Evolution of sequence specificity in a restriction endonuclease by a point mutation

Restriction endonucleases (REases) protect bacteria from invading foreign DNAs and are endowed with exquisite sequence specificity. REases have originated from the ancestral proteins and evolved new sequence specificities by genetic recombination, gene duplication, replication slippage, and transpositional events. They are also speculated to have evolved from nonspecific endonucleases, attaining a high degree of sequence specificity through point mutations. We describe here an example of generation of exquisitely site-specific REase from a highly-promiscuous one by a single point mutation.

Dynamics after a sweep through a quantum critical point

The coherent quantum evolution of a one-dimensional many-particle system after slowly sweeping the Hamiltonian through a critical point is studied using a generalized quantum Ising model containing both integrable and nonintegrable regimes. It is known from previous work that universal power laws of the sweep rate appear in such quantities as the mean number of excitations created by the sweep. Several other phenomena are found that are not reflected by such averages: there are two different scaling behaviors of the entanglement entropy and a relaxation that is power law in time rather than exponential. The final state of evolution after the quench is not characterized by any effective temperature, and the Loschmidt echo converges algebraically for long times, with cusplike singularities in the integrable case that are dynamically broadened by nonintegrable perturbations.

Average-Delay Optimal Policies for the Point-to-Point Channel

Average-delay optimal scheduflng of messages arriving to the transmitter of a point-to-point channel is considered in this paper. We consider a discrete time batch-arrival batch-service queueing model for the communication scheme, with service time that may be a function of batch size. The question of delay optimality is addressed within the semi-Markov decision-theoretic framework. Approximations to the average-delay optimal policy are obtained.

New insights from a fixed-point analysis of single cell IEEE 802.11 WLANs

We study a fixed-point formalization of the well-known analysis of Bianchi. We provide a significant simplification and generalization of the analysis. In this more general framework, the fixed-point solution and performance measures resulting from it are studied. Uniqueness of the fixed point is established. Simple and general throughput formulas are provided. It is shown that the throughput of any flow will be bounded by the one with the smallest transmission rate. The aggregate throughput is bounded by the reciprocal of the harmonic mean of the transmission rates. In an asymptotic regime with a large number of nodes, explicit formulas for the collision probability, the aggregate attempt rate, and the aggregate throughput are provided. The results from the analysis are compared with ns2 simulations and also with an exact Markov model of the backoff process. It is shown how the saturated network analysis can be used to obtain TCP transfer throughputs in some cases.

Tendency toward crossover of the effective susceptibility exponent from its doubled Ising value to its doubled mean-field value near a double critical point

The critical behavior of osmotic susceptibility in an aqueous electrolyte mixture 1-propanol (1P)+water (W)+potassium chloride is reported. This mixture exhibits re-entrant phase transitions and has a nearly parabolic critical line with its apex representing a double critical point (DCP). The behavior of the susceptibility exponent is deduced from static light-scattering measurements, on approaching the lower critical solution temperatures (TL’s) along different experimental paths (by varying t) in the one-phase region. The light-scattering data analysis substantiates the existence of a nonmonotonic crossover behavior of the susceptibility exponent in this mixture. For the TL far away from the DCP, the effective susceptibility exponent γeff as a function of t displays a nonmonotonic crossover from its single limit three-dimensional (3D)-Ising value ( ∼ 1.24) toward its mean-field value with increase in t. While for that closest to the DCP, γeff displays a sharp, nonmonotonic crossover from its nearly doubled 3D-Ising value toward its nearly doubled mean-field value with increase in t. The renormalized Ising regime extends over a relatively larger t range for the TL closest to the DCP, and a trend toward shrinkage in the renormalized Ising regime is observed as TL shifts away from the DCP. Nevertheless, the crossover to the mean-field limit extends well beyond t>10−2 for the TL’s studied. The observed crossover behavior is attributed to the presence of strong ion-induced clustering in this mixture, as revealed by various structure probing techniques. As far as the critical behavior in complex or associating mixtures with special critical points (like the DCP) is concerned, our results indicate that the influence of the DCP on the critical behavior must be taken into account not only on the renormalization of the critical exponent but also on the range of the Ising regime, which can shrink with decrease in the influence of the DCP and with the extent of structuring in the system. The utility of the field variable tUL in analyzing re-entrant phase transitions is demonstrated. The effective susceptibility exponent as a function of tUL displays a nonmonotonic crossover from its asymptotic 3D-Ising value toward a value slightly lower than its nonasymptotic mean-field value of 1. This behavior in the nonasymptotic, high tUL region is interpreted in terms of the possibility of a nonmonotonic crossover to the mean-field value from lower values, as foreseen earlier in micellar systems.

Neutral-point balancing of neutral-point-clamped three-level inverter with a front end switched rectifier DC source for the full modulationn range

A switched rectifier DC voltage source three-level neutral-point-clamped (NPC) converter topology is proposed here to alleviate the inverter from capacitor voltage balancing in three-level drive systems. The proposed configuration requires only one DC link with a voltage of half of that needed in a conventional NPC inverter. To obtain a rated DC link voltage, the rectifier DC source is alternately connected in parallel to one of the two series capacitors using two switches and two diodes with device voltage ratings of half the total DC bus voltage. The frequency at which the voltage source is switched is independent of the inverter and will not affect its operation since the switched voltage source in this configuration balances the capacitors automatically. The proposed configuration can also be used as a conventional two-level inverter in the lower modulation index range, thereby increasing the reliability of the drivesystem. A space-vector-based PWM scheme is used to verify this proposed topology on a laboratory system.

Suitability of a point-contact SAW-based stiffness transducer for biomedical applications

Methods of diagnosis in Biomedical applications can be broadly divided into contact and non-contact based methods. So far, ultrasound based methods have been found to be most favorable for non-contact, non-invasive diagnosis, especially in the case of tissue stiffness analysis. We report here, the fabrication and characterization details of a new contact based transducer system for qualitative determination of the stiffnesses of non-piezoelectric substrates using the phenomenon of Surface Acoustic Waves (SAW). Preliminary trials to study the functionality of this system were carried out on various metallic and non-metallic substrates, and the results were found to be satisfactory. To confirm the suitability of this system for biomedical applications, similar trials have been conducted on tissue mimicking phantoms with varying degrees of stiffness.

Unsteady mixed convection on the stagnation-point flow adjacent to a vertical plate with a magnetic field

An analysis is performed to study the unsteady combined forced and free convection flow (mixed convection flow) of a viscous incompressible electrically conducting fluid in the vicinity of an axisymmetric stagnation point adjacent to a heated vertical surface. The unsteadiness in the flow and temperature fields is due to the free stream velocity, which varies arbitrarily with time. Both constant wall temperature and constant heat flux conditions are considered in this analysis. By using suitable transformations, the Navier-Stokes and energy equations with four independent variables (x, y, z, t) are reduced to a system of partial differential equations with two independent variables (eta, tau). These transformations also uncouple the momentum and energy equations resulting in a primary axisymmetric flow, in an energy equation dependent on the primary flow and in a buoyancy-induced secondary flow dependent on both primary flow and energy. The resulting system of partial differential equations has been solved numerically by using both implicit finite-difference scheme and differential-difference method. An interesting result is that for a decelerating free stream velocity, flow reversal occurs in the primary flow after certain instant of time and the magnetic field delays or prevents the flow reversal. The surface heat transfer and the surface shear stress in the primary flow increase with the magnetic field, but the surface shear stress in the buoyancy-induced secondary flow decreases. Further the heat transfer increases with the Prandtl number, but the surface shear stress in the secondary flow decreases.

Some experimental observations on the use of activated sludge as fertilizer for fish culture

Experiments were conducted in cement cisterns to find out the effect of adding different dosages of activated sludge on fish growth and plankton production. Three dosages of sludge,viz., 62·5 gm., 125 gm. and 250 gm. per 240 litres of water were used. Fingerlings ofCyprinus carpio, Cirrhina mrigala andCatla catla responded positively,C. mrigala showing maximum growth. The results indicate that the sludge has a direct influence on increasing growth of fish and production of plankton due to the release of nutrients into the water. The increase in plankton content stops after about 30 days. When greater quantities of sludge were added in the cisterns, fish mortality took place.

Reversible polyelectrolyte capsules as carriers for protein delivery

A reversible drug delivery system based on spontaneous deposition of a model protein into preformed microcapsules has been demonstrated for protein delivery applications. Layer-by-Layer assembly of poly(allylamine hydrochloride) (PAH) and poly(methacrylic acid) (PMA) onto polystyrene sulfonate (PSS) doped CaCO3 particles, followed by core removal yielded intact hollow microcapsules having a unique property to induce spontaneous deposition of bovine serum albumin (BSA) at pH below its isoelectric point of 4.8, where it was positively charged. These capsules showed reversible pH dependent open and closed states to fluorescence labeled dextran (FITC-Dextran) and BSA (FITC-BSA). The loading capacity of BSA increased from 9.1 x 10(7) to 2.03 x 10(8) molecules per capsule with decrease in pH from 4.5 to 3.The loading of BSA-FITC was observed by confocal laser scanning microscopy (CLSM), which showed homogeneous distribution of protein inside the capsule. Efficient loading of BSA was further confirmed by atomic force microscopy (AFM) and scanning electron microscopy (SEM).The interior capsule concentration was as high as 209 times the feeding concentration when the feeding concentration was increased from 1 to 10 mg/ml. The deposition was initially controlled by spontaneous loading mechanism at lower BSA concentration followed by diffusion controlled loading at higher concentration; which decreased the loading efficiency from 35% to 7%. Circular dichroism (CD) measurements and Fourier transform infrared spectroscopy (FTIR) confirmed that there was no significant change in conformation of released BSA in comparison with native BSA. The release was initially burst in the first 0.5 h and sustained up to 5 h. The hollow capsules were found to be biocompatible with mouse embryonic fibroblast (MEF) cells during in vitro cell culture studies. Thus these pH sensitive polyelectrolyte microcapsules may offer a promising delivery system for water soluble proteins and peptides. (C) 2010 Elsevier B.V. All rights reserved.

Microbial Production Of Amino-Acids .3. Nutritional Studies And Effects Of Organic Growth Promoters And Thiamine On Dl-Alanine Fermentation By Arthrobacter Strain C19d

The study of the nutritional requirements of Arthrobacter strain C19d which accumulates alanine in large amounts in the culture medium. 1evealed that the organism needs thiamine for its growth. A Iso the alanine accumulation by this strain was found to be related to thiamine concentration in the medium. The optimum concentration of thiamine for alanine accumulation (20 tJ.g/mJ) Was also optimum for the growth of the organism indicating thereby that alanine accumulation by this strain is a growth associated process rather than far removed from it. Among the various growth promoters tried yeast extract was found to be superior from the point of view of alanine yield and it wa5 also superior to giving thiamine alone in the medium. A concentration of 0.02% yeast extract was found to be optimum for alanine occumulation.

Folding a Polymer via Two-Point Interaction with an External Folding Agent: Use of H-Bonding and Charge-Transfer Interactions

A polymer containing electron-rich aromatic donors (1,5-dialkoxynaphthalene (DAN)) was coerced into a folded state by an external folding agent that contained an electron-deficient aromatic acceptor (pyromellitic diimide (PM)) unit. The donor-containing polymer was designed to carry a tertiary amine moiety in the linking segment, which served as an H-bonding site for reinforcing the interaction with the acceptor containing folding agent that also bore a carboxylic acid group. The H-bonding interaction of the carboxylic acid and the tertiary amine brings the PDI unit between two adjacent DAN units along the polymer backbone to induce charge-transfer (C-T) interactions, and this in turn causes the polymer chain to form a pleated structure. Evidence for the formation of such a pleated structure was obtained from NMR titration studies and also by monitoring the C-T band in their UV-visible spectra. By varying the length of the segment that links the PDI acceptor to the carboxylic acid group, we showed that the most effective folding agent was the one that had a single carbon spacer, as evident from the highest value of the association constant. Control experiments with propionic acid clearly demonstrated the importance of the additional C-T interactions for venerating the folded structures. Further, solution viscosity measurements in the presence of varying amounts of the folding agent revealed a gradual stiffening of the chain in the case of the PDI carrying carboxylic acid, whereas no such affect was seen in the case of simple propionic acid. These observations were supported by D FT calculations of the interactions of a dimeric model of the polymer with the various folding agents; here too the stability of the complex was seen to be highest in the case of the single carbon spacer.

Note: Dynamic point spread function for single and multiphoton fluorescence microscopy

We propose and demonstrate a dynamic point spread function (PSF) for single and multiphoton fluorescence microscopy. The goal is to generate a PSF whose shape and size can be maneuvered from highly localized to elongated one, thereby allowing shallow-to-depth excitation capability during active imaging. The PSF is obtained by utilizing specially designed spatial filter and dynamically altering the filter parameters. We predict potential applications in nanobioimaging and fluorescence microscopy.