• 한국패류학회지
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• 제32권3호
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• pp.185-188
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• 2016

본 연구를 통하여 업데이트된 PANM 데이터베이스 버전 II는 버전 I 에 비해 많은 양의 정보가 추가되었다. 하지만 여전히 NCBI nr 데이터베이스에 비해 적은 양으로서, NGS 분석에 있어 많은 시간을 절약하게 해줄 수 있다. 또한 웹 인터페이스의 개선으로 인하여 직관성 및 신뢰성을 더욱 더 확보할 수 있었다. 개별적인 서버를 운용하여 NGS 데이터를 분석하는 연구자들을 위해 PANM 데이터베이스의 다운로드가 가능하도록 하였고 이로 인해 NGS 데이터 분석 시간이 줄어들 수 있을 것이다. 앞으로 꾸준한 PANM 데이터베이스 업데이트를 통하여 연체동물을 연구하는 연구자들은 물론 절지동물, 선형동물을 연구하는 연구자들에게도 많은 도움이 될 것으로 생각되며, 추가적으로 구축된 두족류 전용 데이터베이스 역시 두족류를 연구하는 연구자들에게 매우 유용하리라 사료되어진다.

• Bioinformatics and Biosystems
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• 제1권1호
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• pp.46-50
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• 2006

According to the advancement of experimental techniques in molecular biology, genomic and protein sequence databases are increasing in size exponentially, and mean sequence lengths are also increasing. Because the sizes of these databases become larger, it is difficult to search similar sequences in biological databases with significant homologies to a query sequence. In this paper, we present the N-gram indexing method to retrieve similar sequences fast, precisely and comparably. This method regards a protein sequence as a text written in language of 20 amino acid codes, adapts N-gram tokens of fixed-length as its indexing scheme for sequence strings. After such tokens are indexed for all the sequences in the database, sequences can be searched with information retrieval algorithms. Using this new method, we have developed a protein sequence search system named as ProSeS (PROtein Sequence Search). ProSeS is a protein sequence analysis system which provides overall analysis results such as similar sequences with significant homologies, predicted subcellular locations of the query sequence, and major keywords extracted from annotations of similar sequences. We show experimentally that the N-gram indexing approach saves the retrieval time significantly, and that it is as accurate as current popular search tool BLAST.

• Computers and Concrete
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• 제10권6호
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• pp.557-573
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• 2012

This paper discusses the combined application of two different techniques, Neural Networks (NN) and Principal Component Analysis (PCA), for improved prediction of concrete properties. The combination of these approaches allowed the development of six neural networks models for predicting slump and compressive strength of concrete with mineral additives such as blast furnace slag, fly ash and silica fume. The Back-Propagation Multi-Layer Perceptron (BPMLP) with Bayesian regularization was used in all these models. They are produced to implement the complex nonlinear relationship between the inputs and the output of the network. They are also established through the incorporation of a huge experimental database on concrete organized in the form Mix-Property. Thus, the data comprising the concrete mixtures are much correlated to each others. The PCA is proposed for the compression and the elimination of the correlation between these data. After applying the PCA, the uncorrelated data were used to train the six models. The predictive results of these models were compared with the actual experimental trials. The results showed that the elimination of the correlation between the input parameters using PCA improved the predictive generalisation performance models with smaller architectures and dimensionality reduction. This study showed also that using the developed models for numerical investigations on the parameters affecting the properties of concrete is promising.

• Journal of Microbiology and Biotechnology
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• 제20권7호
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• pp.1114-1120
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• 2010

A chitosan-degrading fungus, BSF114, was isolated from soil. The culture preparation showed strong chitosanolytic enzyme activity at an optimum pH of 4.0 and optimum temperature of $60^{\circ}C$ after 36-40 h fermentation. The rapid decrease in the viscosity of the chitosan solution early in the reaction suggested an endo-type cleavage of the polymeric chitosan chains. To identify the isolated fungus, molecular biological and morphological methods were used. The fungal internal transcribed spacer (ITS) region 1 was amplified, sequenced, and then compared with related sequences in the GenBank database using BLAST. The phylogenetic relationships were then analyzed, and the results showed that the fungus belongs to Aspergillus fumigatus. Morphological observations were also used to confirm the above conclusion. The chitooligosaccharides (COS) obtained through hydrolyzing the colloidal chitosan showed that A. fumigatus BSF114 is suitable for degrading chitosan and producing chitooligosaccharides on a large scale. High concentrations of the COS (1,000 and 500 ${\mu}g/ml$) significantly proliferated mice marrow cells.

• 한국자기공명학회논문지
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• 제14권1호
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• pp.45-54
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• 2010

HP1423 (Y1423_HELPY) is a conserved hypothetical protein from H. pylori strain 26695. However, Sequence Blast result indicates that HP1423 belongs to S4 (PF01479) superfamily. According to Pfam database, the S4 domain is a small domain consisting of 60-65 amino acid residues, that probably mediates binding to RNA. In this study, we report the sequence-specific backbone resonance assignment of HP1423, which has 84 amino acid residues. We could assign unambiguously about 88% of all $^{1}H_{N}$, $^{15}N$, $^{13}C_{\alpha}$, $^{13}C_{\beta}$ and $^{13}C=O$ resonances. We could not detect the resonances from residues 15-20, and disappearance of these peaks seems to be related with the intermediate-conformational exchange. These assigned NMR peaks of HP1423 can be used for studying the role of protein dynamics in millisecond timescale, and Protein-RNA binding.

• Fisheries and Aquatic Sciences
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• 제3권1호
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• pp.64-70
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• 2000

DNA probes for the l6S rRNA have been designed for the detection of Edwardsiella tarda. In order to accomplish this purpose, the l6S rRNA gene from E. tarda has been cloned and sequenced. Two highly feasible oligonucleotide probe sites have been determined by the database analysis programs presented by PCGENE and BLAST. These two probes have been evaluated by slot blot hybridization analysis. Hetero- and homo-trimeric templates have been synthesized using these two probe sites. The templates have been further multimerized by PCR to generate between 150 and 300 bp long DIG-11-dUTP labeled probes. Unlike 3' end labeled oligonucleotide probes or templates, multimerized probes showed no cross­hybridization in the given experimental condition. Furthermore, a significant increase in sensitivity has been observed with these probes. This method, we presented here, may be useful for the designing of probes for the detection of other fish pathogenic microorganisms also.

• Journal of Ecology and Environment
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• 제34권3호
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• pp.323-331
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• 2011

Biodiversity and the community composition of micro-eukaryotic organisms were investigated in the Upo wetland in Korea using molecular analysis. Molecular identification was performed using cytochrome oxidase I (COI) and small subunit ribosomal DNA (SSU rDNA). The genomic DNA was isolated directly from soil samples. The COI and SSU rDNA regions were amplified using universal primers and then sequenced after cloning. In a similarity search of the obtained sequences with BLAST in the Genbank database, the closely related sequences from NCBI were used to identify the amplified sequences. A total of six eukaryotic groups (Annelida, Arthropoda, Rotifera, Chlorophyta, Bacillariophyta, and Stramenopiles) with COI and six groups (Annelida, Arthropoda, Rotifera, Alveolata, Fungi, and Apicomplexa) with SSU rDNA genes were determined in the Upo wetland. Among 38 taxa in 20 genera, which are closely related to the amplified sequences, 10 genera (50%) were newly reported in Korea and five genera (25%) were shown to be distributed in the Upo wetland. This approach is applicable to the development of an efficient method for monitoring biodiversity without traditional taxonomic processes and is expected to produce more accurate results in depositing molecular barcode data in the near future.

• 정보처리학회논문지D
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• 제11D권4호
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• pp.765-774
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• 2004

이질의 생물 정보원을 통합하기 위해서는 각 정보원의 이질적인 내용을 숨기고 하나의 관점으로 표현하는 뷰를 정의해야 한다. 본 논문은 생물 정보원 통합 미들웨어를 설계함에 있어서 XML 기반의 뷰 정의모델을 제시하고 그 동작 원리를 보인다. 제시된 모델은 통합시스템 구축을 위한 융통성을 증대시키고, 보다 추상화된 수준에서 통합 질의를 수행할 수 있도록 하기 위하여 사용자 정의 XML 뷰를 지원한다. 제시된 뷰 정의 모델을 기반으로 관계형 데이터베이스와 웹 자원에 대한 랩핑 모델을 제시하고, 아울러 응용 프로그램에 대해서도 같은 모델을 사용한 램핑 결과를 제시한다.

• Journal of Microbiology and Biotechnology
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• 제26권2호
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• pp.364-372
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• 2016

Sand tubules, made up of sand grains cemented by microbe-induced calcium carbonate precipitation, have been found in China's Ningxia Province. Sand tubules grow like a tree's roots about 40-60 cm below the surface. The properties of sand tubules and their bacterial community were examined. X-Ray diffraction analysis revealed that the sand tubules were associated with crystalline calcite. Scanning electron microscopy showed that the crystalline solid had a lamellar structure and lacked the presence of cells, suggesting that no bacteria acted as nucleation sites, nor that the crystalline solid was formed by the aggregation of bacteria. Denaturing gradient gel electrophoresis analysis showed 11 of the 12 detectable bands were uncultured bacteria by BLAST analysis in the GenBank database, and the rest were closely related to Paenibacillus sp. (100% identity). By cultivation techniques, the only strain isolated from the sand tubule was suggested to be related to Paenibacillus sp.; no archaea were found. Furthermore, Paenibacillus sp. was demonstrated to induce calcium carbonate precipitation in vitro.

• 대한의생명과학회지
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• 제18권1호
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• pp.49-55
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• 2012

Numerous biochemical molecules have been implicated in the development of muscular atrophy. However, control mechanisms associated with muscular disease are not clear. The present study was conducted to investigate gene expression profiles of rat muscle during the denervation to atrophy transition processes. We isolated total RNA from rats suffering from partial muscle atrophy (P) and electromyostimulated atrophy (PE) and synthesized cDNA using annealing control primers. Using 20 ACPs for PCR, we cloned 18 DEGs using TOPO TA cloning vector, sequenced, and analyzed their identities using BLAST search. Sequences of 14 clones significantly matched database entries, while one clone was ESTs, and 3 clones were unidentified. Different expression profiles of selected DEGs between P and PE were confirmed. The troponin T, Fkbp1a, RGD1307554, Phtf1, Atp1a1 and Commd3 were highly expressed genes in the P and PE groups, while Krox-25 and TCOX2 were only expressed genes in the P group, the Sv2b and Marcks were only expressed genes in PE group. also, Cox8h was highly expressed genes in PE groups. The ASPH, ND1, and ARPL1 were highly expressed genes in the P and PE groups. List of genes obtained from the present study might provide an insight for the study of mechanism regulating muscle atrophy and electrostimulated muscle atrophy transitions. These data suggest that troponin T, Fkbp1a, RGD1307554, Phtf1, Atp1a1, and Commd3 are potentially useful as clinical biomarkers of age-related muscle atrophy and dysfunction.