• Journal of Photoscience
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• v.9 no.3
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• pp.45-48
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• 2002

Microbial rhodopsins, photoactive 7-transmembrane helix proteins that use retinal as their chromophore, were observed initially in the Archaea and appeared to be restricted to extreme halophilic environments. Our understanding of the abundance and diversity of this family has been radically transformed by findings over the past three years. Genome sequencing of cultivated microbes as well as environmental genomics have unexpectedly revealed archaeal rhodopsin homologs in the other two domains of life as well, namely Bacteria and Eucarya. Organisms containing these homologs inhabit such diverse environments as salt flats, soil, freshwater, and surface and deep ocean waters, and they comprise a broad phylogenetic range of microbial life, including haloarchaea, proteobacteria, cyanobacteria, fungi, and algae. Analysis of the new microbial rhodopsins and their expression and structural and functional characterization reveal that they fulfill both ion transport and sensory functions in various organisms, and use a variety of signaling mechanisms. We have obtained the first crystallographic structure for a photosensory member of this family, the phototaxis receptor sensory rhodopsin II (SRII, also known as phoborhodopsin) that mediates blue-light avoidance by the haloarchaeon Natronobacterium pharaonis. The structure obtained from x-ray diffraction of 3D crystals prepared in a cubic lipid phase reveals key features responsible for its spectral tuning and its sensory function. The mechanism of SRII signaling fits a unified model for transport and signaling in this widespread family of phototransducers.

• Animal Systematics, Evolution and Diversity
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• v.29 no.4
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• pp.272-278
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• 2013

Accurate identification of fish and fish products, from eggs to adults, is important in many areas. Grey mullets of the family Mugilidae are distributed worldwide and inhabit marine, estuarine, and freshwater environments in all tropical and temperate regions. Various Mugilid species are commercially important species in fishery and aquaculture of many countries. For the present study we have chosen two Mugilid genes with different phylogenetic signals: relatively variable mitochondrial cytochrome oxidase subunit I (COI) and conservative nuclear rhodopsin (RHO). We examined their diversity within and among 9 Mugilid species belonging to 4 genera, many of which have been examined from multiple specimens, with the goal of determining whether DNA barcoding can achieve unambiguous species recognition of Mugilid species. The data obtained showed that information based on COI sequences was diagnostic not only for species-level identification but also for recognition of intraspecific units, e.g., allopatric populations of circumtropical Mugil cephalus, or even native and acclimatized specimens of Chelon haematocheila. All RHO sequences appeared strictly species specific. Based on the data obtained, we conclude that COI, as well as RHO sequencing can be used to unambiguously identify fish species. Topologies of phylogeny based on RHO and COI sequences coincided with each other, while together they had a good phylogenetic signal.

• Fisheries and Aquatic Sciences
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• v.14 no.3
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• pp.218-225
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• 2011

Dual frequency identification sonar (DIDSON) is an imaging sonar that has been used for numerous fisheries investigations in a diverse range of freshwater and marine environments. The main purpose of DIDSON is fish counting, fish sizing, and fish behavioral studies. DIDSON records video-quality data, so processing power for handling the vast amount of data with high speed is a priority. Therefore, a semiautomated analysis of DIDSON data for fish counting, sizing, and fish behavior in Echoview (fisheries acoustic data analysis software) was accomplished using testing data collected on the Rakaia River, New Zealand. Using this data, the methods and algorithms for background noise subtraction, image smoothing, target (fish) detection, and conversion to single targets were precisely illustrated. Verification by visualization identified the resulting targets. As a result, not only fish counts but also fish sizing information such as length, thickness, perimeter, compactness, and orientation were obtained. The alpha-beta fish tracking algorithm was employed to extract the speed, change in depth, and the distributed depth relating to fish behavior. Tail-beat pattern was depicted using the maximum intensity of all beams. This methodology can be used as a template and applied to data from BlueView two-dimensional imaging sonar.

• Journal of Ecology and Environment
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• v.35 no.3
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• pp.227-234
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• 2012

Quercus aliena and Q. serrata are both occur as natural vegetation alongside natural freshwater bodies of the southern Korea Peninsula. Q. serrata dominates over Q. aliena as secondary forest vegetation in the present day. In order to explain these natural distributional traits of the oak species, we conducted some experiments with oak seedlings which treated with major important environmental resources, including light, moisture and nutrients, under controlled conditions. We then measured the ecological niche breadths and overlap from 15 eco-morphological characteristics. The ecological niche breadth of Q. aliena and Q. serrata were higher in terms of the nutrient factor applied, but was lower terms of light. The niche breadth of Q. serrata was wider than that of Q. aliena in light and moisture exposure. On the other hand, the niche breadth of Q. aliena was similar with that of Q. serrata in terms of the nutrient factor applied. These results imply that Q. serrata has a broader ecological distribution in over a wider variety of light and moisture environments than that of Q. alien. Ecological niche overlap between two oak species was the widest in terms of the light treatment factor applied, and narrowest in terms of moisture. This response pattern was also verified by cluster and principle component analysis. These results suggest competitive interactions between Q. serrata and Q. aliena seedlings may be higher for light resources than moisture or nutrient resources, and that Q. serrata is more shade tolerant than Q. aliena.

• Journal of Species Research
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• v.7 no.2
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• pp.123-134
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• 2018

A total of 22 bacterial strains belonging to the phylum Bacteroidetes were isolated primarily from aquatic environments such as seawater, freshwater, lagoon and tidal flat. One of these 22 strains was isolated from ginseng soil. Phylogenetic analyses based on 16S rRNA gene sequences revealed that 21 strains showed the high sequence similarities(${\geq}98.7%$) to the closest type strains and formed robust phylogenetic clades with closely related species in the phylum Bacteroidetes. One strain, which had been previously classified as Balneola vulgaris in the phylum Bacteroidetes, was identified as a member of the newly described phylum Rhodothermaeota. These strains had not been previously reported in Korea. Here, we report 21 species of 13 genera in the phylum Bacteroidetes and one species in the phylum Rhodothermaeota which were not reported in Korea. Morphological, biochemical, and physiological characteristics, isolation sources, and NIBR deposit numbers are described in the species descriptions.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.52 no.6
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• pp.625-630
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• 2019

The pathogenic Vibrio genus contains halophilic bacteria that are distributed in marine and freshwater environments. Vibrio cholerae, Vibrio vulnificus, and Vibrio parahaemolyticus are potent human pathogens and leading causes of septicemia, wound infection, and seafood-borne gastroenteritis. The aim of this study was to investigate the presence of pathogenic Vibrio species in seawater off the west coast of Korea. Sixty-four seawater samples were obtained from different sites in Gomso Bay and Byeonsan from April 2018 to November 2018. Pathogenic Vibrio species were detected using a combination of most probable number (MPN)-polymerase chain reaction methods. V. cholerae, V. vulnificus, and V. parahaemolyticus were found in 0.0%, 20.3%, and 65.6% of seawater samples, respectively. Quantitative results revealed 3.6-23 MPN/100 mL of V. vulnificus, and 3.6-930 MPN/100 mL of V. parahaemolyticus in the samples. Overall, these results provide new insight into the necessity for seawater sanitation in Gomso Bay and Byunsan; they also provide evidence that will help reduce outbreaks of seafood-borne illness caused by pathogenic Vibrio species.

• Journal of Industrial and Engineering Chemistry
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• v.68
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• pp.416-424
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• 2018

Oil spill and oily wastewater have now become a serious threat to the freshwater and marine environments. Porous materials with super-hydrophobicity and super-oleophilicity are good candidates for the oil adsorption and oil/water separation. Here, flexible hybrid nanofibrous membrane (FHNM) containing $SiO_2$/polyvinylidene fluoride (PVDF) microspheres was prepared by simultaneous electrospinning and electrospraying. The obtained FHNM combined the flexibility of the nanofiber mat and super-hydrophobicity of the microspheres, which could not be achieved by either only electrospinning or only electrospraying. It was found that when the weight ratio between the $SiO_2$ and PVDF reached a critical value, the $SiO_2$ nanoparticles were present on the PVDF microsphere surface, significantly improving the surface roughness and hence the contact angle of the FHNM. Compared with the pure electrospun PVDF nanofiber mat, most of the FHNMs have a higher oil adsorption capacity. The FHNM could separate the oil with water quickly under the gravity and displayed a high efficiency and good reusability for the oil/water separation. More importantly, the FHNM could not only separate the oil with the pure water but also the corrosive solution including the salt, acid and alkali solution.

• The Korean Journal of Mycology
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• v.47 no.3
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• pp.187-197
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• 2019

Ascomycota is the largest phylum of the Fungi, including approximately 6,600 genera. They are often isolated from soils, indoor air, and freshwater environments, but also from plants as pathogens or endophytes. In this study, four species of Ascomycota (two of Cladosporium and one of each Daldinia and Nigrospora) were collected from the leaves of four woody plants (Camellia japonica, Ginkgo biloba, Quercus sp., Vitis vinifera). Their cultural characteristics were investigated on five different media (PDA, V8A, CMA, MEA, CZA) at 3 days after incubation at $25^{\circ}C$ in darkness. BLASTn search and phylogenetic analysis were performed using the internal transcribed spacer (ITS) rDNA sequences, in addition to tef1 gene sequences for Cladosporium species. Based on the cultural, morphological, and phylogenetic data, the isolates were identified as Cladosporium anthropophilum, Cladosporium pseudocladosporioides, Daldinia eschscholtzii, and Nigrospora chinensis. Previously, some members of Cladosporium and Nigrospora have been recorded as endophytes inhabiting the leaves and stems of various plants, whereas Daldinia eschscholtzii is a wood-inhabiting endophyte or wood-decaying fungus. To our knowledge, this is the first report of these four ascomycetes in Korea.

• Ocean and Polar Research
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• v.43 no.4
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• pp.245-253
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• 2021

Surirella atomus Hustedt 1955, surirelloid diatom, were obtained from Hampyeong Bay, Mu-an, in the west coast of Korea. We describe the first record of S. atomus in Korea and report its ultrastructure and molecular characteristics for the first time. For molecular analysis, rbcL gene and cob gene were sequenced. This species is very small in size, making it difficult to observe its morphological features under a light microscope. Even with a scanning electron microscope, it has no unique structure in the valve. It is morphologically very simple. This rare species was known as a marine benthic species. However, it appears to be widely distributed in marine, freshwater, and brackish environments according to the literature documenting this species. In terms of phylogeny, S. atomus has been tentatively linked to Petrodictyon gemma, but the phylogenetic placement of S. atomus seems to be still uncertain, in a manner that is similar to S. febigeri. However, morphological observations derived from this study suggest that this species belongs to the genus Surirella.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.55 no.6
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• pp.844-849
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• 2022

The pathogenic Vibrio genus denotes halophilic bacteria that are distributed in aquatic environments, including both sea and freshwater. V. cholerae, V. vulnificus, and V. parahaemolyticus are the main species that can be potent human pathogens and the leading cause of septicemia, wound infections, and seafood borne gastroenteritis. The aim of this study was to investigate the presence of pathogenic Vibrios in seawater. We obtained a total of 80 seawater samples from the Geum River estuary area in the west coast of Korea from April to December 2021. Pathogenic Vibrios was determined using a combination of the most probable number-polymerase chain reaction (MPN-PCR) methods. The detection levels of V. cholerae, V. parahaemolyticus, and V. vulnificus in the seawater samples were 7.5%, 68.8%, and 30.0%, respectively. The quantitative results were as follows: 3.6-3.6 MPN/100 mL in V. cholerae, 3.6-3,400 MPN/100 mL in V. parahaemolyticus, and 3.6-4,300 MPN/100 mL in V. vulnificus. Overall, these results provide novel insight into the necessity for seawater sanitation in the Geum River estuary area, and could help reduce the risk of seafood-borne outbreaks caused by pathogenic Vibrios.