• Journal of the Korean Society of Marine Environment & Safety
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• v.29 no.7
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• pp.779-793
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• 2023

Intensive and long-term aquaculture activities in Korea have generated considerable amounts of organic matter, deteriorating the sedimentary environment and ecosystem. The Korean government enacted the Fishery Management Act to preserve and manage the environment of fish farms. Based on this, a fisheries environment assessment has been conducted on fish cage farms since 2014, necessitating the development of a scientific and objective evaluation method suitable for the domestic environment. Therefore, a benthic health index (BHI) was developed using the relationship between benthic polychaete communities and organic matter, a major source of pollution in fish farms. In this study, the development process and calculation method of the BHI have been introduced. The BHI was calculated by classifying 225 species of polychaetes appearing in domestic coastal and aquaculture areas into four groups by linking the concentration gradient of the total organic carbon in the sediment and the distributional characteristics of each species and assigning differential weights to each group. Using BHI, the benthic fauna communities were assigned to one of the four ecological classes (Grade 1: Normal, Grade 2: Slightly polluted, Grade 3: Moderately polluted, and Grade 4: Heavily polluted). The application of the developed index in the field enabled effective evaluation of the Korean environment, being relatively more accurate and less affected by the season compared with the existing evaluation methods like the diversity index or AZTI's Marine Biotic Index developed overseas. In addition, using BHI will be useful in the environmental management of fish farms, as the environment can be graded in quantified figures.

• Journal of Microbiology
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• v.45 no.2
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• pp.158-167
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• 2007

In this study, we have cloned a novel cDNA encoding for a papain-family cysteine protease from the Uni-ZAP XR cDNA library of the polychaete, Periserrula leucophryna. This gene was expressed in Escherichia coli using the T7 promoter system, and the protease was characterized after partial purification. First, the partial DNA fragment (498 bp) was amplified from the total RNA via RT-PCR using degenerated primers derived from the conserved region of cysteine protease. The full-length cDNA of cysteine protease (PLCP) was prepared via the screening of the Uni-ZAP XR cDNA library using the $^{32}P-labeled$ partial DNA fragment. As a result, the PLCP gene was determined to consist of a 2591 bp nucleotide sequence (CDS: 173-1024 bp) which encodes for a 283-amino acid polypeptide, which is itself composed of an 59-residue signal sequence, a 6-residue propeptide, a 218-residue mature protein, and a long 3'-noncoding region encompassing 1564 bp. The predicted molecular weights of the preproprotein and the mature protein were calculated as 31.8 kDa and 25 kDa, respectively. The results of sequence analysis and alignment revealed a significant degree of sequence similarity with other eukaryotic cysteine proteases, including the conserved catalytic triad of the $Cys^{90},\;His^{226},\;and\;Asn^{250}$ residues which characterize the C1 family of papain-like cysteine protease. The nucleotide and amino acid sequences of the novel gene were deposited into the GenBank database under the accession numbers, AY390282 and AAR27011, respectively. The results of Northern blot analysis revealed the 2.5 kb size of the transcript and ubiquitous expression throughout the entirety of the body, head, gut, and skin, which suggested that the PLCP may be grouped within the cathepsin F-like proteases. The region encoding for the mature form of the protease was then subcloned into the pT7-7 expression vector following PCR amplification using the designed primers, including the initiation and termination codons. The recombinant cysteine proteases were generated in a range of 6.3 % to 12.5 % of the total cell proteins in the E. coli BL21(DE3) strain for 8 transformants. The results of SDS-PAGE and Western blot analysis indicated that a cysteine protease of approximately 25 kDa (mature form) was generated. The optimal pH and temperature of the enzyme were determined to be approximately 9.5 and $35^{\circ}C$, respectively, thereby indicating that the cysteine protease is a member of the alkaline protease group. The evaluation of substrate specificity indicated that the purified protease was more active towards Arg-X or Lys-X and did not efficiently cleave the substrates with non-polar amino acids at the P1 site. The PLCP evidenced fibrinolytic activity on the plasminogen-free fibrin plate test.

• The Sea:JOURNAL OF THE KOREAN SOCIETY OF OCEANOGRAPHY
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• v.9 no.1
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• pp.30-39
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• 2004

In order to understand the environmental impact of marine cage fish farms, we measured the vertical fluxes of particulate to the sediment, the distribution of organic carbon in core samples, sediment oxygen consumption rate (SOD), and macrobenthos with increasing distance from a fish cage in Miruk island located in Tongyong. The experiment was performed in August 2003. Measured values gradually decreased with distance, indicating that the organic matter in the sediment derived from the fish farm. The dominant macrobenthos species were Tharyx mulifilis, Lumbrineris longifolia, Sigambra tentaculata, and Capitella capitata, occupying 88% of the total population. Capirella capirata, an opportunistic polychaete species, were especially abundant between 0 to 5 m radius range. The estimated impact regions of organic matter enrichment based on sediment consilmption rates and compositions of macrobenthos were in good agreement. Most organic matter derived from the fish farm was deposited within a 10 m radius and then dispersed horizontally to nearby (at least 50 m) surface sediment. The vertical organic carbon fluxes to the sediment at the fish farm were higher by a factor of two than those outside the area. The remineralization organic carbon in the upper sediment layer was estimated to be 50% (1.07 g C m$^{-2}$ day$^{-1}$ ) at the fish farm. In contrast, outside the area, 30% (0.30 g C m$^{-2}$ day$^{-1}$ ) of organic carbon was recycled and the remaining 70% was deposited to the deep sediment layer.

• Korean Journal of Environmental Biology
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• v.29 no.4
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• pp.326-344
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• 2011

Although anthropogenic disturbance of 20 years duration affects benthic habitats, few studies have examined its effects on the macrobenthic communities of a bay. The aim of this study was to determine the influence of environmental variables on the macrobenthic communities after the construction of the Hwaong dike. Macrobenthos were collected at 22 sites using a Smith McIntyre grab (0.1 $m^2$) in August 2007 and February 2008. Total organic content was very low around the Hwaong dike. Sediment grain size increased from the Hwaong dike to the outer bay. In total, 317 species of macrobenthic fauna were collected and the mean density was 1,155 ind. $m^{-2}$, both of which were higher than the results of previous studies. The dominant species, $Hetermastus$ $filiformis$, known to be a potential pollution indicator, was more abundant near the Hwaong dike. Conversely, species sensitive to organic pollution, such as the polychaete $Ampharete$ $arctica$ and the ophiuroid $Amphioplus$ $squamata$, exhibited higher mean densities in areas distant from the dike. A cluster analysis indicated that the macrobenthic community was divided into two distinct groups: group I near the dike and group II in the outer bay, which were affected by sediment grain size and total organic content. This study suggests that variations in sediment grain size and organic content after dike construction are important factors controlling the macrobenthic community in Asan Bay.

• Journal of Microbiology
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• v.44 no.1
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• pp.54-63
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• 2006

Ferritin is a major eukaryotic protein and in humans is the protein of iron storage. A partial gene fragment of ferritin (255 bp) taken from the total RNA of Periserrula leucophryna, was amplified by RT-PCR using oligonucleotide primers designed from the conserved metal binding domain of eukaryotic ferritin and confirmed by DNA sequencing. Using the $^{32}P-labeled$ partial ferritin cDNA fragment, 28 different clones were obtained by the screening of the P. leucophryna cDNA library prepared in the Uni-ZAP XR vector, sequenced and characterized. The longest clone was named the PLF (Periserrula leucophryna ferritin) gene and the nucleotide and amino acid sequences of this novel gene were deposited in the GenBank databases with accession numbers DQ207752 and ABA55730, respectively. The entire cDNA of PLF clone was 1109 bp (CDS: 129-653), including a coding nucleotide sequence of 525 bp, a 5' -untranslated region of 128 bp, and a 3'-noncoding region of 456 bp. The 5'-UTR contains a putative iron responsive element (IRE) sequence. Ferritin has an open reading frame encoding a polypeptide of 174 amino acids including a hydrophobic signal peptide of 17 amino acids. The predicted molecular weights of the immature and mature ferritin were calculated to be 20.3 kDa and 18.2 kDa, respectively. The region encoding the mature ferritin was subcloned into the pT7-7 expression vector after PCR amplification using the designed primers and included the initiation and termination codons; the recombinant clones were expressed in E. coli BL21(DE3) or E. coli BL21(DE3)pLysE. SDS-PAGE and western blot analysis showed that a ferritin of approximately 18 kDa (mature form) was produced and that by iron staining in native PAGE, it is likely that the recombinant ferritin is correctly folded and assembled into a homopolymer composed of a single subunit.

• 한국해양학회지
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• v.27 no.1
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• pp.46-54
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• 1992

An investigation on the benthic polychaete community in Youngil Bay was conducted during four seasons of 1991. Polychaetes. the dominant macrofaunal group occupying 71.3% in total macro-faunal density, comprised a total of 72 species with a mean density of 1,485 indiv. m/SUP -2/. The highest species number of 54 spp. and density of 3,207 undiv. m/SUP -2/ was recorded in summer, while the lowest in autumn. The most abundant species was Spiophanes nombyx (37.5%), followed by Pseudopolydora sp.(8.4%), Lumbrineris longifolia(7.0%), Madden cristata(6.5%), Polydora ciliata(4.9%) and so on. Maldane cristata was dominated in winter, Polydora ciliata in spring and Spiophanes bombyx in summer and autumn. The density and species number of Polychaetes were high in the southeastern area of Youngil Bay, and poor near the mouth of Hyoungsan River. Based on the species composition, study area was divided into three regions. Each region sustained its specific benthic faunal assemblage; Maldane-Praxillella assemblage from the middle to the southeastern region of Youngil Bay, Spiophanes-Nephtys assemblage in the northwestern region, and Pseudopolydora-Polydora-Capitella assemblage from the mouth of Hyoungsan River to Pohang Hobour. Maldane Praxillella assemblage showed the highest species number of 55 spp.. and the highest species diversity and species richness indices. Spiophanes-Nephtys assemblage had the highest density of 2,675 indiv. m/SUP -2/ and the highest dominance index because of the predominance of Spiophanes bombyx with a density of 2,073 indiv. m/SUP -2/. Pseudopolydora-Polydora-Capitella assemblage was found in the polluted area and it was a specific assemblage mainly composed of the dominance of organic pollution indicator species. The dominant Polychaetes were Pseudopolydora sp., Polydora ciliata, Capitella capitata, and Dorvillea sp.

• Korean Journal of Environmental Biology
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• v.19 no.2
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• pp.159-171
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• 2001

Community structure, horizontal distribution, density, and ratio between nematodes and benthic harpacticoid copepods of the meiobenthos within the sediments of inner Sihwa Lake were investigated in May 1999 and May 2000. A total of 11 and 8 classes of meiobenthic animals were identified in 1999 and 2000, respectively, which were much lower than other coastal areas. The dominant animals during both sampling periods was the nematodes, followed by sarco-mastigophorans, nauplius of crustaceans, benthic harpacticoid copepods and polychaetes. These five classes of animals comprised more than 90% of total abundance of neiobenthos presented in the samples. In 2000, a lot of polychaete larvae were identified. The most abundant animal were the size that fits in 0.063 mm sieve size. Lower density was observed upper inner part of the Sihwa Lake during both sampling periods, and higher density was observed around the Sihwa floodgates. The average density between those two numbers were observed in the samples collected in the middle of the lake. Lower nematodes to betnhic harpacticoides (N/C) ratio, a relative indicator of environmental pollution, was observed to be lower around the floodgate but higher ratios were observed in the upper inner Sihwa Lake. The present study indicated that inner upper part of the lake becomes unsuitable for the meiobenthos, and the most inner upper lake was considered to be polluted.

• Journal of the Korean Society for Marine Environment & Energy
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• v.19 no.4
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• pp.297-309
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• 2016

This study was carried out to investigate the differences in sedimentary environments and benthic polychaete communities between farming grounds and natural habitats (non-farming ground) in Gamak Bay. Sampling stations of natural habitats were evenly distributed in the entire bay. And mussel farm, oyster farm and ark-shell farm were selected as farming grounds. Dominant sedimentary facies was mud in most sampling stations of farming grounds and natural habitats. However organic contents were higher in the farming grounds than natural habitats of the bay. The species number and mean density of polychaetous community in the natural habitats were greater than those from the farming grounds. Lumbrineris longifolia, known as potential organic enrichment indicator species, was first dominant species both in farming grounds and natural habitats of the bay. However, the next dominant species consisted of different species between two benthic habitats. As a result of community analysis using cluster analysis and nMDS, the natural habitats were divided into several station groups, but most of stations in farming grounds were clustered into one group. Pearson' correlation analysis and PCA showed high relationships between sedimentary environmental factors and benthic polychaetous community in natural habitats, but low or no relationships in farming grounds. That means benthic polychaetous community established in farming ground was under unusual condition such as high input of organic matter. Thus it is necessary to improve the benthic environmental quality of the farming grounds as well as the north-western inner part in Gamak Bay through long-term monitoring efforts.

• Journal of the Korean Society of Fisheries and Ocean Technology
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• v.49 no.4
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• pp.404-418
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• 2013

In this study, we conducted field surveys to investigate and analyze species and length composition of catch from gape net with wings being set in two areas - Masari, Supomri - located in southern part of Jin-do for understanding fishing characteristics of gape net with wings fishery from March to September of 2011. And with those results, we attempted to propose fishery management strategy to harvest fisheries resources continuously. Catch obtained from field surveys comprised total 78 species, which accounted for 53 species of fish, 20 species of crustacean, 4 species of cephalopod and one of polychaete. As to species composition in weight, it showed that there was 88.5% for pisces, 9.0% for cephalopoda and 2.5% for crustacea. As to catch specifics by area, there was 36 species (596,891 individual, 456,551g) of pisces, 17 species (35,815 individual, 12,909g) of crustacea and 3 species (2,876 individual, 3,004g) of cephalopoda in Masari area. In Supumri area, there was 41 species (396,898 individual, 281,457g) of pisces, 15 species (16,113 individual, 7,772g) of crustacea and 4 species (6,792 individual, 72,329g) of cephalopoda and one polychaeta (36 individual, 11g). Catch of anchovy by month recorded on high level on June, July, September in both areas. When considering size composition by month, it was found that new populations recruit to these fishing grounds on June and September. Most of bycatch species including hairtail (Trichiurus lepturus), dotted gizzard shad (Konosirus punctatus), conger eel (Leptocephalous), Pacific sandlance (Ammodytes personatus), horse mackerel (Trachurus japonicus) were juvenile, and grass puffer (Takifugu niphobles), Kammal thryssa (Thryssa kammalensis), Japanese sardinella (Sardinella zunasi) were also small in size. As a result, it is considered that gape net with wings fishery which is likely to catch juvenile needs to be set fishing prohibit period for conserving above stocks during the period excluding main fishing periods of anchovy or fisheries management such as expanding mesh size for preventing juvenile catch.

• Ocean and Polar Research
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• v.30 no.3
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• pp.303-312
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• 2008

Despite the impacts of the climate changes on the pelagic ecosystem, few studies have examined the pelagic-benthic coupling in the adjacent East China Sea and Korea Strait. Therefore, the species composition and abundance of the macrobenthic community, as well as the potential food sources of benthic fauna were investigated in the present study using stable isotope analysis (${\delta}^{13}C\;and\;{\delta}^{15}N$) for suspended particulate organic matter (SPOM), sedimentary organic matter (SOM), phytoplankton, and zooplankton. A total of 157 macrobenthic fauna were collected, and the density of the macrobenthic fauna ranged from 4 to 434 ind./0.25 $m^2$, with an average density of 149 ind./0.25 $m^2$. The density of the benthic fauna increased moving from offshore shelf sites to coastal sites adjacent to the Korea Strait. Cluster analysis showed that the macrobenthic communities consisted of three distinct groups: group A in the Korea Strait, group B in the East China Sea, and group C near Ieodo. The dominant species in group A were the amphipods Photis japonica and Ampelisca miharaensis, followed by the polychaete Scolotoma longifolia. Environmental variables, such as the temperature of the seawater and sediment, and oxygen, and chlorophyll a levels, appeared to affect the structure of the community, suggesting the importance of coupling with the pelagic system. The ${\delta}^{13}C$ values of SPOM and zooplankton ranged from -22.97 to -23.5% and -19.92 to -21.86%, respectively, showing a relatively narrow range(<1%) between the two components. The difference between the ${\delta}^{13}C$ values of SOM and pelagic organic matter was also within 1%, suggesting that the SOM originated from the pelagic system, which is an important factor controlling the macrobenthic community.