• The Korean Journal of Mycology
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• v.43 no.4
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• pp.231-238
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• 2015

Genome-wide reanalyzed data of 25 Flammulina strains were compared against the reference genome (KACC42780) to establish a genome-wide single nucleotide polymorphism (SNP). The rate of mapping differences between the strains reflected in the strain variation in its result. Genome-wide SNPs distribution divided into types of homozygous SNP and heterozygous SNP moreover all of the strains demonstrated a wide variation in all of the regions. In the further study of topological relationship between the collected strains, phylogenetic tree was separated into 3 major groups. Group I contained F. velutipes var. related strains of ASI 4062, 4148, 4195. Group 2 contained strains that are different species of ASI 4188 F. elastica, ASI 4190 F. fennae, and ASI 4194 F. rossica. The other 19 strains F. velutipes were classified as a single group. However, further experiment to discriminate its genetic relationship between the white group and brown group did not verify its validity. The inferred tree exhibited a phylogenetic relationship between Korea white fruitbody forming strains of ASI 4210, 4166, 4178 and Japan white fruitbody forming strains of ASI 4209, 4167 confirmed to be genetically closely related.

• Journal of Life Science
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• v.23 no.2
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• pp.182-189
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• 2013

Halophytes are unique land plants that are capable of thriving in a high-salt environment. They are attracting public attention due to their ability to synthesize bioactive substances such as UV protectants or antioxidizing agents. To achieve unaffected growth under high salinity, halophytes may take advantage of the activities of cell growth factors such as expansins. Expansins are well-known cell wall proteins that are responsible for cell enlargement. They loosen cell walls, thereby contributing to actual plant growth. This study aimed to identify positive roles of expansins in the growth of halophytes. Three expansin cDNA clones were isolated from seedlings of Suaeda japonica. Comparing the deduced amino acid sequences of the expansin genes of S. japonica with those of other plant species suggested that the cDNA clones isolated from S. japonica belong to the EXPA (${\alpha}$-expansin) gene family. A phylogenetic tree based on the deduced amino acid sequences revealed that the expansins of S. japonica share a close evolutionary relationship with those of strawberry (Fragaria ananassa) and jujube (Ziziphus jujuba), both of which are woody dicots. SjEXPAs did not show any remarkable change in the gene expression level in different NaCl concentrations, providing a clue to the unaffected seedling growth of S. japonica in a high-salt environment. In conclusion, the present study presents the first report of expansin genes from halophytes and suggests a putative role for these genes in plant growth under high salinity.

• Korean Journal of Ecology and Environment
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• v.54 no.3
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• pp.240-246
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• 2021

The Chironomidae is a benthic macroinvertebrate commonly found in freshwater ecosystems, along with Ephemeroptera and Trichoptera, which can be used for environmental health assessments. There are approximately 15,000 species of Chironomidae worldwide, but there are limited studies on species identification of domestic Chironomidae larvae. In the present study, we carried out species classification of the Chironomidae larvae that found in Jeju's tap water purification plants using morphological characteristics and genetic identification based on cytochrome c oxidase subunit I (COI) gene of the mitochondrial DNA. Body shape, mentum, antenna, mandible in the head capsule, and claws were observed in the larvae for morphological classification. Analysis of 17 larvae collected from faucets and fire hydrants of domestic tap water purification plants revealed the presence of two species, including 14 Orthocladius tamarutilus and 3 Paratrichocladius tammaater. These results will aid the use of the criteria information about species classification of the Chironomidae for water quality management in water purification plants and diversity monitoring of freshwater environments.

• The Korean Journal of Malacology
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• v.30 no.4
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• pp.399-408
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• 2014

Glutathione S-transferases (GSTs) are a superfamily of detoxification enzymes that primarily catalyze the nucleophilic addition of reduced glutathione to both endogenous and exogenous electrophiles. In this study, we isolated and characterized a full-length of alpha class GST cDNA from the abalone (Haliotis discus hannai). The abalone GST cDNA encodes a 223-amino acid polypeptide with a calculated molecular mass of 25.8 kDa and isoelectric point of 5.69. Multiple alignments and phylogenetic analysis with the deduced abalone GST protein revealed that it belongs to the alpha class GSTs and showed strong homology with disk abalone (Haliotis discus discus) putative alpha class GST. Abalone GST mRNA was ubiquitously detected in all tested tissues. GST mRNA expression was comparatively high in the mantle, gill, liver, and digestive duct, however, lowest in the hemocytes. Expression level of abalone GST mRNA in the mantle, gill, liver, and digestive duct was 182.7-fold, 114.8-fold, 4675.8-fold, 406.1-fold higher than in the hemocytes, respectively. Expression level of abalone GST mRNA in the liver was peaked at 6 h post-infection with Vibrio parahemolyticus and decreased at 12 h post-infection. While the expression level of abalone GST mRNA in the hemocytes was drastically increased at 3 h post-infection with Vibrio parahemolyticus. These results suggest that abalone GST is conserved through evolution and may play roles similar to its mammalian counterparts.

• Korean Journal of Ecology and Environment
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• v.47 no.4
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• pp.342-349
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• 2014

This study was conducted to identify the bloom-forming Anabaena strains with two phenotypes (straight-type and coil-type) isolated from North Han River (Sambong-ri Joam-myun) using 16S rDNA sequence. The odor material producing potential was also examined using the geosmin-synthesizing gene cluster. Despite of striking morphological difference of the two stains, resembling A. circinalis and A. crassa species, the phylogenetic analysis using 16S rDNA identified the both strains as a single species of A. circinalis with high genetic similarity (98%~100%). Also, two Anabaena strains showed to possess the geosmin-synthesizing gene cluster, indicating that they are capable of producing the odor substance. This study is the first report that provides the direct evidence of geosmin production in the gene level by A. circinalis in Korea, and provides important basic information to identify the source alga of geosmin increase and its management in North Han River.

• Korean Journal of Plant Taxonomy
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• v.32 no.4
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• pp.383-396
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• 2002

RAPD analyses were compared for 17 taxa of Korean Iris including the subgenus Sisyrinchium and Belamcanda. Eighty scorable RAPD markers were formed from the PCR reactions using 10 random oligoprimers. In this systematic analyses which used neighbor-joining methods including bootstrapping analyses with genetic coefficients, the Korean Iris were divided into three subgenera (Limniris, Crossiris, Pardanthopsis), or two genera (Limniris, Pardanthopsis). The molecular data agree with the previous classification system that recognized two sections and six series for the subgenus Limniris because the subgenus is comprised of four clades in the RAPD analyses. According to the molecula data, the series Chinensis should be divided into two groups. The minutoaurea group is composed of I. koreana, I. odaesanensis, and I. minitoaurea, while the rossi group is comprised of two varieties of I. rossi. The series Tripetalae is closely allied with the series Sibiricae, whereas the series Ensatae is recognized as a sister group to the series Ruthencae. The molecular phylogeny, which was based on RAPD analysis, for the most part agreed with the data proposed by previous authors. This is because the basis of morphological and ITS sequence data suggests that the RAPD markers should be very useful in addressing phylogenetic questions about the genus Iris.

• Korean Journal of Microbiology
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• v.37 no.1
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• pp.9-14
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• 2001

In order to investigate the pathogenicity and development of differential identification technique in the Yersinia species and other entericbacteria, we isolated 5 strains of Y.pseudotuberculosis from spring water sites in Seoul. The biochemical characteristics of isolated strains revealed that indole, VP($25^{\circ}C$, $37^{\circ}C$), $H_2S$, phenylalanine, lysine, arginine, ornithine, gas from glucose, lactose, sucrose, sorbitol, oxidase and motility($37^{\circ}C$) were all negative and urease, glucose, mannitol, salicin, catalase and motility($25^{\circ}C$) were all positive. To detect the causative agent of pseudotuberculosis(Y.pseudotuberculosis), we carried out a study using a PCR with inv primers complementary to the pathogenic region and found that all strains were positive, this revealed that strains from spring waters were pathogenic. Also 16S rDNA for total 5 strains of Y. pseudotuberculosis were amplified and a stretch of approximately 1,450 nucleotides were sequenced and analyzed. The 16S rDNA nucleotide sequence homologies among Yersinia species ranged 97.5% to 100% and between Y.pseudotuberculosis and other entericbacteria they ranged 93.0% to 95.1%. The Phylogenetic tree generated from the sequence analysis of the 16S rDNA gene showed 3 coherent clusters that could be separated into Y.pseudotuberculsis strains, some Yersinia species strains and other entericbacteria strains.

• Microbiology and Biotechnology Letters
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• v.31 no.2
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• pp.103-110
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• 2003

The regulation of pyrimidine nucleotide synthesis has been proved to be controlled by a regulatory protein PyrR-mediated attenuation in the Gram-positive bacteria. After several bacterial genome sequencing projects, we have discovered the PyrR orthologues in the databases for Haemophilus influenzae and Synechocystis and sp. PCC6803 genome sequences. To investigate whether these PyrR orthologue proteins regulate pyrimidine nucleotide synthesis as well as the cases of Bacillus, the PyrR regions of each strains were amplified by PCR and cloned with pUC19 or T-vector in Escherichia coli and with a shuttle vector pHPS9 for E. coli and B. subtilis. For the regulation test of the PyrR orthologues, the aspartate-transcarbamylase (ATCase) assay was carried out. From the results of the ATCase assay, it was confirmed that Synechocystis sp. PCC6803 could not restore by pyrimidines to a B. subtilis, PyrR but H. influenzae PyrR could. For Purification of PyrR orthologue proteins, PyrR orthologue genes were cloned into the expression vector (pET14b). Over-expressed product of PyrR orthologue genes was purified and analyzed by the SDS-PACE. The purified PyrR orthologue proteins from H. influenzae and Synechocystis sp. PCC6803 turned out to be molecular mass of 18 kDa and 21 kDa, respectively. The result of uracil phosphoribosyl transferase (UPRTase) assay with purified PyrR orthologue proteins showed that H. influenzae PyrR protein only has UPRTase activity. In addition, we could predict several regulatory mechanisms that PyrR orthologue proteins regulate pyrimidine de novo synthesis in bacteria, through phylogenetic analysis for PyrR orthologue protein sequences.

• Journal of Life Science
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• v.25 no.2
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• pp.189-196
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• 2015

Bacterial diversity was studied in the rhizosphere of Suaeda japonica Makino, which is native to Suncheon Bay in South Korea. Soil samples from several sites were diluted serially, and pure isolation was performed by subculture using marine agar and tryptic soy agar media. Genomic DNA was extracted from 29 pure, isolated bacterial strains, after which their 16S rDNA sequences were amplified and analyzed. Phylogenetic analysis was performed to confirm their genetic relationship. The 29 bacterial strains were classified into five groups: phylum Firmicutes (44.8%), Gamma proteobacteria group (27.6%), Alpha proteobacteria group (10.3%), phylum Bacteriodetes (10.3%), and phylum Actinobacteria (6.8%). The most widely distributed genera were Bacillus (phylum Firmicutes), and Marinobacterium, Halomonas, and Vibrio (Gamma proteobacteria group). To confirm the bacterial diversity in rhizospheres of S. japonica, the diversity index was used at the genus level. The results show that bacterial diversity differed at each of the sampling sites. These 29 bacterial strains are thought to play a major role in material cycling at Suncheon Bay, in overcoming the sea/mud flat-specific environmental stress. Furthermore, some strains are assumed to be involved in a positive interaction with the halophyte S. japonica, as rhizospheric flora, with induction of growth promotion and plant defense mechanism.

• Korean Journal of Microbiology
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• v.52 no.1
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• pp.65-73
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• 2016

The aim of this study was to investigate the UV-resistance of radiation-resistant bacteria isolated from the water of Han River, South Korea. The water sample was irradiated with 3 kGy gamma radiation prior to isolation. Radiation-resistant bacterial strains were isolated by standard serial dilution method on R2A and 1/10 diluted R2A agar. The resulting purely isolated 60 cultures of bacteria were analysed for UV resistance and used in further studies. Based on the comparative analyses of 16S rRNA gene sequences, the bacterial isolates were divided into 3 phyla (4 genera): the phylum Deinococcus-Thermus (the genus Deinococcus) was 61.7%, Bacteroidetes (Hymenobacter and Spirosoma) was 23.4%, and Firmicutes (Exiguobacterium) was 15%. The results suggested that twenty-nine isolates are candidates new species belonging to Deinococcus, Hymenobacter, and Spirosoma, or other new genera. Nine bacterial strains were selected among the novel candidates and the UV-resistance analysis was conducted. All the candidate bacterial strains showed high UV resistance, similar to that of D. radiodurans R1.