Analysis of the circadian rhythm of biological processes in mouse liver and kidney

Podkolodnyy, I. N.; Tverdokhleb, N. N.; Podkolodnaya, O. A.

doi:10.18699/vj17.311

Cited by 2 publications

(1 citation statement)

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“…In the article (Podkolodnyy et al, 2017), the authors considered genes located in liver and kidney cells that are overexpressed with a certain periodicity during the 24-hour cycle. In a subsequent paper, the authors provided an overview of various mathematical models used to model the autonomous circadian clock in mammalian cells (Podkolodnaya et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

The finding and researching algorithm for potentially oscillating enzymatic systems

et al. 2021

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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.

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Section: Introductionmentioning

confidence: 99%

The finding and researching algorithm for potentially oscillating enzymatic systems

et al. 2021

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Detection and analysis of dynamic patterns of diurnal expression of mammalian genes

2019

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The purpose of the study is to identify and analyze patterns of the diurnal dynamics of the expression of genes that diﬀer in the shape of the curve. It can be expected that the similarity of the patterns of daily expression (shape of the curve) of genes is a reﬂection of the synchronization of gene expression by common external and internal signals or participation in similar biological processes. Diﬀerent signals that have daily dynamics (light, activity, nutrition, stress, temperature, etc.) can aﬀect diﬀerent levels of expression regulation, which can be manifested in various forms of patterns of daily gene expression. In our research, we used experimental data on gene expression at the level of translation (ribosome profling) in the liver and kidney of a mouse (GSE67305 and GSE81283). To identify genes with a daily rhythm of expression, we used a oneway analysis of variance. To identify similarinshape curves of the daily dynamics of gene expression, we propose an approach based on cluster analysis. The distance between the genes was calculated by aligning the phases and fnding the maximum crosscorrelation between the patterns of the daily expression of these genes by the cyclic shift. This approach allowed us to identify genes that have not only expression patterns with a single maximum (sinusoidal, asymmetrical, shifted to the left or right, pulsed), but also complex composite signals with several extremes. As a result, the groups of genes united by the similarity of the shape of the daily expression curve without regard to their phase characteristics were identifed. GO enrichment analysis of groups of genes with sharply different patterns of daily expression (sinusoidal and pulsed) in the mouse kidneys and liver showed that the group of genes with a sinusoidal pattern was more associated with regulation of circadian rhythm and metabolism. The group of genes with a pulsed pattern is largely associated with the protective functions of the organism, which require the quick response. Thus, our studies have confrmed the eﬀectiveness of the proposed approach to the analysis of the diurnal dynamics of gene expression. The identifed dynamic patterns of diurnal expression are important for the further study of complex circadian regulation, synchronization and interaction of biological processes with diurnal dynamics in mammals.

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Analysis of the circadian rhythm of biological processes in mouse liver and kidney

Cited by 2 publications

References 37 publications

The finding and researching algorithm for potentially oscillating enzymatic systems

The finding and researching algorithm for potentially oscillating enzymatic systems

Detection and analysis of dynamic patterns of diurnal expression of mammalian genes

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