Probing the role of the fully conserved Cys126 in triosephosphate isomerase by site-specific mutagenesis - distal effects on dimer stability

Cys126 is a completely conserved residue in triosephosphate isomerase that is proximal to the active site but has been ascribed no specific role in catalysis. A previous study of the C126S and C126A mutants of yeast TIM reported substantial catalytic activity for the mutant enzymes, leading to the suggestion that this residue is implicated in folding and stability [Gonzalez-Mondragon E et al. (2004) Biochemistry43, 3255–3263]. We re-examined the role of Cys126 with the Plasmodium falciparum enzyme as a model. Five mutants, C126S, C126A, C126V, C126M, and C126T, were characterized. Crystal structures of the 3-phosphoglycolate-bound C126S mutant and the unliganded forms of the C126S and C126A mutants were determined at a resolution of 1.7–2.1 Å. Kinetic studies revealed an approximately five-fold drop in kcat for the C126S and C126A mutants, whereas an approximately 10-fold drop was observed for the other three mutants. At ambient temperature, the wild-type enzyme and all five mutants showed no concentration dependence of activity. At higher temperatures (> 40 °C), the mutants showed a significant concentration dependence, with a dramatic loss in activity below 15 μm. The mutants also had diminished thermal stability at low concentration, as monitored by far-UV CD. These results suggest that Cys126 contributes to the stability of the dimer interface through a network of interactions involving His95, Glu97, and Arg98, which form direct contacts across the dimer interface.

Nonequilibrium phase transition in the kinetic Ising model: Divergences of fluctuations and responses near the transition point

The nonequilibrium dynamic phase transition in the kinetic Ising model in the presence of an oscillating magnetic field is studied by Monte Carlo simulation. The fluctuation of the dynamic older parameter is studied as a function of temperature near the dynamic transition point. The temperature variation of appropriately defined ''susceptibility'' is also studied near the dynamic transition point. Similarly, the fluctuation of energy and appropriately defined ''specific heat'' is studied as a function of temperature near the dynamic transition point. In both cases, the fluctuations (of dynamic order parameter and energy) and the corresponding responses diverge (in power law fashion) near the dynamic transition point with similar critical behavior (with identical exponent values).

Crystallization and preliminary X-ray studies of a galactose-specific lectin from the seeds of Spatholobus parviflorus

A galactose-specific seed lectin was purified from the legume Spatholobus parviflorus and crystallized using the hanging-drop vapour-diffusion technique. The crystals belonged to space group P1, with unit-cell parameters a = 60.998, b = 60.792, c = 78.179 angstrom, alpha = 101.32, beta = 91.38, gamma = 104.32 degrees. X-ray diffraction data were collected under cryoconditions (100 K) to a resolution of 2.04 angstrom using a MAR image-plate detector system mounted on a rotating-anode X-ray (Cu K alpha) generator. Molecular replacement using legume-lectin coordinates as a search model gave a tetrameric structure.

Phase diagram of a two-species lattice model with a linear instability

We discuss the properties of a one-dimensional lattice model of a driven system with two species of particles in which the mobility of one species depends on the density of the other. This model was introduced by Lahiri and Ramaswamy (Phys. Rev. Lett., 79, 1150 (1997)) in the context of sedimenting colloidal crystals, and its continuum version was shown to exhibit an instability arising from linear gradient couplings. In this paper we review recent progress in understanding the full phase diagram of the model. There are three phases. In the first, the steady state can be determined exactly along a representative locus using the condition of detailed balance. The system shows phase separation of an exceptionally robust sort, termed strong phase separation, which survives at all temperatures. The second phase arises in the threshold case where the first species evolves independently of the second, but the fluctuations of the first influence the evolution of the second, as in the passive scalar problem. The second species then shows phase separation of a delicate sort, in which long-range order coexists with fluctuations which do not damp down in the large-size limit. This fluctuation-dominated phase ordering is associated with power law decays in cluster size distributions and a breakdown of the Porod law. The third phase is one with a uniform overall density, and along a representative locus the steady state is shown to have product measure form. Density fluctuations are transported by two kinematic waves, each involving both species and coupled at the nonlinear level. Their dissipation properties are governed by the symmetries of these couplings, which depend on the overall densities. In the most interesting case,, the dissipation of the two modes is characterized by different critical exponents, despite the nonlinear coupling.

Particle dynamics in a turbulent particle–gas suspension at high Stokes number. Part 2. The fluctuating-force model

A fluctuating-force model is developed for representing the effect of the turbulent fluid velocity fluctuations on the particle phase in a turbulent gas–solid suspension in the limit of high Stokes number, where the particle relaxation time is large compared with the correlation time for the fluid velocity fluctuations. In the model, a fluctuating force is incorporated in the equation of motion for the particles, and the force distribution is assumed to be an anisotropic Gaussian white noise. It is shown that this is equivalent to incorporating a diffusion term in the Boltzmann equation for the particle velocity distribution functions. The variance of the force distribution, or equivalently the diffusion coefficient in the Boltzmann equation, is related to the time correlation functions for the fluid velocity fluctuations. The fluctuating-force model is applied to the specific case of a Couette flow of a turbulent particle–gas suspension, for which both the fluid and particle velocity distributions were evaluated using direct numerical simulations by Goswami & Kumaran (2010). It is found that the fluctuating-force simulation is able to quantitatively predict the concentration, mean velocity profiles and the mean square velocities, both at relatively low volume fractions, where the viscous relaxation time is small compared with the time between collisions, and at higher volume fractions, where the time between collisions is small compared with the viscous relaxation time. The simulations are also able to predict the velocity distributions in the centre of the Couette, even in cases in which the velocity distribution is very different from a Gaussian distribution.

Insulin Growth Factor-2 Binding Protein 3 (IGF2BP3) Is a Glioblastoma-specific Marker That Activates Phosphatidylinositol 3-Kinase/Mitogen-activated Protein Kinase (PI3K/MAPK) Pathways by Modulating IGF-2

Glioblastoma is the most common and malignant form of primary astrocytoma. Upon investigation of the insulin-like growth factor (IGF) pathway, we found the IGF2BP3/IMP3 transcript and protein to be up-regulated in GBMs but not in lower grade astrocytomas (p<0.0001). IMP3 is an RNA binding protein known to bind to the 5'-untranslated region of IGF-2 mRNA, thereby activating its translation. Overexpression-and knockdown-based studies establish a role for IMP3 in promoting proliferation, anchorage-independent growth, invasion, and chemoresistance. IMP3 overexpressing B16F10 cells also showed increased tumor growth, angiogenesis, and metastasis, resulting in poor survival in a mouse model. Additionally, the infiltrating front, perivascular, and subpial regions in a majority of the GBMs stained positive for IMP3. Furthermore, two different murine glioma models were used to substantiate the above findings. In agreement with the translation activation functions of IMP3, we also found increased IGF-2 protein in the GBM tumor samples without a corresponding increase in its transcript levels. Also, in vitro IMP3 overexpression/knockdown modulated the IGF-2 protein levels without altering its transcript levels. Additionally, IGF-2 neutralization and supplementation studies established that the proproliferative effects of IMP3 were indeed mediated through IGF-2. Concordantly, PI3K and MAPK, the downstream effectors of IGF-2, are activated by IMP3 and are found to be essential for IMP3-induced cell proliferation. Thus, we have identified IMP3 as a GBM-specific proproliferative and proinvasive marker acting through IGF-2 resulting in the activation of oncogenic PI3K and MAPK pathways.

An Empirical Model of the Process of Synthesis of Multiple State Mechanical Devices

Automated synthesis of mechanical designs is an important step towards the development of an intelligent CAD system. Research into methods for supporting conceptual design using automated synthesis has attracted much attention in the past decades. The research work presented here is based on the processes of synthesizing multiple state mechanical devices carried out individually by ten engineering designers. The designers are asked to think aloud, while carrying out the synthesis. The ten design synthesis processes are video recorded, and the records are transcribed and coded for identifying activities occurring in the synthesis processes, as well as for identifying the inputs to and outputs from the activities. A mathematical representation for specifying multi-state design task is proposed. Further, a descriptive model capturing all the ten synthesis processes is developed and presented in this paper. This will be used to identify the outstanding issues to be resolved before a system for supporting design synthesis of multiple state mechanical devices that is capable of creating a comprehensive variety of solution alternatives could be developed.

Describing Hand Postures: Inspirations from Classical Mudras

The objective of this work is to develop a systematic methodology for describing hand postures and grasps which is independent of the kinematics and geometry of the hand model which in turn can be used for developing a universal referencing scheme. It is therefore necessary that the scheme be general enough to describe the continuum of hand poses. Indian traditional classical dance form, “Bharathanatyam”, uses 28 single handed gestures, called “mudras”. A Mudra can be perceived as a hand posture with a specific pattern of finger configurations. Using modifiers, complex mudras could be constructed from relatively simple mudras. An adjacency matrix is constructed to describe the relationship among mudras. Various mudra transitions can be obtained from the graph associated with this matrix. Using this matrix, a hierarchy of the mudras is formed. A set of base mudras and modifiers are used for describing how one simple posture of hand can be transformed into another relatively complex one. A canonical set of predefined hand postures and modifiers can be used in digital human modeling to develop standard hand posture libraries.

Distributed Source Coding for Sensor Data Model and Estimation of Cluster Head Errors Using Bayesian and K-Near Neighborhood Classifiers in Deployment of Dense Wireless Sensor Networks

The lifetime calculation of large dense sensor networks with fixed energy resources and the remaining residual energy have shown that for a constant energy resource in a sensor network the fault rate at the cluster head is network size invariant when using the network layer with no MAC losses.Even after increasing the battery capacities in the nodes the total lifetime does not increase after a max limit of 8 times. As this is a serious limitation lots of research has been done at the MAC layer which allows to adapt to the specific connectivity, traffic and channel polling needs for sensor networks. There have been lots of MAC protocols which allow to control the channel polling of new radios which are available to sensor nodes to communicate. This further reduces the communication overhead by idling and sleep scheduling thus extending the lifetime of the monitoring application. We address the two issues which effects the distributed characteristics and performance of connected MAC nodes. (1) To determine the theoretical minimum rate based on joint coding for a correlated data source at the singlehop, (2a) to estimate cluster head errors using Bayesian rule for routing using persistence clustering when node densities are the same and stored using prior probability at the network layer, (2b) to estimate the upper bound of routing errors when using passive clustering were the node densities at the multi-hop MACS are unknown and not stored at the multi-hop nodes a priori. In this paper we evaluate many MAC based sensor network protocols and study the effects on sensor network lifetime. A renewable energy MAC routing protocol is designed when the probabilities of active nodes are not known a priori. From theoretical derivations we show that for a Bayesian rule with known class densities of omega1, omega2 with expected error P* is bounded by max error rate of P=2P* for single-hop. We study the effects of energy losses using cross-layer simulation of - large sensor network MACS setup, the error rate which effect finding sufficient node densities to have reliable multi-hop communications due to unknown node densities. The simulation results show that even though the lifetime is comparable the expected Bayesian posterior probability error bound is close or higher than Pges2P*.

The advection-condensation model and water-vapour probability density functions

The statistically steady humidity distribution resulting from an interaction of advection, modelled as an uncorrelated random walk of moist parcels on an isentropic surface, and a vapour sink, modelled as immediate condensation whenever the specific humidity exceeds a specified saturation humidity, is explored with theory and simulation. A source supplies moisture at the deep-tropical southern boundary of the domain and the saturation humidity is specified as a monotonically decreasing function of distance from the boundary. The boundary source balances the interior condensation sink, so that a stationary spatially inhomogeneous humidity distribution emerges. An exact solution of the Fokker-Planck equation delivers a simple expression for the resulting probability density function (PDF) of the wate-rvapour field and also the relative humidity. This solution agrees completely with a numerical simulation of the process, and the humidity PDF exhibits several features of interest, such as bimodality close to the source and unimodality further from the source. The PDFs of specific and relative humidity are broad and non-Gaussian. The domain-averaged relative humidity PDF is bimodal with distinct moist and dry peaks, a feature which we show agrees with middleworld isentropic PDFs derived from the ERA interim dataset. Copyright (C) 2011 Royal Meteorological Society

Voltage and Temperature-Aware SSTA Using Neural Network Delay Model

With the emergence of voltage scaling as one of the most powerful power reduction techniques, it has been important to support voltage scalable statistical static timing analysis (SSTA) in deep submicrometer process nodes. In this paper, we propose a single delay model of logic gate using neural network which comprehensively captures process, voltage, and temperature variation along with input slew and output load. The number of simulation programs with integrated circuit emphasis (SPICE) required to create this model over a large voltage and temperature range is found to be modest and 4x less than that required for a conventional table-based approach with comparable accuracy. We show how the model can be used to derive sensitivities required for linear SSTA for an arbitrary voltage and temperature. Our experimentation on ISCAS 85 benchmarks across a voltage range of 0.9-1.1V shows that the average error in mean delay is less than 1.08% and average error in standard deviation is less than 2.85%. The errors in predicting the 99% and 1% probability point are 1.31% and 1%, respectively, with respect to SPICE. The two potential applications of voltage-aware SSTA have been presented, i.e., one for improving the accuracy of timing analysis by considering instance-specific voltage drops in power grids and the other for determining optimum supply voltage for target yield for dynamic voltage scaling applications.

Extracting Three Dimensional Surface Model of Human Kidney from the Visible Human Data Set using Free Software

Three dimensional digital model of a representative human kidney is needed for a surgical simulator that is capable of simulating a laparoscopic surgery involving kidney. Buying a three dimensional computer model of a representative human kidney, or reconstructing a human kidney from an image sequence using commercial software, both involve (sometimes significant amount of) money. In this paper, author has shown that one can obtain a three dimensional surface model of human kidney by making use of images from the Visible Human Data Set and a few free software packages (ImageJ, ITK-SNAP, and MeshLab in particular). Images from the Visible Human Data Set, and the software packages used here, both do not cost anything. Hence, the practice of extracting the geometry of a representative human kidney for free, as illustrated in the present work, could be a free alternative to the use of expensive commercial software or to the purchase of a digital model.