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 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.

Electrodeposition Characteristics of Bismuth-Telluride Films

2004 ◽  
Vol 845 ◽  
Author(s):  
A. Prabhakar ◽  
E. J. Podlaha-Murphy ◽  
M. C. Murphy ◽  
R. V. Devireddy
Keyword(s):  
Mathematical Models ◽  
Bismuth Telluride ◽  
Low Temperatures ◽  
Research Effort ◽  
Biological Systems ◽  
Cellular Level ◽  
Thermoelectric Coolers ◽  
Artificial Tissue ◽  
Tissue System

ABSTRACTThis work is a part of an on-going research effort to develop an array of micro thermoelectric coolers (TECs) for highly localized control of temperature at the cellular level. Prefabrication experimentation and modeling were carried out to understand the behavior of the proposed device. Mathematical models were used to identify important device parameters and optimal device dimensions. Preliminary experiments have shown that it is feasible to produce the TECs through electrodeposition of bismuth and telluride on modules produced using a modified multistep LIGA (Lithographie, Galvanoformung and Abformung) technique. The development and characterization of the proposed TECs would enable the bioengineer highly localized control of temperature in a native or artificial tissue system. Thus enabling further usage of low temperatures in biological systems for both destructive (cryosurgical) and beneficial (cryopreservation) procedures.

scholarly journals trans-dominant inhibition of poly(ADP-ribosyl)ation sensitizes cells against gamma-irradiation and N-methyl-N'-nitro-N-nitrosoguanidine but does not limit DNA replication of a polyomavirus replicon.

1995 ◽  
Vol 15 (6) ◽  
pp. 3154-3163 ◽  
Author(s):  
J H Küpper ◽  
M Müller ◽  
M K Jacobson ◽  
J Tatsumi-Miyajima ◽  
D L Coyle ◽  
...  
Keyword(s):  
Dna Replication ◽  
Dna Binding ◽  
Gamma Irradiation ◽  
Cellular Proliferation ◽  
Molecular Genetic ◽  
Genetic System ◽  
Binding Domain ◽  
Dominant Negative ◽  
Dominant Negative Mutant ◽  
Dna Binding Domain

Poly(ADP-ribosyl)ation is a posttranslational modification of nuclear proteins catalyzed by poly(ADP-ribose) polymerase (PARP; EC 2.4.2.30), with NAD+ serving as the substrate. PARP is strongly activated upon recognition of DNA strand breaks by its DNA-binding domain. Experiments with low-molecular-weight inhibitors of PARP have led to the view that PARP activity plays a role in DNA repair and possibly also in DNA replication, cell proliferation, and differentiation. Accumulating evidence for nonspecific inhibitor effects prompted us to develop a molecular genetic system to inhibit PARP in living cells, i.e., to overexpress selectively the DNA-binding domain of PARP as a dominant negative mutant. Here we report on a cell culture system which allows inducible, high-level expression of the DNA-binding domain. Induction of this domain leads to about 90% reduction of poly(ADP-ribose) accumulation after gamma-irradiation and sensitizes cells to the cytotoxic effect of gamma-irradiation and of N-methyl-N'-nitro-N-nitrosoguanidine. In contrast, induction does not affect normal cellular proliferation or the replication of a transfected polyomavirus replicon. Thus, trans-dominant inhibition of the poly(ADP-ribose) accumulation occurring after gamma-irradiation or N-methyl-N'-nitro-N-nitrosoguanidine is specifically associated with a disturbance of the cellular recovery from the inflicted damage.

A molecular genetic system for the pathogenic yeast Candida dubliniensis

Gene ◽  
2000 ◽  
Vol 242 (1-2) ◽  
pp. 393-398 ◽  
Author(s):  
Peter Staib ◽  
Sonja Michel ◽  
Gerwald Köhler ◽  
Joachim Morschhäuser
Keyword(s):  
Molecular Genetic ◽  
Genetic System ◽  
Candida Dubliniensis ◽  
Pathogenic Yeast

scholarly journals Hyperbolic Rules of the Oligomer Cooperative Organization of Eukaryotic and Prokaryotic Genomes

2020 ◽  
Author(s):  
Sergey Petoukhov
Keyword(s):  
Quantum Information ◽  
Dna Sequences ◽  
Coding System ◽  
Harmonic Progression ◽  
General Rules ◽  
Prokaryotic Genomes ◽  
Algebraic Invariants ◽  
Cooperative Organization ◽  
Long Genes

The author's method of oligomer sums for analysis of oligomer compositions of eukaryotic and prokaryotic genomes is described. The use of this method revealed the existence of general rules for cooperative oligomeric organization of a wide list of genomes. These rules are called hyperbolic because they are associated with hyperbolic sequences including the harmonic progression 1, 1/2, 1/3, .., 1/n. These rules are demonstrated by examples of quantitative analysis of many genomes from the human genome to the genomes of archaea and bacteria. The hyperbolic (harmonic) rules, speaking about the existence of algebraic invariants in full genomic sequences, are considered as candidates for the role of universal rules for cooperative organization of genomes. The described phenomenological results were obtained as consequences of the previously published author's quantum-information model of long DNA sequences. The oligomer sums method was also applied to the analysis of long genes and viruses including the COVID-19 virus; this revealed, in characteristics of many of them, the phenomenon of rhythmically repeating deviations from model hyperbolic sequences; these deviations are associated with DNA triplets and should be systematically analyzed for a deeper understanding the genetic coding system. The topics of the algebraic harmony in living bodies and of the quantum-information approach in biology are discussed.

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