• Korean Journal of Veterinary Research
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• v.43 no.1
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• pp.77-86
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• 2003

Pullorum disease due to Salmonella enterica subspecies enterica bioserovar Pullorum (S. pullorum) is reported to be an endemic disease in domestic poultry flocks. The pulsed-field gel electrophoresis (PFGE) subtyping method was used to assess the extent of genetic diversity and clonality of most of salmonella serotypes and other diverse bacterial species from animals and environmental samples in worldwide. Nowadays, PFGE has already been evaluated as a gold standards for molecular subtyping of salmonella serotypes compared with other molecular analysis methods. PFGE of XbaI digested chromosomal DNA from 23 strains of S. pullorum gave 5 distinctive pulsotypes (from SXPI to SXPV) with 5% confidence range of Dice coefficients, indicating that PFGE is very discriminative and that multiple clones of S. pullorum have been existed and diffused all of domestic poultry flocks industries since 1995. Two dominant pulsogroups (SXA & SXB) appeared as a major clones in this country, because they had consistently been recovered from diverse sources including both chicken organs and raw feed materials between 1995 and 1998. In addition, the matching percentage of PFGE profiles (PFP) among strains from both chickens and feed ingredients provides indirect evidence of the possible transmission of pullorum disease from contaminated raw feed ingredients for chicken production. In calculating of discrimination index (DI) for PFGE method by Simpson's index, DI was appeared as 0.917. Therefore, this index suggested that the present PFGE would seem to be a desirable and confident molecular typing method for S. pullorum strains. To our knowledge for pullorum disease, this is the first study to compare S. pullorum strains from chicken organs and feed samples using the PFGE.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2018.10a
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• pp.64-64
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• 2018

The genus Cenchrus (Poaceae), containing ca. 97 species, is distributed throughout Australia, Africa and Indian sub-continent and which was introduced to the United States and Mexico for use in improved pasture. In Korea, especially Daecheong Island, it is one of the most hazardous invasive plant, which causes serious environmental threats, biodiversity damages and physically negative impact on humans and animals. It can cause serious damage to farms, fields and white sand beaches. However, the chloroplast (cp) genome sequences and information of Cenchrus longispinus have been not addressed, so we provide the complete cp genome of Cenchrus longispinus using next-generation sequencing technology. The size of cp genomes of this Daecheong Island species (Cenchrus longispinus) is 137,144 bp, and it shows a typical quadripartite structure. Consisting of the large single copy (LSC; 80,223 bp), small single copy (SSC; 12,449 bp), separated by a pair of inverted repeats (IRs; 22,236 bp). This cp genome contains 75 unique genes, 4 rRNA coding genes, 33 tRNA coding genes and 21 duplicated in the IR regions, with the gene content and organization are similar to other Poaceae cp genomes. Our comparative analysis identified four cpDNA regions (rpl16, rbcL, ndhH and ndhF) from three Cenchrus species, two Setaria species and one Pennisetum species which may be useful for molecular identification.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.18
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• pp.8093-8100
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• 2016

Background: Genetic and environmental factors play important roles in pathogenesis of digestive tract cancers like those in the esophagus, stomach and colorectum. Folate deficiency and methylenetetrahydrofolate reductase (MTHFR) as an important enzyme of folate and methionine metabolism are considered crucial for DNA synthesis and methylation. MTHFR variants may cause genomic hypomethylation, which may lead to the development of cancer, and MTHFR gene polymorphisms (especially C677T and A1298C) are known to influence predispositions for cancer development. Several case control association studies of MTHFR C677T polymorphisms and colorectal cancer (CRC) have been reported in different populations with contrasting results, possibly reflecting inadequate statistical power. Aim: The present meta-analysis was conducted to investigate the association between the C677T polymorphism and the risk of colorectal cancer. Materials and Methods: A literature search of the PubMed, Google Scholar, Springer link and Elsevier databases was carried out for potential relevant articles. Pooled odds ratio (OR) with corresponding 95 % confidence interval (95 % CI) was calculated to assess the association of MTHFR C677T with the susceptibility to CRC. Cochran's Q statistic and the inconsistency index (I2) were used to check study heterogeneity. Egger's test and funnel plots were applied to assess publication bias. All statistical analyses were conducted by with MetaAnalyst and MIX version 1.7. Results: Thirty four case-control studies involving a total of 9,143 cases and 11,357 controls were retrieved according to the inclusion criteria. Overall, no significant association was found between the MTHFR C677T polymorphism and colorectal cancer in Asian populations (for T vs. C: OR=1.03; 95% CI= 0.92-1.5; p= 0.64; for TT vs CC: OR=0.88; 95%CI= 0.74-1.04; p= 0.04; for CT vs. CC: OR = 1.02; 95%CI= 0.93-1.12; p=0.59; for TT+ CT vs. CC: OR=1.07; 95%CI= 0.94-1.22; p=0.87). Conclusions: Evidence from the current meta-analysis indicated that the C677T polymorphism is not associated with CRC risk in Asian populations. Further investigations are needed to offer better insight into any role of this polymorphism in colorectal carcinogenesis.

• KSBB Journal
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• v.32 no.2
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• pp.124-132
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• 2017

A methane-oxidizing bacterium was isolated from rice paddy field soil around Jeollanam-do province, Korea, and characterized. The isolate was gram-negative, orange pigmented and short rod ($1.1-1.2{\times}1.6-1.9{\mu}m$). It was catalase and urease-negative but oxidase-positive. The strain utilized methane and methanol as sole carbon and energy sources. It had an ability to grow with an optimum pH 7.0 and an optimum growth temperature $30^{\circ}C$. The strain was resistant to antibiotic polymyxin B but sensitive to streptomycin, kanamycin, ampicillin, chloramphenicol and rifampicin. The isolate required copper for their growth with concentration range of $2-25{\mu}M$, with an optimum of $10{\mu}M$. Under optimal culture condition, specific cell growth rate and generation time were found to be $0.046hr^{-1}$ and 15.13 hr, respectively. Phylogenetic analysis based on 16S rDNA sequences indicated that the strain formed a tight phylogenetic lineage with Methylomonas koyamae with a value of 99.4% gene sequence homology. So, we named the isolate as Methylomonas sp. SM4. 8.6 mM methanol was accumulated in the reaction mixture containing 70 mM sodium formate and 40 mM $MgCl_2$ (MDH inhibitor) under atmosphere of methane:air (40:60) mixture for 24 hr at $30^{\circ}C$.

• Journal of the Korean Institute of Intelligent Systems
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• v.14 no.5
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• pp.545-550
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• 2004

The study of available genotypes (biodiversity analysis) in bacterial communities is of growing importance in several fields such as ecology, environmental technology, clinical diagnostics, etc. These culture-independent genotyping techniques, especially amplifying 16S rRNA genes, attempt to overcome some shortcomings of conventional cultivation method. Biodiversity analysis based on molecular technique were laborious for base-calling chromatogram, trimming primer sites, correcting strand directions, electing representative operation taxonomic units (OTU), etc. Also, biologists wanted intuitively to confirm results of the above processes. For making up these demands, we developed the web application based on Folder-Process-Filter (FPF) modeling with correspondence to classical Model-View-Controller model. The model of web application leads to keep virtues of simplicity and directness for development and management of the stepwise web interfaces. The web application was developed in Perl and CGI on Linux workstation. It can be freely accessed from http://home.pusan.ac.kr/～genome/tools/rat.htm.

• 한국생물공학회:학술대회논문집
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• 2005.10a
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• pp.450-455
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• 2005

To treat wastewater efficiently by a one-step process of nitrogen removal, a new strain of $N_2-producing$ bacteria from $NH{_4}{^+}$ under an aerobic condition was isolated and identified. By 16S-rDNA analysis, the isolate was identified as Enterobacter asburiae with 96% similarity. The isolate shows that the capacity of $N_2$ production under an oxic condition was approximately three times higher than that under an anoxic condition. The optimal conditions (pH, temperature and C/N ratio) of the immobilized isolate for $N_2$ production were found to be 7.0, $30^{\circ}C$ and 5, respectively. Under all the optimum reaction conditions, the removal efficiency of $COD_{Cr}$ and TN reached 56.1 and 60.9%, respectively. The removal rates of $COD_{Cr}$ and TN were highest for the first 2.5 hrs (with the removal $COD_{Cr}$ ratios of 32.1), and afterwards the rates decreased as reaction proceeded. For application of the immobilized isolate to a practical process of ammonium removal, a continuous bioreactor system exhibited a satisfactory performance at HRT of 12.1 hr, in which the effluent concentrations of $NH{_4}{^+}-N$ was measured to be 15.4 mg/L with its removal efficiency of 56.0%. The maximum removal rate of $NH{_4}{^+}-N$ reached 1.6 mg $NH{_4}{^+}-N/L/hr$ at HRT of 12.1 hr (with N loading rate of 0.08 $Kg-N/m^3-carrier/d)$. As a result, the application of the immobilized isolate appears a viable alternative to the nitrification-denitrification processes.

• Proceedings of the Korean Aquaculture Society Conference
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• 2004.05a
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• pp.513-513
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• 2004

Manila clam, Ruditapes philippinarum, is commercially and ecologically important marine bivalve in Korea and japan. However, clam landings in the two countries have dramatically declined since the 1980-1990's. In the present study, the protozoan parasite, Perkinsus sp., lectin (host's defense-related glycoprotein) and histopathological features were investigated in Manila clams collected from Gomso Bay in Korea and Ariake Bay in japan (one of the largest clam beds in each country) during summer and fall, 2002-2003. DNA sequences of non-transcribe spacer (NTS), internal transcribed space. (ITS) and 5.85 rRNA of Perkinsus sp. were identical to those of P. atlanticus that was reported in Europe and Korea. For diagnosis of Perkinsus, the fluid thioglycollate medium (FTM) and the 2 M NaOH lysis methods were used. Prevalence of the parasite varied from 92.5-98.7% in Gomso Bay and 35.5-37.9% in Ariake Bay. Infection intensity, in terms of the number of Perkinsuscells per gram tissue wet weight, in the clams of Gomso Bay in fall 2002 averaged 1,010,077-470,937 recording approximately100 times higher than that of Ariake Bay, and these were twice higher than those of summer samples in each location. Mean hemagglutination titer of the clams from Gomso Bay was approximately 60-folds higher than that of clams from Ariake Bay in 2002. In histological preparation of the clams from Gomso Bay in 2002, trophozoites of P. atlanticus were in groups and resulted in severe inflammatory response of host clam. Prevalence of the trematod, Cercaria tapes-like in the clams of Gomso Bay and Ariake Bay were 8.8 % and 10.5% respectively. In conclusion, the clams from Gomso Bay showed more severe pathologic symptoms and higher immune response than those of the clams from Ariake Bay.

• Korean Journal of Biological Psychiatry
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• v.13 no.2
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• pp.110-116
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• 2006

Objectives : Alteration of hippocampus was demonstrated in the maternal social separation(MSS) pups, separated from dams on postnatal day(pnd) 14 and placed alone. Therefore, to understand the molecular events involved in the MSS, we have initiated a search for gene profiles that are up or down-regulated in the hippocampus of MSS pups. Methods : Analysis of cDNA microarray was performed by using total RNA extracted from the hippocampus of control and MSS pups on pnd 17. Also, passive-avoidance test was demonstrated on pnd 35. Results : Up-regulation of Nedd4a was observed in the hippocampus of MSS pups. Also, MSS rats showed less elongation of latency in passive avoidance test. Conclusion : We suggest that environmental effects of MSS may be altered the neural and/or glial differentiation and synapse formation-related genes which may lead cognitive alterations in MSS rats.

• Toxicological Research
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• v.21 no.4
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• pp.355-360
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• 2005

Epidemiological and laboratory studies provide insight into the anti-carcinogenic potential of garlic and its constituent compounds. Garlic is appealing as an anti-carcinogenic agent due to its ability to induce apoptosis in vitro. Diallyl disulfide (DADS) is one of the major components of garlic that used to determine inhibition of cell proliferation and induced apoptosis in human colon cell lines. In this study, human colorectal cancer cell lines (LOVO, HCT-116, SW-480) were exposed to DADS. The inhibitory effects of DADS dose level more than $50\;{\mu}M$ in the cell viability of all cell lines. Cell growth activity inhibits of human colon cancer cell lines. The inhibitory effects of DADS dose level more than $25\~50\;{\mu}M$ in the cell growth using MTT assay. We found that DADS may have the apoptosis action (chromatin condensation, DNA fragmentation) using DAPI staining and increased the expression of caspase-3 at the dose level more than $100\;{\mu}M$, decreased the expression level of $\beta-catenin$ at dose dependent in the western blotting. We suggest that DADS may have a potential candidate as cancer chemopreventive agents.

• Toxicological Research
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• v.18 no.2
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• pp.129-138
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• 2002

The mouse lymphoma assay (MLA) has been recently validated as a sensitive and specific test system to determine the genotoxic potential for a chemical. The objective of this study is to evaluate the utility of MLA for detecting mutagens. Especially, to compare MLA with the in vitro chromosomal aberration test (CA), we performed MLA using the microwell method with three chemicals (hydroxyurea, theophylline and amino acid copper complex), which were reportedly positive in the CA. In cell treated with hydroxyurea, anti-neoplastic agent that blocks DNA replication, evidence of a positive response was obtained without S9 mix for 4 h and 24 h. In addition, analysis of colony size distribution at concentration that gave an elevated mutant fraction showed that hydroxyurea induced a high proportion of small type colonies, indicating that hydroxyurea-induced mutation is associated with large chromosomal deletion. Conversely, negative MLA result was obtained for theophylline, which was wed as central nervous system stimulator. Although theophylline increased the mutant frequency at concentration of 1250 $\mu\textrm{g}$/$\textrm{m}{\ell}$ with S9 mix for 4 h, a concentration-related increase in mutant frequency was not observed. The MLA result of amino acid copper complex was considered equivocal because the positive result was obtained at concentration showing 10% or less RS or RTG. Thus, among 3 CA-positive chemicals, positive MLA result was obtained for one. The other two chemicals were negative and equivocal. However MLA, which evaluates mutagenic potential of chemicals through colony formation by cell grouth, may provide a higher predictivity of carcinogenesis than CA.