Use of Mycobacterium smegmatis Deficient in ADP-Ribosyltransferase as Surrogate for Mycobacterium tuberculosis in Drug Testing and Mutation Analysis

Rifampicin (Rif) is a first line drug used for tuberculosis treatment. However, the emergence of drug resistant strains has necessitated synthesis and testing of newer analogs of Rif. Mycobacterium smegmatis is often used as a surrogate for M. tuberculosis. However, the presence of an ADP ribosyltransferase (Arr) in M. smegmatis inactivates Rif, rendering it impractical for screening of Rif analogs or other compounds when used in conjunction with them (Rif/Rif analogs). Rifampicin is also used in studying the role of various DNA repair enzymes by analyzing mutations in RpoB (a subunit of RNA polymerase) causing Rif resistance. These analyses use high concentrations of Rif when M. smegmatis is used as model. Here, we have generated M. smegmatis strains by deleting arr (Delta arr). The M. smegmatis Delta arr strains show minimum inhibitory concentration (MIC) for Rif which is similar to that for M. tuberculosis. The MICs for isoniazid, pyrazinamide, ethambutol, ciprofloxacin and streptomycin were essentially unaltered for M. smegmatis Delta arr. The growth profiles and mutation spectrum of Delta arr and, Delta arr combined with Delta udgB (udgB encodes a DNA repair enzyme that excises uracil) strains were similar to their counterparts wild-type for arr. However, the mutation spectrum of Delta fpg Delta arr strain differed somewhat from that of the Delta fpg strain (fpg encodes a DNA repair enzyme that excises 8-oxo-G). Our studies suggest M. smegmatis Delta arr strain as an ideal model system in drug testing and mutation spectrum determination in DNA repair studies.

Spatio-temporal correlations in aqueous systems: computational studies of static and dynamic heterogeneity by 2D-IR spectroscopy

Local heterogeneity is ubiquitous in natural aqueous systems. It can be caused locally by external biomolecular subsystems like proteins, DNA, micelles and reverse micelles, nanoscopic materials etc., but can also be intrinsic to the thermodynamic nature of the aqueous solution itself (like binary mixtures or at the gas-liquid interface). The altered dynamics of water in the presence of such diverse surfaces has attracted considerable attention in recent years. As these interfaces are quite narrow, only a few molecular layers thick, they are hard to study by conventional methods. The recent development of two dimensional infra-red (2D-IR) spectroscopy allows us to estimate length and time scales of such dynamics fairly accurately. In this work, we present a series of interesting studies employing two dimensional infra-red spectroscopy (2D-IR) to investigate (i) the heterogeneous dynamics of water inside reverse micelles of varying sizes, (ii) supercritical water near the Widom line that is known to exhibit pronounced density fluctuations and also study (iii) the collective and local polarization fluctuation of water molecules in the presence of several different proteins. The spatio-temporal correlation of confined water molecules inside reverse micelles of varying sizes is well captured through the spectral diffusion of corresponding 2D-IR spectra. In the case of supercritical water also, we observe a strong signature of dynamic heterogeneity from the elongated nature of the 2D-IR spectra. In this case the relaxation is ultrafast. We find remarkable agreement between the different tools employed to study the relaxation of density heterogeneity. For aqueous protein solutions, we find that the calculated dielectric constant of the respective systems unanimously shows a noticeable increment compared to that of neat water. However, the `effective' dielectric constant for successive layers shows significant variation, with the layer adjacent to the protein having a much lower value. Relaxation is also slowest at the surface. We find that the dielectric constant achieves the bulk value at distances more than 3 nm from the surface of the protein.

Solid state structure of p-bromo phenyl 4,5,7-tri-O-benzyl-beta-D-glycero-D-talo-septanoside and an analysis of non-covalent interactions

The solid state structure of a new seven-membered sugar oxepane derivative, namely, p-bromo phenyl 4,5,7-tri-O-benzyl-beta-D-glycero-D-talo-septanoside is discussed, as determined through single crystal X-ray structural determination and in relation to their conformational features. The molecule adopts twist-chair as the preferred conformation, with conformational descriptor (TC2,3)-T-0,1. The solid state packing of molecules is governed by a rich network of non-covalent bonding originating from O-H center dot center dot center dot O, C-H center dot center dot center dot pi, C-H center dot center dot center dot Br and aromatic pi center dot center dot center dot pi interactions that stabilize the packing of molecules in the crystal. (C) 2015 Elsevier Ltd. All rights reserved.

Zinc acetylacetonate hydrate adducted with nitrogen donor ligands: Synthesis, spectroscopic characterization, and thermal analysis

We report synthesis, spectroscopic characterization, and thermal analysis of zinc acetylacetonate complex adducted by nitrogen donor ligands, such as pyridine, bipyridine, and phenanthroline. The pyridine adducted complex crystallizes to monoclinic crystal structure, whereas other two adducted complexes have orthorhombic structure. Addition of nitrogen donor ligands enhances the thermal property of these complexes as that with parent metal-organic complex. Zinc acetylacetonate adducted with pyridine shows much higher volatility (106 degrees C), decomposition temperature (202 degrees C) as that with zinc acetylacetonate (136 degrees C, 220 degrees C), and other adducted complexes. All the adducted complexes are thermally stable, highly volatile and are considered to be suitable precursors for metal organic chemical vapor deposition. The formation of these complexes is confirmed by powder X-ray diffraction, Fourier transform infrared spectroscopy, mass spectroscopy, and elemental analysis. The complexes are widely used as starting precursor materials for the synthesis of ZnO nanostructures by microwave irradiation assisted coating process. (c) 2015 Elsevier B.V. All rights reserved.

A Cause and Effect Analysis of Motion Trajectories for Modeling Actions

An action is typically composed of different parts of the object moving in particular sequences. The presence of different motions (represented as a 1D histogram) has been used in the traditional bag-of-words (BoW) approach for recognizing actions. However the interactions among the motions also form a crucial part of an action. Different object-parts have varying degrees of interactions with the other parts during an action cycle. It is these interactions we want to quantify in order to bring in additional information about the actions. In this paper we propose a causality based approach for quantifying the interactions to aid action classification. Granger causality is used to compute the cause and effect relationships for pairs of motion trajectories of a video. A 2D histogram descriptor for the video is constructed using these pairwise measures. Our proposed method of obtaining pairwise measures for videos is also applicable for large datasets. We have conducted experiments on challenging action recognition databases such as HMDB51 and UCF50 and shown that our causality descriptor helps in encoding additional information regarding the actions and performs on par with the state-of-the art approaches. Due to the complementary nature, a further increase in performance can be observed by combining our approach with state-of-the-art approaches.

Nanoflowers of PdRu on PEDOT for Electrooxidation of Glycerol and Its Analysis

Poly(3,4-ethylenedioxythiophene) (PEDOT) supported PdRu catalysts with various Pd:Ru atomic ratios are prepared by one step electrodeposition method. The catalysts are characterised by several physico-chemical techniques. The morphology depends on Pd:Ru ratio. The nanoflowers of Pd5Ru catalyst are deposited on PEDOT surface in an alloy form. Cyclic voltammetry experiments indicate that Ru improves the catalytic activity of Pd for glycerol oxidation significantly. However, the oxidation of glycerol is not observed on Ru-PEDOT/C electrode. Amongst all compositions, Pd5Ru nanoflowers on PEDOT exhibit the highest electrocatalytic activity and stability. Cyclic voltammetry and differential pulse voltammetry experiments are performed for the analysis of glycerol. Pd5Ru-PEDOT/C electrode is highly sensitive towards glycerol detection with sensitivity of 99.8 mu A cm(-2) mu M-1 and low detection limit of 0.1 mu M. Thus, electrochemically deposited nanoflowers Pd5Ru on PEDOT are efficient catalysts for direct glycerol oxidation as well as for analysis in alkaline media. (C) 2015 Elsevier Ltd. All rights reserved.

A Study of Pressure-Dependent Squeeze Film Stiffness as a Resonance Modulator Using Static and Dynamic Measurements

We report on the resonant frequency modulation of inertial microelectromechanical systems (MEMS) structures due to squeeze film stiffness over a range of working pressures. Squeeze film effects have been studied extensively, but mostly in the context of damping and Q-factor determination of dynamic MEMS structures, typically suspended over a fixed substrate with a very thin air gap. Here, we show with experimental measurements and analytical calculations how the pressure-dependent air springs (squeeze film stiffness) change the resonant frequency of an inertial MEMS structure by as much as five times. For capturing the isolated effect of the squeeze film stiffness, we first determine the static stiffness of our structure with atomic force microscope probing and then study the effect of the air spring by measuring the dynamic response of the structure, thus finding the resonant frequencies while varying the air pressure from 1 to 905 mbar. We also verify our results by analytical and Finite Element Method calculations. Our findings show that the pressure-dependent squeeze film stiffness can affect a rather huge range of frequency modulation (>400%) and, therefore, can be used as a design parameter for exploiting this effect in MEMS devices. 2014-0310]

Gasification of wood particles in a co-current packed bed: Experiments and model analysis

This study focuses on addressing the propagation front movement in a co-current downdraft gasification system. A detailed single particle modeling analysis extended to the packed bed reactor is used to compare with the experimental measurement as well those available in the literature. This model for biomass gasification systems considered pyrolysis process, gas phase volatile combustion, and heterogeneous char reactions along with gas phase reactions in the packed bed. The pyrolysis kinetics has a critical influence on the gasification process. The propagation front has been shown to increase with air mass flux, attains a peak and then decreases with further increase in air mass flux and finally approaches negative propagation rate. This indicates that front is receding, or no upward movement() bra her it is moving downward towards the char bed. The propagation rate correlates with mass flux as (m) over dot `'(0.883) during the increasing regimes of the front movement The study clearly identifies that bed movement is an important parameter for consideration in a co-current configuration towards establishing the effective bed movement. The study also highlights the importance of surface area to volume ratio of the particles in the packed bed and its influence on the volatile generation. Finally, the gas composition for air gasification under various air mass fluxes is compared with the experimental results. (C) 2016 Elsevier B.V. All rights reserved.