Functional characterization, homology modeling and docking studies of beta-glucosidase responsible for bioactivation of cyanogenic hydroxynitrile glucosides from Leucaena leucocephala (subabul)

Glycosyl hydrolase family 1 beta-glucosidases are important enzymes that serve many diverse functions in plants including defense, whereby hydrolyzing the defensive compounds such as hydroxynitrile glucosides. A hydroxynitrile glucoside cleaving beta-glucosidase gene (Llbglu1) was isolated from Leucaena leucocephala, cloned into pET-28a (+) and expressed in E. coli BL21 (DE3) cells. The recombinant enzyme was purified by Ni-NTA affinity chromatography. The optimal temperature and pH for this beta-glucosidase were found to be 45 A degrees C and 4.8, respectively. The purified Llbglu1 enzyme hydrolyzed the synthetic glycosides, pNPGlucoside (pNPGlc) and pNPGalactoside (pNPGal). Also, the enzyme hydrolyzed amygdalin, a hydroxynitrile glycoside and a few of the tested flavonoid and isoflavonoid glucosides. The kinetic parameters K (m) and V (max) were found to be 38.59 mu M and 0.8237 mu M/mg/min for pNPGlc, whereas for pNPGal the values were observed as 1845 mu M and 0.1037 mu M/mg/min. In the present study, a three dimensional (3D) model of the Llbglu1 was built by MODELLER software to find out the substrate binding sites and the quality of the model was examined using the program PROCHEK. Docking studies indicated that conserved active site residues are Glu 199, Glu 413, His 153, Asn 198, Val 270, Asn 340, and Trp 462. Docking of rhodiocyanoside A with the modeled Llbglu1 resulted in a binding with free energy change (Delta G) of -5.52 kcal/mol on which basis rhodiocyanoside A could be considered as a potential substrate.

A generic variant of NIST’s KAS2 key agreement protocol

We propose a generic three-pass key agreement protocol that is based on a certain kind of trapdoor one-way function family. When specialized to the RSA setting, the generic protocol yields the so-called KAS2 scheme that has recently been standardized by NIST. On the other hand, when specialized to the discrete log setting, we obtain a new protocol which we call DH2. An interesting feature of DH2 is that parties can use different groups (e.g., different elliptic curves). The generic protocol also has a hybrid implementation, where one party has an RSA key pair and the other party has a discrete log key pair. The security of KAS2 and DH2 is analyzed in an appropriate modification of the extended Canetti-Krawczyk security model.

Experiments and zero D modeling studies using specific Wiebe coefficients for producer gas as fuel in spark-ignited engines

The paper addresses experiments and modeling studies on the use of producer gas, a bio-derived low energy content fuel in a spark-ignited engine. Producer gas, generated in situ, has thermo-physical properties different from those of fossil fuel(s). Experiments on naturally aspirated and turbo-charged engine operation and subsequent analysis of the cylinder pressure traces reveal significant differences in the heat release pattern within the cylinder compared with a typical fossil fuel. The heat release patterns for gasoline and producer gas compare well in the initial 50% but beyond this, producer gas combustion tends to be sluggish leading to an overall increase in the combustion duration. This is rather unexpected considering that producer gas with nearly 20% hydrogen has higher flame speeds than gasoline. The influence of hydrogen on the initial flame kernel development period and the combustion duration and hence on the overall heat release pattern is addressed. The significant deviations in the heat release profiles between conventional fuels and producer gas necessitates the estimation of producer gas-specific Wiebe coefficients. The experimental heat release profiles are used for estimating the Wiebe coefficients. Experimental evidence of lower fuel conversion efficiency based on the chemical and thermal analysis of the engine exhaust gas is used to arrive at the Wiebe coefficients. The efficiency factor a is found to be 2.4 while the shape factor m is estimated at 0.7 for 2% to 90% burn duration. The standard Wiebe coefficients for conventional fuels and fuel-specific coefficients for producer gas are used in a zero D model to predict the performance of a 6-cylinder gas engine under naturally aspirated and turbo-charged conditions. While simulation results with standard Wiebe coefficients result in excessive deviations from the experimental results, excellent match is observed when producer gas-specific coefficients are used. Predictions using the same coefficients on a 3-cylinder gas engine having different geometry and compression ratio(s) indicate close match with the experimental traces highlighting the versatility of the coefficients.

EESM-Based Link Adaptation in Point-to-Point and Multi-Cell OFDM Systems: Modeling and Analysis

In contemporary wideband orthogonal frequency division multiplexing (OFDM) systems, such as Long Term Evolution (LTE) and WiMAX, different subcarriers over which a codeword is transmitted may experience different signal-to-noise-ratios (SNRs). Thus, adaptive modulation and coding (AMC) in these systems is driven by a vector of subcarrier SNRs experienced by the codeword, and is more involved. Exponential effective SNR mapping (EESM) simplifies the problem by mapping this vector into a single equivalent fiat-fading SNR. Analysis of AMC using EESM is challenging owing to its non-linear nature and its dependence on the modulation and coding scheme. We first propose a novel statistical model for the EESM, which is based on the Beta distribution. It is motivated by the central limit approximation for random variables with a finite support. It is simpler and as accurate as the more involved ad hoc models proposed earlier. Using it, we develop novel expressions for the throughput of a point-to-point OFDM link with multi-antenna diversity that uses EESM for AMC. We then analyze a general, multi-cell OFDM deployment with co-channel interference for various frequency-domain schedulers. Extensive results based on LTE and WiMAX are presented to verify the model and analysis, and gain new insights.

Modeling Time-Varying Aggregate Interference in Cognitive Radio Systems, and Application to Primary Exclusive Zone Design

Accurately characterizing the time-varying interference caused to the primary users is essential in ensuring a successful deployment of cognitive radios (CR). We show that the aggregate interference at the primary receiver (PU-Rx) from multiple, randomly located cognitive users (CUs) is well modeled as a shifted lognormal random process, which is more accurate than the lognormal and the Gaussian process models considered in the literature, even for a relatively dense deployment of CUs. It also compares favorably with the asymptotically exact stable and symmetric truncated stable distribution models, except at high CU densities. Our model accounts for the effect of imperfect spectrum sensing, which depends on path-loss, shadowing, and small-scale fading of the link from the primary transmitter to the CU; the interweave and underlay modes or CR operation, which determine the transmit powers of the CUs; and time-correlated shadowing and fading of the links from the CUs to the PU-Rx. It leads to expressions for the probability distribution function, level crossing rate, and average exceedance duration. The impact of cooperative spectrum sensing is also characterized. We validate the model by applying it to redesign the primary exclusive zone to account for the time-varying nature of interference.

An Exponential Lower Bound for Homogeneous Depth Four Arithmetic Formulas

We show here a 2(Omega(root d.log N)) size lower bound for homogeneous depth four arithmetic formulas. That is, we give an explicit family of polynomials of degree d on N variables (with N = d(3) in our case) with 0, 1-coefficients such that for any representation of a polynomial f in this family of the form f = Sigma(i) Pi(j) Q(ij), where the Q(ij)'s are homogeneous polynomials (recall that a polynomial is said to be homogeneous if all its monomials have the same degree), it must hold that Sigma(i,j) (Number of monomials of Q(ij)) >= 2(Omega(root d.log N)). The above mentioned family, which we refer to as the Nisan-Wigderson design-based family of polynomials, is in the complexity class VNP. Our work builds on the recent lower bound results 1], 2], 3], 4], 5] and yields an improved quantitative bound as compared to the quasi-polynomial lower bound of 6] and the N-Omega(log log (N)) lower bound in the independent work of 7].

Saturated duration for dynamic structural plastic response and fundamental periods of elastic vibration

The relationship is determined between saturated duration of rectangular pressure pulses applied to rigid, perfectly plastic structures and their fundamental periods of elastic vibration. It is shown that the ratio between the saturated duration and the fundamental period of elastic vibration of a structure is dependent upon two factors: the first one is the slenderness or thinness ratio of the structure; and the second one is the square root of ratio between the Young's elastic modulus and the yield stress of the structural material. Dimensional analysis shows that the aforementioned ratio is one of the basic similarity parameters for elastic-plastic modeling under dynamic loading.

Saturated duration of rectangular pressure pulse applied to rectangular plates with finite-deflections

The inequities in health care and housing access experienced by low-income women in the United States are a continuing concern. This article addresses the interrelationships between housing and health as experienced by low-income clients so that health care practitioners can begin to build active and effective health-promoting partnerships with clients, their families, and their communities. A case study is presented that describes the actual experience of a woman living in a low-income housing development and its effect on her health and access to health care. The importance of the role of midwives in addressing the health care and advocacy needs of women in substandard housing is highlighted.

Statistical modeling of damage evolution in spallation

In order to understand the mechanism of the incipient spallation in rolled metals, a one dimensional statistical mode1 on evolution of microcracks in spallation was proposed. The crack length appears to be the fundamental variable in the statistical description. Two dynamic processes, crack nucleation and growth, were involved in the model of damage evolution. A simplified case was examined and preliminary correlation to experimental observations of spallation was made.

Numerical modeling of optical levitation and trapping of the "stuck" particles with a pulsed optical tweezers

We present the theoretical analysis and the numerical modeling of optical levitation and trapping of the stuck particles with a pulsed optical tweezers. In our model, a pulsed laser was used to generate a large gradient force within a short duration that overcame the adhesive interaction between the stuck particles and the surface; and then a low power continuous - wave (cw) laser was used to capture the levitated particle. We describe the gradient force generated by the pulsed optical tweezers and model the binding interaction between the stuck beads and glass surface by the dominative van der Waals force with a randomly distributed binding strength. We numerically calculate the single pulse levitation efficiency for polystyrene beads as the function of the pulse energy, the axial displacement from the surface to the pulsed laser focus and the pulse duration. The result of our numerical modeling is qualitatively consistent with the experimental result. (C) 2005 Optical Society of America.

New insights to the molecular phylogenetics and generic assessment in the Rhacophoridae (Amphibia: Anura) based on five nuclear and three mitochondrial genes, with comments on the evolution of reproduction

The phylogenetic relationships among 12 genera of treefrogs (Family, Rhacophoridae), were investigated based on a large sequence data set, including five nuclear (brain-derived neurotrophic factor, proopiomelanocortin, recombination activating gene 1, tyr

Modular risk modeling and management of water infrastructure disaster incidents

Water supply and wastewater control are critical elements of society's infrastructure. The objective of this study will be to provide a generic risk assessment tool to provide municipalities and the nation as a whole with a quantifiable assessment of their vulnerability to water infrastructure threats. The approach will prioritize countermeasures and identify where research and development is required to further minimize risk. This paper outlines the current context, primary concerns and state-of-the art in critical infrastructure risk management for the water sector and proposes a novel approach to resolve existing questions in the field. The proposed approach is based on a modular framework that derives a quantitative risk index for varied domains of interest. The approach methodology is scaleable and based on formal definitions of event probability and severity. The framework is equally applicable to natural and human-induced hazard types and can be used for analysis of compound risk events.

Structural and functional characterization of the human CCR5 receptor in complex with HIV gp120 envelope glycoprotein and CD4 receptor by molecular modeling studies

The entry of human immunodeficiency virus (HIV) into cells depends on a sequential interaction of the gp120 envelope glycoprotein with the cellular receptors CD4 and members of the chemokine receptor family. The CC chemokine receptor CCR5 is such a receptor for several chemokines and a major coreceptor for the entry of R5 HIV type-1 (HIV-1) into cells. Although many studies focus on the interaction of CCR5 with HIV-1, the corresponding interaction sites in CCR5 and gp120 have not been matched. Here we used an approach combining protein structure modeling, docking and molecular dynamics simulation to build a series of structural models of the CCR5 in complexes with gp120 and CD4. Interactions such as hydrogen bonds, salt bridges and van der Waals contacts between CCR5 and gp120 were investigated. Three snapshots of CCR5-gp120-CD4 models revealed that the initial interactions of CCR5 with gp120 are involved in the negatively charged N-terminus (Nt) region of CCR5 and positively charged bridging sheet region of gp120. Further interactions occurred between extracellular loop2 (ECL2) of CCR5 and the base of V3 loop regions of gp120. These interactions may induce the conformational changes in gp120 and lead to the final entry of HIV into the cell. These results not only strongly support the two-step gp120-CCR5 binding mechanism, but also rationalize extensive biological data about the role of CCR5 in HIV-1 gp120 binding and entry, and may guide efforts to design novel inhibitors.

Modeling natural sounds with modulation cascade processes

Natural sounds are structured on many time-scales. A typical segment of speech, for example, contains features that span four orders of magnitude: Sentences ($\sim1$s); phonemes ($\sim10$−$1$ s); glottal pulses ($\sim 10$−$2$s); and formants ($\sim 10$−$3$s). The auditory system uses information from each of these time-scales to solve complicated tasks such as auditory scene analysis [1]. One route toward understanding how auditory processing accomplishes this analysis is to build neuroscience-inspired algorithms which solve similar tasks and to compare the properties of these algorithms with properties of auditory processing. There is however a discord: Current machine-audition algorithms largely concentrate on the shorter time-scale structures in sounds, and the longer structures are ignored. The reason for this is two-fold. Firstly, it is a difficult technical problem to construct an algorithm that utilises both sorts of information. Secondly, it is computationally demanding to simultaneously process data both at high resolution (to extract short temporal information) and for long duration (to extract long temporal information). The contribution of this work is to develop a new statistical model for natural sounds that captures structure across a wide range of time-scales, and to provide efficient learning and inference algorithms. We demonstrate the success of this approach on a missing data task.

Cooperation of Mtmr8 with PI3K Regulates Actin Filament Modeling and Muscle Development in Zebrafish

Background: It has been shown that mutations in at least four myotubularin family genes (MTM1, MTMR1, 2 and 13) are causative for human neuromuscular disorders. However, the pathway and regulative mechanism remain unknown. Methodology/Principal Findings: Here, we reported a new role for Mtmr8 in neuromuscular development of zebrafish. Firstly, we cloned and characterized zebrafish Mtmr8, and revealed the expression pattern predominantly in the eye field and somites during early somitogenesis. Using morpholino knockdown, then, we observed that loss-of-function of Mtmr8 led to defects in somitogenesis. Subsequently, the possible underlying mechanism and signal pathway were examined. We first checked the Akt phosphorylation, and observed an increase of Akt phosphorylation in the morphant embryos. Furthermore, we studied the PH/G domain function within Mtmr8. Although the PH/G domain deletion by itself did not result in embryonic defect, addition of PI3K inhibitor LY294002 did give a defective phenotype in the PH/G deletion morphants, indicating that the PH/G domain was essential for Mtmr8's function. Moreover, we investigated the cooperation of Mtmr8 with PI3K in actin filament modeling and muscle development, and found that both Mtmr8-MO1 and Mtmr8-MO2+LY294002 led to the disorganization of the actin cytoskeleton. In addition, we revealed a possible participation of Mtmr8 in the Hedgehog pathway, and cell transplantation experiments showed that Mtmr8 worked in a non-cell autonomous manner in actin modeling. Conclusion/Significance: The above data indicate that a conserved functional cooperation of Mtmr8 with PI3K regulates actin filament modeling and muscle development in zebrafish, and reveal a possible participation of Mtmr8 in the Hedgehog pathway. Therefore, this work provides a new clue to study the physiological function of MTM family members.