Novel ATPase activity of the polyprotein intermediate, Viral Protein genome-linked-Nuclear Inclusion-a protease, of Pepper vein banding potyvirus

Potyviruses temporally regulate their protein function by polyprotein processing. Previous studies have shown that VPg (Viral Protein genome-linked) of Pepper vein banding virus interacts with the NIa-Pro (Nuclear Inclusion-a protease) domain, and modulates the kinetics of the protease. In the present study, we report for the first time that VPg harbors the Walker motifs A and B, and the presence of NIa-Pro, especially in cis (cleavage site (E191A) VPg-Pro mutant), is essential for manifestation of the ATPase activity. Mutation of Lys47 (Walker motif A) and Asp88:Glu89 (Walker motif B) to alanine in E191A VPg-Pro lead to reduced ATPase activity, confirming that this activity was inherent to VPg. We propose that potyviral VPg, established as an intrinsically disordered domain, undergoes plausible structural alterations upon interaction with globular NIa-Pro which induces the ATPase activity. (C) 2012 Elsevier Inc. All rights reserved.

Influence of the Blade Hub Geometry on the Performance of Low-Head Axial Flow Turbines

The influence of geometric parameters, such as blade profile and hub geometry on axial flow turbines for micro hydro application remains poorly characterized. This paper first introduces a holistic theoretical model for studying the hydraulic phenomenon resulting from geometric modification to the blades. It then describes modification carried out on two runner stages, of which one has untwisted blades and the other has twisted blades obtained by modifying the inlet hub. The experimental results showed that the performance of the untwisted blade runner was satisfactory with a maximum efficiency of 68%. However, positive effects of twisted blades were clearly evident with an efficiency rise of more than 2%. This study also looks into the possible limitations of the model and suggests the extension of the experimental work and the use of computational tools to conduct a progressive validation of all experimental findings, especially on the flow physics within the hub region and the slip phenomena. The paper finally underlines the importance of developing a standardization philosophy for axial flow turbines specific for micro hydro requirements. DOI:10.1061/(ASCE)EY.1943-7897.0000060. (C) 2012 American Society of Civil Engineers.

Cloning, expression, purification, crystallization and preliminary X-ray crystallographic study of thymidylate kinase (TTHA1607) from Thermus thermophilus HB8

Nucleotide biosynthesis plays a key role in cell survival and cell proliferation. Thymidylate kinase is an enzyme that catalyses the conversion of dTMP to dTDP using ATP-Mg2+ as a phosphoryl-donor group. This enzyme is present at the junction of the de novo and salvage pathways; thus, any inhibitor designed against it will result in cell death. This highlights the importance of this enzyme as a drug target. Thymidylate kinase from the extremely thermophilic organism Thermus thermophilus HB8 has been expressed, purified and crystallized using the microbatch method. The crystals diffracted to a resolution of 1.83 angstrom and belonged to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 39.50, b = 80.29, c = 122.55 angstrom. Preliminary studies revealed the presence of a dimer in the asymmetric unit with a Matthews coefficient (V-M) of 2.18 angstrom(3) Da(-1).

Short- and long-term temporal variations in salinity and the oxygen, carbon and hydrogen isotopic compositions of the Hooghly Estuary water, India

The Hooghly River estuary provides a unique experimental site to understand the effect of monsoonal river discharge on freshwater and seawater mixing. Water samples collected bi-weekly for a duration of 17 months were analyzed for salinity, delta O-18,delta C-13(DIC), as well as delta D to investigate the differential mixing of freshwater and seawater. The differences in salinity and delta O-18 of samples collected during low and high tides on the same day are strongly correlated suggesting a well mixed water column at our sampling site. Low salinity and depleted delta O-18 during monsoon is consistent with increased river discharge as well as high rainfall. We identified different slopes in a delta O-18 versus salinity plot for the estuary water samples collected during monsoon and non-monsoon seasons. This is driven by composition of the freshwater source which is dominated by rainwater during monsoon and rivers during non-monsoon months. Selected delta D analyses of samples indicate that groundwater contributes significantly to the Hooghly Estuary during low rainfall times of the year. delta C-13(DIC) measured in the water recorded low values towards the end of monsoon indicating low productivity (i.e. increased organic respiration) while progressively increasing delta C-13(DIC) values from October till January as well as during some of the pre-monsoon months can be explained by increasing productivity. Very low delta C-13(DIC) (similar to-20%0) suggests involvement of carbon derived from anaerobic oxidation of organics and/or methane with potential contribution from increased anthropogenic water supply. An estimate of seawater incursion into the Hooghly Estuary at different times of the year is obtained by using salinity data in a two-component mixing model. Presence of seawater was found maximum (31-37%) during February till July and lowest (less than or equal to 6%) from September till November. We notice a temporal offset between Ganges River discharge farther upstream at Farakka and salinity variation at the Hooghly Estuary. We believe that this time lag is a result of the physical distance between Farakka and Kakdweep (our sampling location) and put constraints on the travel time of river water during early monsoon. (c) 2012 Published by Elsevier B.V.

EXIT Chart Based Design of Irregular LDPC Codes for Large-MIMO Systems

In this letter, we characterize the extrinsic information transfer (EXIT) behavior of a factor graph based message passing algorithm for detection in large multiple-input multiple-output (MIMO) systems with tens to hundreds of antennas. The EXIT curves of a joint detection-decoding receiver are obtained for low density parity check (LDPC) codes of given degree distributions. From the obtained EXIT curves, an optimization of the LDPC code degree profiles is carried out to design irregular LDPC codes matched to the large-MIMO channel and joint message passing receiver. With low complexity joint detection-decoding, these codes are shown to perform better than off-the-shelf irregular codes in the literature by about 1 to 1.5 dB at a coded BER of 10(-5) in 16 x 16, 64 x 64 and 256 x 256 MIMO systems.

Tuning of the extended concentric tube resonators

It has been shown recently that the acoustic performance of the extended tube expansion chambers can be improved substantially by making the extended inlet and outlet equal to half and quarter chamber lengths, duly incorporating the end corrections due to the evanescent higher order modes that would be generated at the discontinuities. Such chambers however suffer from the disadvantages of high back pressure and generation of aerodynamic noise at the area discontinuities. These two disadvantages can be overcome by means of a perforated bridge between the extended inlet and extended outlet. This paper deals with design or tuning of these extended concentric tube resonators.

Predicting the lithospheric stress field and plate motions by joint modeling of lithosphere and mantle dynamics

The way in which basal tractions, associated with mantle convection, couples with the lithosphere is a fundamental problem in geodynamics. A successful lithosphere-mantle coupling model for the Earth will satisfy observations of plate motions, intraplate stresses, and the plate boundary zone deformation. We solve the depth integrated three-dimensional force balance equations in a global finite element model that takes into account effects of both topography and shallow lithosphere structure as well as tractions originating from deeper mantle convection. The contribution from topography and lithosphere structure is estimated by calculating gravitational potential energy differences. The basal tractions are derived from a fully dynamic flow model with both radial and lateral viscosity variations. We simultaneously fit stresses and plate motions in order to delineate a best-fit lithosphere-mantle coupling model. We use both the World Stress Map and the Global Strain Rate Model to constrain the models. We find that a strongly coupled model with a stiff lithosphere and 3-4 orders of lateral viscosity variations in the lithosphere are best able to match the observational constraints. Our predicted deviatoric stresses, which are dominated by contribution from mantle tractions, range between 20-70 MPa. The best-fitting coupled models predict strain rates that are consistent with observations. That is, the intraplate areas are nearly rigid whereas plate boundaries and some other continental deformation zones display high strain rates. Comparison of mantle tractions and surface velocities indicate that in most areas tractions are driving, although in a few regions, including western North America, tractions are resistive. Citation: Ghosh, A., W. E. Holt, and L. M. Wen (2013), Predicting the lithospheric stress field and plate motions by joint modeling of lithosphere and mantle dynamics.

Ages and relative sizes of pre-2004 tsunamis in the Bay of Bengal inferred from geologic evidence in the Andaman and Nicobar Islands

Geologic evidence along the northern part of the 2004 Aceh-Andaman rupture suggests that this region generated as many as five tsunamis in the prior 2000years. We identify this evidence by drawing analogy with geologic records of land-level change and the tsunami in 2004 from the Andaman and Nicobar Islands (A&N). These analogs include subsided mangrove swamps, uplifted coral terraces, liquefaction, and organic soils coated by sand and coral rubble. The pre-2004 evidence varies in potency, and materials dated provide limiting ages on inferred tsunamis. The earliest tsunamis occurred between the second and sixth centuries A.D., evidenced by coral debris of the southern Car Nicobar Island. A subsequent tsunami, probably in the range A.D. 770-1040, is inferred from deposits both in A&N and on the Indian subcontinent. It is the strongest candidate for a 2004-caliber earthquake in the past 2000years. A&N also contain tsunami deposits from A.D. 1250 to 1450 that probably match those previously reported from Sumatra and Thailand, and which likely date to the 1390s or 1450s if correlated with well-dated coral uplift offshore Sumatra. Thus, age data from A&N suggest that within the uncertainties in estimating relative sizes of paleo-earthquakes and tsunamis, the 1000year interval can be divided in half by the earthquake or earthquakes of A.D. 1250-1450 of magnitude >8.0 and consequent tsunamis. Unlike the transoceanic tsunamis generated by full or partial rupture of the subduction interface, the A&N geology further provides evidence for the smaller-sized historical tsunamis of 1762 and 1881, which may have been damaging locally.

Yanai waves in the western equatorial Indian Ocean

Observations and models have shown the presence of intraseasonal fluctuations in 20-30-day and 10-20-day bands in the equatorial Indian Ocean west of 60 degrees E (WEIO). Their spatial and temporal structures characterize them as Yanai waves, which we label low-frequency (LFYW) and high-frequency (HFYW) Yanai waves, respectively. We explore the dynamics of these intraseasonal signals, using an ocean general circulation model (Modular Ocean Model) and a linear, continuously stratified model. Yanai waves are forced by the meridional wind tau(y) everywhere in the WEIO most strongly during the monsoon seasons. They are forced both directly in the interior ocean and by reflection of the interior response from the western boundary; interference between the interior and boundary responses results in a complex surface pattern that propagates eastward and has nodes. Yanai waves are also forced by instabilities primarily during June/July in a region offshore from the western boundary (52-55 degrees E). At that time, eddies, generated by barotropic instability of the Southern Gyre, are advected southward to the equator. There, they generate a westward-propagating, cross-equatorial flow field, v(eq), with a wave number/frequency spectrum that fits the dispersion relation of a number of Yanai waves, and these waves are efficiently excited. Typically, Yanai waves associated with several baroclinic modes are excited by both wind and eddy forcing; and typically, they superpose to create beams that carry energy vertically and eastward along ray paths. The same processes generate LFYWs and HFYWs, and hence, their responses are similar; differences are traceable to the property that HFYWs have longer wavelengths than LFYWs for each baroclinic mode.

WEAR AND SLIDING-FRICTION CHARACTERISTICS OF STAINLESS STEEL SS316LN WITHOUT A COATING AND WITH A CrN COATING AT ELEVATED TEMPERATURES AND IN A VACUUM

Stainless steel of type AISI 316LN - one of the structural materials of fast neutron reactors - must have a long service life under conditions that subject it to different types of wear (galling, adhesion, fretting, and abrasion). Cobalt-based hard facings are generally avoided due to induced radioactivity. Nickel-based hard facings are strongly preferred instead. One alternative to both types of coatings is a hard-alloy coating of CrN. This article examines wear and friction characteristics during the sliding of uncoated steel SS316LN and the same steel with a CrN coating. In addition, a specially designed pin-on-disk tribometer is used to perform tests in a vacuum at temperatures of up to 1000 degrees C in order to study the effect of oxygen on the wear of these materials. The morphology of the wear surface and the structure of the subsurface were studied by scanning electron microscopy. The formation of an adhesion layer and the self-welding of mating parts are seen to take place in the microstructure at temperatures above 500 degrees C. It is also found that steel SS316LN undergoes shear strain during sliding wear. The friction coefficient depends on the oxygen content, load, and temperature, while the wear rate depends on the strain-hardening of the surface of the material being tested.

Role of Crystal Field in Mixed Alkali Metal Effect: Electron Paramagnetic Resonance Study of Mixed Alkali Metal Oxyfluoro Vanadate Glasses

The mixed alkali metal effect is a long-standing problem in glasses. Electron paramagnetic resonance (EPR) is used by several researchers to study the mixed alkali metal effect, but a detailed analysis of the nearest neighbor environment of the glass former using spin-Hamiltonian parameters was elusive. In this study we have prepared a series of vanadate glasses having general formula (mol %) 40 V2O5-30BaF(2)-(30 - x)LiF-xRbF with x = 5, 10, 15, 20, 25, and 30. Spin-Hamiltonian parameters of V4+ ions were extracted by simulating and fitting to the experimental spectra using EasySpin. From the analysis of these parameters it is observed that the replacement of lithium ions by rubidium ions follows a ``preferential substitution model''. Using this proposed model, we were able to account for the observed variation in the ratio of the g parameter, which goes through a maximum. This reflects an asymmetric to symmetric changeover of. the alkali metal ion environment around the vanadium site. Further, this model also accounts for the variation in oxidation state of vanadium ion, which was confirmed from the variation in signal intensity of EPR spectra.

Surface freshwater storage and variability in the Amazon basin from multi-satellite observations, 1993-2007

The amount of water stored and moving through the surface water bodies of large river basins (river, floodplains, wetlands) plays a major role in the global water and biochemical cycles and is a critical parameter for water resources management. However, the spatiotemporal variations of these freshwater reservoirs are still widely unknown at the global scale. Here, we propose a hypsographic curve approach to estimate surface freshwater storage variations over the Amazon basin combining surface water extent from a multi-satellite-technique with topographic data from the Global Digital Elevation Model (GDEM) from Advance Spaceborne Thermal Emission and Reflection Radiometer (ASTER). Monthly surface water storage variations for 1993-2007 are presented, showing a strong seasonal and interannual variability, and are evaluated against in situ river discharge and precipitation. The basin-scale mean annual amplitude of similar to 1200 km(3) is in the range of previous estimates and contributes to about half of the Gravity Recovery And Climate Experiment (GRACE) total water storage variations. For the first time, we map the surface water volume anomaly during the extreme droughts of 1997 (October-November) and 2005 (September-October) and found that during these dry events the water stored in the river and floodplains of the Amazon basin was, respectively, similar to 230 (similar to 40%) and 210 (similar to 50%) km(3) below the 1993-2007 average. This new 15 year data set of surface water volume represents an unprecedented source of information for future hydrological or climate modeling of the Amazon. It is also a first step toward the development of such database at the global scale.

Trends in aerosol optical depth over Indian region: Potential causes and impact indicators

The first regional synthesis of long-term (back to similar to 25 years at some stations) primary data (from direct measurement) on aerosol optical depth from the ARFINET (network of aerosol observatories established under the Aerosol Radiative Forcing over India (ARFI) project of Indian Space Research Organization over Indian subcontinent) have revealed a statistically significant increasing trend with a significant seasonal variability. Examining the current values of turbidity coefficients with those reported similar to 50 years ago reveals the phenomenal nature of the increase in aerosol loading. Seasonally, the rate of increase is consistently high during the dry months (December to March) over the entire region whereas the trends are rather inconsistent and weak during the premonsoon (April to May) and summer monsoon period (June to September). The trends in the spectral variation of aerosol optical depth (AOD) reveal the significance of anthropogenic activities on the increasing trend in AOD. Examining these with climate variables such as seasonal and regional rainfall, it is seen that the dry season depicts a decreasing trend in the total number of rainy days over the Indian region. The insignificant trend in AOD observed over the Indo-Gangetic Plain, a regional hot spot of aerosols, during the premonsoon and summer monsoon season is mainly attributed to the competing effects of dust transport and wet removal of aerosols by the monsoon rain. Contributions of different aerosol chemical species to the total dust, simulated using Goddard Chemistry Aerosol Radiation and Transport model over the ARFINET stations, showed an increasing trend for all the anthropogenic components and a decreasing trend for dust, consistent with the inference deduced from trend in Angstrom exponent.

A simple model for spatial disaggregation of evaporative fraction: Comparative study with thermal sharpened land surface temperature data over India

[1] Evaporative fraction (EF) is a measure of the amount of available energy at the earth surface that is partitioned into latent heat flux. The currently operational thermal sensors like the Moderate Resolution Imaging Spectroradiometer (MODIS) on satellite platforms provide data only at 1000 m, which constraints the spatial resolution of EF estimates. A simple model (disaggregation of evaporative fraction (DEFrac)) based on the observed relationship between EF and the normalized difference vegetation index is proposed to spatially disaggregate EF. The DEFrac model was tested with EF estimated from the triangle method using 113 clear sky data sets from the MODIS sensor aboard Terra and Aqua satellites. Validation was done using the data at four micrometeorological tower sites across varied agro-climatic zones possessing different land cover conditions in India using Bowen ratio energy balance method. The root-mean-square error (RMSE) of EF estimated at 1000 m resolution using the triangle method was 0.09 for all the four sites put together. The RMSE of DEFrac disaggregated EF was 0.09 for 250 m resolution. Two models of input disaggregation were also tried with thermal data sharpened using two thermal sharpening models DisTrad and TsHARP. The RMSE of disaggregated EF was 0.14 for both the input disaggregation models for 250 m resolution. Moreover, spatial analysis of disaggregation was performed using Landsat-7 (Enhanced Thematic Mapper) ETM+ data over four grids in India for contrasted seasons. It was observed that the DEFrac model performed better than the input disaggregation models under cropped conditions while they were marginally similar under non-cropped conditions.