Nonspecific Interaction between DNA and Protein allows for Cooperativity: A Case Study with Mycobacterium DNA Binding Protein

Different DNA-binding proteins have different interaction modes with DNA. Sequence-specific DNA protein interaction has been mostly associated with regulatory processes inside a cell, and as such extensive studies have been made. Adequate data is also available on nonspecific DNA protein interaction, as an intermediate to protein's search for its cognate partner. Multidomain nonspecific DNA protein interaction involving physical sequestering of DNA has often been implicated to regulate gene expression indirectly. However, data available on this type of interaction is limited. One such interaction is the binding of DNA with mycobacterium DNA binding proteins. We have used the Langmuir-Blodgett technique to evaluate for the first time the kinetics and thermodynamics of Mycobacterium smegmatis Dps 1 binding to DNA. By immobilizing one of the interacting partners, we have shown that, when a kinetic bottleneck is applied, the binding mechanism showed cooperative binding (n = 2.72) at lower temperatures, but the degree of cooperativity gradually reduces (n = 1.38) as the temperature was increased We have also compared the kinetics and thermodynamics of sequence-specific and nonspecific DNA protein interactions under the same set of conditions.

India's biodiversity hotspot under anthropogenic pressure: A case study of Nilgiri Biosphere Reserve

This paper presents data on the impact of biotic pressure in terms of grazing by livestock and wood cutting by humans on the plant community in the Nilgiri Biosphere Reserve of India. Grass, and herbaceous plant biomass, number of cattle dung piles, number of woody stems available and damaged by human activities and weed biomass were assessed at different proximity along transects radiating from village-forest boundary to forest interior to measure the ecological impact of livestock grazing and fire wood collection. The grass biomass was positively correlated to overgrazing indicating the adverse effect on natural vegetation by cattle. Woodcutting was intense along the forest boundary and significantly declined as distance increased. Similarly, weed biomass and number of thorny species declined positively with proximity from village-forest boundary and the weed biomass was significantly higher in the pastoral sites compared to residential sites. The results suggest that human impact adversely affects natural vegetation and promotes weed proliferation in forest areas adjoining human settlements in the ecologically important Nilgiri Biosphere Reserve. Continued anthropogenic pressure could cause reduction in fodder availability to large herbivores like elephants, which in turn leads to an increase in human-elephant conflict. (C) 2011 Elsevier GmbH. All rights reserved.

A neural network based power system stabilizer suitable for on-line training-a practical case study for EGAT system

This paper presents the development of a neural network based power system stabilizer (PSS) designed to enhance the damping characteristics of a practical power system network representing a part of Electricity Generating Authority of Thailand (EGAT) system. The proposed PSS consists of a neuro-identifier and a neuro-controller which have been developed based on functional link network (FLN) model. A recursive on-line training algorithm has been utilized to train the two neural networks. Simulation results have been obtained under various operating conditions and severe disturbance cases which show that the proposed neuro-PSS can provide a better damping to the local as well as interarea modes of oscillations as compared to a conventional PSS

On the linkage of mesospheric planetary waves with those of the lower atmosphere and ionosphere: A case study from Indian low latitudes

In this paper we study the planetary-scale wave features using concurrent observations of mesospheric wind and temperature, ionospheric h'F, and tropospheric wind from Tirunelveli, Gadanki, and Kolhapur, all located in the Indian low latitudes, made during February 2009. Our investigations reveal that 3 to 5 day periodicity, characterized as ultrafast Kelvin (UFK) waves, was persistent throughout the atmosphere during this period. These waves show clear signatures of upward wave propagation from troposphere to the upper mesosphere, linking the ionosphere through a clear correlation between mesospheric winds and h'F variations. We also note that the amplitude of this wave decreased as we moved away from the equator. These results are the first of their kind from Indian sector, portraying the vertical as well as latitudinal characteristics of the 3 to 5 day UFK waves simultaneously from the troposphere to the ionosphere.

Identification of source of heavy metal contamination in a site - a case study

Accidental spills and improper disposal of industrial effluent/sludge containing heavy metals onto the open land or into subsurface result in soil and water contamination. Detailed investigations are carried out to identify the source of contamination of heavy metals in an industrial suburb near Bangalore in India. Detailed investigation of ground water and subsurface soil analysis for various heavy metals has been carried out. Ground water samples were collected in the entire area through the cluster of borewells. Subsurface soil samples were collected from near borewells which were found to contain heavy metals. Water samples and soils samples (after acid digestion) were analysed as per APHO-standard method of analysis. While the results of Zn, Ni and Cd showed that they are within allowable limits in the soil, the ground water and soils in the site have concentration of Cr+6 far exceeding the allowable limits (up to 832 mg/kg). Considering the topography of the area, ground water movement and results of chromium concentration in the borewells and subsurface it was possible to identify the origin, zone of contamination and the migration path of Cr+6. The results indicated that the predominant mechanism of migration of Cr+6 is by diffusion.

A GIS (geographical information system)-based spatial data mining approach for optimal location and capacity planning of distributed biomass power generation facilities: A case study of Tumkur district, India

This paper primarily intends to develop a GIS (geographical information system)-based data mining approach for optimally selecting the locations and determining installed capacities for setting up distributed biomass power generation systems in the context of decentralized energy planning for rural regions. The optimal locations within a cluster of villages are obtained by matching the installed capacity needed with the demand for power, minimizing the cost of transportation of biomass from dispersed sources to power generation system, and cost of distribution of electricity from the power generation system to demand centers or villages. The methodology was validated by using it for developing an optimal plan for implementing distributed biomass-based power systems for meeting the rural electricity needs of Tumkur district in India consisting of 2700 villages. The approach uses a k-medoid clustering algorithm to divide the total region into clusters of villages and locate biomass power generation systems at the medoids. The optimal value of k is determined iteratively by running the algorithm for the entire search space for different values of k along with demand-supply matching constraints. The optimal value of the k is chosen such that it minimizes the total cost of system installation, costs of transportation of biomass, and transmission and distribution. A smaller region, consisting of 293 villages was selected to study the sensitivity of the results to varying demand and supply parameters. The results of clustering are represented on a GIS map for the region.

Synthon identification in co-crystals and polymorphs with IR spectroscopy. Primary amides as a case study

IR spectroscopy has been widely employed to distinguish between different crystal forms such as polymorphs, clathrates, hydrates and co-crystals. IR has been used to monitor co-crystal formation and single synthon detection. In this work, we have developed a strategy to identify multiple supramolecular synthons in polymorphs and co-crystals with this technique. The identification of multiple synthons in co-crystals with IR is difficult for several reasons. In this paper, a four step method involving well assigned IR spectral markers that correspond to bonds in a synthon is used. IR spectra of three forms of the co-crystal system, 4-hydroxybenzoic acid: 4,4'-bipyridine (2 : 1), show clear differences that may be attributed to differences in the synthon combinations existing in the forms (synthon polymorphism). These differences were picked out from the three IR spectra and the bands analysed and assigned to synthons. Our method first identifies IR marker bands corresponding to (covalent) bonds in known/model crystals and then the markers are mapped in known co-crystals having single synthons. Thereafter, the IR markers are queried in known co-crystals with multiple synthons. Finally they are queried in unknown co-crystals with multiple synthons. In the last part of the study, the N-H stretching absorptions of primary amides that crystallize with the amide dimers linked in a ladder like chain show two specific absorptions which are used as marker absorptions and all variations of this band structure have been used to provide details on the environment around the dimer. The extended dimer can accordingly be easily distinguished from the isolated dimer.

Sea-level changes and its impact on coastal archaeological monuments: seven pagodas of Mahabalipuram, a case study

The name `Seven Pagodas' has served as a nickname for the south Indian port of Mahabalipuram since the early European explorers used it as landmark for navigation as they could see summits of seven temples from the sea. There are many theories concerning the name Seven Pagodas. The present study has compared coastline and adjacent seven monuments illustrated in a 17th century Portolan Chart (maritime map) with recent remote sensing data. This analysis throws new light on the name ``Seven Pagodas'' for the city. This study has used DEM of the site to simulate the coastline which is similar to the one depicted in the old portolan chart. Through this, the then sea level and corresponding flooding extent according to topography of the area and their effect on monuments could be analyzed. Most importantly this work has in the process identified possibly the seven monuments that constituted the name Seven Pagodas and this provides an alternative explanation to one of the mysteries of history. This work has demonstrated unique method of studying coastal archaeological sites. As large numbers of heritage sites around the world are on coastlines, this methodology has potential to be very useful for coastal heritage preservation and management.

Spark plasma sintering may lead to phase instability and inferior mechanical properties: A case study with TiB2

In contrast to the widely reported beneficial aspects of spark plasma sintering in developing materials with better properties, we report here two interesting aspects recorded with difficult-to-sinter titanium diboride: (a) in situ formation of second phase (TiB) and (b) inferior hardness (by similar to 30%) and elastic modulus (by similar to 20%) for spark plasma sintered TiB2, with respect to hot pressed TiB2. The formation of TiB is discussed with reference to the enhanced reaction kinetics in the presence of pulsed electric field. (C) 2013 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Corporate social responsibilities of Indian public sector enterprises-a case study of Bharat Heavy Electricals Limited (BHEL)

The high level of public accountability attached to Public Sector Enterprises as a result of public ownership makes them socially responsible. The Committee of Public Undertakings in 1992 examined the issue relating to social obligations of Central Public Sector Enterprises and observed that ``being part of the `State', every Public Sector enterprise has a moral responsibility to play an active role in discharging the social obligations endowed on a welfare state, subject to the financial health of the enterprise''. It issued the Corporate Social Responsibility Guidelines in 2010 where all Central Public Enterprises, through a Board Resolution, are mandated to create a CSR budget as a specified percentage of net profit of the previous year. This paper examines the CSR activities of the biggest engineering public sector organization in India, Bharath Heavy Electricals Limited. The objectives are twofold, one, to develop a case study of the organization about the funds allocated and utilized for various CSR activities, and two, to examine its status with regard to other organizations, the 2010 guidelines, and the local socio-economic development. Secondary data analysis results show three interesting trends. One, it reveals increasing organizational social orientation with the formal guidelines in place. Two, Firms can no longer continue to exploit environmental resources and escape from their responsibilities by acting separate entities regardless of the interest of the society and Three the thrust of CSR in public sector is on inclusive growth, sustainable development and capacity building with due attention to the socio-economic needs of the neglected and marginalized sections of the society.

Low embodied energy cement stabilised rammed earth building-A case study

Rammed earth is a monolithic construction and the construction process involves compaction of processed soil in progressive layers in a rigid formwork. Durable and thinner load bearing walls can be built using stabilised rammed earth. Use of inorganic additives such as cement for rammed earth walls has been in practice since the last 5-6 decades and cement stabilised rammed earth (CSRE) buildings can be seen across the world. The paper deals with the construction aspects, structural design and embodied energy analysis of a three storey load bearing school building complex. The CSRE school complex consists of 15 classrooms, an open air theatre and a service block. The complex has a built-up area of 1691.3 m(2) and was constructed employing manual construction techniques. This case study shows low embodied energy of 1.15 GJ/m(2) for the CSRE building as against 3-4 GJ/m(2) for conventional burnt clay brick load bearing masonry buildings. (C) 2013 Elsevier B.V. All rights reserved.

Molecular Dynamics Perspective on the Protein Thermal Stability: A Case Study Using SAICAR Synthetase

The enzyme SAICAR synthetase ligates aspartate with CAIR (5'-phosphoribosyl-4-carboxy-5-aminoimidazole) forming SAICAR (5-amino-4-imidazole-N-succinocarboxamide ribonucleotide) in the presence of ATP. In continuation with our previous study on the thermostability of this enzyme in hyper-/thermophiles based on the structural aspects, here, we present the dynamic aspects that differentiate the mesophilic (E. coli, E. chaffeensis), thermophilic (G. kaustophilus), and hyperthermophilic (M. jannaschii, P. horikoshii) SAICAR synthetases by carrying out a total of 11 simulations. The five functional dimers from the above organisms were simulated using molecular dynamics for a period of 50 ns each at 300 K, 363 K, and an additional simulation at 333 K for the thermophilic protein. The basic features like root-mean-square deviations, root-mean-square fluctuations, surface accessibility, and radius of gyration revealed the instability of mesophiles at 363 K. Mean square displacements establish the reduced flexibility of hyper-/thermophiles at all temperatures. At the simulations time scale considered here, the long-distance networks are considerably affected in mesophilic structures at 363 K. In mesophiles, a comparatively higher number of short-lived (having less percent existence time) C alpha, hydrogen bonds, hydrophobic interactions are formed, and long-lived (with higher percentage existence time) contacts are lost. The number of time-averaged salt-bridges is at least 2-fold higher in hyperthermophiles at 363 K. The change in surface accessibility of salt-bridges at 363 K from 300 K is nearly doubled in mesophilic protein compared to proteins from other temperature classes.

Solvent polarity and nanoscale morphology in bulk heterojunction organic solar cells: A case study

Organic bulk heterojunction solar cells were fabricated under identical experimental conditions, except by varying the solvent polarity used for spin coating the active layer components and their performance was evaluated systematically. Results showed that presence of nitrobenzene-chlorobenzene composition governs the morphology of active layer formed, which is due to the tuning of solvent polarity as well as the resulting solubility of the P3HT:PCBM blend. Trace amount of nitrobenzene favoured the formation of better organised P3HT domains, as evident from conductive AFM, tapping mode AFM and surface, and cross-sectional SEM analysis. The higher interfacial surface area thus generated produced cells with high efficiency. But, an increase in the nitrobenzene composition leads to a decrease in cell performance, which is due to the formation of an active layer with larger size polymer domain networks with poor charge separation possibility. (C) 2014 AIP Publishing LLC.