• Proceedings of the Korean Society for Bioinformatics Conference
• /
• 2005.09a
• /
• pp.278-283
• /
• 2005

Cell cycle is regulated cooperatively by several genes. The dynamic regulatory mechanism of protein interaction network of cell cycle will be presented taking the budding yeast as a sample system. Based on the mathematical model developed by Chen et at. (MBC, 11,369), at first, the dynamic role of the feedback loops is investigated. Secondly, using a bifurcation diagram, dynamic analysis of the cell cycle regulation is illustrated. The bifurcation diagram is a kind of ‘dynamic road map’ with stable and unstable solutions. On the map, a stable solution denotes a ‘road’ attracting the state and an unstable solution ‘a repelling road’ The ‘START’ transition, the initiation of the cell cycle, occurs at the point where the dynamic road changes from a fixed point to an oscillatory solution. The 'FINISH' transition, the completion of a cell cycle, is returning back to the initial state. The bifurcation analysis for the mutants could be used uncovering the role of proteins in the cell cycle regulation network.

• Proceedings of the Korean Society for Bioinformatics Conference
• /
• 2005.09a
• /
• pp.191-196
• /
• 2005

Genetic networks are a key to unraveling dynamic properties of biological processes and regulation of genes plays an essential role in dynamic behavior of the genetic networks. A popular characterization of regulation of the gene is a kinetic model. However, many kinetic parameters in the genetic regulation have not been available. To overcome this difficulty, in this report, state-space approach to modeling gene regulation is presented. Second-order systems are used to characterize gene regulation. Interpretation of coefficients in the second order systems as resistance, capacitance and inductance is studied. The mathematical methods for transient response analysis of gene regulation to external perturbation are investigated. Criterion for classifying gene into three categories: underdamped, overdamped and critical damped is discussed. The proposed models are applied to yeast cell cycle gene expression data.

• Proceedings of the Korean Biophysical Society Conference
• /
• 2003.06a
• /
• pp.77-77
• /
• 2003

Gene expression in a cell is regulated by mutual activations or repressions between genes. Identifying the gene regulation network will be one of the most important research topics in the post genomic era. We propose a linear dynamic model of gene regulation for the yeast cell cycle. A small gene network consisting of about 40 genes is reconstructed from the analysis of micro-array gene expression data of yeast S. cerevisiae published by P. Spellman et al. We show that the network construction is consistent with the result of the hierarchical cluster analysis.

• Genomics & Informatics
• /
• v.5 no.3
• /
• pp.107-112
• /
• 2007

MicroRNAs (miRNAs) are known to negatively control protein-coding genes by binding to messenger RNA (mRNA) in the cytoplasm. In innate immunity, the role of miRNA gene silencing is largely unknown. In this study, we performed microarray-based experiments using lipopolysaccharide (LPS)-stimulated macrophages derived from wild-type, MyD88 knockout (KO), TRIF KO, and MyD88/TRIF double KO mice. We employed a statistical approach to determine the importance of the commonality and specificity of miRNA binding sites among groups of temporally co-regulated genes. We demonstrate that both commonality and specificity are irrelevant to define a priori groups of co-down regulated genes. In addition, analyzing the various experimental conditions, we suggest that miRNA regulation may not only be a late-phase process (after transcription) but can also occur even early (1h) after stimulation in knockout conditions. This further indicates the existence of dynamic interactions between miRNA and signaling molecules/transcription factor regulation; this is another proof for the need of shifting from a 'hard-wired' paradigm of gene regulation to a dynamical one in which the gene co-regulation is established on a case-by-case basis.

• BMB Reports
• /
• v.49 no.11
• /
• pp.598-606
• /
• 2016

ARF is an alternative reading frame product of the INK4a/ARF locus, inactivated in numerous human cancers. ARF is a key regulator of cellular senescence, an irreversible cell growth arrest that suppresses tumor cell growth. It functions by sequestering MDM2 (a p53 E3 ligase) in the nucleolus, thus activating p53. Besides MDM2, ARF has numerous other interacting partners that induce either cellular senescence or apoptosis in a p53-independent manner. This further complicates the dynamics of the ARF network. Expression of ARF is frequently disrupted in human cancers, mainly due to epigenetic and transcriptional regulation. Vigorous studies on various transcription factors that either positively or negatively regulate ARF transcription have been carried out. However, recent focus on posttranslational modifications, particularly ubiquitination, indicates wider dynamic controls of ARF than previously known. In this review, we discuss the role and dynamic regulation of ARF in senescence and cancer.

• Advances in Computational Design
• /
• v.5 no.3
• /
• pp.233-260
• /
• 2020

The main purpose to introduce model based controller in proposed control technique is to provide better and fast learning of the floating dynamics by means of fuzzy logic controller and also cancelling effect of nonlinear terms of the system. An iterative adaptive dynamic programming algorithm is proposed to deal with the optimal trajectory-tracking control problems for autonomous underwater vehicle (AUV). The optimal tracking control problem is converted into an optimal regulation problem by system transformation. Then the optimal regulation problem is solved by the policy iteration adaptive dynamic programming algorithm. Finally, simulation example is given to show the performance of the iterative adaptive dynamic programming algorithm.

• Journal of Microbiology and Biotechnology
• /
• v.29 no.6
• /
• pp.923-932
• /
• 2019

Current strategies of strain improvement processes are mainly focused on enhancing the synthetic pathways of the products. However, excessive metabolic flux often creates metabolic imbalances, which lead to growth retardation and ultimately limit the yield of the product. To solve this problem, we applied a dynamic regulation strategy to produce $\text\tiny{L}$-phenylalanine ($\text\tiny{L}$-Phe) in Escherichia coli. First, we constructed a series of Phe-induced promoters that exhibited different strengths through modification of the promoter region of tyrP. Then, two engineered promoters were separately introduced into a Phe-producing strain xllp1 to dynamically control the expression level of one pathway enzyme AroK. Batch fermentation results of the strain xllp3 showed that the titer of Phe reached 61.3 g/l at 48 h, representing a titer of 1.36-fold of the strain xllp1 (45.0 g/l). Moreover, the $\text\tiny{L}$-Phe yields on glucose of xllp3 (0.22 g/g) were also greatly improved, with an increase of 1.22-fold in comparison with the xllp1 (0.18 g/g). In summary, we successfully improved the titer of Phe by using dynamic regulation of one key enzyme and this strategy can be applied for improving the performance of strains producing other aromatic amino acids and derived compounds.

• International Journal of Naval Architecture and Ocean Engineering
• /
• v.10 no.3
• /
• pp.282-293
• /
• 2018

This paper attempts to address the motion parameter skip problem associated with three-dimensional trajectory tracking of an underactuated Autonomous Underwater Vehicle (AUV) using backstepping-based control, due to the unsmoothness of tracking trajectory. Through kinematics concepts, a three-dimensional dynamic velocity regulation controller is derived. This controller makes use of the surge and angular velocity errors with bio-inspired models and backstepping techniques. It overcomes the frequently occurring problem of parameter skip at inflection point existing in backstepping tracking control method and increases system robustness. Moreover, the proposed method can effectively avoid the singularity problem in backstepping control of virtual velocity error. The control system is proved to be uniformly ultimately bounded using Lyapunov stability theory. Simulation results illustrate the effectiveness and efficiency of the developed controller, which can realize accurate three-dimensional trajectory tracking for an underactuated AUV with constant external disturbances.

• The Bulletin of The Korean Astronomical Society
• /
• v.35 no.2
• /
• pp.74.1-74.1
• /
• 2010

Using two-dimensional numerical hydrodynamic simulations, we investigate the regulation of star ormation rates in turbulent, multiphase, galactic gaseous disks. Our simulation domain is xisymmetric, and local in the radial direction and global in the vertical direction. Our models nclude galactic rotation, vertical stratification, self-gravity, heating and cooling, and thermal onduction. Turbulence in our models is driven by momentum feedback from supernova events ccurring in localized dense regions formed by thermal and gravitational instabilities. Self-onsistent radiative heating, representing enhanced/reduced FUV photons from the star formation, s also taken into account. Evolution of our model disks is highly dynamic, but reaches a quasi-teady state. The disks are overall in effective hydrostatic equilibrium with the midplane thermal ressure set by the vertical gravity. The star formation rate is found to be proportional pproximately linearly to the midplane thermal pressure. These results are in good agreement with the predictions of a recent theory by Ostriker, McKee, and Leroy (2010) for the thermal/dynamic equilibrium model of star formation regulation.

• Proceedings of the Korean Institute of Information and Commucation Sciences Conference
• /
• 2003.10a
• /
• pp.749-753
• /
• 2003

This paper presents an output voltage regulation system using PWM Buck-Boost AC-AC converter for power qualify improvement of custom power. This paper proposes dynamic modeling of the system for control object and in addition, a controller design example. Therefore, system state equation is derived whereby the transfer function could be obtained. The paper shows a regulation controller for tracking the output voltage to the reference under specific operating point. Finally, this paper shows validity and practical applicability of the proposed modelling and system design by experimental results.