• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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• pp.69-70
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• 2000

The completion of sequencing human genome would motivate us to map millions of human cDNAs onto the unique ruler "genome sequence", in order to identify the exact address of each cDNA together with its exons, its promoter region, and its alternative splicing patterns. The expression patterns of some cDNAs could therefore be associated with these precise gene addresses, which further accelerate studies on mining correlations between motifs of promoters and expressions of genes in tissues. Towards the realization of this goal, we have developed a time-and-space efficient software named SQUALL that is able to map one cDNA sequence of length a few thousand onto a long genome sequence of length thirty million in a couple of minutes on average. Using SQUALL, we have mapped twenty thousand of our Bodymap (http://bodymap.ims.u-tokyo.ac.jp) cDNAs onto the genome sequences of Chr.21st and 22nd. In this talk, I will report the status of this ongoing project.

• Journal of Plant Biology
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• v.38 no.4
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• pp.359-364
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• 1995

As the first step to elucidate the relationship between the structure and function of CTP:phosphocholine cytidylyltransferase (EC 2.7.7.15) in plants, the partial nucleotide sequence of soybean cytidylyltransferase cDNA was determined using a polymerase chain reaction (PCR). Degenerate oligonucleotide primers were synthesized from the conserved region revealed from the rat and yeast cytidylyltransferase DNA sequences. The catalytic domain region showed 78 and 76% homology with the rat and yeast amino acid sequences, respectivly. The hydropathy profile indicated that the C-terminal non-catalytic portion of the protein was very hydrophilic, and in the region between the catalytic domain and the C-terminal region, there was a large amphipathic $\alpha$-helical domain that was believed to bind the membrane surface in the active formation. There are 7 potential sites for phosphorylation by protein kinase C and 4 potential sites for phosphorylation by Ca2+/calmodulin kinase within the determined sequence.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.34 no.2
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• pp.137-144
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• 2001

Sequences of partial 18S rDNA have been analyzed to elucidate genetic diversity of scallops collected around Korean sea, The scallops used in genetic comparison are Argopecten irradians concentricus, Amusium japonicum japonicum, Chlamys farreri farreri, Chlamys (Swiftopecten) swifti and Patinopecten yessoensis. The 18S rDNA sequences were aligned by Clustalx program. Phylogenetic tree was drawn by Treecon program, The scallops were divided into two groups-the Family Pectinidae containing A. japonicum japonicum and the Family Propeamussiidae containing Argopecten, Chlamys and Patinopecten genera. The Family Propeamussiidae was also divided into the Supergenera Aequipecten containing A. irradians concentricus and Supergenera Chlamys containing C. farreri farreri, C. swifti and P. yessoensis. The species of C. swifti was closer to the P. yessoensis rather than C. farreri farreri in respect to nuclear 18S rDNA sequence.

• International Journal of Industrial Entomology and Biomaterials
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• v.6 no.1
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• pp.87-92
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• 2003

We describe here the cloning, expression and characterization of a cDNA encoding a putative chemosensory protein (CSP) from the mole cricket, Gryllotalpa orientalis. The G. orientalis chemosensory protein cDNA sequences comprised of 384 bp with 128 amino acid residues. The G. orientalis chemosensory protein showed 75.4% protein sequence identity to the Locusta migratoria CSP, Northern blot analysis revealed that signal was stronger in head than leg and cuticle, indicating that the head part containing antennae is a main site for G. orientalis chemosensory protein synthesis. The cDNA encoding G. orientalis chemosensory protein was expressed as approximately 12 kDa polypeptide in baculovirus-infected insect cells.

• Mycobiology
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• v.28 no.1
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• pp.17-26
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• 2000

The orchid symbiotic fungi were isolated from the roots of Korean native orchid (Cymbidium goeringii) collected and Chinese orchid (C. sinense) obtained from greenhouses. They were identified as a species of Rhizoctonia, based on the sequences of 18r rDNA, the microscopic observations of mycelia, and the symbiotic relationships with commercial orchids. The isolate collected from Chinese orchids was revealed to be a species of Ceratobasidium endophytica, and to be different from the other isolates at the thickness of the mycelia stained in the root cells of Korean native orchids. The other isolates collected from the Korean native orchids were considered to be a species of Tulsanella repens (anamorphic: Epulorhiza repens) or its related one. The physiologic or microscopic variations were oftenly observed among them, but the tendency of grouping these in the 18s rDNA sequences were observed to be consistent with those of the localities collected. The further taxonomical segregating for Korean symbiotic fungi was not made because the information concerned were limited in this moment, but was recognized as based on the sequences of 18s DNA.

• Journal of Microbiology and Biotechnology
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• v.17 no.11
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• pp.1765-1771
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• 2007

A polymerase chain reaction (PCR)-based method was developed to detect the DNA of Ralstonia solanacearum, the causal agent of bacterial wilt in various crop plants. One pair of primers (RALSF and RALSR), designed using cytochrome c1 signal peptide sequences specific to R. solanacearum, produced a PCR product of 932 bp from 13 isolates of R. solanacearum from several countries. The primer specificity was then tested using DNA from 21 isolates of Ralstonia, Pseudomonas, Burkholderia, Xanthomonas, and Fusarium oxysporum f. sp. dianthi. The specificity of the cytochrome c1 signal peptide sequences in R. solanacearum was further confirmed by a DNA-dot blot analysis. Moreover, the primer pair was able to detect the pathogen in artificially inoculated soil and tomato plants. Therefore, the present results indicate that the primer pair can be effectively used for the detection of R. solanacearum in soil and host plants.

• Journal of Life Science
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• v.11 no.2
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• pp.74-80
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• 2001

The nucleotide sequences of the internal transcribed spacer regions (ITS1 and ITS2) of ribosomal DNA (rDNA), and the 5.85 rRNA gene, have been determined for 13 strains of dinoflagellates in order to analyze the phylo-genetic relationship. The DNA sequences contained considerable variation in the ITS regions, but little in the 5.85 rDNA. In addition, the ITS1 was more variable than the ITS2 in all species examined. The nucleotide length of this region varied from 519 bp to 596 bp depending on the taxa. The investigated taxa were divided into three large groups based on the ITS length, i. e., a group with short ITS region (A. fraterculus and Alexandrium sp.), a with ITS region group (P. micans, P. minimum and P. triestinum) and a with ITS region group (G. impudicum, C. polykrikoides, G. sanguineum, G. catenatum and H. triquetra). The relationship between nucleotide length of ITS1 and that of ITS2 was negative, whereas G+C content and nucleotide length showed positive correlation. In phylogenetic analyses producing NJ trees, the topology was similar cluster and clearly divided the taxa into three groups based on 5.8S rDNA that were similar to those based on morphological characteristics. In particular, G. impudicum was more closely related to G. catenatum than to C. polykrikoides using phylogenetic analysis. From this study, we chew that the length of ITS region contributes to discriminate Korean harmful algal species and ITS analysis is a useful method for resolving the systematic relationships of dinoflagellates.

• Animal Systematics, Evolution and Diversity
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• v.37 no.3
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• pp.229-234
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• 2021

Scolelepis (Scolelepis) daphoinos is newly reported in Korean fauna. This species can be distinguished from its congeners by the following characteristics: the presence of reddish pigment patches on the posterior part of the prostomium, notopodial postchaetal lamellae that are partially fused to the branchiae, and the presence of only the bidentate hooded hooks. The morphological diagnosis and photographs of S. (S.) daphoinos are provided. The partial mitochondrial cytochrome c oxidase subunit I (COI), 16S ribosomal DNA(16S rDNA), and the nuclear 18S ribosomal DNA (18S rDNA) sequences from Korean specimens of S. (S.) daphoinos were determined. Species identification was supported by a comparison of DNA barcode sequences of COI and 16S rDNA with morphological examination from the specimens of type locality, China.

• Korean Journal of Agricultural Science
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• v.30 no.1
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• pp.59-65
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• 2003

To investigate the relationship of endogenous retroviruses in peccaries and pigs, a set of degenerate primers was used in this study to amplify peccary retroviral sequences. The sequences of two putative retroviral clones showed close homology to mouse and pig retroviral sequences. The peccary endogenous retroviral sequences are significant in that they are the first such sequences reported in peccary species and repudiate old claims in the literature that peccaries do not have C-type retroviral sequences.

• Parasites, Hosts and Diseases
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• v.42 no.3
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• pp.129-135
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• 2004

We compared the DNA sequences of the genus Metagonimus: M. yokogawai, M. takahashii, and M. miyatai. We obtained 288 D1 ribosomal DNA (rDNA) and mitochondrial cytochrome c oxidase subunit I (mtCOI) fragments from the adult worms by PCR, that were cloned and sequenced. Phylogenetic relationships inferred from the nucleotide sequences of the 28S D1 rDNA and mtCOI gene. M. takahashii and M. yokogawai are placed in the same clade supported by DNA sequence and phylogenie tree analysis in 28S D1 rDNA and mtCOI gene region. The above findings tell us that M. takahashii is closer to M. yokogawai than to M. miyatai genetically. This phylogenetic data also support the nomination of M. miyatai as a separate species.