• Korean Journal of Microbiology
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• v.40 no.3
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• pp.244-247
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• 2004

To investigate the effects of elevated $CO_2$ on the denitrifying bacterial community structure in a wetland soil, dynamics of bacterial community structure was explored in an artificial wetland ecosystem with one of three plant species (T. latifolia, S. lacustris, and 1. effusus) under two levels of $CO_2$(370 ppm or 740 ppm) after 110day incubation. For the analysis of bacterial community structure, functional genes such as nitrite reductase genes (nirS) were PCR-amplified followed by cloning of PCR products and screening by restriction fragment length polymorphism (RFLP). nirS gene fragments were amplified in all analyzed soil samples. Species richness estimated by the number of distinct phylotypes were 83 and 95 in the ambient $CO_2$ treatment and the elevated treatment, respectively. Two phylotypes (type 1 and type 2) were dominant in both of the treatments. Elevated $CO_2$ treatment increased species richness of denitrifying as well as changed a large proportion of denitrifier phylotypes compared to those of the ambient treatment. Overall, the data in this study suggested that the denitrifying communities in the wetland soil are diverse and that the richness of denitrifying bacterial community might be affected by elevated $CO_2$ treatment.

• Journal of Life Science
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• v.30 no.11
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• pp.1012-1020
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• 2020

Remicade is a therapeutic biosimilar natural antibody in which the mouse variable domain has been linked to the human constant domain. It is a chimeric monoclonal antibody specific to tumor necrosis factor-alpha (TNF-α) and has been developed for the treatment of rheumatoid arthritis. To investigate the biological activity of the Remicade antibody, we carried out a bioinformatics study using a protein data bank to characterize the TNF-α antigen binding mechanism of the Remicade natural antibody. Because the production of the Remicade antibody is often limited by genetic instability of the natural antibody-producing cell, we generated a Remicade single-chain variable domain fragment antibody (Remicade) in which a heavy chain variable domain (VH) is joined with a light chain variable domain (VL) by a polypeptide linker. Furthermore, Remicade was fused to a leucine zipper (RemicadeScZip) for higher production and higher antigen-binding activity than Remicade. The Remicade and Remicade ScZip were expressed in Escherichia coli and purified by a Ni⁺-NTA-agarose column. As expected, the purified proteins had migrated as 28.80 kDa and 33.96 kDa in sodium dodecyl sulfate-polyacrylamide electrophoresis. The TNF-α antigen binding activity of Remicade was not observed by ELISA and western blot. In contrast, RemicadeScZip showed antigen-binding activity. Additional bio-layer interferometry analysis confirmed the antigen-binding activity of RemicadeScZip, suggesting that the leucine zipper stabilized the folding of RemicadeScZip in a denatured condition and improved the TNF-α antigenbinding activity.

• Fisheries and Aquatic Sciences
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• v.8 no.3
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• pp.151-160
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• 2005

Genomic DNA samples isolated from Fenneropenaeus chinensis (fleshy prawn; FP) and Palaemon gravieri (Chinese ditch prawn; CDP) collected in the West Sea, off the Korean Peninsula, at Buan, were PCR-amplified repeatedly. The sizes of the DNA fragments generated by seven different primers varied from 50 bp to 1,600 bp. We identified 358 fragments for the FP species and 301 fragments for the CDP species. There were 18 polymorphic fragments (5.03$\%$) for the FP species and 12 (3.99$\%$) for the CDP species. In total, 66 common fragments (average of 9.4 fragments per primer) were observed for the FP species and 44 fragments (average of 6.3 fragments per primer) were observed for the CDP species. The numbers of specific fragments seen for the FP species and CDP species were 38 and 47, respectively. The complexity of the banding patterns varied dramatically between the primers and the two species. In the FP species, a specific fragment of approximately 1,200 bp generated by primer OPB-04 exhibited inter-individual-specific characteristics that were indicative of DNA polymorphisms. Moreover, in the CDP species, a major fragment of approximately 550 bp generated by primer OPB-20 was found to be specific for the CDP. The average bandsharing value between the two prawn species was 0.421$\pm$0.006, and ranged from 0.230 to 0.611. The dendrogram obtained using the data from the seven primers indicated seven genetic clusters: cluster 1, FLESHY 01, 02, 03, and 04; cluster 2, FLESHY 05, 06, and 07; cluster 3, FLESHY 08, 09, 10, and 11; cluster 4, DITCH 13, 14, 16, and 18; cluster 5, DITCH 12, 15, and 17; cluster 6, DITCH 19, 20, and 21; and cluster 7, DITCH 22. The genetic distance between the two prawn species ranged from 0.071 to 0.642. Thus, RAPD-PCR analysis revealed a significant genetic distance between the two prawn species. Using various arbitrary primers, RAPD-PCR may be applied to identify specific/polymorphic markers that are particular to a species and geographic population, and to define genetic diversity, polymorphisms, and similarities among shrimp species.

• Korean Journal of Ecology and Environment
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• v.41 no.1
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• pp.98-103
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• 2008

Genetic diversity and population genetic structure within or among three stream populations (Gab, Baekgok and Ji streams) of Korean endangered natural monument fish, Iksookimia choii, were assessed by amplified fragment length polymorphism (AFLP). AFLP analysis using three primer combinations generated 104 to 106 AFLP bands, and percent polymorphic bands were similar in those three populations ranging 21.5 to 24.5%. Heterozygosity and genetic diversity within or among populations were quite low for all of these populations with average values ranging from 0.067 to 0.084 and from 0.076 to 0.087, respectively. Analyses of pairwise distance and genetic similarity among three populations of I. choii also revealed the similar results with very low genetic differentiation one another. Although pairwise Fst values were very low, our data clearly indicated distinct genetic differentiation among the three populations. This is the first report concerning the genetic diversity and differentiation of this species, and provides basic genetic information that should facilitate attempts to conserve this species.

• Journal of Microbiology
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• v.45 no.2
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• pp.105-112
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• 2007

The objective of this study was to analyze the phylogenetic composition of bacterial community in the soil of an earth-cave (Niu Cave) using a culture-independent molecular approach. 16S rRNA genes were amplified directly from soil DNA with universally conserved and Bacteria-specific rRNA gene primers and cloned. The clone library was screened by restriction fragment length polymorphism (RFLP), and representative rRNA gene sequences were determined. A total of 115 bacterial sequence types were found in 190 analyzed clones. Phylogenetic sequence analyses revealed novel 16S rRNA gene sequence types and a high diversity of putative bacterial community. Members of these bacteria included Proteobacteria (42.6%), Acidobacteria (18.6%), Planctomycetes (9.0 %), Chloroflexi (Green nonsulfur bacteria, 7.5%), Bacteroidetes (2.1%), Gemmatimonadetes (2.7%), Nitrospirae (8.0%), Actinobacteria (High G+C Gram-positive bacteria, 6.4%) and candidate divisions (including the OP3, GN08, and SBR1093, 3.2%). Thirty-five clones were affiliated with bacteria that were related to nitrogen, sulfur, iron or manganese cycles. The comparison of the present data with the data obtained previously from caves based on 16S rRNA gene analysis revealed similarities in the bacterial community components, especially in the high abundance of Proteobacteria and Acidobacteria. Furthermore, this study provided the novel evidence for presence of Gemmatimonadetes, Nitrosomonadales, Oceanospirillales, and Rubrobacterales in a karstic hypogean environment.

• The Transactions of the Korea Information Processing Society
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• v.7 no.9
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• pp.2797-2806
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• 2000

Recently, DDSs(Distributed Database Systems) have been implemented on V AN(V alue Added Network) as we know the amazing expansion of information network. DDS can yield significant cost and response time advantages over centralized systems for geographically distributed organizations. However, inappropriate design can result in high cost and poor response time to maintain the database at each site. In a DDS design, the main problem is how to select proper computer and how to allocate data fragment into a proper site. In this paper, we address DDS design problem of selecting the proper class of computers and the allocating data files on VAN. Also, the formulated model includes two objectives, the waited response time and the investment cost to include their relationship. Specially, the formulation of waited response time is based on M/M/1 queueing system to evaluate more precisely. GA(Genetic Algorithm), a kind of heuristic search method, is developed to search an optimal solution in the proposed design model and we show the simulation result to examine the algorithm performance.

• Korean Journal of Biological Psychiatry
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• v.7 no.2
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• pp.147-151
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• 2000

Objective : Major depression is known to have immunologic dysfunctions, the recent studies revealed that cytokines including IL-6 and IL-$1{\beta}$ were increased in patients with major depression. Since molecular genetic methods have been progressed, this study was to investigate the relationship between major depression and immunologic aspects by analyzing polymorphism of IL-10 gene. Method : 92 patients with major depression were included and data of 146 normal controls obtained from the Catholic Hemopoietic Stem Cell Information Bank of Korea were used in this study. DNA was extracted from whole blood, thereafter amplified by polymerase chain reaction, and digested by Mae III After that procedure, we obtained and assessed RFLP of two alleles, IL-10T and IL-10C. All data were analyzed by ${\chi}^2$ test. Results : 1) There were no significant difference in genotype frequencies of $IL-10^*T/T$, $IL-10^*T/C$, and $IL-10^*C/C$ between major depression patients group and control group. 2) There were no significant difference in allelic frequencies of $IL-10^*T$ and $IL-10^*C$ between major depression patients group and control group. Conclusion : We did not verified the differences in frequencies of $IL-10^*T/^*IL-10^*C$ gene between the major depression patients group and control group, respectively. But the results of this study do not declare that the IL-10 gene has no association with major depression. We do suggest that further systematic studies including various clinical variables should be conducted.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.18
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• pp.8405-8410
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• 2016

Hepatitis B virus (HBV) infection is the leading cause of hepatocellular carcinoma (HCC) development. Recent studies demonstrated that single nucleotide polymorphisms (SNPs) rs2293152 in signal transducer and activator of transcription 3 (STAT3) and rs7574865 in signal transducer and activator of transcription 4 (STAT4) are associated with chronic hepatitis B (CHB)-related HCC in the Chinese population. We hypothesized that these polymorphisms might be related to HCC susceptibility in Thai population as well. Study subjects were divided into 3 groups consisting of CHB-related HCC (n=192), CHB without HCC (n=200) and healthy controls (n=190). The studied SNPs were genotyped using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). The results showed that the distribution of different genotypes for both polymorphisms were in Hardy-Weinberg equilibrium (P>0.05). Our data demonstrated positive association of rs7574865 with HCC risk when compared to healthy controls under an additive model (GG versus TT: odds ratio (OR)=2.07, 95% confidence interval (CI)=1.06-4.03, P=0.033). This correlation remained significant under allelic and recessive models (OR=1.46, 95% CI=1.09-1.96, P=0.012 and OR=1.71, 95% CI=1.13-2.59, P=0.011, respectively). However, no significant association between rs2293152 and HCC development was observed. These data suggest that SNP rs7574865 in STAT4 might contribute to progression to HCC in the Thai population.

• Journal of Environmental Science International
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• v.14 no.5
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• pp.499-511
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• 2005

This study was performed to determine the effects of genetic polymorphisms, such as glutathione S-transferase ${\mu}1(GSTM1)$, glutathione S-transferase ${\Theta}1\;(GSTM1)$, glutathione S-transferase ${\pi}l (GSTP1)$, aryl hydrocarbon N-acetyltransferase 2 (NAT2), cytochrome P450 2E1 (CYP2E1), cytochrome P450 1A1 (CYP1A1) on the concentrations of urinary 1-hydroxypyrene (1-OHP) and 2-naphthol in general population with no occupational exposure to polycyclic aromatic hydrocarbons (PAHs). Study subjects were 257 men who visited a health promotion center in Susan. A questionnaire was used to obtain detailed data about age, smoking, drinking, body fat mass, intake of fat etc. Urinary l-OHP and 2-naphthol concentration were analyzed by HPLC system with a fluorescence detector. A multiplex PCR method was used to identify the genotypes for GSTM1 and GSTT1. The polymorphisms of GSTP1, NAT2, CYP1A1 and CYP2E1 were determined by the polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) method. Urinary 1-OHP concentration was higher in deleted genotype of GSTM1, increased as smoking and alcohol drinking increased. Urinary 2-naphthol concentration was also rely on the age and smoking. Neither genetic polymorphism nor drinking-related factors were significantly related to urinary 2-naphthol concentration. No significant relation was found between physical characteristics and concentrations of urinary PAHs metabolites in the subjects, but the geometric mean of urinary 1-OHP and 2-naphthol was higher in the group with higher value compared to median value. These data suggest that in general population occupationally not exposed to PAHs, urinary concentration of PAHs metabolites is influenced by smoking, alcohol drinking and deleted genotype of GSTM1 in 1-OHP and smoking in 2-naphthol.

• The Transactions of the Korea Information Processing Society
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• v.6 no.8
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• pp.2000-2007
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• 1999

Recently, DDS (Distributed Database System) has been often implemented on VAN (Value Added Network) as we know the amazing expansion of information network. DDS can yield significant cost and response time advantages over centrailzed systems for geographically distributed organizations. However, inappropriate design can result in high cost and poor response time. In a DDS design, the main problem is 1) how to select proper computer, and 2) how to allocate data fragment into proper nodes. This paper addresses DDS design problem of selecting the proper class of computers and the allocating data files on VAN. Also, the formulated model includes tow objectives, the operating and investment cost. GA (Genetic Algorithm) is developed to solve this mathematical formulation. A numerical experiment shows that the proposed method arrives at a good solution.