• Food Science and Biotechnology
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• v.15 no.5
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• pp.664-671
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• 2006

Modeling the growth kinetics of lactic acid bacteria (LAB), one of the most valuable microbial groups in the food industry, has been actively pursued in order to understand, control, and optimize the relevant fermentation processes. Most modeling approaches have focused on the development of single population models. Primary single population models provide fundamental kinetic information on the proliferation of a primary LAB species, the effects of biological factors on cell inhibition, and the metabolic reactions associated with cell growth. Secondary single population models can evaluate the dependence of primary model parameters, such as the maximum specific growth rate of LAB, on the initial external environmental conditions. This review elucidates some of the most important single population models that are conveniently applicable to the LAB fermentation analyses. Also, a well-defined mixed population model is presented as a valuable tool for assessing potential microbial interactions during fermentation with multiple LAB species.

• Communications for Statistical Applications and Methods
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• v.20 no.3
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• pp.235-240
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• 2013

Generalized linear mixed models(GLMMs) are frequently used for the analysis of longitudinal categorical data when the subject-specific effects is of interest. In GLMMs, the structure of the random effects covariance matrix is important for the estimation of fixed effects and to explain subject and time variations. The estimation of the matrix is not simple because of the high dimension and the positive definiteness; subsequently, we practically use the simple structure of the covariance matrix such as AR(1). However, this strong assumption can result in biased estimates of the fixed effects. In this paper, we introduce Bayesian modeling approaches for the random effects covariance matrix using a modified Cholesky decomposition. The modified Cholesky decomposition approach has been used to explain a heterogenous random effects covariance matrix and the subsequent estimated covariance matrix will be positive definite. We analyze metabolic syndrome data from a Korean Genomic Epidemiology Study using these methods.

• Journal of Ginseng Research
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• v.48 no.1
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• pp.89-97
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• 2024

Background: Ginsenoside F2 (GF2), the protopanaxadiol-type constituent in Panax ginseng, has been reported to attenuate metabolic dysfunction-associated steatotic liver disease (MASLD). However, the mechanism of action is not fully understood. Here, this study investigates the molecular mechanism by which GF2 regulates MASLD progression through liver X receptor (LXR). Methods: To demonstrate the effect of GF2 on LXR activity, computational modeling of protein-ligand binding, Time-resolved fluorescence resonance energy transfer (TR-FRET) assay for LXR cofactor recruitment, and luciferase reporter assay were performed. LXR agonist T0901317 was used for LXR activation in hepatocytes and macrophages. MASLD was induced by high-fat diet (HFD) feeding with or without GF2 administration in WT and LXRα^-/- mice. Results: Computational modeling showed that GF2 had a high affinity with LXRα. LXRE-luciferase reporter assay with amino acid substitution at the predicted ligand binding site revealed that the S264 residue of LXRα was the crucial interaction site of GF2. TR-FRET assay demonstrated that GF2 suppressed LXRα activity by favoring the binding of corepressors to LXRα while inhibiting the accessibility of coactivators. In vitro, GF2 treatments reduced T0901317-induced fat accumulation and pro-inflammatory cytokine expression in hepatocytes and macrophages, respectively. Consistently, GF2 administration ameliorated hepatic steatohepatitis and improved glucose or insulin tolerance in WT but not in LXRα^-/- mice. Conclusion: GF2 alters the binding affinities of LXRα coregulators, thereby interrupting hepatic steatosis and inflammation in macrophages. Therefore, we propose that GF2 might be a potential therapeutic agent for the intervention in patients with MASLD.

• Journal of Microbiology and Biotechnology
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• v.23 no.11
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• pp.1544-1553
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• 2013

Despite the importance of acetate kinase in the metabolism of bacteria, limited structural studies have been carried out on this enzyme. In this study, a three-dimensional structure of the Escherichia coli acetate kinase was constructed by use of molecular modeling methods. In the next stage, by considering the structure of the catalytic intermediate, trifluoroethanol (TFE) and trifluoroethyl butyrate were proposed as potential inhibitors of the enzyme. The putative binding mode of these compounds was studied with the use of a docking program, which revealed that they can fit well into the enzyme. To study the role of these potential enzyme inhibitors in the metabolic pathway of E. coli, their effects on the growth of this bacterium were studied. The results showed that growth was considerably reduced in the presence of these inhibitors. Changes in the profile of the metabolic products were studied by proton nuclear magnetic resonance spectroscopy. Remarkable changes were observed in the quantity of acetate, but other products were less altered. In this study, inhibition of growth by the two inhibitors as reflected by a change in the metabolism of E. coli suggests the potential use of these compounds (particularly TFE) as bacteriostatic agents.

• YAKHAK HOEJI
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• v.49 no.1
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• pp.74-79
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• 2005

Metabonomic analysis has been recognized as a powerful approach for characterizing metabolic changes in biofluids due to toxicity, disease process or environmental influences. To investigate the possibility of relating metabolic changes with $^{1}H-NMR$ spectra, urine samples from Sprague-Dawley rats treated with various dietary restrictions or toxic substances (nicotine) were analysed using $^{1}H-NMR$ spectroscopy and pattern recognition techniques. Dietary restrictions-given to male rats were normal diet and high fat diet and fasting. The nicotine urine samples were collected from SD rats administered with nicotine (25 mg/kg) at the various time intervals. $^{1}H-NMR$ spectra of all urine samples were acquired at 400 MHz on a VARIAN spectrometer. To establish the presence of any intrinsic class-related patterns or clusters in each NMR data, methods of PCA (principal component analysis) and soft independent modeling of class analogy (SIMCA) analysis were used, and the results from these analyses were compared to each other. In all cases of dietary conditions and nicotine treatment, SIMCA analysis gave better results for the discrimination of NMR spectra of urine samples than PCA.

• Genomics & Informatics
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• v.20 no.4
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• pp.41.1-41.9
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• 2022

The pathogen Gallibacterium anatis has caused heavy economic losses for commercial poultry farms around the world. However, despite its importance, the functions of its hypothetical proteins (HPs) have been poorly characterized. The present study analyzed the functions and structures of HPs obtained from Gallibacterium anatis (NCTC11413) using various bioinformatics tools. Initially, all the functions of HPs were predicted using the VICMpred tool, and the physicochemical properties of the identified virulence proteins were then analyzed using Expasy's ProtParam server. A virulence protein (WP_013745346.1) that can act as a potential drug target was further analyzed for its secondary structure, followed by homology modeling and three-dimensional (3D) structure determination using the Swiss-Model and Phyre2 servers. The quality assessment and validation of the 3D model were conducted using ERRAT, Verify3D, and PROCHECK programs. The functional and phylogenetic analysis was conducted using ProFunc, STRING, KEGG servers, and MEGA software. The bioinformatics analysis revealed 201 HPs related to cellular processes (n = 119), metabolism (n = 61), virulence (n = 11), and information/storage molecules (n = 10). Among the virulence proteins, three were detected as drug targets and six as vaccine targets. The characterized virulence protein WP_013745346.1 is proven to be stable, a drug target, and an enzyme related to the citrate cycle in the present pathogen. This enzyme was also found to facilitate other metabolic pathways, the biosynthesis of secondary metabolites, and the biosynthesis of amino acids.

• Korean Chemical Engineering Research
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• v.44 no.1
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• pp.97-105
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• 2006

In order to investigate the effect of inhibitors on L-threonine biosynthesis in Escherichia coli, we have constructed a metabolic network model of amino acid biosynthesis from L-aspartate to L-threonine by using available informations from literatures and databases. In the model, the effects of inhibitors on the biosynthesis of L-threonine was included as an appropriate mathematical form. For simulation study, we used initial values as L-aspartate 5 mM, ATP 5 mM, NADPH 2 mM, and observed the concentration changes of intermediate metabolites over concentration changes of respective inhibitors. As a result, we found that concentrations of intermediate metabolites were not significantly changed over concentration changes of L-lysine, L-methionine, and L-glutamate. But, there were considerable changes of intermediates over concentration changes of L-serine, L-cysteine, and L-threonine, which can be considered as essential effectors on L-threonine synthesis. Contrary, the synthesis of L-threonine seems to be not related to the amounts of L-aspartate, and inversely proportional to the accumulated amount of D,L-aspartic ${\beta}$-semialdehyde.

• Genomics & Informatics
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• v.14 no.4
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• pp.222-229
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• 2016

Kimchi is a traditional Korean food prepared by fermenting vegetables, such as Chinese cabbage and radishes, which are seasoned with various ingredients, including red pepper powder, garlic, ginger, green onion, fermented seafood (Jeotgal), and salt. The various unique microorganisms and bioactive components in kimchi show antioxidant activity and have been associated with an enhanced immune response, as well as anti-cancer and anti-diabetic effects. Red pepper inhibits decay due to microorganisms and prevents food from spoiling. The vast amount of biological information generated by academic and industrial research groups is reflected in a rapidly growing body of scientific literature and expanding data resources. However, the genome, biological pathway, and related disease data are insufficient to explain the health benefits of kimchi because of the varied and heterogeneous data types. Therefore, we have constructed an appropriate semantic data model based on an integrated food knowledge database and analyzed the functional and biological processes associated with kimchi in silico. This complex semantic network of several entities and connections was generalized to answer complex questions, and we demonstrated how specific disease pathways are related to kimchi consumption.

• Journal of the Korean Society for Precision Engineering
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• v.33 no.3
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• pp.173-181
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• 2016

This paper reports on the development of a roller-cam clutch mechanism. This mechanism can transfer bidirectional torque with high backdrivability, as well as increase actuation energy efficiency, in electrical exoskeleton robots. The developed mechanism was installed at the robot knee joint and unclutched during the swing phase which uses less metabolic energy, thereby functioning as a passive joint. The roller-cam clutch aimed to increase actuation energy efficiency while also producing high backdrivability by generating zero impedance for users during the swing phase. To develop the mechanism, mathematical modeling of the roller-cam clutch was conducted, with the design having more than three safety factors following optimization. Titanium (Ti-6AL-4V) material was used. Finally, modeling verification was done using ANSYS software.

• KSBB Journal
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• v.14 no.1
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• pp.45-50
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• 1999

This study was focused on investigating the growth properties of a sulfate reducing bacterium Deslfovibrio sp. B5 which has metabolic ability for desulfurization of petroleum. The optimal temperature and pH for growth of Desulfovibiro sp. B5 were $38^{\circ}C$ and 6.6-7.0, respectively. Addition of 10% corn steep liquor to the Postgate medium C resulted in 0.79 g/L cell concentration, corresponding to a 1.8-fold increase in dry cell mass. Acetate concentrations above 10g/$\ell$ inhibited cell growth significantly. $H_2S$ generated from the sulfate reduction also inhibited the growth of Desulfovibrio sp. B5 at a concentration of 10mM total sulfide. But $N_2$ gassing relieved the growth inhibition by $H_2$S and thereby resulted in a 1.75-fold enhancement in specific growth and lactate consumption pattern of Desulfovibrio sp. B5.