Incorporation of chelating 2,2′-bipyridine (bipy) ligands at the equatorial sites of Cu2(μ-O2CMe)4(H2O)2: an x-ray structure of [Cu2(μ-O2CMe)2(H2O)(bipy)2](PF6)2

The asymmetric dicopper(II) title complex with a [Cu2(μ-O2CMe)22+ core was isolated from the reaction between Cu2(μ-O2CMe)4(H2O)2 and bipy in EtOH in the presence of NH4PF6 and has been characterized by X-ray diffraction analysis.

Identification of Mxr1p-binding sites in the promoters of genes encoding dihydroxyacetone synthase and peroxin 8 of the methylotrophic yeast Pichia pastoris

Expression of genes involved in methanol metabolism of Pichia pastoris is regulated by Mxr1p, a zinc finger transcription factor. In this study, we studied the target gene specificity of Mxr1p by examining its ability to bind to promoters of genes encoding dihydroxyacetone synthase (DHAS) and peroxin 8 (PEX8), since methanol-inducible expression of these genes is abrogated in mxr1-null mutant strains of P. pastoris. Different regions of DHAS and PEX8 promoter were isolated from P. pastoris genomic DNA and their ability to bind to a recombinant Mxr1p protein containing the N-terminal 150 amino acids, including the zinc finger DNA-binding domain, was examined. These studies reveal that Mxr1p specifically binds to promoter regions containing multiple 5'-CYCC-3' sequences, although all DNA sequences containing the 5'-CYCC-3' motif do not qualify as Mxr1p-binding sites. Key DNA-binding determinants are present outside 5'-CYCC-3' motif and Mxr1p preferably binds to DNA sequences containing 5'-CYCCNY-3' than those containing 5'-CYCCNR-3' sequences. This study provides new insights into the molecular determinants of target gene specificity of Mxr1p, and the methodology described here can be used for mapping Mxr1p-binding sites in other methanol-inducible promoters of P. pastoris. Copyright (C) 2010 John Wiley & Sons, Ltd.

Polypurine-polypyrimidine sequences adopt unwound structure in pBR322 form V DNA as probed by single-hit analysis of HpaII sites.

Structure at the polypurine-polypyrimidine sequences flanking the HpaII sites (CCGG) in pBR322 form V DNA was probed employing single-hit analysis using HpaII restriction endonuclease. Reduced cleavage efficiency of HpaII sites flanked by polypurine-polypyrimidine sequences suggested that under high torsional stress these sequences adopt unwound structures rendering these sites insensitive to restriction enzyme cleavage. In addition to polypurine-polypyrimidine sequences. HpaII sites flanked by alternating purine-pyrimidine sequence, a potential motif of left handed Z-DNA, were also found to be resistant to HpaII cleavage. Results obtained from various studies implicating structure sensitivity of restriction endonucleases and methylases were compiled and a direct correlation was observed between the occurrence of altered sites in a domain and its G/C content in pBR322 form V DNA.

Stress-strain response of plastic waste mixed soil

Recycling plastic waste from water bottles has become one of the major challenges worldwide. The present study provides an approach for the use plastic waste as reinforcement material in soil. The experimental results in the form of stress-strain-pore water pressure response are presented. Based on experimental test results, it is observed that the strength of soil is improved and compressibility reduced significantly with addition of a small percentage of plastic waste to the soil. The use of the improvement in strength and compressibility response due to inclusion of plastic waste can be advantageously used in bearing capacity improvement and settlement reduction in the design of shallow foundations. (C) 2010 Elsevier Ltd. All rights reserved.

Combustion synthesis of oxide materials for nuclear waste immobilization

Oxide materials like perovskite, zirconolite, hollandite, pyrochlore, NASICON and sphene which are used for nuclear waste immobilization have been prepared by a solution combustion process. The process involves the combustion of stoichiometric amount of corresponding metal nitrates and carbohydrazide/tetraformyl trisazine/diformyl hydrazide at 450 degrees C. The combustion products have been characterized using powder X-ray diffraction, infrared spectroscopy, and Si-29 MAS-NMR. The fine particle nature of the combustion derived powders has been studied using density, particle size, BET surface area measurements and scanning electron microscopy. Sintering of combustion derived powder yields 85-95% dense ceramics in the temperature range 1000 degrees-1300 degrees C.

Biosorption of copper and zinc using waste Aspergillus niger biomass

Nonliving waste biomass consisting of Aspergillus niger attached to wheat bran was used as a biosorbent for the removal of copper and zinc from aqueous solutions. Copper and zinc uptake by the biomass obeyed Langmuir isotherms. The binding capacity of the biomass for copper was found to be higher than that for zinc. The metal uptake, expressed in milligrams per gram of biomass, was found to be a function of: the initial metal concentration (with the uptake decreasing with increasing initial concentration), the biomass loading (with the uptake decreasing with increasing biomass loading) and pH (with the uptake increasing with increasing pH in the range of 1.5 and 6.0). The metal uptake was significantly affected in the presence of a co-ion. The uptake of copper by the biomass decreased in the presence of zinc and vice versa. The decrease in metal uptake was dependent on the concentrations of metals in the two-component aqueous solutions. The effect of copper on zinc uptake was more pronounced than the effect of zinc on copper uptake.

Dapsone a new diazotizing reagent for the spectrophotometric determination of nitrite in waste and natural water samples

A new diazotizing reagent for the spectrophotometric determination of nitrite is described. The method is based on diazotization-coupling reaction between dapsone and phloroglucinol in hydrochloric acid medium. The reactions were conducted at room temperature, the molor absorptivity at 425 nm is 4.28 x 10(4) 1 Mol, (1)cm(-1) and was stable for 50 h. Beer's law was obeyed in the nitrite range of 0.008 - 1.0 mug ml(-1). Tolerance limits were tested for 33 species. The method has been found to be applicable for the determination of nitrite in natural and wastewater.

The influence of Fe3+ ions at tetrahedral sites on the magnetic properties of nanocrystalline ZnFe2O4

A systematic study on the variation of Mössbauer hyperfine parameters with grain size in nanocrystalline zinc ferrite is lacking. In the present study, nanocrystalline ZnFe2O4 ferrites with different grain sizes were prepared by ball-milling technique and characterised by X-ray, EDAX, magnetisation and Mössbauer studies. The grain size decreases with increasing milling time and lattice parameter is found to be slightly higher than the bulk value. Magnetisation at room temperature (RT) and at 77 K could not be saturated with a magnetic field of 7 kOe and the observed magnetisation at these temperatures can be explained on the basis of deviation of cation distribution from normal spinel structure. The Mössbauer spectra were recorded at different temperatures between RT and 16 K. The values of quadrupole splitting at RT are higher for the milled samples indicating the disordering of ZnFe2O4 on milling. The strength of the magnetic hyperfine interactions increases with grain size reduction and this can be explained on the basis of the distribution of Fe3+ ions at both tetrahedral and octahedral sites.

Crucible Steel in South India-Preliminary Investigations on Crucibles from Some Newly Identified Sites

European accounts from the 17th century onwards have referred to the repute and manufacture of “wootz’, a traditional crucible steel made especially in parts of southern India in the former provinces of Golconda, Mysore and Salem. Pliny's Natural History mentions the import of iron and steel from the Seres which have been thought to refer to the ancient southern Indian kingdom of the Cheras. As yet the scale of excavations and surface surveys is too limited to link the literary accounts to archaeometallurgical evidence, although pioneering exploratory investigations have been made by scholars, especially on the pre-industrial production sites of Konasamudram and Gatihosahalli discussed in 18th-19th century European accounts. In 1991–2 during preliminary surveys of ancient base metal mining sites, Srinivasan came across unreported dumps with crucible fragments at Mel-Siruvalur in Tamil Nadu, and Tintini and Machnur in Karnataka and she collected surface specimens from these sites as well as from the known site of Gatihosahalli. She was also given crucible fragments by the Tamil University, Tanjavur, from an excavated megalithic site at Kodumanal, dated to ca 2nd c. Bc, mentioned in Tamil Sangam literature (ca 3rd c. BC-3rd c. AD), and very near Karur, the ancient capital of the Sangam Cheras. Analyses of crucible fragments from the surface collection at Mel-Siruvalur showed several iron prills with a uniform pearlitic structure of high-carbon hypereutectoid steel (∼1–1.5% C) suggesting that the end product was uniformly a high-carbon steel of a structure consistent with those of high-carbon steels used successfully to experimentally replicate the watered steel patterns on ‘Damascus’ swords. Investigations indicate that the process was of carburisation of molten low carbon iron (m.p. 1400° C) in crucibles packed with carbonaceous matter. The fabric of crucibles from all the above mentioned sites appears similar. Preliminary investigations on these crucibles are thus reported to establish their relationship to crucible production of carbon steel and to thereby extend the known horizons of this technology further.

PocketAlign A Novel Algorithm for Aligning Binding Sites in Protein Structures

A fundamental task in bioinformatics involves a transfer of knowledge from one protein molecule onto another by way of recognizing similarities. Such similarities are obtained at different levels, that of sequence, whole fold, or important substructures. Comparison of binding sites is important to understand functional similarities among the proteins and also to understand drug cross-reactivities. Current methods in literature have their own merits and demerits, warranting exploration of newer concepts and algorithms, especially for large-scale comparisons and for obtaining accurate residue-wise mappings. Here, we report the development of a new algorithm, PocketAlign, for obtaining structural superpositions of binding sites. The software is available as a web-service at http://proline.physicslisc.emetin/pocketalign/. The algorithm encodes shape descriptors in the form of geometric perspectives, supplemented by chemical group classification. The shape descriptor considers several perspectives with each residue as the focus and captures relative distribution of residues around it in a given site. Residue-wise pairings are computed by comparing the set of perspectives of the first site with that of the second, followed by a greedy approach that incrementally combines residue pairings into a mapping. The mappings in different frames are then evaluated by different metrics encoding the extent of alignment of individual geometric perspectives. Different initial seed alignments are computed, each subsequently extended by detecting consequential atomic alignments in a three-dimensional grid, and the best 500 stored in a database. Alignments are then ranked, and the top scoring alignments reported, which are then streamed into Pymol for visualization and analyses. The method is validated for accuracy and sensitivity and benchmarked against existing methods. An advantage of PocketAlign, as compared to some of the existing tools available for binding site comparison in literature, is that it explores different schemes for identifying an alignment thus has a better potential to capture similarities in ligand recognition abilities. PocketAlign, by finding a detailed alignment of a pair of sites, provides insights as to why two sites are similar and which set of residues and atoms contribute to the similarity.

CO adsorption on ionic Pt, Pd and Cu sites in Ce(1-x)M(x)O(2-delta) (M = Pt(2+), Pd(2+), Cu(2+))

Noble metal ion substituted CeO(2) in the form of Ce(0.98)M(0.02)O(2-delta) solid solution (where M = Pt, Pd, Cu) are the new generation catalysts with applications in three-way exhaust catalysis. While adsorption of CO on noble metals ions is well-known, adsorption of CO on noble metal ions has not been studied because creating exclusive ionic sites has been difficult. Using first-principles density functional theory (DFT) we have shown that CO gets adsorbed on the noble metal Pt(2+), Pd(2+), Cu(2+) ionic sites in the respective compounds, and the net energy of the overall system decreases. Adsorption of CO on metal ions is also confirmed by Fourier transform infrared spectroscopy (FTIR).

Novel Algorithm for estimation of Swell Pressure of Fine Grained Soils Based on Diffuse Double Layer (DDL) Theory

Use of engineered landfills for the disposal of industrial wastes is currently a common practice. Bentonite is attracting a greater attention not only as capping and lining materials in landfills but also as buffer and backfill materials for repositories of high-level nuclear waste around the world. In the design of buffer and backfill materials, it is important to know the swelling pressures of compacted bentonite with different electrolyte solutions. The theoretical studies on swell pressure behaviour are all based on Diffuse Double Layer (DDL) theory. To establish a relation between the swell pressure and void ratio of the soil, it is necessary to calculate the mid-plane potential in the diffuse part of the interacting ionic double layers. The difficulty in these calculations is the elliptic integral involved in the relation between half space distance and mid plane potential. Several investigators circumvented this problem using indirect methods or by using cumbersome numerical techniques. In this work, a novel approach is proposed for theoretical estimations of swell pressures of fine-grained soil from the DDL theory. The proposed approach circumvents the complex computations in establishing the relationship between mid-plane potential and diffused plates’ distances in other words, between swell pressure and void ratio.

Environmental audit of Municipal Solid Waste Management

The management of municipal solid waste has become an acute problem due to enhanced economic activities and rapid urbanisation. Increased attention has been given by the government in recent years to handle this problem in a safe and hygienic manner. In this regard, Municipal Solid Waste Management (MSWM) environmental audit has been carried out for Bangalore city through the collection of secondary data from government agencies, and interviews with stakeholders and field surveys. Field surveys were carried out in seven wards (representative samples of the city) to understand the practice and identify the lacunae. The MSWM audit that was carried out functional-element-wise in selected wards to understand the efficacy and shortfalls, if any, is discussed in this paper.