• Korean Journal of Pharmacognosy
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• v.30 no.4
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• pp.404-408
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• 1999

SH2 domains and their associated catalytic or noncatalytic proteins constitute critical signal transduction targets for drug discovery. Grb2 associates with phosphotyrosine sites of the activated receptors or Shc via their SH2 domain to link receptor tyrosine kinases to ras signalling. Blocking of the Grb2-Shc complex may be to intervene the oncogenic signal transduction pathways and to develop a new antitumor drug. In the search for blockers of Grb2 SH2-Shc interaction, Lutein, a family of carotenoids, was isolated from the extract of the leaf of Agastache rugosa O. Kuntze as SH2 domain antagonists. The $IC_{50}$ of Lutein against Grb2-Shc binding was $6.8\;{\mu}M$.

• Journal of Microbiology and Biotechnology
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• v.18 no.9
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• pp.1510-1517
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• 2008

Expresssed sequence tag (EST) analysis was developed from three cDNA libraries constructed from cells of the digestive tract, gonad, and liver of sea squirt. Randomly selected cDNA clones were partially sequenced to generate a total of 922 ESTs, in which 687 unique ESTs were identified respectively. Results of BLASTX search showed that 612 ESTs (89%) have homology to genes of known function whereas 75 ESTs (11%) were unidentified or novel. Based on the major function of their encoded proteins, the identified clones were classified into ten broad categories. We also identified several kinds of immune-related genes as identifying novel genes. Sequence analysis of ESTs revealed the presence of microsatellite-containing genes that may be valuable for further gene mapping studies. The accumulation of a large number of identified cDNA clones is invaluable for the study of sea squirt genetics and developmental biology. Further studies using cDNA microarrays are needed to identify the differentially expressed transcripts after disease infection.

• Asian Journal of Atmospheric Environment
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• v.5 no.3
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• pp.172-180
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• 2011

The transfer of microorganisms is important process for ecosystems. Microorganisms in dryland can transport itself to wetland through atmospheric diffusion, but only few papers reported about the atmospheric bioaerosol present over dryland. We carried out the direct sampling using a tethered balloon over Dunhuang City, China's northwestern dryland. Bioaerosols were collected using a tethered balloon with a bioaerosol collector at 820 m above the ground (1,960 m above the sea level) around noon on August 17, 2007. The bioaerosols were cultured after the collection at Dunhuang Meteorological observatory. Two strains of molds were isolated using the Nutrient agar medium. About 400-bp 18S rRNA partial sequences were amplified by PCR and determined afterwards. The results of a homology search by 18S rRNA sequences of isolates in DNA databases (GenBank, DDBJ, and EMBL) and an observation of the form revealed that two bioaerosols in the convective mixed layer over Dunhuang City were Cladosporium sp. and Aspergillus sp.

• Fisheries and Aquatic Sciences
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• v.7 no.3
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• pp.130-135
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• 2004

The marine dinoflagellate genus Alexandrium, which produces PSP toxins, has a global distribution. As human-assisted dispersal of the species has been suggested, it is important to develop molecular tools to trace the dispersal pathway. To screen population-specific DNA sequences that differentiate Korean and Japanese A. catenella, we targeted the area downstream of the chloroplast psbA gene using PCR with population-specific DNA primers followed by RFLP (restriction fragment length polymorphism) analysis and sequencing. The RFLP patterns of the PCR products divided Korean and Japanese A. catenella regional isolates into three types: Korean, Japanese, and type CMC3, isolated from Korea. We sequenced the PCR products, but found no similar gene in a homology search. The molecular phylogeny inferred from the sequences separated the Korean and Japanese A. catenella strains, as did the RFLP patterns. However, the Japanese isolates included two slightly different sequences (types J and K), while the Korean sequence was the same as the Japanese K type. In addition, a unique sequence was found in the Korean strains CMC2 and CMC3. Population-specific PCR amplification with Japanese A. catenella type-specific PCR primers designed from the type J sequence yielded PCR products for Japanese strains only, showing that the unknown gene can be used for a population analysis of Korean and Japanese A. catenella.

• Genomics & Informatics
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• v.11 no.3
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• pp.155-160
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• 2013

Structural information has been a major concern for biological and pharmaceutical studies for its intimate relationship to the function of a protein. Three-dimensional representation of the positions of protein atoms is utilized among many structural information repositories that have been published. The reliability of the torsional system, which represents the native processes of structural change in the structural analysis, was partially proven with previous structural alignment studies. Here, a web server providing structural information and analysis based on the backbone torsional representation of a protein structure is newly introduced. The web server offers functions of secondary structure database search, secondary structure calculation, and pair-wise protein structure comparison, based on a backbone torsion angle representation system. Application of the implementation in pair-wise structural alignment showed highly accurate results. The information derived from this web server might be further utilized in the field of ab initio protein structure modeling or protein homology-related analyses.

• Biotechnology and Bioprocess Engineering:BBE
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• v.5 no.1
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• pp.23-26
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• 2000

In order to develop the specific genetic marker for Korean native cattle (Hanwoo), randomly amplified polymorphic DNA (RAPD) analysis of 6 different cattle breeds was attempted by using 38 decamer primers. In comparison of RAPD patterns, two distinctive DNA bands specific for Hanwoo were detected. One was 296 bp of DNA fragment found to be specific only for female Hanwoo when primer GTCCACACGG was employed. In individual analysis of this RAPD marker was observed only in female individuals with the possibility of $85.3\%$. The other was 521 bp of RAPD marker amplified using TCGGCGATAG and AGCCAGCGAA primers, which showed $83.0\%$ of genetic frequency in 85 male and 68 female individuals tested. Nucleotide sequencing of these genetic markers revealed that 296 bp marker has a short micro satellite-like sequence, ACCACCACAC, and a tandem repeat sequence of microsatellite GAAAAATG in the determined sequence. Two distinctive tandem repeats of microsatellite sequences, MC and GAAGA, were also appeared in 521 bp DNA marker. In BLAST search, any gene having high homology with these markers was not found.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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• pp.83-85
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• 2000

A lot of microbial genome sequencing projects is being done in many genome centers around the world, since the first genome, Haemophilus influenzae, was sequenced in 1995. The deluge of microbial genome sequence data demands new and highly automatic data flow system in order for genome researchers to manage and analyze their own bulky sequence data from low-level to high-level. In such an aspect, we developed the automatic data management system for microbial genome projects, which consists mainly of local database, analysis programs, and user-friendly interface. We designed and implemented the local database for large-scale sequencing projects, which makes systematic and consistent data management and retrieval possible and is tightly coupled with analysis programs and web-based user interface, That is, parsing and storage of the results of analysis programs in local database is possible and user can retrieve the data in any level of data process by means of web-based graphical user interface. Contig assembly, homology search, and ORF prediction, which are essential in genome projects, make analysis programs in our system. All but Contig assembly program are open as public domain. These programs are connected with each other by means of a lot of utility programs. As a result, this system will maximize the efficiency in cost and time in genome research.

• Journal of Microbiology and Biotechnology
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• v.23 no.6
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• pp.872-877
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• 2013

In a previous study, we isolated and reported a second species of the Saccharophagus genus, Saccharophagus sp. strain Myt-1. In the present study, an alginate lyase gene (algMytC) from the genomic DNA of Myt-1 was cloned and characterized. The DNA sequence fragment obtained contained an open reading frame of 1,032 bp that encoded a protein of 343 amino acids with an estimated molecular mass of 37.6 kDa and a pI of 6.60. The deduced protein, AlgMytC, had the conserved amino acid sequences (RTELREM, QIH, YFKAGVYNQ) of the polysaccharide lyase family 7. A BLAST homology search indicated that AlgMytC shared an amino acid sequence identity of 95.9% with alg7A of S. degradans 2-40. The cloned and purified AlgMytC protein showed optimal activity at $40^{\circ}C$, and retained more than 90% of its total activity even after treatment at $25^{\circ}C$ for 24 h. AlgMytC was very alkaliphilic with an optimal pH of 9.0, and more than 90% of its activity was retained in the pH range 8.5-10.0. Moreover, AlgMytC was stable over a wide pH range. The activity of AlgMytC was also stable in the presence of various detergents.

• Proceedings of the Korea Society of Environmental Toocicology Conference
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• 2002.10a
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• pp.167-167
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• 2002

Methylmercury (MeHg), one of the heavy metal compound, can cause severe damage to the central nervous system in humans. Many reports have contributed MeHg poisoning to contaminated foods and release into the environment. Despite many studies on the pathogenesis of MeHg-induced central neuropathy, no useful mechanism of toxicity has been established. To find genes differentially expressed by MeHg in neuronal cell, we peformed forward and reverse suppression subtractive hybridization (SSH) method on mRNA derived from neuroblastoma cell line, SH-SY5Y treated with solvent (DMSO) and 6.25 uM (IC$\sub$50/) MeHg. Differentially expressed CDNA clones were sequenced and the mRNAs were re-examined on Northern blots. These sequences were identified by BLAST homology search to known genes or expressed sequence tags (ESTs). Analysis of these sequences has provided an insight into the biological effects of MeHg in the pathogenesis of neurodegenerative disease and a possibility to develop more efficient and exact monitoring system of heavy metals as common environmental pollutants.

• Journal of Life Science
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• v.21 no.6
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• pp.865-874
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• 2011

The genus Bryophyllum is best known for many of its species having the ability to produce plantlets on their leaves. This phenomenon is also known as vegetative reproduction. Differential expressed gene (DEG) detecting technique was applied in order to survey the genes involved in the process of asexual reproduction for plantlet formation. Based on homology search using the NCBI database after screening of genes, 38 genes were identified from a total of 69 DEGs. Most of these DEGs were related to cell division, to intercellular signal transduction, and to hormone (cytokinin and ethylene) signaling.