Vibrational spectroscopy and density functional theory analysis of 3-O-caffeoylquinic acid

Density functional theory (DFT) calculations are being performed to investigate the geometric, vibrational, and electronic properties of the chlorogenic acid isomer 3-CQA (1R,3R,4S,5R)-3-{(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-1,4, 5-trihydroxycyclohexanecarboxylic acid), a major phenolic compound in coffee. DFT calculations with the 6-311G(d,p) basis set produce very good results. The electrostatic potential mapped onto an isodensity surface has been obtained. A natural bond orbital analysis (NBO) has been performed in order to study intramolecular bonding, interactions among bonds, and delocalization of unpaired electrons. HOMO-LUMO studies give insights into the interaction of the molecule with other species. The calculated HOMO and LUMO energies indicate that a charge transfer occurs within the molecule. (C) 2012 Elsevier B.V. All rights reserved.

Pseudo-Static and Pseudo-Dynamic Stability Analysis of Tailings Dam Under Seismic Conditions

In this paper the seismic slope stability analyses are performed for a typical section of 44 m high water retention type tailings earthen dam located in the eastern part of India, using both the conventional pseudo-static and recent pseudo-dynamic methods. The tailings earthen dam is analyzed for different upstream conditions of reservoir like filled up with compacted and non-compacted dumped waste materials with different water levels of the pond tailings portion. Phreatic surface is generated using seepage analysis in geotechnical software SEEP/W and that same is used in the pseudo-static and pseudo-dynamic analyses to make the approach more realistic. The minimum values of factor of safety using pseudo-static and pseudo-dynamic method are obtained as 1.18 and 1.09 respectively for the chosen seismic zone in India. These values of factor of safety show clearly the demerits of conventional pseudo-static analysis compared to recent pseudo-dynamic analysis, where in addition to the seismic accelerations, duration, frequency of earthquake, body waves traveling during earthquake and amplification effects are considered.

Polynomial time and parameterized approximation algorithms for boxicity

The boxicity (cubicity) of a graph G, denoted by box(G) (respectively cub(G)), is the minimum integer k such that G can be represented as the intersection graph of axis parallel boxes (cubes) in ℝ k . The problem of computing boxicity (cubicity) is known to be inapproximable in polynomial time even for graph classes like bipartite, co-bipartite and split graphs, within an O(n 0.5 − ε ) factor for any ε > 0, unless NP = ZPP. We prove that if a graph G on n vertices has a clique on n − k vertices, then box(G) can be computed in time n22O(k2logk) . Using this fact, various FPT approximation algorithms for boxicity are derived. The parameter used is the vertex (or edge) edit distance of the input graph from certain graph families of bounded boxicity - like interval graphs and planar graphs. Using the same fact, we also derive an O(nloglogn√logn√) factor approximation algorithm for computing boxicity, which, to our knowledge, is the first o(n) factor approximation algorithm for the problem. We also present an FPT approximation algorithm for computing the cubicity of graphs, with vertex cover number as the parameter.

Expression and function of cyclooxygenase-2 is necessary for hamster blastocyst hatching

Blastocyst hatching is critical for successful implantation leading to pregnancy. Its failure causes infertility. The phenomenon of blastocyst hatching in humans is poorly understood and the available information on this stems from studies of rodents such as mice and hamsters. We and others showed that hamster blastocyst hatching is characterized by firstly blastocyst deflation followed by a dissolution of the zona pellucida (zona) and accompanied by trophectodermal projections (TEPs). We also showed that embryo-derived cathepsins (Cat) proteases, specifically Cat-L, -B and -P act as zonalysins and are responsible for hatching. In this study, we show the expression and function of one of the potential regulators of embryogenesis, cyclooxygenase (COX)-2 during blastocyst development and hatching. The expression of COX-2 mRNA and protein was observed in 8-cell through hatched blastocyst stages and it was also localized to blastocysts TEPs. Specific COX-2 inhibitors, NS-398 and CAY-10404, inhibited blastocyst hatching; percentages achieved were only 28.4 5.3 and 32.3 5.4, respectively, compared with 90 with untreated embryos. Interestingly, inhibitor-treated blastocysts failed to deflate, normally observed during hatching. Supplementation of prostaglandins (PGs)-E-2 or -I-2 to cultured embryos reversed the inhibitors effect on hatching and also the deflation behavior. Importantly, the levels of mRNA and protein of Cat-L, -B and -P showed a significant reduction in the inhibitor-treated embryos compared with untreated embryos, although its mechanism remains to be examined. These data provide the first evidence that COX-2 is critical for blastocyst hatching in the golden hamster.

Form and Function of Proteins. Historical Background and the Indian Effort in Macromolecular Crystallography

Global efforts in macromolecular crystallography started in the thirties of the last century. However, definitive results began to emerge only in the late fifties and the early sixties. India has a long tradition in crystallography. The country had a head start in theoretical and computational structural biology, thanks to the efforts of G.N. Ramachandran and his colleagues in the fifties and the sixties. However, macromolecular crystallography got off the ground in India only in the eighties, particularly after the Bangalore group received adequate support from the Department of Science and Technology under their Thrust Area Programme. The Bangalore centre was also identified as a national nucleus for the development of the area in the country. Since then work in the area has spread widely and is being carried out by several groups, mainly led by scientists trained at Bangalore or their descendents, in about thirty institutions in India. In addition to the Department of Science and Technology, the effort is now supported by other agencies like the Department of Biotechnology and the Council of Scientific and Industrial Research. The problems addressed by macromolecular crystallographers in India encompass almost all aspects of modern biology. Indian efforts in macromolecular crystallography have also become an important component of the international efforts in the area.

Temperature-dependent stability of stacking faults in Al, Cu and Ni: first-principles analysis

We present comparative analysis of microscopic mechanisms relevant to plastic deformation of the face-centered cubic (FCC) metals Al, Cu, and Ni, through determination of the temperature-dependent free energies of intrinsic and unstable stacking faults along 1 (1) over bar 0] and 1 (2) over bar 1] on the (1 1 1) plane using first-principles density-functional-theory-based calculations. We show that vibrational contribution results in significant decrease in the free energy of barriers and intrinsic stacking faults (ISFs) of Al, Cu, and Ni with temperature, confirming an important role of thermal fluctuations in the stability of stacking faults (SFs) and deformation at elevated temperatures. In contrast to Al and Ni, the vibrational spectrum of the unstable stacking fault (USF1 (2) over bar 1]) in Cu reveals structural instabilities, indicating that the energy barrier (gamma(usf)) along the (1 1 1)1 (2) over bar 1] slip system in Cu, determined by typical first-principles calculations, is an overestimate, and its commonly used interpretation as the energy release rate needed for dislocation nucleation, as proposed by Rice (1992 J. Mech. Phys. Solids 40 239), should be taken with caution.

Photoluminescence properties of Eu3+-activated CaMoO4 phosphors for WLEDs applications and its Judd-Ofelt analysis

A series of scheelite-type Eu3+-activated CaMoO4 phosphors were synthesized by the nitrate-citrate gel combustion method. All the compounds crystallized in the tetragonal structure with space group I4(1)/a (No. 88). FESEM results reveal the spherical-like morphology. The CaMoO4 phosphor exhibited broad emission centered at 500 nm under the excitation of 298 nm wavelength, while Eu3+-activated CaMoO4 shows an intense characteristic red emission peak at 615 nm at different excitation wavelengths, due to D-5(0) -> F-7(2) transition of Eu3+ ions. The intensities of transitions between different J levels depend on the symmetry of the local environment of Eu3+ ions and were estimated using the Judd-Ofelt analysis. The high asymmetric ratio revealed that Eu3+ occupies sites with a low symmetry and without an inversion center. The CIE chromaticity co-ordinates (x, y) were calculated from emission spectra, and the values were close to the NTSC standard. Therefore, the present phosphor is highly useful for LEDs applications.

First and second law thermodynamic analysis of air and oxy-steam biomass gasification

Gasification is an energy transformation process in which solid fuel undergoes thermochemical conversion to produce gaseous fuel, and the two most important criteria involved in such process to evaluate the performance, economics and sustainability of the technology are: the total available energy (exergy) and the energy conserved (energy efficiency). Current study focuses on the energy and exergy analysis of the oxy-steam gasification and comparing with air gasification to optimize the H-2 yield, efficiency and syngas energy density. Casuarina wood is used as a fuel, and mixture of oxygen and steam in different proportion and amount is used as a gasifying media. The results are analysed with respect to varying equivalence ratio and steam to biomass ratio (SBR). Elemental mass balance technique is employed to ensure the validity of results. First and second law thermodynamic analysis is used towards time evaluation of energy and exergy analysis. Different component of energy input and output has been studied carefully to understand the influence of varying SBR on the availability of energy and irreversibility in the system to minimize the losses with change in input parameters for optimum performance. The energy and exergy losses (irreversibility) for oxy-steam gasification system are compared with the results of air gasification, and losses are found to be lower in oxy-steam thermal conversion; which has been argued and reasoned due to the presence of N-2 in the air-gasification. The maximum exergy efficiency of 85% with energy efficiency of 82% is achieved at SBR of 0.75 on the molar basis. It has been observed that increase in SBR results in lower exergy and energy efficiency, and it is argued to be due to the high energy input in steam generation and subsequent losses in the form of physical exergy of steam in the product gas, which alone accounts for over 18% in exergy input and 8.5% in exergy of product gas at SBR of 2.7. Carbon boundary point (CBP), is identified at the SBR of 1.5, and water gas shift (WGS) reaction plays a crucial role in H-2 enrichment after carbon boundary point (CBP) is reached. Effects of SBR and CBP on the H-2/CO ratio is analysed and discussed from the perspective of energy as well as the reaction chemistry. Energy density of syngas and energy efficiency is favoured at lower SBR but higher SBR favours H-2 rich gas at the expense of efficiency. Copyright (C) 2014, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.

Enriching the annotation of Mycobacterium tuberculosis H37Rv proteome using remote homology detection approaches: Insights into structure and function

The availability of the genome sequence of Mycobacterium tuberculosis H37Rv has encouraged determination of large numbers of protein structures and detailed definition of the biological information encoded therein; yet, the functions of many proteins in M. tuberculosis remain unknown. The emergence of multidrug resistant strains makes it a priority to exploit recent advances in homology recognition and structure prediction to re-analyse its gene products. Here we report the structural and functional characterization of gene products encoded in the M. tuberculosis genome, with the help of sensitive profile-based remote homology search and fold recognition algorithms resulting in an enhanced annotation of the proteome where 95% of the M. tuberculosis proteins were identified wholly or partly with information on structure or function. New information includes association of 244 proteins with 205 domain families and a separate set of new association of folds to 64 proteins. Extending structural information across uncharacterized protein families represented in the M. tuberculosis proteome, by determining superfamily relationships between families of known and unknown structures, has contributed to an enhancement in the knowledge of structural content. In retrospect, such superfamily relationships have facilitated recognition of probable structure and/or function for several uncharacterized protein families, eventually aiding recognition of probable functions for homologous proteins corresponding to such families. Gene products unique to mycobacteria for which no functions could be identified are 183. Of these 18 were determined to be M. tuberculosis specific. Such pathogen-specific proteins are speculated to harbour virulence factors required for pathogenesis. A re-annotated proteome of M. tuberculosis, with greater completeness of annotated proteins and domain assigned regions, provides a valuable basis for experimental endeavours designed to obtain a better understanding of pathogenesis and to accelerate the process of drug target discovery. (C) 2014 Elsevier Ltd. All rights reserved.

Biocompatibility property of 100% strontium-substituted SiO2-Al2O3-P2O5-CaO-CaF2 glass ceramics over 26 weeks implantation in rabbit model: Histology and micro-Computed Tomography analysis

One of the desired properties for any new biomaterial composition is its long-term stability in a suitable animal model and such property cannot be appropriately assessed by performing short-term implantation studies. While hydroxyapatite (HA) or bioglass coated metallic biomaterials are being investigated for in vivo biocompatibility properties, such study is not extensively being pursued for bulk glass ceramics. In view of their inherent brittle nature, the implant stability as well as impact of long-term release of metallic ions on bone regeneration have been a major concern. In this perspective, the present article reports the results of the in vivo implantation experiments carried out using 100% strontium (Sr)-substituted glass ceramics with the nominal composition of 4.5 SiO2-3Al(2)O(3)-1.5P(2)O(5)-3SrO-2SrF(2) for 26 weeks in cylindrical bone defects in rabbit model. The combination of histological and micro-computed tomography analysis provided a qualitative and quantitative understanding of the bone regeneration around the glass ceramic implants in comparison to the highly bioactive HA bioglass implants (control). The sequential polychrome labeling of bone during in vivo osseointegration using three fluorochromes followed by fluorescence microscopy observation confirmed homogeneous bone formation around the test implants. The results of the present study unequivocally confirm the long-term implant stability as well as osteoconductive property of 100% Sr-substituted glass ceramics, which is comparable to that of a known bioactive implant, that is, HA-based bioglass. (c) 2014 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 103B: 1168-1179, 2015.

Synthesis of Eu3+-activated BaMoO4 phosphors and their Judd-Ofelt analysis: Applications in lasers and white LEDs

Eu3+-activated BaMoO4 phosphors were synthesized by the nitrate citrate gel combustion method. The Rietveld refinement analysis confirmed that all the compounds were crystallized in the scheelite-type tetragonal structure with I4(1)/a (No. 88) space group. Photoluminescence (PL) spectra of BaMoO4 phosphor reveals broad emission peaks at 465 and 605 nm, whereas the Eu3+-activated BaMoO4 phosphors show intense 615 nm (D-5(0) -> F-7(2)) emission peak. Judd-Ofelt theory was applied to evaluate the intensity parameters (Omega(2), Omega(4)) of Eu3+-activated BaMoO4 phosphors. The transition probabilities (A(T)), radiative lifetime (tau(rad)), branching ratio (beta), stimulated emission cross-section (sigma(e)), gain bandwidth (sigma(e) x Delta lambda(eff)) and optical gain (sigma(e) x tau(rad)) were investigated by using the intensity parameters. CIE color coordinates confirmed that the BaMoO4 and Eu3+-activated BaMoO4 phosphors exhibit white and red luminescence, respectively. The obtained results revealed that the present phosphors can be a potential candidate for red lasers and white LEDs applications. (C) 2015 Elsevier B.V. All rights reserved.

Comparative study of Eu3+ -activated LnOCl (Ln=La and Gd) phosphors and their Judd-Ofelt analysis

Eu3+-activated layered LnOCl (Ln=La and Gd) phosphors were synthesized by the conventional solid-state method at relatively low temperature (700 degrees C) and shorter duration of 2 h. The structural parameters were refined by the Rietveld refinement analysis and confirmed by the high resolution transmission electron microscopy (HRTEM). Both the compounds were crystallized in the tetragonal structure with space group P4/nmm (No. 129). The homogeneity of the elements were analyzed by TEM mapping and found to be uniformly distributed. The photoluminescence spectra revealed that the intensity of D-5(0)-> F-7(2) transition (619 nm) was more intense in Eu3+-activated GdOCl compared to LaOCl. This was due to the property of Gd3+ ions to act as an intermediate sublattice to facilitate the energy transfer to Eu3+ ions. Intensity parameters and radiative properties such as transition probabilities, radiative lifetime and branching ratio were calculated using the Judd-Ofelt theory. The CIE color coordinates result revealed that the Eu3+-activated GdOCl (0.641, 0.354) phosphor was close to the commercial red phosphors like, Y2O3:Eu3+ (0.645, 0.347), (Y2OS)-S-2:Eu3+ (0.647, 0.343) and National Television System Committee (NTSC) (0.67, 0.33). The results suggest that the present GdOCl:Eu3+ compound acts as a potential candidate for red phosphor materials.

Ag-doped hydroxyapatite as efficient adsorbent for removal of Congo red dye from aqueous solution: Synthesis, kinetic and equilibrium adsorption isotherm analysis

In the present study a versatile and efficient adsorbent with high adsorption capacity for adsorption of Congo red dye in aqueous solution at ambient temperature without adjusting any pH is presented over the Ag modified calcium hydroxyapatite (CaHAp). CaHAp and Ag-doped CaHAp materials were synthesized using facile aqueous precipitation method. The physico-chemical properties of the materials were determined by powder X-ray diffraction (XRD), Fourier transform infrared (FT-IR) spectroscopy, Transmission electron microscopy (TEM), UV-Visible spectroscopy, N-2 physisorption and acidity was determined by n-butylamine titration and pyridine adsorption methods. XRD analysis confirmed all adsorbents exhibit hexagonal CaHAp structure with P6(3)/m space group. TEM analysis confirms the rod like morphology of the adsorbents and the average length of the rods were in the range of 40-45 nm. Pyridine adsorption results indicate increase in number of Lewis acid sites with Ag doping in CaHAp. Adsorption capacity of CaHAp was found increased with Ag content in the adsorbents. Ag (10): CaHAp adsorbent showed superior adsorption performance among all the adsorbents for various concentrations of Congo red (CR) dye in aqueous solutions. The amount of CR dye adsorbed on Ag (10): CaHAp was found to be 49.89-267.81 mg g(-1) for 50-300 ppm in aqueous solution. A good correlation between adsorption capacity and acidity of the adsorbents was observed. The adsorption kinetic data of adsorbents fitted well with pseudo second-order kinetic model with correlation coefficients ranged from 0.998 to 0.999. The equilibrium adsorption data was found to best fit to the Langmuir adsorption isotherm model. (C) 2015 Elsevier Inc. All rights reserved.

The putative role of some conserved water molecules in the structure and function of human transthyretin

Human transthyretin (hTTR) is a multifunctional protein that is involved in several neurodegenerative diseases. Besides the transportation of thyroxin and vitamin A, it is also involved in the proteolysis of apolipoprotein A1 and A beta peptide. Extensive analyses of 32 high-resolution X-ray and neutron diffraction structures of hTTR followed by molecular-dynamics simulation studies using a set of 15 selected structures affirmed the presence of 44 conserved water molecules in its dimeric structure. They are found to play several important roles in the structure and function of the protein. Eight water molecules stabilize the dimeric structure through an extensive hydrogen-bonding network. The absence of some of these water molecules in highly acidic conditions (pH <= 4.0) severely affects the interfacial hydrogen-bond network, which may destabilize the native tetrameric structure, leading to its dissociation. Three pairs of conserved water molecules contribute to maintaining the geometry of the ligand-binding cavities. Some other water molecules control the orientation and dynamics of different structural elements of hTTR. This systematic study of the location, absence, networking and interactions of the conserved water molecules may shed some light on various structural and functional aspects of the protein. The present study may also provide some rational clues about the conserved water-mediated architecture and stability of hTTR.