Cellular Mechanisms of Aortic Valve Calcification.

Comparative in vitro study examined the osteogenic potential of interstitial cells of aortic valve obtained from the patients with aortic stenosis and from control recipients of orthotopic heart transplantation with intact aortic valve. The osteogenic inductors augmented mineralization of aortic valve interstitial cells (AVIC) in patients with aortic stenosis in comparison with the control level. Native AVIC culture of aortic stenosis patients demonstrated overexpression of osteopontin gene (OPN) and underexpression of osteoprotegerin gene (OPG) in comparison with control levels. In both groups, AVIC differentiation was associated with overexpression of RUNX2 and SPRY1 genes. In AVIC of aortic stenosis patients, expression of BMP2 gene was significantly greater than the control level. The study revealed an enhanced sensitivity of AVIC to osteogenic inductors in aortic stenosis patients, which indicates probable implication of OPN, OPG, and BMP2 genes in pathogenesis of aortic valve calcification.

[Nuclear lamins regulate osteogenic differentiation of mesenchymal stem cells].

Nuclear lamins are the major proteins of nuclear envelope and provide the strength of nuclear membrane as well as the interaction of extra-nuclear structures with components of cell nucleus. Recently, it became clear that lamins not only play a structural role in the cell, but could also regulate cell fate, for example lamins could influence cell differentiation via interaction with components of the Notch signaling pathway. Human mutations in LMNA, encoding lamin A/C lead to diseases commonly referred to as laminopathies. Different mutations cause tissue specific phenotypes that affect predominantly a tissue of mesenchymal origin. The nature of this phenomenon, as well as the mechanisms by which lamins regulate cell differentiation remain poorly understood. The aim of this study was to investigate the effect of different mutations of the LMNA on human mesenchymal stem cell (MSC) osteogenic differentiation, and to explore a possible interaction of lamins and Notch signaling pathway. We modified human MSC with mutant LMNA bearing known mutations with tissue specific phenotype associated with different laminopathies. We have shown that mutations associated with different diseases have different effects on the efficiency of MSC osteogenic differentiation and on the expression of specific osteogenic markers SPP1, IBSP and BGLAP. We have also shown that one of the mechanisms involved in the regulation of MSC differentiation may be an interaction of lamins A/C with components of Notch signaling.

[Regulatory transcription codes in eukaryotic genomes].

Key aspects of gene transcription regulation in multicellular organisms, including the characteristics of their promoters, transcription-factor binding sites, and composition elements are reviewed. The functional role of transcription regulatory proteins (basal factors and regulatory transcription factors), and the mechanisms responsible for regulation of their activity are also discussed. Furthermore, we describe the importance of DNA-encoded nucleosome organization and chromatin modifications in the course of transcription regulation, as well as some mechanisms that regulate the activity of transcription factors associated with genetic networks. The current outlook on regulatory gene expression codes in eukaryotes is presented.

[The analysis of structure of insulin-dependent regulatory contours of mature adipocyte].

Insulin is the important regulator of adipose cell metabolism and activates the branched out network of the signaling pathways supervising glucose transport, glycogen synthesis, lipogenesis stimulation, lipolysis inhibition and adipokine secretion. The purpose of our work is the analysis of structure of regulatory contours providing the response of mammalian adipocytes to insulin. With use of computer technology GeneNet adipocyte regulatory-effector network has been reconstructed. The network generalizes experimental data concerning the main insulin-dependent signaling pathways and their targets in a context insulin-sensitive metabolic processes and transcription events. Analysis of the network revealed positive and negative regulatory contours including MAP kinase-, Cbl/TC10- and P13K-dependent signaling pathways. Regulatory contours functioning with participation of transcription factors SREBP-1c, PPARgamma/RXRalpha, C/EBPalpha, FOXO1 are defined also. The major effectors of regulatory contours are glucose carrier GLUT4, and kinase mTOR.

[Method SiteGA for the recognition of transcription factor binding sites].

A new approach, SiteGA, for the prediction of functional transcription factor binding sites has been developed. The approach is based on the detection of locally positioned dinucleotides by the genetic algorithm and discriminant analysis. The approach has been applied to recognize transcription factor binding sites involved in the regulation of immune responses and cell growth (AP-1, IRF1, ISGF3, NFkappaB, STAT1), obesity and lipid metabolism (HNF4, PPAR, SREBP), and the expression of steroidogenesis genes (SF-1). SiteGA is far superior in accuracy to the traditionally used method of position weight matrices. The approach was implemented in the web tool, SiteGA http://wwwmgs2. bionet.nsc.ru/mgs/programs/sitega.

[Recognition of the potential SF-1 binding sites by SiteGA method, their experimental verification and search for new SF-1 target genes].

The SF-1 (Steroidogenic Factor-1) is a transcription factor known as a key regulator of the steroidogenic gene expression. SF-1 is required for the development and functioning at all levels of the hypothalamic-pituitary-gonadal and adrenal axis. Also it plays an essential role in sex determination. SF-1 is a member of the nuclear receptor superfamily and it activates gene expression by binding to DNA in a monomeric form. Here, we report the results of potential SF-1 binding sites identification by using the SiteGA recognition method. The SiteGA method was implemented using a genetic algorithm (GA) involving a iterative discriminant analyses of local dinucleotide context characteristics. These characteristics were compiled not only over the core binding sites region but over its flanks as well. Developed SiteGA method is characterized by considerably better recognition accuracy when compared to that for the weight matrix method. The experimental tests demonstrated that 83% of the sites recognized by the SiteGA method in the regulatory regions of steroidogenic genes, indeed, interact with the SF-1 factor. We also estimated the density of predicted sites in regulatory region of genes, the members of different functional groups and developed the criterion to search for new SF-1 target genes in genome sequences.

[A generalized chemical-kinetic method for modeling gene networks]. / Obobshchennyi khimiko-kineticheskii metod modelirovaniia gennykh setei.

Development of methods for mathematical simulation of biological systems and building specific simulations is an important trend of bioinformatics development. Here we describe the method of generalized chemokinetic simulation generating flexible and adequate simulations of various biological systems. Adequate simulations of complex nonlinear gene networks--control system of cholesterol by synthesis in the cell and erythrocyte differentiation and maturation--are given as the examples. The simulations were expressed in terms of unit processes--biochemical reactions. Optimal sets of parameters were determined and the systems were numerically simulated under various conditions. The simulations allow us to study possible functional conditions of these gene networks, calculate consequences of mutations, and define optimal strategies for their correction including therapeutic ones. Graphical user interface for these simulations is available at http://wwwmgs.bionet.nsc.ru/systems/MGL/GeneNet/.

[Comparative analysis of methods for recognizing potential transcription factor binding sites]. / Sravnitel'ny analiz metodov raspoznavaniia potentsial'nykh saitov sviazyvaniia transkriptsionnykh faktorov.

A complex approach to recognize transcription factor binding sites (TFBS) has been developed based on four methods: (i) weight matrix, (ii) information content, (iii) multidimensional alignment, and (iv) pairwise alignment with the most similar representative of known sites. It has been shown that no method optimal for all kinds of sites occurs among the considered methods, so in each case, the appropriate way of recognition should be chosen. The approach proposed allows one to minimize the errors of TFBS recognition. The program available through the Internet (http://www.sgi.sscc.ru/mgs/programs/multalig/) has been created to search for the potential TFBS in nucleotide sequences set by the user.

[Regulation of eukaryotic gene transcription: description in the TRRD database]. / Reguliatsiia transkriptsii genov éukariot: opisanie v baze dannykh TRDD.

The structure of the Transcription Regulatory Regions Database (TRRD) and the principles of considering transcription regulation of eukaryotic genes in TRRD are concerned. Formal description of the structural and functional organization of the regulatory gene regions is illustrated with examples. By now, TRRD is based on 3500 original works and contains data on transcription regulation of more than 1100 genes known to possess more than 5000 transcription factor-binding sites and about 1600 regulatory elements (promoters, enhancers, silencers). TRRD is available at http://www.bionet.nsc.ru/trrd/.

[Induction of apoptosis in murine myeloma cells NS0/1, transfected with the gene for the basic heat shock protein HSP70i]. / Induktsiia apoptoza v kletkakh myshinoi mielomy NS0/1, transfitsirovannoi genom osnovnogo belka teplovogo shoka BTSh70i.

Murine myelomas are rare cell variants deficient in inducible isoform of Hsp70 that protects cells from injury. In these cells Hsp70 is absent and is not induced under stress conditions. In this study myeloma cells NS0/1 were transfected with hsp70, and their susceptibility to apoptosis was challenged by serum deprivation or hydrogen peroxide. Expression of Hsp70 in NS0/1 cells made them more resistant to apoptosis in serum-free medium but did not affect their response to hydrogen peroxide. Hsp70 involvement in the protection of myeloma cells from apoptosis caused by different agents is discussed.

[GeneExpress: an integrator for databases and computer systems accessible by the Internet and intended for studying eukaryotic gene expression]. / Gene Express: integrator baz dannykh i komp'iuternykh sistem, dostupnykh po seti internet i prednaznachennykh dlia izucheniia ékspresii genov éukariot.

We have developed GeneExpress that is the WWW-oriented integrator for the databases and systems supporting the investigation of gene expression. The total number of the Web-based resources integrated is 30. The database GeneNet on molecular events forming gene networks was assigned its integrative core. To navigate all these WWW-available resources, the SRS, HTML, and Java viewers were developed, http:@wwwmgs.bionet.nsc.ru/systems/GeneExpress/.

The possible involvement of glucocorticoids in the development of genetically determined autoimmune pathology in NZB mice.

The total blood corticosterone concentration, the reactivity of the adrenal glands to exogenous adrenocorticotrophic hormone, and the binding capacity of corticosteroid-binding globulin (CBG), were determined in male NZB mice that spontaneously develop an autoimmune disease. The appearance of antibodies to endogenous erythrocytes was also monitored. This study was performed on animals of the following age groups: (1) 2-3-month-old animals prior to the appearance of autoantibodies; (2) 6-7-month-old animals in the period when the disease developed; and (3) 10-12-month-old animals, i.e. the period when the autoimmune disease developed. It was demonstrated that in the 10-12-month-old mice there was a sharp decrease in the total corticosterone level in the plasma (from 152 +/- 32 to about 20 micrograms l-1), and the reactivity of the adrenal glands to exogenous corticotrophin decreased (from 400% to 120%). However, the binding capacity of CBG increased with age which led to a decrease in the pool of active corticosterone in the blood. The increase in this capacity was especially pronounced in affected 10-12-month-old animals. (The number of binding sites increased from 0.64 +/- 0.05 to 0.8 +/- 0.03 microM and the values of the association constant for the binding of corticosterone to CBG increased from 0.29 +/- 0.05 to 0.91 +/- 0.07 microM-1). The combination of the above-mentioned changes suggests that there is a direct correlation between the decrease in the glucocorticoid background in the NZB mice and in the appearance of autoantibodies.(ABSTRACT TRUNCATED AT 250 WORDS)

[The effect of thymosin (fraction 5) and taktivin on adrenocortical function in mice]. / Vliianie timozina (fraktsiia 5) i taktivina na funktsiiu kory nadpochechnikov u myshei.

A study was made of the effect of the thymic factors thymosin (fraction 5) and tactivin on adrenocortical function of BALB/C mature mice. A single administration of thymosin at a dose of 1 micrograms/mouse causes a rise of the blood level of corticosterone in 3 h. Dexamethasone, a blocker of ACTH secretion, stops the thymosin effect. Thymosin does not influence adrenocortical production of corticosterone in vitro. A marked tendency to a decrease in the blood level of corticosterone is clearly observed 3 h after tactivin administration at doses of 0.1, 0.5 and 2.5 micrograms/mouse. Tactivin added to the adrenal glands in vitro causes dose-dependent suppression of corticosterone specific production. A conclusion is that both factors act in opposite directions on adrenal functioning, and their influence on the glands is mediated differently.