Evolution of Aromatic beta-Glucoside Utilization by Successive Mutational Steps in Escherichia coli

The bglA gene of Escherichia coli encodes phospho-beta-glucosidase A capable of hydrolyzing the plant-derived aromatic beta-glucoside arbutin. We report that the sequential accumulation of mutations in bglA can confer the ability to hydrolyze the related aromatic beta-glucosides esculin and salicin in two steps. In the first step, esculin hydrolysis is achieved through the acquisition of a four-nucleotide insertion within the promoter of the bglA gene, resulting in enhanced steady-state levels of the bglA transcript. In the second step, hydrolysis of salicin is achieved through the acquisition of a point mutation within the bglA structural gene close to the active site without the loss of the original catabolic activity against arbutin. These studies underscore the ability of microorganisms to evolve additional metabolic capabilities by mutational modification of preexisting genetic systems under selection pressure, thereby expanding their repertoire of utilizable substrates.

Working group report: Dictionary of Large Hadron Collider signatures

We report on a plan to establish a `Dictionary of LHC Signatures', an initiative that started at the WHEPP-X workshop in Chennai, January 2008. This study aims at the strategy of distinguishing 3 classes of dark matter motivated scenarios such as R-parity conserved supersymmetry, little Higgs models with T-parity conservation and universal extra dimensions with KK-parity for generic cases of their realization in a wide range of the model space. Discriminating signatures are tabulated and will need a further detailed analysis.

Physics beyond Standard Model: Working group 3 report

This is a summary of the beyond the Standard Model (including model building working group of the WHEPP-X workshop held at Chennai from January 3 to 15, 2008.

Working group report: Quantum chromodynamics sub-group

This is the report of the QCD working sub-group at the Tenth Workshop on High Energy Physics Phenomenology (WHEPP-X).

targetTB: A target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis

Background: Tuberculosis still remains one of the largest killer infectious diseases, warranting the identification of newer targets and drugs. Identification and validation of appropriate targets for designing drugs are critical steps in drug discovery, which are at present major bottle-necks. A majority of drugs in current clinical use for many diseases have been designed without the knowledge of the targets, perhaps because standard methodologies to identify such targets in a high-throughput fashion do not really exist. With different kinds of 'omics' data that are now available, computational approaches can be powerful means of obtaining short-lists of possible targets for further experimental validation. Results: We report a comprehensive in silico target identification pipeline, targetTB, for Mycobacterium tuberculosis. The pipeline incorporates a network analysis of the protein-protein interactome, a flux balance analysis of the reactome, experimentally derived phenotype essentiality data, sequence analyses and a structural assessment of targetability, using novel algorithms recently developed by us. Using flux balance analysis and network analysis, proteins critical for survival of M. tuberculosis are first identified, followed by comparative genomics with the host, finally incorporating a novel structural analysis of the binding sites to assess the feasibility of a protein as a target. Further analyses include correlation with expression data and non-similarity to gut flora proteins as well as 'anti-targets' in the host, leading to the identification of 451 high-confidence targets. Through phylogenetic profiling against 228 pathogen genomes, shortlisted targets have been further explored to identify broad-spectrum antibiotic targets, while also identifying those specific to tuberculosis. Targets that address mycobacterial persistence and drug resistance mechanisms are also analysed. Conclusion: The pipeline developed provides rational schema for drug target identification that are likely to have high rates of success, which is expected to save enormous amounts of money, resources and time in the drug discovery process. A thorough comparison with previously suggested targets in the literature demonstrates the usefulness of the integrated approach used in our study, highlighting the importance of systems-level analyses in particular. The method has the potential to be used as a general strategy for target identification and validation and hence significantly impact most drug discovery programmes.

Thermal Analysis of Polypropylene Hydroperoxide

Studies on the low temperature oxidation of polyolefins have been the subject matter of several investigations because of interest in understanding the aging and weathering of polymers. One of the key steps in such an oxtdatton is the formation of hydroperoxide. Estimation of the hydroperoxide in oxidized samples, which is conventionally done by iodometric titrations, is quite important to gain knowledge about the kinetics and mechanism of the process. The present investigation is the first report of the thermal analysis of polypropylene hydroperoxide samples from two angles: (1) the thermal behavior of its decomposition and (2) whether such an analysis leads to knowledge of the concentration of hydroperoxide in the sample.

Investigations of separated flow over backward facing steps in IISc hypersonic shock tunnel

Two backward facing step (2 mm and 3 mm step height) models are selected for surface heat transfer measurements. The platinum thin film gauges are deposited on the Macor inserts using both hand paint and vacuum sputtering technique. Using the Eckert reference temperature method the heating rates has been theoretically calculated along the flat plate portion of the model and the theoretical estimates are compared with experimentally determined surface heat transfer rate. Theoretical analysis of heat flux distribution down stream of the backward facing step model has been carried out using Gai’s non-dimensional analysis. Based on the measured surface heating rates on the backward facing step, the reattachment distance is estimated for 2 and 3 mm step height at nominal Mach number of 7.6. It has been found from the present study that for 2 and 3 mm step height, it approximately takes about 10 and 8 step heights downstream of the model respectively for the flow to re-attach.

Electromechanical interactions in a carbon nanotube based thin film field emitting diode

Carbon nanotubes (CNTs) have emerged as promising candidates for biomedical x-ray devices and other applications of field emission. CNTs grown/deposited in a thin film are used as cathodes for field emission. In spite of the good performance of such cathodes, the procedure to estimate the device current is not straightforward and the required insight towards design optimization is not well developed. In this paper, we report an analysis aided by a computational model and experiments by which the process of evolution and self-assembly (reorientation) of CNTs is characterized and the device current is estimated. The modeling approach involves two steps: (i) a phenomenological description of the degradation and fragmentation of CNTs and (ii) a mechanics based modeling of electromechanical interaction among CNTs during field emission. A computational scheme is developed by which the states of CNTs are updated in a time incremental manner. Finally, the device current is obtained by using the Fowler–Nordheim equation for field emission and by integrating the current density over computational cells. A detailed analysis of the results reveals the deflected shapes of the CNTs in an ensemble and the extent to which the initial state of geometry and orientation angles affect the device current. Experimental results confirm these effects.

B Physics: WHEPP-XI working group report

We present the report of the B physics working group of the Workshop on High Energy Physics Phenomenology (WHEPP-XI), held at the Physical Research Laboratory, Ahmedabad, in January 2010.

Enhancement of uniaxial magnetic anisotropy in Fe thin films grown on GaAs(001) with an MgO underlayer

The understanding and control of anisotropy in Fe films grown on cubic systems such as GaAs and MgO has been of interest from the point of view of applications in devices. We report magnetic anisotropy studies on Fe/GaAs(001) and Fe/MgO/GaAs(001) prepared by pulsed laser deposition. In Fe/GaAs(001), magneto optical Kerr effect (MOKE) measurements revealed a dominant uniaxial anisotropy for Fe thickness less than 20 monolayers (ML) and this was confirmed by ferromagnetic resonance (FMR) studies. Multiple steps in the hysteresis loops were observed for Fe films of thickness 20 and 25 ML. Whereas, in Fe/MgO/GaAs(001), even at 25 ML of Fe, the uniaxial anisotropy remained dominant. The anisotropy constants obtained from FMR spectra have shown that the relative strength of uniaxial anisotropy is higher as compared to the cubic anisotropy constant in the case of Fe/MgO/GaAs(001). (C) 2011 American Institute of Physics. doi:10.1063/1.3556941]