• Journal of agriculture & life science
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• v.46 no.4
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• pp.9-20
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• 2012

Eugenol is a volatile compound synthesized by eugenol synthase in various plants and belongs to phenylpropene compounds. However, characteristics of eugenol synthase in tomato has not been known. Therefore, we cloned a full length cDNA of a putative eugenol synthase from tomato 'Micro-Tom' using rapid amplification of cDNA ends (RACE) technique and named a clone SlEGS. Open reading frame of SlEGS was 921bp long and its deduced amino acid sequence was 307bp. The BLAST analysis indicated that SlEGS shared high similarity with PhEGS1 (67.1%) and CbEGS2 (69.4%). Amino acid composition of SlEGS was determined by CLC genomics workbench tool and 3D structure of SlEGS was constructed by homology modeling using Swiss-PDB viewer and validated using PROCHECK and ProSA-web tool. In addition, the physiochemical properties of SlEGS was evaluated using ExPASy's ProtParam tool. Molecular weight was 33.93kDa and isoelectric point was 5.85 showing acidic nature. Other properties such as extinction coefficient, instability index, aliphatic index, and grand average hydropathy was also analyzed.

• 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.

• BMB Reports
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• v.38 no.1
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• pp.28-33
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• 2005

A gene coding a novel isoform of carbamyl phosphate synthetase I (CPS1) was cloned from a human testicular library. As shown by cDNA microarray hybridization, this gene was expressed at a higher level in human adult testes than in fetal testes. The full length of its cDNA was 3831 bp, with a 3149 bp open reading frame, encoding a 1050-amino-acid protein. The cDNA sequence was deposited in the GenBank (AY317138). Sequence analysis showed that it was homologous to the human CPS1 gene. The putative protein contained functional domains composing the intact large subunit of carbamoyl phosphate synthetase, thus indicated it has the capability of arginine biosynthesis. A multiple tissue expression profile showed high expression of this gene in human testis, suggesting the novel alternative splicing form of CPS1 may be correlated with human spermatogenesis.

• Parasites, Hosts and Diseases
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• v.41 no.2
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• pp.89-96
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• 2003

Among the panel of monoclonal antibodies (mAb) against Toxoplasma gondii, mAb of Tg621 (Tg621) clone blotted 38 kDa protein which localized in the cytoplasm of tachyzoites by immunofluorescence microscopy The protein was not released into the parasitophorous vacuole during or after invasion. The cDNA fragment encoding the protein was obtained by screening a T. gondii cDNA expression library with Tg621. The full length cDNA sequence was completed with 5’-RACE as 1,592 bp, which contained open reading frame of 942 bp. The deduced amino acid sequence of Tg621 consisted of a polypeptide of 313 amino acids, with significant homology to ribosomal P proteins (RPP) of other organisms especially high to those of apicomplexan species. The expressed and purified TgRPP was assayed in western blot with the sera of toxoplasmosis patients and normal sera, which resulted in the 74.0% of positive reactions in toxoplasmosis patients whereas 8.3% in normal group. Therefore, the antibody formation against TgRPP in toxoplasmosis patients was regarded as specific for T. gondii infection and suggested a potential autoantibody.

• Plant Resources
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• v.8 no.2
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• pp.110-115
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• 2005

Ribosomal protein complex with ribosomal RNA to form the subunits of the ribosome serve essential functions in protein synthesis. A full-length cDNA (PRPS4) encoding ribosomal protein S4 has been isolated and its nucleotide sequence determined in ginseng plant (Panax ginseng). A PRPS4 cDNA is 1105 nucleotides long and has an open reading frame of 792 bp with a deduced amino acid sequence of 264 residues (pI 10.67). The deduced amino acid sequence of PRPS4 matched to the previously reported ribosomal protein S4 genes. Their degree of amino acid identity ranged from 68 to $92\%$. Phylogenetic analysis based on the amino acid residues showed that the PRPS4 grouped with ribosomal protein S4 of S. tuberosum (CAA54095).

• Journal of Plant Biotechnology
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• v.40 no.2
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• pp.102-110
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• 2013

The novel BrRZFPs genes encoding C3HC4-type RING zinc finger protein were identified from FOX (full length cDNA over-expressing) library of Brassica rapa. Ten full-length cDNAs obtained from the library encode zinc-finger protein containing 346 amino acids, designated BrRZFPs. These genes were classified into four groups by phylogenic analysis showing conserved protein sequences at both termini. The tissue distribution of BrRZFPs transcription was examined by qRT-PCR revealing ubiquitous expression pattern. However, each gene was strongly expressed in the specific tissue. Transcriptional analysis showed that those acquired 10 genes were inducible under abiotic stresses. Likewise, the transcript of BrRZFP3 was strongly induced (~12-folds) by exogenous abscisic acid, whereas the transcripts of BrRZFP1, BrRZFP2 and BrRZFP3 were (> 9-folds) induced by cold. We suggest that these BrRZFPs that function as signal or response to abiotic stress are useful for crop improvement.

• Genomics & Informatics
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• v.3 no.1
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• pp.24-29
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• 2005

TRPV2 is a non-specific cation channel expressed in sensory neurons, and activated by noxious heat. Particularly, TRPV2 has six transmembrane domains and three ankyrin repeats. TRPV2 has been cloned from various species such as human, rat, and mouse. Oocytes of Xenopus laevis - an African clawed frog ­have been widely used for decades in characterization of various receptors and ion channels. The functional property of rat TRPV2 was also identified by this oocyte expression system. However, no TRPV2 orthologue of Xenopus laevis has been reported so far. Hence, we have focused to clone a TRPV2 orthologue of Xenopus laevis with the aid of bioinformatic tools. Because the genome sequence of Xenopus laevis is not available until now, a genome sequence of Xenopus tropicalis - a close relative species of Xenopus laevis - was used. After a number of bioinformatic searches in silico, a predicted full-length sequence of TRPV2 orthologue of Xenopus tropicalis was found. Based on this predicted sequence, various approaches such as RT-PCR and 5' -RACE technique were applied to clone a full length of Xenopus laevis TRV2. Consequently, a full-length Xenopus laevis TRPV2 was cloned from heart cDNA.

• Interdisciplinary Bio Central
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• v.2 no.4
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• pp.13.1-13.8
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• 2010

The National BioResource Project of Japan is a governmental project to promote domestic/international research activities using biological resources. The project has 27 biological resources including three cereal resources. The core center and sub-center which historically collected the cereal resources were selected for each cereal program. These resources are categorized into several different types in the project; germplasm, genetic stocks, genome resources and database information. Contents of rice resources are wild species, local varieties in East and Southwest Asia & wild relatives, MNU-induced chemical mutant lines, marker tester lines, chromosome substitution lines and other experimental lines. Contents of wheat resources are wild strains, cultivated strains, experimental lines, rye wild and cultivated strains; EST clones and full-length cDNA clones. Contents of barley resources are cultivar and experimental lines, core collection, EST/cDNA clones, BAC clones, their filters and superpool DNA. Each resource is accessible from the online database to see the contents and information about the resources. Links to the genome information and genomic tools are also important function of each database. The major contents and some examples are presented here.

• Korean Journal of Agricultural Science
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• v.38 no.1
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• pp.11-16
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• 2011

In this study, we report the generation and analysis of a total of 1,211 expressed sequence tags (ESTs) from Pinus koraiensis. A cDNA library was generated from the young leaf tissue and a total of 1,211 cDNA were partially sequenced. EST and unigene sequence quality were determined by computational filtering, manual review, and BLAST analyses. In all, 857 ESTs were acquired after the removal of the vector sequence and filtering over a minimum length 50 nucleotides. A total of 411 unigene, consisting of 89 contigs and 322 singletons, was identified after assembling. Also, we identified 77 new microsatellite-containing sequences from the unigenes and classified the structure according to their repeat unit. According to homology search with BLASTX against the NCBI database, 63.1% of ESTs were homologous with known function and 22.2% of ESTs were matched with putative or unknown function. The remaining 14.6% of ESTs showed no significant similarity to any protein sequences found in the public database. Gene ontology (GO) classification showed that the most abundant GO terms were transport, nucleotide binding, plastid, in terms biological process, molecular function and cellular component, respectively. The sequence data will be used to characterize potential roles of new genes in Pinus and provided for the useful tools as a genetic resource.

• Fisheries and Aquatic Sciences
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• v.6 no.4
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• pp.180-186
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• 2003

The full-length cDNA encoding the pre-protein growth hormone (sfGH) from spotted flounder (Verasper variegatus) was amplified by the rapid amplification of cDNA ends (RACE) using degenerated oligonucleotide primers derived from conserved growth hormone sequences. It consists of 901 nucleotides in length, including the coding region of 609 nucleotides, 111 nucleotides of a 5' untranslated region, and 181 nucleotides of a 3' untranslated region. The conserved polyadenylation signal (AATAAA) lies 12 bases upstream from the poly (A) tail. The deduced amino acid sequence shows an open reading frame encoding a pre-protein of 203 amino acids and a putative signal peptide of 17 amino acids, suggesting that the mature hormone consists of 186 amino acids. The analyses of sfGH reveal some unique structural features. The repetitive sequences are located in the 5' untranslated region of sfGH cDNA and consist of tandem arrays of imperfect direct repeat monomers. Moreover, sfGH contains six Cys residues, as opposed to four or five in other GHs, and it is clearly distinguishable from olive flounder (Paralichthys olivaceus) GH, which lacks a region corresponding to residues 175-188 in alignment positions. It has important implications from an evolutionary standpoint, suggesting possible divergence among flatfishes.