Engineered dimer interface mutants of triosephosphate isomerase: the role of inter-subunit interactions in enzyme function and stability

The role of inter-subunit interactions in maintaining optimal catalytic activity in triosephosphate isomerase (TIM) has been probed, using the Plasmodium falciparum enzyme as a model. Examination of subunit interface contacts in the crystal structures suggests that residue 75 (Thr, conserved) and residue 13 (Cys, variable) make the largest number of inter-subunit contacts. The mutants Cys13Asp (C13D) and Cys13Glu (C13E) have been constructed and display significant reduction in catalytic activity when compared with wild-type (WT) enzyme (similar to 7.4-fold decrease in k(cat) for the C13D and similar to 3.3-fold for the C13E mutants). Analytical gel filtration demonstrates that the C13D mutant dissociates at concentrations < 1.25 mu M, whereas the WT and the C13E enzymes retain the dimeric structure. The order of stability of the mutants in the presence of chemical denaturants, like urea and guanidium chloride, is WT > Cys13Glu > Cys13Asp. Irreversible thermal precipitation temperatures follow the same order as well. Modeling studies establish that the Cys13Asp mutation is likely to cause a significantly greater structural perturbation than Cys13Glu. Analysis of sequence and structural data for TIMs from diverse sources suggests that residues 13 and 82 form a pair of proximal sites, in which a limited number of residue pairs may be accommodated.

The role of competition and habitat in structuring small mammal communities in a tropical montane ecosystem in southern India

Small mammals were sampled in two natural habitats (montane stunted evergreen forests and montane grassland) and four anthropogenic habitats (tea, wattle, bluegum and pine plantation) in the Upper Nilgiris in southern India. Of the species trapped, eight were in montane evergreen forests and three were in other habitats. Habitat discrimination was studied in the rodents Rattus rattus and Mus famulus and the shrew Suncus montanus in the montane forest habitat. Multivariate tests on five variables (canopy cover, midstorey density, ground cover, tree density, canopy height) showed that R. rattus uses areas of higher tree density and lower canopy cover. Suncus montanus and M. famulus use habitat with higher tree density and ground cover and lower canopy height. Multivariate tests did not discriminate habitat use between the species. Univariate tests, however, showed that M. famulus uses areas of higher tree density than R. rattus and S. montanus. Rattus rattus was the dominant species in the montane forest, comprising 60.9% of total density, while the rodent Millardia meltada was the dominant species in the grassland. Studies of spatial interaction between these two species in habitats where they coexisted showed neither overlap nor avoidance between the species. Rattus rattus, however, did use areas of lower ground cover than did M. meltada. The analysis of spatial interactions between the species, habitat discrimination and use, and the removal experiments suggest that interspecific competition may not be a strong force in structuring these small mammal communities. There are distinct patterns in the use of different habitats by some species, but microhabitat selection and segregation is weak. Other factors such as intraspecific competition may play a more important role in these communities.

Inter and intra crystalline ion exchange equilibria in the system Fe Cr Al O

The tie lines delineating ion-exchange equilibria between FeCr2O4FeAl2O4 spinel solid solution and Cr2O3Al2O3 solid solution with corundum structure have been determined at 1373 K by electron microprobe and EDAX point count analysis of oxide phases equilibrated with metallic iron. Activities in the spinel solid solution are derived from the tie lines and the thermodynamic data on Cr2O3Al2O3 solid solution available in the literature. The oxygen potentials corresponding to the tie-line composition of oxide phases in equilibrium with metallic iron were measured using solid oxide galvanic cells with CaOZrO2 and Y2O3ThO2 electrolytes. These electrochemical measurements also yield activities in the spinel solid solution, in good agreement with those obtained from tie lines. The activity-composition relationship in the spinel solid solution is analysed in terms of the intra-crystalline ion exchange between the tetrahedral and octahedral sites of the spinel structures. The ion exchange is governed by site-preference energies of the cations and the entropy of cations mixing on each site.

A Review of Photo-Induced Inter-Diffusion in Nano-Layered Chalcogenide Films

Abstract | A growing interest in the research of chalcogenide glasses can be currently witnessed, which to a large extent is caused by newly opened fields of applications for these materials. Applications in the field of micro- and opto-electronics, xerography and lithography, acousto-optic and memory switching devices and detectors for medical imaging seem to be most remarkable. Accordingly, photo induced phenomena in chalcogenide glasses are attracting much interest. These phenomena can be found both in uniform thin films as well as multilayered films. Among amorphous multilayers, chalcogenide multilayers are attractive because of the potential it has for tailoring the optical properties. I will be presenting some basic idea of photoinduced effects followed by the diffusion mechanisms of Se, Sb and Bi in to As2S3 films.

Fuzzy logic based TCSC supplementary controller for damping of inter area oscillations in power system

This paper describes an application of a FACTS supplementary controller for damping of inter area oscillations in power systems. A fuzzy logic controller is designed to regulate a thyristor controlled series capacitor (TCSC) in a multimachine environment to produce additional damping in the system. Simultaneous application of the excitation controller and proposed controller is also investigated. Simulation studies have been done with different types of disturbances and the results are shown to be consistent with the expected performance of the supplementary controller.

Prediction of inter-laminar stresses in composite honeycomb sandwich panels under mechanical loading using Variational Asymptotic Method

This work focuses on the formulation of an asymptotically correct theory for symmetric composite honeycomb sandwich plate structures. In these panels, transverse stresses tremendously influence design. The conventional 2-D finite elements cannot predict the thickness-wise distributions of transverse shear or normal stresses and 3-D displacements. Unfortunately, the use of the more accurate three-dimensional finite elements is computationally prohibitive. The development of the present theory is based on the Variational Asymptotic Method (VAM). Its unique features are the identification and utilization of additional small parameters associated with the anisotropy and non-homogeneity of composite sandwich plate structures. These parameters are ratios of smallness of the thickness of both facial layers to that of the core and smallness of 3-D stiffness coefficients of the core to that of the face sheets. Finally, anisotropy in the core and face sheets is addressed by the small parameters within the 3-D stiffness matrices. Numerical results are illustrated for several sample problems. The 3-D responses recovered using VAM-based model are obtained in a much more computationally efficient manner than, and are in agreement with, those of available 3-D elasticity solutions and 3-D FE solutions of MSC NASTRAN. (c) 2012 Elsevier Ltd. All rights reserved.

Inter-domain interactions influence the stability and catalytic activity of the bi-domain protein tyrosine phosphatase PTP99A

The two protein tyrosine phosphatase (PTP) domains in bi-domain PTPs share high sequence and structural similarity. However, only one of the two PIP domains is catalytically active. Here we describe biochemical studies on the two tandem PTP domains of the bi-domain PTP, PTP99A. Phosphatase activity, monitored using small molecule as well as peptide substrates, revealed that the inactive (D2) domain activates the catalytic (D1) domain. Thermodynamic measurements suggest that the inactive D2 domain stabilizes the bi-domain (D1-D2) protein. The mechanism by which the D2 domain activates and stabilizes the bi-domain protein is governed by few interactions at the inter-domain interface. In particular, mutating Lys990 at the interface attenuates inter-domain communication. This residue is located at a structurally equivalent location to the so-called allosteric site of the canonical single domain PIP, PTP1B. These observations suggest functional optimization in bi-domain PTPs whereby the inactive PTP domain modulates the catalytic activity of the bi-domain enzyme. (C) 2012 Elsevier B.V. All rights reserved.

Dung as a potential medium for inter-sexual chemical signaling in Asian elephants (Elephas maximus)

Chemical signaling is a prominent mode of male-female communication among elephants, especially during their sexually active periods. Studies on the Asian elephant in zoos have shown the significance of a urinary pheromone (Z7-12:Ac) in conveying the reproductive status of a female toward the opposite sex. We investigated the additional possibility of an inter-sexual chemical signal being conveyed through dung. Sixteen semi-captive adult male elephants were presented with dung samples of three female elephants in different reproductive phases. Each male was tested in 3 separate trials, within an interval of 1-3 days. The trials followed a double-blind pattern as the male and female elephants used in the trials were strangers, and the observer was not aware of the reproductive status of females during the period of bioassays. Males responded preferentially (P < 0.005), in terms of higher frequency of sniff, check and place behavior toward the dung of females close to pre-ovulatory period (follicular-phase) as compared to those in post-ovulatory period (luteal-phase). The response toward the follicular phase samples declined over repeated trials though was still significantly higher than the corresponding response toward the non-ovulatory phase in each of the trials performed. This is the first study to show that male Asian elephants were able to distinguish the reproductive phase of the female by possibly detecting a pre-ovulatory pheromone released in dung. (C) 2012 Elsevier B.V. All rights reserved.

A Comparative Kinetic and Thermodynamic Perspective of the sigma-Competition Model in Escherichia coli

Transcription is the most fundamental step in gene expression in any living organism. Various environmental cues help in the maturation of core RNA polymerase (RNAP; alpha(2)beta beta'omega) with different sigma-factors, leading to the directed recruitment of RNAP to different promoter DNA sequences. Thus it is essential to determine the sigma-factors that affect the preferential partitioning of core RNAP among various a-actors, and the role of sigma-switching in transcriptional gene regulation. Further, the macromolecular assembly of holo RNAP takes place in an extremely crowded environment within a cell, and thus far the kinetics and thermodynamics of this molecular recognition process have not been well addressed. In this study we used a site-directed bioaffinity immobilization method to evaluate the relative binding affinities of three different Escherichia coli sigma-factors to the same core RNAP with variations in temperature and ionic strength while emulating the crowded cellular milieu. Our data indicate that the interaction of core RNAP-sigma is susceptible to changes in external stimuli such as osmolytic and thermal stress, and the degree of susceptibility varies among different sigma-factors. This allows for a reversible sigma-switching from housekeeping factors to alternate sigma-factors when the organism senses a change in its physiological conditions.

Monoclonal Antibodies against Hepatitis C Genotype 3a Virus Like Particle Inhibit Virus Entry in Cell Culture System

The envelope protein (E1-E2) of Hepatitis C virus (HCV) is a major component of the viral structure. The glycosylated envelope protein is considered to be important for initiation of infection by binding to cellular receptor(s) and also known as one of the major antigenic targets to host immune response. The present study was aimed at identifying mouse monoclonal antibodies which inhibit binding of virus like particles of HCV to target cells. The first step in this direction was to generate recombinant HCV-like particles (HCV-LPs) specific for genotypes 3a of HCV (prevalent in India) using the genes encoding core, E1 and E2 envelop proteins in a baculovirus expression system. The purified HCV-LPs were characterized by ELISA and electron microscopy and were used to generate monoclonal antibodies (mAbs) in mice. Two monoclonal antibodies (E8G9 and H1H10) specific for the E2 region of envelope protein of HCV genotype 3a, were found to reduce the virus binding to Huh7 cells. However, the mAbs generated against HCV genotype 1b (D2H3, G2C7, E1B11) were not so effective. More importantly, mAb E8G9 showed significant inhibition of the virus entry in HCV JFH1 cell culture system. Finally, the epitopic regions on E2 protein which bind to the mAbs have also been identified. Results suggest a new therapeutic strategy and provide the proof of concept that mAb against HCV-LP could be effective in preventing virus entry into liver cells to block HCV replication.

Determination of favorable inter-particle interactions for formation of substitutionally ordered solid phases from a binary mixture of oppositely charged colloidal suspensions

The solid phase formed by a binary mixture of oppositely charged colloidal particles can be either substitutionally ordered or substitutionally disordered depending on the nature and strength of interactions among the particles. In this work, we use Monte Carlo molecular simulations along with the Gibbs-Duhem integration technique to map out the favorable inter-particle interactions for the formation of substitutionally ordered crystalline phases from a fluid phase. The inter-particle interactions are modeled using the hard core Yukawa potential but the method can be easily extended to other systems of interest. The study obtains a map of interactions depicting regions indicating the type of the crystalline aggregate that forms upon phase transition.

Long-Term Environmental Correlates of Invasion by Lantana camara (Verbenaceae) in a Seasonally Dry Tropical Forest

Invasive species, local plant communities and invaded ecosystems change over space and time. Quantifying this change may lead to a better understanding of the ecology and the effective management of invasive species. We used data on density of the highly invasive shrub Lantana camara (lantana) for the period 1990-2008 from a 50 ha permanent plot in a seasonally dry tropical forest of Mudumalai in southern India. We used a cumulative link mixed-effects regression approach to model the transition of lantana from one qualitative density state to another as a function of biotic factors such as indicators of competition from local species (lantana itself, perennial grasses, invasive Chromolaena odorata, the native shrub Helicteres isora and basal area of native trees) and abiotic factors such as fire frequency, inter-annual variability of rainfall and relative soil moisture. The density of lantana increased substantially during the study period. Lantana density was negatively associated with the density of H. isora, positively associated with basal area of native trees, but not affected by the presence of grasses or other invasive species. In the absence of fire, lantana density increased with increasing rainfall. When fires occurred, transitions to higher densities occurred at low rainfall values. In drier regions, lantana changed from low to high density as rainfall increased while in wetter regions of the plot, lantana persisted in the dense category irrespective of rainfall. Lantana seems to effectively utilize resources distributed in space and time to its advantage, thus outcompeting local species and maintaining a population that is not yet self-limiting. High-risk areas and years could potentially be identified based on inferences from this study for facilitating management of lantana in tropical dry forests.

The role of tusks, musth and body size in male-male competition among Asian elephants, Elephas maximus

The evolution of sexually dimorphic, elaborate male traits that are seemingly maladaptive may be driven by sexual selection (male-male competition and or female mate choice). Tusk possession in the Asian elephant is sexually dimorphic and exaggerated but its role in male-male competition has not yet been determined. We examined the role of the tusks in establishing dominance along with two other known male-male signals, namely, body size and musth (a temporary physiologically heightened sexual state) in an Asian elephant population in northeastern India with equal proportions of tusked and tuskless males. We observed 116 agonistic interactions with clear dominance outcomes between adult (>15 years) males during 458 field days in the dry season months of 2008-2011. A generalized linear mixed-effects model was used to predict the probability of winning as a function of body size, tusk possession and musth status relative to the opponent. A hierarchy of the three male-male signals emerged from this analysis, with musth overriding body size and body size overriding tusk possession. In this elephant population tusk possession thus plays a relatively minor role in male-male competition. An important implication of musth and body size being stronger determinants of dominance than tusk possession is that it could facilitate rapid evolution of tuskless males in the population under artificial selection against tusked individuals, which are poached for ivory. (C) 2013 The Association for the Study of Animal Behaviour. Published by Elsevier Ltd. All rights reserved.