Genome analysis: A new approach for visualization of sequence organization in genomes

In this article we describe and demonstrate the versatility of a computer program, GENOME MAPPING, that uses interactive graphics and runs on an IRIS workstation. The program helps to visualize as well as analyse global and local patterns of genomic DNA sequences. It was developed keeping in mind the requirements of the human genome sequencing programme, which requires rapid analysis of the data. Using GENOME MAPPING one can discern signature patterns of different kinds of sequences and analyse such patterns for repetitive as well as rare sequence strings. Further, one can visualize the extent of global homology between different genomic sequences. An application of our method to the published yeast mitochondrial genome data shows similar sequence organizations in the entire sequence and in smaller subsequences.

Fuel drop size measurement in a carburetted induction system with 2 throttling methods

A new throttling system far SI engines is examined. The SMD of the fuel droplets in the induction system is measured to evaluate the performance of the new device with respect to the conventional throttle plate arrangement. The measurements are conducted at steady now conditions. A forward angular scattering technique with a He-Ne laser beam is used for droplet size measurement. The experiments are carried out with different mixture strength, stream velocity and throttle positions. It is observed that A/F ratio has no effect on SMD. However, stream velocity and throttle position have a significant influence on SMD. The new throttling method is found to be more effective in reducing the SMD, particularly at low throttle opening and high stream velocity compared to the conventional throttle plate.

New open-framework phosphate and phosphite compounds of gallium

Five new open-framework compounds of gallium have been synthesized by hydrothermal methods and their structures determined by single crystal X-ray diffraction studies. The compounds, C8N4H26]Ga6F4(PO4)(6)], I, C5N3H11]Ga3F2(PO4)(3)]center dot H2O, II, C6N3H19]Ga-4(C2O4)(PO4)(4)(H2PO4)]center dot 2H(2)O, III, Ga2F3(HPO4)(PO4)]center dot 2H(3)O, IV, and C3N2H5](2)Ga-4(H2O)(3)(HPO3)(7)], V, possess three-dimensional structures. All the compounds are formed by the connectivity between the Ga polyhedra and phosphite/phosphate units. The observation of SBU-6 (I and II) and spiro-5 (IV) secondary building units (SBUs) are noteworthy. The flexibility of the formation of gallium phosphate frameworks has been established by the isolation of two related structures (I and II) from the same SBU units but different organic amines. Some of the present structures have close resemblance to the gallium phosphate phases known earlier. The compounds have been characterized by CHN analysis, powder XRD, IR, and TGA. (C) 2011 Elsevier B. V. All rights reserved.

Biopolymers in nanopores: challenges and opportunities

We review the current status of various aspects of biopolymer translocation through nanopores and the challenges and opportunities it offers. Much of the interest generated by nanopores arises from their potential application to third-generation cheap and fast genome sequencing. Although the ultimate goal of single-nucleotide identification has not yet been reached, great advances have been made both from a fundamental and an applied point of view, particularly in controlling the translocation time, fabricating various kinds of synthetic pores or genetically engineering protein nanopores with tailored properties, and in devising methods (used separately or in combination) aimed at discriminating nucleotides based either on ionic or transverse electron currents, optical readout signatures, or on the capabilities of the cellular machinery. Recently, exciting new applications have emerged, for the detection of specific proteins and toxins (stochastic biosensors), and for the study of protein folding pathways and binding constants of protein-protein and protein-DNA complexes. The combined use of nanopores and advanced micromanipulation techniques involving optical/magnetic tweezers with high spatial resolution offers unique opportunities for improving the basic understanding of the physical behavior of biomolecules in confined geometries, with implications for the control of crucial biological processes such as protein import and protein denaturation. We highlight the key works in these areas along with future prospects. Finally, we review theoretical and simulation studies aimed at improving fundamental understanding of the complex microscopic mechanisms involved in the translocation process. Such understanding is a pre-requisite to fruitful application of nanopore technology in high-throughput devices for molecular biomedical diagnostics.

New Insights into Selective Heterogeneous Nucleation of Metal Nanoparticles on Oxides by Microwave-Assisted Reduction: Rapid Synthesis of High-Activity Supported Catalysts

Microwave-based methods are widely employed to synthesize metal nanoparticles on various substrates. However, the detailed mechanism of formation of such hybrids has not been addressed. In this paper, we describe the thermodynamic and kinetic aspects of reduction of metal salts by ethylene glycol under microwave heating conditions. On the basis of this analysis, we identify the temperatures above which the reduction of the metal salt is thermodynamically favorable and temperatures above which the rates of homogeneous nucleation of the metal and the heterogeneous nucleation of the metal on supports are favored. We delineate different conditions which favor the heterogeneous nucleation of the metal on the supports over homogeneous nucleation in the solvent medium based on the dielectric loss parameters of the solvent and the support and the metal/solvent and metal/support interfacial energies. Contrary to current understanding, we show that metal particles can be selectively formed on the substrate even under situations where the temperature of the substrate Is lower than that of the surrounding medium. The catalytic activity of the Pt/CeO(2) and Pt/TiO(2) hybrids synthesized by this method for H(2) combustion reaction shows that complete conversion is achieved at temperatures as low as 100 degrees C with Pt-CeO(2) catalyst and at 50 degrees C with Pt-TiO(2) catalyst. Our method thus opens up possibilities for rational synthesis of high-activity supported catalysts using a fast microwave-based reduction method.

New possibilities in amplitude- and phase-comparison techniques for distance relays

The paper reports further work on the amplitude-comparison technique described by the same authors in a previous paper. This technique is extended to develop improved polar characteristics. Discontinuous polar characteristics, like directional parallelograms, are obtained by a single measuring gate with a simple mode of relay circuitry, whereas two measuring gates are required to provide a directional-quadrilateral characteristic of potentially general application. The paper also describes some new possibilities in phase-comparison methods for distance-protection schemes. Comparator models which effect the amplitude and phase comparison of the relaying signals are described in their schematic form. A comprehensive theoretical basis for comparison is also presented.

l-pGlu-(2-propyl)-l-His-l-ProNH2 attenuates 4-aminopyridine-induced epileptiform activity and sodium current: a possible action of new thyrotropin-releasing hormone analog for its anticonvulsant potential

L-PGlu-(2-proPyl)-L-His-L-ProNH(2) (NP-647) is a CNS active thyrotropin-releasing hormone (TRH) analog with potential application in various CNS disorders including seizures. In the present study, mechanism of action for protective effect of NP-647 was explored by studying role of NP-647 on epileptiform activity and sodium channels by using patch-clamp methods. Epileptiform activity was induced in subicular pyramidal neurons of hippocampal slice of rat by perfusing 4-aminopyridine (4-AP) containing Mg(+2)-free normal artificial cerebrospinal fluid (nACSF). Increase in mean firing frequency was observed after perfusion of 4-AP and zero Mg(+2) (2.10+/-0.47 Hz) as compared with nACSF (0.12+/-0.08 Hz). A significant decrease in mean firing frequency (0.61+/-0.22 Hz), mean frequency of epileptiform events (0.03+/-0.02 Hz vs. 0.22+/-0.05 Hz of 4-AP+0 Mg), and average number of action potentials in paroxysmal depolarization shift-burst (2.54+/-1.21 Hz vs. 8.16+/-0.88 Hz of 4-AP +0 Mg) was observed. A significant reduction in peak dV/dt (246+/-19 mV ms(-1) vs. 297 18 mV ms-1 of 4-AP+0 Mg) and increase (1.332+/-0.018 ms vs. 1.292+/-0.019 ms of 4-AP+0 Mg) in time required to reach maximum depolarization were observed indicating role of sodium channels. Concentration-dependent depression of sodium current was observed after exposure to dorsal root ganglion neurons to NP-647. NP-647 at different concentrations (1, 3, and 10 mu M) depressed sodium current (15+/-0.5%, 50+/-2.6%, and 75+/-0.7%, respectively). However, NP-647 did not show change in the peak sodium current in CNa18 cells. Results of present study demonstrated potential of NP-647 in the inhibition of epileptiform activity by inhibiting sodium channels indirectly. (C) 2011 IBRO. Published by Elsevier Ltd. All rights reserved.

NMR methods for fast data acquisition

NMR spectroscopy has witnessed tremendous advancements in recent years with the development of new methodologies for structure determination and availability of high-field strength spectrometers equipped with cryogenic probes. Supported by these advancements, a new dimension in NMR research has emerged which aims to increase the speed with data is collected and analyzed. Several novel methodologies have been proposed in this direction. This review focuses on the principles on which these different approaches are based with an emphasis on G-matrix Fourier transform NMR spectroscopy.

Location Area Planning Using Simulated Annealing With A New Solution Representation

Location area planning problem is to partition the cellular/mobile network into location areas with the objective of minimizing the total cost. This partitioning problem is a difficult combinatorial optimization problem. In this paper, we use the simulated annealing with a new solution representation. In our method, we can automatically generate different number of location areas using Compact Index (CI) to obtain the optimal/best partitions. We compare the results obtained in our method with the earlier results available in literature. We show that our methodology is able to perform better than earlier methods.

Familial Diarrhea Syndrome Caused by an Activating GUCY2C Mutation

BACKGROUND Familial diarrhea disorders are, in most cases, severe and caused by recessive mutations. We describe the cause of a novel dominant disease in 32 members of a Norwegian family. The affected members have chronic diarrhea that is of early onset, is relatively mild, and is associated with increased susceptibility to inflammatory bowel disease, small-bowel obstruction, and esophagitis. METHODS We used linkage analysis, based on arrays with single-nucleotide polymorphisms, to identify a candidate region on chromosome 12 and then sequenced GUCY2C, encoding guanylate cyclase C (GC-C), an intestinal receptor for bacterial heat-stable enterotoxins. We performed exome sequencing of the entire candidate region from three affected family members, to exclude the possibility that mutations in genes other than GUCY2C could cause or contribute to susceptibility to the disease. We carried out functional studies of mutant GC-C using HEK293T cells. RESULTS We identified a heterozygous missense mutation (c.2519G -> T) in GUCY2C in all affected family members and observed no other rare variants in the exons of genes in the candidate region. Exposure of the mutant receptor to its ligands resulted in markedly increased production of cyclic guanosine monophosphate (cGMP). This may cause hyperactivation of the cystic fibrosis transmembrane regulator (CFTR), leading to increased chloride and water secretion from the enterocytes, and may thus explain the chronic diarrhea in the affected family members. CONCLUSIONS Increased GC-C signaling disturbs normal bowel function and appears to have a proinflammatory effect, either through increased chloride secretion or additional effects of elevated cellular cGMP. Further investigation of the relevance of genetic variants affecting the GC-C-CFTR pathway to conditions such as Crohn's disease is warranted. (Funded by Helse Vest Western Norway Regional Health Authority] and the Department of Science and Technology, Government of India.)

Crowd Sourcing a New Paradigm for Interactome Driven Drug Target Identification in Mycobacterium tuberculosis

A decade since the availability of Mycobacterium tuberculosis (Mtb) genome sequence, no promising drug has seen the light of the day. This not only indicates the challenges in discovering new drugs but also suggests a gap in our current understanding of Mtb biology. We attempt to bridge this gap by carrying out extensive re-annotation and constructing a systems level protein interaction map of Mtb with an objective of finding novel drug target candidates. Towards this, we synergized crowd sourcing and social networking methods through an initiative `Connect to Decode' (C2D) to generate the first and largest manually curated interactome of Mtb termed `3interactome pathway' (IPW), encompassing a total of 1434 proteins connected through 2575 functional relationships. Interactions leading to gene regulation, signal transduction, metabolism, structural complex formation have been catalogued. In the process, we have functionally annotated 87% of the Mtb genome in context of gene products. We further combine IPW with STRING based network to report central proteins, which may be assessed as potential drug targets for development of drugs with least possible side effects. The fact that five of the 17 predicted drug targets are already experimentally validated either genetically or biochemically lends credence to our unique approach.

Statistical Methods for Accelerated Life Testing with Particular Reference to Resin Impregnated Paper Bushings

Electrical failure of insulation is known to be an extremal random process wherein nominally identical pro-rated specimens of equipment insulation, at constant stress fail at inordinately different times even under laboratory test conditions. In order to be able to estimate the life of power equipment, it is necessary to run long duration ageing experiments under accelerated stresses, to acquire and analyze insulation specific failure data. In the present work, Resin Impregnated Paper (RIP) a relatively new insulation system of choice used in transformer bushings, is taken as an example. The failure data has been processed using proven statistical methods, both graphical and analytical. The physical model governing insulation failure at constant accelerated stress has been assumed to be based on temperature dependent inverse power law model.

Assessment of the Relationships Among Design Methods, Design Activities, and Creativity

This paper presents an experimental study that was conducted to compare the results obtained from using different design methods (brainstorming (BR), functional analysis (FA), and SCAMPER) in design processes. The objectives of this work are twofold. The first was to determine whether there are any differences in the length of time devoted to the different types of activities that are carried out in the design process, depending on the method that is employed; in other words, whether the design methods that are used make a difference in the profile of time spent across the design activities. The second objective was to analyze whether there is any kind of relationship between the time spent on design process activities and the degree of creativity in the solutions that are obtained. Creativity evaluation has been done by means of the degree of novelty and the level of resolution of the designed solutions using creative product semantic scale (CPSS) questionnaire. The results show that there are significant differences between the amounts of time devoted to activities related to understanding the problem and the typology of the design method, intuitive or logical, that are used. While the amount of time spent on analyzing the problem is very small in intuitive methods, such as brainstorming and SCAMPER (around 8-9% of the time), with logical methods like functional analysis practically half the time is devoted to analyzing the problem. Also, it has been found that the amount of time spent in each design phase has an influence on the results in terms of creativity, but results are not enough strong to define in which measure are they affected. This paper offers new data and results on the distinct benefits to be obtained from applying design methods. DOI: 10.1115/1.4007362]

Enhancing reproducibility of ultrasonic measurements by new users

Perception of operator influences ultrasound image acquisition and processing. Lower costs are attracting new users to medical ultrasound. Anticipating an increase in this trend, we conducted a study to quantify the variability in ultrasonic measurements made by novice users and identify methods to reduce it. We designed a protocol with four presets and trained four new users to scan and manually measure the head circumference of a fetal phantom with an ultrasound scanner. In the first phase, the users followed this protocol in seven distinct sessions. They then received feedback on the quality of the scans from an expert. In the second phase, two of the users repeated the entire protocol aided by visual cues provided to them during scanning. We performed off-line measurements on all the images using a fully automated algorithm capable of measuring the head circumference from fetal phantom images. The ground truth (198.1 +/- 1.6 mm) was based on sixteen scans and measurements made by an expert. Our analysis shows that: (1) the inter-observer variability of manual measurements was 5.5 mm, whereas the inter-observer variability of automated measurements was only 0.6 mm in the first phase (2) consistency of image appearance improved and mean manual measurements was 4-5 mm closer to the ground truth in the second phase (3) automated measurements were more precise, accurate and less sensitive to different presets compared to manual measurements in both phases. Our results show that visual aids and automation can bring more reproducibility to ultrasonic measurements made by new users.

Engineering New Layered Solids from Exfoliated Inorganics: a Periodically Alternating Hydrotalcite - Montmorillonite Layered Hybrid

Two-dimensional (2D) nanosheets obtained by exfoliating inorganic layered crystals have emerged as a new class of materials with unique attributes. One of the critical challenges is to develop robust and versatile methods for creating new nanostructures from these 2D-nanosheets. Here we report the delamination of layered materials that belonging to two different classes - the cationic clay, montmorillonite, and the anionic clay, hydrotalcite - by intercalation of appropriate ionic surfactants followed by dispersion in a non-polar solvent. The solids are delaminated to single layers of atomic thickness with the ionic surfactants remaining tethered to the inorganic and consequently the nanosheets are electrically neutral. We then show that when dispersions of the two solids are mixed the exfoliated sheets self-assemble as a new layered solid with periodically alternating hydrotalcite and montmorillonite layers. The procedure outlined here is easily extended to other layered solids for creating new superstructures from 2D-nanosheets by self-assembly.