Splicing Functions and Global Dependency on Fission Yeast Slu7 Reveal Diversity in Spliceosome Assembly

The multiple short introns in Schizosaccharomyces pombe genes with degenerate cis sequences and atypically positioned polypyrimidine tracts make an interesting model to investigate canonical and alternative roles for conserved splicing factors. Here we report functions and interactions of the S. pombe slu7(+) (spslu7(+)) gene product, known from Saccharomyces cerevisiae and human in vitro reactions to assemble into spliceosomes after the first catalytic reaction and to dictate 3' splice site choice during the second reaction. By using a missense mutant of this essential S. pombe factor, we detected a range of global splicing derangements that were validated in assays for the splicing status of diverse candidate introns. We ascribe widespread, intron-specific SpSlu7 functions and have deduced several features, including the branch nucleotide-to-3' splice site distance, intron length, and the impact of its A/U content at the 5' end on the intron's dependence on SpSlu7. The data imply dynamic substrate-splicing factor relationships in multiintron transcripts. Interestingly, the unexpected early splicing arrest in spslu7-2 revealed a role before catalysis. We detected a salt-stable association with U5 snRNP and observed genetic interactions with spprp1(+), a homolog of human U5-102k factor. These observations together point to an altered recruitment and dependence on SpSlu7, suggesting its role in facilitating transitions that promote catalysis, and highlight the diversity in spliceosome assembly.

Synergistic effect of reactor chemistry and compressive stress on dislocation bending during GaN growth

The synergistic effect of compressive growth stresses and reactor chemistry, silane presence, on dislocation bending at the very early stages of GaN growth has been studied using in-situ stress measurements and cross-sectional transmission electron microscopy. A single 100 nm Si-doped GaN layer is found to be more effective than a 1 mu m linearly graded AlGaN buffer layer in reducing dislocation density and preventing the subsequent layer from transitioning to a tensile stress. 1 mu m crack-free GaN layers with a dislocation density of 7 x 10(8)/cm(2), with 0.13 nm surface roughness and no enhancement in n-type background are demonstrated over 2 inch substrates using this simple transition scheme. (C) 2013 AIP Publishing LLC.

Analysis of size quantization and temperature effects on the threshold voltage of thin silicon film double-gate metal-oxide-semiconductor field-effect transistor (MOSFET)

In this paper, we analyze the combined effects of size quantization and device temperature variations (T = 50K to 400 K) on the intrinsic carrier concentration (n(i)), electron concentration (n) and thereby on the threshold voltage (V-th) for thin silicon film (t(si) = 1 nm to 10 nm) based fully-depleted Double-Gate Silicon-on-Insulator MOSFETs. The threshold voltage (V-th) is defined as the gate voltage (V-g) at which the potential at the center of the channel (Phi(c)) begins to saturate (Phi(c) = Phi(c(sat))). It is shown that in the strong quantum confinement regime (t(si) <= 3nm), the effects of size quantization far over-ride the effects of temperature variations on the total change in band-gap (Delta E-g(eff)), intrinsic carrier concentration (n(i)), electron concentration (n), Phi(c(sat)) and the threshold voltage (V-th). On the other hand, for t(si) >= 4 nm, it is shown that size quantization effects recede with increasing t(si), while the effects of temperature variations become increasingly significant. Through detailed analysis, a physical model for the threshold voltage is presented both for the undoped and doped cases valid over a wide-range of device temperatures, silicon film thicknesses and substrate doping densities. Both in the undoped and doped cases, it is shown that the threshold voltage strongly depends on the channel charge density and that it is independent of incomplete ionization effects, at lower device temperatures. The results are compared with the published work available in literature, and it is shown that the present approach incorporates quantization and temperature effects over the entire temperature range. We also present an analytical model for V-th as a function of device temperature (T). (C) 2013 AIP Publishing LLC.

Investigating thermal stability of structural defects and its effect on d(0) ferromagnetism in undoped SnO2

The effect of annealing on structural defects and d(0) ferromagnetism in SnO2 nanoparticles prepared by solution combustion method is investigated. The as-synthesized SnO2 nanoparticles were annealed at 400-800 degrees C for 2 h, in ambient conditions. The crystallinity, size, and morphology of the samples were studied using x-ray diffraction and transmission electron microscopy studies. The annealing results in grain growth due to coarsening as well as reduction in oxygen vacancies as confirmed by Raman spectroscopy, photoluminescence spectroscopy, and x-ray photoelectron spectroscopy. All the as synthesized and annealed samples exhibit room temperature ferromagnetism (RTFM) with distinct hysteresis loops and the saturation magnetization as high as similar to 0.02 emu/g in as-synthesized samples. However, the saturation magnetization is drastically reduced with increasing annealing temperature. Further the presence of singly charged oxygen vacancies (V-o(-) signal at g-value 1.99) is confirmed by electron paramagnetic resonance studies, which also diminish with increasing annealing temperature. The observed diminishing RTFM and simultaneous evidences of diminishing O vacancies clearly indicate that RTFM is driven by defects in oxide lattice and confirms primary role of oxygen vacancies in inducing ferromagnetic ordering in metal oxide semiconductors. The study also provides improved fundamental understanding regarding the ambiguity in the origin of intrinsic RTFM in semiconducting metal oxides and projects their technological application in the field of spintronics. (C) 2013 AIP Publishing LLC.

Influence of operational and geometrical parameters on the performance of twin thermoacoustic prime mover

Thermoacoustics is the interaction between heat and sound, which are useful in designing heat engines and heat pumps. Research in the field of thermoacoustics focuses on the demand to improve the performance which is achieved by altering operational, geometrical and fluid parameters. The present study deals with improving the performance of twin thermoacoustic prime mover, which has gained the significant importance in the recent years for the production of high amplitude sound waves. The performance of twin thermoacoustic prime mover is evaluated in terms of onset temperature difference, resonance frequency and pressure amplitude of the acoustic waves by varying the resonator length and charge pressures of fluid medium nitrogen. DeltaEC, the free simulation software developed by LANL, USA is employed in the present study to simulate the performance of twin thermoacoustic prime mover. Experimental and simulated results are compared and the deviation is found to be within 10%.

Redox regulation of protein tyrosine phosphatase 1B (PTP1B): Importance of steric and electronic effects on the unusual cyclization of the sulfenic acid intermediate to a sulfenyl amide

The redox regulation of protein tyrosine phosphatase 1B (PTP1B) via the unusual transformation of its sulfenic acid (PTP1B-SOH) to a cyclic sulfenyl amide intermediate is studied by using small molecule chemical models. These studies suggest that the sulfenic acids derived from the H2O2-mediated reactions o-amido thiophenols do not efficiently cyclize to sulfenyl amides and the sulfenic acids produced in situ can be trapped by using methyl iodide. Theoretical calculations suggest that the most stable conformer of such sulfenic acids are stabilized by n(O) -> sigma* (S-OH) orbital interactions, which force the -OH group to adopt a position trans to the S center dot center dot center dot O interaction, leading to an almost linear arrangement of the O center dot center dot center dot S-O moiety and this may be the reason for the slow cyclization of such sulfenic acids to their corresponding sulfenyl amides. On the other hand, additional substituents at the 6-position of o-amido phenylsulfenic acids that can induce steric environment and alter the electronic properties around the sulfenic acid moiety by S center dot center dot center dot N or S center dot center dot center dot O nonbonded interactions destabilize the sulfenic acids by inducing strain in the molecule. This may lead to efficient the cyclization of such sulfenic acids. This model study suggests that the amino acid residues in the close proximity of the sulfenic acid moiety in PTP1B may play an important role in the cyclization of PTP1B-SOH to produce the corresponding sulfenyl amide.

The effect of cell size and channel density on neuronal information encoding and energy efficiency

Identifying the determinants of neuronal energy consumption and their relationship to information coding is critical to understanding neuronal function and evolution. Three of the main determinants are cell size, ion channel density, and stimulus statistics. Here we investigate their impact on neuronal energy consumption and information coding by comparing single-compartment spiking neuron models of different sizes with different densities of stochastic voltage-gated Na+ and K+ channels and different statistics of synaptic inputs. The largest compartments have the highest information rates but the lowest energy efficiency for a given voltage-gated ion channel density, and the highest signaling efficiency (bits spike(-1)) for a given firing rate. For a given cell size, our models revealed that the ion channel density that maximizes energy efficiency is lower than that maximizing information rate. Low rates of small synaptic inputs improve energy efficiency but the highest information rates occur with higher rates and larger inputs. These relationships produce a Law of Diminishing Returns that penalizes costly excess information coding capacity, promoting the reduction of cell size, channel density, and input stimuli to the minimum possible, suggesting that the trade-off between energy and information has influenced all aspects of neuronal anatomy and physiology.

Effect of Stress and Interface defects on Photo Luminescence of Si nano-crystals embedded in SiO2

Effect of stress and interface defects on photo luminescence property of a silicon nano-crystal (Si-nc) embedded in amorphous silicon dioxide (a-SiO2) are studied in this paper using a self-consistent quantum-continuum based modeling framework. Si-ncs or quantum dots show photoluminescence at room temperature. Whether its origin is due to Si-nc/a-SiO2 interface defects or quantum confinement of carriers in Si-nc is still an outstanding question. Earlier reports have shown that stresses greater than 12 GPa change the indirect energy band gap structure of bulk Si to a direct energy band gap structure. Such stresses are observed very often in nanostructures and these stresses influence the carrier confinement energy significantly. Hence, it is important to determine the effect of stress in addition to the structure of interface defects on photoluminescence property of Si-nc. In the present work, first a Si-nc embedded in a-SiO2 is constructed using molecular dynamics simulation framework considering the actual conditions they are grown so that the interface and residual stress in the structure evolves naturally during formation. We observe that the structure thus created has an interface of about 1 nm thick consisting of 41.95% of defective states mostly Sin+ (n = 0 to 3) coordination states. Further, both the Si-nc core and the embedding matrix are observed to be under a compressive strain. This residual strain field is applied in an effective mass k.p Hamiltonian formulation to determine the energy states of the carriers. The photo luminescence property computed based on the carrier confinement energy and interface energy states associated with defects will be analysed in details in the paper.

EFFECT OF OFF-STOICHIOMETRY AND TERNARY ADDITIONS ON PLANAR FAULT ENERGIES IN Ni3Al

First principles calculations were done to evaluate the lattice parameter, cohesive energy and stacking fault energies of ordered gamma' (Ll(2)) precipitates in superalloys as a function of composition. It was found that addition of Ti and Ta lead to an increase in lattice parameter and decrease in cohesive energy, while Ni antisites had the opposite effect. Ta and Ti addition to stoichiometric Ni3Al resulted in an initial increase in the energies of APB((111)), CSF(111), APB((001)) and SISF(111). However, at higher concentrations, the fault energies decreased. Addition of Ni antisites decreased the energy of all four faults monotonically. A model based on nearest neighbor bonding was used for Ni-3(Al, Ta), Ni-3(Al, Ti) and Ni-3(Al, Ni) pseudo-binary systems and extended to pseudo- ternary Ni-3(Al, Ta, Ni) and Ni-3(Al, Ti, Ni) systems. Recipes were developed for predicting lattice parameters, cohesive energies and fault energies in pseudo- ternary systems on the basis of coefficients derived from simpler pseudobinary systems. The model predictions were found to be in good agreement with first principles calculations for lattice parameters, cohesive energies, and energies of APB((111)) and CSF(111).

Effect of Texture and Grain Size on Bio-Corrosion Response of Ultrafine-Grained Titanium

The bio-corrosion response of ultrafine-grained commercially pure titanium processed by different routes of equal-channel angular pressing has been studied in simulated body fluid. The results indicate that the samples processed through route B-c that involved rotation of the workpiece by 90 deg in the same sense between each pass exhibited higher corrosion resistance compared to the ones processed by other routes of equal-channel angular pressing, as well as the coarse-grained sample. For a similar grain size, the higher corrosion resistance of the samples exhibiting off-basal texture compared to shear texture indicates the major role of texture in corrosion behavior. It is postulated that an optimum combination of microstructure and crystallographic texture can lead to high strength and excellent corrosion resistance.

Effect of myonuclear number and mitochondrial fusion on Drosophila indirect flight muscle organization and size

Mechanisms involved in establishing the organization and numbers of fibres in a muscle are not completely understood. During Drosophila indirect flight muscle (IFM) formation, muscle growth is achieved by both incorporating hundreds of nuclei, and hypertrophy. As a result, IFMs provide a good model with which to understand the mechanisms that govern overall muscle organization and growth. We present a detailed analysis of the organization of dorsal longitudinal muscles (DLMs), a subset of the IFMs. We show that each DLM is similar to a vertebrate fascicle and consists of multiple muscle fibres. However, increased fascicle size does not necessarily change the number of constituent fibres, but does increase the number of myofibrils packed within the fibres. We also find that altering the number of myoblasts available for fusion changes DLM fascicle size and fibres are loosely packed with myofibrils. Additionally, we show that knock down of genes required for mitochondrial fusion causes a severe reduction in the size of DLM fascicles and fibres. Our results establish the organization levels of DLMs and highlight the importance of the appropriate number of nuclei and mitochondrial fusion in determining the overall organization, growth and size of DLMs. (C) 2013 Elsevier Inc. All rights reserved.

Molecular dynamic simulations of elastomer structure and its influence on anisotropic stress under time-varying strain

We investigate the evolution of polymer structure and its influence on uniaxial anisotropic stress under time-varying uniaxial strain, and the role of external control variables such as temperature, strain rate, chain length, and density, using molecular dynamics simulation. At temperatures higher than glass transition, stress anisotropy in the system is reduced even though the bond stretch is greater at higher temperatures. There is a significant increase in the stress level with increasing density. At higher densities, the uncoiling of the chains is suppressed and the major contribution to the deformation is by internal deformation of the chains. At faster rates of loading stress anisotropy increases. The deformation mechanism is mostly due to bond stretch and bond bending rather than overall shape and size. Stress levels increase with longer chain length. There is a critical value of the functionality of the cross-linkers beyond which the uniaxial stress developed increases caused primarily by bond stretching due to increased constraint on the motion of the monomers. Stacking of the chains in the system also plays a dominant role in the behaviour in terms of excluded volume interactions. Low density, high temperature, low values of functionality of cross-linkers, and short chain length facilitate chain uncoiling and chain slipping in cross-linked polymers.

Local structural disorder and its influence on the average global structure and polar properties in Na0.5Bi0.5TiO3

Na0.5Bi0.5TiO3 (NBT) and its derivatives have prompted a great surge in interest owing to their potential as lead-free piezoelectrics. In spite of five decades since its discovery, there is still a lack of clarity on crucial issues such as the origin of significant dielectric relaxation at room temperature, structural factors influencing its depoling, and the status of the recently proposed monoclinic (Cc) structure vis-a-vis the nanosized structural heterogeneities. In this work, these issues are resolved by comparative analysis of local and global structures on poled and unpoled NBT specimens using electron, x-ray, and neutron diffraction in conjunction with first-principles calculation, dielectric, ferroelectric, and piezoelectric measurements. The reported global monoclinic (Cc) distortion is shown not to correspond to the thermodynamic equilibrium state at room temperature. The global monocliniclike appearance rather owes its origin to the presence of local structural and strain heterogeneities. Poling removes the structural inhomogeneities and establishes a long-range rhombohedral distortion. In the process the system gets irreversibly transformed from a nonergodic relaxor to a normal ferroelectric state. The thermal depoling is shown to be associated with the onset of incompatible in-phase tilted octahedral regions in the field-stabilized long range rhombohedral distortion.

The influence of debris cover and glacial lakes on the recession of glaciers in Sikkim Himalaya, India

We investigated area changes in glaciers covering an area of similar to 200 km(2) in the Tista basin, Sikkim, Eastern Indian Himalaya, between similar to 1990 and 2010 using Landsat Thematic Mapper (TM) and Indian Remote-sensing Satellite (IRS) images and related the changes to debris cover, supraglacial lakes and moraine-dam lakes. The glaciers lost an area of 3.3 +/- 0.8% between 1989/90 and 2010. More detailed analysis revealed an area loss of 2.00 +/- 0.82, 2.56 +/- 0.61 and 2.28 +/- 2.01 km(2) for the periods 1989-97, 1997-2004/05 and 2004-2009/10, respectively. This indicates an accelerated retreat of glaciers after 1997. On further analysis, we observed (1) the formation and expansion of supraglacial lakes on many debris-covered glaciers and (2) the merging of these lakes over time, leading to the development of large moraine-dam lakes. We also observed that debris-covered glaciers with lakes lose a greater area than debris-covered glaciers without lakes and debris-free glaciers. The climatic data for 24 years (1987-2011), measured at the Gangtok meteorological station (1812 m a.s.l.), showed that the region experienced a 1.0 degrees C rise in the summer minimum temperature and a 2.0 degrees C rise in the winter minimum temperature, indicating hotter summers and warmer winters. There was no significant trend in the total annual precipitation. We find that glacier retreat is caused mainly by a temperature increase and that debris-covered glaciers can retreat at a faster rate than debris-free glaciers, if associated with lakes.