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.

Binding of BIS like and other ligands with the GSK-3 beta kinase: a combined docking and MM-PBSA study

Binding of several bisindolylmaleimide (BIS) like (BIS-3, BIS-8 and UCN1) and other ligands (H89, SB203580 and Y27632) with the glycogen synthase kinase-3 (GSK-3 beta) has been studied using combined docking, molecular dynamics and Poisson-Boltzmann surface area analysis approaches. The study generated novel binding modes of these ligands that can rationalize why some ligands inhibit GSK-3 beta while others do not. The relative binding free energies associated with these binding modes are in agreement with the corresponding measured specificities. This study further provides useful insight regarding possible existence of multiple conformations of some ligands like H89 and BIS-8. It is also found that binding modes of BIS-3, BIS-8 and UCN1 with GSK-3 beta and PDK1 kinases are similar. These new insights are expected to be useful for future rational design of novel, more potent GSK-3 beta-specific inhibitors as promising therapeutics.

Rotation field in wedge indentation of metals

A study is made of the rotation field in wedge indentation of metals using copper as the model material system. Wedges with apical angles of 60 and 120 are used to indent annealed copper, and the deformation is mapped using image correlation. The indentation of annealed and strain-hardened copper is simulated using finite element analysis. The rotation field, derived from the deformation measurements, provides a clear way of distinguishing between cutting and compressive modes of deformation. Largely unidirectional rotation on one side of the symmetry line with small spatial rotation gradients is characteristic of compression. Bidirectional rotation with neighboring regions of opposing rotations and locally high rotation gradients characterizes cutting. In addition, the rotation demarcates such characteristic regions as the pile-up zone in indentation of a strain-hardened metal. The residual rotation field obtained after unloading is essentially the same as that at full load, indicating that it is a scalar proxy for plastic deformation as a whole.

Application of vibrational microspectroscopy to biology and medicine

Vibrational microspectroscopic (Raman and infrared (IR)) techniques are rapidly emerging as effective tools to probe the basic processes of life. This review mainly focuses on the applications of Raman and IR microspectroscopy to biology and biomedicine, ranging from studies on cellular components in single cells to advancement in techniques for in vitro to in vivo applications. These techniques have proved to be instrumental in studying the biological specimen with minimum perturbation, i.e. without the use of dyes and contrast-inducing agents. These techniques probe the vibrational modes of the molecules and provide spectra that are specific to the molecular properties and chemical nature of the species.

Analysis and design of machine foundations at resonance

The design of machine foundations are done on the basis of two principal criteria viz., vibration amplitude should be within the permissible limits and natural frequency of machine-foundation-soil system should be away from the operating frequency (i.e. avoidance of resonance condition). In this paper the nondimensional amplitude factor M-m or M-r m and the nondimensional frequency factor a(o m) at resonance are related using elastic half space theory and is used as a new approach for a simplified design procedure for the design of machine foundations for all the modes of vibration fiz. vertical, horizontal, rocking and torsional for rigid base pressure distribution and weighted average displacement condition. The analysis show that one need not know the value of Poisson's ratio for rotating mass system for all the modes of vibration.

Exciting forces due to interaction of water waves with a submerged sphere in an ice-covered two-layer fluid of finite depth

Scattering of water waves by a sphere in a two-layer fluid, where the upper layer has an ice-cover modelled as an elastic plate of very small thickness, while the lower one has a rigid horizontal bottom surface, is investigated within the framework of linearized water wave theory. The effects of surface tension at the surface of separation is neglected. There exist two modes of time-harmonic waves - the one with lower wave number propagating along the ice-cover and the one with higher wave number along the interface. Method of multipole expansions is used to find the particular solution for the problem of wave scattering by a submerged sphere placed in either of the layers. The exciting forces for vertical and horizontal directions are derived and plotted against different values of the wave number for different submersion depths of the sphere and flexural rigidity of the ice-cover. When the flexural rigidity and the density of the ice-cover are taken to be zero, the numerical results for the exciting forces for the problem with free surface are recovered as particular cases. (C) 2011 Elsevier Ltd. All rights reserved.

Switching and fault transient analysis of 765 kV transmission systems

The analysis of electromagnetic transients arising in EHV/UHV power networks gives necessary information about the possible stresses on the different network components, which will determine their proper design, limits of operation as well as their pertinent protection strategies. This paper describes the transient analysis of 765 kV EHV transmission system which is a typical expansion in Indian power grid system. Considering various conditions, switching transient and fault transient studies are carried out. A FORTRAN version of EMTP is developed, to study a practical example, then a comparison with the results available in the literature is made.

Theoretical analysis of photoinduced H-atom elimination in thiophenol

The photoinduced hydrogen elimination reaction in thiophenol via the conical intersections of the dissociative (1)pi sigma* excited state with the bound (1)pi pi* excited state and the electronic ground state has been investigated with ab initio electronic-structure calculations and time-dependent quantum wave-packet calculations. A screening of the coupling constants of the symmetry-allowed coupling modes at the (1)pi pi*-(1)pi sigma* and (1)pi sigma*-S-0 conical intersection shows that the SH torsional mode is by far the most important coupling mode at both conical intersections. A model including three intersecting potential-energy surfaces (S-0, (1)pi pi*, (1)pi sigma*) and two nuclear degrees of freedom (SH stretch and SH torsion) has been constructed on the basis of ab initio complete-active-space self-consistent field and multireference second-order perturbation theory calculations. The nonadiabatic quantum wave-packet dynamics initiated by optical excitation of the (1)pi pi* and (1)pi sigma* states has been explored for this three-state two-coordinate model. The photodissociation dynamics is characterized in terms of snapshots of time-dependent wave packets, time-dependent electronic population probabilities, and the branching ratio of the (2)sigma/(2)pi electronic states of the thiophenoxyl radical. The dependence of the timescale of the photodissociation process and the branching ratio on the initial excitation of the SH stretching and SH torsional vibrations has been analyzed. It is shown that the node structure, which is imposed on the nuclear wave packets by the initial vibrational preparation as well as by the transitions through the conical intersections, has a profound effect on the photodissociation dynamics. The effect of additional weak coupling modes of CC twist (nu(16a)) and ring-distortion (nu(16b)) character has been investigated with three-dimensional and four-dimensional time-dependent wave-packet calculations, and has been found to be minor. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.4709608]

Scaling analysis: Equivalence of convective and radiative heating of levitated droplet

This letter develops theoretical relationships for equilibrium timescale and temperature scale of a vaporizing droplet in a convective and a radiative environment. The transient temperature normalized by the respective scales exhibits a unified profile for both modes of heating. The analysis allows for the prediction of the required laser flux to show its equivalence in a corresponding heated gas stream. The theoretical equivalence shows good agreement with experiments across a range of droplet sizes. Simple experiments can be conducted in a levitator to extrapolate information in realistic convective environments like combustion and spray drying. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.4720092]

Interaction of nucleic acids with carbon nanotubes and dendrimers

Nucleic acid interaction with nanoscale objects like carbon nanotubes (CNTs) and dendrimers is of fundamental interest because of their potential application in CNT separation, gene therapy and antisense therapy. Combining nucleic acids with CNTs and dendrimers also opens the door towards controllable self-assembly to generate various supra-molecular and nano-structures with desired morphologies. The interaction between these nanoscale objects also serve as a model system for studying DNA compaction, which is a fundamental process in chromatin organization. By using fully atomistic simulations, here we report various aspects of the interactions and binding modes of DNA and small interfering RNA (siRNA) with CNTs, graphene and dendrimers. Our results give a microscopic picture and mechanism of the adsorption of single- and double-strand DNA (ssDNA and dsDNA) on CNT and graphene. The nucleic acid-CNT interaction is dominated by the dispersive van der Waals (vdW) interaction. In contrast, the complexation of DNA (both ssDNA and dsDNA) and siRNA with various generations of poly-amido-amine (PAMAM) dendrimers is governed by electrostatic interactions. Our results reveal that both the DNA and siRNA form stable complex with the PAMAM dendrimer at a physiological pH when the dendrimer is positively charged due to the protonation of the primary amines. The size and binding energy of the complex increase with increase in dendrimer generation. We also give a summary of the current status in these fields and discuss future prospects.

Detection of sugar-lectin interactions by multivalent dendritic sugar functionalized single-walled carbon nanotubes

We show that single walled carbon nanotubes (SWNTs) decorated with sugar functionalized poly (propyl ether imine) (PETIM) dendrimer is a very sensitive platform to quantitatively detect carbohydrate recognizing proteins, namely, lectins. The changes in electrical conductivity of SWNT in field effect transistor device due to carbohydrate-protein interactions form the basis of present study. The mannose sugar attached PETIM dendrimers undergo charge-transfer interactions with the SWNTs. The changes in the conductance of the dendritic sugar functionalized SWNT after addition of lectins in varying concentrations were found to follow the Langmuir type isotherm, giving the concanavalin A (Con A)-mannose affinity constant to be 8.5 x 10(6) M-1. The increase in the device conductance observed after adding 10 nM of Con A is same as after adding 20 mu M of a non-specific lectin peanut agglutinin, showing the high specificity of the Con A-mannose interactions. The specificity of sugar-lectin interactions was characterized further by observing significant shifts in Raman modes of the SWNTs. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.4739793]

Space-Time Scales of Northward Propagation of Convection during Boreal Summer

This study uses precipitation estimates from the Tropical Rainfall Measuring Mission to quantify the spatial and temporal scales of northward propagation of convection over the Indian monsoon region during boreal summer. Propagating modes of convective systems in the intraseasonal time scales such as the Madden-Julian oscillation can interact with the intertropical convergence zone and bring active and break spells of the Indian summer monsoon. Wavelet analysis was used to quantify the spatial extent (scale) and center of these propagating convective bands, as well as the time period associated with different spatial scales. Results presented here suggest that during a good monsoon year the spatial scale of this oscillation is about 30 degrees centered around 10 degrees N. During weak monsoon years, the scale of propagation decreases and the center shifts farther south closer to the equator. A strong linear relationship is obtained between the center/scale of convective wave bands and intensity of monsoon precipitation over Indian land on the interannual time scale. Moreover, the spatial scale and its center during the break monsoon were found to be similar to an overall weak monsoon year. Based on this analysis, a new index is proposed to quantify the spatial scales associated with propagating convective bands. This automated wavelet-based technique developed here can be used to study meridional propagation of convection in a large volume of datasets from observations and model simulations. The information so obtained can be related to the interannual and intraseasonal variation of Indian monsoon precipitation.

Theoretical-experimental study of shock wave-assisted metal forming process using a diaphragmless shock tube

The use of high-velocity sheet-forming techniques where the strain rates are in excess of 10(2)/s can help us solve many problems that are difficult to overcome with traditional metal-forming techniques. In this investigation, thin metallic plates/foils were subjected to shock wave loading in the newly developed diaphragmless shock tube. The conventional shock tube used in the aerodynamic applications uses a metal diaphragm for generating shock waves. This method of operation has its own disadvantages including the problems associated with repeatable and reliable generation of shock waves. Moreover, in industrial scenario, changing metal diaphragms after every shot is not desirable. Hence, a diaphragmless shock tube is calibrated and used in this study. Shock Mach numbers up to 3 can be generated with a high degree of repeatability (+/- 4 per cent) for the pressure jumps across the primary shock wave. The shock Mach number scatter is within +/- 1.5 per cent. Copper, brass, and aluminium plates of diameter 60 mm and thickness varying from 0.1 to 1 mm are used. The plate peak over-pressures ranging from 1 to 10 bar are used. The midpoint deflection, circumferential, radial, and thickness strains are measured and using these, the Von Mises strain is also calculated. The experimental results are compared with the numerical values obtained using finite element analysis. The experimental results match well with the numerical values. The plastic hinge effect was also observed in the finite element simulations. Analysis of the failed specimens shows that aluminium plates had mode I failure, whereas copper plates had mode II failure.

Spatial SINR Games of Base Station Placement and Mobile Association

We study the question of determining locations of base stations (BSs) that may belong to the same or to competing service providers. We take into account the impact of these decisions on the behavior of intelligent mobile terminals that can connect to the base station that offers the best utility. The signal-to-interference-plus-noise ratio (SINR) is used as the quantity that determines the association. We first study the SINR association-game: We determine the cells corresponding to each base stations, i.e., the locations at which mobile terminals prefer to connect to a given base station than to others. We make some surprising observations: 1) displacing a base station a little in one direction may result in a displacement of the boundary of the corresponding cell to the opposite direction; 2) a cell corresponding to a BS may be the union of disconnected subcells. We then study the hierarchical equilibrium in the combined BS location and mobile association problem: We determine where to locate the BSs so as to maximize the revenues obtained at the induced SINR mobile association game. We consider the cases of single frequency band and two frequency bands of operation. Finally, we also consider hierarchical equilibria in two frequency systems with successive interference cancellation.

Strain localization effect on system reliability based design of bridge abutments under earthquake loading

The component and system reliability based design of bridge abutments under earthquake loading is presented in the paper. Planar failure surface has been used in conjunction with pseudo-dynamic approach to compute seismic active earth pressures on an abutment. The pseudo-dynamic method, considers the effect of phase difference in shear waves, soil amplification along with the horizontal seismic accelerations, strain localization in backfill soil and associated post-peak reduction in the shear resistance from peak to residual values along a previously formed failure plane. Four modes of stability viz. sliding, overturning, eccentricity and bearing capacity of the foundation soil are considered in the analysis. The series system reliability is computed with an assumption of independent failure modes. The lower and upper bounds of system reliability are also computed by taking into account the correlations between four failure modes, which is evaluated using the direction cosines of the tangent planes at the most probable points of failure.