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.

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

Transcription factor erect wing (EWG) is involved in indirect flight muscle patterning, development and maintenance in Drosophila

Muscle development is a multistep process which includes myoblast diversification, proliferation, migration, fusion, differentiation and growth. A hierarchical exhibition of myogenic factors is important for dexterous execution of progressive events in muscle formation. EWG (erect wing) is a transcription factor known to have a role in indirect flight muscle development (IFM) in Drosophila. We marked out the precise spatio-temporal expression profile of EWG in the myoblasts, and in the developing muscles. Mutant adult flies null for EWG in myoblasts show variable number of IFM, suggesting that EWG is required for patterning of the IFM. The remnant muscle found in the EWG null flies show proper assembly of the structural proteins, which implies that some myoblasts manage to fuse, develop and differentiate normally indicating that EWG is not required for differentiation program per se. However, when EWG expression is extended beyond its expression window in a wild type background, muscle thinning is observed implying EWG function in protein synthesis inhibition. Mis-expression studies in wing disc myoblasts hinted at its role in myoblast proliferation. We thus conclude that EWG is important for regulating fusion events which in turn decides the IFM pattern. Also IFM in EWG null mutants show clumps containing broken fibres and an altered mitochondrial morphology. The vertebrate homolog of EWG is nuclear respiratory factor1 (NRF1) which is known to have a function in mitochondrial biogenesis and protection against oxidative stress. Gene expression for inner mitochondrial membrane protein, Opa1-like was found to be absent in these mutants. Also, these flies were more sensitive to oxidative stress, indicating a compromised mitochondrial functioning. Our results therefore demonstrate that EWG functions in maintaining muscles’ structural integrity by ensuing proper mitochondrial activity.

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.

Primary Microcephaly Gene MCPH1 Shows Signatures of Tumor Suppressors and Is Regulated by miR-27a in Oral Squamous Cell Carcinoma

Mutations in the MCPH1 (microcephalin 1) gene, located at chromosome 8p23.1, result in two autosomal recessive disorders: primary microcephaly and premature chromosome condensation syndrome. MCPH1 has also been shown to be downregulated in breast, prostate and ovarian cancers, and mutated in 1/10 breast and 5/41 endometrial tumors, suggesting that it could also function as a tumor suppressor (TS) gene. To test the possibility of MCPH1 as a TS gene, we first performed LOH study in a panel of 81 matched normal oral tissues and oral squamous cell carcinoma (OSCC) samples, and observed that 14/71 (19.72%) informative samples showed LOH, a hallmark of TS genes. Three protein truncating mutations were identified in 1/15 OSCC samples and 2/5 cancer cell lines. MCPH1 was downregulated at both the transcript and protein levels in 21/41 (51.22%) and 19/25 (76%) OSCC samples respectively. A low level of MCPH1 promoter methylation was also observed in 4/40 (10%) tumor samples. We further observed that overexpression of MCPH1 decreased cellular proliferation, anchorage-independent growth in soft agar, cell invasion and tumor size in nude mice, indicating its tumor suppressive function. Using bioinformatic approaches and luciferase assay, we showed that the 3'-UTR of MCPH1 harbors two non-overlapping functional seed regions for miR-27a which negatively regulated its level. The expression level of miR-27a negatively correlated with the MCPH1 protein level in OSCC. Our study indicates for the first time that, in addition to its role in brain development, MCPH1 also functions as a tumor suppressor gene and is regulated by miR-27a.

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 novel Q-learning algorithm with function approximation for constrained Markov decision processes

We present a novel multi-timescale Q-learning algorithm for average cost control in a Markov decision process subject to multiple inequality constraints. We formulate a relaxed version of this problem through the Lagrange multiplier method. Our algorithm is different from Q-learning in that it updates two parameters - a Q-value parameter and a policy parameter. The Q-value parameter is updated on a slower time scale as compared to the policy parameter. Whereas Q-learning with function approximation can diverge in some cases, our algorithm is seen to be convergent as a result of the aforementioned timescale separation. We show the results of experiments on a problem of constrained routing in a multistage queueing network. Our algorithm is seen to exhibit good performance and the various inequality constraints are seen to be satisfied upon convergence of the algorithm.

On the zeta function of a periodic-finite-type shift

Periodic-finite-type shifts (PFT's) are sofic shifts which forbid the appearance of finitely many pre-specified words in a periodic manner. The class of PFT's strictly includes the class of shifts of finite type (SFT's). The zeta function of a PET is a generating function for the number of periodic sequences in the shift. For a general sofic shift, there exists a formula, attributed to Manning and Bowen, which computes the zeta function of the shift from certain auxiliary graphs constructed from a presentation of the shift. In this paper, we derive an interesting alternative formula computable from certain ``word-based graphs'' constructed from the periodically-forbidden word description of the PET. The advantages of our formula over the Manning-Bowen formula are discussed.

Cl-35 NQR frequency and spin lattice relaxation time in 3,4-dichlorophenol as a function of pressure and temperature

The pressure dependences of Cl-35 nuclear quadrupole resonance (NQR) frequency, temperature and pressure variation of spin lattice relaxation time (T-1) were investigated in 3,4-dichlorophenol. T-1 was measured in the temperature range 77-300 K. Furthermore, the NQR frequency and T-1 for these compounds were measured as a function of pressure up to 5 kbar at 300 K. The temperature dependence of the average torsional lifetimes of the molecules and the transition probabilities W-1 and W-2 for the Delta m = +/- 1 and Delta m = +/- 2 transitions were also obtained. A nonlinear variation of NQR frequency with pressure has been observed and the pressure coefficients were observed to be positive. A thermodynamic analysis of the data was carried out to determine the constant volume temperature coefficients of the NQR frequency. An attempt is made to compare the torsional frequencies evaluated from NQR data with those obtained by IR spectra. On selecting the appropriate mode from IR spectra, a good agreement with torsional frequency obtained from NQR data is observed. The previously mentioned approach is a good illustration of the supplementary nature of the data from IR studies, in relation to NQR studies of compounds in solid state.

Synthesis and application of weight function for edge cracked semicircular disk (ECSD)

We analyze the utility of edge cracked semicircular disk (ECSD) for rapid assessment of fracture toughness using compressive loading. Continuing our earlier work on ECSD, a theoretical examination here leads to a novel way for synthesizing weight functions using two distinct form factors. The efficacy of ECSD mode-I weight function synthesized using displacement and form factor methods is demonstrated by comparing with finite element results. Theory of elasticity in conjunction with finite element method is utilized to analyze crack opening potency of ECSD under eccentric compression to explore newer configurations of ECSD for fracture testing.

Case for multiple views of function in design based on a common definition

Functions are important in designing. However, several issues hinder progress with the understanding and usage of functions: lack of a clear and overarching definition of function, lack of overall justifications for the inevitability of the multiple views of function, and scarcity of systematic attempts to relate these views with one another. To help resolve these, the objectives of this research are to propose a common definition of function that underlies the multiple views in literature and to identify and validate the views of function that are logically justified to be present in designing. Function is defined as a change intended by designers between two scenarios: before and after the introduction of the design. A framework is proposed that comprises the above definition of function and an empirically validated model of designing, extended generate, evaluate, modify, and select of state-change, and an action, part, phenomenon, input, organ, and effect model of causality (Known as GEMS of SAPPhIRE), comprising the views of activity, outcome, requirement-solution-information, and system-environment. The framework is used to identify the logically possible views of function in the context of designing and is validated by comparing these with the views of function in the literature. Describing the different views of function using the proposed framework should enable comparisons and determine relationships among the various views, leading to better understanding and usage of functions in designing.

Transverse single spin asymmetry in e plus p(up arrow) -> e plus J/psi plus X and transverse momentum dependent evolution of the Sivers function

We extend our analysis of transverse single spin asymmetry in electroproduction of J/psi to include the effect of the scale evolution of the transverse momentum dependent (TMD) parton distribution functions and gluon Sivers function. We estimate single spin asymmetry for JLab, HERMES, COMPASS, and eRHIC energies using the color evaporation model of charmonium production, using an analytically obtained approximate solution of TMD evolution equations discussed in the literature. We find that there is a reduction in the asymmetry compared with our predictions for the earlier case considered by us, wherein the Q(2) dependence came only from DGLAP evolution of the unpolarized gluon densities and a different parametrization of the TMD Sivers function was used.

Single electron transfer-driven multi-dimensional signal read-out function of TCNQ as an ``off-the-shelf'' detector for cyanide

Herein we report the first applications of TCNQ as a rapid and highly sensitive off-the-shelf cyanide detector. As a proof-of-concept, we have applied a kinetically selective single-electron transfer (SET) from cyanide to deep-lying LUMO orbitals of TCNQ to generate a persistently stable radical anion (TCNQ(center dot-)), under ambient condition. In contrast to the known cyanide sensors that operate with limited signal outputs, TCNQ(center dot-) offers a unique multiple signaling platform. The signal readability is facilitated through multichannel absorption in the UV-vis-NIR region and scattering-based spectroscopic methods like Raman spectroscopy and hyper Rayleigh scattering techniques. Particularly notable is the application of the intense 840 nm NIR absorption band to detect cyanide. This can be useful for avoiding background interference in the UV-vis region predominant in biological samples. We also demonstrate the fabrication of a practical electronic device with TCNQ as a detector. The device generates multiorder enhancement in current with cyanide because of the formation of the conductive TCNQ(center dot-).