• Plant Biotechnology Reports
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• v.4 no.4
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• pp.329-334
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• 2010

Multiple sequence alignments showed that the prolines at the 25th, 129th, 153rd, 242nd, 322nd, and 434th amino acids in 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) from Agrobacterium sp. strain CP4 are strongly conserved in various prokaryotic EPSPS proteins. Single point mutations of the conserved prolines to alanine (P25A, P153A, P242A, P322A, and P434A) were introduced in the CP4 EPSPS in order to investigate the importance of the conserved prolines for the enzyme properties. The point mutations caused decreases in substrate binding affinity and catalytic efficiency as well as the glyphosate resistance, in general. Especially, the 25th and 242nd prolines located in the polypeptide hinges connecting top and bottom domains of CP4 EPSPS as well as the 434th proline at the C-terminus of the enzyme turned out to be crucial for the enzyme activity.

• Journal of Life Science
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• v.19 no.11
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• pp.1522-1528
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• 2009

A marine bacterium was isolated from brown seaweeds for its ability to degrade alginate. Analysis of 16S ribosomal DNA sequence revealed that the strain belongs to Streptomyces like strain ALG-5 which was reported previously. New alginate lyase gene of Streptomyces sp. M3 was cloned by using PCR with the specific primers designed from homologous nucleotide sequences. The consensus sequences of N-terminal YXRSELREM and C-terminal YFKAGXYXQ were conserved in the M3 alginate lyase amino acid sequences. The homology model for the M3 alginate lyase showed a characteristic structure of $\beta$-jelly roll fold main domain like alyPG from Corynebacterium sp. ALY-1. The homogenate of the recombinant E. coli with the alginate lyase gene showed more degrading activity for polyguluronate block than polymannuronate block. The results from the multiple alignments and the homology modeling elucidated in the M3 alginate lyase can be classified into family PL-7.

• BMB Reports
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• v.44 no.6
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• pp.387-392
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• 2011

To investigate the molecular scavenging capabilities of the larvae of Hermetia illucens, two serine proteases (SPs) were cloned and characterized. Multiple sequence alignments and phylogenetic tree analysis of the deduced amino acid sequences of Hi-SP1 and Hi-SP2 were suggested that Hi-SP1 may be a chymotrypsin- and Hi-SP2 may be a trypsin-like protease. Hi-SP1 and Hi-SP2 3-D homology models revealed that a catalytic triad, three disulfide bonds, and a substrate-binding pocket were highly conserved, as would be expected of a SP. E. coli expressed Hi-SP1 and Hi-SP2 showed chymotrypsin or trypsin activities, respectively. Hi-SP2 mRNAs were consistently expressed during larval development. In contrast, the expression of Hi-SP1 mRNA fluctuated between feeding and molting stages and disappeared at the pupal stages. These expression pattern differences suggest that Hi-SP1 may be a larval specific chymotrypsin-like protease involved with food digestion, while Hi-SP2 may be a trypsin-like protease with diverse functions at different stages.

• The Korean Journal of Malacology
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• v.32 no.4
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• pp.241-247
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• 2016

Macrophage Migration Inhibitory Factor (MIF) are well-defined role as unique cytokine and critical mediator in acute and chronic inflammatory diseases, autoimmune diseases. In this study, we isolated and characterized a full-length of MIF cDNA from the abalone (Haliotis discus hannai). The full-length cDNA of abMIF was of 1264 bp, consisting of a 5'-terminal UTR of 143 bp, an open reading frame of 360 bp and a 3-terminal UTR of 761 bp. The abalone MIF cDNA encodes a 119-amino acid polypeptide with a calculated molecular mass of 13.4 kDa and isoelectric point of 9.07. Multiple alignments and phylogenetic analysis with the deduced abalone MIF protein and showed strong homology with disk abalone (Haliotis discusdiscus). The deduced amino acid sequence of abMIF exhibited homology with other reported MIFs, such as 80%, with that of other disk abalone H. discus discus MIF gene. Quantitative real-time PCR (qRT-PCR) analysis indicated that abMIF was highly expression observed in hapatopacreas, intestine, foot, and gonad of normal conditioned abalone. Even though AbMIF mRNA level in hemocytes was low under the normal condition, it was sharply up-regulated and reached the maximum at 6 h post-infection with Vibrio parahaemolyticus, and then decreased at 24 h post-infection. This result indicates that abMIF plays an important role in responding in the innate immune system.

• The Plant Pathology Journal
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• v.23 no.1
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• pp.13-21
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• 2007

Sweet potato feathery mottle virus(SPFMV) is one of the most prevalent viruses infecting sweet potatoes and occurs widely in sweet potato cultivating areas in Korea. To assess their genetic variation, a total of 28 samples infected with SPFMV were subjected to restriction fragment length polymorphism(RFLP) analysis using DNAs amplified by RT-PCR with specific primer sets corresponding to the coat protein(CP) region of the virus. The similarity matrix by UPGMA procedure indicated that 28 samples infected with SPFMV were classified into three groups based on the number and size of DNA fragments by digestion of CP-encoding regions with 7 enzymes including SalI, AluI, EcoRI, HindIII, FokI, Sau3AI, and DraI bands. Four primer combinations out of 5 designed sets were able to differentiate SPFMV and sweet potato virus G infection, suggesting that these specific primers could be used to differentiate inter-groups of SPFMV. Sequence analysis of the CP genes of 17 SPFMV samples were 97-99% and 91-93% identical at the intra-group and inter-groups of SPFMV, respectively. The N-terminal region of the CP is highly variable and examination of the multiple alignments of amino acid sequences revealed two residues(residues 31 and 32) that were consistently different between SPFMV-O and SPFMV-RC.

• Journal of Veterinary Science
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• v.24 no.4
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• pp.51.1-51.17
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• 2023

Background: To date, various genotypes of infectious bronchitis virus (IBV) have co-circulated and in Korea, GI-15 and GI-19 lineages were prevailing. The spike protein, particularly S1 subunit, is responsible for receptor binding, contains hypervariable regions and is also responsible for the emerging of novel variants. Objective: This study aims to investigate the putative major amino acid substitutions for the variants in GI-19. Methods: The S1 sequence data of IBV isolated from 1986 to 2021 in Korea (n = 188) were analyzed. Sequence alignments were carried out using Multiple alignment using Fast Fourier Transform of Geneious prime. The phylogenetic tree was generated using MEGA-11 (ver. 11.0.10) and Bayesian analysis was performed by BEAST v1.10.4. Selective pressure was analyzed via online server Datamonkey. Highlights and visualization of putative critical amino acid were conducted by using PyMol software (version 2.3). Results: Most (93.5%) belonged to the GI-19 lineage in Korea, and the GI-19 lineage was further divided into seven subgroups: KM91-like (Clade A and B), K40/09-like, QX-like (I-IV). Positive selection was identified at nine and six residues in S1 for KM91-like and QX-like IBVs, respectively. In addition, several positive selection sites of S1-NTD were indicated to have mutations at common locations even when new clades were generated. They were all located on the lateral surface of the quaternary structure of the S1 subunits in close proximity to the receptor-binding motif (RBM), putative RBM motif and neutralizing antigenic sites in S1. Conclusions: Our results suggest RBM surrounding sites in the S1 subunit of IBV are highly susceptible to mutation by selective pressure during evolution.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.135-135
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• 2017

The Gramene database (http://www.gramene.org) is a powerful online resource for agricultural researchers, plant breeders and educators that provides easy access to reference data, visualizations and analytical tools for conducting cross-species comparisons. Learn the benefits of using Gramene to enrich your lectures, accelerate your research goals, and respond to your organismal community needs. Gramene's genomes portal hosts browsers for 44 complete reference genomes, including crops and model organisms, each displaying functional annotations, gene-trees with orthologous and paralogous gene classification, and whole-genome alignments. SNP and structural diversity data, available for 11 species, are displayed in the context of gene annotation, protein domains and functional consequences on transcript structure (e.g., missense variant). Browsers from multiple species can be viewed simultaneously with links to community-driven organismal databases. Thus, while hosting the underlying data for comparative studies, the portal also provides unified access to diverse plant community resources, and the ability for communities to upload and display private data sets in multiple standard formats. Our BioMart data mining interface enable complex queries and bulk download of sequence, annotation, homology and variation data. Gramene's pathway portal, the Plant Reactome, hosts over 240 pathways curated in rice and inferred in 66 additional plant species by orthology projection. Users may compare pathways across species, query and visualize curated expression data from EMBL-EBI's Expression Atlas in the context of pathways, analyze genome-scale expression data, and conduct pathway enrichment analysis. Our integrated search database and modern user interface leverage these diverse annotations to facilitate finding genes through selecting auto-suggested filters with interactive views of the results.

• The Journal of the Korea Contents Association
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• v.18 no.4
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• pp.99-113
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• 2018

Recently, global warming has widened the habitat of mosquitoes and infection chances for mosquito-borne diseases are increasing. Flavivirus is a typical mosquito-borne virus. Flaviviruses with a relatively high frequency of infection in Asian countries include Zika, Dengue, and Japanese encephalitis viruses. Although distinctive diagnosis of flaviviruses is required because the symptoms and therapeutic method differ, there is no diagnostic method that can distinguish them accurately yet. In this study, we propose distinctive diagnosis method of flaviviruses using informations and analysis tools constructed in bioinformatic databases. The envelope protein and non-structural protein 1 which are useful protein for the immuno-diagnostics of three flaviviruses were selected. Their homology was analyzed by multiple sequence alignments and epitope candidates consisting of 10-15 amino acids were selected. Finally two epitopes were suggested to be most useful by immunogenicity analysis and 3D structure prediction. These approaches and results are expected to be great value in the distinctive diagnosis of three flaviviruses with a high frequency of infection in Asian countries.

• Journal of Environmental Health Sciences
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• v.47 no.5
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• pp.479-485
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• 2021

Background: Vibrio vulnificus has been frequently detected in seawater, fish, and shellfish mainly in the coastal areas of Chungcheongnam-do Province. Objectives: This study was conducted to investigate the analyzed biochemical properties, genetic characteristics, and distribution of Vibrio vulnificus isolated from environmental sources in coastal areas of Chungcheongnam-do Province from 2019 to 2020. Methods: A total of 1,510 samples were obtained from six different sites in Chungcheongnam-do Province. Isolated strains from the samples were identified by a VITEK 2 system and MALDI-TOF. Antibiotic susceptibility testing for 85 isolates was done by microdilution minimum inhibitory concentration methods, and 11 isolates were analyzed for 16s rRNA sequences in multiple alignments. Results: Among the 1,510 samples taken during the investigation period, 306 strains were isolated and the detection rate of V. vulnificus was 20.3%. One hundred eighty-eight strains (24.6%) from seawater and 118 strains (15.8%) from mud flats were isolated. It was mainly detected in July (17.3%), August (36.5%), and September (28.8%), and the proportion was 82.0%. Based on the CLSI-recommended breakpoints, V. vulnificus isolates were all susceptible to amoxicillin/clavulanic acid, amikacin, gentamicin, ciprofloxacin and trimethoprim/sulfamethoxazole. However, nonsusceptible isolates to ampicillin, ampicillin/sulbactam, cefazolin, cefoxitin, imipenem, tetracycline and chloramphenicol were identified. In the analysis of the nucleotide sequences for 16s rRNA of V. vulnificus isolates, it was confirmed that mutations frequently occurred between nucleotide number 922 and 952, and 98.2% to 100% nucleotide identities between isolates was verified. Conclusions: The results of this study can be used as a basic data for infection control and prevention of Vibrio vulnificus infection by describing the distribution and characteristics of Vibrio vulnificus strains isolated in coastal areas of Chungcheongnam-do Province.

• Journal of Mushroom
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• v.20 no.4
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• pp.199-207
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• 2022

The demand for novel strains has been rising in the domestic market to increase the production of sclerotia from Wolfiporia hoelen. To improve strain breeding efficiency, we investigated whether single-nucleotide polymorphisms (SNPs) in the RNA polymerase II subunit (RPB2) gene, which may be linked to the mating type locus, are useful for distinguishing monokaryons from dikaryons in Korean W. hoelen strains. We designed a specific primer set to efficiently amplify a region of RPB2 using PCR with the genomic DNA of 12 cultivated strains and 31 wild strains of W. hoelen collected from Korea. Nucleotide sequences of the PCR-amplified RPB2 genes were determined and analyzed for the presence of SNPs among the 43 W. hoelen strains. Previously reported SNP loci were detected in the RPB2 gene of all W. hoelen strains tested. However, these previously reported SNP loci could not be applied to differentiate monokaryons from dikaryons in approximately one-third of Korean wild strains with homozygous genotypes. Three additional SNPs in the RPB2 gene, which may improve the ability to distinguish monokaryons from dikaryons, were identified by searching through the multiple sequence alignments of the 43 W. hoelen strains. The applicability of these three novel SNPs, together with the previously known SNPs, in the RPB2 gene to W. hoelen strain breeding was verified by examining the hybrid strains and their parental strains.