• Journal of Microbiology and Biotechnology
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• v.25 no.9
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• pp.1417-1424
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• 2015

In this study, we tried to characterize Streptomyces peucetius CYP157C4 with homology modeling using three cytochrome P450 (CYP) structures (CYP157C1, CYP164A2, and CYP107L1), having discovered that CYP157C4 lacks the ExxR motif that was considered invariant in all CYPs. We used Discovery Studio 3.5 to build our model after first assessing the stereochemical quality and side-chain environment, and a 7-ethoxycoumarin substrate was docked into the final model. The model-substrate complex allowed us to identify functionally important residues and validate the active-site architecture. We found a distance of 4.56 Å between the 7-ethoxycoumarin and the active site of the heme, and cloning and an in vitro assay of the CYP157C4 showed the dealkylation of the substrate. Since the details regarding this group of CYP structures are still unknown, the findings of this study may provide elucidation to assist with future efforts to find a legitimate substrate.

• Journal of Microbiology and Biotechnology
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• v.24 no.6
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• pp.835-842
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• 2014

Haloperoxidase (HPO, E.C.1.11.1.7) is a metal-containing enzyme oxidizing halonium species, which can be used in the synthesis of halogenated organic compounds, for instance in the production of antimicrobial agents, cosmetics, etc., in the presence of halides and $H_2O_2$. To isolate and evaluate a novel non-metal HPO using a culture-independent method, a cassette PCR library was constructed from marine seawater in Japan. We first isolated a novel HPO gene from Pseudomonas putida ATCC11172 by PCR for constructing the chimeric HPO library (HPO11172). HPO11172 showed each single open-reading frame of 828 base pairs coding for 276 amino acids, respectively, and showed 87% similarity with P. putida IF-3 sequences. Approximately 600 transformants screened for chimeric genes between P. putida ATCC11173 and HPO central fragments were able to identify 113 active clones. Among them, we finally isolated 20 novel HPO genes. Sequence analyses of the obtained 20 clones showed higher homology genes with P. putida or Sinorhizobium or Streptomyces strains. Although the HPO A9 clone showed the lowest homology with HPO11172, clones in group B, including CS19, showed a relatively higher homology of 80%, with 70% identy. E. coli cells expressing these HPO chimeric genes were able to successfully bioconvert chlorodimedone with KBr or KCl as substrate.

• The Journal of the Institute of Internet, Broadcasting and Communication
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• v.18 no.1
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• pp.223-229
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• 2018

This paper proposes a robust technique of image segmentation, which can be obtained if the topological persistence of each connected component is used as the feature vector for the graph-based image segmentation. The topological persistence of the components, which are obtained from the super-level set of the image, is computed from the morse function which is associated with the gray-level or color value of each pixel of the image. The procedure for the components to be born and be merged with the other components is presented in terms of zero-dimensional homology group. Extensive experiments are conducted with a variety of images to show the more correct image segmentation can be obtained by merging the components of small persistence into the adjacent components of large persistence.

• Bulletin of the Korean Chemical Society
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• v.28 no.6
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• pp.941-946
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• 2007

Bacillus halodurans O-methyltransferase (BhOMT) is a S-adenosylmethionine (SAM or AdoMet) dependent methyltransferase. Three dimensional structure of the BhOMT bound to S-adenosyl-L-homocysteine (SAH or AdoHcy) has been determined by comparative homology modeling. BhOMT has 40% sequence identity with caffeoyl-CoA 3-O-methyltransferase (CCoAOMT) from alfalfa. Based on x-ray structure of CCoAOMT, three dimensional structure of BhOMT was determined using MODELLER. The substrate binding sites of these two proteins showed slight differences, but these differences were important to characterize the substrate of BhOMT. Automated docking study showed that four flavonoids, quercetin, fisetin, myricetin, and luteolin which have two hydroxyl groups simultaneously at 3'- and 4'-position in the B-ring and structural rigidity of Cring resulting from the double bond characters between C2 and C3, were well docked as ligands of BhOMT. These flavonoids form stable hydrogen bondings with K211, R170, and hydroxyl group at 3'-position in the Bring has stable electrostatic interaction with Ca2+ ion in BhOMT. This study will be helpful to understand the biochemical function of BhOMT as an O-methyltransferase for flavonoids.

• The Plant Pathology Journal
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• v.18 no.2
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• pp.98-101
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• 2002

Using phytoplasma universal primer pair Pl and P7, a fragment of about 1.8 kb nucleotide sequences of 16S rRNA gene and 16S-23S rRNA intergenic spacer region, and a portion of 23S rRNA gene of jujube witches'broom (JWB) and mulberry dwarf(MD) phytoplasmas were determined. The nucleotide sequences of JWB and MD were 1,850 bp and 1,831 bp long, respectively. The JWB phytoplasma sequence was aligned with the homologous sequence of MD phytoplasma. Twenty-eight base insertions and nine base deletions were found in the JWB phytoplasma sequence compared with that of MD phytoplasma. The similarity of the aligned sequences of JWB and MD was 84.8%. The near-complete 16S rRNA gene DNA sequences of JWB and MD were 1,529 bp and 1,530 bp in length, respectively, and revealed 89.0% homology. The 16S-23S rRNA intergenic spacer region DNA sequences were 263 bp and 243 bp in lengths respectively, while homology was only 70% and the conserved tRNA-lle gene of JWB and MD was located into the intergenic space region between 16S-23S rRNA gene. The nucleotide sequences were 77 bp long in both JWB and MD, and showed 97.4% sequence homology. Based on the phylogenetic analysis of the two phytoplasmas, the JWB phytoplasma belongs to the Elm yellow phytoplasma group (16S rV), whereas, the MD phytoplasma belongs to the Aster yellow group (16S rI).

• Journal of the Korean Mathematical Society
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• v.54 no.2
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• pp.545-561
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• 2017

The signature of a surface bundle over a surface is known to be divisible by 4. It is also known that the signature vanishes if the fiber genus ${\leq}2$ or the base genus ${\leq}1$. In this article, we construct new smooth 4-manifolds with signature 4 which are surface bundles over surfaces with small fiber and base genera. From these we derive improved upper bounds for the minimal genus of surfaces representing the second homology classes of a mapping class group.

• Bulletin of the Korean Mathematical Society
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• v.50 no.4
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• pp.1069-1077
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• 2013

Several authors investigated the properties which are invariant under the passage from a group to its nonabelian tensor square. In the present note we study this problem from the viewpoint of the classes of groups and the methods allow us to prove a result of invariance for some geometric properties of discrete groups.

• Korean Journal Plant Pathology
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• v.14 no.5
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• pp.519-525
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• 1998

Intraspecific genetic diversity of Korean isolates of Phytophthora drechsleri was investigated based on PCR-RFLP of rDNA along with closely related species in the genus; P. cryptogea, P. melonis, P. erythroseptica, P. cinnamomi, P. cambivora and P. cactorum. Gene regions of nuclear small subunit and internal transcribed spacer (ITS) in rDNA were amplified with polymerase chain reaction and digested with 9 restriction enzymes. Phytophthora species was readily differentiated from each other based on the digestion patterns, however, P. cryptogea was not separable from some isolates of P. drechsleri. Twenty one isolates of P. drechsleri originated from 15 host plants were divided into three distinct groups designated as PdG1, PdG2 and PdG3, respectively. Four isolates in PdG1 were originated from green vegetables and tomato and nine isolates in PdG2 were mainly isolated from medicinal plants. The two groups showed 95.3% homology and four isolates of P. cyptogea came under the groups. However, Eight isolates in PdG3 collected from cucurbits were clearly differentiated from those of PdG1 and PdG2 by 66.5% homology, but completely matched with a Taiwan isolate of P. melonis. Results indicated that three distinct groups exist in Korean isolates of P. drechleri and each group has host preference. In addition, reclassification of the cucurbits isolates are reserved because of their distinct genetic characters from other intraspecific groups in P. drechsleri.

• Korean Journal of Veterinary Service
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• v.47 no.1
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• pp.9-17
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• 2024

Porcine epidemic diarrhea (PED) is a highly contagious enteric viral disease of pigs with watery diarrhea in piglets, which ultimately results in huge economic losses in the swine industry. The spike (S) protein plays an important role in viral pathogenicity, tissue tropism, infection, dissemination and the trypsin-dependent proliferation of the PED virus (PEDV). In the present study, we determined the full-length spike (S) gene sequences of twenty PEDV field strains detected in Jeonbuk province in 2022. Phylogenetic analysis showed that the twenty PEDV field strains were classified into G2b group and shared 98.6~100% of nucleotide homology and 97.4~100% of amino acid homology with each other. Mutations of amino acid sequences on the neutralizing epitope of S protein were observed in the twenty field strains compared to the previous vaccine strain SM-98-1 (G1a group). Therefore, these amino acid mutations in the PEDV S protein may result in a new genotype of the virus and highly pathogenic virus, so continuous monitoring is required.

• BMB Reports
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• v.28 no.5
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• pp.402-407
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• 1995

Single-run Partial cDNA sequencing was conducted on 1,592 randomly selected human fetal liver cDNA clones of Korean origin to isolate novel genes related to liver functions. Each partial cDNA sequence determined was analyzed by comparing it with the databases. GenBank, Protein Information Resource (PIR) and SWISS-PROT Protein Sequence Data Bank. From a set of 1.592 cDNA clones reported here, 1,433 (90.0% of the total) were informative cDNA sequences. The other 159 clones were identified as DNA sequences which had originated from the cloning vector. Among 1,433 informative partial cDNA sequences, 851 (59.3%) clones were revealed to be identical to known human genes. These known genes have been classified into 225 different kinds of genes. In addition, 340 clones (23.7%) showed various degrees of homology to previously known human genes. Ninety four (6.6%) clones contained various repeated sequences. Twenty four (1.7%) partial cDNA sequences were found to have considerable homology to known genes from evolutionarily distant organism such as yeast, rice, Arabidopsis, mouse and rat, based on database matches, whereas 124 (8.7%) had no Significant matches. Human homologues to functionally characterized genes from different organisms could be classified as candidates for novel human genes of similar functions. Information from the partial cDNA sequences in this study may facilitate the analysis of genes expressed in human fetal liver.