Influence of phosphate ligands in abolishing the conformational difference between ribonuclease A and its acid-denatured derivative

The initial structural alteration of RNAase A due to acid denaturation (0.5 N HCl, 30 degrees C) that accompanies deamidation (without altering enzymic activity) has been dectected by spectrophotometric titration, fluorescence and ORD/CD measurements. It is shown that acid treated RNAase A has an altered conformation at neutral pH, 25 degrees C. This is characterized by the increased accessibility of buried tyrosine residue(s) towards the solvent. The most altered conformation of RNAase A is found in the 10 h acid-treated derivative. This has about 1.5 additional exposed tyrosine residues and a lesser amount of secondary structure than RNAase A. All three methods (titration, fluorescence and CD) established that the structural transition of RNAase A is biphasic. The first phase occurs within 1 h and the resulting subtle conformational change is constant up to 7 h. Following this, after the release of 0.55 mol of ammonia, the major conformational change begins. The altered conformation of the acid-denatured RNAase A could be reversed completely to the native state through a conformational change induced by substrate analogs like 2'- or 3'-CMP. Thus the monodeamidated derivative isolated from the acid-denatured RNAase A by phosphate is very similar to RNAase A in over-all conformation. The results suggest the possibility of flexibility in the RNAase A molecule that does not affect its catalytic activity, as probed through the tyrosine residues.

Atomic fountain of laser-cooled Yb atoms for precision measurements

We demonstrate launching of laser-cooled Yb atoms in a cold atomic fountain. Atoms in a collimated thermal beam are first cooled and captured in a magneto-optical trap (MOT) operating on the strongly allowed S-1(0) -> P-1(1) transition at 399 nm (blue line). They are then transferred to a MOT on the weakly allowed S-1(0) -> P-3(1) transition at 556 nm (green line). Cold atoms from the green MOT are launched against gravity at a velocity of around 2.5 m/s using a pair of green beams. We trap more than 107 atoms in the blue MOT and transfer up to 70% into the green MOT. The temperature for the odd isotope Yb-171 is similar to 1 mK in the blue MOT, and reduces by a factor of 40 in the green MOT.

High-quality annotation of promoter regions for 913 bacterial genomes

Motivation: The number of bacterial genomes being sequenced is increasing very rapidly and hence, it is crucial to have procedures for rapid and reliable annotation of their functional elements such as promoter regions, which control the expression of each gene or each transcription unit of the genome. The present work addresses this requirement and presents a generic method applicable across organisms. Results: Relative stability of the DNA double helical sequences has been used to discriminate promoter regions from non-promoter regions. Based on the difference in stability between neighboring regions, an algorithm has been implemented to predict promoter regions on a large scale over 913 microbial genome sequences. The average free energy values for the promoter regions as well as their downstream regions are found to differ, depending on their GC content. Threshold values to identify promoter regions have been derived using sequences flanking a subset of translation start sites from all microbial genomes and then used to predict promoters over the complete genome sequences. An average recall value of 72% (which indicates the percentage of protein and RNA coding genes with predicted promoter regions assigned to them) and precision of 56% is achieved over the 913 microbial genome dataset.

Analysis of the evanescent field coupling between a fiber and a planar waveguide using the explicit finite difference method with a nonuniform mesh (Journal Paper)

We investigate an optical waveguide system consisting of an unclad fiber core suspended at a constant distance parallel to the surface of a planar waveguide. The coupling and propagation of light in the combined system is studied using the three-dimensional explicit finite difference beam propagation method with a nonuniform mesh configuration. The power loss in the fiber and the field distribution in the waveguide are studied as a function of various parameters, such as index changes, index profile, and propagation distance, for the combined system.

Finite element estimation of elastic interlaminar stresses in laminates

Low interlaminar strength and the consequent possibility of interlaminar failures in composite laminates demand an examination of interlaminar stresses and/or strains to ensure their satisfactory performance. As a first approximation, these stresses can be obtained from thickness-wise integration of ply equilibrium equations using in-plane stresses from the classical laminated plate theory. Implementation of this approach in the finite element form requires evaluation of third and fourth order derivatives of the displacement functions in an element. Hence, a high precision element developed by Jayachandrabose and Kirkhope (1985) is used here and the required derivatives are obtained in two ways. (i) from direct differentiation of element shape functions; and (ii) by adapting a finite difference technique applied to the nodal strains and curvatures obtained from the finite element analysis. Numerical results obtained for a three-layered symmetric and a two-layered asymmetric laminate show that the second scheme is quite effective compared to the first scheme particularly for the case of asymmetric laminates.

The precision of regulation in Dictyostelium discoideum: implications for cell-type proportioning in the absence of spatial pattern

We have made careful counts of the exact number of spore, stalk and basal disc cells in small fruiting bodies of Dictyostelium discoideum (undifferentiated amoebae are found only rarely and on average their fraction is 4.96 x 10(-4)). (i) Within aggregates of a given size, the relative apportioning of amoebae to the main cell types occurs with a remarkable degree of precision. In most cases the coefficient of variation (c.v.) in the mean fraction of cells that form spores is within 4.86%. The contribution of stalk and basal disc cells is highly variable when considered separately (c.v.'s upto 25% and 100%, respectively), but markedly less so when considered together. Calculations based on theoretical models indicate that purely cell-autonomous specification of cell, fate cannot account for die observed accuracy of proportioning. Cell-autonomous determination to a prestalk or prespore condition followed by cell type interconversion, and stabilised by feedbacks, suffices to explain the measured accuracy. (ii) The fraction of amoebae that differentiates into spores increases monotonically with the total number of cells. This fraction rises from an average of 73.6% for total cell numbers below 30 and reaches 86.0% for cell numbers between 170 and 200 (it remains steady thereafter at around 86%). Correspondingly, the fraction of amoebae differentiating into stalk or basal disc decreases viith total size. These trends are in accordance with evolutionary expectations and imply that a mechanism for sensing the overall size of the aggregate also plays an essential role in the determination of cell-type proportions.

Chopped nonlinear magneto-optic rotation: A technique for precision measurements

We have developed a technique for precise measurement of small magnetic fields using nonlinear magneto-optic rotation (NMOR). The technique relies on the resonant laser beam being chopped. During the on time, the atoms are optically pumped into an aligned ground state (Delta m=2 coherence). During the off time, they freely precess around the magnetic field at the Larmor frequency. If the on-off modulation frequency matches (twice) the Larmor precession frequency, the rotation is resonantly enhanced in every cycle, thereby making the process like a repeated Ramsey measurement of the Larmor frequency. We study chopped-NMOR in a paraffin-coated Cs vapor cell. The out-of-phase demodulated rotation shows a Lorentzian peak of linewidth 85 mu G, corresponding to a sensitivity of 0.15nG/root Hz. We discuss the potential of this technique for the measurement of an atomic electric-dipole moment. Copyright (C) EPLA, 2011

Oscillatory flow and temperature fields in an open tube with temperature difference across the ends

The oscillating flow and temperature field in an open tube subjected to cryogenic temperature at the cold end and ambient temperature at the hot end is studied numerically. The flow is driven by a time-wise sinusoidally varying pressure at the cold end. The conjugate problem takes into account the interaction of oscillatory flow with the heat conduction in the tube wall. The full set of compressible flow equations with axisymmetry assumption are solved with a pressure correction algorithm. Parametric studies are conducted with frequencies of 5-15 Hz, with one end maintained at 100 K and other end at 300 K. The flow and temperature distributions and the cooldown characteristics are obtained. The frequency and pressure amplitude have negligible effect on the time averaged Nusselt number. Pressure amplitude is an important factor determining the enthalpy flow through the solid wall. The frequency of operation has considerable effect on penetration of temperature into the tube. The density variation has strong influence on property profiles during cooldown. The present study is expected to be of interest in applications such as pulse tube refrigerators and other cryocoolers, where oscillatory flows occur in open tubes. (C) 2011 Elsevier Ltd. All rights reserved.

Difference in spin state and covalence between La1-xSrxCoO3 and La2-xSrxLi0.5Co0.5O4

We present a comparative study of the spin states and electronic properties of La1-xSrxCoO3 and La2-xSrxLi0.5Co0.5O4 using X-ray absorption near-edge structure spectroscopy at both the O-K and Co-L-2.3 thresholds. In the La2-xSrxLi0.5Co0.5O4 system the CoO6 octahedra are isolated, the holes induced by Sr doping are trapped in the isolated Co(IV)O-6 octahedra, and a low-spin state is found for the Co ions, which does not change upon Sr doping. In the La1-xSrxCoO3 system, the interconnected CoO6 octahedra, with a 180degrees Co-O-Co bond angle, give rise to a transition from low-spin to intermediate-spin state with a ferromagnetic alignment of the Co spins. The double-exchange, ferromagnetic coupling between Co ions mediated by the 180degrees bond angle is responsible for suppressing the low spin-state. We find that the branching ratio of spectral intensities at the L-2 and L-3 thresholds in the Co-L-2.3 X-ray absorption spectra is sensitive to the spin state of the Co ions allowing its direct spectroscopic determination. (C) 2002 Published by Elsevier Science B.V.

Swam Intelligent Based Inverse Model for Laboratory Double Reservoir Diffusion Experiments

Theoretical approaches are of fundamental importance to predict the potential impact of waste disposal facilities on ground water contamination. Appropriate design parameters are, in general, estimated by fitting the theoretical models to a field monitoring or laboratory experimental data. Double-reservoir diffusion (Transient Through-Diffusion) experiments are generally conducted in the laboratory to estimate the mass transport parameters of the proposed barrier material. These design parameters are estimated by manual parameter adjusting techniques (also called eye-fitting) like Pollute. In this work an automated inverse model is developed to estimate the mass transport parameters from transient through-diffusion experimental data. The proposed inverse model uses particle swarm optimization (PSO) algorithm which is based on the social behaviour of animals for finding their food sources. Finite difference numerical solution of the transient through-diffusion mathematical model is integrated with the PSO algorithm to solve the inverse problem of parameter estimation.The working principle of the new solver is demonstrated by estimating mass transport parameters from the published transient through-diffusion experimental data. The estimated values are compared with the values obtained by existing procedure. The present technique is robust and efficient. The mass transport parameters are obtained with a very good precision in less time

Remote detection and distinction of ants using nest-site specific LISS-derived Normalised Difference Vegetation Index

This study in Western Ghats, India, investigates the relation between nesting sites of ants and a single remotely sensed variable: the Normalised Difference Vegetation Index (NDVI). We carried out sampling in 60 plots each measuring 30 x 30 m and recorded nest sites of 13 ant species. We found that NDVI values at the nesting sites varied considerably between individual species and also between the six functional groups the ants belong to. The functional groups Cryptic Species, Tropical Climate Specialists and Specialist Predators were present in regions with high NDVI whereas Hot Climate Specialists and Opportunists were found in sites with low NDVI. As expected we found that low NDVI values were associated with scrub jungles and high NDVI values with evergreen forests. Interestingly, we found that Pachycondyla rufipes, an ant species found only in deciduous and evergreen forests, established nests only in sites with low NDVI (range = 0.015 - 0.1779). Our results show that these low NDVI values in deciduous and evergreen forests correspond to canopy gaps in otherwise closed deciduous and evergreen forests. Subsequent fieldwork confirmed the observed high prevalence of P. rufipes in these NDVI-constrained areas. We discuss the value of using NDVI for the remote detection and distinction of ant nest sites.