Chimeras of Escherichia coli and Mycobacterium tuberculosis Single-Stranded DNA Binding Proteins: Characterization and Function in Escherichia coli

Single stranded DNA binding proteins (SSBs) are vital for the survival of organisms. Studies on SSBs from the prototype, Escherichia coli (EcoSSB) and, an important human pathogen, Mycobacterium tuberculosis (MtuSSB) had shown that despite significant variations in their quaternary structures, the DNA binding and oligomerization properties of the two are similar. Here, we used the X-ray crystal structure data of the two SSBs to design a series of chimeric proteins (m beta 1, m beta 1'beta 2, m beta 1-beta 5, m beta 1-beta 6 and m beta 4-beta 5) by transplanting beta 1, beta 1'beta 2, beta 1-beta 5, beta 1-beta 6 and beta 4-beta 5 regions, respectively of the N-terminal (DNA binding) domain of MtuSSB for the corresponding sequences in EcoSSB. In addition, m beta 1'beta 2(ESWR) SSB was generated by mutating the MtuSSB specific `PRIY' sequence in the beta 2 strand of m beta 1'beta 2 SSB to EcoSSB specific `ESWR' sequence. Biochemical characterization revealed that except for m beta 1 SSB, all chimeras and a control construct lacking the C-terminal domain (Delta C SSB) bound DNA in modes corresponding to limited and unlimited modes of binding. However, the DNA on MtuSSB may follow a different path than the EcoSSB. Structural probing by protease digestion revealed that unlike other SSBs used, m beta 1 SSB was also hypersensitive to chymotrypsin treatment. Further, to check for their biological activities, we developed a sensitive assay, and observed that m beta 1-beta 6, MtuSSB, m beta 1'beta 2 and m beta 1-beta 5 SSBs complemented E. coli Delta ssb in a dose dependent manner. Complementation by the m beta 1-beta 5 SSB was poor. In contrast, m beta 1'beta 2(ESWR) SSB complemented E. coli as well as EcoSSB. The inefficiently functioning SSBs resulted in an elongated cell/filamentation phenotype of E. coli. Taken together, our observations suggest that specific interactions within the DNA binding domain of the homotetrameric SSBs are crucial for their biological function.

Polycrystal versus single-crystal strain rate sensitivity of cadmium

Taking polycrystalline cadmium as an example and by utilizing the predicted temperature or strain rate-dependence of the (Hall-Petch) stress-grain size parameters, a reasonably quantitative explanation is given for the grain size dependence of apparent activation volume measurements. The explanation involves the theoretical relation of these measurements to single-crystal measurements.

Softening and dynamic recrystallization in magnesium single crystals during c-axis compression

Commercial purity (99.8%) magnesium single crystals were subjected to plane strain compression (PSC) along the c-axis at 200 and 370 degrees C and a constant strain rate of 10(-3) s(-1). Extension was confined to the < 1 1 (2) over bar 0 > direction and the specimens were strained up to a logarithmic true strain of -1. The initial rapid increase in flow stress was followed by significant work softening at different stresses and comparable strains of about -0.05 related to macroscopic twinning events. The microstructure of the specimen after PSC at 200 degrees C was characterized by a high density of {1 0 (1) over bar 1} and {1 0 (1) over bar 3} compression twins, some of which were recrystallized. After PSC at 370 degrees C, completely recrystallized twin bands were the major feature of the observed microstructure. All new grains in these bands retained the same c-axis orientation of their compression twin hosts. The basal plane in these grains was randomly rotated around the c-axis, forming a fiber texture component. The obtained results are discussed with respect to the mechanism of recrystallization, the specific character of the boundaries between new grains and the initial matrix, and the importance of the dynamically recrystallized bands for strain accommodation in these deformed magnesium single crystals. (C) 2011 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Oneand twodimensional single quantumand multiplequantumNMR methodologies: tools for chiral analyses

It is well known that enantiomers cannot be distinguished by NMR spectroscopy unless diastereomorphic interactions are imposed. Several chiral aligning media have therefore been reported for their visualization, although extensive studies are carried out using the liquid crystal made of polypeptide poly-γ-benzyl-L-glutamate (PBLG) in organic solvent. In PBLG medium the spin systems are weakly coupled and the first order analyses of the spectra are generally possible. But due to large number of pair wise interactions of nuclear spins resulting in many degenerate transitions the 1H NMR spectra are not only complex but also broad and featureless, in addition to an indistinguishable overlap of the spectra of enantiomers. This enormous loss of resolution severely hinders the analyses of proton spectra, even for spin systems with 5–6 interacting protons, thereby restricting itsroutine application. In this review we discuss our recently developed several one and multidimensional NMR experiments to circumvent these difficulties taking specific examples of the molecules containing a single chiral centre.

3D Acoustic Analysis Of Spherical Chamber Having Single Inlet And Multiple Outlet: An Impedance Matrix Approach

The transmission loss (TL) performance of spherical chambers having single inlet and multiple outlet is obtained analytically through modal expansion of acoustic field inside the spherical cavity in terms of the spherical Bessel functions and Legendre polynomials. The uniform piston driven model based upon the impedance [Z] matrix is used to characterize the multi-port spherical chamber. It is shown analytically that the [Z] parameters are independent of the azimuthal angle (phi) due to the axisymmetric shape of the sphere; rather, they depend only upon the polar angle (theta) and radius of the chamber R(0). Thus, the effects of relative polar angular location of the ports and number of outlet ports are investigated. The analytical results are shown to be in good agreement with the 3D FEA results, thereby validating the procedure suggested in this work.

Self assembly of bivalent glycolipids on single walled carbon nanotubes and their specific molecular recognition properties

Solubilization of single walled carbon nanotubes (SWNTs) in aqueous milieu by self assembly of bivalent glycolipids is described. Thorough analysis of the resulting composites involving Vis/near-IR spectroscopy, surface plasmon resonance, confocal Raman and atomic force microscopy reveals that glycolipid-coated SWNTs possess specific molecular recognition properties towards lectins.

Thermal decomposition of haloethanols: single pulse shock tube and ab initio studies

This paper reports single pulse shock tube and ab initio studies on thermal decomposition of 2-fluoro and 2-chloroethanol at T=1000–1200 K. Both molecules have HX (X = F/Cl) and H2O molecular elimination channels. The CH3CHO formed by HX elimination is chemically active and undergoes secondary decomposition resulting in the formation of CH4, C2H6, and C2H4. A detailed kinetic simulation indicates that the formation of C2H4 could not be quantitatively explained as arising exclusively from secondary CH3CHO decomposition. Contributions from primary radical processes need to be considered to explain C2H4 quantitatively. Ab initio calculations on HX and H2O elimination reactions from the haloethanols at HF, MP2, and DFT levels with various basis sets up to 6/311++G**are reported. It is pointed out that due to strong correlations between A and Eα, comparison of these two parameters between experimental and theoretical results could be misleading.

Selective synthesis of metallic and semiconducting single-walled carbon nanotubes

As-prepared single-walled carbon nanotubes (SWNTs) are generally mixtures of semiconducting and metallic species, the proportion of the former being around 67%. Since most applications of SWNTs are best served by semiconducting or metallic nanotubes, rather than by mixtures of the two, methods which would directly yield semiconducting and metallic SWNTs in pure form are desirable. In this article, we present the available methods for the direct synthesis of such SWNTs along with the methods available to separate semiconducting and metallic SWNTs from mixtures. We also discuss the synthesis of Y-junction carbon nanotubes.

Unusual dependence of raman mode frequency on excitation wavelength in graphite and single walled carbon nanotubes

In this paper we report resonance Raman scattering from graphite covering excitation energies in the range 2.4 eV to 6 eV. The Raman excitation profile shows a maximum at 4.94 eV (lambda = 251nm) for the G - band (1582 cm(-1)). The D-band at similar to 1350 cm(-1), attributed to disorder activated Raman scattering, does not show up in Raman spectra recorded with excitation wavelengths smaller than 257.3 nm, revealing that the resonance enhancements of the G and D-modes are widely different. Earlier Raman measurements in carbon materials have also revealed a very large and unusual dependence of the D - mode frequency on excitation laser wavelength. This phenomenon is also observed in carbon nanotubes. In this paper we show for the first time that the above unusual dependence arises from the disorder - induced double resonance mechanism.

Non-resonant rf absorption evidence for reentrant melting of vortex lattice in Bi2Sr2CaCu2O8 single crystals

We have studied the magnetic field dependent rf (20 MHz) losses in Bi2Sr2CaCu2O8 single crystals in the low field and high temperature regime. Above HCl the dissipation begins to decrease as the field is increased and exhibits a minimum at HM>HCl. For H>HM the loss increases monotonically. We attribute the decrease in loss above HCl to the stiffening of the vortex lines due to the attractive electromagnetic interaction between the 2D vortices (that comprise the vortex line at low fields) in adjacent CuO bilayers. The minimum at HM implies that the vortex lines are stiffest and hence represents a transition into vortex solid state from the narrow vortex liquid in the vicinity of HCl. The increase in loss for H>HM marks the melting of the vortex lattice and hence a second transition into vortex liquid regime. We discuss our results in the light of recent theory of reentrant melting of the vortex lattice by G. Blatter et al. (Phys. Rev. B 54, 72 (1996)).

A Revisit to Capture the Entire Behavior of Ultrasonic Wave Dispersion Characteristics of Single Walled Carbon Nanotubes Based on Nonlocal Elasticity Theory and Flugge Shell Model

In this paper, an ultrasonic wave propagation analysis in single-walled carbon nanotube (SWCNT) is re-studied using nonlocal elasticity theory, to capture the whole behaviour. The SWCNT is modeled using Flugge's shell theory, with the wall having axial, circumferential and radial degrees of freedom and also including small scale effects. Nonlocal governing equations for this system are derived and wave propagation analysis is also carried out. The revisited nonlocal elasticity calculation shows that the wavenumber tends to infinite at certain frequencies and the corresponding wave velocity tends to zero at those frequencies indicating localization and stationary behavior. This frequency is termed as escape frequency. This behavior is observed only for axial and radial waves in SWCNT. It has been shown that the circumferential waves will propagate dispersively at higher frequencies in nonlocality. The magnitudes of wave velocities of circumferential waves are smaller in nonlocal elasticity as compared to local elasticity. We also show that the explicit expressions of cut-off frequency depend on the nonlocal scaling parameter and the axial wavenumber. The effect of axial wavenumber on the ultrasonic wave behavior in SWCNTs is also discussed. The present results are compared with the corresponding results (for first mode) obtained from ab initio and 3-D elastodynamic continuum models. The acoustic phonon dispersion relation predicted by the present model is in good agreement with that obtained from literature. The results are new and can provide useful guidance for the study and design of the next generation of nanodevices that make use of the wave propagation properties of single-walled carbon nanotubes.

Unzipping and binding of small interfering RNA with single walled carbon nanotube: A platform for small interfering RNA delivery

In an effort to design efficient platform for siRNA delivery, we combine all atom classical and quantum simulations to study the binding of small interfering RNA (siRNA) by pristine single wall carbon nanotube (SWCNT). Our results show that siRNA strongly binds to SWCNT surface via unzipping its base-pairs and the propensity of unzipping increases with the increase in the diameter of the SWCNTs. The unzipping and subsequent wrapping events are initiated and driven by van der Waals interactions between the aromatic rings of siRNA nucleobases and the SWCNT surface. However, molecular dynamics (MD) simulations of double strand DNA (dsDNA) of the same sequence show that the dsDNA undergoes much less unzipping and wrapping on the SWCNT in the simulation time scale of 70 ns. This interesting difference is due to smaller interaction energy of thymidine of dsDNA with the SWCNT compared to that of uridine of siRNA, as calculated by dispersion corrected density functional theory (DFT) methods. After the optimal binding of siRNA to SWCNT, the complex is very stable which serves as one of the major mechanisms of siRNA delivery for biomedical applications. Since siRNA has to undergo unwinding process with the effect of RNA-induced silencing complex, our proposed delivery mechanism by SWCNT possesses potential advantages in achieving RNA interference. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.3682780]

New Insights into Optimal Discrete Rate Adaptation for Average Power Constrained Single and Multi-Node Systems

The throughput-optimal discrete-rate adaptation policy, when nodes are subject to constraints on the average power and bit error rate, is governed by a power control parameter, for which a closed-form characterization has remained an open problem. The parameter is essential in determining the rate adaptation thresholds and the transmit rate and power at any time, and ensuring adherence to the power constraint. We derive novel insightful bounds and approximations that characterize the power control parameter and the throughput in closed-form. The results are comprehensive as they apply to the general class of Nakagami-m (m >= 1) fading channels, which includes Rayleigh fading, uncoded and coded modulation, and single and multi-node systems with selection. The results are appealing as they are provably tight in the asymptotic large average power regime, and are designed and verified to be accurate even for smaller average powers.

Molecular charge-transfer interaction with single-layer graphene

While the effect of electrochemical doping on single-layer graphene (SG) with holes and electrons has been investigated, the effect of charge-transfer doping on SG has not been examined hitherto. Effects of varying the concentration of electron donor and acceptor molecules such as tetrathiafulvalene (TTF) and tetracyanoethylene (TCNE) on SG produced by mechanical exfoliation as well as by the reduction of single-layer graphene oxide have been investigated. TTF softens the G-band in the Raman spectrum, whereas TCNE stiffens the G-band. The full-width-at-half-maximum of the G-band increases on interaction with both TTF and TCNE. These effects are similar to those found with few-layer graphene, but in contrast to those found with electrochemical doping. A common feature between the two types of doping is found in the case of the 2-D band, which shows softening and stiffening on electron and hole doping, respectively. The experimental results are explained on the basis of the frequency shifts, electron-phonon coupling and structural inhomogeneities that are relevant to molecule-graphene interaction.

Construction of Equivalent Circuit of a Single and Isolated Transformer Winding From FRA Data Using the ABC Algorithm

This paper reports the results of employing an artificial bee colony search algorithm for synthesizing a mutually coupled lumped-parameter ladder-network representation of a transformer winding, starting from its measured magnitude frequency response. The existing bee colony algorithm is suitably adopted by appropriately defining constraints, inequalities, and bounds to restrict the search space and thereby ensure synthesis of a nearly unique ladder network corresponding to each frequency response. Ensuring near-uniqueness while constructing the reference circuit (i.e., representation of healthy winding) is the objective. Furthermore, the synthesized circuits must exhibit physical realizability. The proposed method is easy to implement, time efficient, and problems associated with the supply of initial guess in existing methods are circumvented. Experimental results are reported on two types of actual, single, and isolated transformer windings (continuous disc and interleaved disc).