Synthesis, Structure, Spirocyclization Mechanism, and Glutathione Peroxidase-like Antioxidant Activity of Stable Spirodiazaselenurane and Spirodiazatellurane

The first examples of stable spirodiazaselenurane and spirodiazatellurane were synthesized by oxidative spirocyclization of the corresponding diaryl selenide and telluride and were structurally characterized. X-ray crystal structures of the spirodiazaselenurane and spirodiazatellurane suggest that the structures are distorted trigonal bipyramidal (TBP) with the electronegative nitrogen atoms occupying the apical positions and two carbon atoms and the lone pair of Se/Te occupying the equatorial positions. Interestingly, the spirodiazatellurane underwent spontaneous chiral resolution during crystallization, and the absolute configurations of its enantiomers were confirmed by single-crystal X-ray analyses. A detailed mechanistic study indicates that the cyclization to spirodiazaselenurane and spirodiazatellurane occurs via selenoxide and telluroxide intermediates. The chalcogenoxides cyclize to the corresponding spiro compounds in a stepwise manner via the involvement of hydroxyl chalcogenurane intermediates, and the activation energy for them spirocyclization reaction decreases in the order S > Se > Te. In addition to the synthesis, characterization, and mechanism of cyclization, the glutathione peroxidase (GPx) mimetic activity of the newly synthesized compounds was evaluated. These studies suggest that the tellurium compounds are more effective as GPx mimics than their selenium counterparts due to the fast oxidation of the tellurium center in the presence of peroxide and the involvement of an efficient redox cycle between the telluride and telluroxide intermediate.

On the performance analysis of a class of neuron circuits

A new performance metric, Peak-Error Ratio (PER) has been presented to benchmark the performance of a class of neuron circuits to realize neuron activation function (NAF) and its derivative (DNAF). Neuron circuits, biased in subthreshold region, based on the asymmetric cross-coupled differential pair configuration and conventional configuration of applying small external offset voltage at the input have been compared on the basis of PER. It is shown that the technique of using transistor asymmetry in a cross-coupled differential pair performs on-par with that of applying external offset voltage. The neuron circuits have been experimentally prototyped and characterized as a proof of concept on the 1.5 mu m AMI technology.

Observation of a power-law memory kernel for fluctuations within a single protein molecule

The fluctuation of the distance between a fluorescein-tyrosine pair within a single protein complex was directly monitored in real time by photoinduced electron transfer and found to be a stationary, time-reversible, and non-Markovian Gaussian process. Within the generalized Langevin equation formalism, we experimentally determine the memory kernel K(t), which is proportional to the autocorrelation function of the random fluctuating force. K(t) is a power-law decay, t(-0.51 +/- 0.07) in a broad range of time scales (10(-3)-10 s). Such a long-time memory effect could have implications for protein functions.

Self-Assembly of Biopolymers on Colloidal Particles via Hydrogen Bonding

Fabrication of multilayer microcapsules via layer-by-layer approach through hydrogen bonding has attracted enormous interest due to its strong response to pH. In this communication, we have prepared hydrogen-bonded multilayer microcapsule without using any cross-linking agent by using DNA base pair (adenine and thymine) modified biocompatible polymers. The growth of the self-assembly on colloidal (melamine formaldehyde: MF) particles has been monitored with zeta potential measurement. The capsules were obtained on dissolution of MF particles at 0.1N HCl. The capsules were characterized with scanning electron microscopy. Moreover, we have observed the salt induced microscopic change in self-assembly of this system on the surface of colloidal particles.

An automated framework for understanding structural variations in the binding grooves of MHC class II molecules

Background: MHC/HLA class II molecules are important components of the immune system and play a critical role in processes such as phagocytosis. Understanding peptide recognition properties of the hundreds of MHC class II alleles is essential to appreciate determinants of antigenicity and ultimately to predict epitopes. While there are several methods for epitope prediction, each differing in their success rates, there are no reports so far in the literature to systematically characterize the binding sites at the structural level and infer recognition profiles from them. Results: Here we report a new approach to compare the binding sites of MHC class II molecules using their three dimensional structures. We use a specifically tuned version of our recent algorithm, PocketMatch. We show that our methodology is useful for classification of MHC class II molecules based on similarities or differences among their binding sites. A new module has been used to define binding sites in MHC molecules. Comparison of binding sites of 103 MHC molecules, both at the whole groove and individual sub-pocket levels has been carried out, and their clustering patterns analyzed. While clusters largely agree with serotypic classification, deviations from it and several new insights are obtained from our study. We also present how differences in sub-pockets of molecules associated with a pair of autoimmune diseases, narcolepsy and rheumatoid arthritis, were captured by PocketMatch(13). Conclusion: The systematic framework for understanding structuralvariations in MHC class II molecules enables large scale comparison of binding grooves and sub-pockets, which is likely to have direct implications towards predicting epitopes and understanding peptide binding preferences.

A Study of Practical Biological Phantoms with Simple Instrumentation for Electrical Impedance Tomography (EIT)

16-electrode phantoms are developed and studied with a simple instrumentation developed for Electrical Impedance Tomography. An analog instrumentation is developed with a sinusoidal current generator and signal conditioner circuit. Current generator is developed withmodified Howland constant current source fed by a voltage controlled oscillator and the signal conditioner circuit consisting of an instrumentation amplifier and a narrow band pass filter. Electronic hardware is connected to the electrodes through a DIP switch based multiplexer module. Phantoms with different electrode size and position are developed and the EIT forward problem is studied using the forward solver. A low frequency low magnitude sinusoidal current is injected to the surface electrodes surrounding the phantom boundary and the differential potential is measured by a digital multimeter. Comparing measured potential with the simulated data it is intended to reduce the measurement error and an optimum phantom geometry is suggested. Result shows that the common mode electrode reduces the common mode error of the EIT electronics and reduces the error potential in the measured data. Differential potential is reduced up to 67 mV at the voltage electrode pair opposite to the current electrodes. Offset potential is measured and subtracted from the measured data for further correction. It is noticed that the potential data pattern depends on the electrode width and the optimum electrode width is suggested. It is also observed that measured potential becomes acceptable with a 20 mm solution column above and below the electrode array level.

An automated framework for understanding structural variations in the binding grooves of MHC class II molecules

Background: MHC/HLA class II molecules are important components of the immune system and play a critical role in processes such as phagocytosis. Understanding peptide recognition properties of the hundreds of MHC class II alleles is essential to appreciate determinants of antigenicity and ultimately to predict epitopes. While there are several methods for epitope prediction, each differing in their success rates, there are no reports so far in the literature to systematically characterize the binding sites at the structural level and infer recognition profiles from them. Results: Here we report a new approach to compare the binding sites of MHC class II molecules using their three dimensional structures. We use a specifically tuned version of our recent algorithm, PocketMatch. We show that our methodology is useful for classification of MHC class II molecules based on similarities or differences among their binding sites. A new module has been used to define binding sites in MHC molecules. Comparison of binding sites of 103 MHC molecules, both at the whole groove and individual sub-pocket levels has been carried out, and their clustering patterns analyzed. While clusters largely agree with serotypic classification, deviations from it and several new insights are obtained from our study. We also present how differences in sub-pockets of molecules associated with a pair of autoimmune diseases, narcolepsy and rheumatoid arthritis, were captured by PocketMatch(13). Conclusion: The systematic framework for understanding structural variations in MHC class II molecules enables large scale comparison of binding grooves and sub-pockets, which is likely to have direct implications towards predicting epitopes and understanding peptide binding preferences.

On the theory of the indentation test for the measurement of tensile strength of brittle materials

A theoretical solution has been obtained for the state of stress in a rectangular plate under a pair of symmetrically placed rigid indenters. The stress distributions along the two central axes have been calculated for a square plate assuming the pressure distribution under the indenters as uniform, parabolic and one resulting from 'constant displacement' on a semiinfinite boundary, for different ratios of indenter-width to side of square. The results are compared with those of photoelastic analysis of Berenbaum and Brodie and the validity of the solution is discussed. The solution has been extended to orthotropic materials and numerical results for one type of coal are given.

Vitamin C status of vitamin A-deficient rats

IT was initially suggested that vitamin A-deficiency leads to an interference in the biosynthesis of ascorbic acid, because depletion of vitamin A was found to cause a fall in the tissue-levels of ascorbate and diminished urinary ascorbic acid excretion in animals1-3. Mapson4, however, concluded that lowered ascorbic acid-levels in vitamin A-deficient rats is due to inanition only, because he was able to show that following chloretone treatment vitamin A-deficient and pair-fed vitamin A normal rats excrete comparable amounts of ascorbic acid in their urine and that restriction of food intake reduces the urinary ascorbate even in the chloretone-treated normal rats. Results of our preliminary experiments reported here clearly indicate that the synthesis of ascorbic acid in rats is markedly reduced during vitamin A-deficiency.

Crystal structure of an intermolecular 2:1 complex between adenine and thymine.Evidence for both Hoogsteen and `quasi-Watson-Crick' interactions

The titled complex, obtained by co-crystallization (EtOH/25 degrees C),is apparently the only known complex of the free bases. Its crystal structure, as determined by X-ray diffraction at both 90 K and 313 K, showed that one A-T pair involves a Hoogsteen interaction, and the other a Watson-Crick interaction but only with respect to the adenine unit. The absence of a clear-cut Watson-Crick base pair raises intriguing questions about the basis of the DNA double helix. (C) 2010 Elsevier Ltd. All rights reserved.

On Using Projective Relations for Calibration and Estimation in a Structured-Light Scanner

For structured-light scanners, the projective geometry between a projector-camera pair is identical to that of a camera-camera pair. Consequently, in conjunction with calibration, a variety of geometric relations are available for three-dimensional Euclidean reconstruction. In this paper, we use projector-camera epipolar properties and the projective invariance of the cross-ratio to solve for 3D geometry. A key contribution of our approach is the use of homographies induced by reference planes, along with a calibrated camera, resulting in a simple parametric representation for projector and system calibration. Compared to existing solutions that require an elaborate calibration process, our method is simple while ensuring geometric consistency. Our formulation using the invariance of the cross-ratio is also extensible to multiple estimates of 3D geometry that can be analysed in a statistical sense. The performance of our system is demonstrated on some cultural artifacts and geometric surfaces.

Novel composite coded pattern for small angle measurement using imaging method -art.no.62891D

A novel approach for measurement of small rotation angles using imaging method is proposed and demonstrated. A plane mirror placed on a precision rotating table is used for imaging the newly designed composite coded pattern. The imaged patterns are captured with the help of a CCD camera. The angular rotation of the plane mirror is determined from a pair of the images of the pattern, captured once before and once after affecting the tilt of the mirror. Both simulation and experimental results suggest that the proposed approach not only retains the advantages of the original imaging method but also contributes significantly to the enhancement of its measuring range (+/- 4.13 degrees with accuracy of the order of 1 arcsec).

Observation of reduced activation energy and the possible existence of decoupled pancake vortices in superconductor/ferromagnet bilayers

Investigations of different superconducting (S)/ferromagnetic (F) heterostructures grown by pulsed laser deposition reveal that the activation energy (U) for the vortex motion in a high T-c superconductor is reduced remarkably by the presence of F layers. The U exhibits a logarithmic dependence on the applied magnetic field in the S/F bilayers suggesting the existence of decoupled two-dimensional (2D) pancake vortices. This result is discussed in terms of the reduction in the effective S layer thickness and the weakening of the S coherence length due to the presence of F layers. In addition, the U and the superconducting T-c in YBa2Cu3O7-delta/La0.5Sr0.5CoO3 bilayers are observed to be much lower than in the YBa2Cu3O7-delta/La0.7Sr0.3MnO3 ones. This in turn suggests that the degree of spin polarization of the F layer might not play a crucial role for the suppression of superconductivity due to a spin polarized induced pair-breaking effect in S/F bilayers.

The fate of the initiator tRNAs is sensitive to the critical balance between interacting proteins

Formylation of the initiator tRNA is essential for normal growth of Escherichia coil, The initiator tRNA containing the U35A36 mutation (CUA anticodon) initiates from UAG codon, However, an additional mutation at position 72 (72A --> G) renders the tRNA (G72/U35A36) inactive in initiation because it is defective in formylation, In this study, we isolated U1G72/U35A36 tRNA containing a wobble base pair at 1-72 positions as an intragenic suppressor of the G72 mutation. The U1G72/U35A36 tRNA is formylated and participates in initiation. More importantly, we show that the mismatch at 1-72 positions of the initiator tRNA, which was thus far thought to be the hallmark of the resistance of this tRNA against peptidyl-tRNA hydrolase (PTH), is not sufficient, The amino acid attached to the initiator tRNA is also important in conferring protection against PTH. Further, we show that the relative levels of PTH and IF2 influence the path adopted by the initiator tRNAs in protein synthesis. These findings provide an important clue to understand the dual function of the single tRNA(Met) in initiation and elongation, in the mitochondria of various organisms.

Hole pairing within an extended Anderson impurity model applicable to the high-Tc cuprates

We calculate the binding energy of a hole pair within the extended Anderson Hamiltonian for the high-Tc cuprates including a Cu impurity and an oxygen-derived band. The results indicate that stable hole pairs can be formed for intra-atomic and interatomic Coulomb repulsion strengths larger than 6 and 3.5 eV, respectively. It is also shown that the total hybridization strength between the Cu 3d and oxygen p band should be less than 2.5 eV. The hole pairing takes place primarily within the oxygen-derived p band. The range of parameter values for which hole pairing occurs is also consistent with the earlier photoemission results from these cuprates.