• 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.

• Korean Journal of Air-Conditioning and Refrigeration Engineering
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• v.13 no.8
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• pp.692-700
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• 2001

Flow boiling heat transfer coefficients(HTCs) of R22, R134a, R407C, and R410A were measured experimentally for a horizontal plain and a microfin tube. Experimental apparatus was composed of 3 main parts: a refrigerant loop, a water loop and a water-glycol loop. The test section in th refrigerant loop was made of a copper tube of 9.52 mm outer diameter and 1 m length for both tubes. The refrigerant was heated by passing hot water through an annulus surrounding the test section. Tests were performed at a fixed refrigerant saturation temperature of $5^{\circ}C$ with mass fluxes of 100~300 kg/$m^2$s. Test results showed that at similar mass flux the flow boiling HTCs of R134a were similar to those of R22 for both plain and microfin tube. HTCs of R407C were similar to those of R22 for a plain tube but lower than those of R2 by 25~48% for a microfin tube. And HTCs of R410A were higher than those of R2 by 20~63% for a plain tube and were similar to those of R22 for a microfin tube. In general, HTCs of a microfin tube were 1.8~5.7 times higher than those of a plain tube.

• Korean Journal of Air-Conditioning and Refrigeration Engineering
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• v.14 no.2
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• pp.175-183
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• 2002

Flow Condensation heat transfer coefficients (HTCs) of Rl2, R22, R32, Rl23, Rl25, R134a, R142b were measured experimentally on a horizontal plain tube. The experi- mental apparatus was composed of three main parts; a refrigerant loop, a water loop and a water-glycol loop. The test section in a refrigerant loop was made of a copper tube of 8.8 mm inner diameter and 1000 mm length respectively. The refrigerant was cooled by passing cold water through an annulus surrounding the test section. All tests were performed at a filed refrigerant saturation temperature of 4$0^{\circ}C$ with mass fluxes of 100, 200, 300 kg/$m^2$s. The experimental result showed that flow condensation HTCs increase as the quality, mass flux, and latent heat of condensation increase. At the same mass flux, the HTCs of R32 and R142b were higher than those of R22 by 35~45% and 7~14% respectively while HTCs of R134a and Rl23 were similar to those of R22. On the other hand, HTCs of Rl25 and Rl2 were lower than those of R22 by 28 ~30% and 15 ~25% respectively Finally, a new correlation for flow condensation HTCs was developed by modifying Dobson and Chato's correlation with the latent heat of condensation considered. The correlaton showed an average deviation of 13.1% for all pure fluids data indicating an excellent agreement.

• Proceedings of the KSME Conference
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• 2004.11a
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• pp.1270-1275
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• 2004

Flow condensation heat transfer coefficients(HTCs) of R22 and R134a were measured on horizontal aluminum multi-channel tube. The experimental apparatus was composed of three main parts ; a refrigerant loop, a water loop and a water-ethylene glycol loop. The test section in the refrigerant loop was made of aluminum multi-channel tube of 1.4 mm hydraulic diameter and 0.53 m length. The refrigerant was cooled by passing cold water through an annulus surrounding the test section. The data scan vapor qualities $(0.1{\sim}0.9)$, mass flux ($200{\sim}400$ $kg/m^{2}s$) and heat flux ($7.3{\sim}7.7$ $kW/m^{2}$) at $40{\times}0.2^{\circ}C$ saturation temperature in small hydraulic diameter tube. It was found that some well-known previous correlations were not suitable for multichannel tube. So, It must develop new correlations for multi-channel tubes.

• Korean Journal of Air-Conditioning and Refrigeration Engineering
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• v.16 no.5
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• pp.444-451
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• 2004

Flow condensation heat transfer coefficients (HTCs) of R22, R134a, R407C, and R410A were measured on horizontal plain and microfin tubes. The experimental apparatus was composed of three main parts; a refrigerant loop, a water loop and a water/glycol loop. The test section in the refrigerant loop was made of both a plain and a microfin copper tube of 6.0∼6.16 mm inside diameter and 1.0 m length. Refrigerants were cooled by passing cold water through an annulus surrounding the test section. Tests were performed at a fixed refrigerant saturation temperature of 4$0^{\circ}C$ with mass fluxes of 100, 200, and 300 kg/m2s. Test results showed that at similar mass flux the flow condensation HTCs of R134a were similar to those of R22 for both plain and microfin tubes. On the other hand, HTCs of R407C were lower than those of R22 by 4∼16% and 16∼42% for plain and microfin tubes respectively. And HTCs of R410A were similar to those of R22 for a plain tube but lower than those of R22 by 3∼9% for a microfin tube. Heat transfer enhancement factors of a microfin tube were 1.3∼1.9.

• Journal of Life Science
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• v.23 no.10
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• pp.1260-1266
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• 2013

The ribosomal DNA (rDNA) clusters of Hypsizygus marmoreus 3-10 and H. marmoreus 1-1 were analyzed in this study. The small subunit (SSU) and intergenic spacer 2 (IGS 2) was partially sequenced. The internal transcribed spacer 1 (ITS 1), 5.8S, internal transcribed spacer 2 (ITS 2), large subunit (LSU), intergenic spacer 1 (IGS 1), and 5S were completely sequenced. The rDNA clusters of H. marmoreus 3-10 and H. marmoreus 1-1 were 7,049 bp in length. The sequence of SSU rDNA, which corresponded to 18S rDNA, was 1,796 bp in length, and the sequence of LSU rDNA, which corresponded to 28S rDNA, was 3,348 bp in length. The ITS region that variable region and IGS region that non-transcribed spacer was 462 bp and 1,290 bp in length. The sequence of 5.8S rDNA and 5S rDNA was 153 bp and 43 bp in length, respectively. The 17 bp of the rDNA cluster in the H. marmoreus 3-10 strain was different to that in the H. marmoreus 1-1 strain, with 2 bp in the SSU, 3 bp in the ITS, 9 bp in the LSU, and 3 bp in the IGS. The analysis of the secondary structure revealed that the ITS regions of H. marmoreus 3-10 and H. marmoreus 1-1 have five stem-loop structures. Interestingly, among these structures, one different nucleotide sequence resulted in a different secondary structure in stem-loop V.

• Korean Journal of Air-Conditioning and Refrigeration Engineering
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• v.14 no.8
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• pp.656-663
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• 2002

Flow condensation heat transfer coefficients (HTCs) of R22, R134a, R407C, and R410A were measured on horizontal plain and microfin tubes. The experimental apparatus was composed of three main parts; a refrigerant loop, a water loop and a water/glycol loop. The test section in the refrigerant loop was made of both a plain and a microfin copper tube of 9.52 mm outside diameter and 1.0 m length. The refrigerant was cooled by passing cold water through an annulus surrounding the test section. Tests were performed at a fixed refrigerant saturation temperature of $40^{\circ}C$ with mass fluxes of 100, 200, and 300 kg/$m^2s$. Test results showed that at similar mass flux the flow condensation HTCs of R134a were similar to those of R22 for both plain and microfin tubes. On the other hand, HTCs of R407C were lower than those of R22 by 11~l5% and 23~53% for plain and microfin tubes respectively. And HTCs of R410A were similar to those of R22 for a plain tube but lower than those of R22 by 10~21% for a microfin tube. In general, HTCs of a microfin tube were 2.0~3.0 times higher than those of a plain tube.

• Journal of the Korean Chemical Society
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• v.38 no.10
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• pp.769-773
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• 1994

Higher order structure of 5S rRNA isolated from Xanthomonas celebensis was examined using angiogenic extracted from milk. Angiogenin cleaved exclusively 3' P-O bonds on the far sides of pyrimidines in the single-stranded sequences of 5S rRNA. Whereas angiogenin acted only on the loop d of 5S rRNA at pH 7.0 in the presence of 10 mM $Mg^{2+}$, it acted on all the loops (a, b, c and d) except loop e in the absence of $Mg^{2+}$. In the absence of $Mg^{2+}$, bonds $U_{74}$-$G_{75}$, $U_{77}$-$A_{78}$ and $U_{103}$-$A_{104}$ were highly susceptible to the action of angiogenin both at pH 7.0 and at pH 3.5. On the other hand, at pH 3.5 in the absence of $Mg^{2+}$ angiogenin strongly cleaved the bond $C_{17}$-$G_{18}$ of loop a and the bond $U_{55}$-$G_{56}$ of loop b. The results lead us to the following conclusion. First, angiogenin can be used as one of the probes for the tertiary structure analysis of 5S rRNA. Second, the structure of loop d of 5S rRNA is variable depending on the concentrations of $Mg^{2+}$ and $H^{1+}$.

• Journal of the Korean Chemical Society
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• v.37 no.2
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• pp.237-243
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• 1993

The primary and secondary structure of the 5S rRNA isolated from Xanthomonas celebensis were determined by enzymatic and chemical degradation methods. It consists of 119 nucleotides and contains no modified nucleosides. As with the 5S rRNAs of X. maltophilia and X. citri, it contains an additional uridine residue on the 5'-terminus. Its secondary structure was almost identical to the models previously proposed by us for the 5S rRNA of two Xanthomonas species. Its secondary structure consists of five helices, five loops and two bulges. The tertiary interactions in the 5S rRNA molecule were analyzed by Fe(II)-EDTA treatment and hybridization method using deoxyhexamer. From the fact that some adenine residues in loop M, region $I_1-C$, loop $H_1$, and loop $H_2$ become susceptible to diethylpyrocarbonate when the 5S rRNA was hybridized with deoxyhexamer complementary to the sequence $U_{35}CCCAU_{40}$ and that some nucleotide residues in loop M, loop $H_1$ and region $D-I_2$ become resistant Fe(II)-EDTA cleavage in the presence of $Mg^{2+}$, it is presumed that loops $H_1$ and $H_2$ interact with loop M in some way. In the tertiary interaction, the regions $I_1-C$ and $D-I_2$ seem to act as hinges in folding the stems $B-I_1-C$ and $D-I_2-E.$ It was found that loop $H_1$ changes into a smaller loop of three bases by forming noncanonical A : C base-pairs ih acidic environment.

• Proceedings of the Korean Biophysical Society Conference
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• 2003.06a
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• pp.66-66
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• 2003

In skeletal muscle cells, depolarization of the transverse tubules (T-tubules) results in Ca$\^$2+/ release from the sarcoplasmic reticulum (SR), leading to elevated cytoplasmic Ca$\^$2+/ and muscle contraction. This process has been known as excitation-contraction coupling (E-C coupling). Several proteins, such as the ryanodine receptor (RyR), triadin, junctin, and calsequestrin (CSQ), have been identified to be involved in the Ca$\^$2＋/ release process. However, the molecular interactions between the SR proteins have not been resolved. In the present study, the mechanisms of interaction between RyRl and triadin have been studied by in vitro protein binding and $\^$45/Ca$\^$2+/ overlay assays. Our data demonstrate that the intraluminal loop II of RyR1 binds to triadin in Ca$\^$2+/-independent manner. Moreover, we could not find any Ca$\^$2+/ binding sites in the loop II region. GST-pull down assay revealed that a KEKE motif of triadin, which was previously identified as a CSQ binding site (Kobayasi et al.,2000 JBC) was also a binding site for RyR1. Our results suggest that the intraluminal loop II of RyR could participate in the RyR-mediated Ca$\^$2+/ release process by offering a direct binding site to luminal triadin.