ISB_KM_gene_en

More and more attention is lately given to the research of gene expression and processes regulating it. In many respects it is connect with the fact that genome have been sequenced fore more and more organisms, i.e. sequence of all genes in it is defined. Moreover intensive development of such experimentally methods as transcriptomics (mRNA arrays) and proteomics allow to describe quantitatively gene expression in several conditions. All these facts permit to researchers approach to the reconstruction and understanding of organizing of gene expression systems and genetic regulation networks. These problem investigation is very important not only for fundamental basis of cell vital functions but also for number of applied task solution, connected with bioengineering, biotechnology and pharmaceutics (for example the estimation of expression level of foreign genes in the bacterial systems).

On section are given examples of kinetic modeling during research of genes expression systems and regulation realized in them. It is important to underline that kinetic modeling has essential advantages in this field in comparison with other methods.
Determination of gene regulation mechanisms on the basis of experimental data

At present time there are several methods of expression level measuring (RNA amount) for various genes simultaneously (microchips etc). As a rule the experiments are carried out in the following way: the set of genes presumably interacting with each other is selected (genetic network), and external conditions are changing by stepping way. In response of that the levels of selected genes are changing (see figure), and reasoning from that it is possible to see which genes interact with each other.

mRNA_en

Our aim is to generalize these researches for network consisted of many genes, having made certain generalized functions describing well-known regulation mechanisms, and to estimate is it possible to define parameters of these functions on the basis of experimental data and make conclusion not only about the fact of genes interaction but also about its concrete mechanism.
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Prediction of gene expression rate in bacterial system

The idea of this project is to develop the method of predictions of stationary genes expression levels in bacterial systems. In the end of the project we are planning to develop software, which is available to give in the exit the value of stationary expression in case of entering primary gene (or mRNA) sequence and necessary metabolites in it. At first sight, based on the name and problem statement difficulty, is seems that our research have fundamental meaning only. However, in is not completely such case, because it is connected with one very important applied problem. The matter concerns foreign proteins expression in bacterial cells. The importance of this problem confirms the fact that at present time there are no alternative to bacterial cells as factories for protein from other organisms production. At that, researches in this field confront often with the fact that difficulties arise during some protein expression, i.e. the process is not going or its rate is no enough. For these problem removal scientists have to carry out additional researches, which irreversible reflects on time. Software presented in this work would help to the researchers to remove such obstacles.
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