Local Structural and Environmental Factors Define the Efficiency of an RNA Pseudoknot Involved in Programmed Ribosomal Frameshift Process

In programmed -1 ribosomal frameshift, an RNA pseudoknot stalls the ribosome at specific sequence and restarts translation in a new reading frame. A precise understanding of structural characteristics of these pseudoknots and their PRF inducing ability has not been clear to date. To investigate this phenomenon, we have studied various structural aspects of a -1 PRF inducing RNA pseudoknot from BWYV using extensive molecular dynamics simulations. A set of functional and poorly functional forms, for which previous mutational data were available, were chosen for analysis. These structures differ from each other by either single base substitutions or base-pair replacements from the native structure. We have rationalized how certain mutations in RNA pseudoknot affect its function; e.g., a specific base substitution in loop 2 stabilizes the junction geometry by forming multiple noncanonical hydrogen bonds, leading to a highly rigid structure that could effectively resist ribosome-induced unfolding, thereby increasing efficiency. While, a CG to AU pair substitution in stem 1 leads to loss of noncanonical hydrogen bonds between stems and loop, resulting in a less stable structure and reduced PRF inducing ability, inversion of a pair in stem 2 alters specific base-pair geometry that might be required in ribosomal recognition of nucleobase groups, negatively affecting pseudoknot functioning. These observations illustrate that the ability of an RNA pseudoknot to induce -1 PRF with an optimal rate depends on several independent factors that contribute to either the local conformational variability or geometry

LbL Fabricated Poly(Styrene Sulfonate)/TiO2 Multilayer Thin Films for Environmental Applications

Fabrication of multilayer ultrathin composite films composed of nanosized titanium dioxide particles (P25, Degussa) and polyelectrolytes (PELs), such as poly(allyl amine hydrochloride) (PAH) and poly(styrene sulfonate sodium salt) (PSS), on glass substrates using the layer-by-layer (LbL) assembly technique and its potentia application for the photodegradation of rhodamine B under ultraviolet (UV) irradiation has been reported. The polyelectrolytes and TiO2 were deposited on glass substrates at pH 2.5 and the growth of the multilayers was studied using UV/vis speccrophotometer. Thicknes measurements of the films showed a linear increase in film thickness with increase in number of bilayers. The surface microstructure of the thin films was characterized by field emission scanning electron microscope. The ability of the catalysts immobilized by this technique was compared with TiO2 films prepared by drop casting and spin coating methods. Comparison has been made in terms of film stability and photodegradation of rhodamine B. Process variables such as the effect of surface area of the multilayers, umber of bilayers, and initial dye concentration on photodegradation of rhodamine B were studied. Degradation efficiency increased with increase in number of catalysts (total surface area) and bilayers. Kinetics analysis indicated that the photodegradation rates follow first order kinetics. Under maximum loading of TiO2, with five catalyst slides having 20 bilayers of polyelectrolyte/TiO2 on each, 100 mL of 10 mg/L dye solution could be degraded completely in 4 h. The same slides could be reused with the same efficiency for several cycles. This study demonstrates that nanoparticles can be used in wastewater treatment using a simple immobilization technique. This makes the process an attractive option for scale up.

Biomonitoring of Lotic habitats through Diatoms

Freshwater ecosystems vary in size and composition and contain a wide range of organisms which interact with each other and with the environment. These interactions are between organisms and the environment as nutrient cycling, biomass formation and transfer, maintenance of internal environment and interactions with the external environment. The range of organisms present in aquatic communities decides the generation and transfer function of biomass, which defines and characterises the system. These organisms have distinct roles as they occupy particular trophic levels, forming an interconnected system in a food chain. Availability of resources and competition would primarily determine the balance of individual species within the food web, which in turn influences the variety and proportions of the different organisms, with important implications for the overall functioning of the system. This dynamic and diverse relationship decides the physical, chemical and biological elements across spatial and temporal scales in the aquatic ecosystem, which can be recorded by regular inventorying and monitoring to maintain the integrity and conserve the ecosystem. Regular environmental monitoring, particularly water quality monitoring allows us to detect, assess and manage the overall impacts on the rivers. The appreciation of water quality is in constant flux. Water quality assessments derived through the biotic indices, i.e. assessments based on observations of the resident floral and faunal communities has gained importance in recent years. Biological evaluations provide a description of the water quality that is often not achievable from elemental analyses alone. A biological indicator (or bioindicator) is a taxon or taxa selected based on its sensitivity to a particular attribute, and then assessed to make inferences about that attribute. In other words, they are a substitute for directly measuring abiotic features or other biota. Bioindicators are evaluated through presence or absence, condition, relative abundance, reproductive success, community structure (i.e. composition and diversity), community function (i.e. trophic structure), or any combination thereof.Biological communities reflect the overall ecological integrity by integrating various stresses, thus providing a broad measure of their synergistic impacts. Aquatic communities, both plants and animals, integrate and reflect the effects of chemical and physical disturbances that occur over extended periods of time. Monitoring procedures based on the biota measure the health of a river and the ability of aquatic ecosystems to support life as opposed to simply characterising the chemical and physical components of a particular system. This is the central purpose of assessing the biological condition of aquatic communities of a river.Diatoms (Bacillariophyceae), blue green algae (Cyanophyceae), green algae (Chlorophyceae), and red algae (Rhodphyceae) are the main groups of algae in flowing water. These organisms are widely used as biological indicators of environmental health in the aquatic ecosystem because algae occupy the most basic level in the transfer of energy through natural aquatic systems. The distribution of algae in an aquatic ecosystem is directly related to the fundamental factors such as physical, chemical and biological constituents. Soft algae (all the algal groups except diatoms) have also been used as indicators of biological integrity, but they may have less efficiency than diatoms in this respect due to their highly variable morphology. The diatoms (Bacillariophyceae) comprise a ubiquitous, highly successful and distinctive group of unicellular algae with the most obvious distinguishing characteristic feature being siliceous cell walls (frustules). The photosynthetic organisms living within its photic zone are responsible for about one-half of global primary productivity. The most successful organisms are thought to be photosynthetic prokaryotes (cyanobacteria and prochlorophytes) and a class of eukaryotic unicellular algae known as diatoms. Diatoms are likely to have arisen around 240 million years ago following an endosymbiotic event between a red eukaryotic alga and a heterotrophic flagellate related to the Oomycetes.The importance of algae to riverine ecology is easily appreciated when one considers that they are primary producers that convert inorganic nutrients into biologically active organic compounds while providing physical habitat for other organisms. As primary producers, algae transform solar energy into food from which many invertebrates obtain their energy. Algae also transform inorganic nutrients, such as atmospheric nitrogen into organic forms such as ammonia and amino acids that can be used by other organisms. Algae stabilises the substrate and creates mats that form structural habitats for fish and invertebrates. Algae are a source of organic matter and provide habitat for other organisms such as non-photosynthetic bacteria, protists, invertebrates, and fish. Algae's crucial role in stream ecosystems and their excellent indicator properties make them an important component of environmental studies to assess the effects of human activities on stream health. Diatoms are used as biological indicators for a number of reasons: 1. They occur in all types of aquatic ecosystems. 2. They collectively show a broad range of tolerance along a gradient of aquatic productivity, individual species have specific water chemistry requirements. 3. They have one of the shortest generation times of all biological indicators (~2 weeks). They reproduce and respond rapidly to environmental change and provide early measures of both pollution impacts and habitat restoration. 4. It takes two to three weeks before changes are reflected to a measurable extent in the assemblage composition.

Fingerprinting environmental conditions and related stress using stable isotopic composition of rice (Oryza sativa L.) grain organic matter

Sea level rise (SLR) is a primary factor responsible for inundation of low-lying coastal regions across the world, which in turn governs the agricultural productivity. In this study, rice (Oryza sativa L.) cultivated seasonally in the Kuttanad Wetland, a SLR prone region on the southwest coast of India, were analysed for oxygen, hydrogen and carbon isotopic ratios (delta O-18, delta H-2 and delta C-13) to distinguish the seasonal environmental conditions prevalent during rice cultivation. The region receives high rainfall during the wet season which promotes large supply of fresh water to the local water bodies via the rivers. In contrast, during the dry season reduced river discharge favours sea water incursion which adversely affects the rice cultivation. The water for rice cultivation is derived from regional water bodies that are characterised by seasonal salinity variation which co-varies with the delta O-18 and delta H-2 values. Rice cultivated during the wet and the dry season bears the isotopic imprints of this water. We explored the utility of a mechanistic model to quantify the contribution of two prominent factors, namely relative humidity and source water composition in governing the seasonal variation in oxygen isotopic composition of rice grain OM. delta C-13 values of rice grain OM were used to deduce the stress level by estimating the intrinsic water use efficiency (WUEi) of the crop during the two seasons. 1.3 times higher WUE, was exhibited by the same genotype during the dry season. The approach can be extended to other low lying coastal agro-ecosystems to infer the growth conditions of cultivated crops and can further be utilised for retrieving paleo-environmental information from well preserved archaeological plant remains. (c) 2015 Elsevier Ltd. All rights reserved.

Carbon sequestration versus bioenergy: A case study from South India exploring the relative land-use efficiency of two options for climate change mitigation

This case study has been carried out as a comparison between two different land-use strategies for climate change mitigation, with possible application within the Clean Development Mechanisms. The benefits of afforestation for carbon sequestration versus for bioenergy production are compared in the context of development planning to meet increasing domestic and agricultural demand for electricity in Hosahalli village, Karnataka, India. One option is to increase the local biomass based electricity generation, requiring an increased biomass plantation area. This option is compared with fossil based electricity generation where the area is instead used for producing wood for non-energy purposes while also sequestering carbon in the soil and standing biomass. The different options have been assessed using the PRO-COMAP model. The ranking of the different options varies depending on the system boundaries and time period. Results indicate that, in the short term (30 years) perspective, the mitigation potential of the long rotation plantation is largest, followed by the short rotation plantation delivering wood for energy. The bioenergy option is however preferred if a long-term view is taken. Short rotation forests delivering wood for short-lived non-energy products have the smallest mitigation potential, unless a large share of the wood products are used for energy purposes (replacing fossil fuels) after having served their initial purpose. If managed in a sustainable manner all of these strategies can contribute to the improvement of the social and environmental situation of the local community. (C) 2009 Elsevier Ltd. All rights reserved.

Dependence of electron recombination time and light to electricity conversion efficiency on shape of the nanocrystal light sensitizer

Tunability of electron recombination time and light to electricity conversion efficiency to superior values in semiconductor sensitized solar cells via optimized design of nanocrystal light sensitizer shape is discussed here.

Biogeochemical facsimile of the organic matter quality and trophic status of a micro-tidal tropical estuary

Seasonal studies were carried out from 21 stations, comprising of three zones, of Cochin Estuary, to assess the organic matter quality and trophic status. The hydographical parameters showed significant seasonal variations and nutrients and chlorophylls were generally higher during the monsoon season. However, chemical contamination along with the seasonal limitations of light and nitrogen imposed restrictions on the primary production and as a result, mesotrophic conditions generally prevailed in the water column. The nutrient stoichometries and delta C-13 values of surficial sediments indicated significant allochthonous contribution of organic matter. Irrespective of the higher content of total organic matter, the labile organic matter was very low. Dominance of carbohydrates over lipids and proteins indicated the lower nutritive aspect of the organic matter, and their aged and refractory nature. This, along with higher amount of phytodetritus and the low algal contribution to the biopolymeric carbon corroborated the dominance of allochthonous organic matter and the heterotrophic nature. The spatial and seasonal variations of labile organic components could effectively substantiate the observed shift in the productivity pattern. An alternative ratio, lipids to tannins and lignins, was proposed to ascertain the relative contribution of allochthonous organic matter in the estuary. This study confirmed the efficiency of an integrated biogeochemical approach to establish zones with distinct benthic trophic status associated with different degrees of natural and anthropogenic input. Nevertheless, our results also suggest that the biochemical composition alone could lead to erroneous conclusions in the case of regions that receive enormous amounts of anthropogenic inputs.

Nanostructured electrode materials for electrochemical energy storage and conversion

Manipulation of matter at the nanoscale is a way forward to move beyond our current choices in electrochemical energy storage and conversion technologies with promise of higher efficiency, environmental benignity, and cost-effectiveness. Electrochemical processes being basically surface phenomena, tailored multifunctional nanoarchitecturing can lead to improvements in terms of electronic and ionic conductivities, diffusion and mass transport, and electron transfer and electrocatalysis. The nanoscale is also a domain in which queer properties surface: those associated with conversion electrodes, ceramic particles enhancing the conductivity of polymer electrolytes, and transition metal oxide powders catalyzing fuel cell reactions, to cite a few. Although this review attempts to present a bird's eye view of the vast literature that has accumulated in this rather infant field, it also lists a few representative studies that establish the beneficial effects of going `nano'. Investigations on nanostructuring and use of nanoparticles and nanoarchitectures related to lithium-ion batteries (active materials and electrolytes), supercapacitors (electrical double-layer capacitors, supercapacitors based on pseudo-capacitance, and hybrid supercapacitors), and fuel cells (electrocatalysts, membranes and hydrogen storage materials) are highlighted. (C) 2012 John Wiley & Sons, Ltd.

Socio-environmental impact of idol immersion: dimensions and directions

India possesses a diverse and rich cultural heritage and is renowned as a 'land of festivals'. These festivals attract massive community involvement paving way to new materials such as 'Plaster of Paris' being used for 'modernizing' the representation of idols with very little thought given to the issues of toxicity and environmental impacts. Another dimension to the whole issue is the plight of the artisans and the workers involved in the trade. Owing to the unorganized nature of the industry there is minimal or no guidelines pertaining-to the worker safety and health risks of the people involved. This paper attempts to address the complexities of the inherent hazards as a consequence of these socio-environmental issues and trace the scientific rationale in addressing them in a practical and pragmatic way.

Energy harvesting using ionic electro-active polymer thin films with Ag-based electrodes

In this paper we employ the phenomenon of bending deformation induced transport of cations via the polymer chains in the thickness direction of an electro-active polymer (EAP)-metal composite thin film for mechanical energy harvesting. While EAPs have been applied in the past in actuators and artificial muscles, promising applications of such materials in hydrodynamic and vibratory energy harvesting are reported in this paper. For this, functionalization of EAPs with metal electrodes is the key factor in improving the energy harvesting efficiency. Unlike Pt-based electrodes, Ag-based electrodes have been deposited on an EAP membrane made of Nafion. The developed ionic metal polymer composite (IPMC) membrane is subjected to a dynamic bending load, hydrodynamically, and evaluated for the voltage generated against an external electrical load. An increase of a few orders of magnitude has been observed in the harvested energy density and power density in air, deionized water and in electrolyte solutions with varying concentrations of sodium chloride (NaCl) as compared to Pt-based IPMC performances reported in the published literature. This will have potential applications in hydrodynamic and residual environmental energy harvesting to power sensors and actuators based on micro-andn nano-electro-mechanical systems (MEMS and NEMS) for biomedical,maerospace and oceanic applications.

A new Fuzzy-LOGIC based Model for Chlorophyll-a in Pulicat Lagoon, India

Coastal lagoons are complex ecosystems exhibiting a high degree of non-linearity in the distribution and exchange of nutrients dissolved in the water column due to their spatio-temporal characteristics. This factor has a direct influence on the concentrations of chlorophyll-a, an indicator of the primary productivity in the water bodies as lakes and lagoons. Moreover the seasonal variability in the characteristics of large-scale basins further contributes to the uncertainties in the data on the physico-chemical and biological characteristics of the lagoons. Considering the above, modelling the distributions of the nutrients with respect to the chlorophyll-concentrations, hence requires an effective approach which will appropriately account for the non-linearity of the ecosystem as well as the uncertainties in the available data. In the present investigation, fuzzy logic was used to develop a new model of the primary production for Pulicat lagoon, Southeast coast of India. Multiple regression analysis revealed that the concentrations of chlorophyll-a in the lagoon was highly influenced by the dissolved concentrations of nitrate, nitrites and phosphorous to different extents over different seasons and years. A high degree of agreement was obtained between the actual field values and those predicted by the new fuzzy model (d = 0.881 to 0.788) for the years 2005 and 2006, illustrating the efficiency of the model in predicting the values of chlorophyll-a in the lagoon.

Interaction of Bacillus polymyxa with some oxide minerals with reference to mineral beneficiation and environmental control

Interaction of Bacillus polymyxa with calcite, hematite, corundum and quartz resulted in significant surface chemical changes not only of the cells but also in the minerals. Both the cell surfaces as well as quartz particles were rendered more hydrophobic after mutual interaction, whilst the rest of the minerals exhibited enhanced hydrophilicity after interaction with the bacteria. The bacteria were also observed to be capable of dissolving calcite, hematite and corundum and biosorbing the dissolved metal ions to varying extents. An excess of polysaccharides could be observed on biotreated calcite, hematite and corundum while the predominance of a protein-based metabolic product was evident on quartz surfaces. The utility of bioprocessing in the beneficiation of the above minerals through bioflotation and bioflocculation is demonstrated. (C) 1997 Elsevier Science Ltd.

Local environmental structures of Mo in the superionic conducting glass (AgI)(0.6)(Ag2MoO4)(0.4) by anomalous X-ray scattering

The anomalous X-ray scattering (AXS) method using Mo K absorption edges has been employed for obtaining the local structural information of superionic conducting glass having the composition (AgI)(0.6)(Ag2MoO4)(0.4). The possible atomic arrangements in the near-neighbor region of this glass were estimated by coupling the results with the least-squares variational analysis so as to reproduce the differential intensity profile for Mo as well as the ordinary scattering profile. The coordination number of oxygen around Mo is found to be about 4 at the distance of 0.180 mn. This implies that the most probable structural entity in the glass is the MoO4 tetrahedral unit which has been proposed based on infrared spectroscopy. The value of the coordination number of I- around Ag+ is estimated as 4.4 at 0.287 nm, suggesting an arrangement similar to that of crystalline or molten AgI.

Role of Management Decision Variables in Determining Technology Progress and Technical Efficiency in Indian Electronic Industry

This paper analyses the influence of management on Technical Efficiency Change (TEC) and Technological Progress (TP) in the communication equipment and consumer electronics sub-sectors of Indian hardware electronics industry. Each sub-sector comprises 13 sample firms for two time periods.The primary objective is to determine the relative contribution of TP and TEC to TFP Growth (TFPG) and to establish the influence of firm specific operational management decision variables on these two components. The study finds that both the sub-sectors have strived and achieved steady TP but not TEC in the period of economic liberalisation to cope with the intensifying competition. The management decisions with respect to asset and profit utilization, vertical integration, among others, improved TP and TE in the sub-sectors. However, R&D investments and technology imports proved costly for TFP indicating inadequate efforts and/or poor resource utilisation by the management. Management was found to be complacent in terms of improving or developing their own technology as indicated by their higher dependence on import of raw materials and no influence of R&D on TP.

Groundwater Management in India:Physical, Institutional and Policy Alternatives

Groundwater constitutes a vital natural resource for sustaining India’s agricultural economy and meeting the country’s social, ecological and environmental goals. It is a unique resource, widely available, providing security against droughts and yet it is closely linked to surface-water resources and the hydrological cycle. Its availability depends on geo-hydrological conditions and characteristics of aquifers, from deep to alluvium, sediment crystalline rocks to basalt formations; and agro-climate from humid to subhumid and semi-arid to arid. Its reliable supply, uniform quality and temperature, relative turbidity, pollution-safe, minimal evaporation losses, and low cost of development are attributes making groundwater more attractive compared to other resources. It plays a key role in the provision of safe drinking water to rural populations. For example, already almost 80% of domestic water use in rural areas in India is groundwater-supplied, and much of it is being supplied to farms, villages and small towns. Inadequate control of the use of groundwater, indiscriminate application of agrochemicals and unrestrained pollution of the rural environment by other human activities make groundwater usage unsustainable, necessitating proper management in the face of the twin demand for water of good quality for domestic supply and adequate supply for irrigation, ensuring equity, efficiency and sustainability of the resource. Groundwater irrigation has overtaken surface irrigation in the early 1980s, supported by well energization. It is estimated that there are about 24 million energised wells and tube wells now and it is driven by demand rather than availability, evident through the greater occurrence of wells in districts with high population densities. Apart from aquifer characteristics, land fragmentation and landholding size are the factors that decide the density of wells. The ‘rise and fall’ of local economies dependent on groundwater can be summarized as: the green revolution of 1980s, groundwaterbased agrarian boom, early symptoms of groundwater overdraft, and decline of the groundwater socio-ecology. The social characteristics and policy interventions typical of each stage provide a fascinating insight into the human-resource dynamics. This book is a compilation of nine research papers discussing various aspects of groundwater management. It attempts to integrate knowledge about the physical system, the socio-economic system, the institutional set-up and the policy environment to come out with a more realistic analysis of the situation with regard to the nature, characteristics and intensity of resource use, the size of the economy the use generates, and the negative socioeconomic consequences. Complex variables addressed in this regard focusing on northern Gujarat are the stock of groundwater available in the region, its hydrodynamics, its net outflows against inflows, the economics of its intensive use (particularly irrigation in semi-arid and arid regions), its criticality in the regional hydroecological regime, ethical aspects and social aspects of its use. The first chapter by Dinesh Kumar and Singh, dwells on complex groundwater socio-ecology of India, while emphasizing the need for policy measures to address indiscriminate over-exploitation of dwindling resources. The chapter also explores the nature of groundwater economy and the role of electricity prices on it. The next chapter on groundwater issue in north Gujarat provides a description of groundwater resource characteristics followed by a detailed analysis of the groundwater depletion and quality deterioration problems in the region and their undesirable consequences on the economy, ecosystem health and the society. Considering water-buyers and wellowning farmers individually, a methodology for economic valuation of groundwater in regions where its primary usage is in agriculture, and as assessment of the groundwater economy based on case studies from north Gujarat is presented in the fourth chapter. The next chapter focuses on the extent of dependency of milk production on groundwater, which includes the water embedded in green and dry fodder and animal feed. The study made a realistic estimate of irrigation water productivity in terms of the physics and economics of milk production. The sixth chapter analyses the extent of reduction in water usage, increase in yield and overall increase in physical productivity of alfalfa with the use of the drip irrigation system. The chapter also provides a detailed synthesis of the costs and benefits associated with the use of drip irrigation systems. A linear programmingbased optimization model with the objective to minimize groundwater use taking into account the interaction between two distinct components – farming and dairying under the constraints of food security and income stability for different scenarios, including shift in cropping pattern, introduction of water-efficient crops, water- saving technologies in addition to the ‘business as usual’ scenario is presented in the seventh chapter. The results show that sustaining dairy production in the region with reduced groundwater draft requires crop shifts and adoption of water-saving technologies. The eighth chapter provides evidences to prove that the presence of adequate economic incentive would encourage farmers to adopt water-saving irrigation devices, based on the findings of market research with reference to the level of awareness among farmers of technologies and the factors that decide the adoption of water-saving technologies. However, now the marginal cost of using electricity for agricultural pumping is almost zero. The economic incentives are strong and visible only when the farmers are either water-buyers or have to manage irrigation with limited water from tube-well partnerships. The ninth chapter explores the socio-economic viability of increasing the power tariff and inducing groundwater rationing as a tool for managing energy and groundwater demand, considering the current estimate of the country’s annual economic loss of Rs 320 billion towards electricity subsidy in the farm sector. The tenth chapter suggests private tradable property rights and development of water markets as the institutional tool for achieving equity, efficiency and sustainability of groundwater use. It identifies the externalities for local groundwater management and emphasizes the need for managing groundwater by local user groups, supported by a thorough analysis of groundwater socio-ecology in India. An institutional framework for managing the resource based on participatory approach that is capable of internalizing the externalities, comprising implementation of institutional and technical alternatives for resource management is also presented. Major findings of the analyses and key arguments in each chapter are summarized in the concluding chapter. Case studies of the social and economic benefits of groundwater use, where that use could be described as unsustainable, are interesting. The benefits of groundwater use are outlined and described with examples of social and economic impacts of groundwater and the negative aspects of groundwater development with the compilation of environmental problems based on up-to-date research results. This publication with a well-edited compilation of case studies is informative and constitutes a useful publication for students and professionals.