• Journal of Industrial Technology
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• v.26 no.B
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• pp.163-171
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• 2006

Human immunodeficiency virus type 1 (HIV-1) integrase plays a critical role in the life cycle of the HIV virus. An ability to accurately map its electrostatic potential, and then use this information to predict the manner in which DNA will bind to the active site of the catalytic domain could provide a foundation for inhibitory design. Attempts to discern the crystal structure of HIV-1 integrase have proven problematic, especially in the region of enzymatic activity, that being those residues involved in the catalysis of the integration of viral DNA into the host cell. However, there is a structural correlation in to the region of interest with avian sarcoma virus (ASV), so a homology model utilizing this similarity was constructed to approximate the behavior/structure of the undetermined portions of the HIV-1 integrase crystal. After this model was constructed and its energy minimized, electrostatic calculations were carried out on the substance, so that an electrostatic potential map was constructed. Using this information, it was determined that DNA binding was oriented so as to exploit the regions of positive potential nearby the active site, as well as the positive potential of the magnesium cofactors.

• BMB Reports
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• v.37 no.5
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• pp.527-532
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• 2004

A subtracted cDNA library specific to osmotic stress of Haloxylon ammodendron (Mey.) Bge seedlings was constructed by suppression subtractive hybridization (SSH) and T/A cloning. SSH was performed between two groups of H. ammodendron seedlings, one was cultivated in Hoagland (H) solution as a driver and the other group was treated with osmotic stress of the Hoagland solution by the addition of 400 mM mannitol (M), as a tester. The library consisted of about 400 recombinant clones, with the average size being of 500 bp, ranging from 300 bp to 1500 bp. Using a PCR-select differential screening kit, 100 recombinant clones were randomly chosen from the subtracted cDNA library and hybridized with forward,reverse subtracted and unsubtracted probes for two rounds. As a result, 21 positive clones specific to osmotic stress were obtained and some of them were verified by Northern blot analysis. The sequencing analysis of 6 positive clones and the following homology comparison to GenBank [blastx] non-redundant databases characterized that two sequences obtained in this experiment may contribute to novel drought-related genes.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.33 no.6
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• pp.496-500
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• 2000

Partial fragments of nuclear 185 rDNAs from morphologically wide and narrow thalli of the seaweed Porphyra pseudolineazis were amplified and sequenced to compare their DNA homology. Both sequences of 311 base pairs showed $100{\%}$ identical each other. They showed $97.7{\%}$ similarity with a wild strain collected at Sodol in Kangwondo, and $99.4{\%}$ similarity with the GenBank accession number AB013185 of the Japanese P. pseudolinearis. Thus the morphological difference of wide and narrow blades might not be a classification criterion for the sub-species level of P. pseudolinearis.

• 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.

• Journal of fish pathology
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• v.22 no.3
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• pp.391-400
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• 2009

Genetic identification of 17 fish-derived Aeromonas strains was attempted using 5 housekeeping genes. 16S rRNA, gyrB, rpoD, dnaJ and recA genes from the 17 strains were amplified, and total of 85 amplicons were sequenced. DNA sequences of the strains and type strains of the 17 Aeromonas homology groups were used for genetic identification and phylogenetic analyses. None of the strains was identified as a single species using the 16S rRNA gene, showing the same identities (average = 99.7%) with several Aeromonas species. According to gyrB, rpoD, dnaJ, and recA, 9 strains and RFAS-1 used in this study were identified as A. hydrophila and A. salmonicida, respectively. However, the other strains were closely related to 2 or more Aeromonas species (i.e., A. salmonicida, A. veronii, A. jandaei, A. media and A. troda) depending on the genetic marker used. In this study, gyrB, rpoD, dnaJ and recA gene sequences proved to be advantageous over 16S rRNA for the identification of field Aeromonas isolates obtained from fish. However, there are discrepancies between analyses of different phylogenetic markers, indicating there are still difficulties in genetic identification of the genus Aeromonas using the housekeeping genes used in this study. Advantages and disadvantages of each housekeeping gene should be taken into account when the gene is used for identification of Aeromonas species.

• Korean Journal of Plant Resources
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• v.18 no.2
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• pp.240-245
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• 2005

A cDNA clone homologous to glutathione S-transferase gene was isolated and characterized from Codonopsis lanceolata(ClGST). The ClGST is 761 nucleotides long and has an open reading frame of 522 bp with a deduced amino acid sequence of 173 residues. The ClGST shows meaning homology to A. thaliana(AAC63629) $71\%$, C. chinense(CAI51314) $73\%$, E. esula(AAE65767) $75\%$, H. muticus(CAA55039) $70\%$, N. plumbaginifolia(CAA96431) $77\%$, S. commersonii(AAB65163).

• Korean Journal of Plant Resources
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• v.27 no.3
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• pp.249-255
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• 2014

The rice belonging to Oryza sativa is not only has significant economic importance, for it is the major source of nutrition for about 3 billion all around the world. But also plays a vital role as a model organism, because it has a number of advantages to be a model plant, such as efficient transformation system and small genome size. Many methods and techniques have been conducted to attempt to distinguish different Oryza sativa species, such as amplified fragment length polymorphism (AFLP), random amplified polymorphic DNA (RAPD), simple sequence repeat (SSR) and so on. However, studies using sequence analysis of internal transcribed spacer (ITS), a region of ribosomal RNA has not been reported until now. This study was undertaken with an aim to understand the phylogenetic relationships among sixteen isolates of Oryza sativa collected from abroad and fifteen isolates collected from Korea, using ribosomal RNA (rRNA) internal transcribed spacer (ITS) sequences to compare the phylogeny relationships among different Oryza sativa species. The size variation obtained among sequenced nuclear ribosomal DNA (nrDNA) ITS region ranged from 515bp to 1000bp. The highest interspecific genetic distance (GD) was found between Sfejare 45 (FR12) and Anapuruna (FR15). Taebong isolate showed the least dissimilarity of the ITS region sequence with other thirty isolates. This consequence will help us further understanding molecular diversification in intra-species population and their phylogenetic analysis.

• Archives of Pharmacal Research
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• v.19 no.6
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• pp.497-501
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• 1996

A gene coding for triosephosphate isomerase (TPI) from a rat skeletal muscle cDNA library was cloned and its nucleotide sequence was determined. The 1, 348-bp cDNA clone contains 24 bp $5^I$ noncoding region, the entire 750 bp coding region corresponding to a protein of 249 amino acids, $547bp 3^I$ noncoding region and part of a poly(A) tail. It also contains a polyadenylation signal, AATAAA, starting from 17 bp upstream of the poly(A) tail. The calculated molecular weight of rat TPI is 27.8 kDa and the net charge is +4. The deduced amino acid sequence from rat TPI CDNA sequence has 93% and 94% homology with that of mouse and human clones, respectively. The amino acids at the residue of Asn12, Lys14, His96, Glu 166, His96, His101, Ala177, Tyr165, Glu13O, Tyr2O9, and Ser212 in catalytic site are completely identical, confirming that the functional residues in TPI proteins are highly conserved throughout evolution. The most profound characteristic of rat TPI enzyme, compared with other TPIs, is that there are five cysteine substitutions at the residue of 21, 27, 159, 195 and 204. A Glu123 instead of Gly was found in rabbit, rhesus, mouse and human sequences. Through the method of RT-PCR, the mRNA transcription level of TPI gene was found to be different among various tissues and was highest in muscle.

• Journal of Microbiology
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• v.41 no.4
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• pp.295-299
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• 2003

Adenovirus (Ad) precursor to the terminal protein (pTP) plays an essential roles in the viral DNA replication. Ad pTP serves as a primer for the synthesis of a new DNA strand during the initiation step of replication. In addition, Ad pTP forms organized spherical replication foci on the nuclear matrix (NM) and anchors the viral genome to the NM. Here we identified the interferon inducible gene product 1-8D (Inid) as a pTP binding protein by using a two-hybrid screen of a HeLa cDNA library. Of the clones obtained in this assay, nine were identical to the Inid, a 13-kDa polypeptide that shares homology with genes 1-8U and Leu-13/9-27, most of which have little known functions. The entire open reading frame (ORF) of Inid was cloned into the tetracycline inducible expression vector in order to determine the biological functions related with adenoviral infection. When Inid was introduced to the cells along with adenoviruses, fifty to sixty percent of Ad-infected cells expressing Inid had rounded morphology, which was suggestive of apoptosis. Results from the terminal deoxynucleotidyl transferase (TdT) and DNA fragmentation assays confirmed that Inid induces apoptosis in Ad-infected or in uninfected cells. The Inid binding to pTP may target the cell for apoptotic destruction as a host defense mechanism against the viral infection.

• Journal of Microbiology and Biotechnology
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• v.13 no.6
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• pp.1018-1020
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• 2003

The complete 1,486 nucleotide sequence of a cryptic plasmid separated from Lactobacillus bifermentans strain A02 isolated from Kimchi has been determined. The plasmid, designated as pA021, encodes a 33,488 Da putative Rep protein. Based on the sequence similarity, the protein shows homology with coding protein of pRS1, a previously reported plasmid of Oenococcus oeni and the replication initiation protein (Rep) of the Staphylococcal pT181 plasmid family.