scholarly journals The finding and researching algorithm for potentially oscillating enzymatic systems

2021 ◽  
Vol 25 (3) ◽  
pp. 318-330
Author(s):  
T. N. Lakhova ◽  
F. V. Kazantsev ◽  
S. A. Lashin ◽  
Yu. G. Matushkin
Keyword(s):  
Mathematical Models ◽  
Computer Modeling ◽  
Gene Networks ◽  
Biological Systems ◽  
Molecular Genetic ◽  
Structural Models ◽  
Oscillatory Behavior ◽  
Mathematical And Computer Modeling ◽  
Genetic Systems ◽  
Enzymatic Systems

Many processes in living organisms are subject to periodic oscillations at different hierarchical levels of their organization: from molecular-genetic to population and ecological. Oscillatory processes are responsible for cell cycles in both prokaryotes and eukaryotes, for circadian rhythms, for synchronous coupling of respiration with cardiac contractions, etc. Fluctuations in the numbers of organisms in natural populations can be caused by the populations’ own properties, their age structure, and ecological relationships with other species. Along with experimental approaches, mathematical and computer modeling is widely used to study oscillating biological systems. This paper presents classical mathematical models that describe oscillatory behavior in biological systems. Methods for the search for oscillatory molecular-genetic systems are presented by the example of their special case – oscillatory enzymatic systems. Factors influencing the cyclic dynamics in living systems, typical not only of the molecular-genetic level, but of higher levels of organization as well, are considered. Application of different ways to describe gene networks for modeling oscillatory molecular-genetic systems is considered, where the most important factor for the emergence of cyclic behavior is the presence of feedback. Techniques for finding potentially oscillatory enzymatic systems are presented. Using the method described in the article, we present and analyze, in a step-by-step manner, first the structural models (graphs) of gene networks and then the reconstruction of the mathematical models and computational experiments with them. Structural models are ideally suited for the tasks of an automatic search for potential oscillating contours (linked subgraphs), whose structure can correspond to the mathematical model of the molecular-genetic system that demonstrates oscillatory behavior in dynamics. At the same time, it is the numerical study of mathematical models for the selected contours that makes it possible to confirm the presence of stable limit cycles in them. As an example of application of the technology, a network of 300 metabolic reactions of the bacterium Escherichia coli was analyzed using mathematical and computer modeling tools. In particular, oscillatory behavior was shown for a loop whose reactions are part of the tryptophan biosynthesis pathway.

scholarly journals Harmonic Progression in Bioinformatics and Recurrent Series in Inherited Biostructures

2021 ◽  
Vol 248 ◽  
pp. 01011
Author(s):  
Vladimir Verevkin ◽  
Sergey Petoukhov
Keyword(s):  
Mathematical Models ◽  
Biological Systems ◽  
Molecular Genetic ◽  
Standing Waves ◽  
Genetic System ◽  
Coding System ◽  
Harmonic Progression ◽  
Structural Relationships ◽  
Logarithmic Law ◽  
Long Range Communication

The article is devoted to the study of new approaches to the development of mathematical models in genetic biomechanics, which studies the structural relationships of the genetic coding system with genetically inherited biological forms. More specifically, we are talking about models based on the recurrent harmonic progression whose connection with the information sequences of DNA molecules in the genomes of higher and lower organisms was recently revealed. In particular, the article describes previously unknown connections of the function of natural logarithms with the structures of the molecular genetic system, which allow modelling the main psychophysical logarithmic law by Weber-Fechner and also many other logarithmic structures in genetically inherited biological systems. In physics, the harmonic progression is traditionally considered, first of all, as related to standing waves in resonators. Our results are correlated with Frohlich’s vibration-resonant theory about collective quantum effects and long-range communication in biological systems.

scholarly journals On Robust State Estimation of Gene Networks

2010 ◽  
Vol 2 ◽  
pp. 117959721000200 ◽  
Author(s):  
Chia-Hua Chuang ◽  
Chun-Liang Lin
Keyword(s):  
Parameter Estimation ◽  
Kalman Filter ◽  
Quantitative Analysis ◽  
State Estimation ◽  
Gene Networks ◽  
Gene Network ◽  
Biological Systems ◽  
Uncertain Process ◽  
Network Systems ◽  
Internal States

Gene networks in biological systems are not only nonlinear but also stochastic due to noise corruption. How to accurately estimate the internal states of the noisy gene networks is an attractive issue to researchers. However, the internal states of biological systems are mostly inaccessible by direct measurement. This paper intends to develop a robust extended Kalman filter for state and parameter estimation of a class of gene network systems with uncertain process noises. Quantitative analysis of the estimation performance is conducted and some representative examples are provided for demonstration.

scholarly journals MicroRNA-Mediated Regulation in Biological Systems with Oscillatory Behavior

2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
Zhiyong Zhang ◽  
Fengdan Xu ◽  
Zengrong Liu ◽  
Ruiqi Wang ◽  
Tieqiao Wen
Keyword(s):  
Cell Cycle ◽  
Biological Systems ◽  
Noncoding Rnas ◽  
Oscillatory Behavior ◽  
Fine Tuning ◽  
Base Pairing ◽  
Periodic Behavior ◽  
Small Noncoding Rnas ◽  
Regulatory Circuits ◽  
Mrna Transcripts

As a class of small noncoding RNAs, microRNAs (miRNAs) regulate stability or translation of mRNA transcripts. Some reports bring new insights into possible roles of microRNAs in modulating cell cycle. In this paper, we focus on the mechanism and effectiveness of microRNA-mediated regulation in the cell cycle. We first describe two specific regulatory circuits that incorporate base-pairing microRNAs and show their fine-tuning roles in the modulation of periodic behavior. Furthermore, we analyze the effects ofmiR369-3on the modulation of the cell cycle, confirming thatmiR369-3plays a role in shortening the period of the cell cycle. These results are consistent with experimental observations.

scholarly journals Limit cycles in models of circular gene networks regulated by negative feedback loops

2020 ◽  
Vol 21 (S11) ◽  
Author(s):  
Vitaly A. Likhoshvai ◽  
Vladimir P. Golubyatnikov ◽  
Tamara M. Khlebodarova
Keyword(s):  
Negative Feedback ◽  
Gene Networks ◽  
Functional Organization ◽  
Molecular Genetic ◽  
Feedback Loops ◽  
System Structure ◽  
Signal Delay ◽  
Negative Feedback Loops ◽  
Regulatory Signal ◽  
Delay Phenomenon

Abstract Background The regulatory feedback loops that present in structural and functional organization of molecular-genetic systems and the phenomenon of the regulatory signal delay, a time period between the moment of signal reception and its implementation, provide natural conditions for complicated dynamic regimes in these systems. The delay phenomenon at the intracellular level is a consequence of the matrix principle of data transmission, implemented through the rather complex processes of transcription and translation.However, the rules of the influence of system structure on system dynamics are not clearly understood. Knowledge of these rules is particularly important for construction of synthetic gene networks with predetermined properties. Results We study dynamical properties of models of simplest circular gene networks regulated by negative feedback mechanisms. We have shown existence and stability of oscillating trajectories (cycles) in these models. Two algorithms of construction and localization of these cycles have been proposed. For one of these models, we have solved an inverse problem of parameters identification. Conclusions The modeling results demonstrate that non-stationary dynamics in the models of circular gene networks with negative feedback loops is achieved by a high degree of non-linearity of the mechanism of the autorepressor influence on its own expression, by the presence of regulatory signal delay, the value of which must exceed a certain critical value, and transcription/translation should be initiated from a sufficiently strong promoter/Shine-Dalgarno site. We believe that the identified patterns are key elements of the oscillating construction design.

scholarly journals Search for New Candidate Genes Involved in the Comorbidity of Asthma and Hypertension Based on Automatic Analysis of Scientific Literature

2018 ◽  
Vol 15 (4) ◽  
Author(s):  
Olga V. Saik ◽  
Pavel S. Demenkov ◽  
Timofey V. Ivanisenko ◽  
Elena Yu. Bragina ◽  
Maxim B. Freidin ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Gene Networks ◽  
Molecular Mechanisms ◽  
Molecular Genetic ◽  
Genetic Networks ◽  
Positive Sign ◽  
Phenotypic Traits ◽  
Protein Protein Interactions ◽  
Scientific Publications ◽  
Associative Gene Networks

AbstractComorbid states of diseases significantly complicate diagnosis and treatment. Molecular mechanisms of comorbid states of asthma and hypertension are still poorly understood. Prioritization is a way for identifying genes involved in complex phenotypic traits. Existing methods of prioritization consider genetic, expression and evolutionary data, molecular-genetic networks and other. In the case of molecular-genetic networks, as a rule, protein-protein interactions and KEGG networks are used. ANDSystem allows reconstructing associative gene networks, which include more than 20 types of interactions, including protein-protein interactions, expression regulation, transport, catalysis, etc. In this work, a set of genes has been prioritized to find genes potentially involved in asthma and hypertension comorbidity. The prioritization was carried out using well-known methods (ToppGene and Endeavor) and a cross-talk centrality criterion, calculated by analysis of associative gene networks from ANDSystem. The identified genes, including IL1A, CD40LG, STAT3, IL15, FAS, APP, TLR2, C3, IL13 and CXCL10, may be involved in the molecular mechanisms of comorbid asthma/hypertension. An analysis of the dynamics of the frequency of mentioning the most priority genes in scientific publications revealed that the top 100 priority genes are significantly enriched with genes with increased positive dynamics, which may be a positive sign for further studies of these genes.

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