• Journal of the Korean Geotechnical Society
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• v.24 no.12
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• pp.65-73
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• 2008

In the current practice for slope stability problem in Japan, the shear strength, $\tau$, mobilized along the failure surface is usually estimated based on an empirical approximation in which the cohesion, c, is assumed to be equal to the soil thickness above the supposed slip surface, d(m). This approximation is advantageous in that the result of stability analysis is not influenced by the designers in charge. However, since the methodology has little theoretical background, the cohesion may often be grossly overestimated, and conversely the angle of shear resistance, $\phi$, is significantly underestimated, when the soil thickness above the supposed slip surface is quite large. In this paper, a case record of natural slope failure that took place in Hyogo Prefecture in 2007, is described in detail for the case in which the shear strength along the collapsed surface was carefully examined in a series of direct shear box (DSB) tests by considering the effects of in-situ shear stress along the slip surface. It is demonstrated that the factor of safety agrees with that of in-situ conditions when the shear strength from this kind of DSB test was employed for the back-analysis of the slope failure.

• Archives of Pharmacal Research
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• v.24 no.4
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• pp.316-322
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• 2001

Arylsulfate sulfotransferase (ASST) transfers a sulfate group from a phenolic sulfate ester to a phenolic acceptor substrate. In the present study, the gene encoding ASST was cloned from a genomic library copy of Citrobacter freundii, subcloned into the vector pGEM3Zf(-) and sequenced. Sequencing revealed two contiguous open reading frames (ORF1 and ORF2) on the same strand and based on amino acid sequence homologyl they were designated as astA and dsbA, respectively. The amino acid sequence of astA deduced from C. freundii was highly similar to that of the Salmonella typhimurium, Enterobacter amnigenus, Klebsiella, Pseudomonas putida, and Campylobacter jejuni, encoded by the astA genes. However, the ASST activity assay revealed different acceptor specificities. Using p-nitrophenyl sulfate (PNS) as a donor substrate, $\alpha$-naphthol was found to be the best acceptor substrate, followed by phenol, resorcinol, p-acetaminophen, tyramine and tyrosine.

• Korean Journal of Agricultural Science
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• v.47 no.4
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• pp.903-920
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• 2020

Since its first demonstration as a practical genome editing tool in the early 2010s, the use of clustered regularly interspaced short palindromic repeat (CRISPR) along with the endonuclease Cas9 (CRISPR/Cas9) has become an essential choice for generating targeted mutations. Due to its relative simplicity and cost-effectiveness compared to other molecular scissors, i.e., zinc finger nuclease (ZFN) and transcription activator-like effector nuclease (TALEN), the CRISPR/Cas9 system has been shown to have a massive influence on genetic studies regardless of the biological kingdom. Although the system is in the process of being established, numerous protocols have already been released for the system and there have been various topics of CRISPR related papers published each year in ever-increasing manner. Here, we will briefly introduce CRISPR/Cas9 system and discuss the variants of the CRISPR system. Also, their applications to crop improvement will be dealt with mainly ornamental crops among horticultural crops other than Arabidopsis as a model plant. Finally, some issues on the barriers restraining the use of CRISPR system on floricultural crops, the prospect of CRISPR system as a DNA-free genome editing tool with efficient facilitators and finally, the future perspectives on the CRISPR system will be described.

• International Journal of Stem Cells
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• v.16 no.2
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• pp.234-243
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• 2023

The recent advances in human pluripotent stem cells (hPSCs) enable to precisely edit the desired bases in hPSCs to be used for the establishment of isogenic disease models and autologous ex vivo cell therapy. The knock-in approach based on the homologous directed repair with Cas9 endonuclease, causing DNA double-strand breaks (DSBs), produces not only insertion and deletion (indel) mutations but also deleterious large deletions. On the contrary, due to the lack of Cas9 endonuclease activity, base editors (BEs) such as adenine base editor (ABE) and cytosine base editor (CBE) allow precise base substitution by conjugated deaminase activity, free from DSB formation. Despite the limitation of BEs in transition substitution, precise base editing by BEs with no massive off-targets is suggested to be a prospective alternative in hPSCs for clinical applications. Considering the unique cellular characteristics of hPSCs, a few points should be considered. Herein, we describe an updated and optimized protocol for base editing in hPSCs. We also describe an improved methodology for CBE-based C to T substitutions, which are generally lower than A to G substitutions in hPSCs.

• The Bulletin of The Korean Astronomical Society
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• v.37 no.1
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• pp.66.1-66.1
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• 2012

We have developed superconducting mixer receivers for 129 GHz VLBI observation in Korean VLBI Network(KVN). The developed mixer has a radial waveguide probe with simple transmission line LC transformer as a tuning circuit to its 5 series-connected junctions, which can have 125-165 GHz as operation RF frequency. For IF signal path a high impedance quarter-wavelength line connects the probe to one end of symmetric RF chokes. DSB receiver noise of the mixer was about 40 K over 4-6 GHz IF band whereas we achieved about uncorrected SSB noise temperature of 70 K and better than 10 dB IRR in 2SB configuration with 8-10 GHz IF band. Insert-type receiver cartridges using the mixers have been assembled for all three KVN stations. On-site performance summary in commissioning phase is presented.

• Journal of Radiation Industry
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• v.10 no.4
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• pp.243-248
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• 2016

Argonaute 2 (AtAGO2) is a well characterized effector protein in Arabidopsis for its functionalities associated with DNA double-strand break (DSB)-induced small RNAs (diRNAs) and for its inducible expression upon ${\gamma}$-irradiation. However, its transcriptional regulation depending on the recovery time after the irradiation and on the specific response to DSBs has been poorly understood. We analyzed the 1,313 bp promoter sequence of the AtAGO2 gene ($1.3kb_{pro}$) to characterize the transcriptional regulation of AtAGO2 at various recovery times after ${\gamma}$-irradiation. A stable transformant harboring $1.3kb_{pro}$ fused with GUS gene showed that the AtAGO2 is highly expressed in response to ${\gamma}$-irradiation, after which the expression of the gene is gradually decreased until 5 days of DNA damage recovery. We also confirm that the AtAGO2 expression patterns are similar to that of ${\gamma}$-irradiation after the treatments of radiomimetic genotoxins (bleomycin and zeocin). However, methyl methanesulfonate and mitomycin C, which are associated with the inhibition of DNA replication, do not induce the expression of the AtAGO2, suggesting that the expression of the AtAGO2 is closely related with DNA DSBs rather than DNA replication.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2021.04a
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• pp.52-52
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• 2021

Persicaria amphibia as an England native plant, is a rhizomatous perennial, one of the rather amphibious plants. Its aquatic form contains water-soluble sugars, starch, and protein. P. amphibia have up to 18% tannins in stems and rhizomes. Previous studies have confirmed the anti-inflammatory activity of live bacteria roots, but no studies on bioactivity are known. DNA damage responses (DDRs) pathways are considered a crucial factor affecting the alleviation of cellular damage. The ataxia-telangiectasia mutated and Rad3 related (ATM) and checkpoint kinase 2 (Chk2) pathways are the main pathways of DNA damage response. Also, p53 is a key integrator of cellular response to oxidative DNA damage, contributing repair, or leading transcription including apoptosis. In the present study, we conducted an investigation into the inhibitory effects of P. amphibia on oxidative DNA damage for confirming potential to complementary medicine and therapies. In conclusion, P. amphibia can provide protective effects against double-stranded DNA break (DSB) caused by oxidative DNA damage.

• Molecules and Cells
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• v.39 no.3
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• pp.204-210
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• 2016

DNA damage responses are important for the maintenance of genome stability and the survival of organisms. Such responses are activated in the presence of DNA damage and lead to cell cycle arrest, apoptosis, and DNA repair. In Caenorhabditis elegans, double-strand breaks induced by DNA damaging agents have been detected indirectly by antibodies against DSB recognizing proteins. In this study we used a comet assay to detect DNA strand breaks and to measure the elimination of DNA strand breaks in mitotic germline nuclei of C. elegans. We found that C. elegans brc-1 mutants were more sensitive to ionizing radiation and camptothecin than the N2 wild-type strain and repaired DNA strand breaks less efficiently than N2. This study is the first demonstration of direct measurement of DNA strand breaks in mitotic germline nuclei of C. elegans. This newly developed assay can be applied to detect DNA strand breaks in different C. elegans mutants that are sensitive to DNA damaging agents.

• The Journal of Korean Institute of Electromagnetic Engineering and Science
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• v.15 no.8
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• pp.737-743
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• 2004

A fixed-tuned SIS(Superconductor-Insulator-Superconductor) mixer across 120∼180 GHz band has been developed. This mixer employs an SIS chip fabricated by Nobeyama radio observatory which consists of a series array of 6 Nb/Al-Al$_2$O$_3$/Nb junctions in a microstrip line on a fused quartz substrate. The SIS chip is placed at the center of the half-height waveguide mixer mount to have a good incoming signal coupling over the whole frequency band. No mechanical tuner was used in the SIS mixer and the RF signal and local oscillator power are injected to the mixer via a cooled cross-guide coupler. In order to prevent the IF signal loss, the If output impedance of the SIS mixer was matched to the 50 $\Omega$ input impedance of the IF chain. Measured double sideband noise temperatures of a receiver using the SIS mixer are 32∼131 K over 120∼180 GHz band. The developed SIS mixer is now in use for radio astronomical observations on the TRAO 14 m radio telescope.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.7
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• pp.3431-3436
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• 2012

Objective: X-ray cross-complementing group 4 (XRCC4) is a major repair gene for DNA double-strand breaks (DSB) in the non-homologous end-joining (NHEJ) pathway. Several potentially functional polymorphisms of the XRCC4 gene have been implicated in breast cancer risk, but individually published studies showed inconclusive results. The aim of this meta-analysis was to investigate the association between XRCC4 polymorphisms and the risk of breast cancer. Methods: The MEDLINE, EMBASE, Web of science and CBM databases were searched for all relevant articles published up to June 20, 2012. Potential associations were assessed with comparisons of the total mutation rate (TMR), complete mutation rate (CMR) and partial mutation rate (PMR) in cases and controls. Statistical analyses were performed using RevMan 5.1.6 and STATA 12.0 software. Results: Five studies were included with a total of 5,165 breast cancer cases and 4,839 healthy controls. Meta-analysis results showed that mutations of rs2075686 (C>T) and rs6869366 (G>T) in the XRCC4 gene were associated with increased risk of breast cancer, while rs2075685 (G>T) and rs10057194 (A>G) might decrease the risk of breast cancer. However, rs1805377 (A>G), rs1056503 (G>T), rs28360317 (ins>del) and rs3734091 (A>G) polymorphisms of XRCC4 gene did not appear to have an influence on breast cancer susceptibility. Conclusion: Results from the current meta-analysis suggest that the rs2075685 (G>T) and rs6869366 (G>T) polymorphisms of the XRCC4 gene might increase the risk of breast cancer, whereas rs2075685 (G>T) and rs10057194 (A>G) might be protective factors.