• Journal of Microbiology and Biotechnology
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• v.32 no.7
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• pp.911-917
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• 2022

As valuable antibiotics, microbial natural products have been in use for decades in various fields. Among them are polyene compounds including nystatin, amphotericin, and nystatin-like Pseudonocardia polyenes (NPPs). Polyene macrolides are known to possess various biological effects, such as antifungal and antiviral activities. NPP A1, which is produced by Pseudonocardia autotrophica, contains a unique disaccharide moiety in the tetraene macrolide backbone. NPP B1, with a heptane structure and improved antifungal activity, was then developed via genetic manipulation of the NPP A1 biosynthetic gene cluster (BGC). Here, we generated a Streptomyces artificial chromosomal DNA library to isolate a large-sized NPP B1 BGC. The NPP B1 BGC was successfully isolated from P. autotrophica chromosome through the construction and screening of a bacterial artificial chromosome (BAC) library, even though the isolated 140-kb BAC clone (named pNPPB1s) lacked approximately 8 kb of the right-end portion of the NPP B1 BGC. The additional introduction of the pNPPB1s as well as co-expression of the 32-kb portion including the missing 8 kb led to a 7.3-fold increase in the production level of NPP B1 in P. autotrophica. The qRT-PCR confirmed that the transcription level of NPP B1 BGC was significantly increased in the P. autotrophica strain containing two copies of the NPP B1 BGCs. Interestingly, the NPP B1 exhibited a previously unidentified SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) inhibition activity in vitro. These results suggest that the Streptomyces BAC cloning of a large-sized, natural product BGC is a valuable approach for titer improvement and biological activity screening of natural products in actinomycetes.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.210-210
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• 2022

Silybum marianum is an annual or biennial plant from the Asteraceae family. It can grow in low-nutrient soil and drought conditions, making it easy to cultivate. From the seed, a specialized plant metabolite called silymarin (flavonolignan complex) is produced and is known to alleviate the liver from hepatitis and toxins damages. To infer the phylogenetic placement of a Korean milk thistle, we conducted a chloroplast assembly and annotation following by a comparison with existing Chinese reference genome (NC_028027). The chloroplast genome structure was highly similar with an assembly size of 152,642 bp, an 153,202 bp for Korean and Chinese milk thistle respectively. Moreover, there were similarities at the gene level, coding sequence (n = 82), transfer RNA (n = 31) and ribosomal RNA (n = 4). From all coding sequences gene set, the phylogenetic tree inference placed the Korean cultivar into the milk thistle clade; corroborating the expected tree. Moreover, an investigation the tree based only on the ycf1 gene confirmed the same tree; suggesting that ycf1 gene is a potential marker for DNA barcoding and population diversity study in milk thistle genus. Overall, the provided data represents a valuable resource for population genomics and species-centered determination since several species have been reported in the Silybum genus.

• Fisheries and Aquatic Sciences
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• v.26 no.9
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• pp.569-581
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• 2023

The morphology and genetic identification of Rasbora lateristriata and Rasbora argyrotaenia between cultivated and wild populations has never been reported. This study compares morphology and cytochrome c oxidase (COI) genes between farmed and wild stock Rasbora spp. in Java and Sumatra island, Indonesia. We analyzed the truss network measurement (TNM) characters of 80 fish using discriminant function analysis statistical tests. DNA was extracted from muscle tissue of 24 fish specimens, which was then followed by polymerase chain reaction, sequencing, phylogenetic analysis, fixation index analysis, and statistical analysis of haplotype networks. Basic Local Alignment Search Tool analysis validated the following species: R. lateristriata and R. argyrotaenia from farming (Jogjakarta); Rasbora agryotaenia (Purworejo), R. lateristriata (Purworejo and Malang), Rasbora dusonensis (Palembang), and Rasbora einthovenii (Riau) from natural resources. Based on TNM characters, Rasbora spp. were divided into four groups, referring to four distinct characters in the middle of the body. The phylogenetic tree is divided into five clades. The genetic distance between R. argyrotaenia (Jogjakarta) and R. lateristriata (Malang) populations (0.66) was significantly different (p < 0.05). R. lateristriata (Purworejo) has the highest nucleotide diversity (0.43). R. argyrotaenia from Jogjakarta and Purworejo shared the same haplotype. The pattern of gene flow among them results from the two populations' close geographic proximity and environmental effects. R. argyrotaenia had low genetic diversity, therefore, increasing heterozygosity in cultivated populations is necessary to avoid inbreeding. Otherwise, R. lateristriata (Purworejo) had a greater gene variety that could be used to develop breeding. In conclusion, the middle body parts are a distinguishing morphometric character of Rasbora spp., and the COI gene is more heterozygous in the wild population than in farmed fish, therefore, enrichment of genetic variation is required for sustainable Rasbora fish farming.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.56 no.5
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• pp.701-707
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• 2023

We investigated Euphausia pacifica population in Korean waters in 2016 By samplings for genetic structur at five stations. Three sampling stations were located in the middle of the water masses which were clustered by temperature and salinity whereas the other stations were at the boundaries of the water masses. We amplified a 566 bp region and compared it with sequences of E. pacifica distributed in other waters. Sequences were classified two clades, and a clade was formed in the station E. Genetic distance of station E was close to E. pacifica present in Bering Sea, while it was distant to E. pacifica present in Yellow Sea near China. In genetic analysis, seven haplotypes were formed. Hap-1 and Hap-2 were shared in all five stations, while Hap-3 was shared in station W and WS. Four independent haplotypes were present in station E. Haplotype and nucleotide diversity were the highest in station E and the lowest in station S. The F_ST distances between station E and other stations were the highest, but distances among other stations were low. As a result, we concluded that E. pacifica, which is distributed in Korean waters, has a genetic population differentiation in the East Sea (station E).

• Food Science of Animal Resources
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• v.44 no.4
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• pp.779-789
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• 2024

The effects of irradiation on meat constituents including water, proteins, and lipids are multifaceted. Irradiation leads to the decomposition of water molecules, resulting in the formation of free radicals that can have both positive and negative effects on meat quality and storage. Although irradiation reduces the number of microorganisms and extends the shelf life of meat by damaging microbial DNA and cell membranes, it can also accelerate the oxidation of lipids and proteins, particularly sulfur-containing amino acids and unsaturated fatty acids. With regard to proteins, irradiation affects both myofibrillar and sarcoplasmic proteins. Myofibrillar proteins, such as actin and myosin, can undergo depolymerization and fragmentation, thereby altering protein solubility and structure. Sarcoplasmic proteins, including myoglobin, undergo structural changes that can alter meat color. Collagen, which is crucial for meat toughness, can undergo an increase in solubility owing to irradiation-induced degradation. The lipid content and composition are also influenced by irradiation, with unsaturated fatty acids being particularly vulnerable to oxidation. This process can lead to changes in the lipid quality and the production of off-odors. However, the effects of irradiation on lipid oxidation may vary depending on factors such as irradiation dose and packaging method. In summary, while irradiation can have beneficial effects, such as microbial reduction and shelf-life extension, it can also lead to changes in meat properties that need to be carefully managed to maintain quality and consumer acceptability.

• Journal of Environmental Science International
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• v.33 no.1
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• pp.87-95
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• 2024

The giant jellyfish, Nemopilema nomurai, is an endemic species found in Northeast Asian waters and their population structures, such as size and genetics, and their environmental characteristics were investigated. N. nomurai was obtained from the Yellow and Northern East China Seas during the summers of 2006, 2007, and 2009. In the northern Yellow Sea, small-sized jellyfish were found to be dominant and towards the southern seas, the size of the jellyfish increased. In the northern East China Sea, only one mode of jellyfish was found in May, and the number of modes increased up-to five in July. However, at the center of the Yellow Sea, one or two modes were found in July, 2007. Thus, different jellyfish populations were present in the northern East China Sea and the Yellow Sea. However, based on first appearance and a cohort analysis using the bell diameter, the jellyfish population in the northern Yellow Sea might be recognized as a distinct group that differed from those found in the northern East China Sea. Furthermore, mitochondrial DNA sequences (cytochrome c oxidase subunit I) of N. nomurai were, determined and compared with genetic structures obtained from jellyfish in the Yellow Sea. The genetic diversity of N. nomurai was highest in the regions around the northern East China Sea and at the center of the Yellow Sea and was the lowest around the northern Yellow Sea. Thus, N. nomurai populations in the Yellow Sea and northern East China Sea might be different concerning their seeding places.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.57 no.1
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• pp.41-52
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• 2024

Serotransferrin cDNA from the Siberian sturgeon Acipenser baerii was isolated and its expression patterns during early life intervals were characterized. It contained an ORF encoding a 708-aa-long polypeptide, including a 19-aa signal peptide. Bioinfomatic analysis and 3D modeling indicated a typical bi-lobal structure with conserved iron-coordinating residues. During embryonic development, the potential transition of maternally provisioned transcripts to zygotically de novo transcribed ones occurred around blastula stage. The transferrin mRNA levels peaked at stages responsible for pronephros, heart and erythropoietic component differentiation. After hatching, the transferrin mRNA expression gradually increased at early ontogenic phases (0 to 3 DPH) corresponding to the periods in which prolarvae exhibited increased blood circulation and liver differentiation. The expression decreased at subsequent stages in which prolarvae exhibited benthic movement. The tissue distribution assay indicated liver-predominant expression at fingerling stage. From the microinjection-based challenge with Aeromonas hydrophila at day-0 and day-7, the transcriptional response was modulated toward upregulation, in which the amounts induced at 6, 12 and 24 HPI were greater in prolarvae injected at day-7 than at day-0. Therefore, transferrin plays important roles in both early development and host protective responses to pathogens in the Siberian sturgeon.

• Korean Journal of Microbiology
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• v.49 no.2
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• pp.137-145
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• 2013

This study was performed at 2 sites of Nak-Dong River to investigate the changes of nitrifiers depending on the presence and absence of organic pollutants (due to the effluents of domestic wastewater treatment plant, WWTP). Conventional chemical parameters such as T-N, $NH_4$-N, $NO_2$-N, $NO_3$-N were measured and the quantitative nitrifiers at the 2 sites were analyzed comparatively by fluorescent in situ hybridization (FISH) with NSO190 and NIT3, after checking the presence of gene amoA of ammonia oxidizing bacteria (AOB) and 16S rDNA signature sequence for Nitrobacter sp. that belongs to nitrite oxidizing bacteria (NOB). Also ${\alpha}{\cdot}{\beta}{\cdot}{\gamma}$-Proteobacteria were detected using FISH to get a glimpse of the general bacterial community structure of the sites. Based on the distribution structure of the ${\alpha}{\cdot}{\beta}{\cdot}{\gamma}$-Proteobacteria and the measurement of nitrogen in different phases, it could be said that the site 2 was more polluted with organics than site 1. Corresponding to the above conclusion, the average numbers of AOB and NOB detected by NSO160 and NIT3, respectively, at site 2 [AOB, $9.3{\times}10^5$; NOB, $1.6{\times}10^6$ (cells/ml)] was more than those at site 1 [AOB, $7.8{\times}10^5$; NOB, $0.8{\times}10^6$ (cells/ml)] and also their ratios to total counts were higher at site 2 (AOB, 27%; NOB, 34%) than those at site 1 (AOB, 18%; NOB, 23%). Thus, it could be concluded that the nitrification at site 2 was more active due to continuous loading of organics from the effluents of domestic WWTP, compared to site 1 located closed to raw drinking water supply and subsequently less polluted with organics.

• Applied Microscopy
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• v.38 no.4
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• pp.293-306
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• 2008

The essential factor of acute respiratory distress syndrome (ARDS), an acute lung injury accompanied commonly by sepsis syndrome is accumulation of neutrophils in lung tissue. The study attempted to confirm whether a lung injury would be decreased with the anti-inflammatory effect of germanium by the treated germanium prior to the development of ARDS and whether nitric oxide influence in suppressing a lung injury. Test groups were divided in the following structure for experiment; CON that has been administered with sodium chloride to airway, LPS administered with endotoxin for 5 hours in the same amount and 5 hours of endotoxin administered Ge+LPS following 1 hours of pre-treated germanium. The result of a test using experimental animals, infilteration of neutrophils (p<0.001) in bronchoalveolar lavage fluid (BALF) was significantly decreased, the structure of lung tissue was preserved relatively well, and much neutrophils with distinct positive were observed on tunel staining which showed increase of apoptotic neutrophils in the pre-treated germanium group compare to the endotoxin administrated group. In observation of ultrastructural changes of cell in BALF, phagocytic alveolar macrophage was increased in alveolar space, the nucleus of most engulfed neutrophils were condensed, and some apoptosis neutrophils appears to be DNA fragmentation and effacement of cellular organelles were found in intercellular matrix in the pre-treated germanium group. However, the nitric oxide showed increase in all the groups excluding CON, and the nitric oxide effect such as degranulation diminishing of mast cells and apoptosis increase of neutrophils in the pre-treated group only. The situation appears that there was change in internal environment of the experimental animal by the pre-treated germanium before the nitric oxide is produced and the anti-inflammatory effect activated the pre-processed germanium by nitric oxide which activated following the change. Therefore, the nitric oxide created from macrophage in accordance with the pre-treated germanium appears to influence in alleviating a lung injury. Accordingly, acute lung injury is alleviated by the anti-inflammatory effect of germanium such as inhibition of neutrophils migration, induction of neutrophil apoptosis and increase of phagocytic function of phagocyte, and the nitric oxide produced from activated macrophage by germanium would influence in suppressing a lung injury.

• Journal of Embryo Transfer
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• v.27 no.2
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• pp.107-111
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• 2012

Miniature pig sperm cryopreservation is continually researched in biotechnology for breed conservation and reproduction. It is important to control the temperature at each stage of cryopreservation and cryoprotectant. It is also necessary to find the optimal cryoprotectant concentration and chemical elements of the extender. Recently, many studies have used various cryoprotectant materials, such as dimethyl sulphoxide (DMSO), ethylene glycol (EG), antifreeze protein (AFP), amides, and glycerol. Glycerol is a commonly used cryoprotectant. However, glycerol has critical cytotoxic properties, including osmotic pressure and it can cause irreversible damage to live cells. Therefore, We focused on membrane fluidity modifications can reduce cell damage from freezing and thawing procedures and evaluated on the positive effects of trehalose to the viability, chromatin integrity, and motility of boar sperm. Miniature pig sperm was separated from semen by washing with modified- Modena B (mMB) extender. After centrifugation, the pellet was diluted with the prepared first extender. This experiment was designed to compare the effects that sperm cryopreservation using two different extenders has on sperm chromatin. The control group used the glycerol only and it was compared with the glycerol and glycerol plus trehalose extender. Sperm viability and motility were evaluated using WST1 assays and computer-assisted semen assays (CASA). Chromatin structure was examined using acridine orange staining. For the motility descriptors, trehalose caused a significant (p<0.01) increase in total motility ($57.80{\pm}4.60%$ in glycerol vs. $75.50{\pm}6.14%$ in glycerol + trehalose) and progressive ($51.20{\pm}5.45%$ in glycerol vs. $70.74{\pm}8.06%$ in glycerol + trehalose). A significant (p<0.05) increase in VAP ($42.70{\pm}5.73{\mu}m/s$ vs. $59.65{\pm}9.47{\mu}m/s$), VSL ($23.06{\pm}3.27{\mu}m/s$ vs. $34.60{\pm}6.58{\mu}m/s$), VCL ($75.36{\pm}11.36{\mu}m/s$ vs. $99.55{\pm}12.91{\mu}m/s$), STR ($54.4{\pm}2.19%$ vs. $58.0{\pm}1.63%$), and LIN ($32.2{\pm}2.05%$ vs. $36.0{\pm}2.45%$) were also detected, respectively. The sperm DNA fragmentation index was 48.8% to glycerol only and 30.6% to glycerol plus trehalose. Trehalose added group showed higher percentages of sperm motility, stability of chromatin structure than glycerol only. In this study, we suggest that trehalose is effective in reducing freezing damage to miniature pig sperm and can reduce chromatin damage during cryopreservation.