• Journal of Life Science
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• v.18 no.11
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• pp.1617-1624
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• 2008

Chitin and chitosan, which is deacetylated form of chitin, are one of the most abundant biomass on the earth. They showed various biological activities including antimicrobial activity, heavy metal chelating, immune system activation, and have very diverse applications in food, pharmaceutical, medicinal, and environmental industry. There have been reported many chitin/chitosan-hydrolyzing enzymes, their structures and genes from three domains, archaea, bacteria, and eukarya. Carbohydrate hydrolyzing enzymes are classified in CAZy (Carbohydrate Active Enzymes) database according to their amino acid sequence similarity. Interestingly, chitinases and chitosanases are classified in various glycosyl hydrolase(GH) families, GH2, GH5, GH7, GH8, GH18, GH19, GH20, GH46, GH48, GH73, GH75, GH80, GH84, and GH85. Here, we review characteristics and structures of chitin/chitosan hydrolyzing enzymes according to glycosyl hydrolase families in order to provide information about gene mining.

• Journal of Sericultural and Entomological Science
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• v.38 no.1
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• pp.19-24
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• 1996

To investigate the genes which is related to immune reaction of Bombyx mori, differential screening was carried out using naive and induced B. mori mRNA probe. To begin with, we constructed the cDNA library with mRNA isolated from fifth instar larvae injected with E. coli(4 X 106 cells/larva) using Uni ZAP XR vector kit. Thirty-two inducible cDNAs showing higher intensity on the induced mRNA probing membranes were selected. Partial nucleotide sequences of 29 clones were determined and their expessed sequence tags (ESTs) were produced. Nineteen ESTs in 29 ESTs were matched in GenBank database and the rest of them were found to be unknown. These unmatched ESTs were presumed to be novel genes. The nineteen ESTs contained variable genes related to biological process in Bombyx mori and four classes immune genes. Four clones, BmInc 6, 8, 18 and 27 were similar to two antibacterial peptide genes, hemolin gene and transferrin gene, respectively.

• Journal of Life Science
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• v.15 no.3 s.70
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• pp.427-433
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• 2005

With the completely discovery of the Drosophila genome sequence, the next great challenge is to extract its biological information by systematic expression and to perform functional analysis of the gene. Here we reported a proteome analysis of D. melanogaster with two-dimensional electrophoresis (2-DE) and matrix-assisted laser desorption ionization time-of-flight mass spectrometer (MALDI-TOF-MS). The cell extracts of D. melanogaster, $200{\mu}g$ were resolved to more than 400 silver-stained spots by 2-DE. The most abundant protein spots were ranged from 4.0-7.5 of pI and from 15-90 kDa of molecular weight. The excised spots were destained and in-gel digested by trypsin. The masses of the resulting peptide mixtures were measured by MALDI-TOF-MS. Identified proteins were compared with measured peptide mass and a dynamic peptide searching database which is accessible via the internet. The results revealed that identified proteins were produced by 59 genes derived from 65 protein spots.

• The KIPS Transactions:PartD
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• v.11D no.3
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• pp.519-532
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• 2004

With the explosion of bioinformatics data such proteins and genes, biologists need a integrated system to analyze and organize large datasets that interact with heterogeneous types of biological data. In this paper, we propose a integration system based on a mediated data warehouse architecture using a XML model in order to combine protein related data at biology laboratories. A fact constellation model in this system is used at a common model for integration and an integrated schema it translated to a XML schema. In addition, to track source changes and provenance of data in an integrated database employ incremental update and management of sequence version. This paper shows modeling of integration for protein structures, sequences and classification of structures using the proposed system.

• Korean Journal of Microbiology
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• v.54 no.3
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• pp.175-187
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• 2018

Myxobacteria produce diverse secondary metabolites for predation, self-defense, intercellular signaling, and other unknown functions. Many secondary metabolites isolated from myxobacteria show pharmaceutically useful bioactivity such as anticancer, antibacterial, and antifungal activities with a unique mechanism of action. Therefore, a large number of myxobacterial strains have been isolated globally and many bioactive compounds have been purified from them. However, 16S rRNA database analysis indicates that there are far more types of myxobacterial species in the wild than have ever been isolated, and genome sequence analysis suggests that each myxobacterium is capable of producing much more metabolites than already known. In this article, the current status of studies on the secondary metabolites from myxobacteria, their biosynthetic genes, biological functions, and transcriptional regulatory factors governing gene expression were reviewed.

• Korean Journal of Agricultural Science
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• v.45 no.4
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• pp.583-590
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• 2018

Genus Typha L. (Typhaceae; Cattail in common) is one of the hydrophytic plants found in semi-aquatic regions. About nine to 18 species of the genus exist all over the world. In Korea, the most commonly found cattail species are T. laxmanni and T. angustifolia. The aim of this study was to prepare a cDNA library and sequences and analyze expressed sequence tags (ESTs) from these species, T. laxmanni and T. angustifolia. In the case of T. laxmanni, we observed that 715 out of 742 ESTs had high quality sequences, whereas the remaining 27 ESTs were low quality sequences. In this study, we identified 77 contigs, 393 unassembled clones and 65.7% singletons. Furthermore, in the case of T. angustifolia, we recorded 992 high quality EST sequences, and by excluding 28 low quality sequences from among them, we retrieved 120 contigs, 348 unassembled clones and 48.9% singletons. The basic local alignment search tool (BLAST) and Kyoto encyclopedia of genes and genomes (KEGG) database results enabled us to identify the functional categories, i.e., molecular function (16.5%), biological process (22.2%) and cellular components (61.3%). In addition, between these two species, the no hits and anonymous genes were 4.2% and 11.7% and 6.2% and 11.2% in T. laxmanni and T. angustifolia, respectively, based on the BLAST results. The study concluded that they have certain species-specific genes. Hence, the results of this study on these two species could be a valuable resource for further studies.

• Proceedings of the National Institute of Ecology of the Republic of Korea
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• v.4 no.3
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• pp.104-114
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• 2023

In this study, the distribution, bait preference, hosts, symbionts, habitat status, and cytochrome c oxidase subunit-I sequences of the ant Linepithema humile were analyzed. This species habitat comprised approximately 1.5 km along stone crevices, flower gardens, roadsides, and container yards in the vicinity of Busan station, Korea. Feeding activity of this species was confirmed in 9 species of 7 families of plants. Which was approximately 14% of total flora (63 species of 37 families) in the studied area. Particularly, it was observed that Dendranthema indicum and Camellia japonica were the most frequently visited. Further, we verified that they interacted with four species of aphids. We identified 22 species of ants (17 genera, 4 subfamilies) inhabiting the Busan station area, including L. humile, Tetramorium tsushimae, Nylanderia flavipes and the alien species Paratrechina longicornis. In areas where L. humile was the dominant species, the habitat of local native ants was reduced by approximately 30%. Bait preference was ranked in the following order: jelly, water with glucose (25%), and yogurt, with the highest preference for baits containing sugar and protein. The 630-bp cytochrome c oxidase subunit-I sequences of the local L. humile populations were 99% identical to those of L. humile in the National Center for Biotechnology Information database, and the Argentine ants that invaded Korea had a sequence identical to that of other invasive populations from China, Japan, and New Zealand. As L. humile rapidly increases due to domestic adaptation, continuous monitoring and control strategy for eradication are needed to protect domestic biodiversity.

• Parasites, Hosts and Diseases
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• v.54 no.1
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• pp.21-29
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• 2016

The sodium hydrogen exchanger 1 (NHE1), which functions in maintaining the ratio of $Na^+$ and $H^+$ ions, is widely distributed in cell plasma membranes. It plays a prominent role in pH balancing, cell proliferation, differentiation, adhesion, and migration. However, its exact subcellular location and biological functions in Toxoplasma gondii are largely unclear. In this study, we cloned the C-terminal sequence of T. gondii NHE1 (TgNHE1) incorporating the C-terminal peptide of NHE1 (C-NHE1) into the pGEX4T-1 expression plasmid. The peptide sequence was predicted to have good antigenicity based on the information obtained from an immune epitope database. After induction of heterologous gene expression with isopropyl-b-D-thiogalactoside, the recombinant C-NHE1 protein successfully expressed in a soluble form was purified by glutathione sepharose beads as an immunogen for production of a rabbit polyclonal antiserum. The specificity of this antiserum was confirmed by western blotting and immunofluorescence. The antiserum could reduce T. gondii invasion into host cells, indicated by the decreased TgNHE1 expression in T. gondii parasites that were pre-incubated with antiserum in the process of cell entry. Furthermore, the antiserum reduced the virulence of T. gondii parasites to host cells in vitro, possibly by blocking the release of $Ca^{2+}$. In this regard, this antiserum has potential to be a valuable tool for further studies of TgNHE1.

• The Korean Journal of Malacology
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• v.32 no.4
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• pp.263-268
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• 2016

Metallothionein (MT) family of metal-binding proteins are involved in maintaining homeostasis and heavy metal poisoning. Recently, MT has been considered as a biomarker that can identify a particular species, very similar to the use of cytochrome oxidase I (COI) gene. Satsuma myomphala species of land snails have been reported from North-East Asia, including South Korea and Japan. In particular, the land snail species have been known from only a limited area of Geoje Island, Gyeongsangnam-do province of South Korea. Genetic studies of S. myomphala has been limited with only 6 nucleotide, 2 protein registered on the NCBI server. For elucidating the genetic information of S. myomphala, we conducted RNA sequencing analysis using Illumina HiSeq 2500 next-generation platform. We screened the MT gene from the RNA-Seq database to confirm the molecular phylogenetic relationship. After sequencing, the de novo analysis and clustering generated 103,774 unigenes. After annotation against PANM database using BLAST program, we obtained MT sequence of 74 amino acid residues containing the coding region of 222 bp. Based on this sequence, we found about 53 sequences using the BLAST program in NCBI nr database. Using ClustalX alignment, Maximum-Likehood Tree of MEGA program, we confirmed the molecular phylogenetic relationships that showed similarity with mollusks such as Helix pomatia and H. aspersa, Megathura crenulata.

• Journal of Sericultural and Entomological Science
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• v.51 no.2
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• pp.191-196
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• 2013

This study was aimed for development of a useful genes that has a transcript expressional specificity in the early embryonic stage of the silkworm, Bombyx mori. We constructed and analyzed a full-length cDNA library from silkworm's eggs which after a lapse of 2 ~ 6 hours post oviposit. A total 960 clones were randomly selected, and the 5' ends of the inserts were sequenced to generate 652 expressed sequence tags(EST). 334 unique ESTs were generated after the assembly of 652 ESTs. The annotation of 334 unique ESTs by BLAST search revealed that 156(47%) of the sequences represented known genes, whereas 178(53%) of the sequences has no matches in the database. Of the 156 known genes, the most abundant genes were heat shock protein hsp20.8 gene(12 times) and ubiqutin-like protein gene(11 times). The functional groups of these ESTs with matches in the database were constructed according to their putative molecular functions. Among thirteen functional categories, the largest groups were protein synthesis(9.6%) and cellular organization( 8.1%). Further defined studies on molecular functions and biological roles of their promoters will give us wellfined information and its application.