• The Korean Journal of Malacology
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• v.30 no.2
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• pp.155-163
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• 2014

Serpins are a group of proteins involved in the regulation of serine and other type of proteases, and have been identified in many kinds of organisms from invertebrates to vertebrates. Serpins are known to regulate the proteolytic cascades of the innate immune pathways in addition to their roles in blood coagulation, angiogenesis, fibrinolysis, inflammation and tumor suppression. In this study, we have isolated two partial serpin gene fragments from expressed sequence tags (ESTs) of Nesiohelix samarangae. Dotplot analysis indicates that they are of two different types, Ns-serpin type 1 and Ns-serpin type 2. Ns-serpin type 1 has 819 bp coding region (272 amino acids), whereas Ns-serpin type 2 has 555 bp coding region (185 amino acids). Molecular phylogenetic analysis shows that the identified serpins have high similarities to their counterparts in the California see slug, Aplysia californica. Yet, the precise biological and immunological roles of these Ns-serpins remain to be further investigated using RNA interference and other molecular techniques.

• Journal of Ginseng Research
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• v.29 no.4
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• pp.167-175
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• 2005

The $Ca^{2+}-activated$ chloride channel (CLCA) was activated by ginseng total saponin (GTS) in Xenopus oocytes. The reverse transcription PCR (RT-PCR) method was performed with gene specific primers on oocytes. The gene specific primers were deduced from spleen cDNA in expressed sequence tags (EST) database showing high homology to the mouse CLCA. Full length of cDNA sequence was completed by linkage of several 5' and 3'-half cDNA fragments have been sequenced. We named the full cDNA to oCLCA transiently. The oCLCA gene encodes a protein of 911 amino acids with $48.9\%$ identity overall to that of mouse CLCA (mCLCA4). A predicted oCLCA amino acids sequence shows the molecular weight of 108 kDa and has four or more transmembrane domains, and also the one hydrophobic C­terminal domain. oCLCA gene was expressed ubiquitously in various tissues included oocytes, also interfered in oocytes by siRNA for oCLCA. Here, we suggest that oCLCA is a endogenous chloride channel gene in oocytes. We are studying for the identification of oCLCA gene and further physiological research.

• Fisheries and Aquatic Sciences
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• v.12 no.4
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• pp.286-292
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• 2009

We have constructed a cDNA library using brain samples of olive flounder Paralichthys olivaceus. Here, we described the study on gene identification by screening 356 clones from the brain cDNA library of olive flounder. Here, we screened 356 clones from the library to identify genes. Of these, 176 (49.5%) were identified as orthologs of known genes from olive flounder and other organisms. Among the 176 EST clones, 33 (18.7%) represented 11 unique genes that are identical to expressed sequence tags (ESTs) reported for olive flounder, and 120 (68.2%) represented 102 unique genes known from other organisms. The percentage of unknown genes (50.5%) is higher than in other olive flounder cDNA libraries (Lee et al., 2003, 2006, 2007), reflecting the high complexity of brain tissue. Further studies of expression characterization and developmental behavior related to these genes should provide useful insight into the physiological functions of the brain in olive flounder.

• Journal of fish pathology
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• v.21 no.2
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• pp.129-137
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• 2008

We constructed a black rockfish (Sebastes schlegeli) leukocyte cDNA library and a total of 386 expressed sequence tag (EST) clones were generated. Gene annotation procedures and homology searches of the sequenced ESTs were locally done by BLASTX for amino acid similarity comparisons. Of the 386 EST clones, 199 different ESTs showed significant homology to previously described genes while 97 ESTs were unidentified, hypothetical, or unnamed proteins. Encoding 38 different sequences were identified as putative bio-defense genes or genes associated with immune response.

• Plant Breeding and Biotechnology
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• v.6 no.4
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• pp.337-353
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• 2018

We used Illumina/HiSeq sequencing for analysis of gene expression profiling among four maize seed types (dent, CM3 and CM6; waxy, CM5 and CM19) at 10 DAP (days after pollination). A total of 88,993,000 (CM3), 103,817,340 (CM6), 103,139,640 (CM5), and 66,978,958 (CM19) sequence reads were generated with read lengths of about 0.9, 1.0, 1.0, and 0.7 billion bp, respectively. We obtained 69.1 (CM3), 71.0 (CM6), 71.2 (CM5), and 71.8% (CM19) high quality reads from the raw data and compared them with reference RNA sequences in a public DB (NCBI). It was revealed that mapped reads were 58%, 63%, 62%, and 62% of the EST reference in CM3, CM6, CM5 and CM19, respectively; and more than 51,000 genes were expressed based on RPKM criteria (over 0.25 value) in each CM3, CM6, CM5, and CM19 inbred line. In differentially expressed gene (DEG) analysis, we found that 3,527 genes were differentially expressed by at least two-fold with 1,709 upregulated in the two waxy inbred lines and 1,818 upregulated in the two dent inbred lines. We also detected genes for the sucrose and starch biosynthesis pathways based on BINs, and different expression patterns between waxy and dent inbred lines were shown for the gene set for starch synthesis, such as sh2, bt2, du1, wx1, and ae1. Although some genes were more expressed in dent lines, most genes for starch synthesis were much expressed in waxy lines. Especially, there was greater expression of the sus2 gene in both waxy lines compared with the dent lines.

• Journal of fish pathology
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• v.14 no.2
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• pp.59-64
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• 2001

A complementary DNA encoding metallothionein(MT), a heavy metal-responsive protein was cloned from a cartilaginous shark species. Scyliorhinus torazame. An expressed sequence tag(EST)from the shark liver, which showed high similarity with a MT gene, was isolated and its full-length sequence(390bp)was determined. The putative shark MT cDNA sequence contained an open reading frame consisting 68 amino acids and 182bp of 3-untranslated region including the poly (A+) signal. The deduced amino acid sequence was 41-54% identical to those of other animals including mammals and fish species. Tiger shark MT cDNA showed high conservation in the Cys regions. however, peculiarly contained not only additional five amino acids just prior to the conserved beta-domain but also a Ser residue at C terminal, which has not been seen in other MT sequences.

• International Journal of Industrial Entomology and Biomaterials
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• v.18 no.2
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• pp.113-120
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• 2009

Embryonic lethal abnormal visual (elav) is a lethal gene in Drosophila inducing the abnormal development and function of nervous system. We cloned a Bm-elav gene by bioinformatics and biological experiment, based on sequence of ELAV protein and dbEST of Bombyx mori. The full-length of Bm-elav cDNA is 1498 bp, contains a 906 bp open read frame (ORF) encoding a precursor of 301 amino acid residues with a calculated molecular weight of 34 kDa and pI of 8.99. Bm-ELAV protein precursor contains three RNA recognition motifs (RRM) in $24{\sim}91$, $110{\sim}177$ and $222{\sim}295$ bit amino acid residues respectively, and belongs to RNA-binding protein family. Bm-ELAV shared varying positives, ranging from 56% to 60% (Identities from 41% to 45%), with RRM from other species of Xenopus tropicalis, Apis mellifera, Tribolium castaneum, Branchiostoma belcheri and Drosophila. Gene localization indicated that Bm-elav is a single-copy gene, gene mapping within 12-chromosome from 7916.68 knt to 7918.16 knt region of nscaf2993. Spatiotemporal expressions pattern analysis revealed that Bm-elav expressed higher in most tested tissues and developmental stages in whole generation, such as silk gland, fat body, midgut, hemopoietic organ and ovary, but almost no expression in terminated diapause eggs. This suggested that the expression of Bm-elav in early developmental embryonic stages might induce abnormal development like in Drosophila. Cloning of the Bm-elav gene enables us to test its potential role in controlling pests by transferring the gene into field lepidopteran insects in the future.

• Journal of Microbiology and Biotechnology
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• v.26 no.4
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• pp.730-738
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• 2016

est19 is a gene from Bacillus sp. K91 that encodes a new esterase. A comparison of the amino acid sequence showed that Est19 has typical Ser-Gly-Asn-His (SGNH) family motifs and could be grouped into the SGNH hydrolase family. The Est19 protein was functionally cloned, and expressed and purified from Escherichia coli BL21(DE3). The enzyme activity was optimal at 60℃ and pH 9.0, and displayed esterase activity towards esters with short-chain acyl esters (C₂-C₆). A structural model of Est19 was constructed using phospholipase A1 from Streptomyces albidoflavus NA297 as a template. The structure showed an α/β-hydrolase fold and indicated the presence of the typical catalytic triad Ser49-Asp227-His230, which were further investigated by site-directed mutagenesis. To the best of our knowledge, Est19 is a new member of the SGNH hydrolase family identified from thermophiles, which may be applicable in the industrial production of semisynthetic β-lactam antibiotics after modification.

• Parasites, Hosts and Diseases
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• v.49 no.3
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• pp.221-228
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• 2011

Rodent malaria parasites, such as Plasmodium berghei, are practical and useful model organisms for human malaria research because of their analogies to the human malaria in terms of structure, physiology, and life cycle. Exploiting the available genetic sequence information, we constructed a cDNA library from the erythrocytic stages of P. berghei and analyzed the expressed sequence tag (EST). A total of 10,040 ESTs were generated and assembled into 2,462 clusters. These EST clusters were compared against public protein databases and 48 putative new transcripts, most of which were hypothetical proteins with unknown function, were identified. Genes encoding ribosomal or membrane proteins and purine nucleotide phosphorylases were highly abundant clusters in P. berghei. Protein domain analyses and the Gene Ontology functional categorization revealed translation/protein folding, metabolism, protein degradation, and multiple family of variant antigens to be mainly prevalent. The presently-collected ESTs and its bioinformatic analysis will be useful resources to identify for drug target and vaccine candidates and validate gene predictions of P. berghei.

• Journal of the Korea Organic Resources Recycling Association
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• v.18 no.3
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• pp.31-37
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• 2010

Chitinases (EC 3.2.1.14) hydrolyze the ${\beta}$-1,4-linkages in chitin, the second most abundant polymer of N-acetyl-${\beta}$-D-glucosamine which is a structural component of protective biological matrices such as fungal cell walls and insect exoskeletons. The glycosyl hydrolases 18 family including chitinases is an ancient gene family widely expressed in archea, prokaryotes and eukaryotes. Since earthworms live in the soil with a lot of microbial activities and fungi are supposed to be a major component of the diet of earthworm, it has been reported that there would be appropriate immune system to protect themselves from microorganisms attacks. In this study, the novel chitinase, EaChi, from the midgut of earthworm, Eisenia andrei, were identified and characterized. To obtain full-length cDNA sequence of chitinase, RT-PCR and RACE-PCR analyses were carried out by using the previously identified EST sequence amongst cDNA library established from the midgut of E. andrei. EaChi, a partial chitinase gene, was composed of 927 nucleotides encoding 309 amino acids. By the multiple sequence alignments of amino acids with other different species, it was revealed that EaCHI is a member of glycosyl hydrolases 18 family, which has two highly conserved domains, substrate binding and catalytic domain.