• BMB Reports
• /
• v.56 no.5
• /
• pp.265-274
• /
• 2023

Defects in DNA double-strand break (DSB) repair signaling permit cancer cells to accumulate genomic alterations that confer their aggressive phenotype. Nevertheless, tumors depend on residual DNA repair abilities to survive the DNA damage induced by genotoxic stress. This is why only isolated DNA repair signaling is inactivated in cancer cells. DNA DSB repair signaling contributes to general mechanism for various types of lesions in diverse cell cycle phases. DNA DSB repair genes are frequently mutated and amplified in cancer; however, limited data exist regarding the overall genomic prospect and functional result of these modifications. We list the DNA repair genes and related E3 ligases. Mutation and expression frequencies of these genes were analyzed in COSMIC and TCGA. The 11 genes with a high frequency of mutation differed between cancers, and mutations in many DNA DSB repair E3 ligase genes were related to a higher total mutation burden. DNA DSB repair E3 ligase genes are involved in tumor suppressive or oncogenic functions, such as RNF168 and FBXW7, by assisting the functionality of these genomic alterations. DNA damage response-related E3 ligases, such as RNF168, FBXW7, and HERC2, were generated with more than 10% mutation in several cancer cells. This study provides a broad list of candidate genes as potential biomarkers for genomic instability and novel therapeutic targets in cancer. As a DSB related proteins considerably appear the possibilities for targeting DNA repair defective tumors or hyperactive DNA repair tumors. Based on recent research, we describe the relationship between unstable DSB repairs and DSB-related E3 ligases.

• Journal of Ecology and Environment
• /
• v.48 no.2
• /
• pp.163-172
• /
• 2024

Background: Fruit bats are natural carriers of Nipah virus (NiV). The primary objective of this study is to identify potential reservoir species in a selected geographic regions. It is necessary to determine an accurate species identification of the associated reservoir bat species distributed in a specific region. Results: In this study, we collected 20 different bat specimens from the NiV-prone area of the Kushtia district. Among these, 14 were tissue samples (BT-1-14) and six were fecal samples (BF-1-6). We used the mitochondrial gene cytochrome b, one of the most abundant and frequently used genetic markers, for polymerase chain reaction amplification and sequencing. Out of the 20 samples, 12 tissue samples and 2 fecal samples were successfully amplified and sequenced. However, two tissue samples and four fecal samples yielded chimeric sequences, rendering them unsuitable for annotation. The sequences of the successfully amplified samples were compared to those deposited in the National Center for Biotechnology Information database using basic local alignment search tool to identify the bat specimen collected. The study identified six different bat species using both morphological and genetic data, which may carriers of the NiV. Conclusions: Our results suggest that additional research should be conducted to gather more information on fruit bats from different localities across the country. The study contributes to the establishment of appropriate measures for NiV carrying disease control and management.

• Journal of the Korean GEO-environmental Society
• /
• v.19 no.10
• /
• pp.13-19
• /
• 2018

Following the 2016 Gyeongju earthquake, the Pohang Earthquake occurred in 2017, and the south-east region in Korea is under the threat of an earthquake. Especially, in the Pohang Earthquake, the liquefaction phenomenon occurred in the sedimentation area of the coast, and preparation of countermeasures is very important. The soil liquefaction can affect the underground facilities directly as well as various structures on the ground. Therefore, it is necessary to identify the liquefaction risk of facilities and the structures against the possible earthquakes and to prepare countermeasures to minimize them. In this study, we investigated the seismic liquefaction risk about the electric power utility tunnels in the southeast area where the earthquake occurred in Korea recently. In the analysis of seismic liquefaction risk, the earthquake with return period 1000 years and liquefaction potential index are used. The liquefaction risk analysis was conducted in two stages. In the first stage, the liquefaction risk was analyzed by calculating the liquefaction potential index using the ground survey data of the location of electric power utility tunnels in the southeast region. At that time, the seismic amplification in soil layer was considered by soil amplification factor according to the soil classification. In the second stage, the liquefaction risk analysis based on the site response analyses inputted 3 earthquake records were performed for the locations determined to be dangerous from the first step analysis, and the final liquefaction potential index was recalculated. In the analysis, the site investigation data were used from the National Geotechnical Information DB Center. Finally, it can be found that the proposed two stage assessments for liquefaction risk that the macro assessment of liquefaction risk for the underground facilities including the electric power utility tunnel in Korea is carried out at the first stage, and the second risk assessment is performed again with site response analysis for the dangerous regions of the first stage assessment is reasonable and effective.

• Radiation Oncology Journal
• /
• v.22 no.4
• /
• pp.307-315
• /
• 2004

Purpose: The purpose of this work was to study the differences of cyclooxygenase (COX-2) expression between Korean and Caucasian patients with early-onset breast carcinoma by immunohistochemistry. The test were analyzed to find a correlation between COX-2 and other biomarkers including HER-2/neu amplification, because we previously reported that a significant difference had been found in the expression of HER-2/neu between the two races. Furthermore, we investigated prognostic significance of COX-2 in korean patients. Materials and Methods: Sixty Korean women who were diagnosed breast carcinoma at 45 years old or younger and 60 Caucasian women with breast carcinoma were selected for this study. The median age of both groups was 37 years and tumor sizes were distributed evenly between the two group. Paraffin embedded blocks of primary tumor were processed for immunohistochemical staining of COX-2. The COX-2 expression was evaluated according to the percentage of positive cells and the intensity of staining. And the results were compared with the data of the previous studies to find correlation between COX-2 and other parameters and survival data. Results: Proportion of the COX-2 expression in total patients was $27.6\%$. The percentage of tumors that stained positive for COX-2 in korean and Caucasian women with early-onset breast carcinoma were $37.9\%$ and $20.8\%$, respectively. The difference was statistically not significant(p=0.090). Expression of COX-2 was not associated with several clinicopathologic parameters including HER-2/neu overexpression, but negative estrogen receptor status was correlated with significance (p=0.046). The 5 year disease free survival rate for patients with COX-2 expression was $67.9\%$, compared to $81.9\%$ of the COX-2 negative patients and the result was statistically not significant. Conclusions : A significant difference was not found in the expression of COX-2 between the two groups of patients with early-onset breast carcinoma. And correlation between COX-2 and other parameters was not observed except estrogen receptor negativity. Large scaled further research including radiotherapy factors will be needed to identify COX-2 as a prognostic role in patients with early-onset breast carcinoma.

• Geophysics and Geophysical Exploration
• /
• v.16 no.3
• /
• pp.190-195
• /
• 2013

We estimated near-surface shear-wave velocity (${\nu}_s$) at the Hwacheon seismic station using a geologic log of a well, microtremors recorded during a period of 56 days, and records of three teleseismic events ($M_w{\geq}6.0$). The vs of the 10-m thick soil layer (${\nu}^s_s$= 296 m/s) was determined from horizontal-to-vertical spectral ratios of microtremors recorded at the surface. The average ${\nu}_s$ ($\bar{\nu}_s$= 1,309 m/s) from the surface to the 96-m depth of a borehole sensor, was computed using spectral coherence analyses of data recorded by surface- and borehole-sensors for the three teleseismic events. Using these calculated values of ${\nu}^s_s$ and $\bar{\nu}_s$, the computed bedrock ${\nu}_s$ is 2,150 m/s and the time-averaged ${\nu}_s$ to a 30-m depth is 696 m/s. Accordingly the Hwacheon seismic station is regarded as a relatively good site. The deduced near-surface ${\nu}_s$ can be used for further quantitative evaluation of site amplification and earthquake hazard.

• Journal of the Korean Association of Geographic Information Studies
• /
• v.19 no.4
• /
• pp.17-35
• /
• 2016

Earthquake-induced disasters are often more severe in locations with soft soils than firm soils or rocks due to differences in ground motion amplification. On a regional scale, such differences can be estimated by spatially predicting subsurface soil thickness over the entire target area. In general, soil deposits are generally deeper in coastal or riverside areas than in inland regions. In this study, a coastal metropolitan area, Incheon, was selected to assess site effects and provide information on seismic hazards. Spatial prediction of geotechnical layers was performed for the entire study area within the GIS framework. Approximately 7,000 existing borehole drilling data in the Incheon area were gathered and archived into the GIS Database (DB). In addition, surface geotechnical data were acquired from a walkover survey. Based on the built geotechnical DB, spatial zoning maps of site-specific seismic response parameters were created and presented for use in a regional seismic strategy. Site response parameters were performed to determine site coefficients for seismic design over the entire target area and compared with each other. Site classifications and subsequent seismic zoning were assigned based on site coefficients. From this seismic zonation case study in Incheon, we verified that geotechnical GIS-DB can create spatial zoning maps of site-specific seismic response parameters that are useful for seismic hazard mitigation particularly in coastal metropolitan areas.

• Ocean and Polar Research
• /
• v.30 no.4
• /
• pp.453-466
• /
• 2008

In order to examine the generation mechanism of long ocean waves along the west coast of Korea and to understand the amplification process of the long ocean waves, sea level, atmospheric pressure and wind data observed every minute from 2007 March 29 to 2007 April 1 were analyzed and onedimensional numerical ocean model experiments were performed. An atmospheric pressure jump propagated southeastward from Backryungdo to Yeonggwang along the west coast of Korea with speed of $13{\sim}27\;m/s$ between 2007 March 30 23:00 and 2007 April 1 1:30. Average magnitude of pressure jump was 4.2 hPa. As a moving atmospheric jump propagated from north to south along the coast, long ocean waves were generated and the sea level abnormally rose or fell at Anheung, Kunsan, Wido and Yeonggwang. Average amplitude of sea level rise (or fall) was about 113.6 cm. In a one-dimensional numerical ocean model, nonlinear shallow water equations were numerically integrated and a moving atmospheric pressure jump with traveling speed of 24 m/s was used as an external force. While the atmospheric pressure jump travels over 60 m depth ocean, a long ocean wave is generated. Because the propagation speed of the atmospheric jump is almost equal to that of the long ocean wave, Proudman resonance occurs and the long ocean wave amplifies. As the atmospheric pressure jump moves into the coastal area shallower than 60 m, the speed of the long ocean wave decreases and Proudman resonance effect decreases. However, the amplitude of the long ocean wave increases and wave length becomes shorter because of shoaling effect. When the long ocean wave hits the land boundary, amplitude of the long ocean wave drastically amplifies due to reflection. Data analysis and numerical experiments suggest that the southeastward propagation of an atmospheric pressure jump over the shallow ocean, which is a necessary condition for Proudaman resonance, generated the long ocean waves along the west coast of Korea on 2007 March 31 and the ocean waves amplified due to shoaling effect in the coastal area and reflection at the shore.

• Asian Pacific Journal of Cancer Prevention
• /
• v.16 no.7
• /
• pp.2745-2749
• /
• 2015

Objective: To study the PLCE1 gene rs2274223 polymorphism with regard to esophageal cancer and its interaction with diet, lifestyle, psychological and environmental factors in Southwest Shandong province. Materials and Methods: A case series study (case-case) was conducted. Questionnaire data were collected and 3 ml-5ml venous blood was drawn for DNA extraction among the qualified research subjects. PLCE1 gene polymorphism was detected after PCR amplification of DNA. SPSS 13.0 software was used for statistical analysis of the data. Results: The three genotypes A/A, A/G and G/G PLCE1 gene rs2274223 was 31, 16 and 4 cases, accounting for 60.8%, 31.4%, 0.08% respectively. The difference of three genotypes (AA/GA/GG) proportion between negative and positive family history of patients was statistically significant, ${\chi}^2=6.213$, p=0.045. There was no statistically significant relationship between PLCE1 gene rs2274223 polymorphism and smoking, drinking, ${\chi}^2=0.119$, p=0.998, and ${\chi}^2=1.727$, p=0.786. There was no linkage of the three rs2274223 PLCE1 gene genotypes (AA/GA/GG) proportion with eating fried, pickled, hot, mildew, overnight, smoked, excitant food, eat speed, salt taste or not (p>0.05). or with living environment pollution and nine risk factors of occupational exposure (p>0.05). There was no statistically significant difference in TS scores between different genotype of rs2274223 PLCE1 gene. Conclusions: The PLCE1 rs2274223 polymorphism has a relationship with family history of esophageal cancer, but does not have any significant association with age, gender, smoking, alcohol drinking, food hygiene, eating habits, living around the environment and occupation in cases.

• Journal of the Earthquake Engineering Society of Korea
• /
• v.11 no.1 s.53
• /
• pp.45-57
• /
• 2007

The mean shear wave velocity to the depth of 30 m (Vs30) derived from the western Vs is the current site classification criterion for determining the design seismic ground motion taking into account the site amplification potential. In order to evaluate the Vs30 at a site, a shear wave velocity (Vs) Profile extending to at least 30 m in depth must be acquired from in-situ seismic test. In many cases, however, the resultant depth of the Vs profile may not extend to 30 m, owing to the unfavorable field condition and the limitation of adopted testing techniques. In this study, the Vs30 and the mean shear wave velocity to a depth shallower, than 30 m (VsDs) were computed from the Vs profiles more than 30 m in depth obtained by performing various seismic tests at total 72 sites in Korea, and a correlation between Vs30 and VsDs was drawn based on the computed mean Vs data. In addition, a method for extrapolating the Vs profile from shallow depth to 30 m was developed by building a shape curve based on the average data of all Vs profiles. For evaluating the Vs30 from the shallow Vs profiles, both the methods using VsDs and shape curve result in less bias than the simplest method of extending the lowermost Vs equally to 30 m in depth, and are usefully applicable particularly in the cases of the Vs profiles extending to at least 10 m in depth.

• Ocean and Polar Research
• /
• v.26 no.3
• /
• pp.439-451
• /
• 2004

Total solar irradiance (750), total UV irradiunce (TUV) and erythemal UV irradiance (EUV) measured at King Sejong station $(62.22^{\circ}S,\;58.78^{\circ}W)$ in west Antarctica have been used together with total ozone, cloud amount and snow cover to examine the effects of ozone, cloud and snow surface on these surface solar inadiunce over the period of 1998-2003. The data of three solar components for each scan were grouped by cloud amount, n in oktas $(0{\leq}n<3,\;3{\leq}n<4,\;4{\leq}n<5,\;5{\leq}n<6,\;6{\leq}n<7\;and\;7{\leq}n<8)$ and plotted against solar zenith angle (SZA) over the range of $45^{\circ}\;to\;75^{\circ}$. The radiation amplification factor (RAE) is used to quantify ozone effect on EUV. RAF of EUV decreases from 1.51 to 0.94 under clear skies but increases from 0.94 to 1.85 under cloudy skies as SZA increases, and decreases from 1.51 to 1.01 as cloud amount increases. The effects of cloud amount and snow surface on EUV are estimated as a function of SZA and cloud amount after normalization of the data to the reference total ozone of 300 DU. In order to analyse the transmission of solar radiation by cloud, regression analyses have been performed for the maximum values of solar irradiance on clear sky conditions $(0{\leq}n<3)$ and the mean values on cloudy conditions, respectively. The maximum regression values for the clear sky cases were taken to represent minimum aerosol conditions fur the site and thus appropriate for use as a normalization (reference) factor for the other regressions. The overall features for the transmission of the three solar components show a relatively high values around SZAs of $55^{\circ}\;and\;60^{\circ}$ under all sky conditions and cloud amounts $4{\leq}n<5$ and $5{\leq}n<6$. The transmission is, in general, the largest in TUV and the smallest in EUV among the three components of the solar irradiance. If the ground is covered with snow on partly cloudy days $(6{\leq}n<7)$, EUV increases by 20 to 26% compared to snow-free surface around SZA $60^{\circ}-65^{\circ}$, due to multiple reflections and scattering between the surface and the clouds. The relative difference between snow surface and snow-free surface slowly increases from 9% to 20% as total ozone increases from 100 DU to 400 DU under partly cloud conditions $(3{\leq}n<6)$ at SZA $60^{\circ}$. The snow effects on TUV and TSO are relatively high with 32% and 34%, respectively, under clear sky conditions, while the effects changes to 36% and 20% for TUV and TSO, respectively, as cloud amount increases.