Detection of G-Quadruplex DNA Using Primer Extension as a Tool

DNA sequence and structure play a key role in imparting fragility to different regions of the genome. Recent studies have shown that non-B DNA structures play a key role in causing genomic instability, apart from their physiological roles at telomeres and promoters. Structures such as G-quadruplexes, cruciforms, and triplexes have been implicated in making DNA susceptible to breakage, resulting in genomic rearrangements. Hence, techniques that aid in the easy identification of such non-B DNA motifs will prove to be very useful in determining factors responsible for genomic instability. In this study, we provide evidence for the use of primer extension as a sensitive and specific tool to detect such altered DNA structures. We have used the G-quadruplex motif, recently characterized at the BCL2 major breakpoint region as a proof of principle to demonstrate the advantages of the technique. Our results show that pause sites corresponding to the non-B DNA are specific, since they are absent when the G-quadruplex motif is mutated and their positions change in tandem with that of the primers. The efficiency of primer extension pause sites varied according to the concentration of monovalant cations tested, which support G-quadruplex formation. Overall, our results demonstrate that primer extension is a strong in vitro tool to detect non-B DNA structures such as G-quadruplex on a plasmid DNA, which can be further adapted to identify non-B DNA structures, even at the genomic level.

An Evaluation of Inventory Management and Performance in Indian Machine Tool SMEs: An Exploratory Study

Inventory Management (IM) plays a decisive role in the enhancement of efficiency and competitiveness of manufacturing enterprises. Therefore, major manufacturing enterprises are following IM practices as a strategy to improve efficiency and achieve competitiveness. However, the spread of IM culture among Small and Medium Enterprises (SMEs) is limited due to lack of initiation, expertise and financial limitations in developed countries, leave alone developing countries. With this backdrop, this paper makes an attempt to ascertain the role and importance of IM practices and performance of SMEs in the machine tools industry of Bangalore, India. The relationship between inventory management practices and inventory cost are probed based on primary data gathered from 91 SMEs. The paper brings out that formal IM practices have a positive impact on the inventory performance of SMEs.

Defect-selective photothermal imaging: a sensitive tool for damage mapping in optical coatings

A defect-selective photothermal imaging system for the diagnostics of optical coatings is demonstrated. The instrument has been optimized for pump and probe parameters, detector performance, and signal processing algorithm. The imager is capable of mapping purely optical or thermal defects efficiently in coatings of low damage threshold and low absorbance. Detailed mapping of minor inhomogeneities at low pump power has been achieved through the simultaneous action of a low-noise fiber optic photothermal beam defection sensor and a common-mode-rejection demodulation (CMRD) technique. The linearity and sensitivity of the sensor have been examined theoretically and experimentally, and the signal to noise ratio improvement factor is found to be about 110 compared to a conventional bicell photodiode. The scanner is so designed that mapping of static or shock sensitive samples is possible. In the case of a sample with absolute absorptance of 3.8 x 10(-4), a change in absorptance of about 0.005 x 10(-4) has been detected without ambiguity, ensuring a contrast parameter of 760. This is about 1085% improvement over the conventional approach containing a bicell photodiode, at the same pump power. The merits of the system have been demonstrated by mapping two intentionally created damage sites in a MgF2 coating on fused silica at different excitation powers. Amplitude and phase maps were recorded for thermally thin and thick cases, and the results are compared to demonstrate a case which, in conventional imaging, would lead to a deceptive conclusion regarding the type and location of the damage. Also, a residual damage profile created by long term irradiation with high pump power density has been depicted.

Heat shock protein 70 on Neuro2a cells is a putative receptor for Japanese encephalitis virus

Japanese encephalitis virus (JEV) envelope (E) protein has been shown to play a critical role in attachment to cells. However, the receptor interacting with envelope protein has not been conclusively identified. Using mouse neuroblastoma (Neuro2a) cells and purified JEV-E protein in `Virus Overlay Protein Binding Assay' followed by MALDI-TOF analysis, we identified `heat shock protein 70' (Hsp70) as a possible receptor for JEV. Indirect immunofluorescence and flow-cytometry analysis demonstrated localization of Hsp70 on Neuro2a cell surface. Co-immunoprecipitation followed by Western blot analysis reconfirmed the interaction between Hsp70 and JEV-E protein. Further, anti-Hsp70 polyclonal-antibodies were able to block JEV entry into Neuro2a cells. Additionally, using the bioinformatic tool - FTDOCK, clocking between the proteins was performed. Amongst six interacting structural poses studied one pose involving RGD motif on JEV-E and leucine(539) on Hsp70 displayed stable interaction. These observations indicate that Hsp70 serves as putative receptor for JEV in Neuro2A cells.

ESTIMATION OF EVAPOTRANSPIRATION IN AN EXPERIMENTAL WATERSHED IN A DECIDUOUS FOREST OF SOUTH INDIA

Forested areas play a dominant role in the global hydrological cycle. Evapotranspiration is a dominant component most of the time catching up with the rainfall. Though there are sophisticated methods which are available for its estimation, a simple reliable tool is needed so that a good budgeting could be made. Studies have established that evapotranspiration in forested areas is much higher than in agricultural areas. Latitude, type of forests, climate and geological characteristics also add to the complexity of its estimation. Few studies have compared different methods of evapotranspiration on forested watersheds in semi arid tropical forests. In this paper a comparative study of different methods of estimation of evapotranspiration is made with reference to the actual measurements made using all parameter climatological station data of a small deciduous forested watershed of Mulehole (area of 4.5 km2 ), South India. Potential evapotranspiration (ETo) was calculated using ten physically based and empirical methods. Actual evapotranspiration (AET) has been calculated through computation of water balance through SWAT model. The Penman-Montieth method has been used as a benchmark to compare the estimates arrived at using various methods. The AET calculated shows good agreement with the curve for evapotranspiration for forests worldwide. Error estimates have been made with respect to Penman-Montieth method. This study could give an idea of the errors involved whenever methods with limited data are used and also show the use indirect methods in estimation of Evapotranspiration which is more suitable for regional scale studies.

A Case of Simple Tool Use in Wild Liontailed Macaques (Macaca silenus)

Three members of a group of liontailed macaques (Macaea silenus) were seen to use leaves for food preparation. Other examples of prey-selection and hunting behaviour in liontailed macaques reflect individual- and group-specific skills. The absence of similar patterns in bonnet macaques (Macaca radiata) living in the same habitat might be related to differences in the social design and indicate the high significance of social aspects for the occurrence and manifestation of innovative behaviour.

Inventory Management Performance in Indian Machine Tool SMEs: What factors do influence them

These instructions give on basic guidelines for preparing papers for the IEEM 2008 Proceedings. Inventory Management (IM) plays a decisive role in the enhancement of efficiency for manufacturing enterprise competitiveness. Therefore, major manufacturing industries are following inventory management practices as a strategy to improve efficiency and achieve competitiveness. However, the spread of inventory management culture among Small and Medium Enterprises (SMEs) is limited due to lack of initiation, expertise and financial limitations in developed countries, leave alone developing countries.With this backdrop, this paper makes an attempt to ascertain the factors which influence the IM performance of SMEs in the machine tools industry of Bangalore, India. This issue is probed based on primary data gathered from 91 SMEs. The paper brings out that two sets of factors namely organizational support and external pressure have a positive impact on the inventory performance of SMEs.

Mathematical model and rule extraction for tool wear monitoring problem using nature inspired techniques

In this paper, pattern classification problem in tool wear monitoring is solved using nature inspired techniques such as Genetic Programming(GP) and Ant-Miner (AM). The main advantage of GP and AM is their ability to learn the underlying data relationships and express them in the form of mathematical equation or simple rules. The extraction of knowledge from the training data set using GP and AM are in the form of Genetic Programming Classifier Expression (GPCE) and rules respectively. The GPCE and AM extracted rules are then applied to set of data in the testing/validation set to obtain the classification accuracy. A major attraction in GP evolved GPCE and AM based classification is the possibility of obtaining an expert system like rules that can be directly applied subsequently by the user in his/her application. The performance of the data classification using GP and AM is as good as the classification accuracy obtained in the earlier study.

EIT as a tool to observe dual wavelength operation of a semiconductor laser

We propose a simplified technique for dual wavelength operation of an extended cavity semiconductor laser, and its characterization using electromagnetically induced transparency (EIT). In this laser cavity scheme light beam is made converging before it incidences on the cavity grating. The converging angle of the beam creates two longitudinal oscillating modes of resonating cavity. Frequency separation between the longitudinal modes are measured with the help of beat frequency generation in a photodiode and creating pair of EIT spectra in Rb vapor. The pair of EIT dips that are generated due to dual wavelength of this laser (that is used as control laser) can be used to estimate frequency difference between the generated wavelengths. Width of EIT spectra can be used to estimate line width of individual wavelength components.

Fluorescence polarization as a tool to study lectin-sugar interaction. An investigation of the binding of 4-methylumbelliferyl beta-D-galactopyranoside to Abrus precatorious agglutinin

Polarization of ligand fluorescence was used to study the binding of 4-methylumbelliferyl beta-D-galactopyranoside (MeUmb-Galp) to Abrus precatorious agglutinin. The binding of the fluorescent sugar to the lectin led to considerable polarization of the MeUmb-Galp fluorescence, which was also quenched by about 30% on binding to the lectin. The binding of the fluorescent sugar was carbohydrate-specific, as evidenced by inhibition of both fluorescence polarization and quenching when lectin was preincubated with lactose. The association constant as determined by fluorescence polarization is 1.42 x 10(4) M-1 at 25 degrees C and is in excellent agreement with those determined by fluorescence quenching (Ka = 1.51 x 10(4) M-1) and equilibrium dialysis (Ka = 1.62 x 10(4) M-1) at 25 degrees C. The numbers of binding sites as determined by fluorescence polarization, quenching and equilibrium dialysis agree very well with one another, n being equal to 2.0 +/- 0.05. The consistency between the association constant value determined by fluorescence polarization, quenching and equilibrium dialysis shows the validity of this approach to study lectin-sugar interaction.

Influence of tool rake angle on the quality of pure magnesium chip-consolidated product

Chips were produced by orthogonal Cutting of cast pure magnesium billet with three different tool rake angles viz., -15 degrees, -5 degrees and +15 degrees on a lathe. Chip consolidation by solid state recycling technique involved cold compaction followed by hot extrusion. The extruded products were characterized for microstructure and mechanical properties. Chip-consolidated products from -15 degrees rake angle tools showed 19% increase in tensile strength, 60% reduction ingrain size and 12% increase in hardness compared to +15 degrees rake chip-consolidated product indicating better chip bonding and grain refinement. Microstructure of the fracture specimen Supports the abovefinding. On the overall, the present work high lights the importance of tool take angle in determining the quality of the chip-consolidated products. (C) 2009 Elsevier B.V. All rights reserved.

COMPASS – A tool for evaluation of compression strategies for embedded processors

A major concern of embedded system architects is the design for low power. We address one aspect of the problem in this paper, namely the effect of executable code compression. There are two benefits of code compression – firstly, a reduction in the memory footprint of embedded software, and secondly, potential reduction in memory bus traffic and power consumption. Since decompression has to be performed at run time it is achieved by hardware. We describe a tool called COMPASS which can evaluate a range of strategies for any given set of benchmarks and display compression ratios. Also, given an execution trace, it can compute the effect on bus toggles, and cache misses for a range of compression strategies. The tool is interactive and allows the user to vary a set of parameters, and observe their effect on performance. We describe an implementation of the tool and demonstrate its effectiveness. To the best of our knowledge this is the first tool proposed for such a purpose.

Seismic Microzonation: A Tool for Disaster Mitigation Planning

Seismic microzonation has generally been recognized as the most accepted tool in seismic hazard assessment and risk evaluation. In general, risk reduction can be done by reducing the hazard, the vulnerability or the value at risk. Since the earthquake hazard can not be reduced, one has to concentrate on vulnerability and value at risk. The vulnerability of an urban area / municipalities depends on the vulnerability of infrastructure and redundancies within the infrastructure. The earthquake risk is the damage to buildings along with number of people that are killed / hurt and the economic losses during the event due to an earthquake with a return period corresponding to this time period. The principal approaches one can follow to reduce these losses are to avoid, if possible, high hazard areas for the siting of buildings and infrastructure, and further ensure that the buildings and infrastructure are designed and constructed to resist expected earthquake loads. This can be done if one can assess the hazard at local scales. Seismic microzonation maps provide the basis for scientifically based decision-making to reduce earthquake risk for Govt./public agencies, private owners and the general public. Further, seismic microzonation carried out on an appropriate scale provides a valuable tool for disaster mitigation planning and emergency response planning for urban centers / municipalities. It provides the basis for the identification of the areas of the city / municipality which are most likely to experience serious damage in the event of an earthquake.

Do inventory management practices affect economic performance? An empirical evaluation of the machine tool SMEs in Bangalore

Inventory management (IM) has a decisive role in the enhancement of manufacturing industry's competitiveness. Therefore, major manufacturing industries are following IM practices with the intention of improving their performance. However, the effort to introduce IM in SMEs is very limited due to lack of initiation, expertise, and financial constraints. This paper aims to provide a guideline for entrepreneurs in enhancing their IM performance, as it presents the results of a survey based study carried out for machine tool Small and Medium Enterprises (SMEs) in Bangalore. Having established the significance of inventory as an input, we probed the relationship between IM performance and economic performance of these SMEs. To the extent possible all the factors of production and performance indicators were deliberately considered in pure economic terms. All economic performance indicators adopted seem to have a positive and significant association with IM performance in SMEs. On the whole, we found that SMEs which are IM efficient are likely to perform better on the economic front also and experience higher returns to scale.

Interfacial microrheology as a tool to study viscoelastic transitions in nanoconfined soft matter

We present a method to perform in situ microrheological measurements on monolayers of soft materials undergoing viscoelastic transitions under compression. Using the combination of a Langmuir trough mounted on the inverted microscope stage of a laser scanning confocal microscope we track the motion of individual fluorescent quantum dots partly dispersed in monolayers spread at the air-water interface. From the calculated mean square displacement of the probe particles and extending a well established scheme of the generalized Stokes-Einstein relation in bulk to the interface we arrive at the viscoelastic modulus for the respective monolayers as a function of surface density. Measurements on monolayers of glassy as well as nonglassy polymers and a standard fatty acid clearly show sensitivity of our technique to subtle variations, in the viscoelastic properties of the highly confined materials under compression. Evidence for possible spatial variations of such viscoelastic properties at a given surface density for the fatty acid monolayer is also provided.