• 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.

• Molecules and Cells
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• v.38 no.9
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• pp.789-795
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• 2015

A chromosome territory is composed of chromosomal subdomains. The internal structure of chromosomal subdomains provides a structural framework for many genomic activities such as replication and DNA repair, and thus is key to determining the basis of their mechanisms. However, the internal structure and regulating proteins of a chromosomal subdomain remains elusive. Previously, we showed that the chromosome territory expanded after BAF53 knockdown. Because the integrity of chromosomal subdomains is a deciding factor of the volume of a chromosome territory, we examined here the effect of BAF53 knockdown on chromosomal subdomains. We found that BAF53 knockdown led to the disintegration of histone H2B-GFP-visualized chromosomal subdomains and BrdU-labeled replication foci. In addition, the size of DNA loops measured by the maximum fluorescent halo technique increased and became irregular after BAF53 knockdown, indicating DNA loops were released from the residual nuclear structure. These data can be accounted for by the model that BAF53 is prerequisite for maintaining the structural integrity of chromosomal subdomains.

• Bulletin of the Korean Chemical Society
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• v.33 no.2
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• pp.583-588
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• 2012

Functional interaction between Drosophila orphan receptor FTZ-F1 (NR5A3) and a segmentation gene product fushi tarazu (FTZ) is crucial for regulating genes related to define the identities of alternate segmental regions in the Drosophila embryo. FTZ binding to the ligand-binding domain (LBD) of FTZ-F1 is of essence in activating its transcription process. We determined solution structures of the cofactor peptide ($FTZ^{PEP}$) derived from FTZ by NMR spectroscopy. The cofactor peptide showed a nascent helical conformation in aqueous solution, however, the helicity was increased in the presence of TFE. Furthermore, $FTZ^{PEP}$ formed ${\alpha}$-helical conformation upon FTZ-F1 binding, which provides a receptor bound structure of $FTZ^{PEP}$. The solution structure of $FTZ^{PEP}$ in the presence of FTZ-F1 displays a long stretch of the ${\alpha}$-helix with a bend in the middle of helix.

• Journal of Korea Multimedia Society
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• v.23 no.4
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• pp.574-580
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• 2020

Stress induces change to the body functions and causes chronic problems such as worsening a disease. Thus, humans want to evade anxiety and would try any means to reduce stressful situations. Generally, a person would handle their stress by either regulating their emotions or merely coping with the situation, for which the former is most widely used. Our research aims to effectively reduce stress by using the emotional response structure developed by Plutichik and the vitalization method. We extracted the relevant components of the stress-reduction method that would be applicable in any space using digital technologies such as sensors, IoT, and augmented reality. An architect or designer may incorporate these structural components into any structure to effectively reduce people's stress. The research aims to provide a new perspective of architectural space and to show applications of the stress-reducing architectural spaces, which should also fulfill the people's needs. Further research is needed to develop an automatic system to utilize spatial components more effectively.

• Journal of Life Science
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• v.10 no.4
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• pp.422-430
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• 2000

In order to search for the effects of Shine-Dalgarno (SD) sequence and nucleotide sequence of spacer region (SD-ATG) on bGH expression, oligonucleotides containing random SD sequences and a spacer region were chemically synthesized. The distance between SD region and initiation codon (ATG) was fixed to 9 nucleotides in length. The expression vectors have been constructed using pT7-1 vector containing a T7 promoter. Positive clones were screened with colony hybridization and named pT7A or pT7B plasmid series. The selected clones were confirmed by DNA sequencing and finally, 19 clones having various SD combinations were obtained. When bovine growth hormone was induced by IPTG in E. coli BL21(DE3), all cells harboring these plasmids produced a detectable level of bGH in western blot analysis. However, various SD sequences did not affect on bGH expression, indicating that the sequences of SD and the spacer region did not sufficiently destabilize mRNA secondary structure of bGH gene. Therefore, these results indicate that the disruption of mRNA secondary structure might be a major factor for regulating bGH expression in the translational initiation process.

• Bulletin of the Korean Chemical Society
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• v.33 no.8
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• pp.2508-2512
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• 2012

Cold shock proteins (CSPs) are a family of proteins induced at low temperatures. CSPs bind to single-stranded nucleic acids through the ribonucleoprotein 1 and 2 (RNP 1 and 2) binding motifs. CSPs play an essential role in cold adaptation by regulating transcription and translation via molecular chaperones. The solution nuclear magnetic resonance (NMR) or X-ray crystal structures of several CSPs from various microorganisms have been determined, but structural characteristics of psychrophilic CSPs have not been studied. Therefore, we optimized the purification process to obtain highly pure Lm-Csp and determined the three-dimensional structure model of Lm-Csp by comparative homology modeling using MODELLER on the basis of the solution NMR structure of Bs-CspB. Lm-Csp consists of a ${\beta}$-barrel structure, which includes antiparallel ${\beta}$ strands (G4-N10, F15-I18, V26-H29, A46-D50, and P58-Q64). The template protein, Bs-CspB, shares a similar ${\beta}$ sheet structure and an identical chain fold to Lm-Csp. However, the sheets in Lm-Csp were much shorter than those of Bs-CspB. The Lm-Csp side chains, E2 and R20 form a salt bridge, thus, stabilizing the Lm-Csp structure. To evaluate the contribution of this ionic interaction as well as that of the hydrophobic patch on protein stability, we investigated the secondary structures of wild type and mutant protein (W8, F15, and R20) of Lm-Csp using circular dichroism (CD) spectroscopy. The results showed that solvent-exposed aromatic side chains as well as residues participating in ionic interactions are very important for structural stability. Further studies on the three-dimensional structure and dynamics of Lm-Csp using NMR spectroscopy are required.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.39 no.spc1
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• pp.132-141
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• 2006

Artificial structures have been designed as pilot structures to promote the creation and restoration of tidal flats. However, little information is available as to whether such artificial construction affects the macrobenthic community structure. We monitored the variation of the macrobenthic community structure and species composition near natural and artificial structures (seaweed and a timber fence) on the tidal flats near the Iwon Dike, Korea. In total, 137 macrobenthic species were recorded during this study, predominantly crustaceans (47%), polychaetes (18%), and molluscs (27%). Polychaetes comprised over 50% of the total density, followed by gastropods (38%) and crustaceans (11%). Macrobenthic species composition in the artificial and natural areas, was initially similar, but it differed after 7 months. The gastropod Umbonium thomasi, the most dominant species, was present at both sites in the first month after the start of the experiment, but disappeared at the artificial sites within 7 months, suggesting disturbance by the environmental factors. The number of species and diversity (H') varied significantly within sites at the beginning of the experiment, but no difference was observed after 7 months. Multivariate analysis (multidimensional scaling) revealed significant differences in community structure between the artificial and the natural areas from 7 months after the start of the experiment, except from 18 to 21 months. The community structures were mainly influenced by U. thomasi. Community structure at the artificial sites was affected by environmental variables, such as carbon, COD/IL sulfide, loss of ignition, kurtosis and silt, which changed over time. We observed no significant correlations between environmental variables and the dominant species, except in the case of Spio sp. and Macrophthalmus dilatatus, suggesting that the biological interactions and temporary disturbances such as typhoon, as well as the effects of artificial structures may also be important regulating factors in this system.

• Nuclear Engineering and Technology
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• v.54 no.7
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• pp.2427-2434
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• 2022

Series of unequal quantity Nd/Ce co-doped ceramic nuclear waste forms, (Gd, Nd)₂(Zr, Ce)₂O₇, were prepared to tailor its ordered pyrochlore or disordered fluorite structure. The phase transition, microtopography, and elemental composition of the ceramic samples were systematically investigated, especially the effect of order-disorder structure on the chemical stability. It was confirmed that unequal quantity of Nd/Ce could synchronously replace the Gd/Zr-sites of Gd₂Zr₂O₇. And the phase transition of order-disorder structure could be successfully tailored by regulating the average cationic radius ratio of (Gd, Nd)₂(Zr, Ce)₂O₇ series. The elements of Gd, Nd, Zr, and Ce are uniformly distributed in the ordered or disordered structures. The MCC-1 leaching results showed that (Gd, Nd)₂(Zr, Ce)₂O₇ pyrochlore ceramic nuclear waste forms had excellent chemical stability, whose elements' normalized leaching rates were as low as 10^-4-10^-7 g·m^-2·d^-1 after 7 days. In particular, the chemical stability of disordered structure was superior to that of ordered structure. It was proposed that the force constant and the closest packing were changed with the structure transformation resulting the chemical stability difference.

• ALGAE
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• v.35 no.2
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• pp.201-212
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• 2020

The inflammatory bowel diseases (IBD) including ulcerative colitis and Crohn disease are characterized by chronic inflammation throughout the gastrointestinal tract. The prevalence of IBD has been increasing worldwide, and has sometimes led to irreversible impairment of gastrointestinal structure and functions. In the present study, we identified a new sulfoquinovosylmonoacylglycerols (SQMG) (1) together with two known SQMGs (2 and 3) regulating intestinal inflammation from the brown alga Turbinaria ornata. The anti-inflammatory properties of two bioactive SQMGs, 1 and 2 were evaluated using an in vitro co-culture system consisting of human epithelial Caco-2 cells and PMA (phorbol 12-myristate 12-acetate)-differentiated THP-1 macrophages. Treatment with 1 or 2 inhibited the production nitric oxide and prostaglandin E₂ induced by lipopolysaccharide and interferon γ challenge. The expressions of inducible nitric oxide synthase and cyclooxygenase 2 were markedly down-regulated in response to inhibition of nuclear factor κB translocation to nucleus. These findings suggest the potential use of the brown alga T. ornata and its biologically active metabolites SQMGs as pharmaceutical adjuvants in the treatment of inflammation-related diseases, including IBD.

• BMB Reports
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• v.48 no.10
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• pp.583-588
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• 2015

Microtubule actin crosslinking factor 1 (MACF1), a widely expressed cytoskeletal linker, plays important roles in various cells by regulating cytoskeleton dynamics. However, its role in osteoblastic cells is not well understood. Based on our previous findings that the association of MACF1 with F-actin and microtubules in osteoblast-like cells was altered under magnetic force conditions, here, by adopting a stable MACF1-knockdown MC3T3-E1 osteoblastic cell line, we found that MACF1 knockdown induced large cells with a binuclear/multinuclear structure. Further, immunofluorescence staining showed disorganization of F-actin and microtubules in MACF1-knockdown cells. Cell counting revealed significant decrease of cell proliferation and cell cycle analysis showed an S phase cell cycle arrest in MACF1-knockdown cells. Moreover and interestingly, MACF1 knockdown showed a potential effect on cellular MTT reduction activity and mitochondrial content, suggesting an impact on cellular metabolic activity. These results together indicate an important role of MACF1 in regulating osteoblastic cell morphology and function.