Inefficient excision of uracil from loop regions of DNA oligomers by E.coli uracil DNA glycosylase

Kinetic parameters for uracil DNA glycosylase (E.coli)-catalysed excision of uracil from DNA oligomers containing dUMP in different structural contexts were determined. Our results show that single-stranded oligonucleotides (unstructured) are used as somewhat better substrates than the double-stranded oligonucleotides. This is mainly because of the favourable V-max value of the enzyme for single-stranded substrates. More interestingly, however, we found that uracil release from loop regions of DNA hairpins is extremely inefficient. The poor efficiency with which uracil is excised from loop regions is a result of both increased K-m and lowered V-max values. This observation may have significant implications in uracil DNA glycosylase-directed repair of DNA segments that can be extruded as hairpins. In addition, these studies are useful in designing oligonucleotides for various applications in DNA research where the use of uracil DNA glycosylase is sought.

Identification of Local Conformational Similarity in Structurally Variable Regions of Homologous Proteins Using Protein Blocks

Structure comparison tools can be used to align related protein structures to identify structurally conserved and variable regions and to infer functional and evolutionary relationships. While the conserved regions often superimpose well, the variable regions appear non superimposable. Differences in homologous protein structures are thought to be due to evolutionary plasticity to accommodate diverged sequences during evolution. One of the kinds of differences between 3-D structures of homologous proteins is rigid body displacement. A glaring example is not well superimposed equivalent regions of homologous proteins corresponding to a-helical conformation with different spatial orientations. In a rigid body superimposition, these regions would appear variable although they may contain local similarity. Also, due to high spatial deviation in the variable region, one-to-one correspondence at the residue level cannot be determined accurately. Another kind of difference is conformational variability and the most common example is topologically equivalent loops of two homologues but with different conformations. In the current study, we present a refined view of the ``structurally variable'' regions which may contain local similarity obscured in global alignment of homologous protein structures. As structural alphabet is able to describe local structures of proteins precisely through Protein Blocks approach, conformational similarity has been identified in a substantial number of `variable' regions in a large data set of protein structural alignments; optimal residue-residue equivalences could be achieved on the basis of Protein Blocks which led to improved local alignments. Also, through an example, we have demonstrated how the additional information on local backbone structures through protein blocks can aid in comparative modeling of a loop region. In addition, understanding on sequence-structure relationships can be enhanced through our approach. This has been illustrated through examples where the equivalent regions in homologous protein structures share sequence similarity to varied extent but do not preserve local structure.

Contraceptive vaccines: current status and problems in mass application

Progress in the development of contraceptive vaccines for males and females is reviewed. Based on the criteria which need to be met with, none of the proposed candidate antigens meets the requirements for use as a contraceptive vaccine for human application. One of the major problems is the need for periodic injections to maintain required titre and use of an alternate method until effective titres are obtained. Some of the problems associated with active immunization approach can be overcome by the use of preformed, highly specific, potent antibodies. Some progress has been achieved in this direction by the use of humanized single chain monoclonal antibodies to human chorionic gonadotropin.

Abrasive Jet Machining - Process variables and current applications

brusive Jet Machining (AJM) or Micro Blast Machining is a non-traditional machining process, wherein material removal is effected by the erosive action of a high velocity jet of a gas, carrying fine-grained abrasive particles, impacting the work surface. The AJM process differs from conventional sand blasting in that the abrasive is much finer and the process parameters and cutting action are carefully controlled. The process is particularly suitable to cut intricate shapes in hard and brittle materials which are sensitive to heat and have a tendency to chip easily. In other words, AJM can handle virtually any hard or brittle material. Already the process has found its ways Into dozens of applications; sometimes replacing conventional alternatives often doing jobs that could not be done in any other way. This paper reviews the current status of this non-conventional machining process and discusses the unique advantages and possible applications.

Bloch-Nordsieck thermometers: One-loop exponentiation in finite temperature QED

We study the scattering of hard external particles in a heat bath in a real-time formalism for finite temperature QED. We investigate the distribution of the 4-momentum difference of initial and final hard particles in a fully covariant manner when the scale of the process, Q, is much larger than the temperature, T. Our computations are valid for all T subject to this constraint. We exponentiate the leading infra-red term at one-loop order through a resummation of soft (thermal) photon emissions and absorptions. For T > 0, we find that tensor structures arise which are not present at T = 0. These carry thermal signatures. As a result, external particles can serve as thermometers introduced into the heat bath. We investigate the phase space origin of log (Q/M) and log (Q/T) terms.

Catalytic current polarographic determination of traces of titanium in water after preconcentration by coflotation

A new method is reported for the determination of trace levels of Ti(IV) in water by coflotation and polargraphy. Ti(IV) is preconcentrated and separated by coflotation using aluminium hydroxide as coprecipitant and sodium oleate as surfactant. Polarographic determination of titanium content in the froth is based on the catalytic wave of Ti(IV) in the presence of chlorate and oxalate. The effect of various cations and anions on the flotation and determination of titanium has been investigated. The method has been applied to estimation of titanium in natural fresh water samples.

Enhanced sensitivity for the differential pulse polarographic determination of molybdenum(VI) based on adsorption catalytic current

A differential pulse polarographic (DPP) method based on the adsorption catalytic current in a medium containing chlorate and 8-hydroxyquinoline (oxine) is suggested for the determination of molybdenum(VI). Experimental conditions such as pH and the composition of supporting electrolyte have been optimized to get a linear calibration graph at trace levels of Mo(VI). The sensitivity for molybdenum can be considerably enhanced by this method. The influence of possible interferences on the catalytic current has been investigated. The sensitivity of the method is compared with those obtained for other DPP methods for molybdenum. A detection limit of 1.0 x 10(-8) mol/L has been found.

Theory of electron transfer processes via chemisorbed intermediates: Part II. Current-potential characteristics

Current-potential characteristics are obtained numerically for a lone-adsorbate-mediated anodic charge transfer at the electrode-solution interface. An increase in the overpotential leads to the appearance of maxima in the anodic current-potential plots instead of the extended activationless region (i.e. a saturation current at large positive overpotentials) predicted by the direct heterogeneous outer-sphere anodic charge transfer process. A detailed analysis of the dependence of current-potential profiles and other kinetic parameters on various system parameters is also presented.

A profile of adenosine triphosphate

An attempt is made to draw a profile of adenosine triphosphate (ATP) and to project its many actions. The amazing versatility of its participation in a number of synthetic reactions lies in the oligophosphate structure. Many proteins that use ATP have conserved binding 'P-loop' but this gives no clue what makes it so special. The energy transducing reactions leading to synthesis of the terminal phosphodiester had at least three strategies. Of these, direct dehydration and transfer of inorganic phosphate using respiratory energy operate through mechano-coupling in a multisubunit protein. This tripartite, knob-stalk-base structure provides a novel mechanism of rotational catalysis and the tiniest molecular motor, All the reactions occur in concert with no sign of energized chemical intermediate. With the new knowledge on the crystal structure of F-1-ATPase, proton translocation needs a relook. An alternative perspective is emerging on energy being received and stored in polypeptide structure by breaking hydrogen bonds. Membrane serves the purpose of mobilizing the constituent proteins and also as a potential energy carrier of proteins with little loss of energy.

A Rotor Flux Estimation During Zero and Active Vector Periods Using Current Error Space Vector From a Hysteresis Controller for a Sensorless Vector Control of IM Drive

This paper proposes a sensorless vector control scheme for general-purpose induction motor drives using the current error space phasor-based hysteresis controller. In this paper, a new technique for sensorless operation is developed to estimate rotor voltage and hence rotor flux position using the stator current error during zero-voltage space vectors. It gives a comparable performance with the vector control drive using sensors especially at a very low speed of operation (less than 1 Hz). Since no voltage sensing is made, the dead-time effect and loss of accuracy in voltage sensing at low speed are avoided here, with the inherent advantages of the current error space phasor-based hysteresis controller. However, appropriate device on-state drops are compensated to achieve a steady-state operation up to less than 1 Hz. Moreover, using a parabolic boundary for current error, the switching frequency of the inverter can be maintained constant for the entire operating speed range. Simple sigma L-s estimation is proposed, and the parameter sensitivity of the control scheme to changes in stator resistance, R-s is also investigated in this paper. Extensive experimental results are shown at speeds less than 1 Hz to verify the proposed concept. The same control scheme is further extended from less than 1 Hz to rated 50 Hz six-step operation of the inverter. Here, the magnetic saturation is ignored in the control scheme.

Effect of Constant and Cyclic Current Stressing on the Evolution of Intermetallic Compound Layers

In this paper the effects of constant and cyclic power loads on the evolution of interfacial reaction layers in lead-free solder interconnections are presented. Firstly, the differences in the growth behavior of intermetallic compound (IMC) layers at the cathode and anode sides of the interconnections are rationalized. This is done by considering the changes in the intrinsic fluxes of elements owing to electromigration as well as taking into account the fact that the growth of Cu3Sn and Cu6Sn5 are coupled via interfacial reactions. In this way, better understanding of the effect of electron flux on the growth of each individual layer in the Cu-Sn system can be achieved. Secondly, it is shown that there is a distinct difference between steady-state current stressing (constant current, constant temperature) and power cycling with alternating on- and off-cycle periods (accompanied by a change of temperature). The reasons behind the observed differences are subsequently discussed. Finally, special care is taken to ensure that the current densities are chosen in such a way that there is no risk for even partial melting of the solder interconnections.

Influence of the ferromagnetic layer on the pair breaking and low alternating current field magnetic response in superconductor/ferromagnet bilayer

We investigate the influence of the ferromagnetic layer on the magnetic and transport properties of YBa2Cu3O7-delta in YBa2Cu3O7-delta (YBCO)/La0.7Sr0.3MnO3 (LSMO) bilayers. The temperature dependent dc magnetization study reveals the presence of magnetic anisotropy in YBCO/LSMO bilayer as compared to the pure YBCO layer. The ac susceptibility study on YBCO/LSMO bilayers reveals stronger pinning and the temperature dependent critical current is found to be less prone to temperature. Besides, the current (I) dependent electrical transport studies on YBCO/LSMO exhibit a significant reduction in the superconducting T-c with increase in I and it follows I-2/3 dependence in accord with the pair breaking effect. The higher reduction of superconducting T-c in YBCO/LSMO is believed to be due to the enhanced pair-breaking induced by the spin polarized carriers being injected into the superconductor. (C) 2011 American Institute of Physics. doi: 10.1063/1.3560029]

Synthetic aperture radar: A focus on current problems

Synthetic aperture radar (SAR) is a powerful tool for mapping and remote sensing. The theory and operation of SAR have seen a period of intense activity in recent years. This paper attempts to review some of the more advanced topics studied in connection with modern SAR systems based on digital processing. Following a brief review of the principles involved in the operation of SAR, attention is focussed on special topics such as advanced SAR modelling and focussing techniques, in particular clutterlock and autofocus, Doppler centroid (DC) estimation methods involving seismic migration technique, moving target imaging, bistatic radar imaging, effects of system nonlinearities, etc.

Structures of the catalytic site mutants D99A and H48Q and the calcium-loop mutant D49E of phospholipase A(2)

Crystal structures of the active-site mutants D99A and H48Q and the calcium-loop mutant D49E of bovine phospholipase A(2) have been determined at around 1.9 Angstrom resolution. The D99A mutant is isomorphous to the orthorhombic recombinant enzyme, space group P2(1)2(1)2(1), The H48Q and the calcium-loop mutant D49E are isomorphous to the trigonal recombinant enzyme, space group P3(1)21, The two active-site mutants show no major structural perturbations. The structural water is absent in D99A and, therefore, the hydrogen-bonding scheme is changed. In H48Q, the catalytic water is present and hydrogen bonded to Gln48 N, but the second water found in native His48 is absent. In the calcium-loop mutant D49E, the two water molecules forming the pentagonal bipyramid around calcium are absent and only one O atom of the Glu49 carboxylate group is coordinated to calcium, resulting in only four ligands.

A current error space vector based hysteresis controller with constant switching frequency and simple online boundary computation for VSI fed IM drive

This paper proposes a simple current error space vector based hysteresis controller for two-level inverter fed Induction Motor (IM) drives. This proposed hysteresis controller retains all advantages of conventional current error space vector based hysteresis controllers like fast dynamic response, simple to implement, adjacent voltage vector switching etc. The additional advantage of this proposed hysteresis controller is that it gives a phase voltage frequency spectrum exactly similar to that of a constant switching frequency space vector pulse width modulated (SVPWM) inverter. In this proposed hysteresis controller the boundary is computed online using estimated stator voltages along alpha and beta axes thus completely eliminating look up tables used for obtaining parabolic hysteresis boundary proposed in. The estimation of stator voltage is carried out using current errors along alpha and beta axes and steady state model of induction motor. The proposed scheme is simple and capable of taking inverter upto six step mode operation, if demanded by drive system. The proposed hysteresis controller based inverter fed drive scheme is simulated extensively using SIMULINK toolbox of MATLAB for steady state and transient performance. The experimental verification for steady state performance of the proposed scheme is carried out on a 3.7kW IM.