Ligand 5,10,15,20-Tetra(N-methyl-4-pyridyl)porphine (TMPyP4) Prefers the Parallel Propeller-Type Human Telomeric G-Quadruplex DNA over Its Other Polymorphs

The binding of ligand 5,10,15,20-tetra(N-methyl-4-pyridyl)porphine (TMPyP4) with telomeric and genomic G-quadruplex DNA has been extensively studied. However, a comparative study of interactions of TMPyP4 with different conformations of human telomeric G-quadruplex DNA, namely, parallel propeller-type (PP), antiparallel basket-type (AB), and mixed hybrid-type (MH) G-quadruplex DNA, has not been done. We considered all the possible binding sites in each of the G-quadruplex DNA structures and docked TMPyP4 to each one of them. The resultant most potent sites for binding were analyzed from the mean binding free energy of the complexes. Molecular dynamics simulations were then carried out, and analysis of the binding free energy of the TMPyP4-G-quadruplex complex showed that the binding of TMPyP4 with parallel propeller-type G-quadruplex DNA is preferred over the other two G-quadruplex DNA conformations. The results obtained from the change in solvent excluded surface area (SESA) and solvent accessible surface area (SASA) also support the more pronounced binding of the ligand with the parallel propeller-type G-quadruplex DNA.

One-Carbon Metabolic Pathway Rewiring in Escherichia coli Reveals an Evolutionary Advantage of 10-Formyltetrahydrofolate Synthetase (Fhs) in Survival under Hypoxia

In cells, N-10-formyltetrahydrofolate (N-10-fTHF) is required for formylation of eubacterial/organellar initiator tRNA and purine nucleotide biosynthesis. Biosynthesis of N-10-fTHF is catalyzed by 5,10-methylene-tetrahydrofolate dehydrogenase/cyclohydrolase (FolD) and/or 10-formyltetrahydrofolate synthetase (Fhs). All eubacteria possess FolD, but some possess both FolD and Fhs. However, the reasons for possessing Fhs in addition to FolD have remained unclear. We used Escherichia coli, which naturally lacks fhs, as our model. We show that in E. coli, the essential function of folD could be replaced by Clostridium perfringens fhs when it was provided on a medium-copy-number plasmid or integrated as a single-copy gene in the chromosome. The fhs-supported folD deletion (Delta folD) strains grow well in a complex medium. However, these strains require purines and glycine as supplements for growth in M9 minimal medium. The in vivo levels of N-10-fTHF in the Delta folD strain (supported by plasmid-borne fhs) were limiting despite the high capacity of the available Fhs to synthesize N-10-fTHF in vitro. Auxotrophy for purines could be alleviated by supplementing formate to the medium, and that for glycine was alleviated by engineering THF import into the cells. The Delta folD strain (harboring fhs on the chromosome) showed a high NADP(+)-to-NADPH ratio and hypersensitivity to trimethoprim. The presence of fhs in E. coli was disadvantageous for its aerobic growth. However, under hypoxia, E. coli strains harboring fhs outcompeted those lacking it. The computational analysis revealed a predominant natural occurrence of fhs in anaerobic and facultative anaerobic bacteria.

Exploring the Consequences of a Representative ``Disallowed'' Conformation of Aib on a 3(10)-Helical Fold

The structural effects of a representative disallowed conformation of Aib on the 3(10)-helical fold of an octapeptidomimetic are explored. The 1D (H-1, C-13) & 2D NMR, FT-IR and CD data reveal that the octapeptide 1, adopts a 3(10)-helical conformation in solution, as it does in its crystal structure. The C-terminal methyl carboxylate (CO2Me) of 1 was modified into an 1,3-oxazine (Oxa) functional group in the peptidomimetic 2. This modification results in the stabilization of the backbone of the C-terminal Aib (Aib*-Oxa) of 2, in a conformation (phi, =180, 0) that is natively disallowed to Aib. Consequent to the presence of this natively disallowed conformation, the 3(10)-helical fold is not disrupted in the body of the peptidomimetic 2. But the structural distortions that do occur in 2 are primarily in residues in the immediate vicinity of the natively disallowed conformation, rather than in the whole peptide body. Non-native electronic effects resulting from modifications in backbone functional groups can be at the origin of stabilizing residues in natively disallowed conformations. (c) 2014 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 104: 21-36, 2015.

An encaged sigma* orbital in 3-methoxy-2,4,10-trioxaadamantane. Preferred exo-anomeric effect as revealed by the crystal structure

In the titled tricyclic orthocarbonate derivative, the three endocyclic C-O bonds are longer than the exo-cyclic C-O bond (similar to 4.40 angstrom vs. similar to 1.37 angstrom). This indicates an anomeric-type interaction between the two electron lone pairs on the exocyclic oxygen atom and the antibonding orbitals of the two antiperiplanar endocyclic C-O bonds. The remaining endocyclic C-O bond - marginally shorter than the other two apparently adds to this effect. Intriguingly, the antibonding orbital of the exocyclic C-O bond extends into the interior of the adamantyl cage, and is stereoelectronically prevented from overlapping with any of the six adjacent lone pairs. The results also seem to indicate a preference for interaction between a single donor oxygen atom and multiple acceptor antibonding orbitals rather than vice versa. The results add insightfully to the substantial body of evidence favouring the antiperiplanar lone pair hypothesis (ALPH). (C) 2014 Elsevier B.V. All rights reserved.

Cryogenian magmatism and crustal reworking in the Southern Granulite Terrane, India

Understanding Neoproterozoic crustal evolution is fundamental to reconstructing the Gondwana supercontinent, which was assembled at this time. Here we report evidence of Cryogenian crustal reworking in the Madurai Block of the Southern Granulite Terrane of India. The study focuses on a garnet-bearing granite-charnockite suite, where the granite shows in situ dehydration into patches and veins of incipient charnockite along the contact with charnockite. The granite also carries dismembered layers of Mg-Al-rich granulite. Micro-textural evidence for dehydration of granite in the presence of CO2-rich fluids includes the formation of orthopyroxene by the breakdown of biotite, neoblastic zircon growth in the dehydration zone, at around 870 degrees C and 8kbar. The zircon U-Pb ages suggest formation of the granite, charnockite, and incipient charnockite at 836 +/- 73, 831 +/- 31, and 772 +/- 49Ma, respectively. Negative zircon epsilon Hf (t) (-5 to -20) values suggest that these rocks were derived from a reworked Palaeoproterozoic crustal source. Zircon grains in the Mg-Al-rich granulite record a spectrum of ages from ca. 2300 to ca. 500Ma, suggesting multiple provenances ranging from Palaeoproterozoic to mid-Neoproterozoic, with neoblastic zircon growth during high-temperature metamorphism in the Cambrian. We propose that the garnet-bearing granite and charnockite reflect the crustal reworking of aluminous crustal material indicated by the presence of biotite+quartz+aluminosilicate inclusions in the garnet within the granite. This crustal source can be the Mg-Al-rich layers carried by the granite itself, which later experienced high-temperature regional metamorphism at ca. 550Ma. Our model also envisages that the CO2 which dehydrated the garnet-bearing granite generating incipient charnockite was sourced from the proximal massive charnockite through advection. These Cryogenian crustal reworking events are related to prolonged tectonic activities prior to the final assembly of the Gondwana supercontinent.

Estimation of the components of municipal solid waste settlement

Estimation of the municipal solid waste settlements and the contribution of each of the components are essential in the estimation of the volume of the waste that can be accommodated in a landfill and increase the post-usage of the landfill. This article describes an experimental methodology for estimating and separating primary settlement, settlement owing to creep and biodegradation-induced settlement. The primary settlement and secondary settlement have been estimated and separated based on 100% pore pressure dissipation time and the coefficient of consolidation. Mechanical creep and biodegradation settlements were estimated and separated based on the observed time required for landfill gas production. The results of a series of laboratory triaxial tests, creep tests and anaerobic reactor cell setups were conducted to describe the components of settlement. All the tests were conducted on municipal solid waste (compost reject) samples. It was observed that biodegradation accounted to more than 40% of the total settlement, whereas mechanical creep contributed more than 20% towards the total settlement. The essential model parameters, such as the compression ratio (C-c'), rate of mechanical creep (c), coefficient of mechanical creep (b), rate of biodegradation (d) and the total strain owing to biodegradation (E-DG), are useful parameters in the estimation of total settlements as well as components of settlement in landfill.

ADAPTATION OF MW LEVEL NATURAL GAS LEAN BURN ENGINE FOR PRODUCER GAS OPERATION A GRID CONNECTED POWER PLANT

Availability of producer gas engines at MW being limited necessitates to adapt engine from natural gas operation. The present work focus on the development of necessary kit for adapting a 12 cylinder lean burn turbo-charged natural gas engine rated at 900 kWe (Waukesha make VHP5904LTD) to operate on producer and set up an appropriate capacity biomass gasification system for grid linked power generation in Thailand. The overall plant configuration had fuel processing, drying, reactor, cooling and cleaning system, water treatment, engine generator and power evacuation. The overall project is designed for evacuation of 1.5 MWe power to the state grid and had 2 gasification system with the above configuration and 3 engines. Two gasification system each designed for about 1100 kg/hr of woody biomass was connected to the engine using a producer gas carburetor for the necessary Air to fuel ratio control. In the use of PG to fuel IC engines, it has been recognized that the engine response will differ as compared to the response with conventional fueled operation due to the differences in the thermo-physical properties of PG. On fuelling a conventional engine with PG, power de-rating can be expected due to the lower calorific value (LCV), lower adiabatic flame temperature (AFT) and the lower than unity product to reactant more ratio. Further the A/F ratio for producer gas is about 1/10th that of natural gas and requires a different carburetor for engine operation. The research involved in developing a carburetor for varying load conditions. The patented carburetor is based on area ratio control, consisting of a zero pressure regulator and a separate gas and air line along with a mixing zone. The 95 litre engine at 1000 rpm has an electrical efficiency of 33.5 % with a heat input of 2.62 MW. Each engine had two carburetors designed for producer gas flow each capable of handling about 1200 m3/hr in order to provide similar engine heat input at a lower conversion efficiency. Cold flow studies simulating the engine carburetion system results showed that the A/F was maintained in the range of 1.3 +/- 0.1 over the entire flow range. Initially, the gasification system was tested using woody biomass and the gas composition was found to be CO 15 +/- 1.5 % H-2 22 +/- 2% CH4 2.2 +/- 0.5 CO2 11.25 +/- 1.4 % and rest N-2, with the calorific value in the range of 5.0 MJ/kg. After initial trials on the engine to fine tune the control system and adjust various engine operating parameter a peak load of 800 kWe was achieved, while a stable operating conditions was found to be at 750 kWe which is nearly 85 % of the natural gas rating. The specific fuel consumption was found to be 0.9 kg of biomass per kWh.

EXPERIENCE OF OPERATING OPEN TOP BIOMASS GASIFIER USING A LOW DENSITY FUEL-COCONUT FRONDS

Use of fuel other than woody generally has been limited to rice husk and other residues are rarely tried as a fuel in a gasification system. With the availability of woody biomass in most countries like India, alternates fuels are being explored for sustainable supply of fuel. Use of agro residues has been explored after briquetting. There are few feedstock's like coconut fronts, maize cobs, etc, that might require lesser preprocessing steps compared to briquetting. The paper presents a detailed investigation into using coconut fronds as a fuel in an open top down draft gasification system. The fuel has ash content of 7% and was dried to moisture levels of 12 %. The average bulk density was found to be 230 kg/m3 with a fuel size particle of an average size 40 mm as compared to 350 kg/m3 for a standard wood pieces. A typical dry coconut fronds weighs about 2.5kgs and on an average 6 m long and 90 % of the frond is the petiole which is generally used as a fuel. The focus was also to compare the overall process with respect to operating with a typical woody biomass like subabul whose ash content is 1 %. The open top gasification system consists of a reactor, cooling and cleaning system along with water treatment. The performance parameters studied were the gas composition, tar and particulates in the clean gas, water quality and reactor pressure drop apart from other standard data collection of fuel flow rate, etc. The average gas composition was found to be CO 15 1.0 % H-2 16 +/- 1% CH4 0.5 +/- 0.1 % CO2 12.0 +/- 1.0 % and rest N2 compared to CO 19 +/- 1.0 % H-2 17 +/- 1.0 %, CH4 1 +/- 0.2 %, CO2 12 +/- 1.0 % and rest N2. The tar and particulate content in the clean gas has been found to be about 10 and 12 mg/m3 in both cases. The presence of high ash content material increased the pressure drop with coconut frond compared to woody biomass.

BIOMASS GASIFICATION TO SUBSTITUTE FOSSIL FUEL IN FOOD INDUSTRY

Food industries like biscuit and confectionary use significant amount of fossil fuel for thermal energy. Biscuit manufacturing in India is carried out both by organized and unorganized sector. The ratio of organized to unorganized sector is 60 : 40 (1). The total biscuit manufacturing in the organized sector India in 2008 was about 1.7 million metric tons (1). Accounting for the unorganized sector in India, the total biscuit manufacturing would have been about 2.9 million metric tons/annum. A typical biscuit baking is carried in a long tunnel kiln with varying temperature in different zones. Generally diesel is used to provide the necessary heat energy for the baking purpose, with temperature ranging from 190 C in the drying zone to about 300 C in the baking area and has to maintain in the temperature range of +/- 5 C. Typical oil consumption is about 40 litres per ton of biscuit production. The paper discusses the experience in substituting about 120 lts per hour kiln for manufacturing about 70 tons of biscuit daily. The system configuration consists of a 500 kg/hr gasification system comprising of a reactor, multicyclone, water scrubbers, and two blowers for maintaining the constant gas pressure in the header before the burners. Cold producer gas is piped to the oven located about 200 meters away from the gasifier. Fuel used in the gasification system is coconut shells. All the control system existing on the diesel burner has been suitably adapted for producer gas operation to maintain the total flow, A/F control so as to maintain the temperature. A total of 7 burners are used in different zones. Over 17000 hour of operation has resulted in replacing over 1800 tons of diesel over the last 30 months. The system operates for over 6 days a week with average operational hours of 160. It has been found that on an average 3.5 kg of biomass has replaced one liter of diesel.

Doping effect of Ag+, Mn2+ ions on Structural and Optical Properties of ZnO nanoparticles

Pure ZnO and co-doped (Mn, Ag) ZnO nanoparticles have been successfully prepared by chemical co-precipitation method without using a capping agent. X-ray diffraction (XRD) studies confirms the presence of wurtzite (hexagonal) crystal structure similar to undoped ZnO, suggesting that doped Mn, Ag ions are substituted to the regular Zn sites. The morphology of the samples were studied by scanning electron microscopy (SEM). The chemical composition of pure and co-doped ZnO nanoparticles were characterized by energy dispersive X-ray analysis spectroscopy (EDAX). Optical absorption properties were determined by UV-vis Diffuse Reflectance Spectrophotometer. The incorporation of Ag+, Mn2+ in the place of Zn2+ provoked to decrease the size of nanocrystals as compared to pure ZnO. Optical absorption measurements indicates blue shift in the absorption band edge upon Ag, Mn ions doped ZnO nanoparticles.

Impact of Mutating the Key Residues of a Bifunctional 5,10-Methylenetetrahydrofolate Dehydrogenase-Cyclohydrolase from Escherichia coli on Its Activities

Methylenetetrahydrofolate dehydrogenase-cyclohydrolase (FolD) catalyzes interconversion of 5,10-methylene-tetrahydrofolate and 10-formyl-tetrahydrofolate in the one-carbon metabolic pathway. In some organisms, the essential requirement of 10-formyl-tetrahydrofolate may also be fulfilled by formyltetrahydrofolate synthetase (Fhs). Recently, we developed an Escherichia coli strain in which the folD gene was deleted in the presence of Clostridium perfringens fhs (E. coli Delta folD/p-fhs) and used it to purify FolD mutants (free from the host-encoded FolD) and determine their biological activities. Mutations in the key residues of E. coli FolD, as identified from three-dimensional structures (D121A, Q98K, K54S, Y50S, and R191E), and a genetic screen (G122D and C58Y) were generated, and the mutant proteins were purified to determine their kinetic constants. Except for the R191E and K54S mutants, others were highly compromised in terms of both dehydrogenase and cyclohydrolase activities. While the R191E mutant showed high cyclohydrolase activity, it retained only a residual dehydrogenase activity. On the other hand, the K54S mutant lacked the cyclohydrolase activity but possessed high dehydrogenase activity. The D121A and G122D (in a loop between two helices) mutants were highly compromised in terms of both dehydrogenase and cyclohydrolase activities. In vivo and in vitro characterization of wild-type and mutant (R191E, G122D, D121A, Q98K, C58Y, K54S, and Y50S) FolD together with three-dimensional modeling has allowed us to develop a better understanding of the mechanism for substrate binding and catalysis by E. coli FolD.

Discharge Plasma Combined With Bauxite Residue for Biodiesel Exhaust Cleaning: A Case Study on NOx Removal

Experiments were conducted at laboratory level to treat the oxides of nitrogen (NOx) present in raw and dry biodiesel exhaust utilizing a combination of electric discharge plasma and bauxite residue, i. e., red mud, an industrial waste byproduct from the aluminum industry. In this paper, the adsorption and a possible catalytic property of bauxite residue are discussed. Nonthermal plasma was generated using dielectric barrier discharges initiated by ac/repetitive pulse energization. The effect of corona electrodes on the plasma generation was qualitatively studied through NOx cleaning. The plasma reactor and adsorbent reactors were connected in cascade while treating the exhaust. The diesel generator, running on biodiesel fuel, was electrically loaded to study the effectiveness of the cascade system in cleaning the exhaust. Interestingly, under the laboratory conditions studied, plasma-bauxite residue combination has shown good synergistic properties and enhanced the NOx removal up to about 90%. With proper scaling up, the suggested cascade system may become an economically feasible option to treat the exhaust in larger installations. The results were discussed emphasizing the role of bauxite residue as an adsorbent and as a room temperature catalyst.

Single-step synthesis of carbon nanotubes/iron/iron oxide composite films through inert-ambient CVD using ferric acetylacetonate as a precursor

We have developed a unique single-step chemical vapor deposition (CVD) route for the synthesis of composite thin films containing carbon nanotubes (CNTs). CVD was carried out in an inert ambient using only iron(III) acetylacetonate as the precursor. Depositions were conducted at 700 degrees C on stainless steel substrates in argon ambient in the absence of any reactive gases (such as oxygen, hydrogen). By changing the deposition parameters, especially the pressure in the CVD reactor, the form of carbon deposited could be changed from amorphous to carbon nanotubes, the latter resulting in Fe-Fe3O4-CNT films. X-ray diffraction, Raman spectroscopy, X-ray photoelectron spectroscopy, and electron microscopy together confirm the formation of the three-component composite and illustrate the nanoscale mixing of the components. Elemental iron formed in this process was protected from oxidation by the co-deposited carbon surrounding it. Irrespective of the substrate used, a composite coating with CNTs was formed under optimum conditions, as verified by analyses of the film formed on polycrystalline alumina and silicon substrates.

Exploring the Consequences of a Representative ``Disallowed'' Conformation of Aib on a 3(10)-Helical Fold

The structural effects of a representative ``disallowed'' conformation of Aib on the 3(10)-helical fold of an octapeptidomimetic are explored. The 1D (H-1, C-13) & 2D NMR, FT-IR and CD data reveal that the octapeptide 1, adopts a 3(10)- helical conformation in solution, as it does in its crystal structure. The C-terminal methyl carboxylate (CO2Me) of 1 was modified into an 1,3-oxazine (Oxa) functional group in the peptidomimetic 2. This modification results in the stabilization of the backbone of the C-terminal Aib (Aib(star)-Oxa) of 2, in a conformation (phi, psi = 180, 0) that is natively disallowed to Aib. Consequent to the presence of this natively disallowed conformation, the 3(10)- helical fold is not disrupted in the body of the peptidomimetic 2. But the structural distortions that do occur in 2 are primarily in residues in the immediate vicinity of the natively disallowed conformation, rather than in the whole peptide body. Non-native electronic effects resulting from modifications in backbone functional groups can be at the origin of stabilizing residues in natively disallowed conformations. (C) 2014 Wiley Periodicals, Inc. Biopolymers

Exploring the Consequences of a Representative ``Disallowed'' Conformation of Aib on a 3(10)-Helical Fold

The structural effects of a representative ``disallowed'' conformation of Aib on the 3(10)-helical fold of an octapeptidomimetic are explored. The 1D (H-1, C-13) & 2D NMR, FT-IR and CD data reveal that the octapeptide 1, adopts a 3(10)- helical conformation in solution, as it does in its crystal structure. The C-terminal methyl carboxylate (CO2Me) of 1 was modified into an 1,3-oxazine (Oxa) functional group in the peptidomimetic 2. This modification results in the stabilization of the backbone of the C-terminal Aib (Aib(star)-Oxa) of 2, in a conformation (phi, psi = 180, 0) that is natively disallowed to Aib. Consequent to the presence of this natively disallowed conformation, the 3(10)- helical fold is not disrupted in the body of the peptidomimetic 2. But the structural distortions that do occur in 2 are primarily in residues in the immediate vicinity of the natively disallowed conformation, rather than in the whole peptide body. Non-native electronic effects resulting from modifications in backbone functional groups can be at the origin of stabilizing residues in natively disallowed conformations. (C) 2014 Wiley Periodicals, Inc. Biopolymers