DNA looping and translocation provide an optimal cleavage mechanism for the type III restriction enzymes

EcoP15I is a type III restriction enzyme that requires two recognition sites in a defined orientation separated by up to 3.5 kbp to efficiently cleave DNA. The mechanism through which site- bound EcoP15I enzymes communicate between the two sites is unclear. Here, we use atomic force microscopy to study EcoP15I-DNA pre-cleavage complexes. From the number and size distribution of loops formed, we conclude that the loops observed do not result from translocation, but are instead formed by a contact between site- bound EcoP15I and a nonspecific region of DNA. This conclusion is confirmed by a theoretical polymer model. It is further shown that translocation must play some role, because when translocation is blocked by a Lac repressor protein, DNA cleavage is similarly blocked. On the basis of these results, we present a model for restriction by type III restriction enzymes and highlight the similarities between this and other classes of restriction enzymes.

Probing the existing magnetic phases in Pr0.5Ca0.5MnO3 (PCMO) nanowires and nanoparticles: magnetization and magneto-transport investigations

We show from conventional magnetization measurements that the charge order (CO) is completely suppressed in 10 nm Pr0.5Ca0.5MnO3 (PCMO 10) nanoparticles. Novel magnetization measurements, designed by a special high field measurement protocol, show that the dominant ground state magnetic phase is ferromagnetic-metallic (FM-M), which is an equilibrium phase, which coexists with the residual charge ordered anti-ferromagnetic phase (CO AFM) (an arrested phase) and exhibits the characteristic features of a `magnetic glassy state' at low temperatures. It is observed that there is a drastic reduction in the field required to induce the AFM to FM transition (similar to 5-6 T) compared to their bulk counterpart(similar to 27 T); this phase transition is of first order in nature, broad, irreversible and the coexisting phases are tunable with the cooling field. Temperature-dependent magneto-transport data indicate the occurrence of a size-induced insulator-metal transition (TM-I) and anomalous resistive hysteresis (R-H) loops, pointing out the presence of a mixture of the FM-M phase and AFM-I phase.

Relationship between annual rainfall and tree mortality in a tropical dry forest: Results of a 19-year study at Mudumalai, southern India

Variability in rainfall is known to be a major influence on the dynamics of tropical forests, especially rates and patterns of tree mortality. In tropical dry forests a number of contributing factors to tree mortality, including dry season fire and herbivory by large herbivorous mammals, could be related to rainfall patterns, while loss of water potential in trees during the dry season or a wet season drought could also result in enhanced rates of death. While tree mortality as influenced by severe drought has been examined in tropical wet forests there is insufficient understanding of this process in tropical dry forests. We examined these causal factors in relation to inter-annual differences in rainfall in causing tree mortality within a 50-ha Forest Dynamics Plot located in the tropical dry deciduous forests of Mudumalai, southern India, that has been monitored annually since 1988. Over a 19-year period (1988-2007) mean annual mortality rate of all stems >1 cm dbh was 6.9 +/- 4.6% (range = 1.5-17.5%); mortality rates broadly declined from the smaller to the larger size classes with the rates in stems >30 cm dbh being among the lowest recorded in tropical forest globally. Fire was the main agent of mortality in stems 1-5 cm dbh, elephant-herbivory in stems 5-10 cm dbh, and other natural causes in stems > 10 cm dbh. Elephant-related mortality did not show any relationship to rainfall. On the other hand, fire-related mortality was significantly negatively correlated to quantity of rainfall during the preceding year. Mortality due to other causes in the larger stem sizes was significantly negatively correlated to rainfall with a 2-3-year lag, suggesting that water deficit from mild or prolonged drought enhanced the risk of death but only with a time lag that was greater than similar lags in tree mortality observed in other forest types. In this respect, tropical dry forests growing in regions of high rainfall variability may have evolved greater resistance to rainfall deficit as compared to tropical moist or temperate forests but are still vulnerable to drought-related mortality.

Photobiomodulation by Low Power Laser Irradiation Involves Activation of Latent TGF-β1

Laser mediated stimulation of biological process was amongst its very first effects documented by Mester et al. but the ambiguous and tissue-cell context specific biological effects of laser radiation is now termed ‘Photobiomodulation’. We found many parallels between the reported biological effects of lasers and a multiface-ted growth factor, Transforming Growth Factor-β (TGF-β). This review outlines the interestingparallelsbetween the twofieldsand our rationalefor pursuingtheir potential causal correlation. We explored this correlation using an in vitro assay systems and a human clinical trial on healing wound extraction sockets that we reported in a recent publication. In conclusion we report that low power laser irradiation can activate latent TGF-β1 and β3 complexes and suggest that this might be one of the major modes of the photobiomodulatory effects of low power lasers.

Slim P‐E hysteresis loop and anomalous dielectric response in sol-gel derived antiferroelectric PbZrO3 thin films

Sol-gel derived PbZrO3 (PZ) thin films have been deposited on Pt(111)/Ti/SiO2/Si substrate and according to the pseudotetragonal symmetry of PZ, the relatively preferred (110)t oriented phase formation has been noticed. The room temperature P‐E hysteresis loops have been observed to be slim by nature. The slim hysteresis loops are attributed to the [110]t directional antiparallel lattice motion of Pb ions and by the directionality of the applied electric field. Pure PZ formation has been characterized by the dielectric phase transition at 235 °C and antiferroelectric P‐E hysteresis loops at room temperature. Dielectric response has been characterized within a frequency domain of 100 Hz–1 MHz at various temperatures ranging from 40 to 350 °C. Though frequency dispersion of dielectric behaves like a Maxwell–Wagner type of relaxation, ω2 dependency of ac conductivity indicates that there must be G‐C equivalent circuit dominance at high frequency. The presence of trap charges in PZ has been determined by Arrhenius plots of ac conductivity. The temperature dependent n (calculated from the universal power law of ac conductivity) values indicate an anomalous behavior of the trapped charges. This anomaly has been explained by strongly and weakly correlated potential wells of trapped charges and their behavior on thermal activation. The dominance of circuit∕circuits resembling Maxwell–Wagner type has been investigated by logarithmic Nyquist plots at various temperatures and it has been justified that the dielectric dispersion is not from the actual Maxwell–Wagner-type response.

Dielectric, Ferroelectric and Relaxor Behavior of BaLaxBi4-xTi4O15 Ceramics

Monophasic BaLaxBi4-xTi4O15 (x = 0, 0.2, 0.4, 0.6 and 0.8) ceramics, fabricated from the powders synthesized via the solid-state reaction route exhibited relaxor behavior. Dielectric properties of the well sintered ceramics were measured in a wide frequency range (1 kHz-1 MHz) at different temperatures (300-750 K). The temperature of dielectri maximum (T-m) was found to decrease significantly from 696 K for an undoped sample (x = 0) to 395 K for the sample corresponding to the composition x = 0.8 accompanied by a decrease in the magnitude ofdielectric maximum (epsilon(m)). The temperature variation of the dielectric constant on the high temperature slope of the peak (T > T-m) was analyzed by using the Lorentz-ype quadratic law and the diffuseness of the peak was found to increase with increasing x. Vogel-Fulcher modelling of dielectric relaxation showed a decrease in freezing temperature (T-VF) (from 678 to 340 K) and an increase in the activation energy (5 to 24 meV) for the frequency dispersion with increase in x (La-3 divided by content). Strength of frequency dispersion of the phase transition increased with lanthanum content. Polarization (P)-electric field (E) hysteresis loops recorded at 373 showed a transition from a nearly squarish to slim loop hysteresis behavior with increasing lanthanum content.

Handling sectional views in volume-based approach to automatically construct 3D solid from 2D views

This paper presents an algorithm for solid model reconstruction from 2D sectional views based on volume-based approach. None of the existing work in automatic reconstruction from 2D orthographic views have addressed sectional views in detail. It is believed that the volume-based approach is better suited to handle different types of sectional views. The volume-based approach constructs the 3D solid by a boolean combination of elementary solids. The elementary solids are formed by sweep operation on loops identified in the input views. The only adjustment to be made for the presence of sectional views is in the identification of loops that would form the elemental solids. In the algorithm, the conventions of engineering drawing for sectional views, are used to identify the loops correctly. The algorithm is simple and intuitive in nature. Results have been obtained for full sections, offset sections and half sections. Future work will address other types of sectional views such as removed and revolved sections and broken-out sections. (C) 2004 Elsevier Ltd. All rights reserved.

Microcalorimetric indications for ligand binding as a function of the protein for galactoside-specific plant and avian lectins

The process cascade leading to the final accommodation of the carbohydrate ligand in the lectin’s binding site comprises enthalpic and entropic contributions of the binding partners and solvent molecules. With emphasis on lactose, N-acetyllactosamine, and thiodigalactoside as potent inhibitors of binding of galactoside-specific lectins, the question was addressed to what extent these parameters are affected as a function of the protein. The microcalorimetric study of carbohydrate association to the galectin from chicken liver (CG-16) and the agglutinin from Viscum album (VAA) revealed enthalpy–entropy compensation with evident protein type-dependent changes for N-acetyllactosamine. Reduction of the entropic penalty by differential flexibility of loops or side chains and/or solvation properties of the protein will have to be reckoned with to assign a molecular cause to protein type-dependent changes in thermodynamic parameters for lectins sharing the same monosaccharide specificity.

Slow rotation of a sphere in a non-Newtonian fluid with or without suction or injection

The flow generated by the rotation of a sphere in an infinitely extending fluid has recently been studied by Goldshtik. The corresponding problem for non-Newtonian Reiner-Rivlin fluids has been studied by Datta. Bhatnagar and Rajeswari have studied the secondary flow between two concentric spheres rotating about an axis in the non-Newtonian fluids. This last investigation was further generalised by Rajeswari to include the effects of small radial suction or injection. In Part A of the present investigation, we have studied the secondary flow generated by the slow rotation of a single sphere in non-Newtonian fluid obeying the Rivlin-Ericksen constitutive equation. In Part B, the effects of small suction or injection have been studied which is applied in an arbitrary direction at the surface of the sphere. In the absence of suction or injection, the secondary flow for small values of the visco-elastic parameter is similar to that of Newtonian fluids with inclusion of inertia terms in the Oseen approximation. If this parameter exceeds Kc = 18R/219, whereR is the Reynolds number, the breaking of the flow field takes place into two domains, in one of which the stream lines form closed loops. For still higher values of this parameter, the complete reversal of the sense of the flow takes place. When suction or injection is included, the breaking of the flow persists under certain condition investigated in this paper. When this condition is broken, the breaking of the flow is obliterated.

The Line Spectral Frequency Model of a Finite-Length Sequence

The line spectral frequency (LSF) of a causal finite length sequence is a frequency at which the spectrum of the sequence annihilates or the magnitude spectrum has a spectral null. A causal finite-length sequencewith (L + 1) samples having exactly L-LSFs, is referred as an Annihilating (AH) sequence. Using some spectral properties of finite-length sequences, and some model parameters, we develop spectral decomposition structures, which are used to translate any finite-length sequence to an equivalent set of AH-sequences defined by LSFs and some complex constants. This alternate representation format of any finite-length sequence is referred as its LSF-Model. For a finite-length sequence, one can obtain multiple LSF-Models by varying the model parameters. The LSF-Model, in time domain can be used to synthesize any arbitrary causal finite-length sequence in terms of its characteristic AH-sequences. In the frequency domain, the LSF-Model can be used to obtain the spectral samples of the sequence as a linear combination of spectra of its characteristic AH-sequences. We also summarize the utility of the LSF-Model in practical discrete signal processing systems.

A study of the slow reaction in Al-5 wt.% Ag alloy by resistivity measurements

The slow reaction in an Al-5 wt.% Ag alloy has been investigated by resistivity measurements. The "slope change" method gave an activation energy of 1.25 eV for silver diffusion during the slow reaction. The existence of an excess concentration of vacancies in equilibrium with the dislocation loops seems to be responsible for the slow reaction. The presence of silver inhibits the nucleation of dislocation loops by holding up the quenched-in vacancies in solution. There is no indication of the presence of a third stage in the low-temperature ageing process of this alloy.

Investigating novelty-outcome relationships in engineering design

Design creativity involves developing novel and useful solutions to design problems The research in this article is an attempt to understand how novelty of a design resulting from a design process is related to the kind of outcomes. described here as constructs, involved in the design process A model of causality, the SAPPhIRE model, is used as the basis of the analysis The analysis is based on previous research that shows that designing involves development and exploration of the seven basic constructs of the SAPPhIRE model that constitute the causal connection between the various levels of abstraction at which a design can be described The constructs am state change, action, parts. phenomenon. input. organs. and effect The following two questions are asked. Is there a relationship between novelty and the constructs? If them is a relationship, what is the degree of this relationship? A hypothesis is developed to answer the questions an increase in the number and variety of ideas explored while designing should enhance the variety of concept space. leading to an increase in the novelty of the concept space Eight existing observational studies of designing sessions are used to empirically validate the hypothesis Each designing session involves an individual designer. experienced or novice. solving a design problem by producing concepts and following a think-aloud protocol. The results indicate dependence of novelty of concept space on variety of concept space and dependence of variety of concept space on variety of idea space. thereby validating the hypothesis The Jesuits also reveal a strong correlation between novelty and the constructs, correlation value decreases as the abstraction level of the constructs reduces. signifying the importance of using constructs at higher abstraction levels for enhancing novelty

Relation between part position and kinematic freedom: An expository survey

This paper makes explicit the relation between relative part position and kinematic freedom of the parts which is implicitly available in the literature. An extensive set of representative papers in the areas of assembly and kinematic modelling is reviewed to specifically identify how the ideas in the two areas are related and influencing the development of each other. The papers are categorised by the approaches followed in the specification, representation, and solution of the part relations. It is observed that the extent of the part geometry is not respected in modelling schemes and as a result, the causal flow of events (proximity–contact–mobility) during the assembling process is not realised in the existing modelling paradigms, which are focusing on either the relative positioning problem or the relative motion problem. Though an assembly is a static description of part configuration, achievement of this configuration requires availability of relative motion for bringing parts together during the assembly process. On the other hand, the kinematic freedom of a part depends on the nature of contacting regions with other parts in its static configuration. These two problems are thus related through the contact geometry. The chronology of the approaches that significantly contributed to the development of the subject is also included in the paper.

Hysteresis in model spin systems

The authors study the hysteretic response of model spin systems to periodic time-varying fields H(t) as a function of the amplitude H0 and the frequency Omega . At fixed H0, they find conventional, squarish hysteresis loops at low Omega , and rounded, roughly elliptical loops at high Omega , in agreement with experiment. For the O(N to infinity ), d=3, ( Phi 2)2 model with Langevin dynamics, they find a novel scaling behaviour for the area A of the hysteresis loop, of the form (valid for low fields) A approximately=H0066 Omega 0.33.

Estimation of signals in colored non gaussian noise based on Gaussian Mixture models

Non-Gaussianity of signals/noise often results in significant performance degradation for systems, which are designed using the Gaussian assumption. So non-Gaussian signals/noise require a different modelling and processing approach. In this paper, we discuss a new Bayesian estimation technique for non-Gaussian signals corrupted by colored non Gaussian noise. The method is based on using zero mean finite Gaussian Mixture Models (GMMs) for signal and noise. The estimation is done using an adaptive non-causal nonlinear filtering technique. The method involves deriving an estimator in terms of the GMM parameters, which are in turn estimated using the EM algorithm. The proposed filter is of finite length and offers computational feasibility. The simulations show that the proposed method gives a significant improvement compared to the linear filter for a wide variety of noise conditions, including impulsive noise. We also claim that the estimation of signal using the correlation with past and future samples leads to reduced mean squared error as compared to signal estimation based on past samples only.