• Journal of Soil and Groundwater Environment
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• v.14 no.3
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• pp.57-67
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• 2009

In soil and sediment environment, microorganisms play major roles in biochemical cycles of ecological significant elements. Because of its ecological significance, microbial diversity and community structure information are useful as indexes for assessing the quality of subsurface ecological environment and bioremediation. To achieve more accurate assessment, it is requested to gain sufficient yield and purity of DNA extracted from various soil and sediment samples. Although there have been a large number of basic researches regarding soil and sediment DNA extraction methods, little guideline information is given in literature when choosing optimal DNA extraction methods for various purposes such as environmental ecology impact assessment and bioremediation capability evaluation. In this study, we performed a thorough literature review to compare the characteristics of the current DNA extraction methods from soil and sediment samples, and discussed about considerations when selecting and applying DNA extraction methods for environmental impact assessment and bioremediation capability evaluation. This review suggested that one approach is not enough to gain the suitable quantity and yield of DNA for assessing microbial diversity, community structure and population dynamics, and that a careful attention has to be paid for selecting an optimal method for individual environmental purpose.

• KSBB Journal
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• v.20 no.6
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• pp.431-437
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• 2005

Molecular methods were employed to investigate microorganisms in a thermophilic continuous stirred tank reactor(CSTR) used for continuous $H_2$ production. The reactor was inoculated with heat-treated anaerobic sludge and fed with a glucose-based medium. Denaturing gradient gel electrophoresis showed dynamic changes of bacterial populations in the reactor during 43 days of operation. Gas composition was constant from approximately 14 days but population shift still occurred. Populations affiliated with Fervidobactrium gondwanens and Thermoanaerobacterium thermosaccharolyticum were dominant on 21 and 41 days, respectively. Keeping pH of the medium at 5.0 could suppress methanogenic activity that was detected during initial operation period. $CH_4$ and mcrA detected in the samples obtained from the reactor or inoculum suggested the heat treatment condition employed in this study is not enough to remove methanogens in the inoculum. PCR using primer sets specific to 4 main orders of methanogens suggested that major $H_2$-consuming methanogens in the CSTR belong to the order Methanobacteriales.

• KSBB Journal
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• v.22 no.5
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• pp.356-361
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• 2007

Cyanobacteria are a very old group of prokaryotic organisms that produce very diverse secondary metabolites, especially non-ribosomal peptide and polyketide structures. Although some cyanobacteria produce lethal toxins such as microcystins and anatoxins, some may be useful either for development into commercial drugs or as biochemical tools. Detection of unknown secondary metabolites was carried in the present study by a screening of 98 cyanobacterial strains from Cyanobiotech GmbH in order to establish a screening process, isolate pure substances and determine their bioactivities. A degenerated polymerase chain reaction technique as molecular approaches has been used for general screening of NRPS gene and PKS gene in cyanobacteria. A putative PKS gene was detected by DKF/DKR primer in 38 strains (38.8%) and PCR amplicons resulted from a presence of NRPS gene were showed by MTF2/MTR2 primer in 30 strains (30.6%), respectively. A screening of interesting strains was performed by comparing PCR screening results with HPLC analyses of extracts. HPLC analysis for a detection of natural products was performed in extracts from biomass. 5 strains were screened for further scale-up processing. 7 pure substances were isolated from the scale-up cultures and tested for bioactivities under consideration to purity, amount and molecular weight of substances. One substance isolated from CBT 635 showed cytotoxic activity. This substance may be regarded as Microcystin LR.

• Korean Journal of Food Science and Technology
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• v.43 no.1
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• pp.77-82
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• 2011

This study was conducted to provide information for improving the quality characteristics of Buckwheat Soksungjang (BWS). We determined aminotype nitrogen content, total microbial flora counts, the population of Bacillus cereus, presence of volatile compounds, fibrinolytic activity, antioxidant activity, ACE inhibition rate, and a sensory evaluation. The aminotype nitrogen increased gradually during fermentation. We found a decreasing population of B. cereus during fermentation, thus, the edible period for BWS was more than 30 days after fermentation. Acetaldehyde, butanol, and pyrazine were detected as volatile compounds after fermentation. The fibrinolytic activities of a 10% BWS water extract were high at 120.8 units compared to the control (71.6 units). In a sensory evaluation, Soksungjang with 60% added BW showed a significantly higher score (p < 0.001) for color, taste, smell, texture, and overall. The results suggest that a new type of shortened fermented soybean paste had good safety, bioactivities, and sensory characteristics within 4 weeks.

• Korean Journal of Environmental Agriculture
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• v.29 no.3
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• pp.287-292
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• 2010

We aimed to investigate the responses of soil organisms to cover plants and to provide information for the selection of proper plant species. We studied the effects of 7 cover plants, including rye, oat, rattail fescue, Chinese milk vetch, red clover, crimson clover, and hairy vetch, on soil organisms in an apple orchard. An increase in the microbial phospholipid fatty acids (PLFA) and in the number of nematodes and microarthropods in the soil under the cover plants reflects elevated activities of soil organisms. A decrease in the level of some marker PLFA, which is an indicator of environmental stress, suggests that cover plants provide favorable environments for soil organisms. The population of fungi and animals that feed on fungi increased in the soil surface under red clover. The population density of nematodes and mites increased in the soil surface under rattail fescue, and that of mites and omnivorous nematodes increased in the soil surface under Chinese milk vetch. The level of microbial PLFA in the soil surfaces under the tested cover plants was higher than that under clean culture system. These results suggest that proper selection of the cover plants can facilitate the creation of favorable environments for soil organisms.

• Journal of Life Science
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• v.27 no.11
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• pp.1290-1298
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• 2017

Intestinal microbiota is an important factor in the development of immune defense mechanisms in the human body. Treatments with anticancer agents, such as 5-Fluorouracil, Cisplatin, and Oxaliplatin, significantly change the temporal stability and environment of intestinal bacterial flora. The anticancer treatment chemotherapy often depresses the immune system and induces side effects, such as diarrhea. This study investigated the effects anticancer agents have on the intestinal microbial ecosystems of patients with gastric cancer. An exploration of the diversity and temporal stability of the dominant bacteria was undertaken using a DGGE with the 16S rDNA gene. Researchers collected stool samples from patients zero, two and eight weeks after the patients started chemotherapy. After the treatment with anticancer agents, the bacteria strains Sphingomonas paucimobilis, Lactobacillus gasseri, Parabacteroides distasonis and Enterobacter sp. increased. This study focused on the survival of the beneficial microorganisms Bifidobacterium and Lactobacillus in the intestines of cancer patients. The administration of antigastric cancer agents significantly decreased Lactobacillus and Bifidobacterium populations and only moderately affected the main bacterial groups in the patients' intestinal ecosystems. The results showed the versatility of a cultivation independent-PCR DGGE analysis regarding the visual monitoring of ecological diversity and anticancer agent-induced changes in patients' complex intestinal microbial ecosystems.

• Korean Journal of Soil Science and Fertilizer
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• v.45 no.2
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• pp.227-234
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• 2012

Recently, the population of toxic and/or unusable jellyfish is increasing during summer along the east coast of Korea, causing massive economical and ecological damage to fisheries, nuclear power plant and marine environment. To solve this problem, this study was carried out using jellyfish as a potential soil additive for horticulture. The jellyfish was solidified and homogenized, then mixed with a commercial bed soil. Allium tuberosum ROTH was planted to control bed soil (BS) and jellyfish powder mixed bed soil groups (Mixed bed soil, MBS), and following parameters were measured during five weeks: water content, electrical conductivity and growth of leaves. At the end of the experiment, bacterial community structures of each pot were analyzed by DGGE. The relative water adsorption of jellyfish powder was about 2.5 times greater compared to its dry weight. The water content of MBS group was significantly higher than BS group 6.5 to 14.2%, and the electric conductivity of MBS group was measured around 2.8 dS/m where BS group was resulted average of 1.8 dS/m. However, the leaves of BS group were grown 30% longer compared to MBS group. DGGE analysis of MBS group was shown in high number of phylum Bacteroidetes and increased diversity of Sphingobacteriia compared to BS group. Jellyfish powder as a soil additive surely will be a good candidate as humectant and microbiota stimulator, although there are several obstacles such as high electrical conductivity and residual alum salt which used for solidification of jellyfish.

• The Korean Journal of Mycology
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• v.41 no.1
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• pp.1-8
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• 2013

COP9 signalosome (CSN), which is originally identified as the regulator of the photomorphogenic development in plant, is highly conserved protein complex in diverse eukaryotic organisms. Most eukaryotic CSN complex is composed of 8 subunits, which is structurally and functionally similar to the lid subunit of 26S proteasome and eIF3 translation initiation complex. CSN play important functions in the regulation of cell cycle and checkpoint response by controlling Cullin-Ring E3 ubiquitin ligases (CRL) activities. CSN exhibits an isopeptidase activity which cleaves the neddylated moiety of cullin components. In fission yeast, S-phase cell cycle progression was delayed and the sensitivity to g-ray or UV was increased in CSN1 and CSN2 deletion mutants, indicating that yeast CSN is also involved in the checkpoint regulation. CSN in fungal system more closely resembles that of the higher organisms in the structure and assembly of their components. Functionally, CSN is associated with the regulation of conidiation rhythms in Neurospora crassa and the sexual development in Aspsergillus nidulans. Recent studies also revealed that CSN functions as an essential cell cycle regulator, playing key roles in the regulation of DNA replication and DNA damage response in Aspergillus. Overall, CSN of microorganisms, such as fission yeast and fungi, share functionally common aspects with higher organisms, implying that they can be useful tools to study the role of CSN in the CRL-mediated diverse cellular activities.

• Korean Journal of Organic Agriculture
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• v.21 no.4
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• pp.617-627
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• 2013

This study was conducted to survey the current pest occurrence and grower's pest management practices, and to investigate biodiversity including birds, snakes, rodents, and amphibians in organic pear orchards. From the questionnaires and field survey of 22 organic orchards in 2010, the materials such as lime sulphur, plant extracts and their mixtures with microorganisms, and oils were preferred over insecticides. Scab, mealybugs, woollybugs and barkminers were the major pests for organic pear growers. Environment-friendly fungicides and insecticides were applied 9 to 10 and 5 to 6 times respectively. Incidence and severity of scab on Niitaka pear fruits in organic orchards was higher than in conventional ones. Whereas for mealybugs there was no significant difference between organic and conventional orchards. Pear fruits in organic orchards were significantly smaller than those of non-organic orchards. For the biodiversity of amphibians, snakes, pheasants, and rodents, there was no significant difference between organic and conventional orchards, but Rufous turtle doves were monitored more in organic areas than in conventional ones.

• Journal of Veterinary Clinics
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• v.19 no.3
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• pp.312-315
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• 2002

Diagnostic tests often require the determination of cut-off values that discriminate uninfected from infected individuals. The receiver operating characteristic (ROC) curve has been frequently used to attain this purpose and gives a representation of diagnostic accuracy (sensitivity and specificity) of a prediction model when varying the cut-point of a decision rule on a whole spectrum. We have written and tested a visual basic application program in EXCEL for maximum likelihood estimation of a binormal ROC curve, which also computes univariate statistics of a diagnostic test employed. Examples applying for computed tomographic images in radiology and methicillin-resistant Staphylococcus aureus research are given to illustrate this approach. This stand-alone module is available from the first author on request.