• Animal Bioscience
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• v.35 no.7
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• pp.964-974
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• 2022

Objective: The highly pathogenic avian influenza virus (HPAIV) is a threat to the poultry industry and economy and remains a potential source of pandemic infection in humans. Antiviral genes are considered a potential factor for studies on HPAIV resistance. Therefore, in this study, we investigated gene expression related to the mitogen-activated protein kinase (MAPK) signaling pathway by comparing non-infected, HPAI-infected resistant, and susceptible Ri chicken lines. Methods: Resistant (Mx/A; BF2/B21) and susceptible Ri chickens (Mx/G; BF2/B13) were selected by genotyping the Mx and BF2 genes. Then, the tracheal tissues of non-infected and HPAIV H5N1 infected chickens were collected for RNA sequencing. Results: A gene set overlapping test between the analyzed differentially expressed genes (DEGs) and functionally categorized genes was performed, including biological processes of the gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathways. A total of 1,794 DEGs were observed between control and H5N1-infected resistant Ri chickens, 432 DEGs between control and infected susceptible Ri chickens, and 1,202 DEGs between infected susceptible and infected resistant Ri chickens. The expression levels of MAPK signaling pathway-related genes (including MyD88, NF-κB, AP-1, c-fos, Jun, JunD, MAX, c-Myc), cytokines (IL-1β, IL-6, IL-8), type I interferons (IFN-α, IFN-β), and IFN-stimulated genes (Mx1, CCL19, OASL, and PRK) were higher in H5N1-infected than in non-infected resistant Ri chickens. MyD88, Jun, JunD, MAX, cytokines, chemokines, IFNs, and IFN-stimulated expressed genes were higher in resistant-infected than in susceptible-infected Ri chickens. Conclusion: Resistant Ri chickens showed higher antiviral activity compared to susceptible Ri chickens, and H5N1-infected resistant Ri chickens had immune responses and antiviral activity (cytokines, chemokines, interferons, and IFN-stimulated genes), which may have been induced through the MAPK signaling pathway in response to H5N1 infection.

• Animal Bioscience
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• v.37 no.6
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• pp.1021-1030
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• 2024

Objective: R-loops are DNA:RNA triplex hybrids, and their metabolism is tightly regulated by transcriptional regulation, DNA damage response, and chromatin structure dynamics. R-loop homeostasis is dynamically regulated and closely associated with gene transcription in mouse zygotes. However, the factors responsible for regulating these dynamic changes in the R-loops of fertilized mouse eggs have not yet been investigated. This study examined the functions of candidate factors that interact with R-loops during zygotic gene activation. Methods: In this study, we used publicly available next-generation sequencing datasets, including low-input ribosome profiling analysis and polymerase II chromatin immunoprecipitation-sequencing (ChIP-seq), to identify potential regulators of R-loop dynamics in zygotes. These datasets were downloaded, reanalyzed, and compared with mass spectrometry data to identify candidate factors involved in regulating R-loop dynamics. To validate the functions of these candidate factors, we treated mouse zygotes with chemical inhibitors using in vitro fertilization. Immunofluorescence with an anti-R-loop antibody was then performed to quantify changes in R-loop metabolism. Results: We identified DEAD-box-5 (DDX5) and histone deacetylase-2 (HDAC2) as candidates that potentially regulate R-loop metabolism in oocytes, zygotes and two-cell embryos based on change of their gene translation. Our analysis revealed that the DDX5 inhibition of activity led to decreased R-loop accumulation in pronuclei, indicating its involvement in regulating R-loop dynamics. However, the inhibition of histone deacetylase-2 activity did not significantly affect R-loop levels in pronuclei. Conclusion: These findings suggest that dynamic changes in R-loops during mouse zygote development are likely regulated by RNA helicases, particularly DDX5, in conjunction with transcriptional processes. Our study provides compelling evidence for the involvement of these factors in regulating R-loop dynamics during early embryonic development.

• Journal of The Korean Society of Inherited Metabolic disease
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• v.18 no.2
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• pp.62-67
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• 2018

Hunter syndrome, also known as mucopolysaccharidosis Type II (MPS II), is one of the lysosomal storage diseases caused by a lack of the enzyme iduronate 2-sulfatase (I2S). Lack of the I2S enzyme activity leads to accumulation of the glycosaminoglycans (GAG), causing dysfunction of multiple organs and systems. MPS II is an X-linked recessive disease due to mutation of IDS gene located on long arm of the X chromosome (Xq28). To date, more than 350 mutations of IDS gene have been identified in Hunter syndrome. Phenotypes of MPS II are classified as either severe or attenuated depending on the degree of cognitive impairment. Because the phenotype of MPS II is related to the type of mutation, identifying mutations is useful in predicting prognosis. We recently had a case of MPS II diagnosed by exome sequencing in a 7 month old boy with infantile spasm uncontrolled by AED. He was diagnosed with hearing loss at 2 months of age, and he took vigabatrin and prednisolone to control infantile spasms diagnosed at 3 months of age. At 6 months of age, whole exome sequencing was performed to evaluate the infantile spasm and hearing loss in this patient, and the mutation c.851C>T (p.Pro284Leu) inherited from hemizygous mother was revealed. The results of urine Cetylpyridinium Chloride (CPC) precipitation test, which were negative until 8 months of age, were positive from 9 months of age. We report a case of MPS II diagnosed by exome sequencing and treated through enzyme replacement therapy from 9 months after birth.

• Research in Plant Disease
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• v.21 no.2
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• pp.50-57
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• 2015

Control of nematode has become difficult owing to the restricted use of effective soil fumigant, methyl bromide, and other non-fumigant nematicides. Therefore, it is urgently necessary to develop microbial nematicide to replace chemical nematicides. In this study, the 50% aqueous methanol extraction solution of fermentation broths of 2,700 actinomycete strains were tested for their nematicidal activity against second stage of juveniles (J2s) of Meloidogyne incognita. As the results, only the 50% aqueous methanol extraction solution of AN110065, at 20% equivalent to 10% fermentation broth, showed strong nematicidal activity with 78.9% of mortality 24 h after treatment and 94.1% of mortality at 72 h. The 16S rRNA gene sequencing showed that the strain sequence was 99.78% identical to Streptomyces netropsis. The extract of S. netropsis AN110065 fermentation broth was successively partitioned with ethyl acetate and butanol and then the ethyl acetate, butanol and water layers were investigated for their nematicidal activity against the M. incognita. At $1000{\mu}g/ml$, ethyl acetate layer showed the strongest activity of 83.5% of juvenile mortality 72 h after treatment. The pot experiment using the fermentation broth of AN110065 on tomato plant against M. incognita displayed that it evidently suppressed gall formation at a 10-fold diluent treatment. The tomato plants treated with the fermentation broth of S. netropsis AN110065 did not show any phytotoxicity. The results suggest that S. netropsis AN110065 has a potential to serve as microbial nematicide in organic agriculture.

• Microbiology and Biotechnology Letters
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• v.38 no.1
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• pp.24-31
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• 2010

For the research of the natural marine antioxidant, an antioxidant-producing marine actinomycetes was isolated from sea water in Jeju coastal area. The strain was identified based on 16S rDNA sequencing, the morphology by a method of scanning electron microscopy, physiological and biochemical characteristics and cellular fatty acid analysis. The isolated strain ACT-18 was gram positive, aerobic, non-motile spores. Substrate mycelia are dark green and yellow gray aerial mycelia. The cell size of the strain was $0.5{\sim}1.0\;{\mu}m$. 16S rDNA sequence analysis showed that were Gram-positive bacteria grouped on Streptomyces sp. Results of cellular fatty acid analysis showed that major cellular fatty acids were $C_{15:0}$ anteiso (39.33%), $C_{16:1}$ cis 9 (11.96%), $C_{16:0}$ (13.08%) and $C_{17:0}$ anteiso (10.99%). The antioxidant activity of methanol extract from Streptomyce sp. ACT-18 was evaluated by measuring 1,1-diphenyl- 2-picrylhydrazyl (DPPH), hydroxyl, and alkyl radical scavenging activity using an electron spin resonance (ESR) spectrometer. DPPH radical scavenging activity of SBME (Streptomyces Broth Methanol Extract) A-18 was 46% at 0.1 mg/mL. Hydroxyl radical scavenging activity of SBME A-18 was 63% at 0.1 mg/mL. Alkyl radical scavenging activity of SBME A-18 was 39% at 0.1 mg/mL.

• Korean Journal of Food Science and Technology
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• v.36 no.5
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• pp.779-783
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• 2004

New food ingredient was developed to eradicate and protect against re-infection of Helicobacter pylori in fermentation broth of lactic acid bacteria (LAB) showing antimicrobial activity against pathogenic microorganisms such as H. pylori and Listeria monocytogenes. LAB strain CBT SL4 was identified as Pediococcus pentosaceus by 16S rDNA sequencing and its culture broth showed antimicrobial activity of 800 AU/mL against H. pylori in optimized fermentation process. Using thin layer concentration system and spray-typed fluid bed drier system, concentrated powder product showing activity of 12,800 AU/g was harvested. Product showed eradication and protection activities against H. pylori infection on feeding test (50 AU/day) using Mongolian gerbil infection model. After 4 weeks therapy of 8,000 AU/day, ${\Delta}13CO_2$ level (DOB30) decreased about 40% in urea breath test on patient with H. pylori infection. Result show concentrated culture product of P. pentosaceus CBT SL4 has eradicating and protecting activities against H. pylori infection and can be used as food-active ingredient for prevention of gastric and duodenum ulcer caused by H. pylori.

• Korean Journal of Microbiology
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• v.45 no.4
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• pp.397-403
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• 2009

For the research of the natural antioxidant from marine sources, an antioxidant-producing marine actinomycetes was isolated from sea water in Jeju coastal area. The strain was identified based on 16S rDNA sequencing, the morphology by a method of scanning electron microscopy, physiological and biochemical characteristics and cellular fatty acid analysis. The isolated strain ACT-1 cell size was $0.5\sim1.0{\mu}m$ and gram positive, aerobic, nonmotile, substrate mycelium are red and gray aerial mycelium. 16S rRNA sequence analysis showed that were Gram-positive bacteria grouped on Streptomyces genus. Results of cellular fatty acid analysis showed that major cellular fatty acids were $C_{15:0}$ anteiso (39.33%), $C_{16:1}$ cis 9 (11.96%), $C_{16:0}$ (13.08%) and $C_{17:0}$ anteiso (10.99%). Finally, strain was identified Streptomyces sp. ACT-1. The antioxidant activity of methanol extract from Streptomyces sp. ACT-1 was evaluated by measuring DPPH, hydroxyl, and alkyl radical scavenging activity using an electron spin resonance (ESR) spectrometer. DPPH radical scavenging activity of SBME-1 (Streptomyces broth methanol extract) was 67% at $1,000{\mu}g$/ml. Hydroxyl radical scavenging activity of SBME-1 was 84% at $500{\mu}g$/ml. Alkyl radical scavenging activity of SBME-1 was 71% at $1,000{\mu}g$/ml.

• Microbiology and Biotechnology Letters
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• v.43 no.4
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• pp.307-313
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• 2015

Unpolished rice (UR) is considered to be a healthy alternative to white rice when coping with chronic diseases. In the present study, the fermented slurry of unpolished rice (FSUR) was evaluated with respect to its antimicrobial activities and biochemical characteristics, including the quantities of sugar, total soluble sugar, organic acids, free amino acids, pH, and physiological activity. The antimicrobial efficiency of FSUR was assessed using the paper disc-agar diffusion method. FSUR exhibited strong antimicrobial activity against six pathogenic bacterial strains (Staphylococcus aureus, Escherichia coli, Listeria monocytogenes, Pseudomonas aeruginosa, Salmonella typhimurium, and Yersinia enterocolitica) and two fermentation strains (Gluconacetobacter intermedius and Lodderomyces elongisporus). The antimicrobial activity of FSUR was higher than the commercial antibiotics, carbenicillin ($50{\mu}g/ml$) and tetracycline ($50{\mu}g/ml$) against S. aureus, E. coli, L. monocytogenes, P. aeruginosa, S. typhimurium, Y. enterocolitica, and L. elongisporus. Also FSUR had a high antioxidant activity. The microorganisms were isolated from FSUR using tryptic soy broth and yeast extract-peptone-dextrose agar media. The isolated microorganisms were characterized using physiological and biochemical analyses as well as by 16S rRNA gene sequencing and phylogenic analysis. 16S rRNA gene sequence analysis showed that the isolated microorganisms had a high similarity to G. intermedius, Lactobacillus casei, Lactobacillus plantarum, and Acetobacter peroxydans.

• Microbiology and Biotechnology Letters
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• v.40 no.1
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• pp.66-69
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• 2012

Five strains out of 200 candidate strains (SG 1-9, 1-12, SG 2-8, 2-10, and 2-17) were selected to determine their antifungal activity against Raffaelea quercus-mongolicae. The 16S rDNA sequences of the five strains were determined by sequencing analysis and analyzed by the homology of the blast program at NCBI. The homology search showed that SG 1-9 and 1-12 had a 98% homology with Streptomyces cinnamoneus and 98% homology with Burkholderia cepacia, while SG 2-8, 2-10, and 2-17 had a 99% homology with Streptomyces fradiae, a 97% homology with Staphylococcus epidermidis, and a 99% homology with Staphylococcus epidermidis. Out of the five selected strains, organic extract and protein extracts of SG2-17 strain broth were employed to determine antifungal activity against Raffaelea quercus-mongolicae. The organic extract exhibited antifungal activity, but the protein extracts did not demonstrate such an activity. Three organic solvents, butanol, benzene, and ethyl acetate, were also used for determination of antifungal activities. The activity measurements revealed that benzene extract possessed the greatest inhibitory effect on the growth of Raffaelea quercus-mongolicae, with the next highest being butanol extract, and ethyl acetate extract being the lowest.

• Microbiology and Biotechnology Letters
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• v.49 no.1
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• pp.111-119
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• 2021

A bacterial strain isolated from a Malva verticillata leaf was identified as Bacillus velezensis MV2 based on the 16S rRNA sequencing results. Complete genome sequencing revealed that B. velezensis MV2 possessed a single 4,191,702-bp contig with 45.57% GC content. Generally, Bacillus spp. are known to produce diverse antimicrobial compounds including bacteriocins, polyketides, and non-ribosomal peptides. Antimicrobial compounds in the B. velezensis MV2 were extracted from culture supernatants using hydrophobic interaction chromatography. The crude extracts showed antimicrobial activity against both gram-positive bacteria and gram-negative bacteria; however, they were more effective against gram-positive bacteria. The extracts also showed antifungal activity against phytopathogenic fungi such as Fusarium fujikuroi and F. graminearum. In time-kill assays, these antimicrobial compounds showed bactericidal activity against Bacillus cereus, used as indicator strain. To predict the type of antimicrobial compounds produced by this strain, we used the antiSMASH algorithm. Forty-seven secondary metabolites were predicted to be synthesized in MV2, and among them, fourteen were identified with a similarity of 80% or more with those previously identified. Based on the antimicrobial properties, the antimicrobial compounds may be nonribosomal peptides or polyketides. These compounds possess the potential to be used as biopesticides in the food and agricultural industry as an alternative to antibiotics.