MS_RHII-RSD, a Dual-Function RNase HII-(p)ppGpp Synthetase from Mycobacterium smegmatis

In the noninfectious soil saprophyte Mycobacterium smegmatis, intracellular levels of the stress alarmones guanosine tetraphosphate and guanosine pentaphosphate, together termed (p)ppGpp, are regulated by the enzyme Rel(Msm). This enzyme consists of a single, bifunctional polypeptide chain that is capable of both synthesizing and hydrolyzing (p)ppGpp. The rel(Msm), knockout strain of M. smegmatis (Delta rel(Msm)) is expected to show a (p)ppGpp null (p)ppGpp(0)] phenotype. Contrary to this expectation, the strain is capable of synthesizing (p)ppGpp in vivo. In this study, we identify and functionally characterize the open reading frame (ORF), MSMEG_5849, that encodes a second functional (p)ppGpp synthetase in M. smegmatis. In addition to (p)ppGpp synthesis, the 567-amino-acid-long protein encoded by this gene is capable of hydrolyzing RNA(.)DNA hybrids and bears similarity to the conventional RNase HII enzymes. We have classified this protein as actRel(Msm) in accordance with the recent nomenclature proposed and have named it MS_RHII-RSD, indicating the two enzymatic activities present RHII, RNase HII domain, originally identified as (d) under bar omain of (u) under bar nknown (f) under bar unction 429 (DUF429), and RSD, RelA_SpoT nucleotidyl transferase domain, the SYNTH domain responsible for (p)ppGpp synthesis activity]. MS_RHII-RSD is expressed and is constitutively active in vivo and behaves like a monofunctional (p)ppGpp synthetase in vitro. The occurrence of the RNase HII and (p)ppGpp synthetase domains together on the same polypeptide chain is suggestive of an in vivo role for this novel protein as a link connecting the essential life processes of DNA replication, repair, and transcription to the highly conserved stress survival pathway, the stringent response.

PocketAnnotate: towards site-based function annotation

A computational pipeline PocketAnnotate for functional annotation of proteins at the level of binding sites has been proposed in this study. The pipeline integrates three in-house algorithms for site-based function annotation: PocketDepth, for prediction of binding sites in protein structures; PocketMatch, for rapid comparison of binding sites and PocketAlign, to obtain detailed alignment between pair of binding sites. A novel scheme has been developed to rapidly generate a database of non-redundant binding sites. For a given input protein structure, putative ligand-binding sites are identified, matched in real time against the database and the query substructure aligned with the promising hits, to obtain a set of possible ligands that the given protein could bind to. The input can be either whole protein structures or merely the substructures corresponding to possible binding sites. Structure-based function annotation at the level of binding sites thus achieved could prove very useful for cases where no obvious functional inference can be obtained based purely on sequence or fold-level analyses. An attempt has also been made to analyse proteins of no known function from Protein Data Bank. PocketAnnotate would be a valuable tool for the scientific community and contribute towards structure-based functional inference. The web server can be freely accessed at http://proline.biochem.iisc.ernet.in/pocketannotate/.

Model Pseudoconvex Domains and Bumping

The Levi geometry at weakly pseudoconvex boundary points of domains in C-n, n >= 3, is sufficiently complicated that there are no universal model domains with which to compare a general domain. Good models may be constructed by bumping outward a pseudoconvex, finite- type Omega subset of C-3 in such a way that: (i) pseudoconvexity is preserved, (ii) the (locally) larger domain has a simpler defining function, and (iii) the lowest possible orders of contact of the bumped domain with partial derivative Omega, at the site of the bumping, are realized. When Omega subset of C-n, n >= 3, it is, in general, hard to meet the last two requirements. Such well-controlled bumping is possible when Omega is h-extendible/semiregular. We examine a family of domains in C-3 that is strictly larger than the family of h-extendible/semiregular domains and construct explicit models for these domains by bumping.

Model independent bounds on the modulus of the pion form factor on the unitarity cut below the omega pi threshold

We calculate upper and lower bounds on the modulus of the pion electromagnetic form factor on the unitarity cut below the omega pi inelastic threshold, using as input the phase in the elastic region known via the Fermi-Watson theorem from the pi pi P-wave phase shift, and a suitably weighted integral of the modulus squared above the inelastic threshold. The normalization at t = 0, the pion charge radius and experimental values at spacelike momenta are used as additional input information. The bounds are model independent, in the sense that they do not rely on specific parametrizations and do not require assumptions on the phase of the form factor above the inelastic threshold. The results provide nontrivial consistency checks on the recent experimental data on the modulus available below the omega pi threshold from e(+)e(-) annihilation and tau-decay experiments. In particular, at low energies the calculated bounds offer a more precise description of the modulus than the experimental data.

Relation between the work function and Young's modulus of RhSi and estimate of Schottky-barrier height at RhSi/Si interface: An ab-initio study

Density-functional calculations are performed to explore the relationship between the work function and Young's modulus of RhSi, and to estimate the p-Schottky-barrier height (SBH) at the Si/RhSi(010) interface. It is shown that the Young's modulus and the workfunction of RhSi satisfy the generic sextic relation, proposed recently for elemental metals. The calculated p-SBH at the Si/RhSi interface is found to differ only by 0.04 eV in opposite limits, viz., no-pinning and strong pinning. We find that the p-SBH is reduced as much as by 0.28 eV due to vacancies at the interface. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.4761994]

Perturbative expansion of the QCD Adler function improved by renormalization-group summation and analytic continuation in the Borel plane

We examine the large-order behavior of a recently proposed renormalization-group-improved expansion of the Adler function in perturbative QCD, which sums in an analytically closed form the leading logarithms accessible from renormalization-group invariance. The expansion is first written as an effective series in powers of the one-loop coupling, and its leading singularities in the Borel plane are shown to be identical to those of the standard ``contour-improved'' expansion. Applying the technique of conformal mappings for the analytic continuation in the Borel plane, we define a class of improved expansions, which implement both the renormalization-group invariance and the knowledge about the large-order behavior of the series. Detailed numerical studies of specific models for the Adler function indicate that the new expansions have remarkable convergence properties up to high orders. Using these expansions for the determination of the strong coupling from the hadronic width of the tau lepton we obtain, with a conservative estimate of the uncertainty due to the nonperturbative corrections, alpha(s)(M-tau(2)) = 0.3189(-0.0151)(+0.0173), which translates to alpha(s)(M-Z(2)) = 0.1184(-0.0018)(+0.0021). DOI: 10.1103/PhysRevD.87.014008

Spectral analysis on SL(2, R)

Let G be the group . For this group we prove a version of Schwartz's theorem on spectral analysis for the group G. We find the sharp range of Lebesgue spaces L (p) (G) for which a smooth function is not mean periodic unless it is a cusp form. Failure of the Schwartz-like theorem is also proved when C (a)(G) is replaced by L (p) (G) with suitable p. We show that the last result is linked with the failure of the Wiener-tauberian theorem for G.

Spectral moment sum rules for the retarded Green's function and self-energy of the inhomogeneous Bose-Hubbard model in equilibrium and nonequilibrium

We derive exact expressions for the zeroth and the first three spectral moment sum rules for the retarded Green's function and for the zeroth and the first spectral moment sum rules for the retarded self-energy of the inhomogeneous Bose-Hubbard model in nonequilibrium, when the local on-site repulsion and the chemical potential are time-dependent, and in the presence of an external time-dependent electromagnetic field. We also evaluate these expressions for the homogeneous case in equilibrium, where all time dependence and external fields vanish. Unlike similar sum rules for the Fermi-Hubbard model, in the Bose-Hubbard model case, the sum rules often depend on expectation values that cannot be determined simply from parameters in the Hamiltonian like the interaction strength and chemical potential but require knowledge of equal-time many-body expectation values from some other source. We show how one can approximately evaluate these expectation values for the Mott-insulating phase in a systematic strong-coupling expansion in powers of the hopping divided by the interaction. We compare the exact moment relations to the calculated moments of spectral functions determined from a variety of different numerical approximations and use them to benchmark their accuracy. DOI: 10.1103/PhysRevA.87.013628

Toll-Like Receptors 7, 8, and 9 Expression and Function in Primary Human Cervical Cancer Langerhans Cells Evidence of Anergy

Objective: Human papillomavirus oncoproteins E6 and E7 down modulate Toll-like receptor (TLR) 9 expression in infected keratinocytes. We explored the status of expression and function of TLR7, TLR8, and TLR9 in primary human Langerhans cells (LCs) isolated from cervical tumors. Methodology: Single-cell suspensions were made from fresh tissues of squamous cell carcinoma (International Federation of Gynecology and Obstetrics stage IB2); myeloid dendritic cells were purified using CD1c magnetic activated cell separation kits. Langerhans cells were further flow sorted into CD1a(+)CD207(+) cells. Acute monocytic leukemia cell line THP-1-derived LCs (moLCs) formed the controls. mRNA from flow-sorted LCs was reverse transcribed to cDNA and TLR7, TLR8, and TLR9 amplified. Monocyte-derived Langerhans cells and cervical tumor LCs were stimulated with TLR7, TLR8, and TLR9 ligands. Culture supernatants were assayed for interleukin (IL) 1 beta, IL-6, IL-10, IL-12p70, interferon (IFN) alpha, interferon gamma, and tumor necrosis factor (TNF) alpha by Luminex multiplex bead array. Human papillomavirus was genotyped. Results: We have for the first time demonstrated that the acute monocytic leukemia cell line THP-1 can be differentiated into LCs in vitro. Although these moLCs. expressed all the 3 TLRs, tumor LCs expressed TLR7 and TLR8, but uniformly lacked TLR9. Also, moLCs secreted IL-6, IL-1 beta, and tumor necrosis factor alpha to TLR8 ligand and interferon alpha in response to TLR9 ligand; in contrast, tumor LCs did not express any cytokine to any of the 3 TLR ligands. Human papillomavirus type 16 was one of the common human papillomavirus types in all cases. Conclusions: Cervical tumor LCs lacked TLR9 expression and were functionally anergic to all the 3: TLR7, TLR8, and TLR9 ligands, which may play a crucial role in immune tolerance. The exact location of block(s) in TLR7 and TLR8 signaling needs to be investigated, which would have important immunotherapeutic implications.

A nested linear codes approach to distributed function computation over subspaces

In this paper, we consider a distributed function computation setting, where there are m distributed but correlated sources X1,...,Xm and a receiver interested in computing an s-dimensional subspace generated by [X1,...,Xm]Γ for some (m × s) matrix Γ of rank s. We construct a scheme based on nested linear codes and characterize the achievable rates obtained using the scheme. The proposed nested-linear-code approach performs at least as well as the Slepian-Wolf scheme in terms of sum-rate performance for all subspaces and source distributions. In addition, for a large class of distributions and subspaces, the scheme improves upon the Slepian-Wolf approach. The nested-linear-code scheme may be viewed as uniting under a common framework, both the Korner-Marton approach of using a common linear encoder as well as the Slepian-Wolf approach of employing different encoders at each source. Along the way, we prove an interesting and fundamental structural result on the nature of subspaces of an m-dimensional vector space V with respect to a normalized measure of entropy. Here, each element in V corresponds to a distinct linear combination of a set {Xi}im=1 of m random variables whose joint probability distribution function is given.

Point Spread Function Engineering for Super-Resolution Single-Photon and Multiphoton Fluorescence Microscopy

Super-resolution imaging techniques are of paramount interest for applications in bioimaging and fluorescence microscopy. Recent advances in bioimaging demand application-tailored point spread functions. Here, we present some approaches for generating application-tailored point spread functions along with fast imaging capabilities. Aperture engineering techniques provide interesting solutions for obtaining desired system point spread functions. Specially designed spatial filters—realized by optical mask—are outlined both in a single-lens and 4Pi configuration. Applications include depth imaging, multifocal imaging, and super-resolution imaging. Such an approach is suitable for fruitful integration with most existing state-of-art imaging microscopy modalities.

Structural and relaxor characteristics of Ca0.18Sr0.226Ba0.594Nb2O6

Polycrystalline Ca0.18Sr0.226Ba0.594Nb2O6 (CSBN18) was synthesized via the solid-state reaction route. X-ray structural studies confirmed it belonged to the tetragonal tungsten bronze family. Rietveld refinement of the X-ray data has been carried out for CSBN18 where the atomic positions and site occupancy factors for A-sites have been determined. The dielectric properties of CSBN18 ceramic were studied as a function of temperature in the 100 Hz - 1 MHz frequency range. The dielectric relaxation followed the Vogel-Fulcher relation wherein E-a = 37.4 meV; T-f = 131.5 degrees C and omega(0) = 4.31 x 10(9) rad s(-1). A high pyroelectric coefficient of similar to 250 mu C m(-2).K was obtained around the transition temperature (similar to 150 degrees C). This is significantly higher than that reported for polycrystalline SrxBa1-xNb2O6 (SBN). However, the piezoelectric coefficient (d(33)) of the title composition was as low as 6 pC N-1.

Clusters of bound particles in the derivative delta-function Bose gas

In this paper we discuss a novel procedure for constructing clusters of bound particles in the case of a quantum integrable derivative delta-function Bose gas in one dimension. It is shown that clusters of bound particles can be constructed for this Bose gas for some special values of the coupling constant, by taking the quasi-momenta associated with the corresponding Bethe state to be equidistant points on a single circle in the complex momentum plane. We also establish a connection between these special values of the coupling constant and some fractions belonging to the Farey sequences in number theory. This connection leads to a classification of the clusters of bound particles associated with the derivative delta-function Bose gas and allows us to study various properties of these clusters like their size and their stability under the variation of the coupling constant. (C) 2013 Elsevier B.V. All rights reserved.

A unified model for the dynamics of driven ribbon with strain and magnetic order parameters

We develop a unified model to explain the dynamics of driven one dimensional ribbon for materials with strain and magnetic order parameters. We show that the model equations in their most general form explain several results on driven magnetostrictive metallic glass ribbons such as the period doubling route to chaos as a function of a dc magnetic field in the presence of a sinusoidal field, the quasiperiodic route to chaos as a function of the sinusoidal field for a fixed dc field, and induced and suppressed chaos in the presence of an additional low amplitude near resonant sinusoidal field. We also investigate the influence of a low amplitude near resonant field on the period doubling route. The model equations also exhibit symmetry restoring crisis with an exponent close to unity. The model can be adopted to explain certain results on magnetoelastic beam and martensitic ribbon under sinusoidal driving conditions. In the latter case, we find interesting dynamics of a periodic one orbit switching between two equivalent wells as a function of an ac magnetic field that eventually makes a direct transition to chaos under resonant driving condition. The model is also applicable to magnetomartensites and materials with two order parameters. (C) 2013 American Institute of Physics. http://dx.doi.org/10.1063/1.4790845]

Majorana fermions in superconducting 1D systems having periodic, quasiperiodic, and disordered potentials

We present a unified study of the effect of periodic, quasiperiodic, and disordered potentials on topological phases that are characterized by Majorana end modes in one-dimensional p-wave superconducting systems. We define a topological invariant derived from the equations of motion for Majorana modes and, as our first application, employ it to characterize the phase diagram for simple periodic structures. Our general result is a relation between the topological invariant and the normal state localization length. This link allows us to leverage the considerable literature on localization physics and obtain the topological phase diagrams and their salient features for quasiperiodic and disordered systems for the entire region of parameter space. DOI: 10.1103/PhysRevLett.110.146404