The informational concept of searching for periodicity in symbol sequences

Method of informational decomposition has been developed, allowing one to reveal hidden periodicity in any symbol sequences. The informational decomposition is calculated without conversion of a symbol sequence into the numerical one, which facilitates finding periodicities in a symbol sequence. The method permits introducing an analog of the autocorrelation function of a symbol sequence. The method developed by us has been applied to reveal hidden periodicities in nucleotide and amino acid sequences, as well as in different poetical texts. Hidden periodicity has been detected in various genes, testifying to their quantum structure. The functional and structural role of hidden periodicity is discussed.     

Identification of amino acid latent periodicity within 94 protein families.

Here, we have applied information decomposition, cyclic profile alignment, and noise decomposition techniques to search for latent repeats within protein families of various functions. We have identified 94 protein families with a family-specific periodicity. In each case, the periodic element was found in greater than 70% of family members. Latent periodicity profiles with specific length and signature were obtained in each case. The possible relationship between the periodic elements thus identified and the evolutionary development of the protein families are discussed with specific reference to the possibility that there is a correlation between the periodic elements and protein function.     

Effect of Sodium Ions on Calcium-Loaded Rat Heart Mitochondria and Frog Myocardium

Journal of Evolutionary Biochemistry and Physiology - The effect of calcium load on rat heart mitochondria [RHM(K+)], in which K+ ions in the matrix were partially replaced by Na+ ions [RHM(Na+)],...     

ASAP: automated sequence annotation pipeline for web-based updating of sequence information with a local dynamic database

The automated sequence annotation pipeline (ASAP) is designed to ease routine investigation of new functional annotations on unknown sequences, such as expressed sequence tags (ESTs), through querying of web-accessible resources and maintenance of a local database. The system allows easy use of the output from one search as the input for a new search, as well as the filtering of results. The database is used to store formats and parameters and information for parsing data from web sites. The database permits easy updating of format information should a site modify the format of a query or of a returned web page.     

Forest tick Ixodes ricinus (Ixodidae) in the foci of tick-borne borreliosis of the northwestern part of the Moscow region

Monitoring studies during 1996-2001 have shown a natural foci of tick-borne borreliosis with high abundance of Ixodes ricinus and high infection rate with an agent: 19.5-38.4 tick individuals per 1 km of route, infection rate 18.0 +/- 1.7-22.5 +/- 1.5%. A risk to be infected with the Lyme disease in the ricinus focus of the tick-borne borreliosis during the epizootic season did not vary much during the period of study, 3.5-8.2 in different year, mean 6.0 infected ticks per 1 km of route.     

3,5-Substituted phenyl galactosides as leads in designing effective cholera toxin antagonists; synthesis and crystallographic studies

With the aim of developing high-affinity mono and multivalent antagonists of cholera toxin (CT) and Escherichia coli heat-labile enterotoxin (LT) we are using the galactose portion of the natural receptor ganglioside GM1 as an anchoring fragment in structure-based inhibitor design efforts. In order to establish a better structure-activity relationship for guiding these studies, we designed and prepared a small focused library of twenty 3,5-substituted phenylgalactosides based on two previous leads. The compounds were tested for their ability to block CTB(5) binding to immobilized ganglioside receptor and compared to the two previous leads. The crystal structures of the most promising compounds bound to either CTB(5) or LTB(5) were then determined in order to understand the basis for affinity differences. The most potent new compound yielded a six-fold improvement over our benchmark lead m-nitrophenyl-alpha-d-galactopyranoside (MNPG), and a two-fold improvement in IC(50) over a newer MNPG derivative. These results support the notion that the m-nitrophenyl moiety of MNPG and its derivatives is an important element to retain in future optimization efforts. Additionally, a consensus binding-pocket for the alkylmorpholine or piperazine moiety present in all of the designed antagonists was established as an important area of the GM1 binding site to target in future work.     

The regional cerebral blood flow pattern of the normal human brain and its factor structure

The regional cerebral blood flow (rCBF) pattern of the normal human brain was drawn, and its structure was studied. Relative rCBF estimates for 66 regions of interest (cerebral anatomical-functional areas) were obtained using positron emission tomography in 158 healthy subjects aged 18–49 years. The rCBF rate variation range was 89–121% of the rCBF rate averaged over all regions of interest, taken as 100%. The rCBF rates were the highest (>115%) in the paracentral lobule, precuneus, insular cortex, primary visual cortex, and Broca’s area and the lowest (<95%) in the mediobasal regions of the temporal gyri and caudate nuclei. Analysis of the factor structure of the resultant pattern made it possible to classify cerebral anatomical-functional areas according to a predominant effect of one of the following factors on the interdependence between rCBF rates: (1) cytoarchitectonic characteristics; (2) the functional state of the cortex during quiet wakefulness; or (3) the brain vascular region to which the area belongs. The obtained pattern should be taken into account in both mapping of the functions of a normal brain and clinical diagnosis.     

Oligomerization of EpsE coordinates residues from multiple subunits to facilitate ATPase activity

EpsE is an ATPase that powers transport of cholera toxin and hydrolytic enzymes through the Type II secretion (T2S) apparatus in the gram-negative bacterium, Vibrio cholerae. On the basis of structures of homologous Type II/IV secretion ATPases and our biochemical data, we believe that EpsE is active as an oligomer, likely a hexamer, and the binding, hydrolysis, and release of nucleotide cause EpsE to undergo dynamic structural changes, thus converting chemical energy to mechanical work, ultimately resulting in extracellular secretion. The conformational changes that occur as a consequence of nucleotide binding would realign conserved arginines (Arg(210), Arg(225), Arg(320), Arg(324), Arg(336), and Arg(369)) from adjoining domains and subunits to complete the active site around the bound nucleotide. Our data suggest that these arginines are essential for ATP hydrolysis, although their roles in shaping the active site of EpsE are varied. Specifically, we have shown that replacements of these arginine residues abrogate the T2S process due to a reduction of ATPase activity yet do not have any measurable effect on nucleotide binding or oligomerization of EpsE. We have further demonstrated that point mutations in the EpsE intersubunit interface also reduce ATPase activity without disrupting oligomerization, strengthening the idea that residues from multiple subunits must precisely interact in order for EpsE to be sufficiently active to support T2S. Our findings suggest that the action of EpsE is similar to that of other Type II/IV secretion ATPase family members, and thus these results may be widely applicable to the family as a whole.     

Reason for fluctuation in the demographic structure of the taiga tick population (Ixodidae) in dark conifer-leaf forests of Kemchug Upland

It was found out, that mean ratio of unfed taiga ticks Ixodes persulcatus having a life cycle of 3-5 and 6 years counts respectively (N = 6) 33.6, 52.8, 13.2 and 0.4%. Data on absolute number of I. persulcatus individuals in the process of onthogenesis is given. It is shown, that mortality of different unfed stages increases from larva to imago. In the autumn-winter period, the mean ratio of eliminated individuals counted 16% of larvae, 20% of nymphs, and 38 of imago. The mortality in the spring-summer period caused mainly by the deficit of hosts and counted for these stages 3, 82 and 98% respectively. Engorged ticks successfully undertake unfavorable conditions both in the spring-summer and autumn-winter periods. Their mean mortality in the period from feeding to moulting does not exceed 12%.     

Influence of oxidative processes in mitochondria on contractility of the frog Rana temporaria heart muscle. Effects of cadmium

The inotropic Cd2+ action on frog heart is studied with taking into account its toxic effects upon mitochondria. Cd2+ at concentrations of 1, 10, and 20 microM is established to decrease dosedependently (21.3, 50.3, and 72.0%, respectively) the muscle contraction amplitude; this is explained by its competitive action on the potential-controlled Ca2(+)-channels of the L-type (Ca 1.2). In parallel experiments on isolated rat heart mitochondria (RHM) it was shown that Cd2+ at concentrations of 15 and 25 microM produces swelling of non-energized and energized mitochondria in isotonic (with KNO2 and NH4NO3) and hypoosmotic (with 25 mM CH3COOK) media. Study of oxidative processes in RHM by polarographic method has shown 20 microM Cd2+ to disturb activity of respiratory mitochondrial chain. The rate of endogenous respiration of isolated mitochondria in the medium with Cd2+ in the presence of malate and succinate was approximately 5 times lower than in control. In experimental preparations, addition into the medium of DNP-uncoupler of oxidation and phosphorylation did not cause an increase of the oxygen consumption rate. Thus, the obtained data indicate that a decrease in the cardiac muscle contractility caused by Cd2+ is due not only to its direct blocking action on Ca2(+)-channels, but also is mediated by toxic effect on rat heart mitochondria, which was manifested as an increase in ion permeability of the inner mitochondrial membrane (IMM), acceleration of the energy-dependent K+ transport into the matrix of mitochondria, and inhibition of their respiratory chain.