showed strong antioxidant activity. Its total phenolic compounds content were higher than the orders. In addition, anti-inflammatory activity inhibited the protein and mRNA expression of nitric oxide production factor, following the same pattern as contents of phenolic compounds included gallic acid and its antioxidant activity. In conclusion, R. javanica showed effective antioxidant and anti-inflammatory activity. Especially, the roots were evaluated to be highly valuable as a natural resource for reducing inflammation.

• ALGAE
• /
• v.38 no.2
• /
• pp.93-110
• /
• 2023

Progress in phylogenomic analysis has led to a considerable re-evaluation of former cyanobacterial system, with many new taxa being established at different nomenclatural levels. The family Geminocystaceae is among cyanobacterial taxa recently described on the basis of polyphasic approach. Within this family, there are six genera: Geminocystis, Cyanobacterium, Geminobacterium, Annamia, Picocyanobacterium, and Microcrocis. The genus Geminocystis previously encompassed two species: G. herdmanii and G. papuanica. Herein, a new species G. urbisnovae was proposed under the provision of the International Code of Nomenclature for algae, fungi, and plants (ICN). Polyphasic analysis was performed for five strains from the CALU culture collection (St. Petersburg State University, Russian Federation), and they were assigned to the genus Geminocystis in accordance with high 16S rRNA gene similarity to existing species, as well as because of proximity to these species on the phylogenetic trees reconstructed with RaxML and Bayes methods. Plausibility of their assignment to a separate species of the genus Geminocystis was substantiated with smaller cell size; stenohaline freshwater ecotype; capability to complementary chromatic adaptation of second type (CA2); distinct 16S rRNA gene clustering; sequences and folding of D1-D1' and B box domains of the 16S-23S internal transcribed spacer region. The second objective pursued by this communication was to provide a survey of the family Geminocystaceae. The overall assessment was that, despite attention of many researchers, this cyanobacterial family has been understudied and, especially in the case of the crucially important genus Cyanobacterium, taxonomically problematic.

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

• Korean Journal of Microbiology
• /
• v.38 no.4
• /
• pp.235-240
• /
• 2002

Protease producing bacterium, PB16 was isolated from food processing wastewater sludge and paddy field soil samples and selected by the clear zone and enzyme activity test. The isolate was gram negative, rod type and its protease productivity was 6.49 U/ml. As a result of API20NE kit test and 16S rDNA sequencying, the isolated PB16 was identified as Aeromonas hydrophila (99%). The growth rate ($h^{-1}$) was 0.21 in synthetic waste water only and 0.26 in synthetic waste water containing vitamin and mineral using a bioscreen C. Synthetic wastewater removal rate was 59 and 87%, respectively after 1 and 3 day reaction (intial CODcr was 2,472 mg/l).

• Journal of Microbiology and Biotechnology
• /
• v.23 no.2
• /
• pp.189-194
• /
• 2013

In a study of hydrogen-producing bacteria, strain T4384 was isolated from rice field samples in the Republic of Korea. The isolate was identified as Enterobacter sp. T4384 by phylogenetic analysis of 16S rRNA and rpoB gene sequences. Enterobacter sp. T4384 grew at a temperature range of $10-45^{\circ}C$ and at an initial pH range of 4.5-9.5. Strain T4384 produced hydrogen at 0-6% NaCl by using glucose, fructose, and mannose. In serum bottle cultures using a complete medium, Enterobacter sp. T4384 produced 1,098 ml/l $H_2$, 4.0 g/l ethanol, and 1.0 g/l acetic acid. In a pH-regulated jar fermenter culture with the biogas removed, 2,202 ml/l $H_2$, 6.2 g/l ethanol, and 1.0 g/l acetic acid were produced, and the lag-phase time was 4.8 h. Strain T4384 metabolized the hydrolysate of organic waste for the production of hydrogen and volatile fatty acid. The strain T4384 produced 947 ml/l $H_2$, 3.2 g/l ethanol, and 0.2 g/l acetic acid from 6% (w/v) food waste hydrolysate; 738 ml/l $H_2$, 4.2 g/l ethanol, and 0.8 g/l acetic acid from Miscanthus sinensis hydrolysate; and 805 ml/l $H_2$, 5.0 g/l ethanol, and 0.7 g/l acetic acid from Sorghum bicolor hydrolysate.

• Environmental Engineering Research
• /
• v.14 no.1
• /
• pp.19-25
• /
• 2009

In this study, total bacteria, enteric members of the $\gamma$-proteobacteria, and microbial communities in seawater were analyzed as indirect indicators for quantifying biofouling. Biomass in seawater can significantly affect feed water pretreatment and membrane biofouling of reverse osmosis desalination processes. The purpose of this paper is to investigate microbiological quantity and quality of seawater at the potential intake of a desalination plant. For this analysis, the total direct cell count (TDC) using 4'-6-diamidino-2-phenylindole (DAPI)-staining and DNA-based real-time PCR were used to quantify the total bacteria and relative content of enteric members of $\gamma$-proteobacteria in seawater, respectively. In addition, microbial communities were examined using 16S rRNA gene cloning and bacterial isolation to identify the most abundant bacteria for a further biofouling study. The experimental results of this study identified about $10^6$ cells/mL of (total) bacteria, $10^5$ 16S rRNA gene copies/mL of enteric $\gamma$-proteobacteria, and the presence of more than 20 groups of bacteria.

• Food Science of Animal Resources
• /
• v.28 no.3
• /
• pp.355-362
• /
• 2008

This study was carried out to assess the fermentation properties of lactic acid bacteria (LAB) isolated from bovine colostrum and effects of feeding fermented colostrum feed on the growth to piglet. A total of 427 colonies were isolated from bovine colostrum on the BCP plate count agar. These LAB isolated were subcultured in 10% reconstituted skim milk, and seven strain thereof were selected for their highest acid productions, and two strain thereof were finally selected for their excellent sugar utilization. These strains were identified as Streptococcus thermophilus and Streptococcus macedonicus based on l6S rDNA sequencing data, named S. thermophilus CNB-11 and S. macedonicus CNB-11 respectively. For fermentation profiles, sugar utilization, acid production and viable cell counts were excellent in S. thermophilus CNB-11 as compared with S. macedoniclts CNB-11 after 48 hour. The effect of feeding fermented colostrum feed 0.5% using S. thermophilus CNB-11 was investigated for growth rate, analysis of blood and incidence of diarrhea. 24 heads of piglets were divided into two groups: the experimental and the control of 12 animals each. The average growth rate in the pigs fed fermented colostrum feed was higher 16.73% compared with control diet (p<0.05). There were no differences in the concentrations of blood glucose, cholesterol, albumin and globulin in pigs fed fermented colostrum feed as compared with control piglets. Incidence of diarrhea was no in pigs fed fermented colostrum feed as compared with control piglets.

• Nutrition Research and Practice
• /
• v.13 no.4
• /
• pp.302-309
• /
• 2019

BACKGOURND/OBJECTIVES: Vascular inflammation is an important feature in the atherosclerotic process. Recent studies report that leaves and branches of Carpinus turczaninowii (C. turczaninowii) have antioxidant capacity and exert anti-inflammatory effects. However, no study has reported the regulatory effect of C. turczaninowii extract on the arterial inflammatory response. This study therefore investigated modulation of the arterial inflammatory response after exposure to C. turczaninowii extract, using human aortic vascular smooth muscle cells (HAoSMCs). MATERIALS/METHODS: Scavenging activity of free radicals, total phenolic content (TPC), cell viability, mRNA expressions, and secreted levels of cytokines were measured in LPS-stimulated (10 ng/mL) HAoSMCs treated with the C. turczaninowii extract. RESULTS: C. turczaninowii extract contains high amounts of TPC ($225.6{\pm}21.0mg$ of gallic acid equivalents/g of the extract), as well as exerts time-and dose-dependent increases in strongly scavenged free radicals (average $14.8{\pm}1.97{\mu}g/mL$ $IC_{50}$ at 40 min). Cell viabilities after exposure to the extracts (1 and $10{\mu}g/mL$) were similar to the viability of non-treated cells. Cytokine mRNA expressions were significantly suppressed by the extracts (1 and $10{\mu}g/mL$) at 6 hours (h) after exposure. Interleukin-6 secretion was dose-dependently suppressed 2 h after incubation with the extract, at $1-10{\mu}g/mL$ in non-stimulated cells, and at 5 and $10{\mu}g/mL$ in LPS-stimulated cells. Similar patterns were also observed at 24 h after incubation with the extract (at $1-10{\mu}g/mL$ in non-stimulated cells, and at $10{\mu}g/mL$ in the LPS-stimulated cells). Soluble intracellular vascular adhesion molecules (sICAM-1) secreted from non-stimulated cells and LPS-stimulated cells were similarly suppressed in a dose-dependent manner after 24 h exposure to the extracts, but not after 2 h. In addition, sICAM-1 concentration after 24 h treatment was positively related to IL-6 levels after 2 h and 24 h exposure (r = 0.418, P = 0.003, and r = 0.524, P < 0.001, respectively). CONCLUSIONS: This study demonstrates that C. turczaninowii modulates the arterial inflammatory response, and indicates the potential to be applied as a therapeutic use for atherosclerosis.

• Microbiology and Biotechnology Letters
• /
• v.43 no.4
• /
• pp.307-313
• /
• 2015

Unpolished rice (UR) is considered to be a healthy alternative to white rice when coping with chronic diseases. In the present study, the fermented slurry of unpolished rice (FSUR) was evaluated with respect to its antimicrobial activities and biochemical characteristics, including the quantities of sugar, total soluble sugar, organic acids, free amino acids, pH, and physiological activity. The antimicrobial efficiency of FSUR was assessed using the paper disc-agar diffusion method. FSUR exhibited strong antimicrobial activity against six pathogenic bacterial strains (Staphylococcus aureus, Escherichia coli, Listeria monocytogenes, Pseudomonas aeruginosa, Salmonella typhimurium, and Yersinia enterocolitica) and two fermentation strains (Gluconacetobacter intermedius and Lodderomyces elongisporus). The antimicrobial activity of FSUR was higher than the commercial antibiotics, carbenicillin ($50{\mu}g/ml$) and tetracycline ($50{\mu}g/ml$) against S. aureus, E. coli, L. monocytogenes, P. aeruginosa, S. typhimurium, Y. enterocolitica, and L. elongisporus. Also FSUR had a high antioxidant activity. The microorganisms were isolated from FSUR using tryptic soy broth and yeast extract-peptone-dextrose agar media. The isolated microorganisms were characterized using physiological and biochemical analyses as well as by 16S rRNA gene sequencing and phylogenic analysis. 16S rRNA gene sequence analysis showed that the isolated microorganisms had a high similarity to G. intermedius, Lactobacillus casei, Lactobacillus plantarum, and Acetobacter peroxydans.