• BMB Reports
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• v.45 no.4
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• pp.213-220
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• 2012

Viruses have evolved to manipulate the host cell machinery for virus propagation, in part by interfering with the host cellular signaling network. Molecular studies of individual pathways have uncovered many viral host-protein targets; however, it is difficult to predict how viral perturbations will affect the signaling network as a whole. Systems biology approaches rely on multivariate, context-dependent measurements and computational analysis to elucidate how viral infection alters host cell signaling at a network level. Here we describe recent advances in systems analyses of signaling networks in both viral and non-viral biological contexts. These approaches have the potential to uncover virus- mediated changes to host signaling networks, suggest new therapeutic strategies, and assess how cell-to-cell variability affects host responses to infection. We argue that systems approaches will both improve understanding of how individual virus-host protein interactions fit into the progression of viral pathogenesis and help to identify novel therapeutic targets.

• Proceedings of the Korea Society of Environmental Biology Conference
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• 2001.12a
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• pp.80-81
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• 2001

• BMB Reports
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• v.50 no.4
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• pp.208-213
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• 2017

Vascular endothelial growth factor (VEGF) is an essential cytokine that has functions in the formation of new blood vessels and regression of cardiac hypertrophy. VEGF/VEGF-receptor-1 (VEGFR1) signaling plays a key role in the regression of cardiac hypertrophy, whereas VEGF/VEGFR2 signaling leads to cardiac hypertrophy. In this study, we identified the prohypertrophic role of miR-374 using neonatal rat ventricular myocytes (NRVMs). Our results showed that overexpression of miR-374 activated G protein-coupled receptor-mediated prohypertrophic pathways by the inhibition of VEGFR1-dependent regression pathways. Luciferase assays revealed that miR-374 could directly target the 3'-untranslated regions of VEGFR1 and cGMP-dependent protein kinase-1. Collectively, these findings demonstrated that miR-374 was a novel pro-hypertrophic microRNA functioning to suppress the VEGFR1-mediated regression pathway.

• Korean Journal of Environmental Biology
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• v.39 no.4
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• pp.515-522
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• 2021

Jeotgal is a salty and fermented traditional Korean fish sauce. Unlike most other previous studies that investigated samples purchased from retail markets, this study focused on samples of jeotgal with traceable history to Yeonggwang, a timehonored fishing village in Korea. Three jeotgal samples, which were made from small yellow croakers, largehead hairtail, and miscellaneous fish, were selected based on information obtained from interviews with local craftsmen and literature reviews. Bacterial community profiles of the three jeotgal samples were investigated to identify indicator (and potentially core) bacteria for jeotgal ripening. The 16S rRNA gene-based metagenomic analysis revealed that the dominant phyla and classes, (Gammaproteobacteria, Betaproteobacteria, Bacilli, and Clostridia) of the three different jeotgal were identical, albeit with different composition ratios. Diversification was evident beginning at the order level. Interestingly, each dominant order was mainly comprised of single members even at the genus level. The dominant genera included Halomonas, Tetragenococcus, Halanaerobium, Pseudomonas, Massilia, and Lentibacillus. This observed genus-level heterogeneity suggests that there are diverse bacterial signatures in jeotgal and that these can be used as indicators for jeotgal ripening and/or as starters to increase its sensory quality and functionality.

• Journal of Microbiology and Biotechnology
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• v.33 no.1
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• pp.15-27
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• 2023

The incidence of melioidosis cases caused by the gram-negative pathogen Burkholderia pseudomallei (BP) is seeing an increasing trend that has spread beyond its previously known endemic regions. Biofilms produced by BP have been associated with antimicrobial therapy limitation and relapse melioidosis, thus making it urgently necessary to understand the mechanisms of biofilm formation and their role in BP biology. Microbial cells aggregate and enclose within a self-produced matrix of extracellular polymeric substances (EPSs) to form biofilm. The transition mechanism of bacterial cells from planktonic state to initiate biofilm formation, which involves the formation of surface attachment microcolonies and the maturation of the biofilm matrix, is a dynamic and complex process. Despite the emerging findings on the biofilm formation process, systemic knowledge on the molecular mechanisms of biofilm formation in BP remains fractured. This review provides insights into the signaling systems, matrix composition, and the biosynthesis regulation of EPSs (exopolysaccharide, eDNA and proteins) that facilitate the formation of biofilms in order to present an overview of our current knowledge and the questions that remain regarding BP biofilms.

• Molecules and Cells
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• v.27 no.3
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• pp.271-277
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• 2009

Proteins interact with each other within a cell, and those interactions give rise to the biological function and dynamical behavior of cellular systems. Generally, the protein interactions are temporal, spatial, or condition dependent in a specific cell, where only a small part of interactions usually take place under certain conditions. Recently, although a large amount of protein interaction data have been collected by high-throughput technologies, the interactions are recorded or summarized under various or different conditions and therefore cannot be directly used to identify signaling pathways or active networks, which are believed to work in specific cells under specific conditions. However, protein interactions activated under specific conditions may give hints to the biological process underlying corresponding phenotypes. In particular, responsive functional modules consist of protein interactions activated under specific conditions can provide insight into the mechanism underlying biological systems, e.g. protein interaction subnetworks found for certain diseases rather than normal conditions may help to discover potential biomarkers. From computational viewpoint, identifying responsive functional modules can be formulated as an optimization problem. Therefore, efficient computational methods for extracting responsive functional modules are strongly demanded due to the NP-hard nature of such a combinatorial problem. In this review, we first report recent advances in development of computational methods for extracting responsive functional modules or active pathways from protein interaction network and microarray data. Then from computational aspect, we discuss remaining obstacles and perspectives for this attractive and challenging topic in the area of systems biology.

• Biotechnology and Bioprocess Engineering:BBE
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• v.10 no.5
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• pp.418-424
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• 2005

The complexity of the biological system/biological systems has been fascinating and challenging for a long time. With the advent of mathematical tools with various omics technology, systems biology was born and is already ubiquitous in every area of biology and biotechnology. Microalgal biotechnology is no exception in this new trend. As tens of microalgal genomes become publicly available on the Internet, vast amounts of data from genomics, transcriptomics, and proteomics are reported everyday. Though there has not yet been enough data gathered on microalgal metabolomics, the in silica models for relatively simple cyanobacteria or for organelles, such as chloroplasts, will appear presently. With the help of systems biology, a more in-depth understanding of microalgae will be possible. Consequently, most industrially-interested microalgae can be metabolically redesigned/reconfigured as cell factories. Microalgae will be served as the hosts in white biotechnology.

• IMMUNE NETWORK
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• v.14 no.2
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• pp.73-80
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• 2014

Because autoimmune diseases (AIDs) result from a complex combination of genetic and epigenetic factors, as well as an altered immune response to endogenous or exogenous antigens, systems biology approaches have been widely applied. The use of multi-omics approaches, including blood transcriptomics, genomics, epigenetics, proteomics, and metabolomics, not only allow for the discovery of a number of biomarkers but also will provide new directions for further translational AIDs applications. Systems biology approaches rely on high-throughput techniques with data analysis platforms that leverage the assessment of genes, proteins, metabolites, and network analysis of complex biologic or pathways implicated in specific AID conditions. To facilitate the discovery of validated and qualified biomarkers, better-coordinated multi-omics approaches and standardized translational research, in combination with the skills of biologists, clinicians, engineers, and bioinformaticians, are required.

• BMB Reports
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• v.54 no.11
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• pp.541-544
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• 2021

Protein glycosylation is a common post-translational modification found in all living organisms. This modification in bacterial pathogens plays a pivotal role in their infectious processes including pathogenicity, immune evasion, and host-pathogen interactions. Importantly, many key proteins of host immune systems are also glycosylated and bacterial pathogens can notably modulate glycosylation of these host proteins to facilitate pathogenesis through the induction of abnormal host protein activity and abundance. In recent years, interest in studying the regulation of host protein glycosylation caused by bacterial pathogens is increasing to fully understand bacterial pathogenesis. In this review, we focus on how bacterial pathogens regulate remodeling of host glycoproteins during infections to promote the pathogenesis.

• Animal cells and systems
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• v.12 no.4
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• pp.181-191
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• 2008