A Comparative Kinetic and Thermodynamic Perspective of the sigma-Competition Model in Escherichia coli

Transcription is the most fundamental step in gene expression in any living organism. Various environmental cues help in the maturation of core RNA polymerase (RNAP; alpha(2)beta beta'omega) with different sigma-factors, leading to the directed recruitment of RNAP to different promoter DNA sequences. Thus it is essential to determine the sigma-factors that affect the preferential partitioning of core RNAP among various a-actors, and the role of sigma-switching in transcriptional gene regulation. Further, the macromolecular assembly of holo RNAP takes place in an extremely crowded environment within a cell, and thus far the kinetics and thermodynamics of this molecular recognition process have not been well addressed. In this study we used a site-directed bioaffinity immobilization method to evaluate the relative binding affinities of three different Escherichia coli sigma-factors to the same core RNAP with variations in temperature and ionic strength while emulating the crowded cellular milieu. Our data indicate that the interaction of core RNAP-sigma is susceptible to changes in external stimuli such as osmolytic and thermal stress, and the degree of susceptibility varies among different sigma-factors. This allows for a reversible sigma-switching from housekeeping factors to alternate sigma-factors when the organism senses a change in its physiological conditions.

Magneto-Transport Study of Pure and Co Doped ZnO Thin Films

A detailed low temperature magneto-transport study is carried out to understand the transport mechanism in pure and Co doped ZnO thin films grown by pulsed laser deposition (PLD) technique. A negative transverse magneto-resistance (MR) (with a value similar to 4% at 4.5 K) which decreases monotonically with the increase in temperature, is observed for the undoped ZnO film. A competition between positive and negative MR is observed for the Co doped ZnO samples. In this case at higher field values negative MR contribution dominates over the positive MR, which gives rise to a slope change in the MR data. Our data for MR shows excellent agreement with the semi-empirical formula given by Khosla et al., which is originally proposed for the degenerate semiconductors. This formula incorporates the third order perturbation expansion of the s-d exchange scattering of the conduction electrons from the localised spins. We have also obtained the Hall mobility, carrier conc. and mean free path as function of temperature for the pure ZnO film.

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 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.

Water treatment potential in relation to phytoplankton dynamics in tropical sewage-fed urban water bodies

Urban water bodies frequently receive untreated sewage and water levels in such water bodies are maintained by daily inputs of sewage. They function as “variable-zone” anaerobic-aerobic lagoons suffering several macrophyte, biotic and abiotic stresses. We have studied two such lakes in Bangalore (Bellandur-360 ha and Varthur-220 ha) to understand whether such an occurrence could be made beneficial (maintaining water levels as well as treatment). Such hypertrophic water body receives sewage at 180-250mg/L and is discharged at 25-80mg/L COD/BOD in different seasons. In an earlier study we reported macrophyte altering the purification function of the water body. In this paper we studied the impact of phytoplankton dynamics and macrophyte cover on the functions such as organic load removal. Algal community analysis, algal biomass, macrophyte cover, water quality, nutrient status was studied seasonally during 2009-2010. Oxygen deficiency and sometimes anoxia, recorded from surface samples resulted in high quantities of NH4+-N (30-40mg/L) and phosphate (0.5-4mg/L)-characteristics of anoxic hypertrophic urban lakes. The productiveness favoured high phytoplanktonic community characterized by small cells (<10μm; Chlorella sp. - highest numbers). The lake could be clearly demarcated into an initial anaerobic zone (40% area), a facultative zone (20%) and an aerobic zone (40%) based on redox values and GIS/bathymetry. During summer the lake is covered by floating macrophytes converting the lake into an anoxic/anaerobic water pool subduing the water purification function as well as aesthetics. When macrophytes are controlled such sewage fed water bodies can be used for treating urban wastewater while also maintaining water sustainability in these semi-arid ecosystems. This paper reports the community dynamics of phytoplankton, their function and competition with macrophytes.

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.