• Food Science and Industry
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• v.50 no.1
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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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• v.44 no.3
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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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• v.15 no.2
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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.

• Journal of Dairy Science and Biotechnology
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• v.34 no.4
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• pp.203-216
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• 2016

Probiotic microorganisms are thought to provide health benefits when consumed. In 2001, the World Health Organization defined probiotics as "live microorganisms which confer a health benefit on the host, when administered in adequate amounts." Three methods for screening potential probiotics have currently widely available. (1) In vitro assays of potential probiotics are preferred because of their simplicity and low cost. (2) The use of in vivo approaches for exploring various potential probiotics reflects the enormous diversity in biological models with various complex mechanisms. (3) Potential probiotics have been analyzed using several genetic and omics technologies to identify gene expression or protein production patterns under various conditions. However, there is no ideal procedure for selecting potential probiotics than testing cadidate strains on the target population. Hence, in this review, we provide an overview of the different methodologies used to identify new probiotic strains. Furthermore, we describe futre perspectives for the use of in vitro, in vivo and omics in probiotic research.

• Genomics & Informatics
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• v.16 no.3
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• pp.52-58
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• 2018

In this report, we present a case study of how pharmacogenomics and pharmacometabolomics can be useful to characterize safety and pharmacokinetic profiles in early phase new drug development clinical trials. During conducting a first-in-human trial for a new molecular entity, we were able to determine the mechanism of dichotomized variability in plasma drug concentrations, which appeared closely related to adverse drug reactions (ADRs) through integrated omics analysis. The pharmacogenomics screening was performed from whole blood samples using the Affymetrix DMET (Drug-Metabolizing Enzymes and Transporters) Plus microarray, and confirmation of genetic variants was performed using real-time polymerase chain reaction. Metabolomics profiling was performed from plasma samples using liquid chromatography coupled with quadrupole time-of-flight mass spectrometry. A GSTM1 null polymorphism was identified in pharmacogenomics test and the drug concentrations was higher in GSTM1 null subjects than GSTM1 functional subjects. The apparent drug clearance was 13-fold lower in GSTM1 null subjects than GSTM1 functional subjects (p < 0.001). By metabolomics analysis, we identified that the study drug was metabolized by cysteinylglycine conjugation in GSTM functional subjects but those not in GSTM1 null subjects. The incidence rate and the severity of ADRs were higher in the GSTM1 null subjects than the GSTM1 functional subjects. Through the integrated omics analysis, we could understand the mechanism of inter-individual variability in drug exposure and in adverse response. In conclusion, integrated multi-omics analysis can be useful for elucidating the various characteristics of new drug candidates in early phase clinical trials.

• 한국균학회소식:학술대회논문집
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• 2018.05a
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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.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.207-207
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• 2022

Eating and cooking quality (ECQ) is one of the most complex quantitative traits in rice. The understanding of genetic regulation of transcript expression levels attributing to phenotypic variation in ECQ traits is limited. We integrated whole-genome resequencing, transcriptome, and phenotypic variation data from 84 Japonica accessions to build a transcriptome-wide association study (TWAS) based regulatory network. All ECQ traits showed a large phenotypic variation and significant phenotypic correlations among the traits. TWAS analysis identified a total of 285 transcripts significantly associated with six ECQ traits. Genome-wide mapping of ECQ-associated transcripts revealed 66,905 quantitative expression traits (eQTLs), including 21,747 local eQTLs, and 45,158 trans-eQTLs, regulating the expression of 43 genes. The starch synthesis-related genes (SSRGs), starch synthase IV-1 (SSIV-1), starch branching enzyme 1 (SBE1), granule-bound starch synthase 2 (GBSS2), and ADP-glucose pyrophosphorylase small subunit 2a (OsAGPS2a) were found to have eQTLs regulating the expression of ECQ associated transcripts. Further, in co-expression analysis, 130 genes produced at least one network with 22 master regulators. In addition, we developed CRISPR/Cas9-edited glbl mutant lines that confirmed the role of alpha-globulin (glbl) in starch synthesis to validate the co-expression analysis. This study provided novel insights into the genetic regulation of ECQ traits, and transcripts associated with these traits were discovered that could be used in further rice breeding.

• Journal of Microbiology and Biotechnology
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• v.34 no.5
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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.

• Proceedings of the PSK Conference
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• 2002.10a
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• pp.181-182
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• 2002

Recentadvancesin '-omics ' technologies enable us to discover more diverse disease- relevant target proteins, which encourages us to find out more target-specific novel lead compounds as new drug candidates. Therefore, high-throughput screening (HTS) becomes an essential tool in this area. Among many HTS tools, in silico HTS is a very fast and cost-effective tool to try to derive a new lead compound for any new targets, especially when the target protein structures are known or readily modeled. (omitted)

• Proceedings of the Korean Society of Plant Biotechnology Conference
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• 2005.11a
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• pp.397-397
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• 2005