• 한국정보처리학회:학술대회논문집
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• 한국정보처리학회 2023년도 춘계학술발표대회
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• pp.490-492
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• 2023

시퀀싱(sequencing) 기술의 발달로 다양한 오믹스(omics) 데이터의 축적과 인공 지능 기술의 발달로 인하여 다양한 드라이버 유전자 분류기법이 제안되어왔다. 최근에는 암 데이터가 대용량으로 축적되며 기계 학습 기반의 다양한 기법들이 활발히 제안되었다. 특히 다양한 오믹스 데이터를 결합한 고차원 데이터에서 높은 정확도를 확보하기 위한 시도가 활발히 이루어지고 있다. 본 논문에서는 멀티 오믹스와 네트워크 관련 특징을 기반으로 암의 증식 및 발생에 중요한 역할을 하는 드라이버 유전자를 분류하는 딥러닝 모델을 제시한다. 또한 The Cancer Genome Atlas(TCGA) 데이터를 통해서 모델 학습 후 기존 통계 및 머신러닝 기반 기법과 비교하여 성능이 개선되었음을 확인하였다.

• 한국균학회소식:학술대회논문집
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• 한국균학회 2018년도 춘계학술대회 및 임시총회
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• pp.33-33
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• 2018

Air-borne plant pathogenic fungus Fusarium graminearum and seed-borne plant pathogenic bacterium Burkholderia glumae are cause similar disease symptoms in rice heads. Here we showed that two pathogens frequently co-isolated in rice heads and F. graminearum is resistant to toxoflavin produced by B. glumae while other fungal genera are sensitive to the toxin. We have tried to clarify the resistant mechanism of F. graminearum against toxoflavin and the ecological reason of co-existence of the two pathogens in rice. We found that F. graminearum carries resistance to toxoflavin as accumulating lipid in fungal cells. Co-cultivation of two pathogens resulted in increased conidia and enhanced chemical attraction and attachment of the bacterial cells to the fungal conidia. Bacteria physically attached to fungal conidia, which protected bacterium cells from UV light and allowed disease dispersal. Chemotaxis analysis showed that bacterial cells moved toward the fungal exudation compared to a control. Even enhanced the production of phytotoxic trichothecene by the fungal under presence of toxoflavin and disease severity on rice heads was significantly increased by co-inoculation rather than single inoculation. This study suggested that the undisclosed potentiality of air-born infection of bacteria using the fungal spores for survival and dispersal.

• Journal of Microbiology and Biotechnology
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• 제34권5호
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• pp.1109-1118
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• 2024

Probiotics, specifically Lacticaseibacillus rhamnosus, have garnered attention for their potential health benefits. This study focuses on evaluating the probiotic properties of candidate probiotics L. rhamnosus IDCC 3201 (3201) using the Caenorhabditis elegans surrogate animal model, a well-established in vivo system for studying host-bacteria interactions. The adhesive ability to the host's gastrointestinal tract is a crucial criterion for selecting potential probiotic bacteria. Our findings demonstrated that 3201 exhibits significantly higher adhesive capabilities compared with Escherichia coli OP50 (OP50), a standard laboratory food source for C. elegans and is comparable with the widely recognized probiotic L. rhamnosus GG (LGG). In lifespan assay, 3201 significantly increased the longevity of C. elegans compared with OP50. In addition, preconditioning with 3201 enhanced C. elegans immune response against four different foodborne pathogenic bacteria. To uncover the molecular basis of these effects, transcriptome analysis elucidated that 3201 modulates specific gene expression related to the innate immune response in C. elegans. C-type lectin-related genes and lysozyme-related genes, crucial components of the immune system, showed significant upregulation after feeding 3201 compared with OP50. These results suggested that preconditioning with 3201 may enhance the immune response against pathogens. Metabolome analysis revealed increased levels of fumaric acid and succinic acid, metabolites of the citric acid cycle, in C. elegans fed with 3201 compared with OP50. Furthermore, there was an increase in the levels of lactic acid, a well-known antimicrobial compound. This rise in lactic acid levels may have contributed to the robust defense mechanisms against pathogens. In conclusion, this study demonstrated the probiotic properties of the candidate probiotic L. rhamnosus IDCC 3201 by using multi-omics analysis.

• 식품과학과 산업
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• 제50권1호
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• pp.16-25
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• 2017

There is no doubt that accumulation of big data using multi-omics technologies will be useful to solve human's long-standing problems such as development of personalized diet and medicine, overcoming diseases, and longevity. However, in the food industry, big data based on omics is scarcely accumulated. In particular, comprehensive analysis of molecular lipid metabolites directly associated with food quality, such as taste, flavor, and texture has been very limited. Moreover, most of food lipidomics studies are applied to analyze lipid components and discriminate authenticity and freshness of limited foods including vegetable and fish oil. However, if lipid big data through food lipidomics research of various foods and materials can be accumulated, lipidomics can be used in the optimization of food processing, production, delivery system, food safety, and storage as well as functional food.

• Molecules and Cells
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• 제44권3호
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• pp.127-135
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• 2021

Since the introduction of RNA sequencing (RNA-seq) as a high-throughput mRNA expression analysis tool, this procedure has been increasingly implemented to identify cell-level transcriptome changes in a myriad of model systems. However, early methods processed cell samples in bulk, and therefore the unique transcriptomic patterns of individual cells would be lost due to data averaging. Nonetheless, the recent and continuous development of new single-cell RNA sequencing (scRNA-seq) toolkits has enabled researchers to compare transcriptomes at a single-cell resolution, thus facilitating the analysis of individual cellular features and a deeper understanding of cellular functions. Nonetheless, the rapid evolution of high throughput single-cell "omics" tools has created the need for effective hypothesis verification strategies. Particularly, this issue could be addressed by coupling cell engineering techniques with single-cell sequencing. This approach has been successfully employed to gain further insights into disease pathogenesis and the dynamics of differentiation trajectories. Therefore, this review will discuss the current status of cell engineering toolkits and their contributions to single-cell and genome-wide data collection and analyses.

• Mass Spectrometry Letters
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• 제15권2호
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• pp.69 -78
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• 2024

The advancement of high-throughput omics technologies and systems biology is essential for understanding complex biological mechanisms and diseases. The integration of proteomics and metabolomics provides comprehensive insights into cellular functions and disease pathology, driven by developments in mass spectrometry (MS) technologies, including electrospray ionization (ESI). These advancements are crucial for interpreting biological systems effectively. However, integrating these technologies poses challenges. Compared to genomic, proteomics and metabolomics have limitations in throughput, and data integration. This review examines developments in MS equipped electrospray ionization (ESI), and their importance in the effective interpretation of biological mechanisms. The review also discusses developments in sample preparation, such as Simultaneous Metabolite, Protein, Lipid Extraction (SIMPLEX), analytical techniques, and data analysis, highlighting the application of these technologies in the study of cancer or Huntington's disease, underscoring the potential for personalized medicine and diagnostic accuracy. Efforts by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) and integrative data analysis methods such as O2PLS and OnPLS extract statistical similarities between metabolomic and proteomic data. System modeling techniques that mathematically explain and predict system responses are also covered. This practical application also shows significant improvements in cancer research, diagnostic accuracy and therapeutic targeting for diseases like pancreatic ductal adenocarcinoma, non-small cell lung cancer, and Huntington's disease. These approaches enable researchers to develop standardized protocols, and interoperable software and databases, expanding multi-omics research application in clinical practice.

• Mass Spectrometry Letters
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• 제8권4호
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• pp.98-104
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• 2017

Ginseng (Panax ginseng Meyer) is a well-known health functional food used as a traditional herbal drug in Asian countries owing to its diverse pharmacological effects. Herb-drug interactions may cause unexpected side effects of co-administered drugs by the alteration of pharmacokinetics through effects on cytochrome P450 activity. In this study, we investigated the herb-drug interactions between Korean red ginseng extract (KRG) and five CYP-specific probes in mice. The pharmacokinetics of KRG extract induced-drug interactions were studied by cassette dosing of five CYP substrates for CYP1A, 2B, 2C, 2D, and 3A and the LC-MS/MS analysis of the blood concentration of metabolites of each of the five probes. The linearity, precision, and accuracy of the quantification method of the five metabolites were successfully confirmed. The plasma concentrations of five metabolites after co-administration of different doses of the KRG extract (0, 0.5, 1, and 2 g/kg) were quantified by LC-MS/MS and dose-dependent pharmacokinetic parameters were determined. The pharmacokinetic parameters of the five metabolites were not significantly altered by the dose of the KRG extract. In conclusion, the single co-administration of KRG extract up to 2 g/kg in vivo did not cause any significant herb-drug interactions linked to the modulation of CYP activity.

• Journal of Applied Biological Chemistry
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• 제59권4호
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• pp.361-364
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• 2016

본 연구에서는 3-ethyl ascorbic acid를 표준물질로 이용하여, 폴리에톡시레이티드 아스코르빈산의 정량법을 개발하였고, 확립된 시험법으로 시중에서 돼지 및 닭의 면역력 증진과 열에 대한 스트레스 경감제로 유통되고 있는 Poustin-C 검체 내 폴리에톡시레이티드 아스코르빈산의 함량 분석을 실제로 분석하여 시험법의 유효성을 검증하였다. 개발한 분석법의 검증은 직선성, 정확성, 정밀성 및 안정성 시험 등을 통하여 평가하였다. 정밀도 시험은 일내 정밀성과 일간 정밀성으로 나누어 확인하였는데, 일내 및 일간 정밀성은 모두 3.4 % 이내로 매우 우수하였다. 그리고 직선성 실험에서는 상관계수($r^2$)가 0.998 이상으로 우수하였다. 실온에서 6시간까지는 안정하여 실험 도중 분해되지 않음을 확인하였다. 따라서 본 연구에서 개발된 시험법은 검체 내 폴리에톡시레이티드 아스코르빈산의 함량을 분석하기 위한 공정 시험법으로 활용할 수 있을 것으로 사료된다.

• Kyungpook Mathematical Journal
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• 제64권2호
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• pp.287-301
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• 2024

From the mathematical and statistical point of view, a segment of a DNA strand can be viewed as a sequence of four-state (A, C, G, T) trials. Herein, we consider the distributions of runs and patterns related to the run lengths of multi-state sequences, especially for four states (A, B, C, D). Let X₁, X₂, . . . be a sequence of four state independent and identically distributed trials taking values in the set 𝒢 = {A, B, C, D}. In this study, we obtain exact formulas for the probability distribution function for the discrete distribution of runs of B's of order k. We obtain longest run statistics, shortest run statistics, and determine the distributions of waiting times and run lengths.

• 식물병연구
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• 제29권3호
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• pp.220-233
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• 2023

The phenomena of global warming has led to an increase in the average air temperature in temperate climates. Springtime frost damage is becoming more common, and after a period of dormancy, damage to buds, blooms, and developing fruits is greater significant than damage from low winter temperatures. Peaches are a crucial crop among moderate fruits. Spring frost damage in peaches can have a negative effect on crop growth, yield, and quality. It is noteworthy that these plants have evolved defenses against spring frost damage while being exposed to a variety of low temperatures in the early spring. In this current review, recent research advancements on spring frost damage avoidance in peaches were deliberated. Additionally, adaptive mechanisms of peach, such as deacclimation and reacclimation, were emphasized. Moreover, the emerging advancements using various omics approaches revealed the peach physiology and molecular mechanisms comprehensively. Furthermore, the use of chemical products and understanding the spring frost mechanisms through the use of environmental chamber temperature stimulation and infrared thermography studies were also discussed. This review is essential groundwork and paves the way to derive and design future research for agronomists and horticulturalists to overcome the challenges of spring frost damage avoidance and crop management in these circumstances.