Measurement of the Pion Form Factor with CMD-3 Detector and Its Implication to the Hadronic Contribution to Muon (g-2).

The cross section of the process e^{+}e^{-}→π^{+}π^{-} has been measured in the center-of-mass energy range from 0.32 to 1.2 GeV with the CMD-3 detector at the electron-positron collider VEPP-2000. The measurement is based on an integrated luminosity of about 88 pb^{-1}, of which 62 pb^{-1} represent a complete dataset collected by CMD-3 at center-of-mass energies below 1 GeV. In the dominant region near the ρ resonance a systematic uncertainty of 0.7% was achieved. The implications of the presented results for the evaluation of the hadronic contribution to the anomalous magnetic moment of the muon are discussed.

[Early predictive biomarkers of posttraumatic epilepsy]. / Rannie prediktivnye biomarkery posttravmaticheskoi epilepsii.

Traumatic brain injury (TBI) affects about 50 million people in the world every year. Posttraumatic epilepsy (PTE) is a significant complication of TBI of any severity. PTE occurs in 20% of patients with TBI. Treatment of patients with PTE is particularly difficult due to obvious tendency towards drug resistance. Currently, there are no validated predictive biomarkers for PTE. Development of a system of validated predictive markers would improve PTE prediction quality and therapeutic approach for these patients. This review is devoted to the current data on the most perspective predictive biomarkers of PTE for clinical practice.

[The impact of natural climatic factors on level of population morbidity in Russia].

The article considers the influence of natural and climatic factors on population health. According to expert judgments, natural and climatic factors are among causes of unwell feeling of significant part of Russians. The purpose of the study is to determine in what limits and in what way the climate affects citizen health. The various natural and climatic factors were analyzed in the context of their differentiation by regions and the level of impact on human organism. It is determined that natural and climatic factors cause the development of chronic diseases in Russia. On the basis of data comparative analysis concerning nature of acquired diseases and migration level it is concluded that chronic diseases of population can contribute into process of "climate migration".

[Prediction of Bacterial and Archaeal Allergenicity with AllPred Program].

Nowadays, allergic disorders have become one of the most important social problems in the world. This can be related to the advent of new allergenic agents in the environment, as well as an increasing density of human contact with known allergens, including various proteins. Thus, the development of computer programs designed for the prediction of allergenic properties of proteins becomes one of the urgent tasks of mo dern bioinformatics. Previously we developed a web accessible Allpred Program (http://www-bionet.sscc.ru/ psd/cgi-bin/programs/Allpred/allpred.cgi) that allows users to assess the allergenicity of proteins by taking into account the characteristics of their spatial structure. In this paper, using AllPred, we predicted the allergenicity of proteins from 462 archaea and bacteria species for which a complete genome was available. The segregation of considered proteins on archaea and bacteria has shown that allergens are predicted more often among archaea than among bacteria. The division of these proteins into groups according to their intracellular localization has revealed that the majority of allergenic proteins were among the secreted proteins. The application of methods for predicting the level of gene expression of microorganisms based on DNA sequence analysis showed a statistically significant relationship between the expression level of the proteins and their allergenicity. This analysis has revealed that potentially allergenic proteins were more common among highly expressed proteins. Sorting microorganisms into the pathogenic and nonpathogenic groups has shown that pathogens can potentially be more allergenic because of a statistically significant greater number of allergens predicted among their proteins.

[Differential alternative splicing in brain regions of rats selected for aggressive behavior].

Profiles of alternative mRNA isoforms have been determined in three brain regions of rats from an aggressive and a tame line selected for 74 generations. Among 2319 genes with alternatively spliced exons, approximately 84% were confirmed by analyzing public databases. Based on Gene Ontology-guided clustering of alternatively spliced genes, it has been found that the sample was enriched in synapse-specific genes (FDR < 10^(-17)). Patterns of gene expression in the brains of animals with genetically determined high or low aggression were more frequently found to differ in the use of alternatively spliced exons than in animals environmentally conditioned for increased or lowered propensity to aggression. For the Adcyap1r1 gene, five alternatively spliced mRNA isoforms have been represented differentially in aggressive animals. A detailed analysis of the gene that encodes glutamate ionotropic receptor NMDA type subunit 1 (Grin1) has confirmed significant differences in the levels of its alternatively spliced isoforms in certain brain regions of tame and aggressive rats. These differences may affect the behavior in rats genetically selected for aggression levels.

[Computer methods of analysis of chromosome contacts in the cell nucleus based on sequencing technology data]. / Komp'iuternye metody analiza khromosomnykh kontaktov v iadre kletki po dannym tekhnologii sekvenirovaniia.

The study spatial chromosome structure and chromosome folding in the interphase cell nucleus is an important challenge of world science. Detection of eukaryotic genome regions that physically interact with each other could be done by modern sequencing technologies. A basic method of chromosome folding by total sequencing of contacting DNA fragments is HI-C. Long-range chromosomal interactions play an important role in gene transcription and regulation. The study of chromosome interactions, 3D (three-dimensional) genome structure and its effect on gene transcription allows revealing fundamental biological processes from a viewpoint of structural regulation and are important for cancer research. The technique of chromatin immunoprecipitation and subsequent sequencing (ChIP-seq) make possible to determine binding sites of transcription factors that regulate expression of eukaryotic genes; genome transcription factors binding maps have been. The ChIA-PET technology allows exploring not only target protein binding sites, but also pairs of such sites on proximally located and interacting with each other chromosomes co-located in three-dimensional space of the cell nucleus. Here we discuss the principles of the construction of genomic maps and matrices of chromosome contacts according to ChIA-PET and Hi-C data that capture the chromosome conformation and overview existing software for 3D genome analysis including in house programs of gene location analysis in topological domains.

[The experience of application of target sequencing in molecular diagnostic of mucoviscidosis.]

The mucoviscidosis is one of frequent monogenic diseases. In Russia, in case of mucoviscidosis carrying out of DNA-diagnostic is optional. However, its application permits shortening time of diagnosing, increasing efficiency of of therapeutic treatment and preventing secondary manifestation of disease in family. The DNA-diagnostic using panels on frequent mutations in gene CFTR is recommended in cases of uncertain clinical picture and under borderline values of specific laboratory indices. In Russia, application of such panels permit detecting up to 90% of pathological alleles in gene CFTR. To detect more rare alleles the Sanger sequencing is traditionally applied. Lately, highly productive sequencing techniques became available to detect rare mutations. The actual article presents evaluation of efficiency of application of test-system based on technology of target sequencing for detecting mutations unidentified at primary DNA-diagnostic. Besides, in two patients with mucoviscidosis the application of highly productive sequencing techniques permitted to identify previously unknown nonsense mutations Q1038X (c.3112C>T) и W1310X (c.3930G>A).

Variants of Porphyromonas gingivalis lipopolysaccharide alter lipidation of autophagic protein, microtubule-associated protein 1 light chain 3, LC3.

Porphyromonas gingivalis often subverts host cell autophagic processes for its own survival. Our previous studies document the association of the cargo sorting protein, melanoregulin (MREG), with its binding partner, the autophagic protein, microtubule-associated protein 1 light chain 3 (LC3) in macrophages incubated with P. gingivalis (strain 33277). Differences in the lipid A moiety of lipopolysaccharide (LPS) affect the virulence of P. gingivalis; penta-acylated LPS1690 is a weak Toll-like receptor 4 agonist compared with Escherichia coli LPS, whereas tetra-acylated LPS1435/1449 acts as an LPS1690 antagonist. To determine how P. gingivalis LPS1690 affects autophagy we assessed LC3-dependent and MREG-dependent processes in green fluorescent protein (GFP)-LC3-expressing Saos-2 cells. LPS1690 stimulated the formation of very large LC3-positive vacuoles and MREG puncta. This LPS1690 -mediated LC3 lipidation decreased in the presence of LPS1435/1449 . When Saos-2 cells were incubated with P. gingivalis the bacteria internalized but did not traffic to GFP-LC3-positive structures. Nevertheless, increases in LC3 lipidation and MREG puncta were observed. Collectively, these results suggest that P. gingivalis internalization is not necessary for LC3 lipidation. Primary human gingival epithelial cells isolated from patients with periodontitis showed both LC3II and MREG puncta whereas cells from disease-free individuals exhibited little co-localization of these two proteins. These results suggest that the prevalence of a particular LPS moiety may modulate the degradative capacity of host cells, so influencing bacterial survival.

[The development of kit for hybridization extraction of DNA and RNA of agents of hemotransmissive infections from serum and blood plasma].

To decrease dependence of effectiveness of isolation of nucleic acids of composition and amount of applied sample a kit was developed for hybridization extraction of DNA HBV RNA HCV and RNA HIV from blood serum in two formats--using up to 250 mkl and up to 1 ml of sample. This kit, in complex with kits for detection using polymerase chain reaction technique in real-time, forms a test characterized by high analytical sensitivity i.e. HBV50 copies per ml, HCV37.5 copies per ml, HIV 13 copies per ml. The developed kit for extraction of target nucleic acids permits to get rid of total DNA and inhibited effect of heparin. It can be adapted for application wit factors B and automated stations of sample preparation.

Patterns of the UP-Down state in normal and epileptic mice.

Goal of this manuscript is to investigate whether changes that exist in epileptic brain generating spontaneous seizures are reflected in the pattern of the UP-Down state (UDS) recorded from the neocortex and dentate gyrus. Experiments were carried out on naive and epileptic mice under urethane anesthesia. Local field potentials were recorded with chronically implanted microelectrodes and single unit activity was recorded with glass microelectrodes. Recorded neurons were labeled by neurobiotin and identified later as granular cells or interneurons in histological sections. The following major features differentiate the pattern of UDS in epilepsy from normal. (1) The duration of UP and Down phases is significantly longer. (2) Recovery of network excitability after termination of the UP phase is longer. (3) UP-spikes occur during the UP phase, which transiently interrupt the development of the normal electrographic pattern of UP phase. Our data provide evidence that UP-spikes result from gigantic EPSPs generated in response to afferent activity. UP-spikes in the neocortex and dentate gyrus occur in close temporal relationship indicating the existence of direct or indirect pathological functional connections between these areas. Changes in the duration of UP and Down phases as well increased time of recovery of excitability of epileptic brain after termination of UP phase suggest alterations in the homeostatic properties of neuronal network in epileptic brain. We suggest that the existence of UP-spikes in epileptic brain may be an additional electrographic pattern indicating epileptogenicity. Unraveling the neuronal substrates of UP-spikes may further improve our understanding of the mechanisms of epilepsy.

[Oligonucleotide derivatives in the nucleic acid hybridization analysis. II. Isothermal signal amplification in process of DNA analysis by minisequencing].

The isothermal amplification of reporter signal via limited probe extension (minisequencing) upon hybridization of nucleic acids has been studied. The intensity of reporter signal has been shown to increase due to enzymatic labeling of multiple probes upon consecutive hybridization with one DNA template both in homophase and heterophase assays using various kinds of detection signal: radioisotope label, fluorescent label, and enzyme-linked assay. The kinetic scheme of the process has been proposed and kinetic parameters for each step have been determined. The signal intensity has been shown to correlate with physicochemical characteristics of both complexes: probe/DNA and product/DNA. The maximum intensity has been observed at minimal difference between the thermodynamic stability of these complexes, provided the reaction temperature has been adjusted near their melting temperature values; rising or lowering the reaction temperature reduces the amount of reporting product. The signal intensity has been shown to decrease significantly upon hybridization with the DNA template containing single-nucleotide mismatches. Limited probe extension assay is useful not only for detection of DNA template but also for its quantitative characterization.

[Interstrain differences in social and time patterns of agonistic behavior in male laboratory mice].

The aim of present study was to reveal the genetic effects on social dominance and patterns of agonistic behaviors in social partners. The study was carried out in adult male mice of three inbred strains BALB/cLac, CBA/Lac and PT using an ethological model of social hierarchy, which is characterised by the minimal size and genetic heterogeneity (two males of different genotypes). We used a neutral territory as the experimental territorial condition for the establishment of social hierarchy. Rank asymmetry in aggressive and defensive behaviors was quickly formed during the first day after the production of the social. Significant interstrain differences in time patterns ofagonistic behavior in dominants and subordinates as well as in the level of social dominance determined as a proportion of dominant animals in the strain were observed. In was shown that, in laboratory mice, the genotype could markedly influence social dominance and the patterns of agonistic behavior in social partners.

[Development of uncompetitive exogenous internal amplification control for real-time PCR based on UFA method].

An uncompetitive exogenous internal amplification control method (EIAC) was developed on the basis of short synthetic DNA segment, whose amplification can be detected in real time by UFA spectroscopy principle. The EIAC was shown to be useful as internal control in diagnostic test systems based on DNA or RNA detection by multiplex real-time PCR. It can be applied to assess the quality of extracted DNA or RNA, and also to detect and study the factors causing PCR inhibition and earlier plateau effect.

Decontamination of polymerase chain reaction reagents using DEAE-cellulose.

Polymerase chain reaction (PCR) is widely used to detect specific DNA sequences for purposes of microbial identification, clinical diagnosis, and basic research. The most pernicious problem plaguing this technique is contamination of PCR reagents with previously amplified material. We propose a useful tool for PCR reagent purification from contaminating nucleic acid using DEAE-cellulose and present the analysis of this technique for both decontamination efficiency and an effect on the reagent activity. We also show the suitability of the proposed approach for decontamination of the Taq polymerase, monoclonal antibodies to Taq polymerase, and Moloney murine leukemia virus (M-MLV) reverse transcriptase.

Determination of DNA polymerase and nuclease activities of DNA-dependent polymerases using fluorescence detection under real-time conditions.

A new method is proposed for estimation of polymerase activities using fluorescence detection during isothermal reaction. The method allows simultaneous determination of DNA-dependent DNA polymerase and 5'-3'-exonuclease activities using amplifiers supplied with an optical module for fluorescence detection under real-time conditions. Different primer-template combinations used as polymerase substrates were compared. Primer elongation (polymerase reaction) is detected by changes in SYBR Green I fluorescence upon binding to dsDNA during reaction; nuclease activities are detected by changes in fluorescence due to cleavage of the probe, containing the reporter fluorophore and fluorescence quencher, and hybridized in advance to the template single-stranded region. It was also shown that the method can be used for determination of relative activities of DNA polymerase preparations, estimation of temperature-time dissociation parameters of polymerase complexes with specific antibodies to its active center, and analysis of effects of inhibitors and activators of different nature on reaction rates of dsDNA polymerization and 5'-3'-exonuclease cleavage by polymerase. The method can be also used for estimation of endonuclease activities of DNA polymerases.

[Maturation of sexual behavior in laboratory male mice: a role of genotype].

Sexual behaviour and testosterone output in response to a receptive female were investigated in male mice of three inbred strains BALB/cLac, CBA/Lac and PT at puberty (45 days of age) and in adulthood (90 days of age). The animals were exposed for 10 min to a receptive female separated by a plastic grill, which would not allow contact between male and female. Male and female behaviour was recorded by measuring the time the male or female spent at the grill and the number of approaches to it (sexual motivation). The grill was then removed and the number of mounts and chemoinvestigatory behavior towards a female (nasal and anogenital sniffing) was recorded for each male. An increase in serum concentration and testicular content of testosterone was used as an endocrine index of the sensitivity to female pheromones. It has been shown the significant genotype and developmental effects on sexual behaviour and the hormonal response to sexual stimuli. The pubertal BALB/cLac males were characterised by the adult pattern of sexual motivation, chemoinvestigatory behaviour and the evident testosterone respond to a female. Males of the strain PT showed the lowest sexual motivation, chemoinvestigatory behavior towards a receptive female and no testosterone responses at both ages. This is a very different situation with the CBA/Lac's who showed the developmental increase in the sexual motivation, sniffing behaviour and the endocrine reflex, and the highest level of sexual behaviour but the moderate testosterone respond to a female at adulthood. The data obtained suggest genotype related asynchrony in maturation of the olfactory system, pituitary-gonadal axis and neural circuits of sexual behavior, and their independent genetic control. So, the set of mice strains investigated represents a useful tool for genetic and endocrine study of sexual behavior and the chemosensory control of testicular steroidogenesis.

[Individual typological peculiarities of system blood flow, physical capacity for work and cardiac activity regulation in patients with different resistance to periodontal diseases].

From position of typological variability of physiological individuality concept-functional constitution types - the principle of organism integrity was substantiated for stomatological pathology. There were isolated typical and specific reactions of cardiac-vessel system in patients with different resistance to periodontal diseases. Each functional type - patients with different levels of usual motion activity - had their own physiological peculiarities of parameters of system blood flow, physical capacity for work and cardiac activity regulation, that determined individual typological organism reaction in cases of maxillo-facial system pathology. The received data gives the objective base for physiological approach to single out the extreme variants of norm for forming risk contingent and groups of resistant people to periodontal diseases.

[The reproductive correlates of social hierarchy in laboratory male mice].

In laboratory male mice the effects of social hierarchy on hormonal and spermatogenic testicular function, accessory organs and testicular weights, sexual behaviour have been investigated using an experimental model of social hierarchy, which is characterised by a minimal size (two male mice) and 5 days period of social interactions. The social rank of the partners was detected by asymmetry in aggressive behaviour. Using the experimental condition, when the both partners have no preferences for exclusive use of area we demonstrated that there were no rank differences in the number of mounts and testicular testosterone content. Nevertheless a rank asymmetry in the male sniffing behaviour towards a receptive female, weights of the testes, seminal vesicles, epididymes and the number of epididymal sperm was kept up in a stable social group. Social dominance was found to affect negatively on testicular testosterone increase in response to introduction of a receptive female and sexual attractiveness of male to a receptive female in both dominant and subordinate males. The results obtained demonstrate the impact of social hierarchy on reproduction in laboratory male mice, particular in respect of spermatogenesis and the testicular testosterone in response to a receptive female.