Probing the Allosteric Mechanism in Pyrrolysyl-tRNA Synthetase Using Energy-Weighted Network Formalism

Pyrrolysyl-tRNA synthetase (PyIRS) is an atypical enzyme responsible for charging tRNA(Pyl) with pyrrolysine, despite lacking precise tRNA anticodon recognition. This dimeric protein exhibits allosteric regulation of function, like any other tRNA synthetases. In this study we examine the paths of allosteric communication at the atomic level, through energy-weighted networks of Desulfitobacterium hafniense PyIRS (DhPyIRS) and its complexes with tRNA(Pyl) and activated pyrrolysine. We performed molecular dynamics simulations of the structures of these complexes to obtain an ensemble conformation-population perspective. Weighted graph parameters relevant to identifying key players and ties in the context of social networks such as edge/node betweenness, closeness index, and the concept of funneling are explored in identifying key residues and interactions leading to shortest paths of communication in the structure networks of DhPylRS. Further, the changes in the status of important residues and connections and the costs of communication due to ligand induced perturbations are evaluated. The optimal, suboptimal, and preexisting paths are also investigated. Many of these parameters have exhibited an enhanced asymmetry between the two subunits of the dimeric protein, especially in the pretransfer complex, leading us to conclude that encoding of function goes beyond the sequence/structure of proteins. The local and global perturbations mediated by appropriate ligands and their influence on the equilibrium ensemble of conformations also have a significant role to play in the functioning of proteins. Taking a comprehensive view of these observations, we propose that the origin of many functional aspects (allostery rand half-sites reactivity in the case of DhPyIRS) lies in subtle rearrangements of interactions and dynamics at a global level.

A self-supported 40W direct methanol fuel cell system

A self-supported 40W Direct Methanol Fuel Cell (DMFC) system has been developed and performance tested. The auxiliaries in the DMFC system comprise a methanol sensor, a liquid-level indicator, and fuel and air pumps that consume a total power of about 5W. The system has a 15-cell DMFC stack with active electrode-area of 45 cm(2). The self-supported DMFC system addresses issues related to water recovery from the cathode exhaust, and maintains a constant methanol-feed concentration with thermal management in the system. Pure methanol and water from cathode exhaust are pumped to the methanol-mixing tank where the liquid level is monitored and controlled with the help of a liquid-level indicator. During the operation, methanol concentration in the feed solution at the stack outlet is monitored using a methanol sensor, and pure methanol is added to restore the desired methanol concentration in the feed tank by adding the product water from the cathode exhaust. The feed-rate requirements of fuel and oxidant are designed for the stack capacity of 40W. The self-supported DMFC system is ideally suited for various defense and civil applications and, in particular, for charging the storage batteries.

Use of climate information for farm-level decision making: rainfed groundnut in southern India

The production of rainfed crops in semi-arid tropics exhibits large variation in response to the variation in seasonal rainfall. There are several farm-level decisions such as the choice of cropping pattern, whether to invest in fertilizers, pesticides etc., the choice of the period for planting, plant population density etc. for which the appropriate choice (associated with maximum production or minimum risk) depends upon the nature of the rainfall variability or the prediction for a specific year. In this paper, we have addressed the problem of identifying the appropriate strategies for cultivation of rainfed groundnut in the Anantapur region in a semi-arid part of the Indian peninsula. The approach developed involves participatory research with active collaboration with farmers, so that the problems with perceived need are addressed with the modern tools and data sets available. Given the large spatial variation of climate and soil, the appropriate strategies are necessarily location specific. With the approach adopted, it is possible to tap the detailed location specific knowledge of the complex rainfed ecosystem and gain an insight into the variety of options of land use and management practices available to each category of stakeholders. We believe such a participatory approach is essential for identifying strategies that have a favourable cost-benefit ratio over the region considered and hence are associated with a high chance of acceptance by the stakeholders. (C) 2002 Elsevier Science Ltd. All rights reserved.

Mutagenicity associated with O6-methylguanine-DNA damage and mechanism of nucleotide flipping by AGT during repair

Methylated guanine damage at O6 position (i.e. O6MG) is dangerous due to its mutagenic and carcinogenic character that often gives rise to G:C-A:T mutation. However, the reason for this mutagenicity is not known precisely and has been a matter of controversy. Further, although it is known that O6-alkylguanine-DNA alkyltransferase (AGT) repairs O6MG paired with cytosine in DNA, the complete mechanism of target recognition and repair is not known completely. All these aspects of DNA damage and repair have been addressed here by employing high level density functional theory in gas phase and aqueous medium. It is found that the actual cause of O6MG mediated mutation may arise due to the fact that DNA polymerases incorporate thymine opposite to O6MG, misreading the resulting O6MG:T complex as an A:T base pair due to their analogous binding energies and structural alignments. It is further revealed that AGT mediated nucleotide flipping occurs in two successive steps. The intercalation of the finger residue Arg 128 into the DNA double helix and its interaction with the O6MG: C base pair followed by rotation of the O6MG nucleotide are found to be crucial for the damage recognition and nucleotide flipping.

A scanning tunneling microscopy and potentiometry study of epitaxial thin films of La0.7Ca0.3MnO3

To investigate the role of grain boundaries and other growth related microstructure in manganite films, a scanning tunneling microscope is used to simultaneously probe surface topography and local potential distribution under current flow at nanometer level in films of epitaxial thin films of La0.7Ca0.3MnO3 deposited on single crystal SrTiO3 and NdGaO3 substrate by laser ablation. We have studied two types of films strained and strain relaxed. Thin (50nm) films (strained due to lattice mismatch between substrate and the film) show step growth (unit cell steps) and have very smooth surfaces. Relatively thicker films (strain relaxed, thickness 200nm) do not have these step growths and show rather smooth well connected grains. Charge transport in these films is not uniform on the nanometer level and is accompanied by potential jumps at the internal surfaces. In particular scattering from grain boundaries results in large variations in the local potential resulting in fields as high as 104-105V/cm located near the grain boundaries. We discuss the role of local strain and strain inhomogeneties in determining the current transport in these films and their resistance and magnetoresistivity. In this paper we attempt to correlate between bulk electronic properties with microscopic electronic conduction using scanning tunneling microscopy and scanning tunneling potentiometry.

A Seven-Level Inverter Topology for Induction Motor Drive Using Two-Level Inverters and Floating Capacitor Fed H-Bridges

A multilevel inverter topology for seven-level space vector generation is proposed in this paper. In this topology, the seven-level structure is realized using two conventional two-level inverters and six capacitor-fed H-bridge cells. It needs only two isolated dc-voltage sources of voltage rating V(dc)/2 where V(dc) is the dc voltage magnitude required by the conventional neutral point clamped (NPC) seven-level topology. The proposed topology is capable of maintaining the H-bridge capacitor voltages at the required level of V(dc)/6 under all operating conditions, covering the entire linear modulation and overmodulation regions, by making use of the switching state redundancies. In the event of any switch failure in H-bridges, this inverter can operate in three-level mode, a feature that enhances the reliability of the drive system. The two-level inverters, which operate at a higher voltage level of V(dc)/2, switch less compared to the H-bridges, which operate at a lower voltage level of V(dc)/6, resulting in switching loss reduction. The experimental verification of the proposed topology is carried out for the entire modulation range, under steady state as well as transient conditions.

Research bed for unit selection based text to speech synthesis

The paper describes a modular, unit selection based TTS framework, which can be used as a research bed for developing TTS in any new language, as well as studying the effect of changing any parameter during synthesis. Using this framework, TTS has been developed for Tamil. Synthesis database consists of 1027 phonetically rich prerecorded sentences. This framework has already been tested for Kannada. Our TTS synthesizes intelligible and acceptably natural speech, as supported by high mean opinion scores. The framework is further optimized to suit embedded applications like mobiles and PDAs. We compressed the synthesis speech database with standard speech compression algorithms used in commercial GSM phones and evaluated the quality of the resultant synthesized sentences. Even with a highly compressed database, the synthesized output is perceptually close to that with uncompressed database. Through experiments, we explored the ambiguities in human perception when listening to Tamil phones and syllables uttered in isolation,thus proposing to exploit the misperception to substitute for missing phone contexts in the database. Listening experiments have been conducted on sentences synthesized by deliberately replacing phones with their confused ones.

Subnatural linewidth in a strongly-driven degenerate two-level system

We observe linewidths below the natural linewidth for a probe laser on a degenerate two-level F -> F' transition, when the same transition is driven by a strong control laser. We take advantage of the fact that each level of the transition is made of multiple magnetic sublevels, and use the phenomenon of electromagnetically induced transparency (EIT) or absorption ( EIA) in multilevel systems. Optical pumping by the control laser redistributes the population so that only a few sublevels contribute to the probe absorption, an explanation which is verified by a density-matrix analysis of the relevant sublevels. We observe more than a factor of 3 reduction in linewidth in the D(2) line of Rb in room-temperature vapor. Such subnatural features vastly increase the scope of applications of EIT, such as high-resolution spectroscopy and tighter locking of lasers to atomic transitions, since it is not always possible to find a suitable third level. (C) 2011 Elsevier B.V. All rights reserved.

Bounds on Defect Level and Fault Coverage in Linear Analog Circuit Testing

Transfer function coefficients (TFC) are widely used to test linear analog circuits for parametric and catastrophic faults. This paper presents closed form expressions for an upper bound on the defect level (DL) and a lower bound on fault coverage (FC) achievable in TFC based test method. The computed bounds have been tested and validated on several benchmark circuits. Further, application of these bounds to scalable RC ladder networks reveal a number of interesting characteristics. The approach adopted here is general and can be extended to find bounds of DL and FC of other parametric test methods for linear and non-linear circuits.

Microwave spectrum and structure of C(6)H(5)CCH center dot center dot center dot H(2)S complex

Rotational spectra of C(6)H(5)CCH center dot center dot center dot H(2)S, C(6)H(5)CCH center dot center dot center dot H(2)(34)S, C(6)H(5)CCH center dot center dot center dot HDS, C(6)H(5)CCH center dot center dot center dot D(2)S and C(6) H(5)CCD center dot center dot center dot H(2)S complexes have been observed using a pulsed nozzle Fourier transform microwave spectrometer. The observed spectrum is consistent with a structure in which hydrogen sulfide is located over the phenyl ring pi cloud and the distance between the centers of masses of the two monomers is 3.74 +/- 0.01 angstrom. In the complex, the H(2)S unit is shifted from the phenyl ring center towards the acetylene group. The vibrationally averaged structure has an effective Cs symmetry. Ab initio calculations were performed at MP2/aug-cc-pVDZ level of theory to locate the possible geometries of the complex. The calculations reveal the experimentally observed structure to be more stable than a coplanar arrangement of the monomers, which was observed for the C(6)H(5)CCH center dot center dot center dot H(2)O complex. Atoms in molecule theoretical analysis shows the presence of S-H center dot center dot center dot pi hydrogen bond. For the parent isotopologue, each transition frequency was found to split into two resulting from an interchange of the equivalent hydrogens of H(2)S unit in the complex. (C) 2011 Elsevier Inc. All rights reserved.