Structure of d(GT)n repeating sequences with parallel and antiparallel chains]

The ability of oligonucleotides 3'-d(GT)5pO(CH2)5Opd(GT)5-5' (anti[d(GT)]) and 3'-d(GT)5pO(CH2)6Opd(GT)5-3' (par[d(GT)]) to form hairpins and higher associates is studied. Optical methods of thermal denaturation and circular dichroism as well as the fluorescence of ethidium bromide and acridine orange bound to oligonucleotides were used. At room temperatures the formation of hairpin structure with parallel and antiparallel strands is possible. Thermodynamic parameters of par[d(GT)] and anti[d(GT)] are similar and equal to delta H = -15 kcal/mol, delta S = -50 cal/mol. deg. In the temperature range 3-10 degrees C par[d(GT)] and anti[d(GT)] form four-stranded structures with parallel chains, in which layers of four G-residues alternate with unpaired T-residues being bulged out easily. On comparison of occurrence of alternating (GT)n, (GC)n and (G)n sequences in genome it can be stated that (GT)n biological functions could be connected with conformational possibilities of the four-stranded parallel structures with unpaired T-residues.     

Oscillations in Large-Scale Cortical Networks: Map-Based Model

We develop a new computationally efficient approach for the analysis of complex large-scale neurobiological networks. Its key element is the use of a new phenomenological model of a neuron capable of replicating important spike pattern characteristics and designed in the form of a system of difference equations (a map). We developed a set of map-based models that replicate spiking activity of cortical fast spiking, regular spiking and intrinsically bursting neurons. Interconnected with synaptic currents these model neurons demonstrated responses very similar to those found with Hodgkin-Huxley models and in experiments. We illustrate the efficacy of this approach in simulations of one- and two-dimensional cortical network models consisting of regular spiking neurons and fast spiking interneurons to model sleep and activated states of the thalamocortical system. Our study suggests that map-based models can be widely used for large-scale simulations and that such models are especially useful for tasks where the modeling of specific firing patterns of different cell classes is important.     

Iron-blocking the high-affinity Mn-binding site in photosystem II facilitates identification of the type of hydrogen bond participating in proton-coupled electron transport via YZ

Incubation of Mn-depleted PSII membranes [PSII(-Mn)] with Fe(II) is accompanied by the blocking of Y(Z)(*) at the high-affinity Mn-binding site to exogenous electron donors [Semin et al. (2002) Biochemistry 41, 5854-5864] and a shift of the pK(app) of the hydrogen bond partner for Y(Z) (base B) from 7.1 to 6.1 [Semin, B. K., and Seibert, M. (2004) Biochemistry 43, 6772-6782]. Here we calculate activation energies (E(a)) for Y(Z)(*) reduction in PSII(-Mn) and Fe-blocked PSII(-Mn) samples [PSII(-Mn, +Fe)] from temperature dependencies of the rate constants of the fast and slow components of the flash-probe fluorescence decay kinetics. At pH < pK(app) (e.g., 5.5), the decays are fit with one (fast) component in both types of samples, and E(a) is equal to 42.2 +/- 2.9 kJ/mol in PSII(-Mn) and 46.4 +/- 3.3 kJ/mol in PSII(-Mn, +Fe) membranes. At pH > pK(app), the decay kinetics exhibit an additional slow component in PSII(-Mn, +Fe) membranes (E(a) = 36.1 +/- 7.5 kJ/mol), which is much lower than the E(a) of the corresponding component observed for Y(Z)(*) reduction in PSII(-Mn) samples (48.1 +/- 1.7 kJ/mol). We suggest that the above difference results from the formation of a strong low barrier hydrogen bond (LBHB) between Y(Z) and base B in PSII(-Mn, +Fe) samples. To confirm this, Fe-blocking was performed in D(2)O to insert D(+), which has an energetic barrier distinct from H(+), into the LBHB. Measurement of the pH effects on the rates of Y(Z)(*) reduction in PSII(-Mn, +Fe) samples blocked in D(2)O shows a shift of the pK(app) from 6.1 to 7.6, and an increase in the E(a) of the slow component. This approach was also used to measure the stability of the Y(Z)(*) EPR signal at various temperatures in both kinds of membranes. In PSII(-Mn) membranes, the freeze-trapped Y(Z)(*) radical is stable below 190 K, but half of the Y(Z)(*) EPR signal disappears after a 1-min incubation when the sample is warmed to 253 K. In PSII(-Mn, +Fe) samples, the trapped Y(Z)(*) radical is unstable at a much lower temperature (77 K). However, the insertion of D(+) into the hydrogen bond between Y(Z) and base B during the blocking process increases the temperature stability of the Y(Z)(*) EPR signal at 77 K. Again, these results indicate that Fe-blocking involves Y(Z) in the formation of a LBHB, which in turn is consistent with the suggested existence of a LBHB between Y(Z) and base B in intact PSII membranes [Zhang, C., and Styring, S. (2003) Biochemistry 42, 8066-8076].     

The effect of sphyngolipids on the mechanical properties of epidermis and its permeability for water

The effect of water, glycerol, Lipotec(s.a), a hydrophobic sphyngolipid complex, and a liposome water emulsion (prepared from pig brain glycosphyngolipids) on the skin elasticity, evaluated from its resonance frequency, was investigated. It was shown that moistening of skin with water leads to swelling of epidermis cells, which is accompanied by an increase in cellular membrane tension and elasticity growth. This shows up in a statistically authentic (alpha = 0.0025, T-test) growth of skin resonance frequency (on the average by 48.5 +/- 13% in 3 min). Skin moistening by a glycosphyngolipid liposome water emulsion causes a more intensive swelling of epidermis (skin resonance frequency in three minutes increases on the average by 75.8 +/- 22.1%, alpha = 0.0059). No swelling of epidermis was observed if skin was moistened by glycerol or by hydrophobic sphyngolipid complex Lipotec(s.a). It was concluded that pig brain glycosphyngolipid molecules having volumetric negatively charged polar heads are built into lamellar structures of the skin lipid barrier and increase its hydrophilicity and permeability for water.     

22,23-epoxides of sitosterol and related 7-oxygenated delta5-sterols

(22S,23S)-22,23-Epoxysitosterol, (22R,23R)-22,23-epoxysitosterol, (22S,23S)-22,23-epoxy-7-ketositosterol, (22R,23R)-22,23-epoxy-7-ketositosterol, (22S,23S)-22,23-epoxy-7alpha-hydroxysitosterol, (22R,23R)-22,23-epoxy-7alpha-hydroxysitosterol, (22S,23S)-22,23-epoxy-7beta-hydroxysitosterol, and (22R,23R)-22,23-epoxy-7beta-hydroxysitosterol were synthesized. Their 1H and 13C NMR and the mass spectra of their trimethylsilyl derivatives were studied.     

Antiviral action of membranotropic compounds modified by adamantane and norbornene pharmacophores exerted on different HIV-1 strains

The anti-HIV activity of new membranotropic compounds, i.e. of the polycarboxylate matrix and of its derivatives modified by adamantane and norbonene, was studied in respect of HIV-1 strains, whose tropicity to coreceptors CCR5 and CXCR4 was different, as well as in respect of HIV-1 variants resistant to azidothymidine (AZT) in a continuous culture of human lymphoid cells (MT-4) and in mononuclear cells of peripheral blood from healthy donors. Testing of complex compounds in a culture of infected MT-4 human lymphoid cells showed an effective inhibition of viral reproduction of LAV.04 (CXCR4-tropic variant) and of HIV11(EVK) as well as AZT-resistant variants. The studied pharmacophores-modified compounds displayed, in infection of the primary culture of human mononuclear cells of the HIV-1 R5 and X4 strains, a notable antiviral activity with their HIV efficiency significantly exceeding the one of the original matrix.     

Characteristic features of the interaction between Fe(II) cations and the donor side of the manganese-depleted photosystem II

Ferrous iron cations Fe(II) can effectively bind to the donor side of the manganese-depleted photosystem II (PSII(-Mn)) and in this way block electron transfer from diphenylcarbazide (DPC) to the major donor for P680, Y_Z. The present study was focused on the characteristic features of this process. The oxidation and subsequent binding of Fe(II) cations to PSII(-Mn) may proceed in the absence of an artificial electron acceptor, and therefore we investigated the role of O₂ as a putative endogenous acceptor. Oxygen was shown to participate in the blockade of Y_Z by Fe cations, apparently as a structural element of Fe cluster formed at the donor side of PSII(-Mn). The kinetic study of blocking Y_Z by Fe(II) as dependent on light intensity demonstrated that the quantum efficiency of Fe cations binding to the donor side of PSII(-Mn) considerably exceeded that of Mn cations. We also compared the possibilities of extracting the native Mn cluster and reconstructed Fe cations from PSII and an alternative electron transport from DPC to P680⁺ under the conditions of the Y_Z blockade by Fe cations. Neither an alternative donor for P680, Y_D , nor cytochrome b ₅₅₉ participated in the latter process. As a whole, our evidence shows that many features of binding Fe cation to the donor side of PSII(-Mn) are in common with photoassembling the Mn cluster.Translated from Fiziologiya Rastenii, Vol. 52, No. 1, 2005, pp. 12–20.Original Russian Text Copyright © 2005 by Lovyagina, Davletshina, Kultysheva, Timofeev, Ivanov, Semin.     

Egg Size and Formation of the Geographical Range in <Emphasis Type="Italic">Thysanoessa inermis</Emphasis> (Kroyer, 1846) (Crustacea: Euphausiacea) in the Norwegian and Barents Seas

Using materials on the euphausiacean Thysanoessa inermis collected in the Norwegian and Barents seas (from 60°N to 73°N) we studied the variability of size characteristics in the eggs (diameter of embryos and egg capsules and the width of the perivitelline space) and their correlations with water temperature and salinity. The size of embryos showed almost no variability irrespective of the location of the sampling site and the water temperature and salinity; the perivitelline space performs a protective function, and its width showed a tendency to decrease with increasing water temperature and salinity. The similarities in the size of embryos in T. inermis populations thousands of kilometers away from each other might be explained, first, by the relatively small age of the populations (the age of the population from the Barents Sea did not exceed 6000–7000 years) and second, by movement of the crustaceans with currents from the Norwegian Sea to the Barents Sea.     

Isometric contractions of the myocardium: mathematic modeling

A mathematical model describing a single contraction of a cardiac muscle strip under isometric conditions is proposed. The adequacy of the model was checked in experiments on cardiac strips from patients with chronic coronary insufficiency. It was shown that the contraction-relaxation cycle is rather completely characterized by the parameters characterizing the association-dissociation kinetics of actomyosin bridges.     

Protein-free parallel triple-stranded DNA complex formation

A 14 nt DNA sequence 5′-AGAATGTGGCAAAG-3′ from the zinc finger repeat of the human KRAB zinc finger protein gene ZNF91 bearing the intercalator 2-methoxy,6-chloro,9-amino acridine (Acr) attached to the sugar–phosphate backbone in various positions has been shown to form a specific triple helix (triplex) with a 16 bp hairpin (intramolecular) or a two-stranded (intermolecular) duplex having the identical sequence in the same (parallel) orientation. Intramolecular targets with the identical sequence in the antiparallel orientation and a non-specific target sequence were tested as controls. Apparent binding constants for formation of the triplex were determined by quantitating electrophoretic band shifts. Binding of the single-stranded oligonucleotide probe sequence to the target led to an increase in the fluorescence anisotropy of acridine. The parallel orientation of the two identical sequence segments was confirmed by measurement of fluorescence resonance energy transfer between the acridine on the 5′-end of the probe strand as donor and BODIPY-Texas Red on the 3′-amino group of either strand of the target duplex as acceptor. There was full protection from OsO₄-bipyridine modification of thymines in the probe strand of the triplex, in accordance with the presumed triplex formation, which excluded displacement of the homologous duplex strand by the probe–intercalator conjugate. The implications of these results for the existence of protein-independent parallel triplexes are discussed.