Insights into the Fold Organization of TIM Barrel from Interaction Energy Based Structure Networks

There are many well-known examples of proteins with low sequence similarity, adopting the same structural fold. This aspect of sequence-structure relationship has been extensively studied both experimentally and theoretically, however with limited success. Most of the studies consider remote homology or ``sequence conservation'' as the basis for their understanding. Recently ``interaction energy'' based network formalism (Protein Energy Networks (PENs)) was developed to understand the determinants of protein structures. In this paper we have used these PENs to investigate the common non-covalent interactions and their collective features which stabilize the TIM barrel fold. We have also developed a method of aligning PENs in order to understand the spatial conservation of interactions in the fold. We have identified key common interactions responsible for the conservation of the TIM fold, despite high sequence dissimilarity. For instance, the central beta barrel of the TIM fold is stabilized by long-range high energy electrostatic interactions and low-energy contiguous vdW interactions in certain families. The other interfaces like the helix-sheet or the helix-helix seem to be devoid of any high energy conserved interactions. Conserved interactions in the loop regions around the catalytic site of the TIM fold have also been identified, pointing out their significance in both structural and functional evolution. Based on these investigations, we have developed a novel network based phylogenetic analysis for remote homologues, which can perform better than sequence based phylogeny. Such an analysis is more meaningful from both structural and functional evolutionary perspective. We believe that the information obtained through the ``interaction conservation'' viewpoint and the subsequently developed method of structure network alignment, can shed new light in the fields of fold organization and de novo computational protein design.

Insights to urban dynamics through landscape spatial pattern analysis

Urbanisation is a dynamic complex phenomenon involving large scale changes in the land uses at local levels. Analyses of changes in land uses in urban environments provide a historical perspective of land use and give an opportunity to assess the spatial patterns, correlation, trends, rate and impacts of the change, which would help in better regional planning and good governance of the region. Main objective of this research is to quantify the urban dynamics using temporal remote sensing data with the help of well-established landscape metrics. Bangalore being one of the rapidly urbanising landscapes in India has been chosen for this investigation. Complex process of urban sprawl was modelled using spatio temporal analysis. Land use analyses show 584% growth in built-up area during the last four decades with the decline of vegetation by 66% and water bodies by 74%. Analyses of the temporal data reveals an increase in urban built up area of 342.83% (during 1973-1992), 129.56% (during 1992-1999), 106.7% (1999-2002), 114.51% (2002-2006) and 126.19% from 2006 to 2010. The Study area was divided into four zones and each zone is further divided into 17 concentric circles of 1 km incrementing radius to understand the patterns and extent of the urbanisation at local levels. The urban density gradient illustrates radial pattern of urbanisation for the period 1973-2010. Bangalore grew radially from 1973 to 2010 indicating that the urbanisation is intensifying from the central core and has reached the periphery of the Greater Bangalore. Shannon's entropy, alpha and beta population densities were computed to understand the level of urbanisation at local levels. Shannon's entropy values of recent time confirms dispersed haphazard urban growth in the city, particularly in the outskirts of the city. This also illustrates the extent of influence of drivers of urbanisation in various directions. Landscape metrics provided in depth knowledge about the sprawl. Principal component analysis helped in prioritizing the metrics for detailed analyses. The results clearly indicates that whole landscape is aggregating to a large patch in 2010 as compared to earlier years which was dominated by several small patches. The large scale conversion of small patches to large single patch can be seen from 2006 to 2010. In the year 2010 patches are maximally aggregated indicating that the city is becoming more compact and more urbanised in recent years. Bangalore was the most sought after destination for its climatic condition and the availability of various facilities (land availability, economy, political factors) compared to other cities. The growth into a single urban patch can be attributed to rapid urbanisation coupled with the industrialisation. Monitoring of growth through landscape metrics helps to maintain and manage the natural resources. (C) 2012 Elsevier B.V. All rights reserved.

Remarkable photocytotoxicity of curcumin in HeLa cells in visible light and arresting its degradation on oxovanadium(IV) complex formation

Curcumin (Hcur) as a cellular imaging and PDT agent shows remarkable photocytotoxicity in HeLa cells in visible light of 400-700 nm giving IC50 = 8.2 +/- 0.2 mu M and its degradation is arrested on formation of photocytotoxic dipyridophenazine (dppz) complex VO(cur)(dppz)Cl] (IC50 = 3.3 +/- 0.4 mu M), while both are less toxic in the dark.

Light Induced Optical Properties Change in Sb20S40Se40 Thin Films

Thin films of Sb20S40Se40 of thickness 800 nm were prepared by thermal evaporation method. The as-prepared and illuminated thin films were studied by X-ray diffraction, Fourier Transform Infrared Spectroscopy and X-ray Photoelectron Spectroscopy and Raman spectroscopy. The optical band gap was reduced due to photo induced effects along with the increase in disorder. These optical properties changes are due to the change of homopolar bond densities. The core level peak shifting in XPS and Raman spectra supports the optical changes happening in the film due to light exposure.

Visible light photocatalytic inactivation of Escherichia coli with combustion synthesized TiO2

The photocatalytic inactivation of Escherichia coil was studied with combustion synthesized TiO2 photocatalysts in the presence of visible light. A series of 400W lamps irradiating in the visible region of the solar spectrum was used. The effect of various parameters, such as catalyst loading, light intensity, presence of inorganic ions, addition of hydrogen peroxide and pH, on the photocatalytic inactivation of E. coil was investigated. Photolysis alone had a small effect on inactivation while the dark experiment resulted in no inactivation and Ag/TiO2 showed the maximum inactivation. At a catalyst loading of 0.25 g/L, all the combustion synthesized catalysts showed better inactivation of E. coil compared to commercial Degussa P-25 (DP-25) TiO2 catalyst. An improved inactivation was observed with increasing lamp intensity and addition of H2O2. A negative effect on inactivation was observed by addition of inorganic ions such as HCO3-, SO42-, Cl-, NO3-, Na+, K+ and Ca2+. The photocatalytic inactivation of E. coli remained unaltered at different pH of the solution. The inactivation of E. coli was modeled with power law kinetics and was observed to follow first order kinetics. (C) 2012 Elsevier B.V. All rights reserved.

Photocytotoxic Oxidovanadium(IV) Complexes of Polypyridyl Ligands Showing DNA-Cleavage Activity in Near-IR Light

Oxidovanadium(IV) complexes VO(pyphen)(L)]Cl2 (1, 2) and VO(pydppz)(L)]Cl2 (3, 4), where L is 1,10-phenanthroline (phen in 1 and 3) and dipyrido3,2-a:2',3'-c]phenazine (dppz in 2 and 4) are prepared and characterized. The crystal structure of VO(pyphen)(phen)](ClO4)2 (1a) shows a six-coordinate VN5O geometry with a VO2+ moiety in which the polypyridyl ligand binds in a meridional fashion and the phen ligand displays a chelating binding mode with an N-donor site trans to the oxidovanadyl group. The complexes show a dd band within 720-750 nm in DMF. The one-electron paramagnetic complexes are 1:2 electrolytes in DMF. The complexes exhibit an irreversible VIV/VIII redox response near -0.85 V vs. SCE in DMF/0.1 M TBAP. The complexes bind to calf thymus (ct) DNA giving Kb values within 7.5 x 104 to 1.1 x 106 M1. The complexes show poor chemical nuclease activity in the dark and exhibit significant DNA-photocleaving activity in near-IR light of 705 and 785 nm forming .OH radicals. Complexes 2-4 show remarkable photocytotoxicity in HeLa cancer cells. FACS analysis of the HeLa cells treated with complex 4 shows cell death as highlighted by the sub G1 peak. Propidium iodide staining data indicate apoptosis as the primary mode of cell death.

Enhanced Raman Spectroscopy of Molecules Adsorbed on Carbon-Doped TiO2 Obtained from Titanium Carbide: A Visible-Light-Assisted Renewable Substrate

Titanium carbide (TiC) is an electrically conducting material with favorable electrochemical properties. In the present studies, carbon-doped TiO2 (C-TiO2) has been synthesized from TiC particles, as well as TiC films coated on stainless steel substrate via thermal annealing under various conditions. Several C-TiO2 substrates are synthesized by varying experimental, conditions and characterized by UV-visible spectroscopy, photoluminescence, X-ray diffraction and X-ray photoelectron spectroscopic techniques. C-TiO2 in the dry state (in powder form as well as in film form) is subsequently used as a substrate for enhancing Raman signals corresponding to 4-mercaptobenzoic acid and 4-nitrothiophenol by utilizing chemical enhancement based on charge-transfer interactions. Carbon, a nonmetal dopant in TiO2, improves the intensities of Raman signals, compared, to undoped TiO2. Significant dependence of Raman intensity on carbon doping is observed. Ameliorated performance obtained using C-TiO2 is attributed to the presence of surface defects that originate due to carbon as a dopant, which, in turn,, triggers charge transfer between TiO2 and analyte. The C-TiO2 substrates are subsequently regenerated for repetitive use by illuminating an analyte-adsorbed substrate with visible light for a period of 5 h.

Effect of thickness variation of hole injection and hole blocking layers on the performance of fluorescent green organic light emitting diodes

In this paper we present the effect of thickness variation of hole injection and hole blocking layers on the performance of fluorescent green organic light emitting diodes (OLEDs). A number of OLED devices have been fabricated with combinations of hole injecting and hole blocking layers of varying thicknesses. Even though hole blocking and hole injection layers have opposite functions, yet there is a particular combination of their thicknesses when they function in conjunction and luminous efficiency and power efficiency are maximized. The optimum thickness of CuPc (Copper(II) phthalocyanine) layer, used as hole injection layer and BCP (2,9 dimethyl-4,7-diphenyl-1,10-phenanthroline) used as hole blocking layer were found to be 18 nm and 10 nm respectively. It is with this delicate adjustment of thicknesses, charge balancing is achieved and luminous efficiency and power efficiency were optimized. The maximum luminous efficiency of 3.82 cd/A at a current density of 24.45 mA/cm(2) and maximum power efficiency of 2.61 lm/W at a current density of 5.3 mA/cm(2) were achieved. We obtained luminance of 5993 cd/m(2) when current density was 140 mA/cm(2). The EL spectra was obtained for the LEDs and found that it has a peaking at 524 nm of wavelength. (C) 2012 Elsevier B.V. All rights reserved.

Ultrasound modulation of coherent light in a multiple-scattering medium: experimental verification of nonzero average phase carried by light

We demonstrate the phase fluctuation introduced by oscillation of scattering centers in the focal volume of an ultrasound transducer in an optical tomography experiment has a nonzero mean. The conditions to be met for the above are: (i) the frequency of the ultrasound should be in the vicinity of the most dominant natural frequency of vibration of the ultrasound focal volume, (ii) the corresponding acoustic wavelength should be much larger than l(n)*, a modified transport mean-free-path applicable for phase decorrelation and (iii) the focal volume of the ultrasound transducer should not be larger than 4 - 5 times (l(n)*)(3). We demonstrate through simulations that as the ratio of the ultrasound focal volume to (l(n)*)(3) increases, the average of the phase fluctuation decreases and becomes zero when the focal volume becomes greater than around 4(l(n)*)(3); and through simulations and experiments that as the acoustic frequency increases from 100 Hz to 1 MHz, the average phase decreases to zero. Through experiments done in chicken breast we show that the average phase increases from around 110 degrees to 130 degrees when the background medium is changed from water to glycerol, indicating that the average of the phase fluctuation can be used to sense changes in refractive index deep within tissue.

Spatial Filter Based Bessel-Like Beam for Improved Penetration Depth Imaging in Fluorescence Microscopy

Monitoring and visualizing specimens at a large penetration depth is a challenge. At depths of hundreds of microns, several physical effects (such as, scattering, PSF distortion and noise) deteriorate the image quality and prohibit a detailed study of key biological phenomena. In this study, we use a Bessel-like beam in-conjugation with an orthogonal detection system to achieve depth imaging. A Bessel-like penetrating diffractionless beam is generated by engineering the back-aperture of the excitation objective. The proposed excitation scheme allows continuous scanning by simply translating the detection PSF. This type of imaging system is beneficial for obtaining depth information from any desired specimen layer, including nano-particle tracking in thick tissue. As demonstrated by imaging the fluorescent polymer-tagged-CaCO3 particles and yeast cells in a tissue-like gel-matrix, the system offers a penetration depth that extends up to 650 mu m. This achievement will advance the field of fluorescence imaging and deep nano-particle tracking.

Near-infrared light-responsive graphene oxide composite multilayer capsules: a novel route for remote controlled drug delivery

A novel and simple route for near-infrared (NIR)-light controlled release of drugs has been demonstrated using graphene oxide (GO) composite microcapsules based on the unique optical properties of GO. Upon NIR-laser irradiation, the microcapsules were ruptured in a point-wise fashion due to local heating which in turn triggers the light-controlled release of the encapsulated anticancer drug doxorubicin (Dox) from these capsules.

Spatial Modulation and Space Shift Keying in Single Carrier Communication

Spatial modulation (SM) and space shift keying (SSK) are relatively new modulation techniques which are attractive in multi-antenna communications. Single carrier (SC) systems can avoid the peak-to-average power ratio (PAPR) problem encountered in multicarrier systems. In this paper, we study SM and SSK signaling in cyclic-prefixed SC (CPSC) systems on MIMO-ISI channels. We present a diversity analysis of MIMO-CPSC systems under SSK and SM signaling. Our analysis shows that the diversity order achieved by (n(t), n(r)) SSK scheme and (n(t), n(r), Theta(M)) SM scheme in MIMO-CPSC systems under maximum-likelihood (ML) detection is n(r), where n(t), n(r) denote the number of transmit and receive antennas and Theta(M) denotes the modulation alphabet of size M. Bit error rate (BER) simulation results validate this predicted diversity order. Simulation results also show that MIMO-CPSC with SM and SSK achieves much better performance than MIMO-OFDM with SM and SSK.

Spatial SINR Games of Base Station Placement and Mobile Association

We study the question of determining locations of base stations (BSs) that may belong to the same or to competing service providers. We take into account the impact of these decisions on the behavior of intelligent mobile terminals that can connect to the base station that offers the best utility. The signal-to-interference-plus-noise ratio (SINR) is used as the quantity that determines the association. We first study the SINR association-game: We determine the cells corresponding to each base stations, i.e., the locations at which mobile terminals prefer to connect to a given base station than to others. We make some surprising observations: 1) displacing a base station a little in one direction may result in a displacement of the boundary of the corresponding cell to the opposite direction; 2) a cell corresponding to a BS may be the union of disconnected subcells. We then study the hierarchical equilibrium in the combined BS location and mobile association problem: We determine where to locate the BSs so as to maximize the revenues obtained at the induced SINR mobile association game. We consider the cases of single frequency band and two frequency bands of operation. Finally, we also consider hierarchical equilibria in two frequency systems with successive interference cancellation.

Effect of Metal Ions (Ag, Co, Ni, and Pd) on the Visible Light Degradation of Rhodamine B by Carbon-Covered Alumina-Supported TiO2 in Aqueous Solutions

Metal-ion (Ag, Co, Ni, and Pd) doped TiO2 nanocatalysts were successfully embedded on carbon-covered alumina supports. The CCA-embedded catalysts were crystalline and had a high surface area compared to the free metal-ion doped titania nanocatalysts while they still retained the anatase phase of the core TiO2. These catalysts were photocatalytically active under solar light irradiation. Rhodamine B was used as a model pollutant and the reactivity followed a pseudo-first-order reaction kinetics. The reaction rate of the CCA-supported catalysts was Pd > Ag > Co > Ni. Among the ratios of the CCA:catalyst used, it was found that the 1:1 ratio had the fastest reaction rate, followed by the 1:2 ratio, while the 2:1 ratio exhibited the lowest reaction rate. The CCA/metal-ion doped titania were found to have photocatalytic activities comparable with those of CCA-supported titania.

Photocatalytic degradation with combustion synthesized WO3 and WO3-TiO2 mixed oxides under UV and visible light

The photocatalytic activity of commercial titanium dioxide under UV and visible radiation was improved by composites of tungsten trioxide (WO3) with TiO2. WO3 was prepared by solution combustion synthesis and the mixed oxides/composites of WO3-TiO2 were prepared in different weight ratios (0, 0.10, 0.15, 0.20, 0.25, 0.50, 0.75, and 1) by physical mixing. These catalysts were characterized by XRD, DRS, BET, SEM, TEM, pH drift method, TGA and photoluminescence. The photocatalytic activity varies with the WO3 loading in the composites. The optimum loading of WO3 in the composites was found to be 15 wt% for both UV and visible radiation. This loading showed faster dye degradation rate than commercial TiO2 (TiO2-C) and WO3 (WO3-C). The effect of initial concentrations of methylene blue (MB) and orange G (OG) and the effect of the functional group on dye degradation was studied with both anionic and cationic dyes with 15 wt% WO3-TiO2. (C) 2012 Elsevier B.V. All rights reserved.