Ilya Akberdin

Sirius University · Computational Biology

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. The HCV subgenomic replicon-containing cells are widely used for experimental studies of the HCV genome replication mechanisms, for drug testing in vitro and in studies of HCV drug resi...

A mathematical model of the ethanol and lactic acid biosynthesis in the cells of Geobacillus spp. developed and adapted to the available experimental data is presented. It is shown that the mathematical model allows in silico design of genetic engineering experiments with the Geobacillus spp. bacterium and prediction of the dynamics of changes in s...

The results of the model analysis are presented in the article. The model describes of nitrite utilization in E. coli cell under continuous cultivation in the chemostat. The model takes into account expression dynamics of nrf and nir operons encoding the structure of enzymes that participate in the nitrite' metabolism and transport. It has shown th...

The article provides an overview of researches on the in silico cell development. In silico cell or e-cell is an informational and computational resource to simulate the full-scale metabolism of the cell taking into account the processes of genetic regulation as well as mechanisms of cell growth and division. There are also highlighted the key chal...

MGSmodeller (http://biomodelsgroup.ru/projects/) as a computer system contains the next set of modules: "model constructor/editor", "model calculation", "inverse problem", "optimal control". Multifunctionality of the system is based on the facilities of each module. Such module as "model constructor/editor" allows to create and to edit models using...

SEIR (Susceptible–Exposed–Infected–Recovered) approach is a classic modeling method that is frequently used to study infectious diseases. However, in the vast majority of such models transitions from one population group to another are described using the mass-action law. That causes inability to reproduce observable dynamics of an infection such a...

Optimizing physical training regimens to increase muscle aerobic capacity requires an understanding of the internal processes that occur during exercise that initiate subsequent adaptation. During exercise, muscle cells undergo a series of metabolic events that trigger downstream signaling pathways and induce the expression of many genes in working...

Earlier studies aimed at investigating the metabolism of endogenous nucleoside triphosphates in synchronous cultures of E. coli cells revealed an auto-oscillatory mode of functioning of the pyrimidine and purine nucleotide biosynthesis system, which the authors associated with the dynamics of cell division. Theoretically, this system has an intrins...

Cancer treatment and pharmaceutical development require targeted treatment and less toxic therapeutic intervention to achieve real progress against this disease. In this scenario, nanomedicine emerged as a reliable tool to improve drug pharmacokinetics and to translate to the clinical biologics based on large molecules. However, the ability of our...

Patients with COVID-19 can develop pneumonia, severe symptoms of acute respiratory distress syndrome, and multiple organ failure. Nevertheless, the variety of forms of this disease requires further research on the pathogenesis of this disease. Based on the analysis of published data and original experiments on the concentrations of SARS-CoV-2 in bi...

BioUML (https://www.biouml.org)-is a web-based integrated platform for systems biology and data analysis. It supports visual modelling and construction of hierarchical biological models that allow us to construct the most complex modular models of blood pressure regulation, skeletal muscle metabolism, COVID-19 epidemiology. BioUML has been integrat...

Here we describe a toolkit for presenting physiologically based pharmacokinetic (PBPK) models in a modular graphical view in the BioUML platform. Firstly, we demonstrate the BioUML capabilities for PBPK modeling tested on an existing model of nanoparticles delivery to solid tumors in mice. Secondly, we provide guidance on the conversion of the PBPK...

Patients with COVID-19 may develop pneumonia, severe symptoms of acute respiratory distress syndrome, and multiple organ failure. Nevertheless, the variety of forms of this disease, requires further research on the pathogenesis of this disease. Based on the analysis of published data on the concentrations of SARS-CoV-2 in biological fluids of the n...

Skeletal muscle is the principal contributor to exercise-induced changes in human metabolism. Strikingly, although it has been demonstrated that a lot of metabolites accumulating in blood and human skeletal muscle during an exercise activate different signaling pathways and induce the expression of many genes in working muscle fibres, the systemati...

SEIR (Susceptible - Exposed - Infected - Recovered) approach is a classic modeling method that has frequently been applied to the study of infectious disease epidemiology. However, in the vast majority of SEIR models and models derived from them transitions from one population group to another are described using the mass-action law which assumes p...

The prevention of muscle atrophy carries with it clinical significance for the control of increased morbidity and mortality following physical inactivity. While major transcriptional events associated with muscle atrophy-recovery processes are the subject of active research on the gene level, the contribution of non-coding regulatory elements and a...

Skeletal muscle is the principal contributor to exercise-induced changes in human metabolism. Strikingly, although it has been demonstrated that a lot of metabolites accumulating in blood and human skeletal muscle during an exercise activate different signaling pathways and induce expression of many genes in working muscle fibres, the system unders...

YUCCA (YUCCA flavin-dependent monooxygenase) is one of the two enzymes of the main auxin biosynthesis pathway (tryptophan aminotransferase enzyme (TAA)/YUCCA) in land plants. The evolutionary origin of the YUCCA family is currently controversial: YUCCAs are assumed to have emerged via a horizontal gene transfer (HGT) from bacteria to the most recen...

The thermophilic strain of the genus Geobacillus, Geobacillus icigianus is a promising bacterial chassis for a wide range of biotechnological applications. In this study, we explored the metabolic potential of Geobacillus icigianus for the production of 2,3-butanediol (2,3-BTD), one of the cost-effective commodity chemicals. Here we present a genom...

Exercised-induced adaption of skeletal muscle to aerobic endurance training is ensured by instant activation of signaling transduction pathways in the muscle cells with consequent alteration of both metabolic fluxes and expression for a versatile group of genes. Despite the experimentally based efforts to disentangle the complexity of the muscle ad...

The physiological adaptation to aerobic endurance exercises is provided by activation of signaling pathways in skeletal muscle cells. Training-induced activation of specific signaling pathways results in significant transcriptional responses. Despite the ongoing endeavours to experimentally investigate regulatory mechanisms and signal transduction...

Here, we demonstrate bioconversion of methane to muconic acid, a dicarboxylic acid that can be upgraded to an array of platform chemicals, by three gammaproteobacterial methanotrophs. All engineered methanotrophs expressing a heterologous dihydroxyshikimate dehydratase, protocatechuate decarboxylase, and catechol dioxygenase produced muconic acid f...

The paper presents a modification of a multi-compartmental mathematical model describing the dynamics of intracellular species concentrations and fluxes in human muscle at rest. A modular representation of a complex model is proposed, which provides the possibility of rapid expansion and modification of the model compartments to account for the com...

BioUML (homepage: http://www.biouml.org, main public server: https://ict.biouml.org) is a web-based integrated environment (platform) for systems biology and the analysis of biomedical data generated by omics technologies. The BioUML vision is to provide a computational platform to build virtual cell, virtual physiological human and virtual patient...

Complete list of differentially expressed genes.

Schematic components of a continuous culture bioreactor. MTU-Mass Transfer Unit; MSP-Manual Sample Port; MFM-Mass Flow Meter;BS-Bluesens sensors. The protocol is adapted for working with a mini-parallel bioreactor system, such as DasBox (Eppendorf). The system is connected to a custom-built gas-distribution system, which controls the gas-mixture in...

(A) Principal component analysis of analyzed transcriptomic datasets. Individual samples are indicated according to the next notation: light red circle – Ca-regulated growth, blue circle – La-regulated growth; (B) The MA-plot shows the log2 fold changes between Ca- and La-regulated growths of 20 Z over the mean of normalized counts. The x-axis repr...

Background. Rare Earth Elements (REEs) control methanol utilization in both methane- and methanol-utilizing microbes. It has been established that the addition of REEs leads to the transcriptional repression of MxaFI-MeDH (a two-subunit methanol dehydrogenase, calcium-dependent) and the activation of XoxF-MeDH (a one-subunit methanol dehydrogenase,...

Recent developments in experimental technologies have transformed traditional microbial physiology into a data-rich or -omics discipline. As a result, it has caused a renaissance of the mathematical analysis of biological systems and stimulated the development of systems biology workflows which aim to provide a holistic vision of all cellular funct...

Inorganic pyrophosphate (PPi) is a by-product of cellular anabolic processes whose recycle by inorganic pyrophosphatases is essential for biosynthetic reactions. While the metabolic role of PPi in anaerobic microorganisms is widely acknowledged, the contribution of PPi to central metabolic pathways in aerobic organisms is less understood. In methan...

Recent developments in experimental technologies have transformed traditional microbial physiology into a data-rich or -omics discipline. As a result, it has caused a renaissance of the mathematical analysis of biological systems and stimulated the development of systems biology workflows which aim to provide a holistic vision of all cellular funct...

Multiple experimental data demonstrated that the core gene network orchestrating self-renewal and differentiation of mouse embryonic stem cells involves activity of Oct4, Sox2 and Nanog genes by means of a number of positive feedback loops among them. However, recent studies indicated that the architecture of the core gene network should also incor...

A set of MATLAB files: two model modifications, run file and initial values of the model variables. (ZIP)

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.

Biological methane utilization, one of the main sinks of the greenhouse gas in nature, represents an attractive platform for production of fuels and value-added chemicals. Despite the progress made in our understanding of the individual parts of methane utilization, our knowledge of how the whole-cell metabolic network is organized and coordinated...

Motivation: 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 entire biological system, we should use the iterative way for a model reconstruction, which is a consistent composition and combination of its elementary su...

Me.hy.lo.bac'ter. N.L. neut. n. methylum the methyl radical; N.L. masc. n. bacter rod; N.L. masc. n. Methylobacter methyl rod. Proteobacteria / Gammaproteobacteria / Methylococcales / Methylococcaceae / Methylobacter Cells are rods, spherical, or elliptical , 0.8–1.5 × 1.2–3.0 µm. Occur singly, in pairs, and in chains. Gram‐negative . The cells are...

Methane utilization by methanotrophic bacteria is an attractive application for biotechnological conversion of natural or biogas into high-added-value products. Haloalcaliphilic methanotrophic bacteria belonging to the genus Methylomicrobium are among the most promising strains for methane-based biotechnology, providing easy and inexpensive cultiva...

Background Sucrose translocation between plant tissues is crucial for growth, development and reproduction of plants. Systemic analysis of these metabolic and underlying regulatory processes allow a detailed understanding of carbon distribution within the plant and the formation of associated phenotypic traits. Sucrose translocation from ‘source’ t...

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 subsystems. In ac...

Saccharomyces cerevisiae is the most convenient organism widely used for ethanol production from sugars in industry thanks to the high rates of growth and ethanol fermentation and biosynthesis under unaerobic conditions, as well as its tolerance to a high ethanol concentration and low pH level. Lignocellulosic biomass is considered to be the most a...

The tryptophan biosynthesis pathway is universal for the majority of known organisms, although it is absent in animals and some eubacteria. This pathway is conserved in plants, although various species differ in the number of paralogs of the enzymes involved in it. In this work, the possible role of the changes in the number of tryptophan biosynthe...

Analysis of the kinetic and stochastic models describing the dynamics of the core gene network for maintenance of pluripotency and differentiation of embryonic stem cells is represented. The core gene network was modified according to the latest experimental data on the regulation of Nanog expression. Analysis of the kinetic model showed that in th...

The hepatitis C virus (HCV) belongs to Flaviviridae family and causes hazardous liver diseases leading frequently to cirrhosis and hepatocellular carcinoma. HCV is able to rapidly acquire drug resistance and for this reason there is currently no effective anti-HCV therapy in spite of appearance of new potential drugs. Mathematical models are releva...

The hepatitis C virus (HCV) belongs to Flaviviridae family and causes hazardous liver diseases leading frequently to cirrhosis and hepatocellular carcinoma. HCV is able to rapidly acquire drug resistance and for this reason there is currently no effective anti-HCV therapy in spite of appearance of new potential drugs. Mathematical models are releva...

We have represented a new computer system for generation and analysis of mathematical models describing the dynamics of the molecular genetic sys-tems functioning in pro-and eukaryotes. The system consists of two program modules: MGSgenerator and STEP+.

Development of organisms is a very complex process in which a lot of gene networks of different cell types are integrated. Development of a cellular automaton (Ermentrout and Edelshtein-Keshet, J Theor Biol 160:97-133, 1993) that models the morphodynamics of different cell types is the first step in understanding and analysis of the regulatory mech...

Natural populations of the arctic fox (Alopex lagopus, Canidae, Carnivora) differ drastically in their reproductive strategy. Coastal foxes, which depend on stable food resources, produce litters of moderate size. Inland foxes feed on small rodents, whose populations are characterized by cycling fluctuation. In the years with low food supply, inlan...

The pleiotropic effects of mutations resulting in abnormal dentition were analyzed in Kerry Blue Terrier. A decrease in litter size was demonstrated for dogs with dentition anomalies. The mean litter size was 5.72 puppies when both parents had normal dentition and 3.64 puppies when the parents had hypodontia. Analysis showed that the decrease in li...

Development of organisms is a very complex process in that a lot of gene networks of different cell types are to be integrated. Development of cellular automata that model the morphodynamics of different cell types is the first step in understanding and analyzing the regulatory mechanisms that underlie the developmental gene networks. We have devel...

Indole-3-acetic acid (IAA) is physiologically active in the form of the free acid, but can also be found in conjugated forms in plant tissues. IAA can be degraded and redundant pathways lead to its synthesis. Auxin participates in regulation of cell differentiation in development of embryo, leaves, vascular tissue, fruit, primary and lateral root a...