Determining the DNA stability parameters for the breathing dynamics of heterogeneous DNA by stochastic optimization

We suggest that the thermodynamic stability parameters (nearest neighbor stacking and hydrogen bonding free energies) of double-stranded DNA molecules can be inferred reliably from time series of the size fluctuations (breathing) of local denaturation zones (bubbles). On the basis of the reconstructed bubble size distribution, this is achieved through stochastic optimization of the free energies in terms of simulated annealing. In particular, it is shown that even noisy time series allow the identification of the stability parameters at remarkable accuracy. This method will be useful to obtain the DNA stacking and hydrogen bonding free energies from single bubble breathing assays rather than equilibrium data.     

Thermostability of Cromobacterium viscosum lipase in AOT/isooctane reverse micelle

The thermostability of Cromobacterium viscosum lipase (EC 3.1.1.3) entrapped in AOT (sodium bis-[2-ethylhexyl] sulfosuccinate) reverse micelles was increased by the addition of short-chain polyethylene glycol (PEG 400). Two different approaches were considered: (1) the determination of half-life time and (2) the mechanistic analysis of deactivation kinetics. The half-life of lipase entrapped in AOT/isooctane reverse micelles with PEG 400 at 60 degrees C was 28 h, ninefold higher than that in reverse micelles without PEG 400. The lipase entrapped in both reverse micellar systems followed a series-type deactivation mechanism involving two first-order steps. The deactivation constant for the first step at 60 degrees C in PEG containing reverse micelles was 0.055 h!1, 11-fold lower than that in reverse micelles without PEG, whereas it remained almost constant for the second step. The inactivation energy of the lipase entrapped in reverse micelles with and without PEG 400 was 88.12 and 21.97 kJ/mol, respectively.     

A rare ferromagnetically coupled asymmetric doubly azido bridged copper(II) dimer with an N,N, O donor Schiff base

A new end-to-end (EE) doubly azido bridged dinuclear complex [Cu₂L₂(μ_1,3-N₃)₂] (1) [where L = (E)-4-(2-(dimethylamino)ethylimino)-1,1,1-trifluoropentan-2-one)] has been synthesized and characterized by elemental and spectroscopic techniques. Single crystal X-ray diffraction analysis reveals that the dimeric complex possesses a center of inversion. Each copper atom in 1 is in a distorted square pyramidal geometry with a CuN₄O chromophore as revealed from the τ value, 0.19. The four basal positions are occupied by two imine N and one keto O atom of the Schiff base and one N atom from the azide anion. Another N atom from a coordinated azide occupies the apical position. Temperature dependent magnetic susceptibility of 1 was fitted using the Bleaney–Bowers expression which led to the parameters J = 13.6 cm⁻¹ and R = 3.4 × 10⁻⁵. It indicates a ferromagnetic interaction through the double azido bridges connecting the individual copper Schiff base units.     

Effect of the Pretreatment of Lipase with Organic Solvents on its Conformation and Activity in Reverse Micelles

The activity and conformation of Chromobacterium viscosum lipase-pretreated with various organic solvents were investigated. The pretreatment of lipase led to a substantial increase of enzyme activity in AOT (sodium bis [2-ethyl -1-hexyl] sulfosuccinate)/isooctane/water reverse micelles. Among the organic solvents used, n-hexane was found to be most effective. It was observed that higher hexane content with shorter agitation time and vice versa had almost the same effect on the initial activity of lipase. The kinetic study showed that the Michaelis constant (K _m) and the substrate adsorption equilibrium constant (K _ad) were reduced by the pretreatment of lipase with hexane, whereas the change in the maximum reaction rate (V _max) was insignificant. The two spectroscopic techniques (Fluorescence spectra of lipase encapsulated in RMs and Fourier transform infrared [FTIR] spectra of lipase powders) were performed to detect possible conformational changes in the enzyme caused by the pretreatment. A correlation between the maximum fluorescence intensity and the activity of treated lipase was found as a function of agitation time. The FTIR spectrum of lipase showed a new shape peak corresponding to 1,500 cm⁻¹ as a result of pretreatment with organic solvents.     

Improvement of Seed Germination Rate,Agronomic Traits,Enzymatic Activity and Nutritional Composition of Bread Wheat (Triticum aestivum) Using Low-Frequency Glow Discharge Plasma

Plasma Chemistry and Plasma Processing - Plasma agriculture is an emerging field. In this report, we studied the effect of medium pressure (~?10 torr) low-frequency...     

Natural dualities for semilattice-based algebras

While every finite lattice-based algebra is dualisable, the same is not true of semilattice-based algebras. We show that a finite semilattice-based algebra is dualisable if all its operations are compatible with the semilattice operation. We also give examples of infinite semilattice-based algebras that are dualisable. In contrast, we present a general condition that guarantees the inherent non-dualisability of a finite semilattice-based algebra. We combine our results to characterise dualisability amongst the finite algebras in the classes of flat extensions of partial algebras and closure semilattices. Throughout, we emphasise the connection between the dualisability of an algebra and the residual character of the variety it generates. Presented by R. Willard.     

10,000-fold concentration increase in proteins in a cascade microchip using anionic ITP by a 3-D numerical simulation with experimental results

This paper describes both the experimental application and 3-D numerical simulation of isotachophoresis (ITP) in a 3.2 cm long "cascade" poly(methyl methacrylate) (PMMA) microfluidic chip. The microchip includes 10 × reductions in both the width and depth of the microchannel, which decreases the overall cross-sectional area by a factor of 100 between the inlet (cathode) and outlet (anode). A 3-D numerical simulation of ITP is outlined and is a first example of an ITP simulation in three dimensions. The 3-D numerical simulation uses COMSOL Multiphysics v4.0a to concentrate two generic proteins and monitor protein migration through the microchannel. In performing an ITP simulation on this microchip platform, we observe an increase in concentration by over a factor of more than 10,000 due to the combination of ITP stacking and the reduction in cross-sectional area. Two fluorescent proteins, green fluorescent protein and R-phycoerythrin, were used to experimentally visualize ITP through the fabricated microfluidic chip. The initial concentration of each protein in the sample was 1.995 μg/mL and, after preconcentration by ITP, the final concentrations of the two fluorescent proteins were 32.57 ± 3.63 and 22.81 ± 4.61 mg/mL, respectively. Thus, experimentally the two fluorescent proteins were concentrated by over a factor of 10,000 and show good qualitative agreement with our simulation results.     

An antiferromagnetically coupled hexanuclear copper(II) Schiff base complex containing phenoxo and dicyanamido bridges: Structural aspects and magnetic properties

A novel hexanuclear complex [{(CuL)₂Cu}₂(μ-dca)₂](ClO₄)₂·2L′(1) (where H₂L = (OH)C₆H₄C(CH₃)N(CH₂)₃NC(CH₃)C₆H₄(OH) or N,N′-bis(2-hydroxyacetophenone) propylenediimine and dca = N(CN)₂⁻ and L′ = 2-hydroxyacetophenone) has been synthesized and characterized by elemental analysis, UV-Vis, FT-IR spectroscopic and electrochemical methods. Single crystal X-ray structural characterization reveals a centrosymmetric nature of the complex unit, where the metal centers adopt distorted square-planar and distorted octahedral geometries. Structural analysis also reveals μ₂-phenoxo bridges between terminal and the central copper(II) centers of the asymmetric [(CuL)₂Cu(dca)] unit, the latter being interconnected to its symmetry related counterpart by double μ_1,5-dca bridges, leading to the hexanuclear complex ion [{(CuL)₂Cu}₂(μ-dca)₂]²⁺. Low temperature susceptibility measurements of 1 revealed the presence of strong antiferromagnetic coupling (2J = −407 cm⁻¹) between the copper(II) centers.