Excision of uracil from the ends of double stranded DNA by uracil DNA glycosylase and its use in high efficiency cloning of PCR products

We show that uracil DNA glycosylase from E. coli excises uracil residues from the ends of double stranded oligos. This information has allowed us to develop an efficient method of cloning PCR amplified DNA. In this report, we describe use of this method in cloning of E. coli genes for lysyl- and methionyl-tRNA synthetases. Efficiency of cloning by this method was found to be the same as that of subcloning of DNA restriction fragments from one vector to the other vector. Possibilities of using other DNA glycosylases for such applications are discussed.

Probing the inter-tube transport in aligned and random multiwall carbon nanotubes

The temperature and magnetic field dependence of conductivity has been used to probe the inter-tube transport in multiwall carbon nanotubes (MWNTs). The scanning electron microscopy images show highly aligned and random distribution of MWNTs. The conductivity in aligned carbon nanotube (ACNT) and random carbon nanotube (RCNT) samples at low temperature follows T-1/2 (at T < 8 K) and T-3/4 (at T > 8 K) dependence in accordance with the weak localization and electron-electron (e-e) interaction model. The values of diffusion coefficient in ACNT and RCNT are 0.25 x 10(-2) and 0.71 x 10(-2) cm(2) s(-1), respectively, indicating that larger number of inter-tube junctions in later enhances the bulk transport. The positive magnetoconductance (MC) data in both samples show that the weak localization contribution is dominant. However, the saturation of MC at higher fields and lower temperatures indicate that e-e interaction is quite significant in RCNT. The T-3/4 and T-1/2 dependence of inelastic scattering length (l(in)) in ACNT and RCNT samples show that the inelastic e-e scattering is more important in aligned tubes. (C) 2011 American Institute of Physics. doi:10.1063/1.3552911]

Proportioning of fly-ash cement concrete mixes

The accumulation of fly ash throughout the world is several million tons per day. The main problem with the usage of fly ash is the slow rate of strength gain, primarily due to slow pozzolanic reactions. Existing methods of proportioning fly ash concrete are lacking. These methods are involved and do not directly take into account the properties of the constituent materials. The Generalized Approach for Mix Proportioning developed at the Indian Institute of Science, Bangalore, is the basis for the development of the proposed method, which takes into account the characteristics of cement, fly ash, and aggregates. Based on the basic trial mix data obtained by using the American Concrete Institute (ACI 211.1-81) method, the proportions of fly-ash concrete mixes were arrived at using the Generalized Approach for Mix Proportioning. The method proposed was applied to and found applicable for fly-ash concretes using fly ashes from two different sources.

Fatigue crack propagation model and size effect in concrete using dimensional analysis

It is well known that fatigue in concrete causes excessive deformations and cracking leading to structural failures. Due to quasi-brittle nature of concrete and formation of a fracture process zone, the rate of fatigue crack growth depends on a number of parameters, such as, the tensile strength, fracture toughness, loading ratio and most importantly the structural size. In this work, an analytical model is proposed for estimating the fatigue crack growth in concrete by using the concepts of dimensional analysis and including the above parameters. Knowing the governed and the governing parameters of the physical problem and by using the concepts of self-similarity, a relationship is obtained between different parameters involved. It is shown that the proposed fatigue law is able to capture the size effect in plain concrete and agrees well with different experimental results. Through a sensitivity analysis, it is shown that the structural size plays a dominant role followed by loading ratio and the initial crack length in fatigue crack propagation. (C) 2010 Elsevier Ltd. All rights reserved.

High-rate, Double-Symbol-Decodable STBCs from Clifford Algebras

For the number of transmit antennas N = 2(a) the maximum rate (in complex symbols per channel use) of all the Quasi-Orthogonal Designs (QODs) reported in the literature is a/2(a)-1. In this paper, we report double-symbol-decodable Space-Time Block Codes with rate a-1/2(a)-2 for N = 2(a) transmit antennas. In particular, our code for 8 and 16 transmit antennas offer rates 1 and 3/4 respectively, the known QODs offer only 3/4 and 1/2 respectively. Our construction is based on the representations of Clifford algebras and applicable for any number of transmit antennas. We study the diversity sum and diversity product of our codes. We show that our diversity sum is larger than that of all known QODs and hence our codes perform better than the comparable QODs at low SNRs for identical spectral efficiency. We provide simulation results for various spectral efficiencies.

Fracture Analysis of Concrete Structural Components Accounting for Tension Softening Effect

This paper presents methodologies for fracture analysis of concrete structural components with and without considering tension softening effect. Stress intensity factor (SIF) is computed by using analytical approach and finite element analysis. In the analytical approach, SW accounting for tension softening effect has been obtained as the difference of SIP obtained using linear elastic fracture mechanics (LEFM) principles and SIP due to closing pressure. Superposition principle has been used by accounting for non-linearity in incremental form. SW due to crack closing force applied on the effective crack face inside the process zone has been computed using Green's function approach. In finite element analysis, the domain integral method has been used for computation of SIR The domain integral method is used to calculate the strain energy release rate and SIF when a crack grows. Numerical studies have been conducted on notched 3-point bending concrete specimen with and without considering the cohesive stresses. It is observed from the studies that SW obtained from the finite element analysis with and without considering the cohesive stresses is in good agreement with the corresponding analytical value. The effect of cohesive stress on SW decreases with increase of crack length. Further, studies have been conducted on geometrically similar structures and observed that (i) the effect of cohesive stress on SW is significant with increase of load for a particular crack length and (iii) SW values decreases with increase of tensile strength for a particular crack length and load.

Studies on molecular evolution and structural features of double-headed inhibitors of ?-amylase and trypsin in plants

Plant seeds usually have high concentrations of proteinase and amylase inhibitors. These inhibitors exhibit a wide range of specificity, stability and oligomeric structure. In this communication, we report analysis of sequences that show statistically significant similarity to the double-headed alpha-amylase/trypsin inhibitor of ragi (Eleusine coracana). Our aim is to understand their evolutionary and structural features. The 14 sequences of this family that are available in the SWISSPROT database form three evolutionarily distinct branches. The branches relate to enzyme specificities and also probably to the oligomeric state of the proteins and not to the botanical class of the plant from which the enzymes are derived. This suggests that the enzyme specificities of the inhibitors evolved before the divergence of commercially cultivated cereals. The inhibitor sequences have three regions that display periodicity in hydrophobicity. It is likely that this feature reflects extended secondary structure in these segments. One of the most variable regions of the polypeptide corresponds to a loop, which is most probably exposed in the native structure of the inhibitors and is responsible for the inhibitory property.

Antibodies raised against guanosine bind to double-stranded DNA

Antibodies elicited against guanosine have been reported to bind to single-stranded DNA. Using an avidin-biotin microELISA, we report that these antibodies also bind to double-stranded DNA. The binding is specific and is completely inhibited by the homologous hapten. The cross-reactivity of double-stranded DNA binding antibodies to single-stranded DNA is low. The antibodies are shown to bind to the topoisomers of plasmid DNA as assessed by a gel retardation assay.

Origin of magnetism and trend in T-c in Cr-based double perovskites: Interplay of two driving mechanisms

Hamiltonian constructed in a first principles manner, we explored the origin of magnetism and the T-c trend in Cr-based double perovskite series, Sr2CrB'O-6 (B' = W/Re/Os). Our study shows that the apparently puzzling T-c trend in Sr2CrB'O-6 (B' = W/Re/Os) series can be understood in terms of the interplay of the hybridization driven mechanism and the superexchange mechanism.

Analysis of texture evolution in pure magnesium and the magnesium alloy AM30 during rod and tube extrusion

The evolution of microstructure and texture during extrusion of pure magnesium and its single phase alloy AM30 has been studied experimentally as well as by crystal plasticity simulation. Microstructure and micro-texture were characterized by electron back scattered diffraction (EBSD), bulk-texture was measured using X-ray diffraction and deformation texture simulations were carried out using visco-plastic self consistent (VPSC) model. In spite of clear indications of the occurrence of dynamic recrystallization (DRX), simulations were able to reproduce the experimental textures successfully. This was attributed to the fact that the textures were c-type fibers with their axis of rotation parallel to the c-axis and DRX leads to simply rotate the texture around the c-axis. (C) 2011 Elsevier B.V. All rights reserved.

Experimental validation of the 1-D acoustical model for conical concentric tube resonators with moving medium

Variable cross-sectional area ducts are often used for attenuation at lower frequencies (of the order of firing frequency), whereas concentric tube resonators provide attenuation at relatively higher frequencies. In this paper, analysis of one dimensional control volume approach of conical concentric tube resonators is validated experimentally. The effects of mean flow and taper are investigated. The experimental setup is specially designed to measure the pressure transfer function in the form of Level Difference or Noise Reduction across the test muffler. It is shown that there is a reasonably good agreement between the predicted values of the Noise Reduction and the measured ones for incompressible mean flow as well as stationary medium. (C) 2011 Institute of Noise Control Engineering.

Synergetic roles of concrete ingredients in strength development

Concrete is basically a heterogeneous material made up of ingredients with distinct physical and mechanical properties. As a result, the presence of interphases is inevitable. In the processing of concrete, fresh and hardened states are the two distinct stages. In the fresh state, the presence of inert constituents in the cement mortar matrix only dilutes the overall potential of concrete to flow. In the hardened state the synergetics play a dominant role in strength development. When the strength of coarse aggregate is far higher than the strength levels for which the matrix or concrete is processed, interphase bonding plays a dominant role on the strength. When the matrix strength is comparable to that of the aggregate strength, in contrast, the concrete strength is affected by the aggregate strength. Besides these aspects, the effects of the size and the surface texture of coarse aggregates have also been analysed. Copyright (C) 1996 Elsevier Science Ltd.

Effect of Alkyl Chain Arrangement on Conformation and Dynamics in a Surfactant Intercalated Layered Double Hydroxide: Spectroscopic Measurements and MD Simulations

The anionic surfactant dodecyl sulfate (DDS) has been intercalated in an Mg-Al layered double hydroxide (LDH). Monolayer and bilayer arrangements of the alkyl chains of the intercalated surfactant can be engineered by tuning the Al/Mg ratio of the LDH. In both arrangements the anionic headgroup of the surfactant is tethered to the LDH sheets, and consequently translational mobility of the chains is absent. The degrees of freedom of the confined alkyl chains are restricted to changes in conformation. The effects of the arrangement of the intercalated surfactant chains on conformational order and dynamics have been,investigated by spectroscopic measurements and molecular dynamics simulations. Infrared, Raman, and C-13 NMR spectroscopies were used to investigate conformation of the alkyl chains in the monolayer and bilayer arrangements and variable contact time cross-polarization magic angle spinning (VCT CPMAS) NMR measurements to probe molecular motion. The alkyl chains in the monolayer arrangement of the intercalated DDS chains showed considerably greater conformational disorder and faster dynamics as compared to chains in the bilayer arrangement, in spite of the fact that the volume available per chain in the monolayer is smaller than that in the bilayer. Atomistic MD simulations of the two arrangements of the intercalated surfactant were carried out using an isothermal-isobaric ensemble. The simulations are able to reproduce the essential results of the experiment-greater conformational disorder and faster dynamics for the alkyl chains in the monolayer arrangement of the intercalated surfactant. The MD simulations show that these results are a consequence of the fact that the nature of conformational disorder in the two arrangements is different. In the monolayer arrangement the alkyl chains can sustain isolated gauche defects, whereas in the bilayer arrangement gauche conformers occur only as part of a kink a gauche(+) trans gauche(-) sequence.

Peristaltic pumping in a circular tube in the presence of an eccentric catheter

The influence of an eccentrically inserted catheter on the peristaltic pumping in a tube is investigated under long wavelength, low Reynolds number assumptions. The radially asymmetric deformation of the wall arising through an eccentrically inserted catheter is taken into consideration by choosing an appropriate bipolar coordinate system. The effect of the position and size of the catheter on pumping characteristics is studied. The best performance of pumping is noticed at a certain position of the catheter. The size of the catheter, when placed eccentrically, alters the pressure signature significantly inside the bolus, unlike the concentric case discussed by Lykoudis and Roos (1971). Further, the maximum pressure rise in one period of the peristaltic wave is observed to decrease with an increase in the eccentricity.