• Korean Journal of Microbiology
• /
• 제46권4호
• /
• pp.366-374
• /
• 2010

Culture-dependent RFLP and culture-independent DGGE were employed to investigate the bacterial community associated with the marine sponge Spirastrella abata. A total of 164 bacterial strains associated with the sponge were cultivated using Zobell and Natural sea salt media. PCR amplicons of the 16S rDNA from the bacterial strains were digested with the restriction enzymes HaeIII and MspI, and then assigned into different groups according to their restriction patterns. The 16S rDNA sequences derived from RFLP patterns showed more than 95% similarities compared with known bacterial species, and the isolates belonged to four phyla, Proteobacteria (Alphaproteobacteria, Gammaproteobacteria), Actinobacteria, Firmicutes, and Bacteriodetes, of which Alphaproteobacteria was dominant. DGGE fingerprinting of 16S rDNAs amplified from the sponge- derived total gDNA showed five major DGGE bands, and their sequences showed more than 96% similarities compared with available sequences. The sequences derived from DGGE bands revealed high similarity with the uncultured bacterial clones. DGGE revealed that bacterial community consisted of four phyla, including Proteobacteria (Alphaproteobacteria, Gammaproteobacteria), Actinobacteria, Spirochetes, and Chloroflexi. Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria were commonly found in bacteria associated with S. abata by both RFLP and DGGE methods; however, overall bacterial community in the sponge differed depending on the analysis methods.

• The KIPS Transactions:PartB
• /
• 제12B권3호
• /
• pp.239-246
• /
• 2005

Biologist must have to do 2DGE biological experiment for Protein Search and Analysis. This experiment coming into being 2 dimensional image. 2DGE (2D Gel Electrophoresis : two dimensional gel electrophoresis) image is the most widely used method for isolating of the objective protein by comparative analysis of the protein spot pattern in the gel plane. The process of protein spot analysis, firstly segment protein spots that are spread in 2D gel plane by image processing and can find important protein spots through comparative analysis with protein pattern of contrast group. In the algorithm which detect protein spots, previous 2DGE image analysis is applies gaussian fitting, however recently Watersheds region based segmentation algorithm, which is based on morphological segmentation is applied. Watersheds has the benefit that segment rapidly needed field in big sized image, however has under-segmentation and over-segmentation of spot area when gray level is continuous. The drawback was somewhat solved by marker point institution, but needs the split and merge process. This paper introduces a novel marker search of protein spots by watersheds-based hierarchical threshold, which can resolve the problem of marker-driven watersheds.

• Journal of Life Science
• /
• 제22권8호
• /
• pp.1120-1125
• /
• 2012

Cirsium pendulum plants were collected from Hongcheon, Pyeongchang, Wonju, Yangyang in Kangwondo, Gapyeong in Gyeongkido, and Choongju in Choongcheongbukdo. Cirsium setidens plants were collected from Taebaek in Kangwondo and Bonghwa in Kyeongsangbukdo. Genomic DNA was prepared from those plants and used for the amplification of 18S rDNA, ITS1, 5.8S rDNA, ITS2, and part of 28S rDNA. The PCR products were sequenced, and the sequence was deposited in the GenBank. The comparison of those sequences has revealed that the rDNA sequences are identical for all six C. pendulum plants, but that the ITS1 and ITS2 sequences contain variable nucleotides. The two C. setidens plants had different nucleotides in 18S rDNA, ITS1, and ITS2. The comparison of the DNA sequences of C. pendulum and C. setidens collected in this study with C. pendulum of Hokkaido in Japan and C. japonicum of Anhui in China indicated that the plants of those three species are clearly divided into three distinct groups. The silymarin content of the collected plants was analyzed and turned out to be quite high. Therefore, it has been found that both C. pendulum and C. setidens plants are producing large amounts of silymarin, which has been reported to have various medicinal effects.

• Applied Biological Chemistry
• /
• 제49권4호
• /
• pp.270-275
• /
• 2006

[ $2{\beta},\;3{\alpha}$ ], 23-trihydroxyrus-12-ene-28-oic acid was isolated from Trapa pseudoincisa S. et Z. It has a common structure of pentacyclic triterpenes and belongs to the amyrin ursolic acid group. The cytotoxic effect of this compound was investigated in human hepatoma cell line HepG2. $2{\beta},\;3{\alpha}$, 23-trihydroxyrus-12-ene-28-oic acid showed dose-dependent cytotoxicity in HepG2 cells. Confocal microscopy data showed that green fluorescence was increased in $2{\beta},\;3{\alpha}$, 23-trihydroxyrus-12-ene-28-oic acid treated-HepG2 cells in a time-dependent manner. $2{\beta},\;3{\alpha}$, 23-trihydroxyrus-12-ene-28-oic acid also increased the sub-G1 cell population of HepG2 cells as well as ladder-like DNA fragmentation. Taken together, our results indicate that $2{\beta},\;3{\alpha}$, 23-trihydroxyrus-12-ene-28-oic acid induced apoptosis in HepG2 cells.

• Journal of Applied Biological Chemistry
• /
• 제55권1호
• /
• pp.55-59
• /
• 2012

We designed a new rapid detection method for volatilized formaldehyde from wood. The process was installed with volatilizing and collecting parts in an incubator. For rapid sampling of formaldehyde from wood, we pulverized the wood to sawdust, and used 0.15-2.0 mm particles for the tests. The highest sampling rate (94.8%) was obtained at 40 mL/min flow rate and $100^{\circ}C$. Under the optimized condition, we could collect the volatilized formaldehyde with good recovery rate. The developed method was applied to the monitoring of the formaldehyde from wood, and the measured concentrations were 0.7-4.6 ${\mu}g/g$ from natural wood, 5.9-12.3 ${\mu}g/g$ from preserved wood, and 5.9-211.5 ${\mu}g/g$ from chemical adhesive processed wood. From the results, we identified natural wood sawdust and chemically processed wood (medium density fiberboard, high density fiberboard, particle board) by the formaldehyde contents except preserved wood.

• Journal of Animal Science and Technology
• /
• 제53권4호
• /
• pp.289-296
• /
• 2011

Swine industry in Korea plays an important role in providing the meat for domestic consumption, and the number of pigs in Korea was about 9.72 million heads as of June, 2010. Meat quality is used to describe any traits which impact the consumer acceptability of fresh meat products. Meat color, firmness, water holding capacity, ultimate muscle $pH_{24h}$ (measured 24 hours post-mortem), shear force, and intramuscular fat percentage (IMF) are generally accepted as important indicators of meat quality and ultimately, consumer acceptance of fresh pork. The objective of this study was to estimate genetic parameters for meat quality traits in Berkshire pigs. The heritability estimates for muscle $pH_{24h}$, lightness (CIE $L^*$), NPPC marbling were 0.61, 0.56 and 0.57, respectively, The heritability estimates for drip loss, cooking loss, shear force were 0.51, 0.66 and 0.56, respectively. The phenotypic correlations between $pH_{24h}$ and lightness (CIE $L^*$), drip loss, cooking loss were negative, ranging from -.45 ~ -.13. The genetic correlations between muscle $pH_{24h}$ and lightness (CIE $L^*$), drip loss were negative, ranging from -.35 ~ -.32. Genetic parameters obtained herein indicate that genetic improvement of muscle $pH_{24h}$ is not related to the NPPC marbling of meat, but rather to improved lightness(CIE $L^*$) and drip loss. Genetic trends of meat quality traits showed increased muscle $pH_{24h}$ and decreased cooking loss and drip loss.

• Korean Journal of Ecology and Environment
• /
• 제39권2호통권116호
• /
• pp.219-225
• /
• 2006

Bacterial community structure in the Juam Reservoir was analysed using fluorescent in situ hybridization (FISH) technique from April 2005 to January 2006. Total bacterial numbers varied in the range of 1.58 ${\sim}\;2.73{\times}\;10^6\;cells\;mL^{-1}$ proportional to the concentration of chi-a and had the minimal value in January. The ratios of ${\alpha}\;{\cdot}\;{\beta}\;{\cdot}\;{\gamma}$-subclass proteobacteria and Cytophaga-Flavobacterium (CF) group to total bacteria ranged from 45.1% to 77.5%, and the ratios of ${\alpha}\;{\cdot}\;{\beta}\;{\cdot}\;{\gamma}$-subclasses to total bacteria in June and September with the concentration of chi-a measured were lower than those ratios in April and January. It suggests that enriched growth of Microcystis aeruginosa may inhibit the metabolic activlty of ${\alpha}\;{\cdot}\;{\beta}\;{\cdot}\;{\gamma}$-subclass proteobacteria. However, the ratio of CF group bacteria represented no large change depending on algal bloom. In terms of nitrifying bacteria, the numbers of ammonia-oxidizing bacteria ranged from 9.9 ${\times}\;10^4\;to\;25.5\;{\times}10^4\;cells\;mL^{-1}$ with sharp fluctuation whereas those of nitrite-oxidizing bacteria varied in 8.7${\sim}9.8{\times}10^4\;cells\;mL^{-1}$ without noticeable change except the maximal value of $20.3{\times}10^4\;cells\;mL^{-1}$ in January maybe due to the high DO.

• Journal of Life Science
• /
• 제17권2호통권82호
• /
• pp.235-240
• /
• 2007

AvrRpt2 protein triggers hypersensitive response (HR) and strong disease resistance when it is translocated from a bacterial pathogen Pseudomonas sp. to host plant cells containing a cognate RPS2 resistance protein through Type III Secretion System (TTSS). However, AvrRpt2 protein can function as the effector that suppresses a basal defense and enhances the disease symptom when functional RPS2 resistance protein is absent in the infected plant cells. Using Affymetrix Arabidopsis DNA chip, we found that many genes were specifically regulated by AvrRpt2 protein in the rps2 Arabidopsis mutant. Here, we showed that expression of AtERF11 that is known as a member of B1a subcluster of AP2/ERF transcription factor family was down regulated specifically by AvrRpt2. To determine its function in plant resistance, we also generated the Arabidopsis thaliana transgenic plants constitutively overexpressing AtERF11 under CaMV 355 promoter, which conferred an enhanced resistance against a bacterial pathogen, Pseudomonas syringae pv. tomato DC3000. Thus, these results collectively suggest that AtERF11 plays a role as a positive regulator for disease resistance against biotrophic bacterial pathogen in plant.

• The Korean Journal of Mycology
• /
• 제27권4호통권91호
• /
• pp.274-279
• /
• 1999

The internal transcribed spacer regions(ITS) of the ribosomal DNA gene repeat from Coprinus and Psathyrella spp. were amplified using polymerase chain reaction (PCR) and sequenced. Sequences from 11 species including Coprinus comatus, C. atramentarius, C. micaceus, C. cinereus, C. rhizophorus, C. radians, C. echinosporus, C. disseminatus, Psathyrella candolleana, P. spadiceogrisea and Stropharia rugosoannulata were compared. The spacer region I and II were $258{\sim}301\;bp\;and\;253{\sim}275\;bp$ in length respectively and partially contained 17S, 5.8S and 25S. The reciprocal homologies of ITS sequences among these strains were in the range of $43.9{\sim}96.0%$. According to the analysis of ITS sequences, Coprinus and Psathyrella spp. were classified into three clusters. Cluster I consisted of Coprinus lagopus, C. cinereus, C. echinosporus, C. rhizophorus, and C. atramentarius. Cluster II comprised C. micaceus, C. radians, C. disseminatus, Psathyrella candolleana, and P. spadiceogrisea. On the other hand C. comatus is in Cluster III with Stropharia rugosoannulata even though this species is belonging to the section Coprinus in morphological aspect. These results suggest that taxonomic position of Psathyrella would better be inculded in genus Coprinus. Coprinus comatus, the type species of Coprinus, gives a doubt on monophyletic evolution and is assumed to be paraphyletic or polyphyletic.

• Korean Journal of Microbiology
• /
• 제46권3호
• /
• pp.262-269
• /
• 2010

To investigate a quantitative evaluation of the actinobacteria, we have collected samples from various kinds of bamboo forest soil. Each different layers contained $2.7{\times}10^6-2.7{\times}10^8$ CFU/g of actinobacteria which was the highest in litter layers of Sasa boreali forest soil. We obtained 330 actinobacteria from different layers of bamboo forest soil; litter (100 strains), humus (70 strains), and rhizosphere soil (160 strains). Based on the colony morphology (aerial mycelium, substrate mycelium, and soluble pigment), isolates were divided into thirty-six groups and we selected 50 representative isolates. 16S rRNA gene sequence analysis showed Streptomyces was major actinobacteria (94%) and they were categorized as cluster I (2 strains), II (35 strains), III (6 strains), and IV (7 strains), respectively. The diversity index of 50 Streptomyces collected from the bamboo forest soil was calculated with the Shannon-Wiener method. Bamboo litter showed higher diversity index level of 3.33 than that of humus and rhizosphere soil. Also, antibiotic activities of our isolates were investigated against Botrytis cinerea, Xanthomonas campestris, Xanthomonas axonopodis pv. vesicatoria, and Bacillus cereus and found in 74, 16, 25, and 24 strains, respectively.