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Evolution and extinction can occur rapidly: a modeling approach

Vitaly A. Likhoshvai, Tamara M. Khlebodarova
2021 PeerJ  
We developed a model of evolutionary self-development of a large ecosystem.  ...  We have shown that global extinctions and phases of rapid growth and biodiversity stasis can be a reflection of the emergence of bistability in a self-organizing system, which is the Earth's biota.  ...  , 2018; Khlebodarova & Likhoshvai, 2019) .  ... 
doi:10.7717/peerj.11130 pmid:33954033 pmcid:PMC8051336 fatcat:j4q5aqkxdfhsze575w6p6l5j6m

MAMMOTh: a new database for curated MAthematical Models of bioMOlecular sysTems [article]

Fedor Kazantsev, Ilya Akberdin, Sergey Lashin, Natalia Ree, Vladimir Timonov, Alexander Ratushny, Tamara Khlebodarova, Vitaly Likhoshvai
2016 bioRxiv   pre-print
Living systems have a complex hierarchical organization that can be viewed as a set of dynamically interacting subsystems.  ...  Thus, to simulate the internal nature and dynamics of the whole biological system we should use the iterative way for a model reconstruction, which is a consistent composition and combination of its elementary  ...  a given function.  ... 
doi:10.1101/053652 fatcat:33jw3gcyiff4dfuaoiolcru72u

Chaos and Hyperchaos in a Model of Ribosome Autocatalytic Synthesis

Vitaly A. Likhoshvai, Vladislav V. Kogai, Stanislav I. Fadeev, Tamara M. Khlebodarova
2016 Scientific Reports  
However, only a few senior Lyapunov exponents have a significant impact. The presence in the spectrum of at least one positive Lyapunov exponent is a measure of chaos.  ...  Let us give a description of the method of calculation of several senior Lyapunov exponents for the retarded equation based on a modification of a known method of Benettin 58, 59 .  ... 
doi:10.1038/srep38870 pmid:27941909 pmcid:PMC5151018 fatcat:lb774dviyjfwhmuyo5zetdakri

On the dynamical aspects of local translation at the activated synapse

Tamara M. Khlebodarova, Vladislav V. Kogai, Vitaly A. Likhoshvai
2020 BMC Bioinformatics  
Results A mathematical model that describes the maintenance of a specific pool of active receptors on the postsynaptic membrane via two mechanisms – de novo synthesis of receptor proteins and restoration  ...  The indicated condition may cause a number of neuropsychiatric diseases, including autism and epilepsy.  ...  Parameter values: h x = 2, k x = 40, k b = 100 (a-f), k b = 200 (g-i), h b = 5 (a-c), h b = 10 (d-f), h b = 15 (g-i), K a = 1 (a, d, g), K a = 2 (b, e, h), K a = 3 (c, f, i); τ а = 1, τ b = 2, τ r = 3,  ... 
doi:10.1186/s12859-020-03597-0 pmid:32921299 fatcat:tx2ozr75bvb3pnwqgtpkecjhiu

On the control mechanisms of the nitrite level in Escherichia coli cells: the mathematical model

Tamara M. Khlebodarova, Nataly A. Ree, Vitaly A. Likhoshvai
2016 BMC Microbiology  
Due to a high toxicity of nitrite and its metabolites, it is of high interest to study mechanisms underlying the low NO 2 level maintenance in the cell.  ...  NrfA reductase is localized in the cell periplasm and uses NO 2 as an electron acceptor to create a proton gradient; NirB reductase is restricted to the cytoplasm and metabolizes excessive nitrite inside  ...  Nrf A 2 B 2 =K M;Nrf −Nrf A 2 B 2 u À Á ; dNrf A 2 B 2 dt ¼ k dis;Nrf A2B2u u  Nrf A 2 B 2 =K M;Nrf −Nrf A 2 B 2 u À Á −k cat;Nrf Nrf A 2 B 2 u; dNrf A 2 B 2 dt ¼ −k dis;Nrf A2B2u u  Nrf A 2 B 2 =K M  ... 
doi:10.1186/s12866-015-0619-x pmid:26823079 pmcid:PMC4895483 fatcat:sm6qmw2a5vb7xo2xunwtayvjqy

Differentiation of single-cell organisms according to elongation stages crucial for gene expression efficacy

Vitali A. Likhoshvai, Yuri G. Matushkin
2002 FEBS Letters  
We constructed a measure, the elongation efficiency index, that considers simultaneously the information on codon frequencies and the degree of mRNA local self-complementarity.  ...  We analyzed the interrelation between the efficiency of a gene expression and the nucleotide composition of all protein-coding sequences in 38 unicellular organisms whose complete genomic sequences are  ...  A.3.  ... 
doi:10.1016/s0014-5793(02)02507-3 pmid:11959109 fatcat:gg2umjk24nfyhhtzny62ly3n5u

MAMMOTh: A new database for curated mathematical models of biomolecular systems

Fedor Kazantsev, Ilya Akberdin, Sergey Lashin, Natalia Ree, Vladimir Timonov, Alexander Ratushny, Tamara Khlebodarova, Vitaly Likhoshvai
2018 Journal of Bioinformatics and Computational Biology  
Living systems have a complex hierarchical organization that can be viewed as a set of dynamically interacting subsystems.  ...  Thus, to simulate the internal nature and dynamics of the whole biological system we should use the iterative way for a model reconstruction, which is a consistent composition and combination of its elementary  ...  a given function.  ... 
doi:10.1142/s0219720017400108 pmid:29172865 fatcat:yt5zbiwkmferdb3ctxt3tmdtya

A plausible mechanism for auxin patterning along the developing root

Victoria V Mironova, Nadya A Omelyanchuk, Guy Yosiphon, Stanislav I Fadeev, Nikolai A Kolchanov, Eric Mjolsness, Vitaly A Likhoshvai
2010 BMC Systems Biology  
These events may predetermine lateral root initiation in a rhyzotactic pattern.  ...  Results: We propose a reflected flow mechanism for the formation of the auxin maximum in the root apical meristem.  ...  1 1 1 1 = − + − − = +  + + − + − + − + − − = − 1 1 1 1 2 a a D a a K a da j N dt D a j i i j i ji d ji j N j , , , , , , ) ( ) , (   a a D a a K a j N j N jN d jN j , , , , ) ( ) + − − ⎧ ⎨ ⎪ ⎪ ⎪ ⎪  ... 
doi:10.1186/1752-0509-4-98 pmid:20663170 pmcid:PMC2921385 fatcat:abgkxaanifb2bgmyqblaqj37ki

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

Vitaly A. Likhoshvai, Vladimir P. Golubyatnikov, Tamara M. Khlebodarova
2020 BMC Bioinformatics  
from a sufficiently strong promoter/Shine-Dalgarno site.  ...  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  ...  Now, we give a description of a symmetric limit cycle of n-dimensional system (4) with the paraemter α.  ... 
doi:10.1186/s12859-020-03598-z pmid:32921311 fatcat:2h2m4mydwbdlhdktyo5ipis3xe

A New Stochastic Model for Subgenomic Hepatitis C Virus Replication Considers Drug Resistant Mutants

Nikita V. Ivanisenko, Elena L. Mishchenko, Ilya R. Akberdin, Pavel S. Demenkov, Vitaly A. Likhoshvai, Konstantin N. Kozlov, Dmitry I. Todorov, Vitaly V. Gursky, Maria G. Samsonova, Alexander M. Samsonov, Diana Clausznitzer, Lars Kaderali (+3 others)
2014 PLoS ONE  
As an RNA virus, hepatitis C virus (HCV) is able to rapidly acquire drug resistance, and for this reason the design of effective anti-HCV drugs is a real challenge.  ...  We have developed a stochastic model of subgenomic HCV replicon replication, in which the emergence and selection of drug resistant mutant viral RNAs in replicon cells is taken into account.  ...  S2 (a) ).  ... 
doi:10.1371/journal.pone.0091502 pmid:24643004 pmcid:PMC3958367 fatcat:mgbsogq6xbhflh2d7uwx64flqi

A computer system for analysis and integrated description of regulation of the molecular-genetic system of interferon induction and action

Olga E. Belova, Vitaly A. Likhoshvai, Sergey I. Bazhan, Vladimir A. Kulichkov
1995 Bioinformatics  
The knowledge base incorporates: (i) a reference database containing experimental data on the structural-functional organization of a biological system; (ii) a dynamic mathematical model for analysis of  ...  The proposed approach is implemented as a computer system for the IBM PC and compatibles.  ...  This research was supported, in part, by the Russian Human Genome grant and by a grant from the US Department of Energy, Health Effects and Life Science Research Division.  ... 
doi:10.1093/bioinformatics/11.2.213 fatcat:nni5jwqc3bffxhzax2otv5plji

A CELLULAR AUTOMATON TO MODEL THE DEVELOPMENT OF PRIMARY SHOOT MERISTEMS OF ARABIDOPSIS THALIANA

ILYA R. AKBERDIN, EVGENIY A. OZONOV, VICTORIA V. MIRONOVA, NADEZDA A. OMELYANCHUK, VITALY A. LIKHOSHVAI, DMYTRY N. GORPINCHENKO, NIKOLAI A. KOLCHANOV
2007 Journal of Bioinformatics and Computational Biology  
Development of organisms is a very complex process in which a lot of gene networks of different cell types are integrated.  ...  A model of a cellular automaton has been developed, which simulates the embryonic development of 27 shoot meristem in Arabidopsis thaliana.  ...  Vitaly A. Likhoshvai received his Ph.D. degree in Molecular Biology".  ... 
doi:10.1142/s0219720007002862 pmid:17636867 fatcat:tz72c7zquvhhvnne7h5lsfjkom

Mathematical model of the Tat-Rev regulation of HIV-1 replication in an activated cell predicts the existence of oscillatory dynamics in the synthesis of viral components

Vitaly A Likhoshvai, Tamara M Khlebodarova, Sergei I Bazhan, Irina A Gainova, Valery A Chereshnev, Gennady A Bocharov
2014 BMC Genomics  
We analyze the strategy which is based on two feedback mechanisms, one mediating a positive regulation of the virus replication by Tat protein via the antitermination of the genomic RNAs transcription  ...  on TAR (transactivation responsive) element of the proviral DNA and the second mechanism providing a negative regulation of the splicing of the full-length (9 kb) RNAs and incompletely spliced (4 kb) RNAs  ...  We thank Tatyana Likhoshvai for the information support for this study.  ... 
doi:10.1186/1471-2164-15-s12-s1 pmid:25564443 pmcid:PMC4303933 fatcat:73odesga6jds7ajpy4o6tk2c54

Виталий Александрович Лихошвай: первые шаги в науке

2020 Письма в Вавиловский журнал генетики и селекции  
Likhoshvai scientific activity, which he started at the All-Union  ...  Bazhan Vitaly A. Likhoshvai: the first steps in science с его приходом во ВНИИ МБ.  ...  Bazhan Vitaly A. Likhoshvai: the first steps in science • построение и верификацию модели; • проверку гипотез и генерацию новых знаний в данной предметной области.  ... 
doi:10.18699/letters2020-6-20 fatcat:mf52v3lgjvcspfn4r2mz6cunki

Памяти Виталия Александровича Лихошвая: уроки, беседы и воспоминания

2020 Письма в Вавиловский журнал генетики и селекции  
In memory of Vitaly A. Likhoshvai: lessons, conversations and memories  ...  In memory of Vitaly A.  ...  Vitaly A. Likhoshvai: the first steps in science. Pisma v Vavilovskii Zhurnal Genetiki i Selektsii = Letters to Vavilov Journal Автор раздела Мария Савина.  ... 
doi:10.18699/letters2020-6-25 fatcat:tros3mlzv5dl7pn5th7xhb4fji
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