[Morphogenetic Networks which Determine the Spatial Expression of Zygotic Genes in Early Drosophila Embryo].

This review deals with the recent studies expanding the idea of positional information in the early embryogenesis of Drosophila melanogaster. Previous studies showed that, in the course of segment determination in Drosophila, information created by gradients of products of maternal coordinate genes is not "read" statically, being interpreted by their zygotic target genes via regulatory interactions. This leads to spatial shifts in the expression of target genes relative to the original positions as well as to dynamic reduction in the zygotic expression variability. However, according to recent data, interpretation of positional information includes the interaction between not only zygotic target genes but also the maternal coordinate genes themselves. Different systems of maternal coordinate genes (maternal systems)­the posterior-anterior, terminal, and dorsoventral­ can interact with each other. This is usually expressed in the regulation of zygotic target genes of one maternal system by other maternal systems. The concept of a "morphogenetic network" was introduced to define the interaction of maternal systems during determination of spatial gene expression in the early Drosophila embryo.

[Numerical Analysis of Particle Trajectories in Living Cells under Uncertainty Conditions].

We have developed a numerical method for the analysis of particle trajectories in living cells, where a type of movement is determined by Akaike's information criterion, while model parameters are identified by a weighted least squares method. The method is realized in computer software, written in the Java programming language, that enables us to automatically conduct the analysis of trajectories. The method is tested on synthetic trajectories with known parameters, and applied to the analysis of replication complexes in cells, infected with hepatitis C virus. Results of the analysis are in agreement with available data on the movement of biological objects along microtubules.

[The dynamics of feed-forward loop depends on regulator type in indirect pathway].

Gene networks contain a recurring motif, called the feed-forward loop, in which a transcription factor regulates target expression directly and indirectly via the second regulator. Here we present the results of mathematical modeling of feed-forward loops with either the transcription factor or miRNA as a repressor in the indirect pathway. We showed that the substitution of the transcription factor with miRNA changes the dynamic behavior of the feed-forward loop and lends new properties critical for biological system functioning.

[Modelling of Drosophila gap gene network under Bcd morphogen variation].

Expression patterns of segmentation genes are formed under the influence of maternal transcription factor gradients, which initiate spatially localized expression in the cascade of segmentation genes. Bcd is one of these activators. We have studied one model of regulation in the gap gene network by varying the concentration of this protein. We have shown that the known gap gene network topology is not sufficient to explain experimental data on the shifts exhibited by the hb anterior expression domain by change in Bcd concentration in the embryo. As the result of modeling with these experimental data taken into account, a new topology is obtained that determines the correct shifts of the hb expression domain. These results suggest that interactions among the three hb, Kr and gt genes are key regulatory factors for the valid behaviour of the hb expression pattern with Bcd concentration changes. This study made it possible to specify the limits of validity for phenomenological models of gene networks.

[Method of Entirely Parallel Differential Evolution for Model Adaptation in Systems Biology].

We developed a method of entirely parallel differential evolution for identification of unknown parameters of mathematical models by minimization of the objective function that describes the discrepancy of the model solution and the experimental data. The method is implemented in the free and open source software available on the Internet. The method demonstrated a good performance comparable to the top three methods from CEC-2014 and was successfully applied to several biological problems.

[A method for solution of the multi-objective inverse problems under uncertainty].

We describe a method to solve multi-objective inverse problems under uncertainty. The method was tested on non-linear models of dynamic series and population dynamics, as well as on the spatiotemporal model of gene expression in terms of non-linear differential equations. We consider how to identify model parameters when experimental data contain additive noise and measurements are performed in discrete time points. We formulate the multi-objective problem of optimization under uncertainty. In addition to a criterion of least squares difference we applied a criterion which is based on the integral of trajectories of the system spatiotemporal dynamics, as well as a heuristic criterion CHAOS based on the decision tree method. The optimization problem is formulated using a fuzzy statement and is constrained by penalty functions based on the normalized membership functions of a fuzzy set of model solutions. This allows us to reconstruct the expression pattern of hairy gene in Drosophila even-skipped mutants that is in good agreement with experimental data. The reproducibility of obtained results is confirmed by solution of inverse problems using different global optimization methods with heuristic strategies.

[Replication of the subgenomic hepatitis C virus replicon in the presence of the NS3 protease inhibitors: a stochastic model].

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 relevant to predict the efficacy of potential drugs against virus or host targets. One of the promising targets for development of new drugs is the viral NS3 protease. Here we developed a stochastic model of the subgenomic HCV replicon replication in Huh-7 cells and in the presence of the NS3 protease inhibitors. Along with consideration of the stochastic nature of the subgenomic HCV replicon replication the model takes into account the existence and generation of main NS3 protease drug resistant mutants, namely BILN-2061 (A156T, D168V, R155Q), VX-950 (A156S, A156T, T54A) and SCH-503034 (A156T, A156S, T54A). The model reproduces well the viral RNA kinetics in the cell from the moment of the subgenomic HCV replicon transfection to steady state, as well as the viral RNA suppression kinetics in the presence of NS3 protease inhibitors BILN-2061, VX-950 and SCH-503034. We showed that the resistant mutants should be taken into account for the correct description of biphasic kinetics of the viral RNA suppression. The mutants selected in the presence of different inhibitor concentrations have maximal replication capacity in the given inhibitor concentration range. Our model can be used to interpret the results of the new anti-HCV drug testing in replicon systems, as well as to predict the efficacy of new potential drugs and optimize the regimen of their use.

[Studies of stability mechanisms of early embryonal development of fruit fly Drosophila].

Living organisms well adapt themselves to changes in the environment and are robust to potential damage such as mutations. The epigenetic mechanism whereby the suppression of phenotypic variation is achieved has been dubbed canalization. This paper summarizes results of research that employed experimental and theoretical approaches to uncover the mechanisms of canalization of variation in expression of segmentation genes.

[Dynamic filtration of the variability of expression patterns of zygotic segmentation genes in Drosophila].

An analysis of the quantitative data obtained by processing the confocal images showed that the early variability of expression patterns of zygotic segmentation genes in Drosophila drastically decreases by the time of the onset of gastrulation. The following components of variability were examined: the scatter of the levels of gene expression in different embryos, the time and sequence of the formation of expression domains, the type of their formation, and the domain positioning. It was found that the positioning error at the level of zygotic genes is dynamically filtered with time.

[Methods for acquisition of quantitative from confocal images of gene expression in situ].

In this review we summarize original methods for the extraction quantitative information from the confocal images of gene expression patterns. These methods include image segmentation, extraction of quantitative numerical data on gene expression, removal of background signal and spatial registration. Finally it is possible to construct a spatiotemporal atlas of gene expression form individual images obtained at each developmental stage. Initially all methods were developed to extract quantitative numerical information form confocal images of segmentation gene expression in Drosophila melanogaster. Application of these methods to Drosophila images makes it possible to reveal new mechanisms of formation of segmentation gene expression domains, as well as to construct the quantitative atlas of segmentation gene expression. Most image processing procedures can be easily adapted to process a wide range of biological images.

Methods for Acquisition of Quantitative Data from Confocal Images of Gene Expression in situ.

In this review, we summarize original methods for the extraction of quantitative information from confocal images of gene-expression patterns. These methods include image segmentation, the extraction of quantitative numerical data on gene expression, and the removal of background signal and spatial registration. Finally, it is possible to construct a spatiotemporal atlas of gene expression from individual images recorded at each developmental stage. Initially all methods were developed to extract quantitative numerical information from confocal images of segmentation gene expression in Drosophila melanogaster. The application of these methods to Drosophila images makes it possible to reveal new mechanisms in the formation of segmentation gene expression domains, as well as to construct a quantitative atlas of segmentation gene expression. Most image processing procedures can be easily adapted to process a wide range of biological images.

[Spatial registration of data on gene expression in situ]. / Prostranstvennaia registratsiia dannykh ob ékspressii genov in situ.

For registering data on the in situ expression of segmentation genes, a method of image registration was developed basing on the spline approximation. The reference points for the registration were the coordinates of extrema in one-dimensional patterns of gene expression. This registration method is characterized by a very high accuracy. A method of creating a generalized pattern of gene expression in single cells is proposed. Such patterns were constructed for nine segmentation genes belonging to the gap and pair-rule classes of genes.

NetWork: an interactive interface to the tools for analysis of genetic network structure and dynamics.

We designed a Java applet called NetWork which enables a user to interactively construct and visualize a genetic network of interest, and to and to evaluate and explore its dynamics in the framework of a Boolean network model. NetWork displays the mechanism of gene interactions at the level of gene expression and enables the visualization of large genetic networks. NetWork can serve as an interactive interface to tools for the analysis of genetic network structure and behavior.

Spatio-temporal registration of the expression patterns of Drosophila segmentation genes.

The application of image registration techniques resulted in the construction of an integrated atlas of Drosophila segmentation gene expression in both space and time. The registration method was based on a quadratic spline approximation with flexible knots. A classifier for automatic attribution of an embryo to one of the temporal classes according to its gene expression pattern was developed.)

Graphical interface to the genetic network database GeNet.

UNLABELLED: We designed a Java applet which enables the visualization of genetic networks and can be used as a Web publishing tool by molecular biologists studying the mechanisms of gene interactions. AVAILABILITY: http://www. csa.ru/Inst/gorb_dep/inbios/ genet/Graph/Genes_Graph.html CONTACT: samson@fn.csa.ru

[Structural and functional chromatin organization of the SUP35 gene in Saccharomyces cerevisiae yeast]. / Strukturno-funktsional'naia organizatsiia khromatina gena SUP35 drozhzhei Saccharomyces cerevisiae.

Structural and functional organization of the 5' region of the SUP35 gene was analyzed in Saccharomyces cerevisiae yeast. Indirect DNA end labeling allowed two nuclease-hypersensitive sites and a region involved in nucleosomes to be revealed. DNase I and micrococcal nuclease hypersensitive sites were localized to almost the same regions: -461 ... -372 bp and -271 ... -91 bp for DNase I and -461 ... -356 bp and -231 ... -79 for micrococcal nuclease. Nucleosomes were localized to a region +22 ... +339 bp. Both the location of DNase I and micrococcal nuclease hypersensitive sites within the promoter region and the location of nucleosomes within the coding region remain the same at different cell culture growth phases. However, positioning nucleosomes were revealed within the SUP35 coding region only at the late logarithmic phase; the radioautographic pattern of them does not depend on the extent of nuclease digestion.

Reversions to respiratory competence of omnipotent sup45 suppressor mutants may be caused by secondary sup45 mutations.

The molecular nature of the sup45 respiratory deficient omnipotent suppressor, and of three reversions to respiratory competence which removed the suppressor effect of the initial mutation, was examined. All reversions were caused by secondary sup45 mutations which indicates a direct connection between sup45 "respiratory" and "translational" functions. Computer analysis showed the local changes of Sup45 protein characteristics in the suppressor strain and revertants in comparison to the wild-type protein. The distribution of mutant sites in relation to evolutionary conserved, and tentatively functional, regions in the Sup45 protein is discussed.

[The Petergof genetic collection of microorganisms]. / Petergofskie geneticheskie kollektsii mikroorganizmov.

The Petergof Genetic Collection (PGC) of microalgae was created in the 1960s during study of the regularities of mutational processes. A collection of yeasts has been maintained at the Department of Genetics and Selection of St. Petersburg State University since 1977. This collection contains some 1000 genetically marked strains of the yeasts Saccharomyces cerevisiae and Pichia methanolica, and the algae collection comprises about 600 strains of Chlamydomonas reinhardtii, Chlorella vulgaris, and Scenedesmus obliquus. The structure of the collection and the employment of strains in basic and applied research, as well as for educational purposes, are discussed. On the basis of the original software GENESTRAIN, a yeast PGC database (DB) was developed. A visual interface that contains information about selection of Ch. reinhardtii strains and crosses made was created in the HyperCard operational system.

Conservative system for dosage-dependent modulation of translational fidelity in eukaryotes.

Variations in dosage of some genes can alter the level of translational fidelity. The Saccharomyces cerevisiae genes that act as dosage-dependent suppressors and/or modulators of suppression, are the following: some tRNA genes (for example, tRNA(Gln)) inducing readthrough by mispairing; genes coding for either translational elongation factor or other proteins taking part in translation; and some genes of unknown function. We suggest that the SUP35 protein is a factor which may play a major role in balance-dependent regulation of translational fidelity. Homologues of this genes have been identified in other yeast genera (Pichia), green algae (Chlamydomonas) and various animals including man. No homologies have been found in the polychaeta (Nereis) or in insects (Drosophila). Rates of evolution differ for two separate parts of the genes; the N-terminal part, which is important for ambiguous translation in Saccharomyces, is markedly variable in the organisms tested. However, the C-terminal part which is required for yeast viability has a common origin but a separate evolution from that of the EF-Tu protein family.