Modeling of Gap Gene Expression in <i>Drosophila Kruppel</i> Mutants

The segmentation gene network in Drosophila embryo solves the fundamental problem of embryonic patterning: how to establish a periodic pattern of gene expression, which determines both the positions and the identities of body segments. The gap gene network constitutes the first zygotic regulatory tier in this process. Here we have applied the systems-level approach to investigate the regulatory effect of gap gene Kruppel (Kr) on segmentation gene expression. We acquired a large dataset on the expression of gap genes in Kr null mutants and demonstrated that the expression levels of these genes are significantly reduced in the second half of cycle 14A. To explain this novel biological result we applied the gene circuit method which extracts regulatory information from spatial gene expression data. Previous attempts to use this formalism to correctly and quantitatively reproduce gap gene expression in mutants for a trunk gap gene failed, therefore here we constructed a revised model and showed that it correctly reproduces the expression patterns of gap genes in Kr null mutants. We found that the remarkable alteration of gap gene expression patterns in Kr mutants can be explained by the dynamic decrease of activating effect of Cad on a target gene and exclusion of Kr gene from the complex network of gap gene interactions, that makes it possible for other interactions, in particular, between hb and gt, to come into effect. The successful modeling of the quantitative aspects of gap gene expression in mutant for the trunk gap gene Kr is a significant achievement of this work. This result also clearly indicates that the oversimplified representation of transcriptional regulation in the previous models is one of the reasons for unsuccessful attempts of mutant simulations.</p

Decision-making based on the model of functioning of socio-ecological-economic system

The development of regional socio-economic and ecological systems requires informed decisions. In this, decision-making authorities can be helped by models of such systems, which include three interrelated subsystems: social, environmental and economic, which may include subsystems of a lower level. The object of the study is hierarchical socio-ecological-economic systems (SEES) with homogeneous performance characteristics at all levels of management. The subject of the study is the characteristics of the processes of influence of factors on the results of the functioning of a hierarchical SEES in order to develop control actions that provide a given level of target indicators. The purpose of the study is to model the functioning of socio-ecological and economic systems based on a multi-level optimization approach under conditions of uncertainty, with the help of which it is possible to find changes in factors that allow improving the goal indicators of the SEES functioning. Based on the constructed models of the state and functioning of complex systems for the regions of the Central Federal District and the Tula Region using statistical data for 2007-2020, a multilevel optimization approach to the management of socio-economic systems was applied, proposals aimed at ensuring the sustainable development of the Tula region in the ecological subsystem were substantiated

Mechanisms of gap gene expression canalization in the Drosophila blastoderm

<p>Abstract</p> <p>Background</p> <p>Extensive variation in early gap gene expression in the <it>Drosophila </it>blastoderm is reduced over time because of gap gene cross regulation. This phenomenon is a manifestation of canalization, the ability of an organism to produce a consistent phenotype despite variations in genotype or environment. The canalization of gap gene expression can be understood as arising from the actions of attractors in the gap gene dynamical system.</p> <p>Results</p> <p>In order to better understand the processes of developmental robustness and canalization in the early <it>Drosophila </it>embryo, we investigated the dynamical effects of varying spatial profiles of Bicoid protein concentration on the formation of the expression border of the gap gene <it>hunchback</it>. At several positions on the anterior-posterior axis of the embryo, we analyzed attractors and their basins of attraction in a dynamical model describing expression of four gap genes with the Bicoid concentration profile accounted as a given input in the model equations. This model was tested against a family of Bicoid gradients obtained from individual embryos. These gradients were normalized by two independent methods, which are based on distinct biological hypotheses and provide different magnitudes for Bicoid spatial variability. We showed how the border formation is dictated by the biological initial conditions (the concentration gradient of maternal Hunchback protein) being attracted to specific attracting sets in a local vicinity of the border. Different types of these attracting sets (point attractors or one dimensional attracting manifolds) define several possible mechanisms of border formation. The <it>hunchback </it>border formation is associated with intersection of the spatial gradient of the maternal Hunchback protein and a boundary between the attraction basins of two different point attractors. We demonstrated how the positional variability for <it>hunchback </it>is related to the corresponding variability of the basin boundaries. The observed reduction in variability of the <it>hunchback </it>gene expression can be accounted for by specific geometrical properties of the basin boundaries.</p> <p>Conclusion</p> <p>We clarified the mechanisms of gap gene expression canalization in early <it>Drosophila </it>embryos. These mechanisms were specified in the case of <it>hunchback </it>in well defined terms of the dynamical system theory.</p

Modeling of gap gene expression in Drosophila Kruppel mutants.

The segmentation gene network in Drosophila embryo solves the fundamental problem of embryonic patterning: how to establish a periodic pattern of gene expression, which determines both the positions and the identities of body segments. The gap gene network constitutes the first zygotic regulatory tier in this process. Here we have applied the systems-level approach to investigate the regulatory effect of gap gene Kruppel (Kr) on segmentation gene expression. We acquired a large dataset on the expression of gap genes in Kr null mutants and demonstrated that the expression levels of these genes are significantly reduced in the second half of cycle 14A. To explain this novel biological result we applied the gene circuit method which extracts regulatory information from spatial gene expression data. Previous attempts to use this formalism to correctly and quantitatively reproduce gap gene expression in mutants for a trunk gap gene failed, therefore here we constructed a revised model and showed that it correctly reproduces the expression patterns of gap genes in Kr null mutants. We found that the remarkable alteration of gap gene expression patterns in Kr mutants can be explained by the dynamic decrease of activating effect of Cad on a target gene and exclusion of Kr gene from the complex network of gap gene interactions, that makes it possible for other interactions, in particular, between hb and gt, to come into effect. The successful modeling of the quantitative aspects of gap gene expression in mutant for the trunk gap gene Kr is a significant achievement of this work. This result also clearly indicates that the oversimplified representation of transcriptional regulation in the previous models is one of the reasons for unsuccessful attempts of mutant simulations

3 Application of the Neural Networks BasedonMulti-valuedNeurons to Classification of the Images of Gene Expression Patterns

Abstract. Multi-valued neurons (MVN) are the neural processing elements with complex-valued weights and high functionality. It is possible to implement an arbitrary mapping described by partial-defined multiple-valued function on the single MVN. The MVN-based neural networks are applied to temporal classification of images of gene expression patterns, obtained by confocal scanning microscopy. The classification results confirmed the efficiency of this method for image recognition. It was shown that frequency domain of the representation of images is highly effective for their description.

Decision-making based on the model of functioning of socio-ecological-economic system

The development of regional socio-economic and ecological systems requires informed decisions. In this, decision-making authorities can be helped by models of such systems, which include three interrelated subsystems: social, environmental and economic, which may include subsystems of a lower level. The object of the study is hierarchical socio-ecological-economic systems (SEES) with homogeneous performance characteristics at all levels of management. The subject of the study is the characteristics of the processes of influence of factors on the results of the functioning of a hierarchical SEES in order to develop control actions that provide a given level of target indicators. The purpose of the study is to model the functioning of socio-ecological and economic systems based on a multi-level optimization approach under conditions of uncertainty, with the help of which it is possible to find changes in factors that allow improving the goal indicators of the SEES functioning. Based on the constructed models of the state and functioning of complex systems for the regions of the Central Federal District and the Tula Region using statistical data for 2007-2020, a multilevel optimization approach to the management of socio-economic systems was applied, proposals aimed at ensuring the sustainable development of the Tula region in the ecological subsystem were substantiated

Polymeric composite and lubricants for the wearresistant friction units of railway mechanics

For long functioning of the friction unit it is necessary to create the steady layers between friction surfaces, which can lower considerably the friction force, and thereof also the wear reducing. Within the metal-polymer tribocoupling the friction transfer film shall function as a separating layer. The frame and kinetics of filming of friction carry at metal- binary material friction is studied, that creates the base for mining new high-performance self-lubricating polymer compositions.When the unit with a lubricant functions, a role of the uncoupling layer is being fulfilled by the lubricating film, which shall possess the given properties, that is to contain in its composition the nanoclaster additives, capable to function in a tribocoupling for a long time, constantly reappearing in a film due to the chemical reactions at friction. It is shown that introduction of nanomodified additives on the basis of phosphorus molybdate of metals into widely used lubricant compositions allows to create steady lubricant films between friction surfaces. The possible mechanism of action of inorganic phosphoprous-containing additives of the polymeric nature is discussed

ImageServer, a Tool for On-line Processing and Analysis of Biological Images

We present a novel tool for processing and analysis of images of gene expression patterns stored in a relational database. This tool, known as ImageServer, is portable across different software/hardware platforms and supports both basic and subject domain oriented operations on images. The tool is used to process and analyze images stored in FlyEx database (http://urchin.spbcas.ru/flyex); software and documentation are available for download from http://urchin.spbcas.ru/downloads/IS/IS.htm

Phase Transformation in UHMWPE Reactor Powders Synthesized on Various Catalysts in Mechanical and Thermal Fields

Nowadays, a solvent-free method for production of high performance fibers directly from ultrahigh-molecular-weight polyethylene (UHMWPE) reactor powder is being actively developed. It causes the interest in the morphology of the reactor particles and their behavior in thermal and mechanical fields. Changes in the phase composition in virgin particles of ultra-high molecular-weight polyethylene reactor powders and in particles of powders compressed at room temperature under different pressures were studied in real time using synchrotron radiation with heating in the range of 300–370 K. It was found that the content of the monoclinic phase in reactor powders depends on the type of catalyst used for synthesis and on the applied pressure. It is shown that there are monoclinic phases of different nature: a structurally stabilized monoclinic phase formed during synthesis, and a monoclinic phase resulting from plastic deformation during compaction at room temperature. The behavior of these phases in temperature and mechanical fields is compared