• Journal of KIISE:Databases
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• v.30 no.6
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• pp.573-584
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• 2003

Recent massive data generation by genomics and proteomics requires bioinformatic tools to extract the biological meaning from the massive results. Here we introduce ROSPath, a database system to deal with information on reactive oxygen species (ROS)-mediated cell signaling pathways. It provides a structured repository for handling pathway related data and tools for querying, displaying, and analyzing pathways. ROSPath data model provides the extensibility for representing incomplete knowledge and the accessibility for linking the existing biochemical databases via the Internet. For flexibility and efficient retrieval, hierarchically structured data model is defined by using the object-oriented model. There are two major data types in ROSPath data model: ‘bio entity’ and ‘interaction’. Bio entity represents a single biochemical entity: a protein or protein state involved in ROS cell-signaling pathways. Interaction, characterized by a list of inputs and outputs, describes various types of relationship among bio entities. Typical interactions are protein state transitions, chemical reactions, and protein-protein interactions. A complex network can be constructed from ROSPath data model and thus provides a foundation for describing and analyzing various biochemical processes.

• Molecular & Cellular Toxicology
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• v.4 no.3
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• pp.260-266
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• 2008

Recently, there has been scientific discussion on the utility of -omics techniques such as genomics, proteomics, and metabolomics within toxicological research and mechanism-based risk assessment. Toxicogenomics is a novel approach integrating the expression analysis of genes (genomic) or proteins (proteomic) with traditional toxicological methods. Since 1999, the toxicogenomic approach has been extensively applied for regulatory purposes in order to understand the potential toxic mechanisms that result from chemical compound exposures. Therefore, this article's purpose was to consider the utility of toxicogenomic profiles for improved risk assessment, explore the current limitations in applying toxicogenomics to regulation, and finally, to rationalize possible avenues to resolve some of the major challenges. Based on many recent works, the significant impact toxicogenomic techniques would have on human health risk assessment is better identification of toxicity pathways or mode-of-actions (MOAs). In addition, the application of toxicogenomics in risk assessment and regulation has proven to be cost effective in terms of screening unknown toxicants prior to more extensive and costly experimental evaluation. However, to maximize the utility of these techniques in regulation, researchers and regulators must resolve many parallel challenges with regard to data collection, integration, and interpretation. Furthermore, standard guidance has to be prepared for researchers and assessors on the scientifically appropriate use of toxicogenomic profiles in risk assessment. The National Institute of Toxicological Research (NITR) looks forward to an ongoing role as leader in addressing the challenges associated with the scientifically sound use of toxicogenomics data in risk assessment.

• Journal of Plant Biotechnology
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• v.43 no.2
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• pp.223-230
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• 2016

Ascorbic acid (AsA) is a strong antioxidant/reducing agent that can be converted to dehydroascorbate (DHA) by oxidation in plants. DHA, a very short-lived chemical, is recycled to AsA by dehydroascorbate reductase (DHAR). Previously, DHAR cDNA was isolated from the hairy roots of the sesame plant, and DHAR-overexpressing transgenic potato plants were generated under the control of the CaMV35S promoter (CaMV35S::DHAR). An increase in transgene expression and ascorbate levels were observed in the transgenic plants. In the present study, proteomic analysis revealed that transgenic plants not only accumulated DHAR in their cells, but also induced several other antioxidant enzyme-related proteins during plant growth. These results suggest that DHAR is important for stress tolerance via induction of antioxidant proteins, and could improve stress tolerance in transgenic potato plants.

• Journal of Digital Contents Society
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• v.11 no.1
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• pp.99-104
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• 2010

Numerous bio-digital contents have been produced by new technology using biochip and others for analyzing early chemical-induced genes. These contents have little meaning by themselves, and so they should be modified and extracted after consideration of biological meaning. These include genomics, transcriptomics, protenomics, metabolomics, which combined into omics. Omics tools could be applied into toxicology, forming a new field of toxicogenomics. It is possible that approach of toxicogenomics can estimate toxicity more quickly and accurately by analyzing gene/protein/metabolite profiles. These approaches should help not only to discover highly sensitive and predictive biomarkers but also to understand molecular mechanism(s) of toxicity, based on the development of analysing technology. Furthermore, it is important that bio-digital contents should be obtained from specific cells having biological events more than from whole cells. Taken together, many bio-digital contents should be analyzed by careful calculating algorism under well-designed experimental protocols, network analysis using computational algorism and related profound databases.

• Journal of Ginseng Research
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• v.45 no.1
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• pp.58-65
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• 2021

Background: Panax ginseng, as one of the most widely used herbal medicines worldwide, has been studied comprehensively in terms of the chemical components and pharmacology. The proteins from ginseng are also of great importance for both nutrition value and the mechanism of secondary metabolites. However, the proteomic studies are less reported in the absence of the genome information. With the completion of ginseng genome sequencing, the proteome profiling has become available for the functional study of ginseng protein components. Methods: We optimized the protein extraction process systematically by using SDS-PAGE and one-dimensional liquid chromatography mass spectrometry. The extracted proteins were then analyzed by two-dimensional chromatography separation and cutting-edge mass spectrometry technique. Results: A total of 2,732 and 3,608 proteins were identified from ginseng root and cauline leaf, respectively, which was the largest data set reported so far. Only around 50% protein overlapped between the cauline leaf and root tissue parts because of the function assignment for plant growing. Further gene ontology and KEGG pathway revealed the distinguish difference between ginseng root and leaf, which accounts for the photosynthesis and metabolic process. With in-deep analysis of functional proteins related to ginsenoside synthesis, we interestingly found the cytochrome P450 and UDP-glycosyltransferase expression extensively in cauline leaf but not in the root, indicating that the post glucoside synthesis of ginsenosides might be carried out when growing and then transported to the root at withering. Conclusion: The systematically proteome analysis of Panax ginseng will provide us comprehensive understanding of ginsenoside synthesis and guidance for artificial cultivation.

• Journal of Microbiology and Biotechnology
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• v.29 no.7
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• pp.1155-1164
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• 2019

Lichens contain diverse bioactive secondary metabolites with various chemical and biological properties, which have been widely studied. However, details of the inhibitory mechanisms of their secondary metabolites against influenza A virus (IAV) have not been documented. Here, we investigated the antiviral effect of lichen extracts, obtained from South Korea, against IAV in MDCK cells. Of the lichens tested, Nipponoparmelia laevior (LC24) exhibited the most potent inhibitory effect against IAV infection. LC24 extract significantly increased cell viability, and reduced apoptosis in IAV-infected cells. The LC24 extract also markedly reduced (~ 3.2 log-fold) IAV mRNA expression after 48 h of infection. To understand the antiviral mechanism of LC24 against IAV, proteomic (UPLC-$HDMS^E$) analysis was performed to compare proteome modulation in IAV-infected (V) vs. mock (M) and LC24+IAV (LCV) vs. V cells. Based on Ingenuity Pathway Analysis (IPA), LC24 inhibited IAV infection by modulating several antiviral-related genes and proteins (HSPA4, HSPA5, HSPA8, ANXA1, ANXA2, $HIF-1{\alpha}$, AKT1, MX1, HNRNPH1, HNRNPDL, PDIA3, and VCP) via different signaling pathways, including $HIF-1{\alpha}$ signaling, unfolded protein response, and interferon signaling. These molecules were identified as the specific biomarkers for controlling IAV in vitro and further confirmation of their potential against IAV in vivo is required. Our findings provide a platform for further studies on the application of lichen extracts against IAV.

• Journal of Ginseng Research
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• v.47 no.2
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• pp.302-310
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• 2023

Background: The most common type of dementia, Alzheimer's disease (AD), is marked by the formation of extracellular amyloid beta (Aβ) plaques. The impairments of axons and synapses appear in the process of Aβ plaques formation, and this damage could cause neurodegeneration. We previously reported that non-saponin fraction with rich polysaccharide (NFP) from Korean Red Ginseng (KRG) showed neuroprotective effects in AD. However, precise molecular mechanism of the therapeutic effects of NFP from KRG in AD still remains elusive. Methods: To investigate the therapeutic mechanisms of NFP from KRG on AD, we conducted proteomic analysis for frontal cortex from vehicle-treated wild-type, vehicle-treated 5XFAD mice, and NFP-treated 5XFAD mice by using nano-LC-ESI-MS/MS. Metabolic network analysis was additionally performed as the effects of NFP appeared to be associated with metabolism according to the proteome analysis. Results: Starting from 5,470 proteins, 2,636 proteins were selected for hierarchical clustering analysis, and finally 111 proteins were further selected for protein-protein interaction network analysis. A series of these analyses revealed that proteins associated with synapse and mitochondria might be linked to the therapeutic mechanism of NFP. Subsequent metabolic network analysis via genome-scale metabolic models that represent the three mouse groups showed that there were significant changes in metabolic fluxes of mitochondrial carnitine shuttle pathway and mitochondrial beta-oxidation of polyunsaturated fatty acids. Conclusion: Our results suggested that the therapeutic effects of NFP on AD were associated with synaptic- and mitochondrial-related pathways, and they provided targets for further rigorous studies on precise understanding of the molecular mechanism of NFP.

• Journal of Ginseng Research
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• v.47 no.5
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• pp.662-671
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• 2023

Background: 20(S)-protopanaxadiol (PPD), a ginsenoside metabolite, has prominent benefits for the central nervous system, especially in improving learning and memory. However, its transcriptional targets in brain tissue remain unknown. Methods: In this study, we first used mass spectrometry-based drug affinity responsive target stability (DARTS) to identify the potential proteins of ginsenosides and intersected them with the transcription factor library. Second, the transcription factor PURA was confirmed as a target of PPD by biolayer interferometry (BLI) and molecular docking. Next, the effect of PPD on the transcriptional levels of target genes of PURA in brain tissues was determined by qRT-PCR. Finally, bioinformatics analysis was used to analyze the potential biological features of these target proteins. Results: The results showed three overlapping transcription factors between the proteomics of DARTS and transcription factor library. BLI analysis further showed that PPD had a higher direct interaction with PURA than parent ginsenosides. Subsequently, BLI kinetic analysis, molecular docking, and mutations in key amino acids of PURA indicated that PPD specifically bound to PURA. The results of qRT-PCR showed that PPD could increase the transcription levels of PURA target genes in brain. Finally, bioinformatics analysis showed that these target proteins were involved in learning and memory function. Conclusion: The above-mentioned findings indicate that PURA is a transcription target of PPD in brain, and PPD upregulate the transcription levels of target genes related to cognitive dysfunction by binding PURA, which could provide a chemical and biological basis for the study of treating cognitive impairment by targeting PURA.