Under-representation of intrinsic terminators across bacterial genomic islands: Rho as a principal regulator of xenogenic DNA expression

Two transcription termination mechanisms - intrinsic and Rho-dependent - have evolved in bacteria. The Rho factor occurs in most bacterial lineages, and has been hypothesized to play a global regulatory role. Genome-wide studies using microarray, 2D-gel electrophoresis and ChIP-chip provided evidence that Rho serves to silence transcription from horizontally acquired genes and prophages in Escherichia coli K-12, implicating the factor to be a part of the ``cellular immune mechanism'' protecting against deleterious phages and aberrant gene expression from acquired xenogenic DNA. We have investigated this model by adopting an alternate in silico approach and have extended the study to other species. Our analysis shows that several genomic islands across diverse phyla have under-representation of intrinsic terminators, similar to that experimentally observed in E. coli K-12. This implies that Rho-dependent termination is the predominant process operational in these islands and that silencing of foreign DNA is a conserved function of Rho. From the present analysis, it is evident that horizontally acquired islands have lost intrinsic terminators to facilitate Rho-dependent termination. These results underscore the importance of Rho as a conserved, genome-wide sentinel that regulates potentially toxic xenogenic DNA. (C) 2012 Elsevier B.V. All rights reserved.

Conformational dynamics of HIV-1 protease: a comparative molecular dynamics simulation study with multiple amber force fields

Flap dynamics of HIV-1 protease (HIV-pr) controls the entry of inhibitors and substrates to the active site. Dynamical models from previous simulations are not all consistent with each other and not all are supported by the NMR results. In the present work, the er effect of force field on the dynamics of HIV-pr is investigated by MD simulations using three AMBER force fields ff99, ff99SB, and ff03. The generalized order parameters for amide backbone are calculated from the three force fields and compared with the NMR S2 values. We found that the ff99SB and ff03 force field calculated order parameters agree reasonably well with the NMR S2 values, whereas ff99 calculated values deviate most from the NMR order parameters. Stereochemical geometry of protein models from each force field also agrees well with the remarks from NMR S2 values. However, between ff99SB and ff03, there are several differences, most notably in the loop regions. It is found that these loops are, in general, more flexible in the ff03 force field. This results in a larger active site cavity in the simulation with the ff03 force field. The effect of this difference in computer-aided drug design against flexible receptors is discussed.

Methane and carbon dioxide adsorption on edge-functionalized graphene: a comparative DFT study

With a view towards optimizing gas storage and separation in crystalline and disordered nanoporous carbon-based materials, we use ab initio density functional theory calculations to explore the effect of chemical functionalization on gas binding to exposed edges within model carbon nanostructures. We test the geometry, energetics, and charge distribution of in-plane and out-of-plane binding of CO2 and CH4 to model zigzag graphene nanoribbons edge-functionalized with COOH, OH, NH2, H2PO3, NO2, and CH3. Although different choices for the exchange-correlation functional lead to a spread of values for the binding energy, trends across the functional groups are largely preserved for each choice, as are the final orientations of the adsorbed gas molecules. We find binding of CO2 to exceed that of CH4 by roughly a factor of two. However, the two gases follow very similar trends with changes in the attached functional group, despite different molecular symmetries. Our results indicate that the presence of NH2, H2PO3, NO2, and COOH functional groups can significantly enhance gas binding, making the edges potentially viable binding sites in materials with high concentrations of edge carbons. To first order, in-plane binding strength correlates with the larger permanent and induced dipole moments on these groups. Implications for tailoring carbon structures for increased gas uptake and improved CO2/CH4 selectivity are discussed. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.4736568]

Direct Observation of Valley Hybridization and Universal Symmetry of Graphene with Mesoscopic Conductance Fluctuations

In graphene, the valleys represent spinlike quantities and can act as a physical resource in valley-based electronics to produce novel quantum computation schemes. Here we demonstrate a direct route to tune and read the valley quantum states of disordered graphene by measuring the mesoscopic conductance fluctuations. We show that the conductance fluctuations in graphene at low temperatures are reduced by a factor of 4 when valley triplet states are gapped in the presence of short-range potential scatterers at high carrier densities. We also show that this implies a gate tunable universal symmetry class that outlines a fundamental feature arising from graphene's unique crystal structure.

Modified Newton, rank-1 Broyden update and rank-2 BFGS update methods in helicopter trim: A comparative study

Nonlinear equations in mathematical physics and engineering are solved by linearizing the equations and forming various iterative procedures, then executing the numerical simulation. For strongly nonlinear problems, the solution obtained in the iterative process can diverge due to numerical instability. As a result, the application of numerical simulation for strongly nonlinear problems is limited. Helicopter aeroelasticity involves the solution of systems of nonlinear equations in a computationally expensive environment. Reliable solution methods which do not need Jacobian calculation at each iteration are needed for this problem. In this paper, a comparative study is done by incorporating different methods for solving the nonlinear equations in helicopter trim. Three different methods based on calculating the Jacobian at the initial guess are investigated. (C) 2011 Elsevier Masson SAS. All rights reserved.

COMPARATIVE EVALUATION OF THERMAL CONDUCTIVITY OF ZIRCONIA SOLID AND HONEYCOMB STRUCTURES

Porous zirconia ceramic monoliths have been extensively used in thermo-structural applications due to their inherent low thermal conductivity in combination with their adaptability to form complicated shapes through advanced ceramic processing techniques. However, extruded cellular honeycomb structures made from these materials have been less explored for thermal management applications. There exist large potential applications due to their unique configurations, resulting in better heat-management mechanisms. Some of the studies carried out on zirconia honeycombs are safeguarded through patents due to its technical importance, or the information is not in the public domain. In the present study, for the sake of comparison, honeycomb specimens with varying wall thicknesses and unit cell lengths maintaining almost same bulk density of around 90% theoretical and relative density of 0.34-0.37 were prepared and subjected to thermal conductivity evaluation along with the solid samples with relative density of 1.0 using monotonic heating regime methodology. In addition, the effect of channel shape was also evaluated using square and triangular channeled honeycombs with the same relative densities. The results obtained from these specimens were correlated with their configurations to bring out the advantages accrued by using the honeycomb with these configurations. It was observed that a significant decrease in thermal conductivity was achieved in honeycombs, which can be attributed to the behavior of various heat transfer mechanisms that are operative at high temperatures in combination with the considerable reduction in thermal mass and the consequent conduction through the solids.

Identification of mycobacterial lectins from genomic data

Sixty-four sequences containing lectin domains with homologs of known three-dimensional structure were identified through a search of mycobacterial genomes. They appear to belong to the -prism II, the C-type, the Microcystis virdis (MV), and the -trefoil lectin folds. The first three always occur in conjunction with the LysM, the PI-PLC, and the -grasp domains, respectively while mycobacterial -trefoil lectins are unaccompanied by any other domain. Thirty heparin binding hemagglutinins (HBHA), already annotated, have also been included in the study although they have no homologs of known three-dimensional structure. The biological role of HBHA has been well characterized. A comparison between the sequences of the lectin from pathogenic and nonpathogenic mycobacteria provides insights into the carbohydrate binding region of the molecule, but the structure of the molecule is yet to be determined. A reasonable picture of the structural features of other mycobacterial proteins containing one or the other of the four lectin domains can be gleaned through the examination of homologs proteins, although the structure of none of them is available. Their biological role is also yet to be elucidated. The work presented here is among the first steps towards exploring the almost unexplored area of the structural biology of mycobacterial lectins. Proteins 2013. (c) 2012 Wiley Periodicals, Inc.

Characterization and microhardness of Co-W coatings electrodeposited at different pH using gluconate bath: a comparative study

Electrodeposition of Co-W alloy coatings has been carried out with DC and PC using gluconate bath at different pH. These coatings are characterized for their structure, morphology and chemical composition by X-ray diffraction, field emission scanning electron microscopy, differential scanning calorimetry and X-ray photoelectron spectroscopy (XPS). Alloy coatings plated at pH8 are crystalline, whereas coatings electrodeposited at pH5 are nanocrystalline in nature. XPS studies have demonstrated that as-deposited alloy plated at pH8 with DC contain only Co2+ and W6+ species, whereas that alloy plated at pH5 has significant amount of Co-0 and W-0 along with Co2+ and W6+ species. Again, Co2+ and W6+ are main species in all as-deposited PC plated alloys in both pH. Co-0 concentration increases upon successive sputtering of all alloy coatings. In contrast, mainly W6+ species is detected in the following layers of all alloys plated with PC. Alloys plated at pH5 show higher microhardness compared to their pH8 counterparts.

Comparative study on optical properties of Se-Zn-In and Se-Zn-Te-In chalcogenide glasses

In contemporary world optoelectronics materials are used in daily life owing to its verity of applications. Utility of these materials makes them attractive for investigations. Specifically study regarding optical properties of recent developed materials is worth for technical uses. Therefore, this work demonstrates a comparative study of extinction coefficient (K), real dielectric (epsilon') and imaginary dielectric (epsilon `') constants, refractive index (n) and optical energy band gap (E-g) with structural unit < r > for Se98-xZn2Inx (0 <= X-In <= 10) and Se93-yZn2Te5Iny (0 <= Y-In <= 10) chalcogenide glasses. Fixed amount of Te with increasing In concentration as cost of Se is largely influence the optical parameters of the materials. Values of optical parameters are obtained higher and lower respectively at thresholds structural units values. This comparative study demonstrates that enhanced values of optical parameters have been obtained for Te containing Se-Zn-In glasses.

Microcracking and fracture process in cement mortar and concrete: a comparative study using acoustic emission technique

This article reports the acoustic emission (AE) study of precursory micro-cracking activity and fracture behaviour of quasi-brittle materials such as concrete and cement mortar. In the present study, notched three-point bend specimens (TPB) were tested under crack mouth opening displacement (CMOD) control at a rate of 0.0004 mm/sec and the accompanying AE were recorded using a 8 channel AE monitoring system. The various AE statistical parameters including AE event rate , AE energy release rate , amplitude distribution for computing the AE based b-value, cumulative energy (I E) pound and ring down count (RDC) were used for the analysis. The results show that the micro-cracks initiated and grew at an early stage in mortar in the pre peak regime. While in the case of concrete, the micro-crack growth occurred during the peak load regime. However, both concrete and mortar showed three distinct stages of micro-cracking activity, namely initiation, stable growth and nucleation prior to the final failure. The AE statistical behavior of each individual stage is dependent on the number and size distribution of micro-cracks. The results obtained in the laboratory are useful to understand the various stages of micro-cracking activity during the fracture process in quasi-brittle materials such as concrete & mortar and extend them for field applications.

Device Fabrication of insoluble donor-acceptor-donor structured molecule by pulsed laser deposition- A comparative study using different laser source

Many of the conducting polymers though having good material property are not solution processable. Hence an alternate method of fabrication of film by pulsed laser deposition, was explored in this work. PDTCPA, a donor-acceptor-donor type of polymer having absorption from 900 nm to 300 nm was deposited by both UV and IR laser to understand the effect of deposition parameters on the film quality. It was observed that the laser ablation of PDTCPA doesn't alter its chemical structure hence retaining the chemical integrity of the polymer. Microscopic studies of the ablated film shows that the IR laser ablated films were particulate in nature while UV laser ablated films are deposited as smooth continuous layer. The morphology of the film influences its electrical characteristics as current-voltage characteristic of these films shows that films deposited by UV laser are p rectifying while those by IR laser are more of resistor in nature.

A comparative study of room temperature ferromagnetism in MgO films deposited by rf/dc sputtering using high purity Mg and MgO targets

Thin films of nanocrystalline MgO were deposited on glass/Si substrates by rf/dc sputtering from metallic Mg, and ceramic MgO targets. The purpose of this study is to identify the differences in the properties, magnetic in particular, of MgO films obtained on sputter deposition from 99.99% pure metallic Mg target in a controlled Nitrogen + Oxygen partial pressure (O(2)pp)] atmosphere as against those deposited using an equally pure ceramic MgO target in argon + identical oxygen ambience conditions while maintaining the same total pressure in the chamber in both cases. Characterization of the films was carried out by X-ray diffraction, focussed ion beam cross sectioning, atomic force microscopy and SQUID-magnetometry. The `as-obtained' films from pure Mg target are found to be predominantly X-ray amorphous, while the ceramic MgO target gives crystalline films, (002) oriented with respect to the film plane. The films consisted of nano-crystalline grains of size in the range of about 0.4 to 4.15 nm with the films from metallic target being more homogeneous and consisting of mostly subnanometer grains. Both the types of films are found to be ferromagnetic to much above room temperature. We observe unusually high maximum saturation magnetization (MS) values of 13.75 emu/g and similar to 4.2 emu/g, respectively for the MgO films prepared from Mg, and MgO targets. The origin of magnetism in MgO films is attributed to Mg vacancy (V-Mg), and 2p holes localized on oxygen sites. The role of nitrogen in enhancing the magnetic moments is also discussed.

Comparative Evaluation of Switching and Average Models of a DC-DC Boost Converter for Real-Time Simulation

This paper presents a comparative evaluation of the average and switching models of a dc-dc boost converter from the point of view of real-time simulation. Both the models are used to simulate the converter in real-time on a Field Programmable Gate Array (FPGA) platform. The converter is considered to function over a wide range of operating conditions, and could do transition between continuous conduction mode (CCM) and discontinuous conduction mode (DCM). While the average model is known to be computationally efficient from the perspective of off-line simulation, the same is shown here to consume more logical resources than the switching model for real-time simulation of the dc-dc converter. Further, evaluation of the boundary condition between CCM and DCM is found to be the main reason for the increased consumption of resources by the average model.

Comparative Evaluation of Zoledronic Acid, Alfacalcidol and Propranolol in Pharmacological Correction of Experimental Osteoporosis

Propranolol, a beta-adrenergic receptor blocker, is presently considered to be a potential therapeutic intervention under investigation for its role in prevention and treatment of osteoporosis. However, no studies have compared the osteoprotective properties of propranolol with well accepted therapeu-tic interventions for the treatment of osteoporosis. To address this question, this study was designed to evaluate the bone protective effects of zoledronic acid, alfacalcidol and propranolol in an animal model of postmenopausal osteoporosis. Five days after ovariectomy, 36 ovariectomized (OVX) rats were divided in- to 6 equal groups, randomized to treatments zoledronic acid (100 μg/kg, intravenous single dose); alfacal-cidol (0.5 μg/kg, oral gauge daily); propranolol (0.1mg/kg, subcutaneously 5 days per week) for 12 weeks. Untreated OVX and sham OVX were used as controls. At the end of the study, rats were killed under anesthesia. For bone porosity evaluation, whole fourth lumbar vertebrae (LV4) were removed. LV4 were also used to measure bone mechanical propeties. Left femurs were used for bone histology. Propranolol showed a significant decrease in bone porosity in comparison to OVX control. Moreover, propranolol sig- nificantly improved bone mechanical properties and bone quality when compared with OVX control. The osteoprotective effect of propranolol was comparable with zoledronic acid and alfacalcidol. Based on this comparative study, the results strongly suggest that propranolol might be new therapeutic intervention for the management of postmenopausal osteoporosis in humans.