The repertoire of protein kinases encoded in the draft version of the human genome: atypical variations and uncommon domain combinations

Background: Phosphorylation by protein kinases is central to cellular signal transduction. Abnormal functioning of kinases has been implicated in developmental disorders and malignancies. Their activity is regulated by second messengers and by the binding of associated domains, which are also influential in translocating the catalytic component to their substrate sites, in mediating interaction with other proteins and carrying out their biological roles. Results: Using sensitive profile-search methods and manual analysis, the human genome has been surveyed for protein kinases. A set of 448 sequences, which show significant similarity to protein kinases and contain the critical residues essential for kinase function, have been selected for an analysis of domain combinations after classifying the kinase domains into subfamilies. The unusual domain combinations in particular kinases suggest their involvement in ubiquitination pathways and alternative modes of regulation for mitogen-activated protein kinase kinases (MAPKKs) and cyclin-dependent kinase (CDK)-like kinases. Previously unexplored kinases have been implicated in osteoblast differentiation and embryonic development on the basis of homology with kinases of known functions from other organisms. Kinases potentially unique to vertebrates are involved in highly evolved processes such as apoptosis, protein translation and tyrosine kinase signaling. In addition to coevolution with the kinase domain, duplication and recruitment of non-catalytic domains is apparent in signaling domains such as the PH, DAG-PE, SH2 and SH3 domains. Conclusions: Expansion of the functional repertoire and possible existence of alternative modes of regulation of certain kinases is suggested by their uncommon domain combinations. Experimental verification of the predicted implications of these kinases could enhance our understanding of their biological roles.

Reliability Based Design Optimization for Internal Stability of Reinforced Soil Structures Using Pseudo‐Static Method

Seismic design of reinforced soil structures involves many uncertainties that arise from the backfill soil properties and tensile strength of the reinforcement which is not addressed in current design guidelines. This paper highlights the significance of variability in the internal stability assessment of reinforced soil structures. Reliability analysis is applied to estimate probability of failure and pseudo‐static approach has been used for the calculation of the tensile strength and length of the reinforcement needed to maintain the internal stability against tension and pullout failures. Logarithmic spiral failure surface has been considered in conjunction with the limit equilibrium method. Two modes of failure namely, tension failure and pullout failure have been considered. The influence of variations of the backfill soil friction angle, the tensile strength of reinforcement, horizontal seismic acceleration on the reliability index against tension failure and pullout failure of reinforced earth structure have been discussed.

Infrared studies of the phase transitions of alkylammonium halides, RNH3X, and bis-(alkylammonium) tetrahalogenometallates(II), (RNH3)2MX4, (R = alkyl, M = metal, X = Cl or Br)

Internal vibration modes of bis-(alkylammonium) tetrachlorometallates(II) and the corresponding alkylammonium chlorides have been studied through their phase transitions using infrared spectroscopy. The studies show that the vibrational states of alkylammonium ions change markedly through the phase transitions. Spectra of the analogous tetrabromometallates and alkylammonium bromides also confirm this behaviour. There is appreciable motion of the alkylammonium ions in the high-temperature phases; thus, CH3NH+3 ions are essentially undistorted in these phases. The low-temperature, ordered phases show evidence of stronger hydrogen bonding of the cations and for the presence of C—N torsional modes.

Reliability based design optimization of gravity retaining walls

In this paper the use of probability theory in reliability based optimum design of reinforced gravity retaining wall is described. The formulation for computing system reliability index is presented. A parametric study is conducted using advanced first order second moment method (AFOSM) developed by Hasofer-Lind and Rackwitz-Fiessler (HL-RF) to asses the effect of uncertainties in design parameters on the probability of failure of reinforced gravity retaining wall. Totally 8 modes of failure are considered, viz overturning, sliding, eccentricity, bearing capacity failure, shear and moment failure in the toe slab and heel slab. The analysis is performed by treating back fill soil properties, foundation soil properties, geometric properties of wall, reinforcement properties and concrete properties as random variables. These results are used to investigate optimum wall proportions for different coefficients of variation of φ (5% and 10%) and targeting system reliability index (βt) in the range of 3 – 3.2.

Combustion synthesis, characterization and Raman studies of ZnO nanopowders

Spherical shaped ZnO nanopowders (14-50 nm) were synthesized by a low temperature solution combustion method in a short time <5 min. Rietveld analysis show that ZnO has hexagonal wurtzite structure with lattice constants a = 3.2511(1) angstrom, c = 5.2076(2) angstrom, unit cell volume (V) = 47.66(5) (angstrom)(3) and belongs to space group P63mc. SEM micrographs reveal that the particles are spherical in shape and the powders contained several voids and pores. TEM results also confirm spherical shape, with average particle size of 14-50 nm. The values are consistent with the grain sizes measured from Scherrer's method and Williamson-Hall (W-H) plots. A broad UV-vis absorption spectrum was observed at similar to 375 nm which is a characteristic band for the wurtzite hexagonal pure ZnO. The optical energy band gap of 3.24 eV was observed for nanopowder which is slightly lower than that of the bulk ZnO (3.37 eV). The observed Raman peaks at 438 and 588 cm(-1) were attributed to the E(2) (high) and E(1) (LO) modes respectively. The broad band at 564 cm(-1) is due to disorder-activated Raman scattering for the A(1) mode. These bands are associated with the first-order Raman active modes of the ZnO phase. The weak bands observed in the range 750-1000 cm(-1) are due to small defects. (C) 2011 Elsevier B.V. All rights reserved.

Application of composition gradient solid electrolytes in sensors and thermodynamic measurements

New compos~tiong radient solid electrolytes are developed which have application in high temperature solid state galvanic sensors and provide a new tool for thermodynamic measurements. The electrolyte consists oi a solid solution between two ionic conductors with a common mobile ion and spatial variation in composition of otber coxup nents. Incorporation of the composite electrolyte in sensors permits the use oi dissimilar gas electrodes. It is demonsuated, both experimentall y and theoretically, that the composition gradient of the relativeiy immobile species does not give rise to a diffusion potential.The emi of a cell is determined by the activity of the mobile species at the two eiectrodes. The thermodynamic properties of solid solutions can be measured using the gradient solid electrolyte. The experimental stuay is based on model systems A?(COj)x(S04)l-x (A=Na,K),where S \.aria across the electrolyte. The functionally gradient solid electrolytes used for activity measurements consist of pure carbonate at one ena and the solid solution under stuav at the other. The identical vaiues of activity, obtained h m t hree different modes of operation of the ceil. indicate unit transport number for the ddi metal ion in the graciient electrolyte. Tlle activities in the solid solutions exhibit moderate positive deviations from Raoult 's law.

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.

Evolutionary Algorithm for the Determination of Optimal Mode of Bioreactor Operation

Stirred tank bioreactors, employed in the production of a variety of biologically active chemicals, are often operated in batch, fed-batch, and continuous modes of operation. The optimal design of bioreactor is dependent on the kinetics of the biological process, as well as the performance criteria (yield, productivity, etc.) under consideration. In this paper, a general framework is proposed for addressing the two key issues related to the optimal design of a bioreactor, namely, (i) choice of the best operating mode and (ii) the corresponding flow rate trajectories. The optimal bioreactor design problem is formulated with initial conditions and inlet and outlet flow rate trajectories as decision variables to maximize more than one performance criteria (yield, productivity, etc.) as objective functions. A computational methodology based on genetic algorithm approach is developed to solve this challenging multiobjective optimization problem with multiple decision variables. The applicability of the algorithm is illustrated by solving two challenging problems from the bioreactor optimization literature.

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.

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]