A gradient PCR-based screen for use in site-directed mutagenesis

Site-directed mutagenesis is widely used to study protein and nucleic acid structure and function. Despite recent advancements in the efficiency of procedures for site-directed mutagenesis, the fraction of site-directed mutants by most procedures rarely exceeds 50% on a routine basis and is never 100%. Hence it is typically necessary to sequence two or three clones each time a site-directed mutant is constructed. We describe a simple and robust gradient-PCR-based screen for distinguishing site-directed mutants from the starting, unmutated plasmid. The procedure can use either purified plasmid DNA or colony PCR, starting from a single colony. The screen utilizes the primer used for mutagenesis and a common outside primer that can be used for all other mutants constructed with the same template. Over 30 site-specific mutants in a variety of templates were successfully screened and all of the mutations detected were subsequently confirmed by DNA sequencing. A single base pair mismatch could be detected in an oligonucleotide of 36 bases. Detection efficiency was relatively independent of starting template concentration and the nature of the outside primer used. (C) 2003 Elsevier Science (USA). All rights reserved.

Solving a part classification problem using simulated annealing-like hybrid

Part classification and coding is still considered as laborious and time-consuming exercise. Keeping in view, the crucial role, which it plays, in developing automated CAPP systems, the attempts have been made in this article to automate a few elements of this exercise using a shape analysis model. In this study, a 24-vector directional template is contemplated to represent the feature elements of the parts (candidate and prototype). Various transformation processes such as deformation, straightening, bypassing, insertion and deletion are embedded in the proposed simulated annealing (SA)-like hybrid algorithm to match the candidate part with their prototype. For a candidate part, searching its matching prototype from the information data is computationally expensive and requires large search space. However, the proposed SA-like hybrid algorithm for solving the part classification problem considerably minimizes the search space and ensures early convergence of the solution. The application of the proposed approach is illustrated by an example part. The proposed approach is applied for the classification of 100 candidate parts and their prototypes to demonstrate the effectiveness of the algorithm. (C) 2003 Elsevier Science Ltd. All rights reserved.

Strategies for Rescheduling Tightly-Coupled Parallel Applications in Multi-Cluster Grids

As computational Grids are increasingly used for executing long running multi-phase parallel applications, it is important to develop efficient rescheduling frameworks that adapt application execution in response to resource and application dynamics. In this paper, three strategies or algorithms have been developed for deciding when and where to reschedule parallel applications that execute on multi-cluster Grids. The algorithms derive rescheduling plans that consist of potential points in application execution for rescheduling and schedules of resources for application execution between two consecutive rescheduling points. Using large number of simulations, it is shown that the rescheduling plans developed by the algorithms can lead to large decrease in application execution times when compared to executions without rescheduling on dynamic Grid resources. The rescheduling plans generated by the algorithms are also shown to be competitive when compared to the near-optimal plans generated by brute-force methods. Of the algorithms, genetic algorithm yielded the most efficient rescheduling plans with 9-12% smaller average execution times than the other algorithms.

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.

Efficiently Approximating Query Optimizer Plan Diagrams

Given a parametrized n-dimensional SQL query template and a choice of query optimizer, a plan diagram is a color-coded pictorial enumeration of the execution plan choices of the optimizer over the query parameter space. These diagrams have proved to be a powerful metaphor for the analysis and redesign of modern optimizers, and are gaining currency in diverse industrial and academic institutions. However, their utility is adversely impacted by the impractically large computational overheads incurred when standard brute-force exhaustive approaches are used for producing fine-grained diagrams on high-dimensional query templates. In this paper, we investigate strategies for efficiently producing close approximations to complex plan diagrams. Our techniques are customized to the features available in the optimizer's API, ranging from the generic optimizers that provide only the optimal plan for a query, to those that also support costing of sub-optimal plans and enumerating rank-ordered lists of plans. The techniques collectively feature both random and grid sampling, as well as inference techniques based on nearest-neighbor classifiers, parametric query optimization and plan cost monotonicity. Extensive experimentation with a representative set of TPC-H and TPC-DS-based query templates on industrial-strength optimizers indicates that our techniques are capable of delivering 90% accurate diagrams while incurring less than 15% of the computational overheads of the exhaustive approach. In fact, for full-featured optimizers, we can guarantee zero error with less than 10% overheads. These approximation techniques have been implemented in the publicly available Picasso optimizer visualization tool.

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.

Distributed Source Coding for Sensor Data Model and Estimation of Cluster Head Errors Using Bayesian and K-Near Neighborhood Classifiers in Deployment of Dense Wireless Sensor Networks

The lifetime calculation of large dense sensor networks with fixed energy resources and the remaining residual energy have shown that for a constant energy resource in a sensor network the fault rate at the cluster head is network size invariant when using the network layer with no MAC losses.Even after increasing the battery capacities in the nodes the total lifetime does not increase after a max limit of 8 times. As this is a serious limitation lots of research has been done at the MAC layer which allows to adapt to the specific connectivity, traffic and channel polling needs for sensor networks. There have been lots of MAC protocols which allow to control the channel polling of new radios which are available to sensor nodes to communicate. This further reduces the communication overhead by idling and sleep scheduling thus extending the lifetime of the monitoring application. We address the two issues which effects the distributed characteristics and performance of connected MAC nodes. (1) To determine the theoretical minimum rate based on joint coding for a correlated data source at the singlehop, (2a) to estimate cluster head errors using Bayesian rule for routing using persistence clustering when node densities are the same and stored using prior probability at the network layer, (2b) to estimate the upper bound of routing errors when using passive clustering were the node densities at the multi-hop MACS are unknown and not stored at the multi-hop nodes a priori. In this paper we evaluate many MAC based sensor network protocols and study the effects on sensor network lifetime. A renewable energy MAC routing protocol is designed when the probabilities of active nodes are not known a priori. From theoretical derivations we show that for a Bayesian rule with known class densities of omega1, omega2 with expected error P* is bounded by max error rate of P=2P* for single-hop. We study the effects of energy losses using cross-layer simulation of - large sensor network MACS setup, the error rate which effect finding sufficient node densities to have reliable multi-hop communications due to unknown node densities. The simulation results show that even though the lifetime is comparable the expected Bayesian posterior probability error bound is close or higher than Pges2P*.

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.

Synthesis, structural characterization and ferroelectric properties of Pb(0.76)Ca(0.24)TiO(3) nanotubes

A capillary-enforced template-based method has been applied to fabricate Pb(0.76)Ca(0.24)TiO(3) (PCT24) nanotubes via filling PCT24 precursor solution, prepared by modified sol-gel method, into nanochannels of anodic aluminum oxide templates. The morphology and structure of as-prepared PCT24 were examined by scanning electron microscopy, transmission electron microscopy (TEM) and X-ray diffraction techniques. The obtained PCT24 nanotubes with diameter of similar to 200 nm and wall thickness of similar to 20 nm exhibited a tetragonal perovskite structure. High resolution TEM (HRTEM) analysis confirmed that as-obtained PCT24 nanotubes made up of nanoparticles (5-8 nm) which were randomly aligned in the nanotubes. Formation of some solid crystalline PCT24 nanorods, Y-junctions and multi-branches were observed. Interconnections in the pores of template are responsible for the growth of Y-junctions and multi-branches. The possible formation mechanism of PCT24 nanotubes/nanorods was discussed. Ferroelectric hysteresis loops of PCT24 nanotube arrays were measured, showing a room temperature ferroelectric characteristic of as-prepared PCT24 nanotubes. (C) 2011 Elsevier B.V. All rights reserved.

Compositionally modulated Pb(Mg1/3Nb2/3)O-3-PbTiO3 relaxor thin films deposited by pulsed excimer laser ablation technique

Thin films of (1-x)Pb(Mg1/3Nb2/3)O-3 - xPbTiO(3) (x = 0.1 to 0.3)(PMN-PT) were deposited on the platinum coated silicon substrate by pulsed excimer laser ablation technique. A template layer of LaSr0.5Co0.5O3 (LSCO) was deposited on platinum substrate prior to the deposition of PMN-PT thin films. The composition and the structure of the films were modulated via proper variation of the deposition parameter such as substrate temperature, laser fluence and thickness of the template layers. We observed the impact of the thickness of LSCO template layer on the orientation of the films. A room temperature dielectric constant varying from 2000 to 4500 was noted for different composition of the films. The dielectric properties of the films were studied over the frequency range of 100 Hz - 100 kHz over a wide range of temperatures. The films exhibited the relaxor- type behavior that was characterized by the frequency dispersion of the temperature of dielectric constant maxima (T-m) and also diffuse phase transition. C1 Indian Inst Sci, Mat Res Ctr, Bangalore, Karnataka 560012 India.

Chromium Nanowires Grown Inside Lithographically Fabricated U-Trench Templates

Chromium nanowires of diameter 40-120 nm have been grown inside lithographically fabricated U-trench templates on oxidized silicon substrate by RF sputtering deposition technique. Under favourable experimental conditions, very long nanowires can be grown which depends on the trench length and surface homogeneity along the axis. Surface wettability control by the restricted supply of metal vapour is the key for the formation of nanowires. Diameter/depth ratio for the trench template is demonstrated to be crucial for the growth of nanowires.

Compositionally and structurally modulated Pb(Mg1/3Nb2/3)O3-PbTiO3 relaxor thin films for microactuator application

Thin films of (1-x)Pb(Mg1/3Nb2/3)O3-xPbTiO3(x = 0.1 to 0.3) (PMN-PT) were successfully grown on the platinum coated silicon substrate by pulsed excimer laser ablation technique. A thin template layer of LaSr0.5Co0.5O3 (LSCO) was deposited on platinum substrate prior to the deposition of PMN-PT thin films. The composition and the structure of the films were modulated via proper variation of the deposition parameter such as substrate temperature, laser fluence and thickness of the template layers. We observed the impact of the thickness of LSCO template layer on the orientation of the films. The crystallographic structure and compositional variation were confirmed with x-ray diffraction and energy diffraction x-ray (EDX) analysis. A room temperature dielectric constant varying from 2000 to 4500 was noted for different composition of the films. The dielectric properties of the films were studied over the frequency range of 100 Hz - 100 kHz over a wide range of temperatures. The films exhibited the relaxor-type behavior that was characterized by the frequency dispersion of the temperature of dielectric constant maxima (Tm) and also diffuse phase transition. This relaxor nature in PMN-PT thin films was attributed to freezing of the dipole moment, which takes place below a certain temperature. This phenomenon was found to be very similar to spin glass system, where spins are observed to freeze after certain temperature.