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.

Experimental and numerical studies on protection of buried pipelines and underground utilities using geocells

This paper presents the results of the laboratory model tests and the numerical studies conducted on small diameter PVC pipes, buried in geocell reinforced sand beds. The aim of the study was to evaluate the suitability of the geocell reinforcement in protecting the underground utilities and buried pipelines. In addition to geocells, the efficacy of only geogrid and geocell with additional basal geogrid cases were also studied. A PVC (Poly Vinyl Chloride) pipe with external diameter 75 mm and thickness 1.4 mm was used in the experiments. The vehicle tire contact pressure was simulated by applying the pressure on the top of the bed with the help of a steel plate. Results suggest that the use of geocells with additional basal geogrid considerably reduces the deformation of the pipe as compared to other types of reinforcements. Further, the depth of placement of pipe was also varied between 1B to 2B (B is the width of loading plate) below the plate in the presence of geocell with additional basal geogrid. More than 50% reduction in the pressure and more than 40% reduction in the strain values were observed in the presence of reinforcements at different depths as compared to the unreinforced beds. Conversely, the performance of the subgrade soil was also found to be marginally influenced by the position of the pipe, even in the presence of the relatively stiff reinforcement system. Further, experimental results were validated with 3-dimensional numerical studies using FLAC(3D) (Fast Lagrangian Analysis of Continua in 3D). A good agreement in the measured pipe stain values were observed between the experimental and numerical studies. Numerical studies revealed that the geocells distribute the stresses in the lateral direction and thus reduce the pressure on the pipe. In addition, the results of the 1-g model tests were scaled up to the prototype case of the shallow buried pipeline below the pavement using the appropriate scaling laws. (C) 2015 Elsevier Ltd. All rights reserved.

Effects of instabilities and coherent structures on the performance of a thermocline based thermal energy storage

We investigate the transient dynamics of disturbances inside a thermocline based molten salt thermal energy storage (TES). Numerical simulations were conducted with four inlet flow configurations. The disturbances introduced at the inlet grow via Rayleigh Taylor instability. The formed vortical motions inside the tank propagate downstream and destroy the thermocline. The vortex-thermocline interaction upsets the stratification inside the TES. The disturbance growth rate, penetration length and vortex Reynolds number are measured. The growth of penetration length prior to the vortex-thermocline interaction is quadratic. The vortex Reynolds number of the eddy which causes thermocline breakdown increases with increase in Atwood number. The impingement of vortex on thermocline is studied. (C) 2015 Elsevier Ltd. All rights reserved.

A Few Case Studies on the Correlation of Particle Network and Its Stability on the Ionic Conductivity of Solid-Liquid Composite Electrolytes

We discuss here the crucial role of the particle network and its stability on the long-range ion transport in solid liquid composite electrolytes. The solid liquid composite electrolytes chosen for the study here comprise nanometer sized silica (SiO2) particles having various surface chemical functionalities dispersed in nonaqueous lithium salt solutions, viz, lithium perchlorate (LiClO4) in two different polyethylene glycol based solvents. These systems constitute representative examples of an independent class of soft matter electrolytes known as ``soggy sand'' electrolytes, which have tremendous potential in diverse electrochemical devices. The oxide additive acts as a heterogeneous dopant creating free charge carriers and enhancing the local ion transport. For long-range transport, however, a stable spanning particle network is needed. Systematic experimental investigations here reveal that the spatial and time dependent characteristics of the particle network in the liquid solution are nontrivial. The network characteristics are predominantly determined by the chemical makeup of the electrolyte components and the chemical interactions between them. It is noteworthy that in this study the steady state macroscopic ionic conductivity and viscosity of the solid liquid composite electrolyte are observed to be greatly determined by the additive oxide surface chemical functionality, solvent chemical composition, and solvent dielectric constant.

Isolating the impacts of land use and climate change on streamflow

Quantifying the isolated and integrated impacts of land use (LU) and climate change on streamflow is challenging as well as crucial to optimally manage water resources in river basins. This paper presents a simple hydrologic modeling-based approach to segregate the impacts of land use and climate change on the streamflow of a river basin. The upper Ganga basin (UGB) in India is selected as the case study to carry out the analysis. Streamflow in the river basin is modeled using a calibrated variable infiltration capacity (VIC) hydrologic model. The approach involves development of three scenarios to understand the influence of land use and climate on streamflow. The first scenario assesses the sensitivity of streamflow to land use changes under invariant climate. The second scenario determines the change in streamflow due to change in climate assuming constant land use. The third scenario estimates the combined effect of changing land use and climate over the streamflow of the basin. Based on the results obtained from the three scenarios, quantification of isolated impacts of land use and climate change on streamflow is addressed. Future projections of climate are obtained from dynamically downscaled simulations of six general circulation models (GCMs) available from the Coordinated Regional Downscaling Experiment (CORDEX) project. Uncertainties associated with the GCMs and emission scenarios are quantified in the analysis. Results for the case study indicate that streamflow is highly sensitive to change in urban areas and moderately sensitive to change in cropland areas. However, variations in streamflow generally reproduce the variations in precipitation. The combined effect of land use and climate on streamflow is observed to be more pronounced compared to their individual impacts in the basin. It is observed from the isolated effects of land use and climate change that climate has a more dominant impact on streamflow in the region. The approach proposed in this paper is applicable to any river basin to isolate the impacts of land use change and climate change on the streamflow.

Modeling of Effect of Nucleation Rate and Electrodes' Resistance on Discharge Characteristics of Lead-Acid Batteries

Classical models are not successful in describing discharge characteristics of a lead-acid battery when the current density is varied over a wide range. A model is developed in this work to overcome this lacuna by introducing into the standard models two mechanisms that have not been used earlier. Lead sulfate particles nucleate and grow on active materials of electrodes during discharge, resulting in coverage of active area. Increasing rate of discharge builds supersaturation of lead sulfate rapidly, and causes increased extents of nucleation and coverage. Electrodes behave almost like an insulator due to deposition of lead sulfate when active materials are converted to a critical extent, and this can stop discharge process. Influence of this mechanism is also rate dependent. The new model developed is tested against data on polarization behavior, and capacity drawn as a function of current. The model successfully predicts both polarization curves and Peukert behavior. The model is used to predict charge that can be drawn at a current after partial discharge at a different current. Model suggests that altering nucleation behavior can be useful in enhancing capacity available for discharge. (C) 2015 The Electrochemical Society.

In-situ synthesized poly(vinyl butyral)/MMT-clay nanocomposites: The role of degree of acetalization and clay content on thermal, mechanical and permeability properties of PVB matrix

Poly(vinyl butyral) - MMT clay nanocomposites were synthesized in situ with three different degrees of acetalization and with varying clay content for each vinyl butyral polymer ratio. The clay nano-platelet galleries were expanded, as determined by X-ray diffraction and TEM analysis. The glass transition temperature of the polymer nanocomposites were found to be similar to 56 degrees C and similar to 52 degrees C for the neat polymer and the 4% clay loaded samples, respectively. The 4 wt% clay loaded film showed higher strength and low strain to failure. The dynamic mechanical analysis also confirmed the improved stability of the matrix. The matrix with 0.5 butyral to alcohol ratio for 4 wt% clay exhibited good water vapor transmission compared to all other compositions. The encapsulated devices with 2.5 and 4 wt% clay loaded films increases the device life time and the efficiencies of these films were 50% higher than their encapsulated pristine polymer films. (C) 2015 Elsevier Ltd. All rights reserved.

Common effect of chemical and external pressures on the magnetic properties of RCoPO (R = La, Pr, Nd, Sm). II.

We investigate the direct correspondence between Co band ferromagnetism and structural parameters in the pnictide oxides RCoPO for different rare-earth ions (R = La, Pr, Nd, Sm) by means of muon-spin spectroscopy and ab initio calculations, complementing our results published previously G. Prando et al., Common effect of chemical and external pressures on the magnetic properties of RCoPO (R = La, Pr), Phys. Rev. B 87, 064401 (2013)]. We find that both the transition temperature to the ferromagnetic phase T-C and the volume of the crystallographic unit cell V are conveniently tuned by the R ionic radius and/or external pressure. We report a linear correlation between T-C and V and our ab initio calculations unambiguously demonstrate a full equivalence of chemical and external pressures. As such, we show that R ions influence the ferromagnetic phase only via the induced structural shrinkage without involving any active role from the electronic f degrees of freedom, which are only giving a sizable magnetic contribution at much lower temperatures.

In Vitro Production of Echioidinin, 7-O-Methywogonin from Callus Cultures of Andrographis lineata and Their Cytotoxicity on Cancer Cells

Andrographis lineata is an herbal medicinal plant used in traditional medicine as a substitute for Andrographis paniculata. Here, using mature leaf explants of A. lineata we demonstrate for the first time the callus induction established on MS medium containing 1.0 mg l(-1) IAA. Dried callus was subjected to solvent extraction with acetone. Further the acetone residue was separated by silica gel column chromatography, crystallized and characterized on the basis of nuclear magnetic resonance (proton and c13) and liquid chromatographic mass spectroscopy. This analysis revealed the occurrence of two known flavones namely, 7-O-methylwogonin (MW) and Echioidinin (ED). Furthermore, these compounds were tested for their cytotoxicity against leukemic cell line, CEM. We identify that ED and MW induced cytotoxicity in a time-and concentration-dependent manner. Further increase in the LDH release upon treatment with ED and MW further confirmed our cytotoxicity results against leukemic cell line. Strikingly, MW was more potent than ED when compared by trypan blue and MTT assays. Our results recapitulate the utility of callus cultures for the production of plant specific bioactive secondary metabolites instead of using wild plants. Together, our in vitro studies provide new insights of A. lineata callus cultures serving as a source for cancer chemotherapeutic agents.

Scaling analysis and numerical studies on water vapour adsorption in a columnar porous silica gel bed

This article presents a theoretical analysis of heat and mass transfer in a silica gel + water adsorption process using scaling principles. A two-dimensional columnar packed adsorber domain is chosen for the study, with side and bottom walls cooled and vapour inlet from the top. The adsorption process is initiated from the cold walls with a temperature jump of 15 K, whereas the water vapour supply is maintained at a constant inlet pressure of 1 kPa. The first part of the study is dedicated to deriving relevant scales for the adsorption process by an order of magnitude analysis of energy, continuity and momentum equations. In the latter part, the derived scales are compared with the outcome of numerical studies performed for various domain widths and aspect ratio of bed. A good correlation between scaling and simulation results is observed, thereby validating the scaling approach. (C) 2015 Elsevier Ltd. All rights reserved.

Molecular dynamics and simulations study on the vibrational and electronic solvatochromism of benzophenone

Solvent plays a key role in diverse physico-chemical and biological processes. Therefore, understanding solute-solvent interactions at the molecular level of detail is of utmost importance. A comprehensive solvatochromic analysis of benzophenone (Bzp) was carried out in various solvents using Raman and electronic spectroscopy, in conjunction with Density Functional Theory (DFT) calculations of supramolecular solute-solvent clusters generated using classical Molecular Dynamics Simulations (c-MDSs). The >C=O stretching frequency undergoes a bathochromic shift with solvent polarity. Interestingly, in protic solvents this peak appears as a doublet: c-MDS and ad hoc explicit solvent ab initio calculations suggest that the lower and higher frequency peaks are associated with the hydrogen bonded and dangling carbonyl group of Bzp, respectively. Additionally, the dangling carbonyl in methanol (MeOH) solvent is 4 cm(-1) blue-shifted relative to acetonitrile solvent, despite their similar dipolarity/polarizability. This suggests that the cybotactic region of the dangling carbonyl group in MeOH is very different from its bulk solvent structure. Therefore, we propose that this blue-shift of the dangling carbonyl originates in the hydrophobic solvation shell around it resulting from extended hydrogen bonding network of the protic solvents. Furthermore, the 1(1)n pi* (band I) and 1(1)pi pi* (band II) electronic transitions show a hypsochromic and bathochromic shift, respectively. In particular, these shifts in protic solvents are due to differences in their excited state-hydrogen bonding mechanisms. Additionally, a linear relationship is obtained for band I and the >C=O stretching frequency (cm(-1)), which suggests that the different excitation wavelengths in band I correspond to different solvation states. Therefore, we hypothesize that the variation in excitation wavelengths in band I could arise from different solvation states leading to varying solvation dynamics. This will have implications for ultrafast processes associated with electron-transfer, charge transfer, and also the photophysical aspects of excited states. (C) 2016 AIP Publishing LLC.

Comments on ``Influence of chemical reaction and viscous dissipation on MHD mixed convection flow'' by K. Das JMST 28 (5) (2014) 1881 similar to 1885] and ``Cu-water nanofluid flow and heat transfer over a shrinking sheet'' by K. Das JMST 28 (12) 5089 similar to 5094]

In this letter, we submit our comment on the following recently published papers by Kalidas Das: (1) ``Influence of chemical reaction and viscous dissipation on MHD mixed convection flow,'' Journal of Mechanical Science and Technology 28 (5) (2014) 1881-1885; and (2) ``Cu-water nanofluid flow and heat transfer over a shrinking sheet,'' Journal of Mechanical Science and Technology 28 (12) (2014) 5089-5094. The authors attempt to present the similarity solutions in both papers. We comment that the similarity transformations considered in Refs. 1, 2] are incorrect. Thus, the results presented by Kalidas Das lead to invalid conclusions.

Design and Validation of On-chip Planar Mixer Based on Advection and Viscoelastic Effects

Mixing at low Reynolds number is usually due to diffusion and requires longer channel lengths for complete mixing. In order to reduce the mixing lengths, advective flow can be induced by varying the channel geometry. Additionally, in non-newtonian fluids, appropriate modifications to channel geometry can be used to aid the mixing process by capitalizing on their viscoelastic nature. Here we have exploited the advection and viscoelastic effects to implement a planar passive micro-mixer. Microfluidic devices incorporating different blend of mixing geometries were conceived. The optimum design was chosen based on the results of the numerical simulations performed in COMSOL. The chosen design had sudden expansion and contraction along with teeth patterns along the channel walls to improve mixing. Mixing of two different dyes was performed to validate the mixing efficiency. Particle dispersion experiments were also carried out. The results indicated effective mixing. In addition, the same design was also found to be compatible with electrical power free pumping mechanism like suction. The proposed design was then used to carry out on-chip chemical cell lysis with human whole blood samples to establish its use with non-newtonian fluids. Complete lysis of the erythrocytes was observed leaving behind the white blood cells at the outlet.

Effect of strain rate response and pin diameter on mechanically mixed layer formation and wear mechanisms in a Ti6Al4V-SS316L pair

Three mechanisms operate during wear of materials. These mechanisms include the Strain Rate Response (SRR - effect of strain rate on plastic deformation), Tribo-Chemical Reactions (TCR) and formation of Mechanically Mixed Layers (MML). The present work investigates the effect of these three in context of the formation of MML. For this wear experiments are done on a pin-on-disc machine using Ti64 as the pin and SS316L as the disc. It is seen that apart from the speed and load, which control the SRR and TCR, the diameter of the pin controls the formation of MML, especially at higher speeds.

Effects of 'sinking in' and 'piling up' on estimating the contact area under load in indentation

The phenomena of the 'piling up' and 'sinking-in' of surface profiles in conical indentation in elastic-plastic solids with work hardening are studied using dimensional and finite-element analysis. The degree of sinking in and piling up is shown to depend on the ratio of the initial yield strength Y to Young's modulus E and on the work-hardening exponent n. The widely used procedure proposed by Oliver and Pharr for estimating contact depth is then evaluated systematically. By comparing the contact depth obtained directly from finite-element calculations with that obtained from the initial unloading slope using the Oliver-Pharr procedure, the applicability of the procedure is discussed.