Conformational Polymorphism in Telomeric Structures: Loop Orientation and Interloop Pairing in d(G4TnG4),

Sequence repeats constituting the telomeric regions of chromosomes are known to adopt a variety of unusual structures, consisting of a G tetraplex stem and short stretches of thymines or thymines and adenines forming loops over the stem. Detailed model building and molecular mechanics studies have been carried out for these telomeric sequences to elucidate different types of loop orientations and possible conformations of thymines in the loop. The model building studies indicate that a minimum of two thymines have to be interspersed between guanine stretches to form folded-back structures with loops across adjacent strands in a G tetraplex (both over the small as well as large groove), while the minimum number of thymines required to build a loop across the diagonal strands in a G tetraplex is three. For two repeat sequences, these hairpins, resulting from different types of folding, can dimerize in three distinct ways-i.e., with loops across adjacent strands and on same side, with loops across adjacent strands and on opposite sides, and with loops across diagonal strands and on opposite sides-to form hairpin dimer structures. Energy minimization studies indicate that all possible hairpin dimers have very similar total energy values, though different structures are stabilized by different types of interactions. When the two loops are on the same side, in the hairpin dimer structures of d(G(4)T(n)G(4)), the thymines form favorably stacked tetrads in the loop region and there is interloop hydrogen bonding involving two hydrogen bonds for each thymine-thymine pair. Our molecular mechanics calculations on various folded-back as well as parallel tetraplex structures of these telomeric sequences provide a theoretical rationale for the experimentally observed feature that the presence of intervening thymine stretches stabilizes folded-back structures, while isolated stretches of guanines adopt a parallel tetraplex structure

4-Azidomethyl-7-methyl-2-oxo-2H-chromene-6-sulfonyl azide

In the title compound, C11H8N6O4S, the plane of the coumarin aromatic ring is twisted by 17.2 (2)degrees with respect to the plane of the azide group bound to the methylene substituent, whereas it is twisted by 83.2 (2)degrees to the plane of the azide attached to the sulfonyl group. The crystal structure is stabilized by weak C-H center dot center dot center dot O interactions, leading to the formation of dimers with R-2(2)(12) graph-set motifs. These dimers are further linked by weak S-O center dot center dot center dot pi and pi-pi contacts centroid-centroid distance = 3.765 (2) angstrom], leading to the formation of a layered structure.

A new model for coalescence efficiency of drops in stirred dispersions

A model for coalescence efficiency of two drops embedded in an eddy has been developed. Unlike the other models which consider only head-on collisions, the model considers the droplets to approach at an arbitrary angle. The drop pair is permitted to undergo rotation while they approach each other. For coalescence to occur, the drops are assumed to approach each other under a squeezing force acting over the life time of eddy but which can vary with time depending upon the angle of approach. The model accounts for the deformation of tip regions of the approaching drops and, describes the rupture of the intervening film, based on stability considerations while film drainage is continuing under the combined influence of the hydrodynamic and van der Waals forces. The coalescence efficiency is defined as the ratio of the range of angles resulting in coalescence to the total range of all possible approach angles. The model not only reconciles the contradictory predictions made by the earlier models based on similar framework but also brings out the important role of dispersed-phase viscosity. It further predicts that the dispersions involving pure phases can be stabilized at high rps values. Apart from explaining the hitherto unexplained experimental data of Konno et al. qualitatively, the model also offers an alternate explanation for the interesting observations of Shinnar.

Field-dependent changeover from current-to voltage-limiting characteristics by non-linear n-type BaTiO3 ceramics

Non-linear resistors having current-limiting capabilities at lower field strengths, and voltage-limiting characteristics (varistors) at higher field strengths, were prepared from sintered polycrystalline ceramics of (Ba0.6Sr0.4)(Ti0.97Zr0.03)O3+0.3 at % La, and reannealed after painting with low-melting mixtures of Bi2O3 + PbO +B2O3. These types of non-linear characteristics were found to depend upon the non-uniform diffusion of lead and the consequent distribution of Curie points (T c) in these perovskites, resulting in diffuse phase transitions. Tunnelling of electrons across the asymmetric barrier at tetragonak-cubic interfaces changes to tunnelling across the symmetric barrier as the cubic phase is fully stabilized through Joule heating at high field strengths. Therefore the current-limiting characteristics switch over to voltage-limiting behaviour because tunnelling to acceptor-type mid-bandgap states gives way to band-to-band tunnelling.

Suomussalmen varhaisproterotsooisten diabaasien mineralogia tektonisessa tulkinnassa

The object of this research is to study the mineralogy of the diabase dykes in Suomussalmi and the relevance of the mineralogy to tectonic events, specifically large block movements in the Archaean crust. Sharp tectonic lines separate two anomalies in the dyke swarms, shown on a geomagnetic map as positive anomalies. In one of these areas, the Toravaara anomaly, the diabases seem to contain pyroxenes as a main component. Outside the Toravaara anomaly hornblende is the main ferromagnesian mineral in diabases. The aim of this paper is to research the differences in the diabases inside and outside the anomalies and interpret the processes that formed the anomalies. The data for this sudy consist of field observations, 120 thin sections, 334 electron microprobe analyses, 19 whole-rock chemical analyses, a U-Pb age analysis and geomagnetic low-altitude aerial survey maps. The methods are interpretation of field observations, chemical analyses, microprobe analyses of single minerals and radiometric age determination, microscopic studies of the thin sections, geothermometers and geobarometers. On the basis of field observations and petrographic studies the diabases in the area are divided into pyroxene diabases, hornblende diabases and the Lohisärkkä porphyritic dyke swarm. Hornblende diabases are found in the entire study area, while the pyroxene diabases concentrate on the area of the Toravaara geomagnetic anomaly. The Lohisärkkä swarm transects the whole area as a thin line from east to west. The diabases are fairly homogenous both chemically and by mineral composition. The few exceptions are part of rarer older swarms or are significantly altered. The Lohisärkkä dyke swarm was dated as 2,21 Ga old, significantly older than the most common 1,98 Ga swarm in the area. The geothermometers applied showed that the diabases on the Toravaara anomaly were stabilized at a much higher temperature than the dykes outside the anomaly. The geobarometers showed the pyroxenes to have crystallized at varying depths. The research showed the Toravaara anomaly to have formed by a vertical block movement, and the fault on its west side to have a total lateral transfer of only a few kilometers. The formation of the second anomaly was also interpreted to be tectonic in nature. In addition, the results of the geothermobarometry uncovered necessary conditions for the study of diabase emplacement depth: the minerals for the study must be chosen by minimum crystallization depth, and a geobarometer capable of determining the magmatic temperature must be used. In addition, it would be more suitable to conduct this kind of study in an area where the dykes are more exposed.

Molecular structure of Lantadene-B&C, triterpenoids ofantana camara, red variety: Lantadene-B, 22β-angeloyloxy-3-oxoolean-12-en-28-oic acid; Lantadene-C, 22 β-(S)-2′-methyl butanoyloxy-3-oxoolean-12-en-28-oic acid

(I)Lantadene-B: C35H52O5,M r =552.80, MonoclinicC2,a=25.65(1),b=6.819(9),c=18.75(1) Å,beta=100.61(9),V=3223(5) Å3,Z=4,D x =1.14 g cm–3 CuKagr (lambda=1.5418A),mgr=5.5 cm–1,F(000)=1208,R=0.118,wR=0.132 for 1527 observed reflections withF o ge2sgr(F o ). (II)Lantadene-C: C35H54O5·CH3OH,Mr=586.85, Monoclinic,P21,a=9.822(3),b=10.909(3),c=16.120(8)Å,beta=99.82(4),V=1702(1)Å3,Z=2,D x =1.145 g cm–3, MoKagr (lambda=0.7107Å), mgr=0.708 cm–1 F(000)=644,R=0.098, wR=0.094 for 1073 observed reflections. The rings A, B, C, D, and E aretrans, trans, trans, cis fused and are in chair, chair, sofa, half-chair, chair conformations, respectively, in both the structures. In the unit cell the molecules are stabilized by O-HctdotO hydrogen bonds in both the structures, however an additional C-HctdotO interaction is observed in the case of Lantadene-C.

Conformational analysis and design of cross-strand disulfides in antiparallel beta-sheets

Cross-strand disulfides bridge two cysteines in a registered pair of antiparallel beta-strands. A nonredundant data set comprising 5025 polypeptides containing 2311 disulfides was used to study cross-strand disulfides. Seventy-six cross-strand disulfides were found of which 75 and 1 occurred at non-hydrogen-bonded (NHB) and hydrogen-bonded (HB) registered pairs, respectively. Conformational analysis and modeling studies demonstrated that disulfide formation at HB pairs necessarily requires an extremely rare and positive chi(1) value for at least one of the cysteine residues. Disulfides at HB positions also have more unfavorable steric repulsion with the main chain. Thirteen pairs of disulfides were introduced in NHB and HB pairs in four model proteins: leucine binding protein (LBP), leucine, isoleucine, valine binding protein (LIVBP), maltose binding protein (MBP), and Top7. All mutants LIVBP T247C V331C showed disulfide formation either on purification, or on treatment with oxidants. Protein stability in both oxidized and reduced states of all mutants was measured. Relative to wild type, LBP and MBP mutants were destabilized with respect to chemical denaturation, although the sole exposed NHB LBP mutant showed an increase of 3.1 degrees C in T-m. All Top7 mutants were characterized for stability through guanidinium thiocyanate chemical denaturation. Both exposed and two of the three buried NHB mutants were appreciably stabilized. All four HB Top7 mutants were destabilized (Delta Delta G(0) = -3.3 to -6.7 kcal/mol). The data demonstrate that introduction of cross-strand disulfides at exposed NHB pairs is a robust method of improving protein stability. All four exposed Top7 disulfide mutants showed mild redox activity. Proteins 2011; 79: 244-260. (C) 2010 Wiley-Liss, Inc.

Role of Gypsum in the Strength Development of Fly Ashes with Lime

The strength of fly ash mixture often needs to be enhanced for its better utilization in geotechnical and environmental applications. Many fly ashes often improve their strength with lime but may not meet the requirements. Gypsum, which reduces the lime leachability, further improves the strength. An attempt is made in this paper to study the effect of gypsum on the strength development of two Class F fly ashes with different lime contents after curing them for different periods. The sustainability of improved strength has been examined after soaking the cured specimens in water and with different leachates containing heavy-metal ions. The strength of both the fly ashes investigated improved markedly up to a particular amount of the lime content, which can be taken as optimum lime content, and thereafter the improvement is gradual. The improvement in strength at higher lime contents continues for a longer period (even up to 180 days). Gypsum accelerates the gain in strength for lime-stabilized fly ashes, particularly in the initial curing periods at about optimum lime content. At high lime contents gypsum attributes very high strength after curing for long periods mainly due to the alteration of fly ash lime reaction compounds. Gypsum not only improves the reduction in the loss of strength due to soaking even at low curing periods but also improves the durability of stabilized fly ashes due to repeated cycles of wetting and drying.

Forest policies and programs affecting vulnerability and adaptation to climate change

Due to large scale afforestation programs and forest conservation legislations, India's total forest area seems to have stabilized or even increased. In spite of such efforts, forest fragmentation and degradation continues, with forests being subject to increased pressure due to anthropogenic factors. Such fragmentation and degradation is leading to the forest cover to change from very dense to moderately dense and open forest and 253 km(2) of very dense forest has been converted to moderately dense forest, open forest, scrub and non-forest (during 2005-2007). Similarly, there has been a degradation of 4,120 km(2) of moderately dense forest to open forest, scrub and non-forest resulting in a net loss of 936 km(2) of moderately dense forest. Additionally, 4,335 km(2) of open forest have degraded to scrub and non-forest. Coupled with pressure due to anthropogenic factors, climate change is likely to be an added stress on forests. Forest sector programs and policies are major factors that determine the status of forests and potentially resilience to projected impacts of climate change. An attempt is made to review the forest policies and programs and their implications for the status of forests and for vulnerability of forests to projected climate change. The study concludes that forest conservation and development policies and programs need to be oriented to incorporate climate change impacts, vulnerability and adaptation.

2-(4-Methylsulfanylphenyl)-1H-benzimidazol-3-ium bromide

In the cation of the title compound, C14H13N2S+center dot Br-, the essentially planar benzimidazole system (r.m.s. deviation = 0.0082 angstrom) is substituted with a 4-methylsulfanylphenyl ring. The dihedral angle between the benzimidazole system and the 4-methylsulfanylphenyl ring is 2.133 (2)degrees. The crystal structure is characterized by strong and highly directional intermolecular N-H center dot center dot center dot Br hydrogen bonds involving the bromide ion. Moreover, C-H center dot center dot center dot S interactions result in chains of molecules along the c axis. The supramolecular assembly is further stabilized by pi-pi stacking interactions between the benzimidazole system and 4-methylsulfanylphenyl rings centroid-centroid distance = 3.477 (4) angstrom].

Theoretical and Computational Analysis of Static and Dynamic Anomalies in Water-DMSO Binary Mixture at Low DMSO Concentrations

Experiments have repeatedly observed both thermodynamic and dynamic anomalies in aqueous binary mixtures, surprisingly at low solute concentration. Examples of such binary mixtures include water-DMSO, water-ethanol, water-tertiary butyl alcohol (TBA), and water-dioxane, to name a few. The anomalies have often been attributed to the onset of a structural transition, whose nature, however, has been left rather unclear. Here we study the origin of such anomalies using large scale computer simulations and theoretical analysis in water-DMSO binary mixture. At very low DMSO concentration (below 10%), small aggregates of DMSO are solvated by water through the formation of DMSO-(H2O)(2) moieties. As the concentration is increased beyond 10-12% of DMSO, spanning clusters comprising the same moieties appear in the system. Those clusters are formed and stabilized not only through H-bonding but also through the association of CH3 groups of DMSO. We attribute the experimentally observed anomalies to a continuum percolation-like transition at DMSO concentration X-DMSO approximate to 12-15%. The largest cluster size of CH3-CH3 aggregation clearly indicates the formation of such percolating clusters. As a result, a significant slowing down is observed in the decay of associated rotational auto time correlation functions (of the S = O bond vector of DMSO and O-H bond vector of water). Markedly unusual behavior in the mean square fluctuation of total dipole moment again suggests a structural transition around the same concentration range. Furthermore, we map our findings to an interacting lattice model which substantiates the continuum percolation model as the reason for low concentration anomalies in binary mixtures where the solutes involved have both hydrophilic and hydrophobic moieties.

Edge Stabilities of Hexagonal Boron Nitride Nanoribbons: A First-Principles Study

We investigate the comparative stability of sp(2) bonded planar hexagonal boron nitride (h-BN) nanoribbon (BNNR) edges, using first principles calculations. We find that the pristine armchair edges have the highest degree of stability. Pristine zigzag edges are metastable, favoring planar reconstructions in the form of 5-7 rings] that minimizes the energy. Our investigation further reveals that the pristine zigzag edges can be stabilized against 5-7 reconstructions by passivating the dangling bonds at the edges by other elements, such as hydrogen (H) atoms. Electronic and magnetic properties of nanoribbons depend on the edge shapes and are strongly affected by edge reconstructions.

Effect of Substrate Binding Loop Mutations on the Structure, Kinetics, and Inhibition of Enoyl Acyl Carrier Protein Reductase from Plasmodium falciparum

Enoyl acyl carrier protein reductase (ENR), which catalyzes the final and rate limiting step of fatty acid elongation, has been validated as a potential drug target. Triclosan is known to be an effective inhibitor for this enzyme. We mutated the substrate binding site residue Ala372 of the ENR of Plasmodium falciparum (PfENR) to Methionine and Valine which increased the affinity of the enzyme towards triclosan to almost double, close to that of Escherichia coli ENR (EcENR) which has a Methionine at the structurally similar position of Ala372 of PfENR. Kinetic studies of the mutants of PfENR and the crystal structure analysis of the A372M mutant revealed that a more hydrophobic environment enhances the affinity of the enzyme for the inhibitor. A triclosan derivative showed a threefold increase in the affinity towards the mutants compared to the wild type, due to additional interactions with the A372M mutant as revealed by the crystal structure. The enzyme has a conserved salt bridge which stabilizes the substrate binding loop and appears to be important for the active conformation of the enzyme. We generated a second set of mutants to check this hypothesis. These mutants showed loss of function, except in one case, where the crystal structure showed that the substrate binding loop is stabilized by a water bridge network. (C) 2011 IUBMB mum Life, 63(1): 30-41,2011

Bi2W1–xCuxO6–x(0.7[less-than-or-eq]x[less-than-or-eq]0.8): a new oxide-ion conductor

Anion-deficient Aurivillius phases of the general formula, Bi2Wi-xCuxO6-2x, possessing orthorhombic/tetragonal Bi2WO6-like structures, have been synthesized by quenching the oxide melts. The tetragonal phase stabilized for the compositions 0.7 less-than-or-equal-to x less-than-or-equal-to 0.8 is a good oxide-ion conductor in the temperature range 500-900 K, the x = 0.7 composition exhibiting the highest conductivity in the series.

Gibbs energy of formation of orthorhombic CaZrO3

The Gibbs free energy of formation of the orthorhombic form of CaZrO3(o) from monoclinic ZrO2(m) and periclase CaO(p) has been determined as a function of temperature in the range 950-1225 K, using an electrochemical cell incorporating single-crystal CaF2 as the solid electrolyte. The results are corrected for the small solid solubility of CaO in ZrO2. For the reaction, ZrO2(m) + CaO(p) --> CaZrO3(o), DELTAG(phi) = -31590 -13.9T(+/- 180) J mol-1. The ''second-law'' enthalpy of formation of CaZrO3 obtained from the results of this study at a mean temperature of 1090 K is in excellent agreement with the high-temperature solution calorimetric measurements of Muromachi and Navrotsky at 1068 K (J. Solid State Chem., 72 (1988) 244), and the average value of the bomb and acid solution calorimetric studies of Lvova and Feodosev (Zh. Fiz. Khim., 38 (1964) 28), Korneev et al. (Izv. Akad. Nauk SSSR, Neorg. Mater., 7 (1971) 886) and Brown and Bennington (Thermochim. Acta, 106 (1986) 183). The standard entropy of CaZrO3(o) at 298.15 K from the free energy data is 96.4 (+/- 3.5) J K-1 mol-1. The results of this study are discussed in comparison with high-temperture e.m.f. measurements reported in the literature on cubic zirconia solid solutions.