Substrate specificity plays an important role in uncoupling the catalytic and scaffolding activities of rat testis DNA topoisomerase IIalpha

Topoisomerase II (topo II) is a dyadic enzyme found in all eukaryotic cells. Topo II is involved in a number of cellular processes related to DNA metabolism, including DNA replication, recombination and the maintenance of genomic stability. We discovered a correlation between the development of postnatal testis and increased binding of topo IIalpha to the chromatin fraction. We used this observation to characterize DNA-binding specificity and catalytic properties of purified testis topo IIalpha. The results indicate that topo IIalpha binds a substrate containing the preferred site with greater affinity and, consequently, catalyzes the conversion of form I to form IV DNA more efficiently in contrast to substrates lacking such a site. Interestingly, topo IIalpha displayed high-affinity and cooperativity in binding to the scaffold associated region. In contrast to the preferred site, however, high-affinity binding of topo IIalpha to the scaffold-associated region failed to result in enhanced catalytic activity. Intriguingly, competition assays involving scaffold-associated region revealed an additional DNA-binding site within the dyadic topo IIalpha. These results implicate a dual role for topo IIalpha in vivo consistent with the notion that its sequestration to the chromatin might play a role in chromosome condensation and decondensation during spermatogenesis.

Adsorption of Nitrogen on Activated Carbon-Refit of Experimental Data and Derivation of Properties Required for Design of Equipment

Volumetric method based adsorption measurements of nitrogen on two specimens of activated carbon (Fluka and Sarabhai) reported by us are refitted to two popular isotherms, namely, Dubunin−Astakhov (D−A) and Toth, in light of improved fitting methods derived recently. Those isotherms have been used to derive other data of relevance in design of engineering equipment such as the concentration dependence of heat of adsorption and Henry’s law coefficients. The present fits provide a better representation of experimental measurements than before because the temperature dependence of adsorbed phase volume and structural heterogeneity of micropore distribution have been accounted for in the D−A equation. A new correlation to the Toth equation is a further contribution. The heat of adsorption in the limiting uptake condition is correlated with the Henry’s law coefficients at the near zero uptake condition.

Design, Synthesis, and DNA Binding Properties of Photoisomerizable Azobenzene−Distamycin Conjugates: An Experimental and Computational Study

Here, we present the synthesis, photochemical, and DNA binding properties of three photoisomerizable azobenzene−distamycin conjugates in which two distamycin units were linked via electron-rich alkoxy or electron-withdrawing carboxamido moieties with the azobenzene core. Like parent distamycin A, these molecules also demonstrated AT-specific DNA binding. Duplex DNA binding abilities of these conjugates were found to depend upon the nature and length of the spacer, the location of protonatable residues, and the isomeric state of the conjugate. The changes in the duplex DNA binding efficiency of the individual conjugates in the dark and with their respective photoirradiated forms were examined by circular dichroism, thermal denaturation of DNA, and Hoechst displacement assay with poly[d(A-T).d(T-A)] DNA in 150 mM NaCl buffer. Computational structural analyses of the uncomplexed ligands using ab initio HF and MP2 theory and molecular docking studies involving the conjugates with duplex d[(GC(AT)10CG)]2 DNA were performed to rationalize the nature of binding of these conjugates.

Investigation of inter-ion interactions in N,N,N',N'-tetramethylethylenediammonium dithiocyanate via experimental and theoretical charge density studies

The crystal structure of the N,N,N',N'-tetramethylethylenediammonium dithiocyanate salt has been examined by experimental charge density studies from high-resolution X-ray diffraction data. The corresponding results are compared with multipole refinements, using theoretical structure factors obtained from a periodic density functional theory calculation at the B3LYP level with a 6-31G** basis set. The salt crystallizes in space group P (1) over bar and contains only a single ion pair with an inversion center in the cation. The salt has thus one unique classical N+-H center dot center dot center dot(NCS)(-) hydrogen bond but also has six other weaker interactions: four C-H center dot center dot center dot S, one C-H center dot center dot center dot N, and one C-H center dot center dot center dot C-pi. The nature of all these interactions has been examined topologically using Bader's quantum theory of "atoms in molecules" and all eight of the Koch-Popelier criteria. The experimental and theoretical approaches agree well and both show that the inter-ion interactions, even in this simplest of systems, play an integrated and complex role in the packing of the ions in the crystal. Electrostatic potential maps are derived from experimental charge densities. This is the first time such a system has been examined in detail by these methods.

Experimental study on shrinkage behaviour and prediction of shrinkage magnitudes of residual soils

The present study examines the shrinkage behaviour of residually derived black cotton (BC) soil and red soil compacted specimens that were subjected to air-drying from the swollen state. The soil specimens were compacted at varying dry density and moisture contents to simulate varied field conditions. The void ratio and moisture content of the swollen specimens were monitored during the drying process and relationship between them is analyzed. Shrinkage is represented as reduction in void ratio with decrease in water content of soil specimens. It is found to occur in three distinct stages. Total shrinkage magnitude depends on the type of clay mineral present. Variation in compaction conditions effect marginally total shrinkage magnitudes of BC soil specimens but have relatively more effect on red soil specimens. A linear relation is obtained between total shrinkage magnitude and volumetric water content of soil specimens in swollen state and can be used to predict the shrinkage magnitude of soils.

Experimental implementation of a three qubit quantum game with corrupt source using nuclear magnetic resonance quantum information processor

In a three player quantum `Dilemma' game each player takes independent decisions to maximize his/her individual gain. The optimal strategy in the quantum version of this game has a higher payoff compared to its classical counterpart. However, this advantage is lost if the initial qubits provided to the players are from a noisy source. We have experimentally implemented the three player quantum version of the `Dilemma' game as described by Johnson, [N.F. Johnson, Phys. Rev. A 63 (2001) 020302(R)] using nuclear magnetic resonance quantum information processor and have experimentally verified that the payoff of the quantum game for various levels of corruption matches the theoretical payoff. (c) 2007 Elsevier Inc. All rights reserved.

Experimental Demonstration of H{infty} Control based Active Vibration Suppression in Composite Fin-tip of Aircraft using Optimally Placed Piezoelectric Patch Actuators

The goal of this study is the multi-mode structural vibration control in the composite fin-tip of an aircraft. Structural model of the composite fin-tip with surface bonded piezoelectric actuators is developed using the finite element method. The finite element model is updated experimentally to reflect the natural frequencies and mode shapes accurately. A model order reduction technique is employed for reducing the finite element structural matrices before developing the controller. Particle swarm based evolutionary optimization technique is used for optimal placement of piezoelectric patch actuators and accelerometer sensors to suppress vibration. H{infty} based active vibration controllers are designed directly in the discrete domain and implemented using dSpace® (DS-1005) electronic signal processing boards. Significant vibration suppression in the multiple bending modes of interest is experimentally demonstrated for sinusoidal and band limited white noise forcing functions.

Experimental studies on a two stage pulse tube cryocooler reaching 2.5K

A two stage Pulse Tube Cryocooler (PTC) is designed and fabricated which reaches a no-load temperature of 2.5K in the second stage and similar to 60 K in the first stage respectively. The system provides a cooling power of similar to 250 mW at 5K in the second stage. Stainless steel meshes (size 200) and lead (Pb) granules are used as the first stage regenerator materials and combination of Pb with Er3Ni / HoCu2 are used as the second stage regenerator materials. The system operates at 1.6 Hz using a 6 kW water cooled helium compressor. Studies conducted by varying the dimensions of Pulse Tubes and regenerators show that the dimensions of the Pulse Tubes are more critical to the performance of the Cryocooler than those of the regenerators. Experimental studies show that the optimum volume ratios of Er3Ni to Pb and HoCu2 to Pb in the second stage regenerator should be 3:2 and 2:3 respectively for the best performance. Further, systems with HoCu2 performed better than those with Er3Ni. The theoretical analysis of the system has been carried out using a simple isothermal model. The experimentally measured cooling powers are in good agreement with the theoretical predictions.

Novel flutamide regulated genes in the rat ventral prostate: differential modulation of their expression by castration and flutamide treatments

Aim: To identify flutamide regulated genes in the rat ventral prostate. Methods: Total RNA from ventral prostates control and flutamide treated rats were isolated. Differentially expressed transcripts were identified using display reverse transcriptase polymerase chain reaction. The effect of castration on the expression of regulated transcripts was studied. Results: We have identified beta 2-microglobulin, cytoplasmic FMR1 protein 2 and pumilio 1 as flutamide induced and spermine binding protein and ribophorin II as flutamide targets in the rat ventral prostate. Although flutamide treatment caused an induction of pumilio I mRNA, had no effect. Conclusion: Castration and flutamide treatments exert differential effects on gene expression. might also have direct AR independent effects, which might have implications in the emergence of androgen dent prostate cancer and the failure of flutamide therapy.

Detection of alpha(2u)-globulin and its bound putative pheromones in the preputial gland of the Indian commensal rat (Rattus rattus) using mass spectrometry

The role of pheromones and pheromone-binding proteins in the laboratory rat has been extensively investigated. However, we have previously reported that the preputial gland of the Indian commensal rat produces a variety of pheromonal molecules and preputial glands would seem to be the predominant source for pheromonal communication. The presence of pheromone-binding proteins has not yet been identified in the preputial gland of the Indian commensal rat; therefore, the experiments were designed to unravel the alpha(2u)-globulin (alpha 2u) and its bound volatiles in the commensal rat. Total preputial glandular proteins were first fractionated by sodium dodecyl sulfate/polyacrylamide gel electrophoresis (SDS-PAGE) and subsequently analyzed by mass spectrometry. Further, we purified alpha 2u and screened for the presence of bound pheromonal molecules with the aid of gas chromatography/mass spectrometry (GC/MS). A novel alpha 2u was identified with a high score and this protein has not been previously described as present in the preputial gland of Indian commensal rats.This novel alpha 2u was then characterized by tandem mass spectrometry (MS/MS). Peptides with m/z values of 969, 1192, 1303 and 1876 were further fragmented with the aid of MS/MS and generated de novo sequences which provided additional evidence for the presence of alpha 2u in the preputial gland. Finally, we identified the presence of farnesol 1 and 2 bound to alpha 2u. The present investigation confirms the presence of alpha 2u (18.54 kDa) in the preputial gland of the Indian commensal rat and identifies farnesol 1 and 2 as probably involved in chemo-communication by the Indian commensal rat.Copyright (C) 2010 John Wiley & Sons, Ltd.

Experimental and Theoretical Charge Density Analysis of Polymorphic Structures: The Case of Coumarin 314 Dye

Experimental charge density distributions in two known conformational polymorphs (orange and yellow) of coumarin 314 dye are analyzed based on multipole modeling of X-ray diffraction data collected at 100 K. The experimental results are compared with the charge densities derived from multipole modeling of theoretical structure factors obtained from periodic quantum calculation with density functional theory (DFT) method and B3LYP/6-31G(d,p) level of theory. The presence of disorder at the carbonyl oxygen atom of ethoxycarbonyl group in the yellow form, which was not identified earlier, is addressed here. The investigationof intermolecular interactions, based on Hirshfeld surface analysis and topological properties via quantum theory of atoms in molecule and total electrostatic interaction energies, revealed significant differences between the polymorphs. The differences of electrostatic nature in these two polymorphic forms were unveiled via construction of three-dimensional deformation electrostatic potential maps plotted over the molecular surfaces. The lattice energies evaluated from ab initio calculations on the two polymorphic forms indicate that the yellow form is likely to be the most favorable thermodynamically. The dipole moments derived from experimental and theoretical charge densities and also from Lorentz tensor approach are compared with the single-molecule dipole moments. In each case, the differences of dipole moments between the polymorphs are identified.

Accurate determination of interference in pin joints Pin-to-plate interference in experimental models of interference-fit joints is significantly overestimated by direct physical measurements, but it can be accurately determined by a simple photoelastic method

Suitable pin-to-hole interference can significantly increase the fatigue life of a pin joint. In practical design, the initial stresses due to interference are high and they are proportional to the effective interference. In experimental studies on such joints, difficulties have been experienced in estimating the interference accurately from physical measurements of pin and hole diameters. A simple photoelastic method has been developed to determine the effective interference to a high degree of accuracy. This paper presents the method and reports illustrative data from a successful application thereof.

A generalized mathematical theory and experimental verification of proportional notches

A theory and generalized synthesis procedure is advocated for the design of weir notches and orifice-notches having a base in any given shape, to a depth a, such that the discharge through it is proportional to any singular monotonically-increasing function of the depth of flow measured above a certain datum. The problem is reduced to finding an exact solution of a Volterra integral equation in Abel form. The maximization of the depth of the datum below the crest of the notch is investigated. Proof is given that for a weir notch made out of one continuous curve, and for a flow proportional to the mth power of the head, it is impossible to bring the datum lower than (2m − 1)a below the crest of the notch. A new concept of an orifice-notch, having discontinuity in the curve and a division of flow into two distinct portions, is presented. The division of flow is shown to have a beneficial effect in reducing the datum below (2m − 1)a from the crest of the weir and still maintaining the proportionality of the flow. Experimental proof with one such orifice-notch is found to have a constant coefficient of discharge of 0.625. The importance of this analysis in the design of grit chambers is emphasized.

A semi-experimental approach to plane problems in elasticity

A semi-experimental approach to solve two-dimensional problems in elasticity is given. The method has been applied to two problems, (i) a square deep beam, and (ii) a bridge pier with a sloping boundary. For the first problem sufficient analytical results are available and hence the accuracy of the method can be verified. Then the method has been extended to the second problem for which sufficient results are not available.