• Journal of Korea Artificial Intelligence Association
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• 제2권1호
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• pp.7-14
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• 2024

In this paper, we explore the application of RNA-sequencing data and ensemble machine learning to predict lung cancer and treatment strategies for lung cancer, a leading cause of cancer mortality worldwide. The research utilizes Random Forest, XGBoost, and LightGBM models to analyze gene expression profiles from extensive datasets, aiming to enhance predictive accuracy for lung cancer prognosis. The methodology focuses on preprocessing RNA-seq data to standardize expression levels across samples and applying ensemble algorithms to maximize prediction stability and reduce model overfitting. Key findings indicate that ensemble models, especially XGBoost, substantially outperform traditional predictive models. Significant genetic markers such as ADGRF5 is identified as crucial for predicting lung cancer outcomes. In conclusion, ensemble learning using RNA-seq data proves highly effective in predicting lung cancer, suggesting a potential shift towards more precise and personalized treatment approaches. The results advocate for further integration of molecular and clinical data to refine diagnostic models and improve clinical outcomes, underscoring the critical role of advanced molecular diagnostics in enhancing patient survival rates and quality of life. This study lays the groundwork for future research in the application of RNA-sequencing data and ensemble machine learning techniques in clinical settings.

• BMB Reports
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• 제41권8호
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• pp.568-574
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• 2008

Antisense RNA molecules are powerful tools for controlling the expression of specific genes but their use in prokaryotes has been limited by their unpredictable antisense effectiveness. Moreover, appreciation of the molecular mechanisms associated with silencing in bacteria is still restricted. Here we report our attempts to define an effective antisense strategy in E. coli, and to dissect the observed silencing process. Antisense constructs complementary to different regions of lacZ were investigated, and silencing was observed exclusively upon expression of antisense RNA hybridising the 5'UTR of lac messenger. The level of lacZ mRNA was reduced upon expression of this antisense construct, and the silencing competence was found to be closely associated with its stability. These observations may help in the design of antisense molecules directed against prokaryotic genes.

• Asian-Australasian Journal of Animal Sciences
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• 제32권1호
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• pp.38-48
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• 2019

Objective: In this study, the transcriptome profile of cow experiencing miscarriage during peri-implantation was investigated. Methods: Total transcriptomes were checked by RNA sequencing, and the analyzed by bioinformatics methods, the differentially expressed genes (DEGs) were analysed with hierarchical clustering and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis. Results: The results suggested that serum progesterone levels were significantly decreased in cows that miscarried as compared to the pregnant cows at 18, 21, 33, 39, and 51 days after artificial insemination. The RNA sequencing results suggested that 32, 176, 5, 10, and 2 DEGs were identified in the pregnant cows and miscarried cows at 18, 21, 33, 39, and 51 d after artificial insemination. And 15, 101, 1, 2, and 2 DEGs were upregulated, and 17, 74, 4, and 8 DEGs were downregulated in the cows in the pregnant and miscarriage groups, respectively at 18, 21, 33, and 39, but no gene was downregulated at 51 d after artificial insemination. These DEGs were distributed to 13, 20, 3, 6, and 20 pathways, and some pathway essential for pregnancy, such as cell adhesion molecules, tumor necrosis factor signaling pathway and PI3K-Akt signaling pathway. Conclusion: This analysis has identified several genes and related pathways crucial for pregnancy and miscarriage in cows, as well as these genes supply molecular markers to predict the miscarriage in cows.

• Fisheries and Aquatic Sciences
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• 제7권4호
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• pp.192-203
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• 2004

The effects of temperatures, starvation, and kind of foods on growth, RNA/DNA ratio and protein contents during metamorphosis and early juvenile stage of olive flounder (Paralichthys olivaceus) were examined. During metamorphosis, warm-acclimated fish showed higher RNA and DNA content than those of the cold-acclimated fish, excepting H stage (28 DAH) at which the ratio was higher at cold temperature. RNA/DNA ratio during metamorphosis showed similar values at two temperatures tested. However, after 42 DAH warm-acclimated juveniles had higher DNA content compared with cold-acclimated fish, resulted in marked decreases in RNA/DNA ratios. Higher RNA content at H stage of cold-acclimated fish was consistent with an increase in protein content. Growth of fish rearing at warm temperature was higher than those of fish at cold temperature during all experiments. In starvation experiment, contents of DNA, RNA and protein significantly decreased. Even though there were no significant differences in total length (TL) and body weight between the live mysid-fed and artificial pellet-fed fish at 35 mm TL, both RNA/DNA and protein/DNA ratios of the former group was significantly higher than those of the latter due primarily to lower DNA content of the live mysid-fed group. The results from this study suggest that temperature, starvation and kind of foods should be considered when RNA/DNA ratio applied to assessing the cultured larval and juvenile fish condition.

• 대한한의학회지
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• 제24권3호
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• pp.145-154
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• 2003

Background : Production of cytokines by bronchial epithelial cells may contribute to the local accumulation of inflammatory cells in patients with bronchial asthma. In many recent studies, molecular biological methods have been used to investigate the role of cytokines in pathogenesis and new therapeutic targets of asthma. Objective : We aimed to identify the dose-dependent inhibitory effects of Lonicerae Flos and Paeoniae Radix on the mRNA expression of IL-6, IL-16, and GM-CSF involved in the asthma model. Materials and Methods : In the study BEAS-2B cell lines, human epithelial cells were used. These cells were stimulated with tumor necrosis factor $(TNF)-\alpha$ for artificial inflammatory expression. ${\beta}-actin$ messenger RNA (mRNA) was used for internal standard. After 24 hours of Lonicerae Flos, Paeoniae Radix, total cellular RNAs were collected treating RNA zol directly on the living cells. Then the transcriptional activities of IL-6, 16, GM-CSF were measured by RT- PCR with electrophoresis. Results : In the Lonicerae Flos study, the mRNA expression of IL-6, IL-16 and GM-CSF was showed no inhibitory effect compared to the control group in all concentrations. In the Paeoniae Radix study, the mRNA expression of IL-6, IL-l6 and GM-CSF was showed no inhibitory effect compared to the control group in all concentrations. Conclusion : This study shows that Lonicerae Flus and Paeuniae Radix have no inhibitory effects on the mRNA expression of IL-6, IL-16 and GM-CSF in BEAS-2B cell lines, human epithelial cells. Advanced studies are required to investigate the other mechanisms of inhibitory effect by Lonicerae Flus and Paeoniae Radix in the asthma model.

• 미생물학회지
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• 제33권2호
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• pp.105-110
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• 1997

한국에서 분리한 U. maydis에서 바이러스 혹은 dsRNA를 가지고 있는 A series와 SH series를 조합하여 옥수수에서 인위적으로 mating시켜 A45, A23, A211, A310, SH614, SH24의 6개 교배형 균주를 분리하였다. 새로운 교배형 균주에서 바이러스 dsRNA를 비교 분석하여 본 결과, mating전 양친형 균주에서 보이고 있는 H, M, L strand의 dsRNA 양상을 모두 가지고 있고 균주간 특별한 molecular exclusion 현상은 보이지 않았다. 교배형 6개으 균주에서 바이러스를 분리하였다. 분리된 바이러스로부터 dsRNA를 분석한 결과 균주간 mating시 dsRNA 재조합을 통한 새로운 encapsidation은 발생하지 않는다는 것을 확인하였다. Toxin test 결과, SH614는 SH9, SH10, SH11 균주에 대해서, A310과 SH24의 2종은 SH11 균주에 대해 특이적 성장억제 현상을 보였다. 이는 mating에 따른 dsRNA의 재조합이 toxin gene의 발현에 영향을 미치지 않는다는 것을 시사한다.

• 대한한의학회지
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• 제24권1호
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• pp.74-83
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• 2003

Background : Production of cytokines by bronchial epithelial cells may contribute to the local accumulation of inflammatory cells in patients with bronchial asthma. In many recent studies, molecular biological methods have been used to investigate the role of cytokines in pathogenesis and new therapeutic targets of asthma. Objective : We aimed to identify the dose-dependent inhibitory effects of Socheongryong-tang and Socheongryong-tang plus Sasam (Adenophorae Radix) on the mRNA expressions of Interleukin (IL)-6, IL-8 and granulocyte macrophage colony stimulating factor (GM-CSF) involved in the asthma model. Materials and Methods : In this study, BEAS-2B cell lines, human epithelial cells, were used. These cells were stimulated by tumor necrosis factor $(TNF)-{\alpha},{\;}IL-1{\beta}$ and histamine for artificial inflammatory expression. ${\beta}-actin$ messenger RNA (mRNA) was used for the internal standard. After each 24 hours of the Socheongryong-tang (小靑龍湯) and Socheongryong-tang plus Sasam (小靑 龍湯加沙蔘) treatment, total cellular RNAs were collected by applying RNAzol directly to the living cells. Then the transcriptional activities of IL-6, IL-8 and GM-CSF were measured by RT-PCR with electrophoresis. Results : In the Socheongryong-tang (小靑龍湯) study, the mRNA expressions of IL-6, IL-8 and GM-CSF were significantly inhibited compared to that of the control group (p<0.05). In the Socheongryong-tang plus Sasam (小靑龍湯加沙蔘) study, the mRNA expressions of IL-6, IL-8 and GM-CSF were significantly inhibited compared to that of the control group (p<0.05). Conclusions : This study shows that Socheongryong-tang (小靑龍湯) and Socheongryong-tang plus Sasam (小靑龍湯加沙蔘) have dose-dependent inhibitory effects on the mRNA expressions of IL-6, IL-8 and GM-CSF in human epithelial cells, so these herbal medicines may inhibit the inflammatory process of asthma. Advanced studies are required to investigate the mechanisms of inhibition by herbal medicine in the asthma model.

• 대한한의학회지
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• 제23권1호
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• pp.11-23
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• 2002

Objectives: We aimed to identify the dose-dependent inhibitory effects of Maekmundongcheongpye-eum and Liriopis Tuber on the mRNA expression of IL-6, IL-16, GM-CSF involved in the asthma model. Methods: In the study BEAS-2B cell lines, human epithelial cells were used. These cells were stimulated with tumor necrosis factor $(TNF)-{\alpha}$ for artificial inflammatory expression. ${\beta}-actin$ messenger RNA (mRNA) was used by internal standard. After 24 hours of Maekmundongcheongpye-eum, Liriopis Tuber-treatment, total cellular RNAs were collected, treating RNAzol directly on the alive cells. Then the transcriptional activities of IL-6, 16, GM-CSF were measured by RT-PCR with electrophoresis. Results: In the Maekmundongcheongpye-eum study, the mRNA expression of IL-6 showed 48% transcriptional inhibitory effect compared to the control group in the $100{\;}{\mu}l/ml$ category (P<0.001). In the IL-16, there was 53% and 57% transcriptional inhibitory effect compared to the control group in the $20{\;}{\mu}l/ml$ and $100{\;}{\mu}l/ml$ categories (P<0.001). In the GM-CSF, there was no inhibitory effect. In the Liriopis Tuber study, the mRNA expression of IL-6 showed 43% transcriptional inhibitory effect compared to the control group in the $100{\;}{\mu}l/ml$ category (p<0.005). In the IL-16, 34% and 26% of transcriptional inhibitory effect was shown compared to the control group in the $20{\;}{\mu}l/ml$ and $100{\;}{\mu}l/ml$ categories, respectively (P<0.05). In the GM-CSF, there was no inhibitory effect. Conclusions: This study shows that Maekmundongcheongpye-eum and Liriopis Tuber have dose-dependent inhibitory effects on the mRNA expression of IL-6 and IL-16 in BEAS-2B cell lines, human epithelial cells. Advanced studies are required to investigate the mechanisms of inhibition by herbal medicine in the asthma model.

• BMB Reports
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• 제33권5호
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• pp.359-365
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• 2000

Ribozymes are catalytic RNAs that can cleave RNAs at specific sites, thus they have been employed to degrade a target mRNA in vivo. Development of allosterically controllable ribozymes is of great current interest, but it remained difficult to furnish such functions to ribozymes in cultured cells or in animals. Recently, we designed allosterically controllable ribozymes termed maxizymes, which have sensor arms that recognize target mRNA sequences and, in the presence of such target sequences only, they form a cavity that can capture catalytically indispensable $Mg^{2+}$ ions, cleaving the target. The maxizyme was applied to therapy for chronic myelogenous leukemia (CML). It cleaved specifically the chimeric BCR-ABL mRNA, which caused CML, without damaging the normal ABL or BCR mRNA in mammalian cells and also in mice, providing the first successful example for allosteric control of the activity of artificial ribozymes in vivo.

• 한국미생물·생명공학회지
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• 제49권4호
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• pp.534-542
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• 2021

CRISPR/Cas를 이용한 유전체 편집과 유전자 발현 조절을 위한 기술에서 sgRNA는 표적서열을 인식하는 역할을 한다. gal 프로모터를 표적서열로 하여 유전체 편집에 필요한 sgRNA의 표적인식서열의 길이와 유전자 발현 조절에 필요한 sgRNA의 표적인식서열의 길이를 Cas9-NG에서 체계적으로 비교하였다. 유전체 편집의 경우, sgRNA의 표적인식서열을 구성하는 20개의 뉴클레오티드에서 3개의 뉴클레오티드의 결손만을 허용하였다. 하지만, 유전자 발현 조절에는 표적인식서열에서 11개의 뉴클레오티드가 결손되어도 표적서열을 인식하고 결합할 수 있다는 것을 밝혔다. 따라서, sgRNA의 표적인식서열에서 4개 이상의 뉴클레오티드의 결손이 있는 경우에 sgRNA/Cas9-NG는 표적 DNA 서열에 특이적으로 결합을 하지만, 엔도뉴클레아제의 활성을 갖지 못하기 때문에 유전체 편집을 할 수 없는 것으로 판단된다. 이 결과는 인공전사인자 개발과 합성생물학 분야의 다양한 CRISPR 기술 발전에 도움을 줄 것이다.