[Native and chiral modified NMDA-receptor NR1-binding core ligands modeling]

Native and chiral modified (with non-enzymatic Asn racemization) NR1-binding core of NMDA-receptor was modelled by means of molecular dynamic ligand modelling. It was concluded that Gly, D-Ser, D-Asn and D-Thr are ligands of NR1-binding core native NMDA-receptor, whereas the chiral modified NR1-binding core is characterized by the aliphatic non-polar amino acids D-Ala, D-Leu, D-Ile and D-Pro as ligands. The latter amino acids can be considered as effective ligands of NMDA-receptor NR1-binding core in age-related pathology.

[PCR detection of periodontal bacteria and Streptococcus mutans in the biological samples from the oral cavity]

The paper describes an optimized technique for DNA isolation from the Streptococcus mutans cultures and from the clinical samples including proteinase K treatment and detergent lysis, followed by sorbent-based enrichment. This technique was employed for isolating DNA from the periodontal bacteria Porphyromonas gingivalis, Actinobacillus actinomycetemcomitans, and Bacteroides forsythus. A multiplex PCR technique was adapted for large-scale studies of clinical samples. An original PCR method was developed for the semiquantitative detection of Str. mutans, showing the sensitivity of 100 genome copies per reaction. Extensive studies of approximately 2,000 individuals have demonstrated that these methods are applicable to the study of the dental and gingival microflora in the biological sample from the oral cavity of persons with dental diseases from various age groups.

[Streptococcus agalactiae sak0192 gene contains direct repeats and spacers that are genetic markers for characterizing the strains]

A new approach to differentiation of the Streptococcus agalactiae strains was suggested. The approach is based on the nucleotide polymorphism of the sak0192 gene containing variable number of 16 bp direct repeats and 44 bp spacer regions in different S. Agalactiae strains. In general, the direct repeats were identical, while the spacers were variable. Overall, the structure of the sak0192 gene of S. Agalactiae was analogous to direct repeat cluster of Mycobacterium tuberculosis and Streptococcus pyogenes. The applicability of the sak0192 gene polymorphism as a novel genetic marker to identification of S. Agalactiae and differentiation of the strains was demonstrated.

[Energy distribution and ionic selectivity of the bacterial potassium channel]

An explanation for the ionic selectivity of the bacterial potassium channel K(CS)A is offered, which is based on a comparison of energy interactions of lithium, sodium, and potassium cations with the atoms of the selective filter of an protein pore. Using quantum-chemical calculations, the presence of a deeper potential hole for potassium ions was discovered, which explains the energy preferableness in their permeability. It has been shown that the traditional methods of force field AMBER, CHARMM, OPLS in reference parametrization and also at their partial reparametrization give incorrect ratings of energy distribution of ions in the channel.

[Quantum chemical model for prediction of the site of hydroxylation of aromatic substances mediated by cytochrome P450]

An approach based on the oxenoid model of monooxygenase action and semiempirical quantum chemical calculations was applied to the prediction of aromatic hydroxylation sites of cytochrome P450 substrates. The results were compared with experimental data on the metabolism in mammals and human from Metabolite database.

[On the methods of calculation of the electrostatic potential in a protein channel]

The profiles of the electrostatic potential along the axis of a gramicidin channel were calculated using two quantum chemistry methods (EHT and CNDO/2) and three methods of force fields (AMBER, CHARMM, and OPLS). The calculations were performed without taking into account the contribution of water. A comparative analysis of the calculated profiles indicated that the electrostatic field of point charges of the CHARMM force field is close to that obtained by the quantum chemistry methods. It was concluded that there is no need to calculate the electric field using laborious quantum-mechanical methods since the less laborious method of the CHARMM force field gives approximately the same results.

[Study of IS-elements aimed at establishing a degree of the relationship of multiple-serotype Streptococcal strains of group B]

The presence and restriction fragment length polymorphism of IS 861 and IS 1548 were analyzed among 113 streptococcal strains of group B. 13 strains were found to possess both IS 861 and IS 1548, 54 strains were found to possess only IS 861, and 46 strains had neither IS 861 nor IS 1548. 9 HindIII and 6 EcoRI restriction patterns, hybridizing correspondingly with IS 861 and IS 1548, were discovered. A certain correlation between IS 1548 and IS 861 hybridizing patterns, on the one hand, and restriction patterns, found by pulse-electrophoresis, on the other hand, was established. It was demonstrated that restriction fragment length polymorphism of IS 1548 and 861 can be used to evaluate the degree of relationship between the strains.

[Methods of molecular epidemiology of infections caused by group B streptococci]

In this review the comparative analysis of advantages and disadvantages of the known methods for the immunological diagnostics of streptococcal infections (serotyping, phage typing), as well as the methods of molecular epidemiology (PCR typing with the use of "disseminated" priming, ribotyping, electrophoresis in the pulsing electric field, etc.), is presented. Essentially new approaches, capable of being used in future for the control of epidemically topical clones of group B streptococci, are discussed.

Data failures in the "Riabina-2" experiment on MIR orbital station

Experimental data about high-energy particle fluxes obtained in 1990-2000 in the Riabina-2 experiment on board MIR orbital station are analyzed in the sense of data failures. There are two types of failure. The first type is represented as sharp positive or negative spikes on the relatively smooth time profiles of the particle fluxes. The second type is randomly distributed data gaps with durations of up to tens minutes. These two kinds of the data failures are formalized in the form of "failure occurrence probability" (FOP). The comparison analysis of the FOP with solar activity, solar wind conditions and geomagnetic activity shows that one half of the observed data failures are owing to noise originating mostly from electronic equipment on board MIR station. The other half of the data failures are closely connected to geomagnetic storms and interplanetary disturbances. The space station surface charge and radio signal distortion in disturbed ionosphere are considered as possible phenomena responsible for the data failures.

[Energy levels and ion wave functions in gramicidin channels]

A model study of the motion of Na+ ions in the cavity of membrane gramicidin channels was performed by the methods of quantum mechanics. An approximation of the distribution of the electrostatic potential along the channel axis, determined by charges on the atoms of the gramicidin A molecule, was obtained. The energy distribution and the wave functions for the stationary states of the ions were determined. The solutions of the Schrödinger equation for two conformers were compared.

[Interaction of local anesthetics with model ion channels]

A theoretical study of intermolecular interactions between local anesthetics of the acetanilide series and model ionic channels was performed. A dimer of gramicidine A and melittin were used as models of ionic channels. The geometry of molecules was determined by the method of molecular mechanics. Statistically significant correlation equations were derived, which relate the indices of local anesthetizing activity to the characteristics of intermolecular interactions in the anesthetic-peptide system. A comparative analysis of intermolecular interactions in anesthetic-gramicidine A and anesthetic-melittin systems was carried out.

Circadian clock regulation of pH in the rabbit retina

Although it is generally accepted that the acid-base ratio of tissue, as represented by the pH, is strictly regulated to maintain normal function, recent studies in the mammalian nervous system have shown that neuronal activity can result in significant shifts in pH. In the mammalian retina, many cellular phenomena, including neuronal activity, are regulated by a circadian clock. We thus investigated whether a clock regulates retinal pH, using pH-sensitive microelectrodes to measure the extracellular pH (pH(o)) of the in vitro rabbit retina in the subjective day and night, that is, under conditions of constant darkness. These measurements demonstrated that a circadian clock regulates the pH(o) of the rabbit retina so that the pH(o) is lower at night than in the day. This day/night difference in retinal pH(o) was observed when the rabbits were maintained on a normal light/dark cycle and after they were maintained on a light/dark cycle that was phase-delayed by 9 hr. Continuous recordings of retinal pH(o) around subjective dusk indicated that the change from daytime to nighttime pH(o) is relatively fast and suggested that the clock that regulates pH(o) is located in the retina. The lowest pH(o) recorded in the retina in both the day and night was in the vicinity of the inner segments of photoreceptor cells, supporting the idea that photoreceptors serve as the primary source of protons. The circadian-induced shift in pH(o) was several times greater than light-induced pH(o) changes. These findings suggest that a circadian clock in the mammalian retina regulates retinal pH.