The Influence of Polyamines on the Expression of Escherichia Coli Ribosome Hibernation Factor Raia

RaiA is one of the main ribosome hibernation factors in Escherichia coli. Like other ribosome hibernation factors, this protein reversibly inhibits translation under stress conditions. According to published data, being induced by indole, RaiA is involved in bacterial persistence, which is considered to play important role in the recalcitrance of chronic infections to antibiotics. Previously, we showed that the raiA expression on the transcriptional level is stimulated by polyamines, in addition to indole. In this work, we investigated the influence of polyamines on the raiA expression on the translational level. We obtained the predicted secondary structures of raiA mRNA, the analysis of which showed the presence of the bulged-out region in the initiation site with a high probability. This may be a sign of gene involvement in the polyamine modulon. We constructed translational raiA::lacZ reporter fusion. Using this genetic construct, we studied the effects of polyamines on the raiA expression through an addition of putrescine, cadaverine or spermidine at concentrations of 1 mM and 2 mM. According to the results, the raiA expression is primarily stimulated by cadaverine at the stationary phase

DMNP, a Synthetic Analog of Erogorgiaene, Inhibits the ppGpp Synthetase Activity of the Small Alarmone Synthetase RelZ

Suppression of the stringent response is a promising strategy for the treatment of persistent bacterial infections. A novel class of compounds having a mechanism of action based on alarmone synthetase inhibition and suppressing the synthesis of (p)ppGpp alarmones in bacteria may provide a more effective treatment for latent infections and resolve problems associated with bacterial persistence. Conventional antibiotics primarily act on actively growing bacteria, but they are inactive against persister cells with a slowed metabolism. Alarmone synthetase inhibitors have antipersister properties that may enhance conventional antibiotics’ antibacterial action. Two groups of RSH proteins are responsible for the synthesis of alarmones: long RelA/SpoT homologs and small alarmone synthetases. Many species of bacteria possess both types of enzymes. Despite the fact that a number of inhibitors of bifunctional long synthetases/hydrolases have been described to date, their properties with respect to monofunctional small alarmone synthetases have been studied poorly. This study investigated the effect of the alarmone synthetase inhibitor DMNP on the purified RelZ small alarmone synthetase protein from Mycolicibacterium smegmatis

Oscillations of a rapidly rotating annular Bose-Einstein condensate

A time-dependent variational Lagrangian analysis based on the Gross-Pitaevskii energy functional serves to study the dynamics of a metastable giant vortex in a rapidly rotating Bose-Einstein condensate. The resulting oscillation frequencies of the core radius reproduce the trends seen in recent experiments [Engels et al., Phys. Rev. Lett. 90, 170405 (2003)], but the theoretical values are smaller by a factor approximately 0.6-0.8.Comment: 7 pages, revtex

Packing of Compressible Granular Materials

3D Computer simulations and experiments are employed to study random packings of compressible spherical grains under external confining stress. Of particular interest is the rigid ball limit, which we describe as a continuous transition in which the applied stress vanishes as (\phi-\phi_c)^\beta, where \phi is the (solid phase) volume density. This transition coincides with the onset of shear rigidity. The value of \phi_c depends, for example, on whether the grains interact via only normal forces (giving rise to random close packings) or by a combination of normal and friction generated transverse forces (producing random loose packings). In both cases, near the transition, the system's response is controlled by localized force chains. As the stress increases, we characterize the system's evolution in terms of (1) the participation number, (2) the average force distribution, and (3) visualization techniques.Comment: 4 pages, 7 figures, to appear in Phys. Rev. Let

Why Effective Medium Theory Fails in Granular Materials

Experimentally it is known that the bulk modulus, K, and shear modulus, \mu, of a granular assembly of elastic spheres increase with pressure, p, faster than the p^1/3 law predicted by effective medium theory (EMT) based on Hertz-Mindlin contact forces. To understand the origin of these discrepancies, we perform numerical simulations of granular aggregates under compression. We show that EMT can describe the moduli pressure dependence if one includes the increasing number of grain-grain contacts with p. Most important, the affine assumption (which underlies EMT), is found to be valid for K(p) but breakdown seriously for \mu(p). This explains why the experimental and numerical values of \mu(p) are much smaller than the EMT predictions.Comment: 4 pages, 5 figures, http://polymer.bu.edu/~hmaks

Vortices and dynamics in trapped Bose-Einstein condensates

I review the basic physics of ultracold dilute trapped atomic gases, with emphasis on Bose-Einstein condensation and quantized vortices. The hydrodynamic form of the Gross-Pitaevskii equation (a nonlinear Schr{\"o}dinger equation) illuminates the role of the density and the quantum-mechanical phase. One unique feature of these experimental systems is the opportunity to study the dynamics of vortices in real time, in contrast to typical experiments on superfluid $^4$He. I discuss three specific examples (precession of single vortices, motion of vortex dipoles, and Tkachenko oscillations of a vortex array). Other unusual features include the study of quantum turbulence and the behavior for rapid rotation, when the vortices form dense regular arrays. Ultimately, the system is predicted to make a quantum phase transition to various highly correlated many-body states (analogous to bosonic quantum Hall states) that are not superfluid and do not have condensate wave functions. At present, this transition remains elusive. Conceivably, laser-induced synthetic vector potentials can serve to reach this intriguing phase transition.Comment: Accepted for publication in Journal of Low Temperature Physics, conference proceedings: Symposia on Superfluids under Rotation (Lammi, Finland, April 2010

United classification of cosmic gamma-ray bursts and their counterparts

United classification of gamma-ray bursts and their counterparts is established on the basis of measured characteristics: photon energy E and emission duration T. The founded interrelation between the mentioned characteristics of events consists in that, as the energy increases, the duration decreases (and vice versa). The given interrelation reflects the nature of the phenomenon and forms the E-T diagram, which represents a natural classification of all observed events in the energy range from 10E9 to 10E-6 eV and in the corresponding interval of durations from about 10E-2 up to 10E8 s. The proposed classification results in the consequences, which are principal for the theory and practical study of the phenomenon.Comment: Keywords Gamma rays: burst

Force distributions near the jamming and glass transitions

We calculate the distribution of interparticle normal forces $P(F)$ near the glass and jamming transitions in model supercooled liquids and foams, respectively. $P(F)$ develops a peak that appears near the glass or jamming transitions, whose height increases with decreasing temperature, decreasing shear stress and increasing packing density. A similar shape of $P(F)$ was observed in experiments on static granular packings. We propose that the appearance of this peak signals the development of a yield stress. The sensitivity of the peak to temperature, shear stress and density lends credence to the recently proposed generalized jamming phase diagram.Comment: 4 pages, 3 postscript figures;Version 3 replaces figure 1 and removes figure 2 from version 1. Significant rewording of version 1 to emphasize the formation of peak in P(F) when these systems jam along five different routes of the recently proposed jamming phase diagram. Version 2 displayed the incorrect abstrac

Stress Propagation through Frictionless Granular Material

We examine the network of forces to be expected in a static assembly of hard, frictionless spherical beads of random sizes, such as a colloidal glass. Such an assembly is minimally connected: the ratio of constraint equations to contact forces approaches unity for a large assembly. However, the bead positions in a finite subregion of the assembly are underdetermined. Thus to maintain equilibrium, half of the exterior contact forces are determined by the other half. We argue that the transmission of force may be regarded as unidirectional, in contrast to the transmission of force in an elastic material. Specializing to sequentially deposited beads, we show that forces on a given buried bead can be uniquely specified in terms of forces involving more recently added beads. We derive equations for the transmission of stress averaged over scales much larger than a single bead. This derivation requires the Ansatz that statistical fluctuations of the forces are independent of fluctuations of the contact geometry. Under this Ansatz, the $d(d+1)/2$-component stress field can be expressed in terms of a d-component vector field. The procedure may be generalized to non-sequential packings. In two dimensions, the stress propagates according to a wave equation, as postulated in recent work elsewhere. We demonstrate similar wave-like propagation in higher dimensions, assuming that the packing geometry has uniaxial symmetry. In macroscopic granular materials we argue that our approach may be useful even though grains have friction and are not packed sequentially.=17Comment: 15 pages, 4 figures, revised vertion for Phys. Rev.

Geometric origin of mechanical properties of granular materials

Some remarkable generic properties, related to isostaticity and potential energy minimization, of equilibrium configurations of assemblies of rigid, frictionless grains are studied. Isostaticity -the uniqueness of the forces, once the list of contacts is known- is established in a quite general context, and the important distinction between isostatic problems under given external loads and isostatic (rigid) structures is presented. Complete rigidity is only guaranteed, on stability grounds, in the case of spherical cohesionless grains. Otherwise, the network of contacts might deform elastically in response to load increments, even though grains are rigid. This sets an uuper bound on the contact coordination number. The approximation of small displacements (ASD) allows to draw analogies with other model systems studied in statistical mechanics, such as minimum paths on a lattice. It also entails the uniqueness of the equilibrium state (the list of contacts itself is geometrically determined) for cohesionless grains, and thus the absence of plastic dissipation. Plasticity and hysteresis are due to the lack of such uniqueness and may stem, apart from intergranular friction, from small, but finite, rearrangements, in which the system jumps between two distinct potential energy minima, or from bounded tensile contact forces. The response to load increments is discussed. On the basis of past numerical studies, we argue that, if the ASD is valid, the macroscopic displacement field is the solution to an elliptic boundary value problem (akin to the Stokes problem).Comment: RevTex, 40 pages, 26 figures. Close to published paper. Misprints and minor errors correcte