Role of free valences and spin densities on the migrating atom in location of saddle points in radical-exchange reactions

The principle of the conservation of bond orders during radical-exchange reactions is examined using Mayer's definition of bond orders. This simple intuitive approximation is not valid in a quantitative sense. Ab initio results reveal that free valences (or spin densities) develop on the migrating atom during reactions. For several examples of hydrogen-transfer reactions, the sum of the reaction coordinate bond orders in the transition state was found to be 0.92 +/- 0.04 instead of the theoretical 1.00 because free valences (or spin densities) develop on the migrating atom during reactions. It is shown that free valence is almost equal to the square of the spin density on the migrating hydrogen atom and the maxima in the free valence (or spin density) profiles coincide (or nearly coincide) with the saddle points in the corresponding energy profiles.

Functional Significance of an Evolutionarily Conserved Alanine (GCA) Resume Codon in tmRNA in Escherichia coli

Occasionally, ribosomes stall on mRNAs prior to the completion of the polypeptide chain. In Escherichia coli and other eubacteria, tmRNA-mediated trans-translation is a major mechanism that recycles the stalled ribosomes. The tmRNA possesses a tRNA-like domain and a short mRNA region encoding a short peptide (ANDENYALAA in E. coli) followed by a termination codon. The first amino acid (Ala) of this peptide encoded by the resume codon (GCN) is highly conserved in tmRNAs in different species. However, reasons for the high evolutionary conservation of the resume codon identity have remained unclear. In this study, we show that changing the E. coli tmRNA resume codon to other efficiently translatable codons retains efficient functioning of the tmRNA. However, when the resume codon was replaced with the low-usage codons, its function was adversely affected. Interestingly, expression of tRNAs decoding the low-usage codon from plasmid-borne gene copies restored efficient utilization of tmRNA. We discuss why in E. coli, the GCA (Ala) is one of the best codons and why all codons in the short mRNA of the tmRNA are decoded by the abundant tRNAs.

Mathematical model of COREX melter gasifier: Part I. Steady-state model

The COREX melter gasifier is a countercurrent reactor to produce liquid iron. Directly reduced iron (DRI), noncoking coal, and other additives are charged to the melter gasifier at their respective temperatures, and O-2 is blown through the tuyeres. Functionally, a melter gasifier is divided into three zones: a moving bed, fluidized bed, and free board. A model has been developed for the moving bed, where the tuyere region is two-dimensional (2-D) and the rest is one-dimensional (1-D). It is based on multiphase conservation of mass, momentum, and heat. The fluidized bed has been treated as 1-D. Partial equilibrium is calculated for the free board. The calculated temperature of the hot metal, the top gas, and the chemistry of the top gas agree with the reported plant data. The model has been used to study the effects of bed height, injection of impure O-2, coal chemistry, and reactivity on the process performance.

Environment Education for Ecosystem Conservation

Conservation of natural resources through sustainable ecosystem management and development is the key to our secured future. The management of ecosystem involves inventorying and monitoring, and applying integrated technologies, methodologies and interdisciplinary approaches for its conservation. Hence, now it is even more critical than ever before for the humans to be environmentally literate. To realise this vision, both ecological and environmental education must become a fundamental part of the education system at all levels of education. Currently, it is even more critical than ever before for the humankind as a whole to have a clear understanding of environmental concerns and to follow sustainable development practices. The degradation of our environment is linked to continuing problems of pollution, loss of forest, solid waste disposal, and issues related to economic productivity and national as well as ecological security. Environmental management has gained momentum in the recent years with the initiatives focussing on managing environmental hazards and preventing possible disasters. Environmental issues make better sense, when one can understand them in the context of one’s own cognitive sphere. Environmental education focusing on real-world contexts and issues often begins close to home, encouraging learners to understand and forge connections with their immediate surroundings. The awareness, knowledge, and skills needed for these local connections and understandings provide a base for moving out into larger systems, broader issues, and a more sophisticated comprehension of causes, connections, and consequences. Environmental Education Programme at CES in collaboration with Karnataka Environment Research Foundation (KERF) referred as ‘Know your Ecosystem’ focuses on the importance of investigating the ecosystems within the context of human influences, incorporating an examination of ecology, economics, culture, political structure, and social equity as well as natural processes and systems. The ultimate goal of environment education is to develop an environmentally literate public. It needs to address the connection between our conception and practice of education and our relationship as human cultures to life-sustaining ecological systems. For each environmental issue there are many perspectives and much uncertainty. Environmental education cultivates the ability to recognise uncertainty, envision alternative scenarios, and adapt to changing conditions and information. These knowledge, skills, and mindset translate into a citizenry who is better equipped to address its common problems and take advantage of opportunities, whether environmental concerns are involved or not.

Present status of Gottigere Tank : Indicator of Decision maker’s apathy

Gottigere lake with a water spread area of about 14.98 ha is located in the Bellandur Lake catchment of the South Pennar River basin. In recent years, this lake catchment has been subjected to environmental stress mainly due to the rampant unplanned developmental activities in the catchment. The functional ability of the ecosystem is impaired due to structural changes in the ecosystem. This is evident from poor water quality, breeding of disease vectors, contamination of groundwater in the catchment, frequent flooding in the catchment due to topography alteration, decline in groundwater table, erosion in lake bed, etc. The development plans of the region (current as well as the proposed) ignore the integrated planning approaches considering all components of the ecosystem. Serious threats to the sustainability of the region due to lack of holistic approaches in aquatic resources management are land use changes (removal of vegetation cover, etc.), point and non-point sources of pollution impairing water quality, dumping of solid waste (building waste, etc.). Conservation of lake ecosystem is possible only when the physical and chemical integrity of its catchment is maintained. Alteration in the catchment either due to land use changes (leading to paved surface area from vegetation cover), alteration in topography, construction of roads in the immediate vicinity are detrimental to water yield in the catchment and hence, the sustenance of the lake. Open spaces in the form of lakes and parks aid as kidney and lung in an urban ecosystem, which maintain the health of the people residing in the locality. Identification of core buffer zones and conservation of buffer zones (500 to 1000 m from shore) is to be taken up on priority for conservation and sustainable management of Bangalore lakes. Bangalore is located over a ridge delineating four watersheds, viz. Hebbal, Koramangala, Challaghatta and Vrishabhavathi. Lakes and tanks are an integral part of natural drainage and help in retaining water during rainfall, which otherwise get drained off as flash floods. Each lake harvests rainwater from its catchment and surplus flows downstream spilling into the next lake in the chain. The topography of Bangalore has uniquely supported the creation of a large number of lakes. These lakes form chains, being a series of impoundments across streams. This emphasises the interconnectivity among Bangalore lakes, which has to be retained to prevent Bangalore from flooding or from water scarcity. The main source of replenishment of groundwater is the rainfall. The slope of the terrain allows most of the rainwater to flow as run-off. With the steep gradients available in the major valleys of Bangalore, the rainwater will flow out of the city within four to five hours. Only a small fraction of the rainwater infiltrates into the soil. The infiltration of water into the subsoil has declined with more and more buildings and paved road being constructed in the city. Thus the natural drainage of Bangalore is governed by flows from the central ridge to all lower contours and is connected with various tanks and ponds. There are no major rivers flowing in Bangalore and there is an urgent need to sustain these vital ecosystems through proper conservation and management measures. The proposed peripheral ring road connecting Hosur Road (NH 7) and Mysore Road (SH 17) at Gottigere lake falls within the buffer zone of the lake. This would alter the catchment integrity and hence water yield affecting flora, fauna and local people, and ultimately lead to the disappearance of Gottigere lake. Developmental activities in lake catchments, which has altered lake’s ecological integrity is in violation of the Indian Fisheries Act – 1857, the Indian Forest Act – 1927, Wildlife (Protection) Act – 1972, Water (Prevention and Control of Pollution) Act – 1974, Water (Prevention and Control of Pollution) Act – 1977, Forest (Conservation Act) – 1980, Environmental (Protection) Act – 1986, Wildlife (Protection) Amendment Act – 1991 and National Conservation Strategy and Policy Statement on Environment and Development – 1992. Considering 65% decline of waterbodies in Bangalore (during last three decades), decision makers should immediately take preventive measures to ensure that lake ecosystems are not affected. This report discusses the impacts due to the proposed infrastructure developmental activities in the vicinity of Gottigere tank.

Environment Education for Ecosystem Conservation

Conservation of natural resources through sustainable ecosystem management and development is the key to our secured future. The management of ecosystem involves inventorying and monitoring, and applying integrated technologies, methodologies and interdisciplinary approaches for its conservation. Hence, now it is even more critical than ever before for the humans to be environmentally literate. To realise this vision, both ecological and environmental education must become a fundamental part of the education system at all levels of education. Currently, it is even more critical than ever before for the humankind as a whole to have a clear understanding of environmental concerns and to follow sustainable development practices. The degradation of our environment is linked to continuing problems of pollution, loss of forest, solid waste disposal, and issues related to economic productivity and national as well as ecological security. Environmental management has gained momentum in the recent years with the initiatives focussing on managing environmental hazards and preventing possible disasters. Environmental issues make better sense, when one can understand them in the context of one’s own cognitive sphere. Environmental education focusing on real-world contexts and issues often begins close to home, encouraging learners to understand and forge connections with their immediate surroundings. The awareness, knowledge, and skills needed for these local connections and understandings provide a base for moving out into larger systems, broader issues, and a more sophisticated comprehension of causes, connections, and consequences. Environmental Education Programme at CES in collaboration with Karnataka Environment Research Foundation (KERF) referred as ‘Know your Ecosystem’ focuses on the importance of investigating the ecosystems within the context of human influences, incorporating an examination of ecology, economics, culture, political structure, and social equity as well as natural processes and systems. The ultimate goal of environment education is to develop an environmentally literate public. It needs to address the connection between our conception and practice of education and our relationship as human cultures to life-sustaining ecological systems. For each environmental issue there are many perspectives and much uncertainty. Environmental education cultivates the ability to recognise uncertainty, envision alternative scenarios, and adapt to changing conditions and information. These knowledge, skills, and mindset translate into a citizenry who is better equipped to address its common problems and take advantage of opportunities, whether environmental concerns are involved or not.

Environment Education for Ecosystem Conservation

Conservation of natural resources through sustainable ecosystem management and development is the key to our secured future. The management of ecosystem involves inventorying and monitoring, and applying integrated technologies, methodologies and interdisciplinary approaches for its conservation. Hence, now it is even more critical than ever before for the humans to be environmentally literate. To realise this vision, both ecological and environmental education must become a fundamental part of the education system at all levels of education. Currently, it is even more critical than ever before for the humankind as a whole to have a clear understanding of environmental concerns and to follow sustainable development practices. The degradation of our environment is linked to continuing problems of pollution, loss of forest, solid waste disposal, and issues related to economic productivity and national as well as ecological security. Environmental management has gained momentum in the recent years with the initiatives focussing on managing environmental hazards and preventing possible disasters. Environmental issues make better sense, when one can understand them in the context of one’s own cognitive sphere. Environmental education focusing on real-world contexts and issues often begins close to home, encouraging learners to understand and forge connections with their immediate surroundings. The awareness, knowledge, and skills needed for these local connections and understandings provide a base for moving out into larger systems, broader issues, and a more sophisticated comprehension of causes, connections, and consequences. Environmental Education Programme at CES in collaboration with Karnataka Environment Research Foundation (KERF) referred as ‘Know your Ecosystem’ focuses on the importance of investigating the ecosystems within the context of human influences, incorporating an examination of ecology, economics, culture, political structure, and social equity as well as natural processes and systems. The ultimate goal of environment education is to develop an environmentally literate public. It needs to address the connection between our conception and practice of education and our relationship as human cultures to life-sustaining ecological systems. For each environmental issue there are many perspectives and much uncertainty. Environmental education cultivates the ability to recognise uncertainty, envision alternative scenarios, and adapt to changing conditions and information. These knowledge, skills, and mindset translate into a citizenry who is better equipped to address its common problems and take advantage of opportunities, whether environmental concerns are involved or not.

Assessment of estrus cyclicity in the Asian elephant (Elephas maximus) by measurement of fecal progesterone metabolite 5 alpha-P-3OH, using a non-invasive assay

Reproductive management of the Asian elephant (Elephas maximus) is important for its conservation. To monitor its estrous cyclicity, we earlier used an indirect ELISA to show that levels of fecal progesterone (P(4))-metabolite (allopregnanolone: 5 alpha-P-3OH) in semi-captive females sampled randomly positively correlated with serum P(4) levels [12]. In this longitudinal study (51 weeks), we measured levels of fecal 5 alpha-P-3OH and serum P(4) in seven semi-captive female elephants. Females exhibited three types of hormonal profiles. Four females showed cyclical patterns of fecal 5 alpha-P-3OH and serum P(4) typical of normal estrous cycles, two showed acyclic pattern while one showed high values indicative of a pregnant animal. Values for anestrous or follicular phases were <= 0.3 mu g g(-1), (5 alpha-P-3OH) and <= 0.3 ng mL(-1) (P(4)); for luteal phase 0.32-11.09 mu g g(-1) (5 alpha-P-3OH) and 0.32-1.48 ng mL(-1) (P(4)); for pregnancy 1.41-7.38 mu g g(-1) (5 alpha-P-3OH) and 0.39-1.6 ng mL(-1) (R(4)). A positive correlation (t = 8.8, p < 0.01, n = 321) between levels of fecal 5 alpha-P-3OH and serum P4 was observed. A random sample of 30 free-ranging female elephants showed fecal 5 alpha-P-3OH values of 0.06-23.4 mu g g(-1), indicating them to be in different stages of estrous cyclicity. This study is the first to assess the reproductive phases of female Asian elephants based on the correlative-patterns of both the fecal 5 alpha-P-3OH and serum P(4) values over multiple estrous cycles. This has a potential application in the reproductive management and conservation of Asian elephants. (C) 2011 Elsevier Inc. All rights reserved.

Arbitrary Lagrangian-Eulerian finite-element method for computation of two-phase flows with soluble surfactants

A finite-element scheme based on a coupled arbitrary Lagrangian-Eulerian and Lagrangian approach is developed for the computation of interface flows with soluble surfactants. The numerical scheme is designed to solve the time-dependent Navier-Stokes equations and an evolution equation for the surfactant concentration in the bulk phase, and simultaneously, an evolution equation for the surfactant concentration on the interface. Second-order isoparametric finite elements on moving meshes and second-order isoparametric surface finite elements are used to solve these equations. The interface-resolved moving meshes allow the accurate incorporation of surface forces, Marangoni forces and jumps in the material parameters. The lower-dimensional finite-element meshes for solving the surface evolution equation are part of the interface-resolved moving meshes. The numerical scheme is validated for problems with known analytical solutions. A number of computations to study the influence of the surfactants in 3D-axisymmetric rising bubbles have been performed. The proposed scheme shows excellent conservation of fluid mass and of the total mass of the surfactant. (C) 2012 Elsevier Inc. All rights reserved.

Insights into the Fold Organization of TIM Barrel from Interaction Energy Based Structure Networks

There are many well-known examples of proteins with low sequence similarity, adopting the same structural fold. This aspect of sequence-structure relationship has been extensively studied both experimentally and theoretically, however with limited success. Most of the studies consider remote homology or ``sequence conservation'' as the basis for their understanding. Recently ``interaction energy'' based network formalism (Protein Energy Networks (PENs)) was developed to understand the determinants of protein structures. In this paper we have used these PENs to investigate the common non-covalent interactions and their collective features which stabilize the TIM barrel fold. We have also developed a method of aligning PENs in order to understand the spatial conservation of interactions in the fold. We have identified key common interactions responsible for the conservation of the TIM fold, despite high sequence dissimilarity. For instance, the central beta barrel of the TIM fold is stabilized by long-range high energy electrostatic interactions and low-energy contiguous vdW interactions in certain families. The other interfaces like the helix-sheet or the helix-helix seem to be devoid of any high energy conserved interactions. Conserved interactions in the loop regions around the catalytic site of the TIM fold have also been identified, pointing out their significance in both structural and functional evolution. Based on these investigations, we have developed a novel network based phylogenetic analysis for remote homologues, which can perform better than sequence based phylogeny. Such an analysis is more meaningful from both structural and functional evolutionary perspective. We believe that the information obtained through the ``interaction conservation'' viewpoint and the subsequently developed method of structure network alignment, can shed new light in the fields of fold organization and de novo computational protein design.

Characterization of structural and free energy properties of promoters associated with Primary and Operon TSS in Helicobacter pylori genome and their orthologs

Promoter regions in the genomes of all domains of life show similar trends in several structural properties such as stability, bendability, curvature, etc. In current study we analysed the stability and bendability of various classes of promoter regions (based on the recent identification of different classes of transcription start sites) of Helicobacter pylori 26695 strain. It is found that primary TSS and operon-associated TSS promoters show significantly strong features in their promoter regions. DNA free-energy-based promoter prediction tool PromPredict was used to annotate promoters of different classes, and very high recall values (similar to 80%) are obtained for primary TSS. Orthologous genes from other strains of H. pylori show conservation of structural properties in promoter regions as well as coding regions. PromPredict annotates promoters of orthologous genes with very high recall and precision.

Costs and benefits of the presence of leopards to the sport-hunting industry and local communities in Niassa national reserve, mozambique

Sport hunting is often proposed as a tool to support the conservation of large carnivores. However, it is challenging to provide tangible economic benefits from this activity as an incentive for local people to conserve carnivores. We assessed economic gains from sport hunting and poaching of leopards (Panthera pardus), costs of leopard depredation of livestock, and attitudes of people toward leopards in Niassa National Reserve, Mozambique. We sent questionnaires to hunting concessionaires (n = 8) to investigate the economic value of and the relative importance of leopards relative to other key trophy-hunted species. We asked villagers (n = 158) the number of and prices for leopards poached in the reserve and the number of goats depredated by leopard. Leopards were the mainstay of the hunting industry; a single animal was worth approximately U.S.$24,000. Most safari revenues are retained at national and international levels, but poached leopard are illegally traded locally for small amounts ($83). Leopards depredated 11 goats over 2 years in 2 of 4 surveyed villages resulting in losses of $440 to 6 households. People in these households had negative attitudes toward leopards. Although leopard sport hunting generates larger gross revenues than poaching, illegal hunting provides higher economic benefits for households involved in the activity. Sport-hunting revenues did not compensate for the economic losses of livestock at the household level. On the basis of our results, we propose that poaching be reduced by increasing the costs of apprehension and that the economic benefits from leopard sport hunting be used to improve community livelihoods and provide incentives not to poach.

A landscape-level assessment of Asian elephant habitat, its population and elephant-human conflict in the Anamalai hill ranges of southern Western Ghats, India

Spatial information at the landscape scale is extremely important for conservation planning, especially in the case of long-ranging vertebrates. The biodiversity-rich Anamalai hill ranges in the Western Ghats of southern India hold a viable population for the long-term conservation of the Asian elephant. Through rapid but extensive field surveys we mapped elephant habitat, corridors, vegetation and land-use patterns, estimated the elephant population density and structure, and assessed elephant-human conflict across this landscape. GIS and remote sensing analyses indicate that elephants are distributed among three blocks over a total area of about 4600 km(2). Approximately 92% remains contiguous because of four corridors; however, under 4000 km2 of this area may be effectively used by elephants. Nine landscape elements were identified, including five natural vegetation types, of which tropical moist deciduous forest is dominant. Population density assessed through the dung count method using line transects covering 275 km of walk across the effective elephant habitat of the landscape yielded a mean density of 1.1 (95% Cl = 0.99-1.2) elephant/km(2). Population structure from direct sighting of elephants showed that adult male elephants constitute just 2.9% and adult females 42.3% of the population with the rest being subadults (27.4%), juveniles (16%) and calves (11.4%). Sex ratios show an increasing skew toward females from juvenile (1:1.8) to sub-adult (1:2.4) and adult (1:14.7) indicating higher mortality of sub-adult and adult males that is most likely due to historical poaching for ivory. A rapid questionnaire survey and secondary data on elephant-human conflict from forest department records reveals that villages in and around the forest divisions on the eastern side of landscape experience higher levels of elephant-human conflict than those on the western side; this seems to relate to a greater degree of habitat fragmentation and percentage farmers cultivating annual crops in the east. We provide several recommendations that could help maintain population viability and reduce elephant-human conflict of the Anamalai elephant landscape. (C) 2013 Deutsche Gesellschaft far Saugetierkunde. Published by Elsevier GmbH. All rights reserved.

Investigations of Ramachandran disallowed conformations in protein domain families

In peptide and protein structures, occurrence of (phi,psi.) angles in the disallowed region of the Ramachandran map almost always suggests local regions of error or poor accuracy. However, very rarely genuine disallowed conformations occur as noted in the current study in proteins of known structure available at ultra-high resolution (<= 1.2 (A) over circle). In the current work, extent of conservation of genuine disallowed conformations in homologous proteins of known structures has been analyzed. From a dataset of 124 protein domain families, with structure of at least one constituent member in each family available at a resolution of 1.2 (A) over circle or better, we have analyzed the conservation of 221 disallowed conformations. It is observed that the disallowed conformation is only moderately conservedin protein domain families. In the gross dataset no particular residue type adopting disallowed conformation elicit high conservation of residue type though there are alignment positions in the dataset with complete conservation of both the residue type and the disallowed conformation. Conserved disallowed conformation in protein domain families play biologically significant role in roughly 50% of the cases. The residues with the disallowed conformation or its flanking residues are often located within or around the functional site of the protein. (C) 2013 Elsevier B.V. All rights reserved.

Identification of heat shock factor binding protein in Plasmodium falciparum

Background: Heat shock factor binding protein (HSBP) was originally discovered in a yeast two-hybrid screen as an interacting partner of heat shock factor (HSF). It appears to be conserved in all eukaryotes studied so far, with yeast being the only exception. Cell biological analysis of HSBP in mammals suggests its role as a negative regulator of heat shock response as it appears to interact with HSF only during the recovery phase following exposure to heat stress. While the identification of HSF in the malaria parasite is still eluding biologists, this study for the first time, reports the presence of a homologue of HSBP in Plasmodium falciparum. Methods: PfHSBP was cloned and purified as his-tag fusion protein. CD (Circular dichroism) spectroscopy was performed to predict the secondary structure. Immunoblots and immunofluorescence approaches were used to study expression and localization of HSBP in P. falciparum. Cellular fractionation was performed to examine subcellular distribution of PfHSBP. Immunoprecipitation was carried out to identify HSBP interacting partner in P. falciparum. Results: PfHSBP is a conserved protein with a high helical content and has a propensity to form homo-oligomers. PfHSBP was cloned, expressed and purified. The in vivo protein expression profile shows maximal expression in trophozoites. The protein was found to exist in oligomeric form as trimer and hexamer. PfHSBP is predominantly localized in the parasite cytosol, however, upon heat shock, it translocates to the nucleus. This study also reports the interaction of PfHSBP with PfHSP70-1 in the cytoplasm of the parasite. Conclusions: This study emphasizes the structural and biochemical conservation of PfHSBP with its mammalian counterpart and highlights its potential role in regulation of heat shock response in the malaria parasite. Analysis of HSBP may be an important step towards identification of the transcription factor regulating the heat shock response in P. falciparum.