• Bioinformatics and Biosystems
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• v.1 no.2
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• pp.99-102
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• 2006

The Basic Local Alignment Search Tool (BLAST) is one of the most established software in bioinformatics research and it compares a query sequence against the libraries of known sequences in order to investigate sequence similarity. Expressed Sequence Tags (ESTs) are single-pass sequence reads from mRNA (or cDNA) and represent the expression for a given cDNA library and the snapshot of genes expressed in a given tissue and/or at a given developmental stage. Therefore, ESTs can be very valuable information for functional genomics and bioinformatics researches. Although major bio database (DB) websites including NCBI are providing BLAST services and EST data, local DB and search system is demanding for better performance and security issue. Here we present animal EST DBs and local BLAST search system. The animal ESTs DB in NCBI Genbank were divided by animal species using the Perl script we developed. and we also built the new extended DB search systems fur the new data (Local Animal BLAST Search System: http://bioinfo.kohost.net), which was constructed on the high-capacity PC Cluster system fur the best performance. The new local DB contains 650,046 sequences for Bos taurus(cattle), 368,120 sequences for Sus scrofa (pig), 693,005 sequences for Gallus gallus (fowl), respectively.

• Molecules and Cells
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• v.27 no.5
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• pp.563-570
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• 2009

We previously isolated the OsCBT gene, which encodes a calmodulin (CaM)-binding protein, from a rice expression library constructed from fungal elicitor-treated rice suspension cells. In order to understand the function of OsCBT in rice, we isolated and characterized a T-DNA insertion mutant allele named oscbt-1. The oscbt-1 mutant exhibits reduced levels of OsCBT transcripts and no significant morphological changes compared to wild-type plant although the growth of the mutant is stunted. However, oscbt-1 mutants showed significant resistance to two major rice pathogens. The growth of the rice blast fungus Magnaporthe grisea, as well as the bacterial pathogen Xanthomonas oryzae pv. oryzae was significantly suppressed in oscbt-1 plants. Histochemical analysis indicated that the hypersensitive-response was induced in the oscbt-1 mutant in response to compatible strains of fungal pathogens. OsCBT expression was induced upon challenge with fungal elicitor. We also observed significant increase in the level of pathogenesis-related genes in the oscbt-1 mutant even under pathogen-free condition. Taken together, the results support an idea that OsCBT might act as a negative regulator on plant defense.

• Journal of Internet Computing and Services
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• v.6 no.6
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• pp.139-148
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• 2005

The desired level for multimedia services in the mobile web environment, the next generation web environment, is expected to be of PC level quality. And great efforts have been made in the development of hadware technology, communication technology, various kinds of services and standardization to support these services, In the mobile web environment, multimedia contents adaptation services should be available through supporting various kinds of devices, network abilities and users' preferences. It means that due to the variety of both desired devices' hardware specifications, called destinations, and desired QoSes, the QoSes in the destinations are not fixed or defined. If a new user wants to stream multimedia contents in a server through a new kind of terminal device, it should be considered whether the existing transcoders are able to adapt the multimedia contents. However, the existing libraries for multimedia adaptation have heavy transcoder figures which include all adaptive functions in one library, The challenge of universal access is too complex to be solved with these all in one solutions. Therefore, in this paper we propose an application independent multimedia adaptation framework which meets the QoS of new and varied mobile devices. This framework is composed of a group of unit transcoders having only one transcoding function respectively, Instead of heavy transcoders. Also, It includes the transcoder manager supporting the dynamic connections of the unit transcoders in order to satisfy end to end QoS.

• Journal of Life Science
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• v.19 no.5
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• pp.566-572
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• 2009

A recombinant plasmid, pDH3, was obtained from the genomic library of Serattia marcescens KCTC 2172, and several recombinant subclones constructed from pDH3. The nucleotide sequence of a 5,137 bp segment, pPH4, was determined and three open reading frames were detected. The three ORFs encoded the phosphate specific transport (pst) operon, which was pstC, pstA, and pstB, with the same direction of transcription. Comparison of the pst operon of S. marcescens with that of other organisms revealed that the genes for pstS and phoU were missing. A potential CRP bonding site and pho box sequence was found in the upstream of the putative promoter at the regulatory region. Analysis of the nucleotide sequence showed that homology in amino acid sequences between the PstC protein and Yersinia sp., Vibrio sp., and Pseudomonas sp. were 49, 37 and 33%, respectively. The PstA protein and Yersinia sp., Vibrio sp., and Pseudomonas sp. showed homologies of 64, 51, and 47%, respectively. PstB protein and Methanocaldococcus sp., E. coli, and Mycoplasma sp. showed homologies of 60, 50, and 48%, respectively. The pst genes could be expressed in vivo and positively regulated by cAMP-CRP. The E. coli strain harboring plasmid pPH7, with pst genes, increased with the transport of phosphate.

• BMB Reports
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• v.45 no.3
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• pp.183-188
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• 2012

Participates in actin remodeling through Rac and receptor endocytosis via Rab5. Here, we used yeast two-hybrid system with Eps8 as bait to screen a human brain cDNA library. ITSN2 was identified as the novel binding factor of Eps8. The interaction between ITSN2 and Eps8 was demonstrated by the in vivo co-immunoprecipitation and colocalization assays and the in vitro GST pull-down assays. Furthermore, we mapped the interaction domains to the region between amino acids 260-306 of Eps8 and the coiled-coil domain of ITSN2. In addition, protein stability assays and immunofluorescence analysis showed ITSN2 overexpression induced the degradation of Eps8 proteins, which was markedly alleviated with the lysosome inhibitor NH4Cl treatment. Taken together, our results suggested ITSN2 interacts with Eps8 and stimulates the degradation of Eps8 proteins.

• Korean Journal of Microbiology
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• v.49 no.4
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• pp.336-342
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• 2013

Trichloroethylene (TCE) is a widely used substance in commercial and industrial applications, yet it must be removed from the contaminated soil and groundwater environment due to its toxic and carcinogenic nature. We investigated bacterial community structure, dominant bacterial strain, and removal efficiency in a TCE contaminated groundwater treatment system using immobilized carrier. The microbial diversity was determined by the nucleotide sequences of 16S rRNA gene library. The major bacterial population of the contaminated groundwater treatment system was belonging to BTEX degradation bacteria. The bacterial community consisted mainly of one genus of Pseudomonas (Pseudomonas putida group). The domination of Pseudomonas putida group may be caused by high concentration of toluene and TCE. Furthermore, we isolated a toluene and TCE degrading bacterium, named Pseudomonas sp. DHC8, from the immobilized carrier in bioreactor which was designed to remove TCE from the contaminated ground water. Based on the results of morphological and physiological characteristics, and 16S rRNA gene sequence analysis, strain DHC8 was identified as a member of Pseudomonas putida group. When TCE (0.83 mg/L) and toluene (60.61 mg/L) were degraded by this strain, removal efficiencies were 72.3% and 100% for 12.5 h, respectively. Toluene removal rate was 2.89 ${\mu}mol/g$-DCW/h and TCE removal rate was 0.02 ${\mu}mol/g$-DCW/h. These findings will be helpful for maintaining maximum TCE removal efficiency of a reactor for bioremediation of TCE.

• Journal of Acupuncture Research
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• v.21 no.3
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• pp.265-282
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• 2004

Objective : The aim of this study was to review systemically clinical trials on the effectiveness and safety of herbal medicines in the treatment of osteoarthritis. Methods : Computerized literature searches were carried out on seven electronic databases, and hand-searching on some chinese medical journals in library of Kyung Hee Medical Center. Trial data were extracted in a standardized, predefined manner and assessed independently. Results : 1. Thirty reports of clinical trials and two reports of meta-analyses concerning herbal medicine were collected and reviewed. Among these reports three medical herbs were applied as topical medicine and others as internal medicine. 2. The western studies established NSAIDs or placebo as their control group. Five chinese reports established formulated herb pill(Ruanshnagshenjin pill) as their control group and Six did not establish a control group at all. 3. ACR was the most highly used diagnostic criteria in the western studies while the Chinese used their official criteria established by their government or the criteria of their text books. 4. 20 reports chose the Lequesne functional index, SHAQ, WOMAC OA index, AIMS, and their own unique scoring system as the criteria of analysing the effect. Others chose clinical symptoms, articular functions, and lab finding as their criteria. 5. 7 single herbs and 19 formulated herbs were studied. Among the formulated herbs, Achyranthes japonica was studied in 10 of the studies and Angelica gigantis Radix in 8, making them the most often studied herbs among the studies.

• Journal of Acupuncture Research
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• v.33 no.2
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• pp.135-150
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• 2016

Objectives : The aim of this study is to review the combination effects and adverse effects of Yerba Mate (Ilex paraguariensis) on the treatment of obesity. Methods : Four databases were searched, including Pubmed, National assembly library, RISS4u, and NDSL, for studies published before March 31, 2016 using the keywords 'yerba mate', 'Ilex paraguariensis', and those related to 'obesity'. Clinical trials, and both in vivo and in vitro studies were classified according to the following categories: publication year, nationality, types and composition of test compounds, combination effects, adverse effects, and safety. Results : A total of 16 articles (14 clinical trials, one in vivo, one in vitro) were included in the analysis. Combination effects were reported from six YGD (Yerba Mate, Guarana, Damiana, Zotrim), five Meltdown, one Shred-matrix, one DBX (DymaBurn Xtreme), one XSIII research study, and adverse effects were reported from two YGD (Zotrim), four Meltdown, one Shred-matrix and one MetEF research study. YGD and Shred-matrix increased satiety while YGD and MetEF had adverse gastrointestinal effects potentially due to guarana. Meltdown and Shred-matrix increased energy expenditure and fat oxidation and had the adverse effects of increased heart rate and blood pressure due to the thermogenic effect of caffeine and yohimbine. DBX increased resting energy expenditure but no difference was observed in respiratory exchange ratio. XSIII reduced body weight gain and food intake more than each of the extracts did on their own. Conclusion : Taken together, the combination effects and adverse effects differed according to the composition of test compounds and the ratio of ingredients. Multicomponent approaches should be used for treating multifactorial diseases such as obesity. As a general conclusion, there is a place for a combination of herbal components including yerba mate, based on the principle of Kun-Shin-Choa-Sa for the treatment of obesity.

• Korean Journal of Microbiology
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• v.50 no.2
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• pp.164-168
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• 2014

The ecosystem of the Arctic region has been increasingly affected by global warming. Archaeal ammonia monooxygenase alpha subunit coding gene (amoA) which is a key enzyme for nitrification was used to investigate the effect of runoff water of ice melt on microbial community of nitrogen cycle. The archaeal amoA genes at coastal area of Svalbard, Arctic region were PCR-amplified and sequenced after clone library construction. Analysis of archaeal amoA gene clone libraries suggested that the station 188 which is in the vicinity to the area of runoff water harbor lower ammonia-oxidizing archaeal diversity than the station 176 and 184. The average amino acid sequence identity within all archaeal amoA gene clones was 94% (with 91% nucleotide sequence identity). While all the clones of the station 188 were affiliated with Nitrosoarchaeaum clade containing strains isolated from low-salinity and terrestrial environments, about 45% of total clones of the station 176 and 184 were related to marine Nitosopumilus clade. Interestingly, other typical archaeal amoA gene clones of thaumarchaeal I.1b clade frequently retrieved from terrestrial environments was identified at station 188. Microbial community of nitrogen cycle in marine sediment might be affected by input of sediments caused by runoff glacier melt waters.

• Journal of Life Science
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• v.8 no.3
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• pp.263-271
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• 1998

One of the better-characterized transcription factor of E. coli is the cAMP receptor protein(CRP) and the CRP binds cAMP and DNA. The cAMP-CRP complex is involved in regulation of many genes at bacteria. The cAMP-CRP regulatory element represents, in some respects, a global regulatory network. The aim of this work was to study the structure and the mechanisms controlling the expression of CRP in Serratia marcescens. We have been get 5 different clones from Serratia which stimulated the cells to use maltose as a sole carbon source in E. coli TP2139. The crp gene clone, pCKB12, was confirmed by Southern hybridization with E. coli crp gene. The location of the crp gene was determined by construction subclones carrying various portions of pCKB12. To investigate the potential role of CRP in E. coli, lacZ fused plasmids were constructed and investigated the ${\beta}$-galactosidase activity of the fused plasmid. The Serratiamarcescens cAMP receptor protein can substitute the E. coli CRP in transcriptional activation at the lacZ gene. These results suggest that Serratia marcescens cAMP receptor protein complex functions to regulate several promoters in E. coli.