• Molecules and Cells
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• v.45 no.12
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• pp.896-910
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• 2022

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly transmissible and potentially fatal virus. So far, most comprehensive analyses encompassing clinical and transcriptional manifestation have concentrated on the lungs. Here, we confirmed evident signs of viral infection in the lungs and spleen of SARS-CoV-2-infected K18-hACE2 mice, which replicate the phenotype and infection symptoms in hospitalized humans. Seven days post viral detection in organs, infected mice showed decreased vital signs, leading to death. Bronchopneumonia due to infiltration of leukocytes in the lungs and reduction in the spleen lymphocyte region were observed. Transcriptome profiling implicated the meticulous regulation of distress and recovery from cytokine-mediated immunity by distinct immune cell types in a time-dependent manner. In lungs, the chemokine-driven response to viral invasion was highly elevated at 2 days post infection (dpi). In late infection, diseased lungs, post the innate immune process, showed recovery signs. The spleen established an even more immediate line of defense than the lungs, and the cytokine expression profile dropped at 7 dpi. At 5 dpi, spleen samples diverged into two distinct groups with different transcriptome profile and pathophysiology. Inhibition of consecutive host cell viral entry and massive immunoglobulin production and proteolysis inhibition seemed that one group endeavored to survive, while the other group struggled with developmental regeneration against consistent viral intrusion through the replication cycle. Our results may contribute to improved understanding of the longitudinal response to viral infection and development of potential therapeutics for hospitalized patients affected by SARS-CoV-2.

• Geophysics and Geophysical Exploration
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• v.12 no.2
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• pp.192-198
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• 2009

Side scan sonar and SBP (sub-bottom profiler) play a very important role in the survey for seafloor imaging and sub-bottom profiling. In this study, we have acquired side scan sonar and SBP data from the artificial reef area. We applied digital image processing techniques to side scan sonar data in order to improve an image quality. For the enhancement of data quality and image resolution, we applied the typical seismic data processing sequence including gain recovery, muting, spectrum analysis, predictive deconvolution, migration to SBP data. We could easily estimate if artificial reef structures were settled properly and their distribution on the seafloor from the integrated interpretation of side scan sonar and SBP data. From the sampling analysis of seabed sediments, texture filtering of side scan sonar data and SBP data interpretation, we could evaluate the sediment type, distribution and thickness of seafloor sediments in detail.

• YAKHAK HOEJI
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• v.51 no.3
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• pp.179-185
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• 2007

Gastric cancer is one of the most common malignancies in Korea, but the predominant molecular event underlying gastric carcinogenesis remain unknown. Recently, DNA microarray technology has enabled the comprehensive analysis of gene expression level, and as such has yielded great insight into the molecular nature of cancer, However, despite the powerful approach of this techniques, the technical artifacts and/or bias in applied array platform limited the liability of resultant tens of thousand data points from microarray experiments. Therefore, we applied two different any platforms, such as olignucleotide microarray and cDNA microarray, to identify gastric cancer related large-scale molecular signature of the same human specimens. When thirty sets of matched human gastric cancer and normal tissues subjected to oligonucleotide microarray, total 623 genes were resulted as differently expressed genes in gastric cancer compared to normal tissues, and 252 genes for cDNA microarray analysis. In addition, forty three outlier genes which reflect the characteristic expression signature of gastric cancer beyond array platform and analytical protocol was recapitulated from two different expression profile. In conclusion, we were able to identify robust large-scale molecular changes in gastric cancer by applying two different platform of DNA microarray, this may facilitate to understand molecular carcinogenesis of gastric cancer.

• YAKHAK HOEJI
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• v.51 no.2
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• pp.96-102
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• 2007

Measurement of globotriaosylceramide (Gb3, ceramide trihexoside) in urine has clinical importance for monitoring after enzyme replacement therapy in Fabry disease patients. The disease is an X-linked lipid storage disorder that results from a deficiency of the enzyme ${\alpha}$-galactosidase A (${\alpha}$-Gal A). The lack of ${\alpha}$-Gal A causes an intracellular accumulation of glycosphingolipids, mainly Gb3. A simple, rapid, and highly sensitive analytical method for Gb3 in urine was developed without labor-extensive pre-treatment by electrospray ionization MS/MS (ESI-MS/MS). Only simple 5-fold dilution of urine is necessary for the extraction and isolation of Gb3 in urine. Gb3 in diluted urine was dissolved in dioxane containing C17:0 Gb3 as an internal standard. After centrifugation it was directly injected and analyzed through guard column by in combination with multiple reaction monitoring mode of ESI-MS/MS. Eight isoforms of Gb3 were completely resolved from urine matrix. C24:0 Gb3 occupied 50% of total Gb3 as a major component in urine. Linear relationship for Gb3 isoforms was found in the range of 0.005${\sim}$5.0 ${\mu}$g/ml. The limit of detection (S/N=5) was 0.005 ${\mu}$g/ml and limit of quantification was 0.05 ${\mu}$g/ml for C24:0 Gb3 with acceptable precision and accuracy. Correlation coefficient of calibration curves for 8 Gb3 isoforms ranged from 0.9598 to 0.9975. This method could be useful for rapid and sensitive 1st line Fabry disease screening, monitoring and/or diagnostic tool for Fabry disease.

• 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.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.20
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• pp.8893-8900
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• 2014

Dysregulated expression of microRNAs (miRNAs) has been shown to be closely associated with tumor development, progression, and carcinogenesis. However, their clinical implications for gastric cancer remain elusive. To investigate the hypothesis that genome-wide alternations of miRNAs differentiate gastric cancer tissues from those matched adjacent non-tumor tissues (ANTTs), miRNA arrays were employed to examine miRNA expression profiles for the 5-pair discovery stage, and the quantitative real-time polymerase chain reaction (qRTPCR) was applied to validate candidate miRNAs for 48-pair validation stage. Furthermore, the relationship between altered miRNA and clinicopathological features and prognosis of gastric cancer was explored. Among a total of 1,146 miRNAs analyzed, 16 miRNAs were found to be significantly different expressed in tissues from gastric cancer compared to ANTTs (p<0.05). qRT-PCR further confirmed the variation in expression of miR-193b and miR-196a in the validation stage. Down-expression of miR-193b was significantly correlated with Lauren type, differentiation, UICC stage, invasion, and metastasis of gastric cancer (p<0.05), while over-expression of miR-196a was significantly associated with poor differentiation (p=0.022). Moreover, binary logistic regression analysis demonstrated that the UICC stage was a significant risk factor for down-expression of miR-193b (adjusted OR=8.69; 95%CI=1.06-56.91; p=0.043). Additionally, Kaplan-Meier survival curves indicated that patients with a high fold-change of down-regulated miR-193b had a significantly shorter survival time (n=19; median survival=29 months) compared to patients with a low fold-change of down-regulated miR-193b (n=29; median survival=54 months) (p=0.001). Overall survival time of patients with a low fold-change of up-regulated miR-196a (n=27; median survival=52 months) was significantly longer than that of patients with a high fold-change of up-regulated miR-196a (n=21; median survival=46 months) (p=0.003). Hence, miR-193b and miR-196a may be applied as novel and promising prognostic markers in gastric cancer.

• Journal of the Korean Chemical Society
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• v.42 no.3
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• pp.266-276
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• 1998

Cholesterol supersaturation in bile, which causes gallstone formation, is the result of low bile acid secretion or high cholesterol secretion. The quantitative analysis of cholesterol, bile acids and sterols which are precursors of cholesterol have been used to examine the changes in bile component. We described a simple, sensitive and reproducible method for simultaneous determination of cholesterol, five bile acids and seven sterols in human bile juices and gallstones by capillary column gas chromatography-mass spectrometry (GC/MS). Clinical samples were hydrolyzed by alcoholic KOH, extracted twice (pH 14 and 1) and derivatized to trimethylsilyl (TMS) ether with $MSTFA/NH_4I$ (N-methyl-N-trimethylsilyltrifluoroacetamide/ammonium iodide) mixture in order to be detected on the GC/MS. The good quality control data were obtained through within-a-day and day-to-day test (RSD values were 1.72-13.79, 0.68-14.10, respectively) and the recovery range of them was 73.56-96. 95 Using this method, biliary and gallstone compositions in the patients with intrahepatic stones were analyzed. The amounts and its relative distribution of cholesterol, bile acids and sterols showed different pattern in bile juices and gallstones.

• The Korea Journal of Herbology
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• v.22 no.4
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• pp.253-260
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• 2007

Objectives : Intracerebral hemorrhage (ICH) is characterized by breakdown of blood vessels within the brain parenchyma. Fundamental therapeutic strategies for ICH, particularly those aimed at neuroprotection, have to be established. So in this experiment, the effects of Woowhangchongshim-won, a traditional prescription formula for treating Cerebral Apoplexy in Asian countries, were investigated. Methods : After intraperitoneal injection of chloralhydrate, rats were placed in a stereotaxic frame. ICH was induced by injection of 1 U collagenase type IV and drug was administered orally for 10 days. The molecular profile of cerebral hemorrhage in rat brain tissue was measured using micro array technique to identify up- or down- regulated genes in brain tissue. These genes induced by brain damage were mainly concerned with general metabolic process such as primary metabolic process, cellular metabolic process, macromolecule metabolic process, and biosynthetic process. Results : The number of genes increased in control and not-changed in experiment was 374, and decreased in control and not-changed in experiment was 527. We are concerned with genes that can be recovered by treatment with medicine, it is especially interesting to above types of genes. Conclusions : Upon medicine treatment to the rat having cerebral hemorrhage, expressions of some genes were restored to normal level. Further analysis using protein interaction database identified some key molecules that can be used for elucidation of therapeutical mechanism of medicine in future.

• Korean Journal of Food Science and Technology
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• v.26 no.6
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• pp.665-669
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• 1994

A rapid gas chromatographic (GC) profiling method was applied to dairy products (milk and cheeses) for the simultaneous analysis of volatile and nonvolatile organic acids. Cheese samples were first made into aqueous samples by dissolving in water. The aqueous samples were then extracted with organic solvents after the acidification and NaCI saturation. The organic layers (diethyl ether : hexane= 1 : 1) were extracted with $NaHCO_3$ saturated solution with subsequent solid-phase extraction of the aqueous phases using Chromosorb P column/diethyl ether followed by triethylamine treatment. The resulting triethylammonium salts of acids were directly converted into volatile tert.-butyldimethylsilyl derivatives, which were analyzed by dual-capillary column GC, and GC-mass spectrometry. From milk and four cheese samples studied, 31 organic acids including 21 fatty acids and other hydroxy and dioic acids were tentatively identified. The amounts of the fatty acids were different among the kinds of cheese and thus the simplified retention index (RI) spectra of organic acids were useful for the visual pattern recognition of each sample, when the Direct Comparision method between cheese and a blind sample were attempted, it was quickly recognized to be a gouda cheese with the 999 ppt match quality value.

• The Korean Journal of Malacology
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• v.32 no.2
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• pp.127-131
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• 2016

The natives of the genus Corbicula have shown worldwide dispersion in recent times, which has caused great ecological and economic impacts on the introduced ecosystems. The species reported from the genus have been consumed as food and explored for medicine with pharmacological activity. Consequently, the demand of Corbicula sp. in the South Korean domestic market has increased and so also it's associated import to the country. However, due to the absence of identification keys of imported Corbicula, the market is facing confronting situations. We hypothesized that the mitochondrial Cytochrome Oxidase I gene (CO-I) based molecular profiling could be a necessary technique for identification of Corbicula sp. in the South Korea domestic market. The genetic analysis identified both Corbicula japonica and Corbicula fluminea from the market foods. C. japonica and C. fluminea are inhabitants in Korea, but C. fluminea production has decreased in Seomjingang river basin. Therefore, C. fluminea identified from this study, is expected to be imported from China and would have a mixed sales in Seomjingang river side basin.