RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach

RegPredict web server is designed to provide comparative genomics tools for reconstruction and analysis of microbial regulons using comparative genomics approach. The server allows the user to rapidly generate reference sets of regulons and regulatory motif profiles in a group of prokaryotic genomes. The new concept of a cluster of co-regulated orthologous operons allows the user to distribute the analysis of large regulons and to perform the comparative analysis of multiple clusters independently. Two major workflows currently implemented in RegPredict are: (i) regulon reconstruction for a known regulatory motif and (ii) ab initio inference of a novel regulon using several scenarios for the generation of starting gene sets. RegPredict provides a comprehensive collection of manually curated positional weight matrices of regulatory motifs. It is based on genomic sequences, ortholog and operon predictions from the MicrobesOnline. An interactive web interface of RegPredict integrates and presents diverse genomic and functional information about the candidate regulon members from several web resources. RegPredict is freely accessible at http://regpredict.lbl.gov

Homogeneous spaces with symmetries

We give a brief survey of main recent results about invariant pseudo-Riemannian metrics and classical affinor structures on homogeneous spaces with symmetries obtained by the participants of the joint BRFFI-RFFI project “Homogeneous spaces with symmetries”

Analysis of 6.4 KEV Moessbauer Spectra Obtained with MIMOS II on MER on Cobbles at Meridiani Planum, Mars and Considerations on Penetration Depths

The miniaturized Moessbauer (MB) spectrometers MIMOS II [1] on board of the two Mars Exploration Rovers Spirit and Opportunity have obtained more than 600 spectra of more than 300 different rock and soil targets [2-7]. Both instruments have simultaneously collected 6.4 keV X-ray and 14.4 keV .-ray spectra in backscattering geometry [1]. With Spirit's MB spectrometer, 6.4 keV and 14.4 keV spectra have been obtained for all targets through sol 461. After this date, only 14.4 keV spectra were collected. With Opportunity's spectrometer, 6.4 keV and 14.4 keV spectra have been collected for all targets to date. The Fe-mineralogy of rock and soil targets at both landing sites reported to date has been exclusively extracted from 14.4 keV spectra [2-5]. The comparison of 6.4 keV and 14.4 keV spectra provides depth selective information about a sample, but interpretation is not always straightforward [8]

Out-of-Equilibrium Admittance of Single Electron Box Under Strong Coulomb Blockade

We study admittance and energy dissipation in an out-of-equlibrium single electron box. The system consists of a small metallic island coupled to a massive reservoir via single tunneling junction. The potential of electrons in the island is controlled by an additional gate electrode. The energy dissipation is caused by an AC gate voltage. The case of a strong Coulomb blockade is considered. We focus on the regime when electron coherence can be neglected but quantum fluctuations of charge are strong due to Coulomb interaction. We obtain the admittance under the specified conditions. It turns out that the energy dissipation rate can be expressed via charge relaxation resistance and renormalized gate capacitance even out of equilibrium. We suggest the admittance as a tool for a measurement of the bosonic distribution corresponding collective excitations in the system

Estimating the Dark Halo Mass from the Relative Thickness of Stellar Disks

We analyze the relationship between the mass of a spherical component and the minimum possible thickness of stable stellar disks. This relationship for real galaxies allows the lower limit on the dark halo mass to be estimated (the thinner the stable stellar disk is, the more massive the dark halo must be). In our analysis, we use both theoretical relations and numerical N-body simulations of the dynamical evolution of thin disks in the presence of spherical components with different density profiles and different masses. We conclude that the theoretical relationship between the thickness of disk galaxies and the mass of their spherical components is a lower envelope for the model data points. We recommend using this theoretical relationship to estimate the lower limit for the dark halo mass in galaxies. The estimate obtained turns out to be weak. Even for the thinnest galaxies, the dark halo mass within four exponential disk scale lengths must be more than one stellar disk mass.Comment: 20 pages including 6 figures. To be published in Astronomy Letters (v. 32, No. 10, pp. 649-660, 2006

The first applications of novel gaseous detectors for UV visualization

We have demonstrated experimentally that recently developed gaseous detectors combined with solid or gaseous photo-cathodes have exceptionally low noise and high quantum efficiency for UV photons while being solar blind. For this reason they can be used for the detection of weak UV sources in daylight conditions. These detectors are extremely robust, can operate in poor gas conditions and are cheap. We present the first results of their applications to hyper-spectroscopy and flame detection in daylight conditions

The Energy Level Shifts, Wave Functions and the Probability Current Distributions for the Bound Scalar and Spinor Particles Moving in a Uniform Magnetic Field

We discuss the equations for the bound one-active electron states based on the analytic solutions of the Schrodinger and Pauli equations for a uniform magnetic field and a single attractive $\delta({\bf r})$-potential. It is vary important that ground electron states in the magnetic field differ essentially from the analogous state of spin-0 particles, whose binding energy was intensively studied more than forty years ago. We show that binding energy equations for spin-1/2 particles can be obtained without using the language of boundary conditions in the $\delta$-potential model developed in pioneering works. We use the obtained equations to calculate the energy level displacements analytically and demonstrate nonlinear dependencies on field intensity. We show that the magnetic field indeed plays a stabilizing role in considered systems in a case of the weak intensity, but the opposite occurs in the case of strong intensity. These properties may be important for real quantum mechanical fermionic systems in two and three dimensions. We also analyze the exact solution of the Pauli equation for an electron moving in the potential field determined by the three-dimensional $\delta$-well in the presence of a strong magnetic field. We obtain asymptotic expressions for this solution for different values of the problem parameters. In addition, we consider electron probability currents and their dependence on the magnetic field. We show that including the spin in the framework of the nonrelativistic approach allows correctly taking the effect of the magnetic field on the electric current into account. The obtained dependencies of the current distribution, which is an experimentally observable quantity, can be manifested directly in scattering processes, for example.Comment: 31 pages, 10 figure

Optimizing a low-temperature preservation technique for Bacillus anthracis strains

The use of pure microbial cultures is associated with the following key challenges: storage, transportation and resuscitation after a long-term preservation. The currently used anthrax vaccines are produced using various strains of Bacillus anthracis. According to the storage passport data, anthrax strains are now stored in 30–40% glycerin solutions, which helps to preserve a sufficient number of viable cells without losses to their pathogenic properties for three years. It is obviously an urgent task to develop a long-term preservation technique for Bacillus anthracis strains. The aim of this study was to optimize a low-temperature preservation method for Bacillus anthracis strains that ensures viability and no losses to biological properties of the pathogen. Two vaccine strains of Bacillus anthracis were selected for the research: i.e. K-STI-79 and 55-VNIIVViM and two cryoprotective media (No. 1 – 15% glycerin solution with 15% glucose solution and No. 2 – 30% neutral glycerin solution in saline solution). At first biological properties of the strains were studied and the number of viable cells was calculated. Later on, the strains were placed into low-temperature preservation facilities, at the temperature of –40 and –70 °C. Six months later, the effect of three thawing cycles on viability and biological properties of the agent was tested: i.e. at room temperature (22 ± 2) °C, in a water bath at a temperature of (37 ± 1) °C and in a household refrigerator at a temperature of (6 ± 2) °C. As demonstrated, the best option is to preserve the cells at –70 °C and thaw them in a water bath at (37 ± 1) °C. Further research will be focused on duration of the low-temperature preservation that will ensure appropriate viability and biological properties of the pathogen