Element free Galerkin formulation of composite beam with longitudinal slip

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ahmad, Dzulkarnain; Mokhtaram, Mokhtazul Haizad; Badli, Mohd Iqbal

2015-05-15

Behaviour between two materials in composite beam is assumed partially interact when longitudinal slip at its interfacial surfaces is considered. Commonly analysed by the mesh-based formulation, this study used meshless formulation known as Element Free Galerkin (EFG) method in the beam partial interaction analysis, numerically. As meshless formulation implies that the problem domain is discretised only by nodes, the EFG method is based on Moving Least Square (MLS) approach for shape functions formulation with its weak form is developed using variational method. The essential boundary conditions are enforced by Langrange multipliers. The proposed EFG formulation gives comparable results, after beenmore » verified by analytical solution, thus signify its application in partial interaction problems. Based on numerical test results, the Cubic Spline and Quartic Spline weight functions yield better accuracy for the EFG formulation, compares to other proposed weight functions.« less

Particle-based and meshless methods with Aboria

NASA Astrophysics Data System (ADS)

Robinson, Martin; Bruna, Maria

Aboria is a powerful and flexible C++ library for the implementation of particle-based numerical methods. The particles in such methods can represent actual particles (e.g. Molecular Dynamics) or abstract particles used to discretise a continuous function over a domain (e.g. Radial Basis Functions). Aboria provides a particle container, compatible with the Standard Template Library, spatial search data structures, and a Domain Specific Language to specify non-linear operators on the particle set. This paper gives an overview of Aboria's design, an example of use, and a performance benchmark.

Simulation of the hot rolling of steel with direct iteration

NASA Astrophysics Data System (ADS)

Hanoglu, Umut; Šarler, Božidar

2017-10-01

In this study a simulation system based on the meshless Local Radial Basis Function Collocation Method (LRBFCM) is applied for the hot rolling of steel. Rolling is a complex, 3D, thermo-mechanical problem; however, 2D cross-sectional slices are used as computational domains that are aligned with the rolling direction and no heat flow or strain is considered in the direction that is orthogonal to the slices. For each predefined position with respect to the rolling direction, the solution procedure is repeated until the slice reaches the final rolling position. Collocation nodes are initially distributed over the domain and boundaries of the initial slice. A local solution is achieved by considering the overlapping influence domains with either 5 or 7 nodes. Radial Basis Functions (RBFs) are used for the temperature discretization in the thermal model and displacement discretization in the mechanical model. The meshless solution procedure does not require a mesh-generation algorithm in the classic sense. Strong-form mechanical and thermal models are run for each slice regarding the contact with the roll's surface. Ideal plastic material behavior is considered for the mechanical results, where the nonlinear stress-strain relation is solved with a direct iteration. The majority of the Finite Element Model (FEM) simulations, including commercial software, use a conventional Newton-Raphson algorithm. However, direct iteration is chosen here due to its better compatibility with meshless methods. In order to overcome any unforeseen stability issues, the redistribution of the nodes by Elliptic Node Generation (ENG) is applied to one or more slices throughout the simulation. The rolling simulation presented here helps the user to design, test and optimize different rolling schedules. The results can be seen minutes after the simulation's start in terms of temperature, displacement, stress and strain fields as well as important technological parameters, like the roll-separating forces, roll toque, etc. An example of a rolling simulation, in which an initial size of 110x110 mm steel is rolled to a round bar with 80 mm diameter, is shown in Fig. 3. A user-friendly computer application for industrial use is created by using the C# and .NET frameworks.

Meshless method for solving fixed boundary problem of plasma equilibrium

NASA Astrophysics Data System (ADS)

Imazawa, Ryota; Kawano, Yasunori; Itami, Kiyoshi

2015-07-01

This study solves the Grad-Shafranov equation with a fixed plasma boundary by utilizing a meshless method for the first time. Previous studies have utilized a finite element method (FEM) to solve an equilibrium inside the fixed separatrix. In order to avoid difficulties of FEM (such as mesh problem, difficulty of coding, expensive calculation cost), this study focuses on the meshless methods, especially RBF-MFS and KANSA's method to solve the fixed boundary problem. The results showed that CPU time of the meshless methods was ten to one hundred times shorter than that of FEM to obtain the same accuracy.

A novel partitioning method for block-structured adaptive meshes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fu, Lin, E-mail: lin.fu@tum.de; Litvinov, Sergej, E-mail: sergej.litvinov@aer.mw.tum.de; Hu, Xiangyu Y., E-mail: xiangyu.hu@tum.de

We propose a novel partitioning method for block-structured adaptive meshes utilizing the meshless Lagrangian particle concept. With the observation that an optimum partitioning has high analogy to the relaxation of a multi-phase fluid to steady state, physically motivated model equations are developed to characterize the background mesh topology and are solved by multi-phase smoothed-particle hydrodynamics. In contrast to well established partitioning approaches, all optimization objectives are implicitly incorporated and achieved during the particle relaxation to stationary state. Distinct partitioning sub-domains are represented by colored particles and separated by a sharp interface with a surface tension model. In order to obtainmore » the particle relaxation, special viscous and skin friction models, coupled with a tailored time integration algorithm are proposed. Numerical experiments show that the present method has several important properties: generation of approximately equal-sized partitions without dependence on the mesh-element type, optimized interface communication between distinct partitioning sub-domains, continuous domain decomposition which is physically localized and implicitly incremental. Therefore it is particularly suitable for load-balancing of high-performance CFD simulations.« less

A novel partitioning method for block-structured adaptive meshes

NASA Astrophysics Data System (ADS)

Fu, Lin; Litvinov, Sergej; Hu, Xiangyu Y.; Adams, Nikolaus A.

2017-07-01

We propose a novel partitioning method for block-structured adaptive meshes utilizing the meshless Lagrangian particle concept. With the observation that an optimum partitioning has high analogy to the relaxation of a multi-phase fluid to steady state, physically motivated model equations are developed to characterize the background mesh topology and are solved by multi-phase smoothed-particle hydrodynamics. In contrast to well established partitioning approaches, all optimization objectives are implicitly incorporated and achieved during the particle relaxation to stationary state. Distinct partitioning sub-domains are represented by colored particles and separated by a sharp interface with a surface tension model. In order to obtain the particle relaxation, special viscous and skin friction models, coupled with a tailored time integration algorithm are proposed. Numerical experiments show that the present method has several important properties: generation of approximately equal-sized partitions without dependence on the mesh-element type, optimized interface communication between distinct partitioning sub-domains, continuous domain decomposition which is physically localized and implicitly incremental. Therefore it is particularly suitable for load-balancing of high-performance CFD simulations.

Experimental and AI-based numerical modeling of contaminant transport in porous media.

PubMed

Nourani, Vahid; Mousavi, Shahram; Sadikoglu, Fahreddin; Singh, Vijay P

2017-10-01

This study developed a new hybrid artificial intelligence (AI)-meshless approach for modeling contaminant transport in porous media. The key innovation of the proposed approach is that both black box and physically-based models are combined for modeling contaminant transport. The effectiveness of the approach was evaluated using experimental and real world data. Artificial neural network (ANN) and adaptive neuro-fuzzy inference system (ANFIS) were calibrated to predict temporal contaminant concentrations (CCs), and the effect of noisy and de-noised data on the model performance was evaluated. Then, considering the predicted CCs at test points (TPs, in experimental study) and piezometers (in Myandoab plain) as interior conditions, the multiquadric radial basis function (MQ-RBF), as a meshless approach which solves partial differential equation (PDE) of contaminant transport in porous media, was employed to estimate the CC values at any point within the study area where there was no TP or piezometer. Optimal values of the dispersion coefficient in the advection-dispersion PDE and shape coefficient of MQ-RBF were determined using the imperialist competitive algorithm. In temporal contaminant transport modeling, de-noised data enhanced the performance of ANN and ANFIS methods in terms of the determination coefficient, up to 6 and 5%, respectively, in the experimental study and up to 39 and 18%, respectively, in the field study. Results showed that the efficiency of ANFIS-meshless model was more than ANN-meshless model up to 2 and 13% in the experimental and field studies, respectively. Copyright © 2017. Published by Elsevier B.V.

Meshless Modeling of Deformable Shapes and their Motion

PubMed Central

Adams, Bart; Ovsjanikov, Maks; Wand, Michael; Seidel, Hans-Peter; Guibas, Leonidas J.

2010-01-01

We present a new framework for interactive shape deformation modeling and key frame interpolation based on a meshless finite element formulation. Starting from a coarse nodal sampling of an object’s volume, we formulate rigidity and volume preservation constraints that are enforced to yield realistic shape deformations at interactive frame rates. Additionally, by specifying key frame poses of the deforming shape and optimizing the nodal displacements while targeting smooth interpolated motion, our algorithm extends to a motion planning framework for deformable objects. This allows reconstructing smooth and plausible deformable shape trajectories in the presence of possibly moving obstacles. The presented results illustrate that our framework can handle complex shapes at interactive rates and hence is a valuable tool for animators to realistically and efficiently model and interpolate deforming 3D shapes. PMID:24839614

A numerical scheme based on radial basis function finite difference (RBF-FD) technique for solving the high-dimensional nonlinear Schrödinger equations using an explicit time discretization: Runge-Kutta method

NASA Astrophysics Data System (ADS)

Dehghan, Mehdi; Mohammadi, Vahid

2017-08-01

In this research, we investigate the numerical solution of nonlinear Schrödinger equations in two and three dimensions. The numerical meshless method which will be used here is RBF-FD technique. The main advantage of this method is the approximation of the required derivatives based on finite difference technique at each local-support domain as Ωi. At each Ωi, we require to solve a small linear system of algebraic equations with a conditionally positive definite matrix of order 1 (interpolation matrix). This scheme is efficient and its computational cost is same as the moving least squares (MLS) approximation. A challengeable issue is choosing suitable shape parameter for interpolation matrix in this way. In order to overcome this matter, an algorithm which was established by Sarra (2012), will be applied. This algorithm computes the condition number of the local interpolation matrix using the singular value decomposition (SVD) for obtaining the smallest and largest singular values of that matrix. Moreover, an explicit method based on Runge-Kutta formula of fourth-order accuracy will be applied for approximating the time variable. It also decreases the computational costs at each time step since we will not solve a nonlinear system. On the other hand, to compare RBF-FD method with another meshless technique, the moving kriging least squares (MKLS) approximation is considered for the studied model. Our results demonstrate the ability of the present approach for solving the applicable model which is investigated in the current research work.

The meshless local Petrov-Galerkin method based on moving Kriging interpolation for solving the time fractional Navier-Stokes equations.

PubMed

Thamareerat, N; Luadsong, A; Aschariyaphotha, N

2016-01-01

In this paper, we present a numerical scheme used to solve the nonlinear time fractional Navier-Stokes equations in two dimensions. We first employ the meshless local Petrov-Galerkin (MLPG) method based on a local weak formulation to form the system of discretized equations and then we will approximate the time fractional derivative interpreted in the sense of Caputo by a simple quadrature formula. The moving Kriging interpolation which possesses the Kronecker delta property is applied to construct shape functions. This research aims to extend and develop further the applicability of the truly MLPG method to the generalized incompressible Navier-Stokes equations. Two numerical examples are provided to illustrate the accuracy and efficiency of the proposed algorithm. Very good agreement between the numerically and analytically computed solutions can be observed in the verification. The present MLPG method has proved its efficiency and reliability for solving the two-dimensional time fractional Navier-Stokes equations arising in fluid dynamics as well as several other problems in science and engineering.

A compatible high-order meshless method for the Stokes equations with applications to suspension flows

NASA Astrophysics Data System (ADS)

Trask, Nathaniel; Maxey, Martin; Hu, Xiaozhe

2018-02-01

A stable numerical solution of the steady Stokes problem requires compatibility between the choice of velocity and pressure approximation that has traditionally proven problematic for meshless methods. In this work, we present a discretization that couples a staggered scheme for pressure approximation with a divergence-free velocity reconstruction to obtain an adaptive, high-order, finite difference-like discretization that can be efficiently solved with conventional algebraic multigrid techniques. We use analytic benchmarks to demonstrate equal-order convergence for both velocity and pressure when solving problems with curvilinear geometries. In order to study problems in dense suspensions, we couple the solution for the flow to the equations of motion for freely suspended particles in an implicit monolithic scheme. The combination of high-order accuracy with fully-implicit schemes allows the accurate resolution of stiff lubrication forces directly from the solution of the Stokes problem without the need to introduce sub-grid lubrication models.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Ch.; Gao, X. W.; Sladek, J.

This paper reports our recent research works on crack analysis in continuously non-homogeneous and linear elastic functionally graded materials. A meshless boundary element method is developed for this purpose. Numerical examples are presented and discussed to demonstrate the efficiency and the accuracy of the present numerical method, and to show the effects of the material gradation on the crack-opening-displacements and the stress intensity factors.

Meshless Local Petrov-Galerkin Method for Bending Problems

NASA Technical Reports Server (NTRS)

Phillips, Dawn R.; Raju, Ivatury S.

2002-01-01

Recent literature shows extensive research work on meshless or element-free methods as alternatives to the versatile Finite Element Method. One such meshless method is the Meshless Local Petrov-Galerkin (MLPG) method. In this report, the method is developed for bending of beams - C1 problems. A generalized moving least squares (GMLS) interpolation is used to construct the trial functions, and spline and power weight functions are used as the test functions. The method is applied to problems for which exact solutions are available to evaluate its effectiveness. The accuracy of the method is demonstrated for problems with load discontinuities and continuous beam problems. A Petrov-Galerkin implementation of the method is shown to greatly reduce computational time and effort and is thus preferable over the previously developed Galerkin approach. The MLPG method for beam problems yields very accurate deflections and slopes and continuous moment and shear forces without the need for elaborate post-processing techniques.

Meshless Method for Simulation of Compressible Flow

NASA Astrophysics Data System (ADS)

Nabizadeh Shahrebabak, Ebrahim

In the present age, rapid development in computing technology and high speed supercomputers has made numerical analysis and computational simulation more practical than ever before for large and complex cases. Numerical simulations have also become an essential means for analyzing the engineering problems and the cases that experimental analysis is not practical. There are so many sophisticated and accurate numerical schemes, which do these simulations. The finite difference method (FDM) has been used to solve differential equation systems for decades. Additional numerical methods based on finite volume and finite element techniques are widely used in solving problems with complex geometry. All of these methods are mesh-based techniques. Mesh generation is an essential preprocessing part to discretize the computation domain for these conventional methods. However, when dealing with mesh-based complex geometries these conventional mesh-based techniques can become troublesome, difficult to implement, and prone to inaccuracies. In this study, a more robust, yet simple numerical approach is used to simulate problems in an easier manner for even complex problem. The meshless, or meshfree, method is one such development that is becoming the focus of much research in the recent years. The biggest advantage of meshfree methods is to circumvent mesh generation. Many algorithms have now been developed to help make this method more popular and understandable for everyone. These algorithms have been employed over a wide range of problems in computational analysis with various levels of success. Since there is no connectivity between the nodes in this method, the challenge was considerable. The most fundamental issue is lack of conservation, which can be a source of unpredictable errors in the solution process. This problem is particularly evident in the presence of steep gradient regions and discontinuities, such as shocks that frequently occur in high speed compressible flow problems. To solve this discontinuity problem, this research study deals with the implementation of a conservative meshless method and its applications in computational fluid dynamics (CFD). One of the most common types of collocating meshless method the RBF-DQ, is used to approximate the spatial derivatives. The issue with meshless methods when dealing with highly convective cases is that they cannot distinguish the influence of fluid flow from upstream or downstream and some methodology is needed to make the scheme stable. Therefore, an upwinding scheme similar to one used in the finite volume method is added to capture steep gradient or shocks. This scheme creates a flexible algorithm within which a wide range of numerical flux schemes, such as those commonly used in the finite volume method, can be employed. In addition, a blended RBF is used to decrease the dissipation ensuing from the use of a low shape parameter. All of these steps are formulated for the Euler equation and a series of test problems used to confirm convergence of the algorithm. The present scheme was first employed on several incompressible benchmarks to validate the framework. The application of this algorithm is illustrated by solving a set of incompressible Navier-Stokes problems. Results from the compressible problem are compared with the exact solution for the flow over a ramp and compared with solutions of finite volume discretization and the discontinuous Galerkin method, both requiring a mesh. The applicability of the algorithm and its robustness are shown to be applied to complex problems.

Meshless collocation methods for the numerical solution of elliptic boundary valued problems the rotational shallow water equations on the sphere

NASA Astrophysics Data System (ADS)

Blakely, Christopher D.

This dissertation thesis has three main goals: (1) To explore the anatomy of meshless collocation approximation methods that have recently gained attention in the numerical analysis community; (2) Numerically demonstrate why the meshless collocation method should clearly become an attractive alternative to standard finite-element methods due to the simplicity of its implementation and its high-order convergence properties; (3) Propose a meshless collocation method for large scale computational geophysical fluid dynamics models. We provide numerical verification and validation of the meshless collocation scheme applied to the rotational shallow-water equations on the sphere and demonstrate computationally that the proposed model can compete with existing high performance methods for approximating the shallow-water equations such as the SEAM (spectral-element atmospheric model) developed at NCAR. A detailed analysis of the parallel implementation of the model, along with the introduction of parallel algorithmic routines for the high-performance simulation of the model will be given. We analyze the programming and computational aspects of the model using Fortran 90 and the message passing interface (mpi) library along with software and hardware specifications and performance tests. Details from many aspects of the implementation in regards to performance, optimization, and stabilization will be given. In order to verify the mathematical correctness of the algorithms presented and to validate the performance of the meshless collocation shallow-water model, we conclude the thesis with numerical experiments on some standardized test cases for the shallow-water equations on the sphere using the proposed method.

A class of renormalised meshless Laplacians for boundary value problems

NASA Astrophysics Data System (ADS)

Basic, Josip; Degiuli, Nastia; Ban, Dario

2018-02-01

A meshless approach to approximating spatial derivatives on scattered point arrangements is presented in this paper. Three various derivations of approximate discrete Laplace operator formulations are produced using the Taylor series expansion and renormalised least-squares correction of the first spatial derivatives. Numerical analyses are performed for the introduced Laplacian formulations, and their convergence rate and computational efficiency are examined. The tests are conducted on regular and highly irregular scattered point arrangements. The results are compared to those obtained by the smoothed particle hydrodynamics method and the finite differences method on a regular grid. Finally, the strong form of various Poisson and diffusion equations with Dirichlet or Robin boundary conditions are solved in two and three dimensions by making use of the introduced operators in order to examine their stability and accuracy for boundary value problems. The introduced Laplacian operators perform well for highly irregular point distribution and offer adequate accuracy for mesh and mesh-free numerical methods that require frequent movement of the grid or point cloud.

Biomechanical Model for Computing Deformations for Whole-Body Image Registration: A Meshless Approach

PubMed Central

Li, Mao; Miller, Karol; Joldes, Grand Roman; Kikinis, Ron; Wittek, Adam

2016-01-01

Patient-specific biomechanical models have been advocated as a tool for predicting deformations of soft body organs/tissue for medical image registration (aligning two sets of images) when differences between the images are large. However, complex and irregular geometry of the body organs makes generation of patient-specific biomechanical models very time consuming. Meshless discretisation has been proposed to solve this challenge. However, applications so far have been limited to 2-D models and computing single organ deformations. In this study, 3-D comprehensive patient-specific non-linear biomechanical models implemented using Meshless Total Lagrangian Explicit Dynamics (MTLED) algorithms are applied to predict a 3-D deformation field for whole-body image registration. Unlike a conventional approach which requires dividing (segmenting) the image into non-overlapping constituents representing different organs/tissues, the mechanical properties are assigned using the Fuzzy C-Means (FCM) algorithm without the image segmentation. Verification indicates that the deformations predicted using the proposed meshless approach are for practical purposes the same as those obtained using the previously validated finite element models. To quantitatively evaluate the accuracy of the predicted deformations, we determined the spatial misalignment between the registered (i.e. source images warped using the predicted deformations) and target images by computing the edge-based Hausdorff distance. The Hausdorff distance-based evaluation determines that our meshless models led to successful registration of the vast majority of the image features. PMID:26791945

Meshless Lagrangian SPH method applied to isothermal lid-driven cavity flow at low-Re numbers

NASA Astrophysics Data System (ADS)

Fraga Filho, C. A. D.; Chacaltana, J. T. A.; Pinto, W. J. N.

2018-01-01

SPH is a recent particle method applied in the cavities study, without many results available in the literature. The lid-driven cavity flow is a classic problem of the fluid mechanics, extensively explored in the literature and presenting a considerable complexity. The aim of this paper is to present a solution from the Lagrangian viewpoint for this problem. The discretization of the continuum domain is performed using the Lagrangian particles. The physical laws of mass, momentum and energy conservation are presented by the Navier-Stokes equations. A serial numerical code, written in Fortran programming language, has been used to perform the numerical simulations. The application of the SPH and comparison with the literature (mesh methods and a meshless collocation method) have been done. The positions of the primary vortex centre and the non-dimensional velocity profiles passing through the geometric centre of the cavity have been analysed. The numerical Lagrangian results showed a good agreement when compared to the results found in the literature, specifically for { Re} < 100.00 . Suggestions for improvements in the SPH model presented are listed, in the search for better results for flows with higher Reynolds numbers.

Biomechanical model for computing deformations for whole-body image registration: A meshless approach.

PubMed

Li, Mao; Miller, Karol; Joldes, Grand Roman; Kikinis, Ron; Wittek, Adam

2016-12-01

Patient-specific biomechanical models have been advocated as a tool for predicting deformations of soft body organs/tissue for medical image registration (aligning two sets of images) when differences between the images are large. However, complex and irregular geometry of the body organs makes generation of patient-specific biomechanical models very time-consuming. Meshless discretisation has been proposed to solve this challenge. However, applications so far have been limited to 2D models and computing single organ deformations. In this study, 3D comprehensive patient-specific nonlinear biomechanical models implemented using meshless Total Lagrangian explicit dynamics algorithms are applied to predict a 3D deformation field for whole-body image registration. Unlike a conventional approach that requires dividing (segmenting) the image into non-overlapping constituents representing different organs/tissues, the mechanical properties are assigned using the fuzzy c-means algorithm without the image segmentation. Verification indicates that the deformations predicted using the proposed meshless approach are for practical purposes the same as those obtained using the previously validated finite element models. To quantitatively evaluate the accuracy of the predicted deformations, we determined the spatial misalignment between the registered (i.e. source images warped using the predicted deformations) and target images by computing the edge-based Hausdorff distance. The Hausdorff distance-based evaluation determines that our meshless models led to successful registration of the vast majority of the image features. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

A second order radiative transfer equation and its solution by meshless method with application to strongly inhomogeneous media

NASA Astrophysics Data System (ADS)

Zhao, J. M.; Tan, J. Y.; Liu, L. H.

2013-01-01

A new second order form of radiative transfer equation (named MSORTE) is proposed, which overcomes the singularity problem of a previously proposed second order radiative transfer equation [J.E. Morel, B.T. Adams, T. Noh, J.M. McGhee, T.M. Evans, T.J. Urbatsch, Spatial discretizations for self-adjoint forms of the radiative transfer equations, J. Comput. Phys. 214 (1) (2006) 12-40 (where it was termed SAAI), J.M. Zhao, L.H. Liu, Second order radiative transfer equation and its properties of numerical solution using finite element method, Numer. Heat Transfer B 51 (2007) 391-409] in dealing with inhomogeneous media where some locations have very small/zero extinction coefficient. The MSORTE contains a naturally introduced diffusion (or second order) term which provides better numerical property than the classic first order radiative transfer equation (RTE). The stability and convergence characteristics of the MSORTE discretized by central difference scheme is analyzed theoretically, and the better numerical stability of the second order form radiative transfer equations than the RTE when discretized by the central difference type method is proved. A collocation meshless method is developed based on the MSORTE to solve radiative transfer in inhomogeneous media. Several critical test cases are taken to verify the performance of the presented method. The collocation meshless method based on the MSORTE is demonstrated to be capable of stably and accurately solve radiative transfer in strongly inhomogeneous media, media with void region and even with discontinuous extinction coefficient.

A well-balanced meshless tsunami propagation and inundation model

NASA Astrophysics Data System (ADS)

Brecht, Rüdiger; Bihlo, Alexander; MacLachlan, Scott; Behrens, Jörn

2018-05-01

We present a novel meshless tsunami propagation and inundation model. We discretize the nonlinear shallow-water equations using a well-balanced scheme relying on radial basis function based finite differences. For the inundation model, radial basis functions are used to extrapolate the dry region from nearby wet points. Numerical results against standard one- and two-dimensional benchmarks are presented.

Meshless Geometric Subdivision

DTIC Science & Technology

2004-10-01

Michelangelo Youthful data set is shown on the right. for p ∈ M and with boundary condition dM (q, q) = 0 is approximated by |∇dΩrP (p, ·)| = F̃ (p), (2...dealing with more complex geometry. We apply our meshless subdivision operator to a base point set of 10088 points generated from the Michelangelo ...acknowledge the permission to use the Michelangelo point sets granted by the Stanford Computer Graphics group. The Isis, 50% decimated and non

Boundary particle method for Laplace transformed time fractional diffusion equations

NASA Astrophysics Data System (ADS)

Fu, Zhuo-Jia; Chen, Wen; Yang, Hai-Tian

2013-02-01

This paper develops a novel boundary meshless approach, Laplace transformed boundary particle method (LTBPM), for numerical modeling of time fractional diffusion equations. It implements Laplace transform technique to obtain the corresponding time-independent inhomogeneous equation in Laplace space and then employs a truly boundary-only meshless boundary particle method (BPM) to solve this Laplace-transformed problem. Unlike the other boundary discretization methods, the BPM does not require any inner nodes, since the recursive composite multiple reciprocity technique (RC-MRM) is used to convert the inhomogeneous problem into the higher-order homogeneous problem. Finally, the Stehfest numerical inverse Laplace transform (NILT) is implemented to retrieve the numerical solutions of time fractional diffusion equations from the corresponding BPM solutions. In comparison with finite difference discretization, the LTBPM introduces Laplace transform and Stehfest NILT algorithm to deal with time fractional derivative term, which evades costly convolution integral calculation in time fractional derivation approximation and avoids the effect of time step on numerical accuracy and stability. Consequently, it can effectively simulate long time-history fractional diffusion systems. Error analysis and numerical experiments demonstrate that the present LTBPM is highly accurate and computationally efficient for 2D and 3D time fractional diffusion equations.

Reconstruction and analysis of hybrid composite shells using meshless methods

NASA Astrophysics Data System (ADS)

Bernardo, G. M. S.; Loja, M. A. R.

2017-06-01

The importance of focusing on the research of viable models to predict the behaviour of structures which may possess in some cases complex geometries is an issue that is growing in different scientific areas, ranging from the civil and mechanical engineering to the architecture or biomedical devices fields. In these cases, the research effort to find an efficient approach to fit laser scanning point clouds, to the desired surface, has been increasing, leading to the possibility of modelling as-built/as-is structures and components' features. However, combining the task of surface reconstruction and the implementation of a structural analysis model is not a trivial task. Although there are works focusing those different phases in separate, there is still an effective need to find approaches able to interconnect them in an efficient way. Therefore, achieving a representative geometric model able to be subsequently submitted to a structural analysis in a similar based platform is a fundamental step to establish an effective expeditious processing workflow. With the present work, one presents an integrated methodology based on the use of meshless approaches, to reconstruct shells described by points' clouds, and to subsequently predict their static behaviour. These methods are highly appropriate on dealing with unstructured points clouds, as they do not need to have any specific spatial or geometric requirement when implemented, depending only on the distance between the points. Details on the formulation, and a set of illustrative examples focusing the reconstruction of cylindrical and double-curvature shells, and its further analysis, are presented.

Meshless Method with Operator Splitting Technique for Transient Nonlinear Bioheat Transfer in Two-Dimensional Skin Tissues

PubMed Central

Zhang, Ze-Wei; Wang, Hui; Qin, Qing-Hua

2015-01-01

A meshless numerical scheme combining the operator splitting method (OSM), the radial basis function (RBF) interpolation, and the method of fundamental solutions (MFS) is developed for solving transient nonlinear bioheat problems in two-dimensional (2D) skin tissues. In the numerical scheme, the nonlinearity caused by linear and exponential relationships of temperature-dependent blood perfusion rate (TDBPR) is taken into consideration. In the analysis, the OSM is used first to separate the Laplacian operator and the nonlinear source term, and then the second-order time-stepping schemes are employed for approximating two splitting operators to convert the original governing equation into a linear nonhomogeneous Helmholtz-type governing equation (NHGE) at each time step. Subsequently, the RBF interpolation and the MFS involving the fundamental solution of the Laplace equation are respectively employed to obtain approximated particular and homogeneous solutions of the nonhomogeneous Helmholtz-type governing equation. Finally, the full fields consisting of the particular and homogeneous solutions are enforced to fit the NHGE at interpolation points and the boundary conditions at boundary collocations for determining unknowns at each time step. The proposed method is verified by comparison of other methods. Furthermore, the sensitivity of the coefficients in the cases of a linear and an exponential relationship of TDBPR is investigated to reveal their bioheat effect on the skin tissue. PMID:25603180

Meshless method with operator splitting technique for transient nonlinear bioheat transfer in two-dimensional skin tissues.

PubMed

Zhang, Ze-Wei; Wang, Hui; Qin, Qing-Hua

2015-01-16

A meshless numerical scheme combining the operator splitting method (OSM), the radial basis function (RBF) interpolation, and the method of fundamental solutions (MFS) is developed for solving transient nonlinear bioheat problems in two-dimensional (2D) skin tissues. In the numerical scheme, the nonlinearity caused by linear and exponential relationships of temperature-dependent blood perfusion rate (TDBPR) is taken into consideration. In the analysis, the OSM is used first to separate the Laplacian operator and the nonlinear source term, and then the second-order time-stepping schemes are employed for approximating two splitting operators to convert the original governing equation into a linear nonhomogeneous Helmholtz-type governing equation (NHGE) at each time step. Subsequently, the RBF interpolation and the MFS involving the fundamental solution of the Laplace equation are respectively employed to obtain approximated particular and homogeneous solutions of the nonhomogeneous Helmholtz-type governing equation. Finally, the full fields consisting of the particular and homogeneous solutions are enforced to fit the NHGE at interpolation points and the boundary conditions at boundary collocations for determining unknowns at each time step. The proposed method is verified by comparison of other methods. Furthermore, the sensitivity of the coefficients in the cases of a linear and an exponential relationship of TDBPR is investigated to reveal their bioheat effect on the skin tissue.

Accurate, meshless methods for magnetohydrodynamics

NASA Astrophysics Data System (ADS)

Hopkins, Philip F.; Raives, Matthias J.

2016-01-01

Recently, we explored new meshless finite-volume Lagrangian methods for hydrodynamics: the `meshless finite mass' (MFM) and `meshless finite volume' (MFV) methods; these capture advantages of both smoothed particle hydrodynamics (SPH) and adaptive mesh refinement (AMR) schemes. We extend these to include ideal magnetohydrodynamics (MHD). The MHD equations are second-order consistent and conservative. We augment these with a divergence-cleaning scheme, which maintains nabla \\cdot B≈ 0. We implement these in the code GIZMO, together with state-of-the-art SPH MHD. We consider a large test suite, and show that on all problems the new methods are competitive with AMR using constrained transport (CT) to ensure nabla \\cdot B=0. They correctly capture the growth/structure of the magnetorotational instability, MHD turbulence, and launching of magnetic jets, in some cases converging more rapidly than state-of-the-art AMR. Compared to SPH, the MFM/MFV methods exhibit convergence at fixed neighbour number, sharp shock-capturing, and dramatically reduced noise, divergence errors, and diffusion. Still, `modern' SPH can handle most test problems, at the cost of larger kernels and `by hand' adjustment of artificial diffusion. Compared to non-moving meshes, the new methods exhibit enhanced `grid noise' but reduced advection errors and diffusion, easily include self-gravity, and feature velocity-independent errors and superior angular momentum conservation. They converge more slowly on some problems (smooth, slow-moving flows), but more rapidly on others (involving advection/rotation). In all cases, we show divergence control beyond the Powell 8-wave approach is necessary, or all methods can converge to unphysical answers even at high resolution.

Solving Reynolds Equation in the Head-Disk Interface of Hard Disk Drives by Using a Meshless Method

NASA Astrophysics Data System (ADS)

Bao-Jun, Shi; Ting-Yi, Yang; Jian, Zhang; Yun-Dong, Du

2010-05-01

With the decrease of the flying height of the magnetic head/slider in hard disk drives (HDDs), Reynolds equation, which is used to describe the pressure distribution of the air bearing film in HDDs, must be modified to account for the rarefaction effect. Meshless local Petrov-Galerkin (MLPG) method has been successfully used in some fields of solid mechanics and fluid mechanics and was proven to be an efficacious method. No meshes are needed in MLPG method either for the interpolation of the trial and test functions, or for the integration of the weak form of the related differential equation. We solve Reynolds equation in the head-disk interface (HDI) of HDDs by using MLPG method. The pressure distribution of the air baring film by using MLPG method is obtained and compared with the exact solution and that obtained by using a least square finite difference (LSFD) method. We also investigate effects of the bearing number on the pressure value and the center of pressure based on this meshless method for different film-thickness ratios.

A meshless EFG-based algorithm for 3D deformable modeling of soft tissue in real-time.

PubMed

Abdi, Elahe; Farahmand, Farzam; Durali, Mohammad

2012-01-01

The meshless element-free Galerkin method was generalized and an algorithm was developed for 3D dynamic modeling of deformable bodies in real time. The efficacy of the algorithm was investigated in a 3D linear viscoelastic model of human spleen subjected to a time-varying compressive force exerted by a surgical grasper. The model remained stable in spite of the considerably large deformations occurred. There was a good agreement between the results and those of an equivalent finite element model. The computational cost, however, was much lower, enabling the proposed algorithm to be effectively used in real-time applications.

Object-constrained meshless deformable algorithm for high speed 3D nonrigid registration between CT and CBCT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen Ting; Kim, Sung; Goyal, Sharad

2010-01-15

Purpose: High-speed nonrigid registration between the planning CT and the treatment CBCT data is critical for real time image guided radiotherapy (IGRT) to improve the dose distribution and to reduce the toxicity to adjacent organs. The authors propose a new fully automatic 3D registration framework that integrates object-based global and seed constraints with the grayscale-based ''demons'' algorithm. Methods: Clinical objects were segmented on the planning CT images and were utilized as meshless deformable models during the nonrigid registration process. The meshless models reinforced a global constraint in addition to the grayscale difference between CT and CBCT in order to maintainmore » the shape and the volume of geometrically complex 3D objects during the registration. To expedite the registration process, the framework was stratified into hierarchies, and the authors used a frequency domain formulation to diffuse the displacement between the reference and the target in each hierarchy. Also during the registration of pelvis images, they replaced the air region inside the rectum with estimated pixel values from the surrounding rectal wall and introduced an additional seed constraint to robustly track and match the seeds implanted into the prostate. The proposed registration framework and algorithm were evaluated on 15 real prostate cancer patients. For each patient, prostate gland, seminal vesicle, bladder, and rectum were first segmented by a radiation oncologist on planning CT images for radiotherapy planning purpose. The same radiation oncologist also manually delineated the tumor volumes and critical anatomical structures in the corresponding CBCT images acquired at treatment. These delineated structures on the CBCT were only used as the ground truth for the quantitative validation, while structures on the planning CT were used both as the input to the registration method and the ground truth in validation. By registering the planning CT to the CBCT, a displacement map was generated. Segmented volumes in the CT images deformed using the displacement field were compared against the manual segmentations in the CBCT images to quantitatively measure the convergence of the shape and the volume. Other image features were also used to evaluate the overall performance of the registration. Results: The algorithm was able to complete the segmentation and registration process within 1 min, and the superimposed clinical objects achieved a volumetric similarity measure of over 90% between the reference and the registered data. Validation results also showed that the proposed registration could accurately trace the deformation inside the target volume with average errors of less than 1 mm. The method had a solid performance in registering the simulated images with up to 20 Hounsfield unit white noise added. Also, the side by side comparison with the original demons algorithm demonstrated its improved registration performance over the local pixel-based registration approaches. Conclusions: Given the strength and efficiency of the algorithm, the proposed method has significant clinical potential to accelerate and to improve the CBCT delineation and targets tracking in online IGRT applications.« less

A meshless method using radial basis functions for numerical solution of the two-dimensional KdV-Burgers equation

NASA Astrophysics Data System (ADS)

Zabihi, F.; Saffarian, M.

2016-07-01

The aim of this article is to obtain the numerical solution of the two-dimensional KdV-Burgers equation. We construct the solution by using a different approach, that is based on using collocation points. The solution is based on using the thin plate splines radial basis function, which builds an approximated solution with discretizing the time and the space to small steps. We use a predictor-corrector scheme to avoid solving the nonlinear system. The results of numerical experiments are compared with analytical solutions to confirm the accuracy and efficiency of the presented scheme.

Solution of Grad-Shafranov equation by the method of fundamental solutions

NASA Astrophysics Data System (ADS)

Nath, D.; Kalra, M. S.; Kalra

2014-06-01

In this paper we have used the Method of Fundamental Solutions (MFS) to solve the Grad-Shafranov (GS) equation for the axisymmetric equilibria of tokamak plasmas with monomial sources. These monomials are the individual terms appearing on the right-hand side of the GS equation if one expands the nonlinear terms into polynomials. Unlike the Boundary Element Method (BEM), the MFS does not involve any singular integrals and is a meshless boundary-alone method. Its basic idea is to create a fictitious boundary around the actual physical boundary of the computational domain. This automatically removes the involvement of singular integrals. The results obtained by the MFS match well with the earlier results obtained using the BEM. The method is also applied to Solov'ev profiles and it is found that the results are in good agreement with analytical results.

A nearest-neighbour discretisation of the regularized stokeslet boundary integral equation

NASA Astrophysics Data System (ADS)

Smith, David J.

2018-04-01

The method of regularized stokeslets is extensively used in biological fluid dynamics due to its conceptual simplicity and meshlessness. This simplicity carries a degree of cost in computational expense and accuracy because the number of degrees of freedom used to discretise the unknown surface traction is generally significantly higher than that required by boundary element methods. We describe a meshless method based on nearest-neighbour interpolation that significantly reduces the number of degrees of freedom required to discretise the unknown traction, increasing the range of problems that can be practically solved, without excessively complicating the task of the modeller. The nearest-neighbour technique is tested against the classical problem of rigid body motion of a sphere immersed in very viscous fluid, then applied to the more complex biophysical problem of calculating the rotational diffusion timescales of a macromolecular structure modelled by three closely-spaced non-slender rods. A heuristic for finding the required density of force and quadrature points by numerical refinement is suggested. Matlab/GNU Octave code for the key steps of the algorithm is provided, which predominantly use basic linear algebra operations, with a full implementation being provided on github. Compared with the standard Nyström discretisation, more accurate and substantially more efficient results can be obtained by de-refining the force discretisation relative to the quadrature discretisation: a cost reduction of over 10 times with improved accuracy is observed. This improvement comes at minimal additional technical complexity. Future avenues to develop the algorithm are then discussed.

Numerical study of the shape parameter dependence of the local radial point interpolation method in linear elasticity.

PubMed

Moussaoui, Ahmed; Bouziane, Touria

2016-01-01

The method LRPIM is a Meshless method with properties of simple implementation of the essential boundary conditions and less costly than the moving least squares (MLS) methods. This method is proposed to overcome the singularity associated to polynomial basis by using radial basis functions. In this paper, we will present a study of a 2D problem of an elastic homogenous rectangular plate by using the method LRPIM. Our numerical investigations will concern the influence of different shape parameters on the domain of convergence,accuracy and using the radial basis function of the thin plate spline. It also will presents a comparison between numerical results for different materials and the convergence domain by precising maximum and minimum values as a function of distribution nodes number. The analytical solution of the deflection confirms the numerical results. The essential points in the method are: •The LRPIM is derived from the local weak form of the equilibrium equations for solving a thin elastic plate.•The convergence of the LRPIM method depends on number of parameters derived from local weak form and sub-domains.•The effect of distributions nodes number by varying nature of material and the radial basis function (TPS).

Meshless Local Petrov-Galerkin Euler-Bernoulli Beam Problems: A Radial Basis Function Approach

NASA Technical Reports Server (NTRS)

Raju, I. S.; Phillips, D. R.; Krishnamurthy, T.

2003-01-01

A radial basis function implementation of the meshless local Petrov-Galerkin (MLPG) method is presented to study Euler-Bernoulli beam problems. Radial basis functions, rather than generalized moving least squares (GMLS) interpolations, are used to develop the trial functions. This choice yields a computationally simpler method as fewer matrix inversions and multiplications are required than when GMLS interpolations are used. Test functions are chosen as simple weight functions as in the conventional MLPG method. Compactly and noncompactly supported radial basis functions are considered. The non-compactly supported cubic radial basis function is found to perform very well. Results obtained from the radial basis MLPG method are comparable to those obtained using the conventional MLPG method for mixed boundary value problems and problems with discontinuous loading conditions.

2D modeling of direct laser metal deposition process using a finite particle method

NASA Astrophysics Data System (ADS)

Anedaf, T.; Abbès, B.; Abbès, F.; Li, Y. M.

2018-05-01

Direct laser metal deposition is one of the material additive manufacturing processes used to produce complex metallic parts. A thorough understanding of the underlying physical phenomena is required to obtain a high-quality parts. In this work, a mathematical model is presented to simulate the coaxial laser direct deposition process tacking into account of mass addition, heat transfer, and fluid flow with free surface and melting. The fluid flow in the melt pool together with mass and energy balances are solved using the Computational Fluid Dynamics (CFD) software NOGRID-points, based on the meshless Finite Pointset Method (FPM). The basis of the computations is a point cloud, which represents the continuum fluid domain. Each finite point carries all fluid information (density, velocity, pressure and temperature). The dynamic shape of the molten zone is explicitly described by the point cloud. The proposed model is used to simulate a single layer cladding.

gpuSPHASE-A shared memory caching implementation for 2D SPH using CUDA

NASA Astrophysics Data System (ADS)

Winkler, Daniel; Meister, Michael; Rezavand, Massoud; Rauch, Wolfgang

2017-04-01

Smoothed particle hydrodynamics (SPH) is a meshless Lagrangian method that has been successfully applied to computational fluid dynamics (CFD), solid mechanics and many other multi-physics problems. Using the method to solve transport phenomena in process engineering requires the simulation of several days to weeks of physical time. Based on the high computational demand of CFD such simulations in 3D need a computation time of years so that a reduction to a 2D domain is inevitable. In this paper gpuSPHASE, a new open-source 2D SPH solver implementation for graphics devices, is developed. It is optimized for simulations that must be executed with thousands of frames per second to be computed in reasonable time. A novel caching algorithm for Compute Unified Device Architecture (CUDA) shared memory is proposed and implemented. The software is validated and the performance is evaluated for the well established dambreak test case.

A Meshless Method Using Radial Basis Functions for Beam Bending Problems

NASA Technical Reports Server (NTRS)

Raju, I. S.; Phillips, D. R.; Krishnamurthy, T.

2004-01-01

A meshless local Petrov-Galerkin (MLPG) method that uses radial basis functions (RBFs) as trial functions in the study of Euler-Bernoulli beam problems is presented. RBFs, rather than generalized moving least squares (GMLS) interpolations, are used to develop the trial functions. This choice yields a computationally simpler method as fewer matrix inversions and multiplications are required than when GMLS interpolations are used. Test functions are chosen as simple weight functions as they are in the conventional MLPG method. Compactly and noncompactly supported RBFs are considered. Noncompactly supported cubic RBFs are found to be preferable. Patch tests, mixed boundary value problems, and problems with complex loading conditions are considered. Results obtained from the radial basis MLPG method are either of comparable or better accuracy than those obtained when using the conventional MLPG method.

Meshless Solution of the Problem on the Static Behavior of Thin and Thick Laminated Composite Beams

NASA Astrophysics Data System (ADS)

Xiang, S.; Kang, G. W.

2018-03-01

For the first time, the static behavior of laminated composite beams is analyzed using the meshless collocation method based on a thin-plate-spline radial basis function. In the approximation of a partial differential equation by using a radial basis function, the shape parameter has an important role in ensuring the numerical accuracy. The choice of a shape parameter in the thin plate spline radial basis function is easier than in other radial basis functions. The governing differential equations are derived based on Reddy's third-order shear deformation theory. Numerical results are obtained for symmetric cross-ply laminated composite beams with simple-simple and cantilever boundary conditions under a uniform load. The results found are compared with available published ones and demonstrate the accuracy of the present method.

A New Hybrid Viscoelastic Soft Tissue Model based on Meshless Method for Haptic Surgical Simulation

PubMed Central

Bao, Yidong; Wu, Dongmei; Yan, Zhiyuan; Du, Zhijiang

2013-01-01

This paper proposes a hybrid soft tissue model that consists of a multilayer structure and many spheres for surgical simulation system based on meshless. To improve accuracy of the model, tension is added to the three-parameter viscoelastic structure that connects the two spheres. By using haptic device, the three-parameter viscoelastic model (TPM) produces accurate deformationand also has better stress-strain, stress relaxation and creep properties. Stress relaxation and creep formulas have been obtained by mathematical formula derivation. Comparing with the experimental results of the real pig liver which were reported by Evren et al. and Amy et al., the curve lines of stress-strain, stress relaxation and creep of TPM are close to the experimental data of the real liver. Simulated results show that TPM has better real-time, stability and accuracy. PMID:24339837

Modeling Soft Tissue Damage and Failure Using a Combined Particle/Continuum Approach.

PubMed

Rausch, M K; Karniadakis, G E; Humphrey, J D

2017-02-01

Biological soft tissues experience damage and failure as a result of injury, disease, or simply age; examples include torn ligaments and arterial dissections. Given the complexity of tissue geometry and material behavior, computational models are often essential for studying both damage and failure. Yet, because of the need to account for discontinuous phenomena such as crazing, tearing, and rupturing, continuum methods are limited. Therefore, we model soft tissue damage and failure using a particle/continuum approach. Specifically, we combine continuum damage theory with Smoothed Particle Hydrodynamics (SPH). Because SPH is a meshless particle method, and particle connectivity is determined solely through a neighbor list, discontinuities can be readily modeled by modifying this list. We show, for the first time, that an anisotropic hyperelastic constitutive model commonly employed for modeling soft tissue can be conveniently implemented within a SPH framework and that SPH results show excellent agreement with analytical solutions for uniaxial and biaxial extension as well as finite element solutions for clamped uniaxial extension in 2D and 3D. We further develop a simple algorithm that automatically detects damaged particles and disconnects the spatial domain along rupture lines in 2D and rupture surfaces in 3D. We demonstrate the utility of this approach by simulating damage and failure under clamped uniaxial extension and in a peeling experiment of virtual soft tissue samples. In conclusion, SPH in combination with continuum damage theory may provide an accurate and efficient framework for modeling damage and failure in soft tissues.

Modeling Soft Tissue Damage and Failure Using a Combined Particle/Continuum Approach

PubMed Central

Rausch, M. K.; Karniadakis, G. E.; Humphrey, J. D.

2016-01-01

Biological soft tissues experience damage and failure as a result of injury, disease, or simply age; examples include torn ligaments and arterial dissections. Given the complexity of tissue geometry and material behavior, computational models are often essential for studying both damage and failure. Yet, because of the need to account for discontinuous phenomena such as crazing, tearing, and rupturing, continuum methods are limited. Therefore, we model soft tissue damage and failure using a particle/continuum approach. Specifically, we combine continuum damage theory with Smoothed Particle Hydrodynamics (SPH). Because SPH is a meshless particle method, and particle connectivity is determined solely through a neighbor list, discontinuities can be readily modeled by modifying this list. We show, for the first time, that an anisotropic hyperelastic constitutive model commonly employed for modeling soft tissue can be conveniently implemented within a SPH framework and that SPH results show excellent agreement with analytical solutions for uniaxial and biaxial extension as well as finite element solutions for clamped uniaxial extension in 2D and 3D. We further develop a simple algorithm that automatically detects damaged particles and disconnects the spatial domain along rupture lines in 2D and rupture surfaces in 3D. We demonstrate the utility of this approach by simulating damage and failure under clamped uniaxial extension and in a peeling experiment of virtual soft tissue samples. In conclusion, SPH in combination with continuum damage theory may provide an accurate and efficient framework for modeling damage and failure in soft tissues. PMID:27538848

Calculation of steady and unsteady transonic flow using a Cartesian mesh and gridless boundary conditions with application to aeroelasticity

NASA Astrophysics Data System (ADS)

Kirshman, David

A numerical method for the solution of inviscid compressible flow using an array of embedded Cartesian meshes in conjunction with gridless surface boundary conditions is developed. The gridless boundary treatment is implemented by means of a least squares fitting of the conserved flux variables using a cloud of nodes in the vicinity of the surface geometry. The method allows for accurate treatment of the surface boundary conditions using a grid resolution an order of magnitude coarser than required of typical Cartesian approaches. Additionally, the method does not suffer from issues associated with thin body geometry or extremely fine cut cells near the body. Unlike some methods that consider a gridless (or "meshless") treatment throughout the entire domain, multi-grid acceleration can be effectively incorporated and issues associated with global conservation are alleviated. The "gridless" surface boundary condition provides for efficient and simple problem set up since definition of the body geometry is generated independently from the field mesh, and automatically incorporated into the field discretization of the domain. The applicability of the method is first demonstrated for steady flow of single and multi-element airfoil configurations. Using this method, comparisons with traditional body-fitted grid simulations reveal that steady flow solutions can be obtained accurately with minimal effort associated with grid generation. The method is then extended to unsteady flow predictions. In this application, flow field simulations for the prescribed oscillation of an airfoil indicate excellent agreement with experimental data. Furthermore, it is shown that the phase lag associated with shock oscillation is accurately predicted without the need for a deformable mesh. Lastly, the method is applied to the prediction of transonic flutter using a two-dimensional wing model, in which comparisons with moving mesh simulations yield nearly identical results. As a result, applicability of the method to transient and vibrating fluid-structure interaction problems is established in which the requirement for a deformable mesh is eliminated.

Radiation effects on bifurcation and dual solutions in transient natural convection in a horizontal annulus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Luo, Kang; Yi, Hong-Liang, E-mail: yihongliang@hit.edu.cn; Tan, He-Ping, E-mail: tanheping@hit.edu.cn

2014-05-15

Transitions and bifurcations of transient natural convection in a horizontal annulus with radiatively participating medium are numerically investigated using the coupled lattice Boltzmann and direct collocation meshless (LB-DCM) method. As a hybrid approach based on a common multi-scale Boltzmann-type model, the LB-DCM scheme is easy to implement and has an excellent flexibility in dealing with the irregular geometries. Separate particle distribution functions in the LBM are used to calculate the density field, the velocity field and the thermal field. In the radiatively participating medium, the contribution of thermal radiation to natural convection must be taken into account, and it ismore » considered as a radiative term in the energy equation that is solved by the meshless method with moving least-squares (MLS) approximation. The occurrence of various instabilities and bifurcative phenomena is analyzed for different Rayleigh number Ra and Prandtl number Pr with and without radiation. Then, bifurcation diagrams and dual solutions are presented for relevant radiative parameters, such as convection-radiation parameter Rc and optical thickness τ. Numerical results show that the presence of volumetric radiation changes the static temperature gradient of the fluid, and generally results in an increase in the flow critical value. Besides, the existence and development of dual solutions of transient convection in the presence of radiation are greatly affected by radiative parameters. Finally, the advantage of LB-DCM combination is discussed, and the potential benefits of applying the LB-DCM method to multi-field coupling problems are demonstrated.« less

Efficient multiscale magnetic-domain analysis of iron-core material under mechanical stress

NASA Astrophysics Data System (ADS)

Nishikubo, Atsushi; Ito, Shumpei; Mifune, Takeshi; Matsuo, Tetsuji; Kaido, Chikara; Takahashi, Yasuhito; Fujiwara, Koji

2018-05-01

For an efficient analysis of magnetization, a partial-implicit solution method is improved using an assembled domain structure model with six-domain mesoscopic particles exhibiting pinning-type hysteresis. The quantitative analysis of non-oriented silicon steel succeeds in predicting the stress dependence of hysteresis loss with computation times greatly reduced by using the improved partial-implicit method. The effect of cell division along the thickness direction is also evaluated.

Singular boundary method for global gravity field modelling

NASA Astrophysics Data System (ADS)

Cunderlik, Robert

2014-05-01

The singular boundary method (SBM) and method of fundamental solutions (MFS) are meshless boundary collocation techniques that use the fundamental solution of a governing partial differential equation (e.g. the Laplace equation) as their basis functions. They have been developed to avoid singular numerical integration as well as mesh generation in the traditional boundary element method (BEM). SBM have been proposed to overcome a main drawback of MFS - its controversial fictitious boundary outside the domain. The key idea of SBM is to introduce a concept of the origin intensity factors that isolate singularities of the fundamental solution and its derivatives using some appropriate regularization techniques. Consequently, the source points can be placed directly on the real boundary and coincide with the collocation nodes. In this study we deal with SBM applied for high-resolution global gravity field modelling. The first numerical experiment presents a numerical solution to the fixed gravimetric boundary value problem. The achieved results are compared with the numerical solutions obtained by MFS or the direct BEM indicating efficiency of all methods. In the second numerical experiments, SBM is used to derive the geopotential and its first derivatives from the Tzz components of the gravity disturbing tensor observed by the GOCE satellite mission. A determination of the origin intensity factors allows to evaluate the disturbing potential and gravity disturbances directly on the Earth's surface where the source points are located. To achieve high-resolution numerical solutions, the large-scale parallel computations are performed on the cluster with 1TB of the distributed memory and an iterative elimination of far zones' contributions is applied.

Meshless deformable models for 3D cardiac motion and strain analysis from tagged MRI.

PubMed

Wang, Xiaoxu; Chen, Ting; Zhang, Shaoting; Schaerer, Joël; Qian, Zhen; Huh, Suejung; Metaxas, Dimitris; Axel, Leon

2015-01-01

Tagged magnetic resonance imaging (TMRI) provides a direct and noninvasive way to visualize the in-wall deformation of the myocardium. Due to the through-plane motion, the tracking of 3D trajectories of the material points and the computation of 3D strain field call for the necessity of building 3D cardiac deformable models. The intersections of three stacks of orthogonal tagging planes are material points in the myocardium. With these intersections as control points, 3D motion can be reconstructed with a novel meshless deformable model (MDM). Volumetric MDMs describe an object as point cloud inside the object boundary and the coordinate of each point can be written in parametric functions. A generic heart mesh is registered on the TMRI with polar decomposition. A 3D MDM is generated and deformed with MR image tagging lines. Volumetric MDMs are deformed by calculating the dynamics function and minimizing the local Laplacian coordinates. The similarity transformation of each point is computed by assuming its neighboring points are making the same transformation. The deformation is computed iteratively until the control points match the target positions in the consecutive image frame. The 3D strain field is computed from the 3D displacement field with moving least squares. We demonstrate that MDMs outperformed the finite element method and the spline method with a numerical phantom. Meshless deformable models can track the trajectory of any material point in the myocardium and compute the 3D strain field of any particular area. The experimental results on in vivo healthy and patient heart MRI show that the MDM can fully recover the myocardium motion in three dimensions. Copyright © 2014. Published by Elsevier Inc.

Meshless deformable models for 3D cardiac motion and strain analysis from tagged MRI

PubMed Central

Wang, Xiaoxu; Chen, Ting; Zhang, Shaoting; Schaerer, Joël; Qian, Zhen; Huh, Suejung; Metaxas, Dimitris; Axel, Leon

2016-01-01

Tagged magnetic resonance imaging (TMRI) provides a direct and noninvasive way to visualize the in-wall deformation of the myocardium. Due to the through-plane motion, the tracking of 3D trajectories of the material points and the computation of 3D strain field call for the necessity of building 3D cardiac deformable models. The intersections of three stacks of orthogonal tagging planes are material points in the myocardium. With these intersections as control points, 3D motion can be reconstructed with a novel meshless deformable model (MDM). Volumetric MDMs describe an object as point cloud inside the object boundary and the coordinate of each point can be written in parametric functions. A generic heart mesh is registered on the TMRI with polar decomposition. A 3D MDM is generated and deformed with MR image tagging lines. Volumetric MDMs are deformed by calculating the dynamics function and minimizing the local Laplacian coordinates. The similarity transformation of each point is computed by assuming its neighboring points are making the same transformation. The deformation is computed iteratively until the control points match the target positions in the consecutive image frame. The 3D strain field is computed from the 3D displacement field with moving least squares. We demonstrate that MDMs outperformed the finite element method and the spline method with a numerical phantom. Meshless deformable models can track the trajectory of any material point in the myocardium and compute the 3D strain field of any particular area. The experimental results on in vivo healthy and patient heart MRI show that the MDM can fully recover the myocardium motion in three dimensions. PMID:25157446

Fast multipole methods on a cluster of GPUs for the meshless simulation of turbulence

NASA Astrophysics Data System (ADS)

Yokota, R.; Narumi, T.; Sakamaki, R.; Kameoka, S.; Obi, S.; Yasuoka, K.

2009-11-01

Recent advances in the parallelizability of fast N-body algorithms, and the programmability of graphics processing units (GPUs) have opened a new path for particle based simulations. For the simulation of turbulence, vortex methods can now be considered as an interesting alternative to finite difference and spectral methods. The present study focuses on the efficient implementation of the fast multipole method and pseudo-particle method on a cluster of NVIDIA GeForce 8800 GT GPUs, and applies this to a vortex method calculation of homogeneous isotropic turbulence. The results of the present vortex method agree quantitatively with that of the reference calculation using a spectral method. We achieved a maximum speed of 7.48 TFlops using 64 GPUs, and the cost performance was near 9.4/GFlops. The calculation of the present vortex method on 64 GPUs took 4120 s, while the spectral method on 32 CPUs took 4910 s.

On automating domain connectivity for overset grids

NASA Technical Reports Server (NTRS)

Chiu, Ing-Tsau

1994-01-01

An alternative method for domain connectivity among systems of overset grids is presented. Reference uniform Cartesian systems of points are used to achieve highly efficient domain connectivity, and form the basis for a future fully automated system. The Cartesian systems are used to approximated body surfaces and to map the computational space of component grids. By exploiting the characteristics of Cartesian Systems, Chimera type hole-cutting and identification of donor elements for intergrid boundary points can be carried out very efficiently. The method is tested for a range of geometrically complex multiple-body overset grid systems.

Progress on the development of FullWave, a Hot and Cold Plasma Parallel Full Wave Code

NASA Astrophysics Data System (ADS)

Spencer, J. Andrew; Svidzinski, Vladimir; Zhao, Liangji; Kim, Jin-Soo

2017-10-01

FullWave is being developed at FAR-TECH, Inc. to simulate RF waves in hot inhomogeneous magnetized plasmas without making small orbit approximations. FullWave is based on a meshless formulation in configuration space on non-uniform clouds of computational points (CCP) adapted to better resolve plasma resonances, antenna structures and complex boundaries. The linear frequency domain wave equation is formulated using two approaches: for cold plasmas the local cold plasma dielectric tensor is used (resolving resonances by particle collisions), while for hot plasmas the conductivity kernel is calculated. The details of FullWave and some preliminary results will be presented, including: 1) a monitor function based on analytic solutions of the cold-plasma dispersion relation; 2) an adaptive CCP based on the monitor function; 3) construction of the finite differences for approximation of derivatives on adaptive CCP; 4) results of 2-D full wave simulations in the cold plasma model in tokamak geometry using the formulated approach for ECRH, ICRH and Lower Hybrid range of frequencies. Work is supported by the U.S. DOE SBIR program.

On automating domain connectivity for overset grids

NASA Technical Reports Server (NTRS)

Chiu, Ing-Tsau; Meakin, Robert L.

1995-01-01

An alternative method for domain connectivity among systems of overset grids is presented. Reference uniform Cartesian systems of points are used to achieve highly efficient domain connectivity, and form the basis for a future fully automated system. The Cartesian systems are used to approximate body surfaces and to map the computational space of component grids. By exploiting the characteristics of Cartesian systems, Chimera type hole-cutting and identification of donor elements for intergrid boundary points can be carried out very efficiently. The method is tested for a range of geometrically complex multiple-body overset grid systems. A dynamic hole expansion/contraction algorithm is also implemented to obtain optimum domain connectivity; however, it is tested only for geometry of generic shapes.

Efficient physics-based tracking of heart surface motion for beating heart surgery robotic systems.

PubMed

Bogatyrenko, Evgeniya; Pompey, Pascal; Hanebeck, Uwe D

2011-05-01

Tracking of beating heart motion in a robotic surgery system is required for complex cardiovascular interventions. A heart surface motion tracking method is developed, including a stochastic physics-based heart surface model and an efficient reconstruction algorithm. The algorithm uses the constraints provided by the model that exploits the physical characteristics of the heart. The main advantage of the model is that it is more realistic than most standard heart models. Additionally, no explicit matching between the measurements and the model is required. The application of meshless methods significantly reduces the complexity of physics-based tracking. Based on the stochastic physical model of the heart surface, this approach considers the motion of the intervention area and is robust to occlusions and reflections. The tracking algorithm is evaluated in simulations and experiments on an artificial heart. Providing higher accuracy than the standard model-based methods, it successfully copes with occlusions and provides high performance even when all measurements are not available. Combining the physical and stochastic description of the heart surface motion ensures physically correct and accurate prediction. Automatic initialization of the physics-based cardiac motion tracking enables system evaluation in a clinical environment.

Conjunction of radial basis function interpolator and artificial intelligence models for time-space modeling of contaminant transport in porous media

NASA Astrophysics Data System (ADS)

Nourani, Vahid; Mousavi, Shahram; Dabrowska, Dominika; Sadikoglu, Fahreddin

2017-05-01

As an innovation, both black box and physical-based models were incorporated into simulating groundwater flow and contaminant transport. Time series of groundwater level (GL) and chloride concentration (CC) observed at different piezometers of study plain were firstly de-noised by the wavelet-based de-noising approach. The effect of de-noised data on the performance of artificial neural network (ANN) and adaptive neuro-fuzzy inference system (ANFIS) was evaluated. Wavelet transform coherence was employed for spatial clustering of piezometers. Then for each cluster, ANN and ANFIS models were trained to predict GL and CC values. Finally, considering the predicted water heads of piezometers as interior conditions, the radial basis function as a meshless method which solves partial differential equations of GFCT, was used to estimate GL and CC values at any point within the plain where there is not any piezometer. Results indicated that efficiency of ANFIS based spatiotemporal model was more than ANN based model up to 13%.

Understanding casing flow in Pelton turbines by numerical simulation

NASA Astrophysics Data System (ADS)

Rentschler, M.; Neuhauser, M.; Marongiu, J. C.; Parkinson, E.

2016-11-01

For rehabilitation projects of Pelton turbines, the flow in the casing may have an important influence on the overall performance of the machine. Water sheets returning on the jets or on the runner significantly reduce efficiency, and run-away speed depends on the flow in the casing. CFD simulations can provide a detailed insight into this type of flow, but these simulations are computationally intensive. As in general the volume of water in a Pelton turbine is small compared to the complete volume of the turbine housing, a single phase simulation greatly reduces the complexity of the simulation. In the present work a numerical tool based on the SPH-ALE meshless method is used to simulate the casing flow in a Pelton turbine. Using improved order schemes reduces the numerical viscosity. This is necessary to resolve the flow in the jet and on the casing wall, where the velocity differs by two orders of magnitude. The results are compared to flow visualizations and measurement in a hydraulic laboratory. Several rehabilitation projects proved the added value of understanding the flow in the Pelton casing. The flow simulation helps designing casing insert, not only to see their influence on the flow, but also to calculate the stress in the inserts. In some projects, the casing simulation leads to the understanding of unexpected behavior of the flow. One such example is presented where the backsplash of a deflector hit the runner, creating a reversed rotation of the runner.

The Role of Structural Dynamics of Actin in Class-Specific Myosin Motility

PubMed Central

Noguchi, Taro Q. P.; Morimatsu, Masatoshi; Iwane, Atsuko H.; Yanagida, Toshio; Uyeda, Taro Q. P.

2015-01-01

The structural dynamics of actin, including the tilting motion between the small and large domains, are essential for proper interactions with actin-binding proteins. Gly146 is situated at the hinge between the two domains, and we previously showed that a G146V mutation leads to severe motility defects in skeletal myosin but has no effect on motility of myosin V. The present study tested the hypothesis that G146V mutation impaired rotation between the two domains, leading to such functional defects. First, our study showed that depolymerization of G146V filaments was slower than that of wild-type filaments. This result is consistent with the distinction of structural states of G146V filaments from those of the wild type, considering the recent report that stabilization of actin filaments involves rotation of the two domains. Next, we measured intramolecular FRET efficiencies between two fluorophores in the two domains with or without skeletal muscle heavy meromyosin or the heavy meromyosin equivalent of myosin V in the presence of ATP. Single-molecule FRET measurements showed that the conformations of actin subunits of control and G146V actin filaments were different in the presence of skeletal muscle heavy meromyosin. This altered conformation of G146V subunits may lead to motility defects in myosin II. In contrast, distributions of FRET efficiencies of control and G146V subunits were similar in the presence of myosin V, consistent with the lack of motility defects in G146V actin with myosin V. The distribution of FRET efficiencies in the presence of myosin V was different from that in the presence of skeletal muscle heavy meromyosin, implying that the roles of actin conformation in myosin motility depend on the type of myosin. PMID:25945499

2005 22nd International Symposium on Ballistics. Volume 3 Thursday - Friday

DTIC Science & Technology

2005-11-18

QinetiQ; Vladimir Titarev, Eleuterio Toro , Umeritek Limited The Mechanism Analysis of Interior Ballistics of Serial Chamber Gun, Dr. Sanjiu Ying, Charge...Elements and Meshless Particles, Gordon R. Johnson and Robert A. Stryk, Network Computing Services, Inc. Experimental and Numerical Study of the...Internal Ballistics Clive R. Woodley, David Finbow, QinetiQ; Vladimir Titarev, Eleuterio Toro , Numeritek Limited 22nd International Symposium on

Simbol-X Mirror Module Thermal Shields: I-Design and X-Ray Transmission

NASA Astrophysics Data System (ADS)

Collura, A.; Barbera, M.; Varisco, S.; Basso, S.; Pareschi, G.; Tagliaferri, G.; Ayers, T.

2009-05-01

The Simbol-X mission is designed to fly in formation flight configuration. As a consequence, the telescope has both ends open to space, and thermal shielding at telescope entrance and exit is required to maintain temperature uniformity throughout the mirrors. Both mesh and meshless solutions are presently under study for the shields. We discuss the design and the X-ray transmission.

Ageing influences myonuclear domain size differently in fast and slow skeletal muscle of rats.

PubMed

Brooks, Naomi E; Schuenke, M D; Hikida, R S

2009-09-01

In multinucleated skeletal muscle, a myonuclear domain is the region of cytoplasm governed by one nucleus, and myofibres are mosaics of overlapping myonuclear domains. Association of ageing and myonuclear domain is important in the understanding of sarcopenia and with prevention or combating age-related muscle declines. This study examined the effects of age, fibre type and muscle on nucleo-cytoplasmic (N/C) relationships as reflecting myonuclear domain size. The N/C was compared in fibre types of soleus and plantaris muscles from young (n = 6) and ageing (n = 8) male Fisher 344 rats. There were no significant differences in fibre type composition or cross-sectional area of the soleus across ages. The old soleus had significantly more myonuclei, resulting in a significantly smaller myonuclear domain size. The plantaris muscle showed a higher percentage of slow fibres in old compared with young fibres. There were no differences in the number of myonuclei or in myonuclear domain size between young and older animals. We found muscle-specific differences in the effects of ageing on myonuclear domain, possibly as a result of reduced efficiency of the myonuclei in the slow muscles.

Revealed distributional preferences: Individuals vs. teams☆☆☆

PubMed Central

Balafoutas, Loukas; Kerschbamer, Rudolf; Kocher, Martin; Sutter, Matthias

2014-01-01

We compare experimentally the revealed distributional preferences of individuals and teams in allocation tasks. We find that teams are significantly more benevolent than individuals in the domain of disadvantageous inequality while the benevolence in the domain of advantageous inequality is similar across decision makers. A consequence for the frequency of preference types is that while a substantial fraction of individuals is classified as inequality averse, this type disappears completely in teams. Spiteful types are markedly more frequent among individuals than among teams. On the other hand, by far more teams than individuals are classified as efficiency lovers. PMID:25843995

Heuristic Chemistry--A Qualitative Study on Teaching Domain-Specific Strategies for the Six-Electron Case

ERIC Educational Resources Information Center

Graulich, Nicole; Tiemann, Rudiger; Schreiner, Peter R.

2012-01-01

We investigate the efficiency of domain-specific heuristic strategies in mastering and predicting pericyclic six-electron rearrangements. Based on recent research findings on these types of reactions a new concept has been developed that should help students identify and describe six-electron rearrangements more readily in complex molecules. The…

Refolding and characterization of the functional ligand-binding domain of human lectin-like oxidized LDL receptor.

PubMed

Xie, Qiuhong; Matsunaga, Shigeru; Shi, Xiaohua; Ogawa, Setsuko; Niimi, Setsuko; Wen, Zhesheng; Tokuyasu, Ken; Machida, Sachiko

2003-11-01

Lectin-like oxidized low-density lipoprotein receptor (LOX-1), a type II membrane protein that can recognize a variety of structurally unrelated macromolecules, plays an important role in host defense and is implicated in atherogenesis. To understand the interaction between human LOX-1 and its ligands, in this study the functional C-type lectin-like domain (CTLD) of LOX-1 was reconstituted at high efficiency from inactive aggregates in Escherichia coli using a refolding technique based on an artificial chaperone. The CD spectra of the purified domain suggested that the domain has alpha-helical structure and the blue shift of Trp residues was observed on refolding of the domain. Like wild-type hLOX-1, the refolded CTLD domain was able to bind modified LDL. Thus, even though CTLD contains six Cys residues that form disulfide bonds, it recovered its specific binding ability on refolding. This suggests that the correct disulfide bonds in CTLD were formed by the artificial chaperone technique. Although the domain lacked N-glycosylation, it showed high affinity for its ligand in surface plasmon resonance experiments. Thus, unglycosylated CTLD is sufficient for binding modified LDL.

2005 22nd International Symposium on Ballistics Volume 2 Wednesday

DTIC Science & Technology

2005-11-18

Information 1 Experimental and Numerical Study of the Penetration of Tungsten Carbide Into Steel Targets During High Rates of Strain John F . Moxnes...QinetiQ; Vladimir Titarev, Eleuterio Toro , Umeritek Limited The Mechanism Analysis of Interior Ballistics of Serial Chamber Gun, Dr. Sanjiu Ying, Charge...Elements and Meshless Particles, Gordon R. Johnson and Robert A. Stryk, Network Computing Services, Inc. Experimental and Numerical Study of the

Modeling RF Fields in Hot Plasmas with Parallel Full Wave Code

NASA Astrophysics Data System (ADS)

Spencer, Andrew; Svidzinski, Vladimir; Zhao, Liangji; Galkin, Sergei; Kim, Jin-Soo

2016-10-01

FAR-TECH, Inc. is developing a suite of full wave RF plasma codes. It is based on a meshless formulation in configuration space with adapted cloud of computational points (CCP) capability and using the hot plasma conductivity kernel to model the nonlocal plasma dielectric response. The conductivity kernel is calculated by numerically integrating the linearized Vlasov equation along unperturbed particle trajectories. Work has been done on the following calculations: 1) the conductivity kernel in hot plasmas, 2) a monitor function based on analytic solutions of the cold-plasma dispersion relation, 3) an adaptive CCP based on the monitor function, 4) stencils to approximate the wave equations on the CCP, 5) the solution to the full wave equations in the cold-plasma model in tokamak geometry for ECRH and ICRH range of frequencies, and 6) the solution to the wave equations using the calculated hot plasma conductivity kernel. We will present results on using a meshless formulation on adaptive CCP to solve the wave equations and on implementing the non-local hot plasma dielectric response to the wave equations. The presentation will include numerical results of wave propagation and absorption in the cold and hot tokamak plasma RF models, using DIII-D geometry and plasma parameters. Work is supported by the U.S. DOE SBIR program.

Convergence of the Critical Cooling Rate for Protoplanetary Disk Fragmentation Achieved: The Key Role of Numerical Dissipation of Angular Momentum

NASA Astrophysics Data System (ADS)

Deng, Hongping; Mayer, Lucio; Meru, Farzana

2017-09-01

We carry out simulations of gravitationally unstable disks using smoothed particle hydrodynamics (SPH) and the novel Lagrangian meshless finite mass (MFM) scheme in the GIZMO code. Our aim is to understand the cause of the nonconvergence of the cooling boundary for fragmentation reported in the literature. We run SPH simulations with two different artificial viscosity implementations and compare them with MFM, which does not employ any artificial viscosity. With MFM we demonstrate convergence of the critical cooling timescale for fragmentation at {β }{crit}≈ 3. Nonconvergence persists in SPH codes. We show how the nonconvergence problem is caused by artificial fragmentation triggered by excessive dissipation of angular momentum in domains with large velocity derivatives. With increased resolution, such domains become more prominent. Vorticity lags behind density, due to numerical viscous dissipation in these regions, promoting collapse with longer cooling times. Such effect is shown to be dominant over the competing tendency of artificial viscosity to diminish with increasing resolution. When the initial conditions are first relaxed for several orbits, the flow is more regular, with lower shear and vorticity in nonaxisymmetric regions, aiding convergence. Yet MFM is the only method that converges exactly. Our findings are of general interest, as numerical dissipation via artificial viscosity or advection errors can also occur in grid-based codes. Indeed, for the FARGO code values of {β }{crit} significantly higher than our converged estimate have been reported in the literature. Finally, we discuss implications for giant planet formation via disk instability.

A Novel Functional Role of Collagen Glycosylation

PubMed Central

Jürgensen, Henrik J.; Madsen, Daniel H.; Ingvarsen, Signe; Melander, Maria C.; Gårdsvoll, Henrik; Patthy, Laszlo; Engelholm, Lars H.; Behrendt, Niels

2011-01-01

Collagens make up the most abundant component of interstitial extracellular matrices and basement membranes. Collagen remodeling is a crucial process in many normal physiological events and in several pathological conditions. Some collagen subtypes contain specific carbohydrate side chains, the function of which is poorly known. The endocytic collagen receptor urokinase plasminogen activator receptor-associated protein (uPARAP)/Endo180 plays an important role in matrix remodeling through its ability to internalize collagen for lysosomal degradation. uPARAP/Endo180 is a member of the mannose receptor protein family. These proteins all include a fibronectin type II domain and a series of C-type lectin-like domains, of which only a minor part possess carbohydrate recognition activity. At least two of the family members, uPARAP/Endo180 and the mannose receptor, interact with collagens. The molecular basis for this interaction is known to involve the fibronectin type II domain but nothing is known about the function of the lectin domains in this respect. In this study, we have investigated a possible role of the single active lectin domain of uPARAP/Endo180 in the interaction with collagens. By expressing truncated recombinant uPARAP/Endo180 proteins and analyzing their interaction with collagens with high and low levels of glycosylation we demonstrated that this lectin domain interacts directly with glycosylated collagens. This interaction is functionally important because it was found to modulate the endocytic efficiency of the receptor toward highly glycosylated collagens such as basement membrane collagen IV. Surprisingly, this property was not shared by the mannose receptor, which internalized glycosylated collagens independently of its lectin function. This role of modulating its uptake efficiency by a specific receptor is a previously unrecognized function of collagen glycosylation. PMID:21768090

Structure-transfection activity relationships in a series of novel cationic lipids with heterocyclic head-groups.

PubMed

Ivanova, Ekaterina A; Maslov, Mikhail A; Kabilova, Tatyana O; Puchkov, Pavel A; Alekseeva, Anna S; Boldyrev, Ivan A; Vlassov, Valentin V; Serebrennikova, Galina A; Morozova, Nina G; Zenkova, Marina A

2013-11-07

Cationic liposomes are promising candidates for the delivery of various therapeutic nucleic acids. Here, we report a convenient synthesis of carbamate-type cationic lipids with various hydrophobic domains (tetradecanol, dialkylglycerol, cholesterol) and positively charged head-groups (pyridinium, N-methylimidazolium, N-methylmorpholinium) and data on the structure-transfection activity relationships. It was found that single-chain lipids possess high surface activity, which correlates with high cytotoxicity due to their ability to disrupt the cellular membrane by combined hydrophobic and electrostatic interactions. Liposomes containing these lipids also display high cytotoxicity with respect to all cell lines. Irrespective of chemical structures, all cationic lipids form liposomes with similar sizes and surface potentials. The characteristics of complexes composed of cationic liposomes and nucleic acids depend mostly on the type of nucleic acid and P/N ratios. In the case of oligodeoxyribonucleotide delivery, the transfection activity depends on the type of cationic head-group regardless of the type of hydrophobic domain: all types of cationic liposomes mediate efficient oligonucleotide transfer into 80-90% of the eukaryotic cells, and liposomes based on lipids with N-methylmorpholinium cationic head-group display the highest transfection activity. In the case of plasmid DNA and siRNA, the type of hydrophobic domain determines the transfection activity: liposomes composed of cholesterol-based lipids were the most efficient in DNA transfer, while liposomes containing glycerol-based lipids exhibited reasonable activity in siRNA delivery under serum-free conditions.

Normalized Implicit Radial Models for Scattered Point Cloud Data without Normal Vectors

DTIC Science & Technology

2009-03-23

points by shrinking a discrete membrane, Computer Graphics Forum, Vol. 24-4, 2005, pp. 791-808 [8] Floater , M. S., Reimers, M.: Meshless...Parameterization and Surface Reconstruction, Computer Aided Geometric Design 18, 2001, pp 77-92 [9] Floater , M. S.: Parameterization of Triangulations and...Unorganized Points, In: Tutorials on Multiresolution in Geometric Modelling, A. Iske, E. Quak and M. S. Floater (eds.), Springer , 2002, pp. 287-316 [10

Smoothed Particle Hydrodynamics and its applications for multiphase flow and reactive transport in porous media

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tartakovsky, Alexandre M.; Trask, Nathaniel; Pan, K.

2016-03-11

Smoothed Particle Hydrodynamics (SPH) is a Lagrangian method based on a meshless discretization of partial differential equations. In this review, we present SPH discretization of the Navier-Stokes and Advection-Diffusion-Reaction equations, implementation of various boundary conditions, and time integration of the SPH equations, and we discuss applications of the SPH method for modeling pore-scale multiphase flows and reactive transport in porous and fractured media.

Critical domain interactions for type A RNase P RNA catalysis with and without the specificity domain

PubMed Central

Mao, Guanzhong; Srivastava, Abhishek S.; Wu, Shiying; Kosek, David; Lindell, Magnus

2018-01-01

The natural trans-acting ribozyme RNase P RNA (RPR) is composed of two domains in which the catalytic (C-) domain mediates cleavage of various substrates. The C-domain alone, after removal of the second specificity (S-) domain, catalyzes this reaction as well, albeit with reduced efficiency. Here we provide experimental evidence indicating that efficient cleavage mediated by the Escherichia coli C-domain (Eco CP RPR) with and without the C5 protein likely depends on an interaction referred to as the "P6-mimic". Moreover, the P18 helix connects the C- and S-domains between its loop and the P8 helix in the S-domain (the P8/ P18-interaction). In contrast to the "P6-mimic", the presence of P18 does not contribute to the catalytic performance by the C-domain lacking the S-domain in cleavage of an all ribo model hairpin loop substrate while deletion or disruption of the P8/ P18-interaction in full-size RPR lowers the catalytic efficiency in cleavage of the same model hairpin loop substrate in keeping with previously reported data using precursor tRNAs. Consistent with that P18 is not required for cleavage mediated by the C-domain we show that the archaeal Pyrococcus furiosus RPR C-domain, which lacks the P18 helix, is catalytically active in trans without the S-domain and any protein. Our data also suggest that the S-domain has a larger impact on catalysis for E. coli RPR compared to P. furiosus RPR. Finally, we provide data indicating that the absence of the S-domain and P18, or the P8/ P18-interaction in full-length RPR influences the charge distribution near the cleavage site in the RPR-substrate complex to a small but reproducible extent. PMID:29509761

Fungal-type carbohydrate binding modules from the coccolithophore Emiliania huxleyi show binding affinity to cellulose and chitin.

PubMed

Rooijakkers, Bart J M; Ikonen, Martina S; Linder, Markus B

2018-01-01

Six fungal-type cellulose binding domains were found in the genome of the coccolithophore Emiliania huxleyi and cloned and expressed in Escherichia coli. Sequence comparison indicate high similarity to fungal cellulose binding domains, raising the question of why these domains exist in coccolithophores. The proteins were tested for binding with cellulose and chitin as ligands, which resulted in the identification of two functional carbohydrate binding modules: EHUX2 and EHUX4. Compared to benchmark fungal cellulose binding domain Cel7A-CBM1 from Trichoderma reesei, these proteins showed slightly lower binding to birch and bacterial cellulose, but were more efficient chitin binders. Finally, a set of cellulose binding domains was created based on the shuffling of one well-functioning and one non-functional domain. These were characterized in order to get more information of the binding domain's sequence-function relationship, indicating characteristic differences between the molecular basis of cellulose versus chitin recognition. As previous reports have showed the presence of cellulose in coccoliths and here we find functional cellulose binding modules, a possible connection is discussed.

Development of full wave code for modeling RF fields in hot non-uniform plasmas

NASA Astrophysics Data System (ADS)

Zhao, Liangji; Svidzinski, Vladimir; Spencer, Andrew; Kim, Jin-Soo

2016-10-01

FAR-TECH, Inc. is developing a full wave RF modeling code to model RF fields in fusion devices and in general plasma applications. As an important component of the code, an adaptive meshless technique is introduced to solve the wave equations, which allows resolving plasma resonances efficiently and adapting to the complexity of antenna geometry and device boundary. The computational points are generated using either a point elimination method or a force balancing method based on the monitor function, which is calculated by solving the cold plasma dispersion equation locally. Another part of the code is the conductivity kernel calculation, used for modeling the nonlocal hot plasma dielectric response. The conductivity kernel is calculated on a coarse grid of test points and then interpolated linearly onto the computational points. All the components of the code are parallelized using MPI and OpenMP libraries to optimize the execution speed and memory. The algorithm and the results of our numerical approach to solving 2-D wave equations in a tokamak geometry will be presented. Work is supported by the U.S. DOE SBIR program.

Library of electrocatalytic sites in nano-structured domains: electrocatalysis of hydrogen peroxide.

PubMed

Pandey, Prem C; Singh, Bhupendra

2008-12-01

Electrochemical detection of hydrogen peroxide at eight types of ormosil-modified electrodes, referred as hexacyanoferrate-system; Prussian blue systems (PB-1, PB-2, and PB-3), palladium (Pd-) system, graphite (Gr-) system, gold nanoparticle (AuNPs) system and palladium-gold nanoparticle (Pd-AuNPs) system were studied. The results on electrochemical detection suggested that hydrogen peroxide does not undergo homogeneous electrochemical mediation; however, the presence of redox mediator within nano-structured domains facilitates the electro-analysis of the same via redox electrocatalysis. Four approaches causing manipulation in nano-structured domains are described: (a) increase in the molecular size of the components generating nano-structured domains; (b) modulation via chemical reactivity; (c) modulation by non-reactive moieties and known nanoparticles; and (d) modulation by mixed approaches (a-c), all leading to decrease in a nano-structured domains. The results demonstrated that an increase in the size of nano-structured domains or decrease in micro-porous geometry increases the efficiency of electrocatalysis. The basic reaction protocol adopted in generating nano-structured domains, followed by manipulation protocols, supported the introduction of a library for creating electrocatalytic sites with varying electrocatalytic efficiency within the same basic nano-structured platform.

The solitary wave solution of coupled Klein-Gordon-Zakharov equations via two different numerical methods

NASA Astrophysics Data System (ADS)

Dehghan, Mehdi; Nikpour, Ahmad

2013-09-01

In this research, we propose two different methods to solve the coupled Klein-Gordon-Zakharov (KGZ) equations: the Differential Quadrature (DQ) and Globally Radial Basis Functions (GRBFs) methods. In the DQ method, the derivative value of a function with respect to a point is directly approximated by a linear combination of all functional values in the global domain. The principal work in this method is the determination of weight coefficients. We use two ways for obtaining these coefficients: cosine expansion (CDQ) and radial basis functions (RBFs-DQ), the former is a mesh-based method and the latter categorizes in the set of meshless methods. Unlike the DQ method, the GRBF method directly substitutes the expression of the function approximation by RBFs into the partial differential equation. The main problem in the GRBFs method is ill-conditioning of the interpolation matrix. Avoiding this problem, we study the bases introduced in Pazouki and Schaback (2011) [44]. Some examples are presented to compare the accuracy and easy implementation of the proposed methods. In numerical examples, we concentrate on Inverse Multiquadric (IMQ) and second-order Thin Plate Spline (TPS) radial basis functions. The variable shape parameter (exponentially and random) strategies are applied in the IMQ function and the results are compared with the constant shape parameter.

Complexity of type-specific 56 kDa antigen CD4 T-cell epitopes of Orientia tsutsugamushi strains causing scrub typhus in India

PubMed Central

Dasch, Gregory A.

2018-01-01

Orientia tsutsugamushi (Ots) is an obligate, intracellular, mite-transmitted human pathogen which causes scrub typhus. Understanding the diversity of Ots antigens is essential for designing specific diagnostic assays and efficient vaccines. The protective immunodominant type-specific 56 kDa antigen (TSA) of Ots varies locally and across its geographic distribution. TSA contains four hypervariable domains. We bioinformatically analyzed 345 partial sequences of TSA available from India, most of which contain only the three variable domains (VDI-III) and three spacer conserved domains (SVDI, SVDII/III, SVDIII). The total number (152) of antigenic types (amino acid variants) varied from 14–36 in the six domains of TSA that we studied. Notably, 55% (787/1435) of the predicted CD4 T-cell epitopes (TCEs) from all the six domains had high binding affinities (HBA) to at least one of the prevalent Indian human leukocyte antigen (HLA) alleles. A surprisingly high proportion (61%) of such TCEs were from spacer domains; indeed 100% of the CD4 TCEs in the SVDI were HBA. TSA sequences from India had more antigenic types (AT) than TSA from Korea. Overall, >90% of predicted CD4 TCEs from spacer domains were predicted to have HBA against one or more prevalent HLA types from Indian, Korean, Asia-Pacific region or global population data sets, while only <50% of CD4 TCEs in variable domains exhibited such HBA. The phylogenetically and immunologically important amino acids in the conserved spacer domains were identified. Our results suggest that the conserved spacer domains are predicted to be functionally more important than previously appreciated in immune responses to Ots infections. Changes occurring at the TCE level of TSA may contribute to the wide range of pathogenicity of Ots in humans and mouse models. CD4 T-cell functional experiments are needed to assess the immunological significance of these HBA spacer domains and their role in clearance of Ots from Indian patients. PMID:29698425

Mechanics of cantilever beam: Implementation and comparison of FEM and MLPG approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Trobec, Roman

2016-06-08

Two weak form solution approaches for partial differential equations, the well known meshbased finite element method and the newer meshless local Petrov Galerkin method are described and compared on a standard test case - mechanics of cantilever beam. The implementation, solution accuracy and calculation complexity are addressed for both approaches. We found out that FEM is superior in most standard criteria, but MLPG has some advantages because of its flexibility that results from its general formulation.

Computational Study of Colloidal Droplet Interactions with Three Dimensional Structures

DTIC Science & Technology

2015-05-18

on the meshless SPH method for droplet impact on and sorption into a powder bed considering free surface flow above the powder bed surface ...considering free surface flow above the powder bed surface , infiltration of the liquid in the porous matrix, and the interfacial forces on the free moving...infiltration of the liquid in the porous matrix, and the interfacial forces on the free moving surface . The model has been used to study the effect of impact

MUFASA: galaxy formation simulations with meshless hydrodynamics

NASA Astrophysics Data System (ADS)

Davé, Romeel; Thompson, Robert; Hopkins, Philip F.

2016-11-01

We present the MUFASA suite of cosmological hydrodynamic simulations, which employs the GIZMO meshless finite mass (MFM) code including H2-based star formation, nine-element chemical evolution, two-phase kinetic outflows following scalings from the Feedback in Realistic Environments zoom simulations, and evolving halo mass-based quenching. Our fiducial (50 h-1 Mpc)3 volume is evolved to z = 0 with a quarter billion elements. The predicted galaxy stellar mass functions (GSMFs) reproduces observations from z = 4 → 0 to ≲ 1.2σ in cosmic variance, providing an unprecedented match to this key diagnostic. The cosmic star formation history and stellar mass growth show general agreement with data, with a strong archaeological downsizing trend such that dwarf galaxies form the majority of their stars after z ˜ 1. We run 25 and 12.5 h-1 Mpc volumes to z = 2 with identical feedback prescriptions, the latter resolving all hydrogen-cooling haloes, and the three runs display fair resolution convergence. The specific star formation rates broadly agree with data at z = 0, but are underpredicted at z ˜ 2 by a factor of 3, re-emphasizing a longstanding puzzle in galaxy evolution models. We compare runs using MFM and two flavours of smoothed particle hydrodynamics, and show that the GSMF is sensitive to hydrodynamics methodology at the ˜×2 level, which is sub-dominant to choices for parametrizing feedback.

A multiphysics and multiscale model for low frequency electromagnetic direct-chill casting

NASA Astrophysics Data System (ADS)

Košnik, N.; Guštin, A. Z.; Mavrič, B.; Šarler, B.

2016-03-01

Simulation and control of macrosegregation, deformation and grain size in low frequency electromagnetic (EM) direct-chill casting (LFEMC) is important for downstream processing. Respectively, a multiphysics and multiscale model is developed for solution of Lorentz force, temperature, velocity, concentration, deformation and grain structure of LFEMC processed aluminum alloys, with focus on axisymmetric billets. The mixture equations with lever rule, linearized phase diagram, and stationary thermoelastic solid phase are assumed, together with EM induction equation for the field imposed by the coil. Explicit diffuse approximate meshless solution procedure [1] is used for solving the EM field, and the explicit local radial basis function collocation method [2] is used for solving the coupled transport phenomena and thermomechanics fields. Pressure-velocity coupling is performed by the fractional step method [3]. The point automata method with modified KGT model is used to estimate the grain structure [4] in a post-processing mode. Thermal, mechanical, EM and grain structure outcomes of the model are demonstrated. A systematic study of the complicated influences of the process parameters can be investigated by the model, including intensity and frequency of the electromagnetic field. The meshless solution framework, with the implemented simplest physical models, will be further extended by including more sophisticated microsegregation and grain structure models, as well as a more realistic solid and solid-liquid phase rheology.

Two-dimensional fracture analysis of piezoelectric material based on the scaled boundary node method

NASA Astrophysics Data System (ADS)

Shen-Shen, Chen; Juan, Wang; Qing-Hua, Li

2016-04-01

A scaled boundary node method (SBNM) is developed for two-dimensional fracture analysis of piezoelectric material, which allows the stress and electric displacement intensity factors to be calculated directly and accurately. As a boundary-type meshless method, the SBNM employs the moving Kriging (MK) interpolation technique to an approximate unknown field in the circumferential direction and therefore only a set of scattered nodes are required to discretize the boundary. As the shape functions satisfy Kronecker delta property, no special techniques are required to impose the essential boundary conditions. In the radial direction, the SBNM seeks analytical solutions by making use of analytical techniques available to solve ordinary differential equations. Numerical examples are investigated and satisfactory solutions are obtained, which validates the accuracy and simplicity of the proposed approach. Project supported by the National Natural Science Foundation of China (Grant Nos. 11462006 and 21466012), the Foundation of Jiangxi Provincial Educational Committee, China (Grant No. KJLD14041), and the Foundation of East China Jiaotong University, China (Grant No. 09130020).

Shallow boomerang-shaped influenza hemagglutinin G13A mutant structure promotes leaky membrane fusion.

PubMed

Lai, Alex L; Tamm, Lukas K

2010-11-26

Our previous studies showed that an angled boomerang-shaped structure of the influenza hemagglutinin (HA) fusion domain is critical for virus entry into host cells by membrane fusion. Because the acute angle of ∼105° of the wild-type fusion domain promotes efficient non-leaky membrane fusion, we asked whether different angles would still support fusion and thus facilitate virus entry. Here, we show that the G13A fusion domain mutant produces a new leaky fusion phenotype. The mutant fusion domain structure was solved by NMR spectroscopy in a lipid environment at fusion pH. The mutant adopted a boomerang structure similar to that of wild type but with a shallower kink angle of ∼150°. G13A perturbed the structure of model membranes to a lesser degree than wild type but to a greater degree than non-fusogenic fusion domain mutants. The strength of G13A binding to lipid bilayers was also intermediate between that of wild type and non-fusogenic mutants. These membrane interactions provide a clear link between structure and function of influenza fusion domains: an acute angle is required to promote clean non-leaky fusion suitable for virus entry presumably by interaction of the fusion domain with the transmembrane domain deep in the lipid bilayer. A shallower angle perturbs the bilayer of the target membrane so that it becomes leaky and unable to form a clean fusion pore. Mutants with no fixed boomerang angle interacted with bilayers weakly and did not promote any fusion or membrane perturbation.

Shallow Boomerang-shaped Influenza Hemagglutinin G13A Mutant Structure Promotes Leaky Membrane Fusion*

PubMed Central

Lai, Alex L.; Tamm, Lukas K.

2010-01-01

Our previous studies showed that an angled boomerang-shaped structure of the influenza hemagglutinin (HA) fusion domain is critical for virus entry into host cells by membrane fusion. Because the acute angle of ∼105° of the wild-type fusion domain promotes efficient non-leaky membrane fusion, we asked whether different angles would still support fusion and thus facilitate virus entry. Here, we show that the G13A fusion domain mutant produces a new leaky fusion phenotype. The mutant fusion domain structure was solved by NMR spectroscopy in a lipid environment at fusion pH. The mutant adopted a boomerang structure similar to that of wild type but with a shallower kink angle of ∼150°. G13A perturbed the structure of model membranes to a lesser degree than wild type but to a greater degree than non-fusogenic fusion domain mutants. The strength of G13A binding to lipid bilayers was also intermediate between that of wild type and non-fusogenic mutants. These membrane interactions provide a clear link between structure and function of influenza fusion domains: an acute angle is required to promote clean non-leaky fusion suitable for virus entry presumably by interaction of the fusion domain with the transmembrane domain deep in the lipid bilayer. A shallower angle perturbs the bilayer of the target membrane so that it becomes leaky and unable to form a clean fusion pore. Mutants with no fixed boomerang angle interacted with bilayers weakly and did not promote any fusion or membrane perturbation. PMID:20826788

Fungal-type carbohydrate binding modules from the coccolithophore Emiliania huxleyi show binding affinity to cellulose and chitin

PubMed Central

Rooijakkers, Bart J. M.

2018-01-01

Six fungal-type cellulose binding domains were found in the genome of the coccolithophore Emiliania huxleyi and cloned and expressed in Escherichia coli. Sequence comparison indicate high similarity to fungal cellulose binding domains, raising the question of why these domains exist in coccolithophores. The proteins were tested for binding with cellulose and chitin as ligands, which resulted in the identification of two functional carbohydrate binding modules: EHUX2 and EHUX4. Compared to benchmark fungal cellulose binding domain Cel7A-CBM1 from Trichoderma reesei, these proteins showed slightly lower binding to birch and bacterial cellulose, but were more efficient chitin binders. Finally, a set of cellulose binding domains was created based on the shuffling of one well-functioning and one non-functional domain. These were characterized in order to get more information of the binding domain’s sequence–function relationship, indicating characteristic differences between the molecular basis of cellulose versus chitin recognition. As previous reports have showed the presence of cellulose in coccoliths and here we find functional cellulose binding modules, a possible connection is discussed. PMID:29782536

EBNA-2 of herpesvirus papio diverges significantly from the type A and type B EBNA-2 proteins of Epstein-Barr virus but retains an efficient transactivation domain with a conserved hydrophobic motif.

PubMed Central

Ling, P D; Ryon, J J; Hayward, S D

1993-01-01

EBNA-2 contributes to the establishment of Epstein-Barr virus (EBV) latency in B cells and to the resultant alterations in B-cell growth pattern by up-regulating expression from specific viral and cellular promoters. We have taken a comparative approach toward characterizing functional domains within EBNA-2. To this end, we have cloned and sequenced the EBNA-2 gene from the closely related baboon virus herpesvirus papio (HVP). All human EBV isolates have either a type A or type B EBNA-2 gene. However, the HVP EBNA-2 gene falls into neither the type A category nor the type B category, suggesting that the separation into these two subtypes may have been a recent evolutionary event. Comparison of the predicted amino acid sequences indicates 37% amino acid identity with EBV type A EBNA-2 and 35% amino acid identity with type B EBNA-2. To define the domains of EBNA-2 required for transcriptional activation, the DNA binding domain of the GAL4 protein was fused to overlapping segments of EBV EBNA-2. This approach identified a 40-amino-acid (40-aa) EBNA-2 activation domain located between aa 437 and 477. Transactivation ability was completely lost when the amino-terminal boundary of this domain was moved to aa 441, indicating that the motif at aa 437 to 440, Pro-Ile-Leu-Phe, contains residues critical for function. The aa 437 boundary identified in these experiments coincides precisely with a block of conserved sequences in HVP EBNA-2, and the comparable carboxy-terminal region of HVP EBNA-2 also functioned as a strong transcriptional activation domain when fused to the Gal4(1-147) protein. The EBV and HVP EBNA-2 activation domains share a mixed proline-rich, negatively charged character with a striking conservation of positionally equivalent hydrophobic residues. The importance of the individual amino acids making up the Pro-Ile-Leu-Phe motif was examined by mutagenesis. Any alteration of these residues was found to reduce transactivation efficiency, with changes at the Pro-437 and Phe-440 positions producing the most deleterious effects. Activation of the EBV latency C promoter by EBNA-2 was shown to be dependent on the presence of the carboxy-terminal activation domain. However, this requirement was generic, rather than specific, since the EBNA-2 activation domain could be replaced with those from the herpes simplex virus (HSV) VP16 protein or the EBV Rta protein. Potential karyophilic signals within EBNA-2 were examined by introducing oligonucleotides encoding positively charged amino acid groupings that might serve in this capacity into a cytoplasmic test protein, HSV delta IE175, and by examining the intracellular localization of the resulting proteins. This assay identified a strong nuclear localization signal between EBV amino acids (aa) 478 to 485, which was conserved in HVP, and a weaker noncanonical signal between EBV aa 341 to 355, which was not conserved in HVP. Images PMID:8388484

EBNA-2 of herpesvirus papio diverges significantly from the type A and type B EBNA-2 proteins of Epstein-Barr virus but retains an efficient transactivation domain with a conserved hydrophobic motif.

PubMed

Ling, P D; Ryon, J J; Hayward, S D

1993-06-01

EBNA-2 contributes to the establishment of Epstein-Barr virus (EBV) latency in B cells and to the resultant alterations in B-cell growth pattern by up-regulating expression from specific viral and cellular promoters. We have taken a comparative approach toward characterizing functional domains within EBNA-2. To this end, we have cloned and sequenced the EBNA-2 gene from the closely related baboon virus herpesvirus papio (HVP). All human EBV isolates have either a type A or type B EBNA-2 gene. However, the HVP EBNA-2 gene falls into neither the type A category nor the type B category, suggesting that the separation into these two subtypes may have been a recent evolutionary event. Comparison of the predicted amino acid sequences indicates 37% amino acid identity with EBV type A EBNA-2 and 35% amino acid identity with type B EBNA-2. To define the domains of EBNA-2 required for transcriptional activation, the DNA binding domain of the GAL4 protein was fused to overlapping segments of EBV EBNA-2. This approach identified a 40-amino-acid (40-aa) EBNA-2 activation domain located between aa 437 and 477. Transactivation ability was completely lost when the amino-terminal boundary of this domain was moved to aa 441, indicating that the motif at aa 437 to 440, Pro-Ile-Leu-Phe, contains residues critical for function. The aa 437 boundary identified in these experiments coincides precisely with a block of conserved sequences in HVP EBNA-2, and the comparable carboxy-terminal region of HVP EBNA-2 also functioned as a strong transcriptional activation domain when fused to the Gal4(1-147) protein. The EBV and HVP EBNA-2 activation domains share a mixed proline-rich, negatively charged character with a striking conservation of positionally equivalent hydrophobic residues. The importance of the individual amino acids making up the Pro-Ile-Leu-Phe motif was examined by mutagenesis. Any alteration of these residues was found to reduce transactivation efficiency, with changes at the Pro-437 and Phe-440 positions producing the most deleterious effects. Activation of the EBV latency C promoter by EBNA-2 was shown to be dependent on the presence of the carboxy-terminal activation domain. However, this requirement was generic, rather than specific, since the EBNA-2 activation domain could be replaced with those from the herpes simplex virus (HSV) VP16 protein or the EBV Rta protein. Potential karyophilic signals within EBNA-2 were examined by introducing oligonucleotides encoding positively charged amino acid groupings that might serve in this capacity into a cytoplasmic test protein, HSV delta IE175, and by examining the intracellular localization of the resulting proteins. This assay identified a strong nuclear localization signal between EBV amino acids (aa) 478 to 485, which was conserved in HVP, and a weaker noncanonical signal between EBV aa 341 to 355, which was not conserved in HVP.

Application of the Fourier pseudospectral time-domain method in orthogonal curvilinear coordinates for near-rigid moderately curved surfaces.

PubMed

Hornikx, Maarten; Dragna, Didier

2015-07-01

The Fourier pseudospectral time-domain method is an efficient wave-based method to model sound propagation in inhomogeneous media. One of the limitations of the method for atmospheric sound propagation purposes is its restriction to a Cartesian grid, confining it to staircase-like geometries. A transform from the physical coordinate system to the curvilinear coordinate system has been applied to solve more arbitrary geometries. For applicability of this method near the boundaries, the acoustic velocity variables are solved for their curvilinear components. The performance of the curvilinear Fourier pseudospectral method is investigated in free field and for outdoor sound propagation over an impedance strip for various types of shapes. Accuracy is shown to be related to the maximum grid stretching ratio and deformation of the boundary shape and computational efficiency is reduced relative to the smallest grid cell in the physical domain. The applicability of the curvilinear Fourier pseudospectral time-domain method is demonstrated by investigating the effect of sound propagation over a hill in a nocturnal boundary layer. With the proposed method, accurate and efficient results for sound propagation over smoothly varying ground surfaces with high impedances can be obtained.

Mapping of the self-interaction domains in the simian immunodeficiency virus Gag polyprotein.

PubMed

Rauddi, María L; Mac Donald, Cecilia L; Affranchino, José L; González, Silvia A

2011-03-01

To gain a better understanding of the assembly process in simian immunodeficiency virus (SIV), we first established the conditions under which recombinant SIV Gag lacking the C-terminal p6 domain (SIV GagΔp6) assembled in vitro into spherical particles. Based on the full multimerization capacity of SIV GagΔp6, and to identify the Gag sequences involved in homotypic interactions, we next developed a pull-down assay in which a panel of histidine-tagged SIV Gag truncation mutants was tested for its ability to associate in vitro with GST-SIVGagΔp6. Removal of the nucleocapsid (NC) domain from Gag impaired its ability to interact with GST-SIVGagΔp6. However, this Gag mutant consisting of the matrix (MA) and capsid (CA) domains still retained 50% of the wild-type binding activity. Truncation of SIV Gag from its N-terminus yielded markedly different results. The Gag region consisting of the CA and NC was significantly more efficient than wild-type Gag at interacting in vitro with GST-SIVGagΔp6. Notably, a small Gag subdomain containing the C-terminal third of the CA and the entire NC not only bound to GST-SIVGagΔp6 in vitro at wild-type levels, but also associated in vivo with full-length Gag and was recruited into extracellular particles. Interestingly, when the mature Gag products were analyzed, the MA and NC interacted with GST-SIVGagΔp6 with efficiencies representing 20% and 40%, respectively, of the wild-type value, whereas the CA failed to bind to GST-SIVGagΔp6, despite being capable of self-associating into multimeric complexes.

Free vibrations and buckling analysis of laminated plates by oscillatory radial basis functions

NASA Astrophysics Data System (ADS)

Neves, A. M. A.; Ferreira, A. J. M.

2015-12-01

In this paper the free vibrations and buckling analysis of laminated plates is performed using a global meshless method. A refined version of Kant's theorie which accounts for transverse normal stress and through-the-thickness deformation is used. The innovation is the use of oscillatory radial basis functions. Numerical examples are performed and results are presented and compared to available references. Such functions proved to be an alternative to the tradicional nonoscillatory radial basis functions.

Mingus Discontinuous Multiphysics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pat Notz, Dan Turner

Mingus provides hybrid coupled local/non-local mechanics analysis capabilities that extend several traditional methods to applications with inherent discontinuities. Its primary features include adaptations of solid mechanics, fluid dynamics and digital image correlation that naturally accommodate dijointed data or irregular solution fields by assimilating a variety of discretizations (such as control volume finite elements, peridynamics and meshless control point clouds). The goal of this software is to provide an analysis framework form multiphysics engineering problems with an integrated image correlation capability that can be used for experimental validation and model

Meshless Local Petrov-Galerkin Method for Solving Contact, Impact and Penetration Problems

DTIC Science & Technology

2006-11-30

Crack Growth 3 point of view, this approach makes the full use of the ex- isting FE models to avoid any model regeneration , which is extremely high in...process, at point C, the pressure reduces to zero, but the volumet- ric strain does not go to zero due to the collapsed void volume. 2.2 Damage...lease rate to go beyond the critical strain energy release rate. Thus, the micro-cracks begin to growth inside these areas. At 10 micro-seconds, these

Improved catalytic efficiency, thermophilicity, anti-salt and detergent tolerance of keratinase KerSMD by partially truncation of PPC domain

PubMed Central

Fang, Zhen; Zhang, Juan; Du, Guocheng; Chen, Jian

2016-01-01

The keratinase from Stenotrophomonas maltophilia (KerSMD) is known for its high activity and pH stability in keratin degradation. However, catalytic efficiency and detergent tolerability need to be improved in order to be used for industrial application. In this work, we obtained several keratinase variants with enhanced catalytic efficiency, thermophilicity, and anti-salt and detergent tolerability by partially truncating the PPC domain of KerSMD. The variants all showed improved catalytic efficiency to synthetic substrate AAPF, with the V355 variant having the highest kcat /Km value of 143.6 s−1 mM−1. The truncation of keratinase had little effect on alkaline stability but obviously decreased collagenase activity, developing its potential application in leather treatment. The variants V380, V370, and V355 were thermophilic, with a 1.7-fold enhancement of keratinlytic activity at 60 °C when compared to the wild type. The entire truncation of PPC domain obtained the variant V355 with improved tolerance to alkalinity, salt, chaotropic agents, and detergents. The V355 variant showed more than a 40% improvement in activity under 15% (w/v) NaCl or 4% (w/v) SDS solution, showing excellent stability under harsh washing and unhairing conditions. Our work investigated how protein engineering affects the function of PPC domain of KerSMD. PMID:27298079

Improved catalytic efficiency, thermophilicity, anti-salt and detergent tolerance of keratinase KerSMD by partially truncation of PPC domain.

PubMed

Fang, Zhen; Zhang, Juan; Du, Guocheng; Chen, Jian

2016-06-14

The keratinase from Stenotrophomonas maltophilia (KerSMD) is known for its high activity and pH stability in keratin degradation. However, catalytic efficiency and detergent tolerability need to be improved in order to be used for industrial application. In this work, we obtained several keratinase variants with enhanced catalytic efficiency, thermophilicity, and anti-salt and detergent tolerability by partially truncating the PPC domain of KerSMD. The variants all showed improved catalytic efficiency to synthetic substrate AAPF, with the V355 variant having the highest kcat /Km value of 143.6 s(-1) mM(-1). The truncation of keratinase had little effect on alkaline stability but obviously decreased collagenase activity, developing its potential application in leather treatment. The variants V380, V370, and V355 were thermophilic, with a 1.7-fold enhancement of keratinlytic activity at 60 °C when compared to the wild type. The entire truncation of PPC domain obtained the variant V355 with improved tolerance to alkalinity, salt, chaotropic agents, and detergents. The V355 variant showed more than a 40% improvement in activity under 15% (w/v) NaCl or 4% (w/v) SDS solution, showing excellent stability under harsh washing and unhairing conditions. Our work investigated how protein engineering affects the function of PPC domain of KerSMD.

Segregated nodal domains of two-dimensional multispecies Bose-Einstein condensates

NASA Astrophysics Data System (ADS)

Chang, Shu-Ming; Lin, Chang-Shou; Lin, Tai-Chia; Lin, Wen-Wei

2004-09-01

In this paper, we study the distribution of m segregated nodal domains of the m-mixture of Bose-Einstein condensates under positive and large repulsive scattering lengths. It is shown that components of positive bound states may repel each other and form segregated nodal domains as the repulsive scattering lengths go to infinity. Efficient numerical schemes are created to confirm our theoretical results and discover a new phenomenon called verticillate multiplying, i.e., the generation of multiple verticillate structures. In addition, our proposed Gauss-Seidel-type iteration method is very effective in that it converges linearly in 10-20 steps.

Error analysis of multipoint flux domain decomposition methods for evolutionary diffusion problems

NASA Astrophysics Data System (ADS)

Arrarás, A.; Portero, L.; Yotov, I.

2014-01-01

We study space and time discretizations for mixed formulations of parabolic problems. The spatial approximation is based on the multipoint flux mixed finite element method, which reduces to an efficient cell-centered pressure system on general grids, including triangles, quadrilaterals, tetrahedra, and hexahedra. The time integration is performed by using a domain decomposition time-splitting technique combined with multiterm fractional step diagonally implicit Runge-Kutta methods. The resulting scheme is unconditionally stable and computationally efficient, as it reduces the global system to a collection of uncoupled subdomain problems that can be solved in parallel without the need for Schwarz-type iteration. Convergence analysis for both the semidiscrete and fully discrete schemes is presented.

Species-Specific Elements in the Large T-Antigen J Domain Are Required for Cellular Transformation and DNA Replication by Simian Virus 40

PubMed Central

Sullivan, Christopher S.; Tremblay, James D.; Fewell, Sheara W.; Lewis, John A.; Brodsky, Jeffrey L.; Pipas, James M.

2000-01-01

The J domain of simian virus 40 (SV40) large T antigen is required for efficient DNA replication and transformation. Despite previous reports demonstrating the promiscuity of J domains in heterologous systems, results presented here show the requirement for specific J-domain sequences in SV40 large-T-antigen-mediated activities. In particular, chimeric-T-antigen constructs in which the SV40 T-antigen J domain was replaced with that from the yeast Ydj1p or Escherichia coli DnaJ proteins failed to replicate in BSC40 cells and did not transform REF52 cells. However, T antigen containing the JC virus J domain was functional in these assays, although it was less efficient than the wild type. The inability of some large-T-antigen chimeras to promote DNA replication and elicit cellular transformation was not due to a failure to interact with hsc70, since a nonfunctional chimera, containing the DnaJ J domain, bound hsc70. However, this nonfunctional chimeric T antigen was reduced in its ability to stimulate hsc70 ATPase activity and unable to liberate E2F from p130, indicating that transcriptional activation of factors required for cell growth and DNA replication may be compromised. Our data suggest that the T-antigen J domain harbors species-specific elements required for viral activities in vivo. PMID:10891510

Spatiotemporal groundwater level modeling using hybrid artificial intelligence-meshless method

NASA Astrophysics Data System (ADS)

Nourani, Vahid; Mousavi, Shahram

2016-05-01

Uncertainties of the field parameters, noise of the observed data and unknown boundary conditions are the main factors involved in the groundwater level (GL) time series which limit the modeling and simulation of GL. This paper presents a hybrid artificial intelligence-meshless model for spatiotemporal GL modeling. In this way firstly time series of GL observed in different piezometers were de-noised using threshold-based wavelet method and the impact of de-noised and noisy data was compared in temporal GL modeling by artificial neural network (ANN) and adaptive neuro-fuzzy inference system (ANFIS). In the second step, both ANN and ANFIS models were calibrated and verified using GL data of each piezometer, rainfall and runoff considering various input scenarios to predict the GL at one month ahead. In the final step, the simulated GLs in the second step of modeling were considered as interior conditions for the multiquadric radial basis function (RBF) based solve of governing partial differential equation of groundwater flow to estimate GL at any desired point within the plain where there is not any observation. In order to evaluate and compare the GL pattern at different time scales, the cross-wavelet coherence was also applied to GL time series of piezometers. The results showed that the threshold-based wavelet de-noising approach can enhance the performance of the modeling up to 13.4%. Also it was found that the accuracy of ANFIS-RBF model is more reliable than ANN-RBF model in both calibration and validation steps.

A parallel multi-domain solution methodology applied to nonlinear thermal transport problems in nuclear fuel pins

DOE PAGES

Philip, Bobby; Berrill, Mark A.; Allu, Srikanth; ...

2015-01-26

We describe an efficient and nonlinearly consistent parallel solution methodology for solving coupled nonlinear thermal transport problems that occur in nuclear reactor applications over hundreds of individual 3D physical subdomains. Efficiency is obtained by leveraging knowledge of the physical domains, the physics on individual domains, and the couplings between them for preconditioning within a Jacobian Free Newton Krylov method. Details of the computational infrastructure that enabled this work, namely the open source Advanced Multi-Physics (AMP) package developed by the authors are described. The details of verification and validation experiments, and parallel performance analysis in weak and strong scaling studies demonstratingmore » the achieved efficiency of the algorithm are presented. Moreover, numerical experiments demonstrate that the preconditioner developed is independent of the number of fuel subdomains in a fuel rod, which is particularly important when simulating different types of fuel rods. Finally, we demonstrate the power of the coupling methodology by considering problems with couplings between surface and volume physics and coupling of nonlinear thermal transport in fuel rods to an external radiation transport code.« less

Efficient Modeling of Gravity Fields Caused by Sources with Arbitrary Geometry and Arbitrary Density Distribution

NASA Astrophysics Data System (ADS)

Wu, Leyuan

2018-01-01

We present a brief review of gravity forward algorithms in Cartesian coordinate system, including both space-domain and Fourier-domain approaches, after which we introduce a truly general and efficient algorithm, namely the convolution-type Gauss fast Fourier transform (Conv-Gauss-FFT) algorithm, for 2D and 3D modeling of gravity potential and its derivatives due to sources with arbitrary geometry and arbitrary density distribution which are defined either by discrete or by continuous functions. The Conv-Gauss-FFT algorithm is based on the combined use of a hybrid rectangle-Gaussian grid and the fast Fourier transform (FFT) algorithm. Since the gravity forward problem in Cartesian coordinate system can be expressed as continuous convolution-type integrals, we first approximate the continuous convolution by a weighted sum of a series of shifted discrete convolutions, and then each shifted discrete convolution, which is essentially a Toeplitz system, is calculated efficiently and accurately by combining circulant embedding with the FFT algorithm. Synthetic and real model tests show that the Conv-Gauss-FFT algorithm can obtain high-precision forward results very efficiently for almost any practical model, and it works especially well for complex 3D models when gravity fields on large 3D regular grids are needed.

Structure, replication efficiency and fragility of yeast ARS elements.

PubMed

Dhar, Manoj K; Sehgal, Shelly; Kaul, Sanjana

2012-05-01

DNA replication in eukaryotes initiates at specific sites known as origins of replication, or replicators. These replication origins occur throughout the genome, though the propensity of their occurrence depends on the type of organism. In eukaryotes, zones of initiation of replication spanning from about 100 to 50,000 base pairs have been reported. The characteristics of eukaryotic replication origins are best understood in the budding yeast Saccharomyces cerevisiae, where some autonomously replicating sequences, or ARS elements, confer origin activity. ARS elements are short DNA sequences of a few hundred base pairs, identified by their efficiency at initiating a replication event when cloned in a plasmid. ARS elements, although structurally diverse, maintain a basic structure composed of three domains, A, B and C. Domain A is comprised of a consensus sequence designated ACS (ARS consensus sequence), while the B domain has the DNA unwinding element and the C domain is important for DNA-protein interactions. Although there are ∼400 ARS elements in the yeast genome, not all of them are active origins of replication. Different groups within the genus Saccharomyces have ARS elements as components of replication origin. The present paper provides a comprehensive review of various aspects of ARSs, starting from their structural conservation to sequence thermodynamics. All significant and conserved functional sequence motifs within different types of ARS elements have been extensively described. Issues like silencing at ARSs, their inherent fragility and factors governing their replication efficiency have also been addressed. Progress in understanding crucial components associated with the replication machinery and timing at these ARS elements is discussed in the section entitled "The replicon revisited". Copyright © 2012 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Helicase Domain of West Nile Virus NS3 Protein Plays a Role in Inhibition of Type I Interferon Signalling.

PubMed

Setoh, Yin Xiang; Periasamy, Parthiban; Peng, Nias Yong Gao; Amarilla, Alberto A; Slonchak, Andrii; Khromykh, Alexander A

2017-11-02

West Nile virus (WNV) is a neurotropic flavivirus that can cause encephalitis in mammalian and avian hosts. In America, the virulent WNV strain (NY99) is causing yearly outbreaks of encephalitis in humans and horses, while in Australia the less virulent Kunjin strain of WNV strain has not been associated with significant disease outbreaks until a recent 2011 large outbreak in horses (but not in humans) caused by NSW2011 strain. Using chimeric viruses between NY99 and NSW2011 strains we previously identified a role for the non-structural proteins of NY99 strain and especially the NS3 protein, in enhanced virus replication in type I interferon response-competent cells and increased virulence in mice. To further define the role of NY99 NS3 protein in inhibition of type I interferon response, we have generated and characterised additional chimeric viruses containing the protease or the helicase domains of NY99 NS3 on the background of the NSW2011 strain. The results identified the role for the helicase but not the protease domain of NS3 protein in the inhibition of type I interferon signalling and showed that helicase domain of the more virulent NY99 strain performs this function more efficiently than helicase domain of the less virulent NSW2011 strain. Further analysis with individual amino acid mutants identified two amino acid residues in the helicase domain primarily responsible for this difference. Using chimeric replicons, we also showed that the inhibition of type I interferon (IFN) signalling was independent of other known functions of NS3 in RNA replication and assembly of virus particles.

Helicase Domain of West Nile Virus NS3 Protein Plays a Role in Inhibition of Type I Interferon Signalling

PubMed Central

Periasamy, Parthiban; Peng, Nias Yong Gao; Amarilla, Alberto A.; Slonchak, Andrii; Khromykh, Alexander A.

2017-01-01

West Nile virus (WNV) is a neurotropic flavivirus that can cause encephalitis in mammalian and avian hosts. In America, the virulent WNV strain (NY99) is causing yearly outbreaks of encephalitis in humans and horses, while in Australia the less virulent Kunjin strain of WNV strain has not been associated with significant disease outbreaks until a recent 2011 large outbreak in horses (but not in humans) caused by NSW2011 strain. Using chimeric viruses between NY99 and NSW2011 strains we previously identified a role for the non-structural proteins of NY99 strain and especially the NS3 protein, in enhanced virus replication in type I interferon response-competent cells and increased virulence in mice. To further define the role of NY99 NS3 protein in inhibition of type I interferon response, we have generated and characterised additional chimeric viruses containing the protease or the helicase domains of NY99 NS3 on the background of the NSW2011 strain. The results identified the role for the helicase but not the protease domain of NS3 protein in the inhibition of type I interferon signalling and showed that helicase domain of the more virulent NY99 strain performs this function more efficiently than helicase domain of the less virulent NSW2011 strain. Further analysis with individual amino acid mutants identified two amino acid residues in the helicase domain primarily responsible for this difference. Using chimeric replicons, we also showed that the inhibition of type I interferon (IFN) signalling was independent of other known functions of NS3 in RNA replication and assembly of virus particles. PMID:29099073

Numerical treatment for solving two-dimensional space-fractional advection-dispersion equation using meshless method

NASA Astrophysics Data System (ADS)

Cheng, Rongjun; Sun, Fengxin; Wei, Qi; Wang, Jufeng

2018-02-01

Space-fractional advection-dispersion equation (SFADE) can describe particle transport in a variety of fields more accurately than the classical models of integer-order derivative. Because of nonlocal property of integro-differential operator of space-fractional derivative, it is very challenging to deal with fractional model, and few have been reported in the literature. In this paper, a numerical analysis of the two-dimensional SFADE is carried out by the element-free Galerkin (EFG) method. The trial functions for the SFADE are constructed by the moving least-square (MLS) approximation. By the Galerkin weak form, the energy functional is formulated. Employing the energy functional minimization procedure, the final algebraic equations system is obtained. The Riemann-Liouville operator is discretized by the Grünwald formula. With center difference method, EFG method and Grünwald formula, the fully discrete approximation schemes for SFADE are established. Comparing with exact results and available results by other well-known methods, the computed approximate solutions are presented in the format of tables and graphs. The presented results demonstrate the validity, efficiency and accuracy of the proposed techniques. Furthermore, the error is computed and the proposed method has reasonable convergence rates in spatial and temporal discretizations.

Deformation of Soft Tissue and Force Feedback Using the Smoothed Particle Hydrodynamics

PubMed Central

Liu, Xuemei; Wang, Ruiyi; Li, Yunhua; Song, Dongdong

2015-01-01

We study the deformation and haptic feedback of soft tissue in virtual surgery based on a liver model by using a force feedback device named PHANTOM OMNI developed by SensAble Company in USA. Although a significant amount of research efforts have been dedicated to simulating the behaviors of soft tissue and implementing force feedback, it is still a challenging problem. This paper introduces a kind of meshfree method for deformation simulation of soft tissue and force computation based on viscoelastic mechanical model and smoothed particle hydrodynamics (SPH). Firstly, viscoelastic model can present the mechanical characteristics of soft tissue which greatly promotes the realism. Secondly, SPH has features of meshless technique and self-adaption, which supply higher precision than methods based on meshes for force feedback computation. Finally, a SPH method based on dynamic interaction area is proposed to improve the real time performance of simulation. The results reveal that SPH methodology is suitable for simulating soft tissue deformation and force feedback calculation, and SPH based on dynamic local interaction area has a higher computational efficiency significantly compared with usual SPH. Our algorithm has a bright prospect in the area of virtual surgery. PMID:26417380

A Galleria Boundary Element Method for two-dimensional nonlinear magnetostatics

NASA Astrophysics Data System (ADS)

Brovont, Aaron D.

The Boundary Element Method (BEM) is a numerical technique for solving partial differential equations that is used broadly among the engineering disciplines. The main advantage of this method is that one needs only to mesh the boundary of a solution domain. A key drawback is the myriad of integrals that must be evaluated to populate the full system matrix. To this day these integrals have been evaluated using numerical quadrature. In this research, a Galerkin formulation of the BEM is derived and implemented to solve two-dimensional magnetostatic problems with a focus on accurate, rapid computation. To this end, exact, closed-form solutions have been derived for all the integrals comprising the system matrix as well as those required to compute fields in post-processing; the need for numerical integration has been eliminated. It is shown that calculation of the system matrix elements using analytical solutions is 15-20 times faster than with numerical integration of similar accuracy. Furthermore, through the example analysis of a c-core inductor, it is demonstrated that the present BEM formulation is a competitive alternative to the Finite Element Method (FEM) for linear magnetostatic analysis. Finally, the BEM formulation is extended to analyze nonlinear magnetostatic problems via the Dual Reciprocity Method (DRBEM). It is shown that a coarse, meshless analysis using the DRBEM is able to achieve RMS error of 3-6% compared to a commercial FEM package in lightly saturated conditions.

Truncation of the human immunodeficiency virus type 1 transmembrane glycoprotein cytoplasmic domain blocks virus infectivity.

PubMed Central

Dubay, J W; Roberts, S J; Hahn, B H; Hunter, E

1992-01-01

Human immunodeficiency virus type 1 contains a transmembrane glycoprotein with an unusually long cytoplasmic domain. To determine the role of this domain in virus replication, a series of single nucleotide changes that result in the insertion of premature termination codons throughout the cytoplasmic domain has been constructed. These mutations delete from 6 to 192 amino acids from the carboxy terminus of gp41 and do not affect the amino acid sequence of the regulatory proteins encoded by rev and tat. The effects of these mutations on glycoprotein biosynthesis and function as well as on virus infectivity have been examined in the context of a glycoprotein expression vector and the viral genome. All of the mutant glycoproteins were synthesized, processed, and transported to the cell surface in a manner similar to that of the wild-type glycoprotein. With the exception of mutants that remove the membrane anchor domain, all of the mutant glycoproteins retained the ability to cause fusion of CD4-bearing cells. However, deletion of more than 19 amino acids from the C terminus of gp41 blocked the ability of mutant virions to infect cells. This defect in virus infectivity appeared to be due at least in part to a failure of the virus to efficiently incorporate the truncated glycoprotein. Similar data were obtained for mutations in two different env genes and two different target cell lines. These results indicate that the cytoplasmic domain of gp41 plays a critical role during virus assembly and entry in the life cycle of human immunodeficiency virus type 1. Images PMID:1357190

Compressive sensing for sparse time-frequency representation of nonstationary signals in the presence of impulsive noise

NASA Astrophysics Data System (ADS)

Orović, Irena; Stanković, Srdjan; Amin, Moeness

2013-05-01

A modified robust two-dimensional compressive sensing algorithm for reconstruction of sparse time-frequency representation (TFR) is proposed. The ambiguity function domain is assumed to be the domain of observations. The two-dimensional Fourier bases are used to linearly relate the observations to the sparse TFR, in lieu of the Wigner distribution. We assume that a set of available samples in the ambiguity domain is heavily corrupted by an impulsive type of noise. Consequently, the problem of sparse TFR reconstruction cannot be tackled using standard compressive sensing optimization algorithms. We introduce a two-dimensional L-statistics based modification into the transform domain representation. It provides suitable initial conditions that will produce efficient convergence of the reconstruction algorithm. This approach applies sorting and weighting operations to discard an expected amount of samples corrupted by noise. The remaining samples serve as observations used in sparse reconstruction of the time-frequency signal representation. The efficiency of the proposed approach is demonstrated on numerical examples that comprise both cases of monocomponent and multicomponent signals.

Probabilistic numerical methods for PDE-constrained Bayesian inverse problems

NASA Astrophysics Data System (ADS)

Cockayne, Jon; Oates, Chris; Sullivan, Tim; Girolami, Mark

2017-06-01

This paper develops meshless methods for probabilistically describing discretisation error in the numerical solution of partial differential equations. This construction enables the solution of Bayesian inverse problems while accounting for the impact of the discretisation of the forward problem. In particular, this drives statistical inferences to be more conservative in the presence of significant solver error. Theoretical results are presented describing rates of convergence for the posteriors in both the forward and inverse problems. This method is tested on a challenging inverse problem with a nonlinear forward model.

Comparison of Response Surface Construction Methods for Derivative Estimation Using Moving Least Squares, Kriging and Radial Basis Functions

NASA Technical Reports Server (NTRS)

Krishnamurthy, Thiagarajan

2005-01-01

Response construction methods using Moving Least Squares (MLS), Kriging and Radial Basis Functions (RBF) are compared with the Global Least Squares (GLS) method in three numerical examples for derivative generation capability. Also, a new Interpolating Moving Least Squares (IMLS) method adopted from the meshless method is presented. It is found that the response surface construction methods using the Kriging and RBF interpolation yields more accurate results compared with MLS and GLS methods. Several computational aspects of the response surface construction methods also discussed.

The Transcription Elongation Factor CA150 Interacts with RNA Polymerase II and the Pre-mRNA Splicing Factor SF1

PubMed Central

Goldstrohm, Aaron C.; Albrecht, Todd R.; Suñé, Carles; Bedford, Mark T.; Garcia-Blanco, Mariano A.

2001-01-01

CA150 represses RNA polymerase II (RNAPII) transcription by inhibiting the elongation of transcripts. The FF repeat domains of CA150 bind directly to the phosphorylated carboxyl-terminal domain of the largest subunit of RNAPII. We determined that this interaction is required for efficient CA150-mediated repression of transcription from the α4-integrin promoter. Additional functional determinants, namely, the WW1 and WW2 domains of CA150, were also required for efficient repression. A protein that interacted directly with CA150 WW1 and WW2 was identified as the splicing-transcription factor SF1. Previous studies have demonstrated a role for SF1 in transcription repression, and we found that binding of the CA150 WW1 and WW2 domains to SF1 correlated exactly with the functional contribution of these domains for repression. The binding specificity of the CA150 WW domains was found to be unique in comparison to known classes of WW domains. Furthermore, the CA150 binding site, within the carboxyl-terminal half of SF1, contains a novel type of proline-rich motif that may be recognized by the CA150 WW1 and WW2 domains. These results support a model for the recruitment of CA150 to repress transcription elongation. In this model, CA150 binds to the phosphorylated CTD of elongating RNAPII and SF1 targets the nascent transcript. PMID:11604498

The transcription elongation factor CA150 interacts with RNA polymerase II and the pre-mRNA splicing factor SF1.

PubMed

Goldstrohm, A C; Albrecht, T R; Suñé, C; Bedford, M T; Garcia-Blanco, M A

2001-11-01

CA150 represses RNA polymerase II (RNAPII) transcription by inhibiting the elongation of transcripts. The FF repeat domains of CA150 bind directly to the phosphorylated carboxyl-terminal domain of the largest subunit of RNAPII. We determined that this interaction is required for efficient CA150-mediated repression of transcription from the alpha(4)-integrin promoter. Additional functional determinants, namely, the WW1 and WW2 domains of CA150, were also required for efficient repression. A protein that interacted directly with CA150 WW1 and WW2 was identified as the splicing-transcription factor SF1. Previous studies have demonstrated a role for SF1 in transcription repression, and we found that binding of the CA150 WW1 and WW2 domains to SF1 correlated exactly with the functional contribution of these domains for repression. The binding specificity of the CA150 WW domains was found to be unique in comparison to known classes of WW domains. Furthermore, the CA150 binding site, within the carboxyl-terminal half of SF1, contains a novel type of proline-rich motif that may be recognized by the CA150 WW1 and WW2 domains. These results support a model for the recruitment of CA150 to repress transcription elongation. In this model, CA150 binds to the phosphorylated CTD of elongating RNAPII and SF1 targets the nascent transcript.

Clumpy Disks as a Testbed for Feedback-regulated Galaxy Formation

NASA Astrophysics Data System (ADS)

Mayer, Lucio; Tamburello, Valentina; Lupi, Alessandro; Keller, Ben; Wadsley, James; Madau, Piero

2016-10-01

We study the dependence of fragmentation in massive gas-rich galaxy disks at z > 1 on stellar feedback schemes and hydrodynamical solvers, employing the GASOLINE2 SPH code and the lagrangian mesh-less code GIZMO in finite mass mode. Non-cosmological galaxy disk runs with the standard delayed-cooling blastwave feedback are compared with runs adopting a new superbubble feedback, which produces winds by modeling the detailed physics of supernova-driven bubbles and leads to efficient self-regulation of star formation. We find that, with blastwave feedback, massive star-forming clumps form in comparable number and with very similar masses in GASOLINE2 and GIZMO. Typical clump masses are in the range 107-108 M ⊙, lower than in most previous works, while giant clumps with masses above 109 M ⊙ are exceedingly rare. By contrast, superbubble feedback does not produce massive star-forming bound clumps as galaxies never undergo a phase of violent disk instability. In this scheme, only sporadic, unbound star-forming overdensities lasting a few tens of Myr can arise, triggered by non-linear perturbations from massive satellite companions. We conclude that there is severe tension between explaining massive star-forming clumps observed at z > 1 primarily as the result of disk fragmentation driven by gravitational instability and the prevailing view of feedback-regulated galaxy formation. The link between disk stability and star formation efficiency should thus be regarded as a key testing ground for galaxy formation theory.

Structural and functional dissection reveals distinct roles of Ca2+-binding sites in the giant adhesin SiiE of Salmonella enterica

PubMed Central

Klingl, Stefan; Sandmann, Achim; Taccardi, Nicola; Sticht, Heinrich; Muller, Yves A.; Hensel, Michael

2017-01-01

The giant non-fimbrial adhesin SiiE of Salmonella enterica mediates the first contact to the apical site of epithelial cells and enables subsequent invasion. SiiE is a 595 kDa protein composed of 53 repetitive bacterial immunoglobulin (BIg) domains and the only known substrate of the SPI4-encoded type 1 secretion system (T1SS). The crystal structure of BIg50-52 of SiiE revealed two distinct Ca2+-binding sites per BIg domain formed by conserved aspartate or glutamate residues. In a mutational analysis Ca2+-binding sites were disrupted by aspartate to serine exchange at various positions in the BIg domains of SiiE. Amounts of secreted SiiE diminish with a decreasing number of intact Ca2+-binding sites. BIg domains of SiiE contain distinct Ca2+-binding sites, with type I sites being similar to other T1SS-secreted proteins and type II sites newly identified in SiiE. We functionally and structurally dissected the roles of type I and type II Ca2+-binding sites in SiiE, as well as the importance of Ca2+-binding sites in various positions of SiiE. Type I Ca2+-binding sites were critical for efficient secretion of SiiE and a decreasing number of type I sites correlated with reduced secretion. Type II sites were less important for secretion, stability and surface expression of SiiE, however integrity of type II sites in the C-terminal portion was required for the function of SiiE in mediating adhesion and invasion. PMID:28558023

The B7-1 Cytoplasmic Tail Enhances Intracellular Transport and Mammalian Cell Surface Display of Chimeric Proteins in the Absence of a Linear ER Export Motif

PubMed Central

Lin, Yi-Chieh; Chen, Bing-Mae; Lu, Wei-Cheng; Su, Chien-I; Prijovich, Zeljko M.; Chung, Wen-Chuan; Wu, Pei-Yu; Chen, Kai-Chuan; Lee, I-Chiao; Juan, Ting-Yi; Roffler, Steve R.

2013-01-01

Membrane-tethered proteins (mammalian surface display) are increasingly being used for novel therapeutic and biotechnology applications. Maximizing surface expression of chimeric proteins on mammalian cells is important for these applications. We show that the cytoplasmic domain from the B7-1 antigen, a commonly used element for mammalian surface display, can enhance the intracellular transport and surface display of chimeric proteins in a Sar1 and Rab1 dependent fashion. However, mutational, alanine scanning and deletion analysis demonstrate the absence of linear ER export motifs in the B7 cytoplasmic domain. Rather, efficient intracellular transport correlated with the presence of predicted secondary structure in the cytoplasmic tail. Examination of the cytoplasmic domains of 984 human and 782 mouse type I transmembrane proteins revealed that many previously identified ER export motifs are rarely found in the cytoplasmic tail of type I transmembrane proteins. Our results suggest that efficient intracellular transport of B7 chimeric proteins is associated with the structure rather than to the presence of a linear ER export motif in the cytoplasmic tail, and indicate that short (less than ~ 10-20 amino acids) and unstructured cytoplasmic tails should be avoided to express high levels of chimeric proteins on mammalian cells. PMID:24073236

A 2D-3D strategy for resolving tsunami-generated debris flow in urban environments

NASA Astrophysics Data System (ADS)

Birjukovs Canelas, Ricardo; Conde, Daniel; Garcia-Feal, Orlando; João Telhado, Maria; Ferreira, Rui M. L.

2017-04-01

The incorporation of solids, either sediment from the natural environment or remains from buildings or infrastructures is a relevant feature of tsunami run-up in urban environments, greatly increasing the destructive potential of tsunami propagation. Two-dimensional (2D) models have been used to assess the propagation of the bore, even in dense urban fronts. Computational advances are introduced in this work, namely a fully lagrangian, 3D description of the fluid-solid flow, coupled with a high performance meshless implementation capable of dealing with large domains and fine discretizations. A Smoothed Particle Hydrodynamics (SPH) Navier-Stokes discretization and a Distributed Contact Discrete Element Method (DCDEM) description of solid-solid interactions provide a state-of the-art fluid-solid flow description. Together with support for arbitrary geometries, centimetre scale resolution simulations of a city section in Lisbon downtown are presented. 2D results are used as boundary conditions for the 3D model, characterizing the incoming wave as it approaches the coast. It is shown that the incoming bore is able to mobilize and incorporate standing vehicles and other urban hardware. Such fully featured simulation provides explicit description of the interactions among fluid, floating debris (vehicles and urban furniture), the buildings and the pavement. The proposed model presents both an innovative research tool for the study of these flows and a powerful and robust approach to study, design and test mitigation solutions at the local scale. At the same time, due to the high time and space resolution of these methodologies, new questions are raised: scenario-building and initial configurations play a crucial role but they do not univocally determine the final configuration of the simulation, as the solution of the Navier-Stokes equations for high Reynolds numbers possesses a high number of degrees of freedom. This calls for conducting the simulations in a statistical framework, involving both initial conditions generation and interpretation of results, which is only attainable under very high standards of computational efficiency. This research as partially supported by Portuguese and European funds, within programs COMPETE2020 and PORL-FEDER, through project PTDC/ECM-HID/6387/2014 granted by the National Foundation for Science and Technology (FCT).

Optimizing Cubature for Efficient Integration of Subspace Deformations

PubMed Central

An, Steven S.; Kim, Theodore; James, Doug L.

2009-01-01

We propose an efficient scheme for evaluating nonlinear subspace forces (and Jacobians) associated with subspace deformations. The core problem we address is efficient integration of the subspace force density over the 3D spatial domain. Similar to Gaussian quadrature schemes that efficiently integrate functions that lie in particular polynomial subspaces, we propose cubature schemes (multi-dimensional quadrature) optimized for efficient integration of force densities associated with particular subspace deformations, particular materials, and particular geometric domains. We support generic subspace deformation kinematics, and nonlinear hyperelastic materials. For an r-dimensional deformation subspace with O(r) cubature points, our method is able to evaluate subspace forces at O(r2) cost. We also describe composite cubature rules for runtime error estimation. Results are provided for various subspace deformation models, several hyperelastic materials (St.Venant-Kirchhoff, Mooney-Rivlin, Arruda-Boyce), and multimodal (graphics, haptics, sound) applications. We show dramatically better efficiency than traditional Monte Carlo integration. CR Categories: I.6.8 [Simulation and Modeling]: Types of Simulation—Animation, I.3.5 [Computer Graphics]: Computational Geometry and Object Modeling—Physically based modeling G.1.4 [Mathematics of Computing]: Numerical Analysis—Quadrature and Numerical Differentiation PMID:19956777

Life Events, Sibling Warmth, and Youths' Adjustment

ERIC Educational Resources Information Center

Waite, Evelyn B.; Shanahan, Lilly; Calkins, Susan D.; Keane, Susan P.; O'Brien, Marion

2011-01-01

Sibling warmth has been identified as a protective factor from life events, but stressor-support match-mismatch and social domains perspectives suggest that sibling warmth may not efficiently protect youths from all types of life events. We tested whether sibling warmth moderated the association between each of family-wide, youths' personal, and…

Gas phase electrodeposition: a programmable multimaterial deposition method for combinatorial nanostructured device discovery.

PubMed

Lin, En-Chiang; Cole, Jesse J; Jacobs, Heiko O

2010-11-10

This article reports and applies a recently discovered programmable multimaterial deposition process to the formation and combinatorial improvement of 3D nanostructured devices. The gas-phase deposition process produces charged <5 nm particles of silver, tungsten, and platinum and uses externally biased electrodes to control the material flux and to turn deposition ON/OFF in selected domains. Domains host nanostructured dielectrics to define arrays of electrodynamic 10 × nanolenses to further control the flux to form <100 nm resolution deposits. The unique feature of the process is that material type, amount, and sequence can be altered from one domain to the next leading to different types of nanostructures including multimaterial bridges, interconnects, or nanowire arrays with 20 nm positional accuracy. These features enable combinatorial nanostructured materials and device discovery. As a first demonstration, we produce and identify in a combinatorial way 3D nanostructured electrode designs that improve light scattering, absorption, and minority carrier extraction of bulk heterojunction photovoltaic cells. Photovoltaic cells from domains with long and dense nanowire arrays improve the relative power conversion efficiency by 47% when compared to flat domains on the same substrate.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Sun -Ki; Chung, Daehwan; Himmel, Michael E.

Here, CelA is the most abundant enzyme secreted by Caldicellulosiruptor bescii and has been shown to outperform mixtures of commercially available exo- and endoglucanases in vitro. CelA contains both a glycoside hydrolase family 9 endoglucanase and a glycoside hydrolase family 48 exoglucanase known to be synergistic in their activity, connected by three cellulose-binding domains via linker peptides. Here, repeated aspartate residues were introduced into the N-terminal ends of CelA GH9 and GH48 domains to improve secretion efficiency and/or catalytic efficiency of CelA. Among several constructs, the highest activity on carboxymethylcellulose (CMC), 0.81 ± 0.03 mg/mL was observed for the C.more » bescii strain containing CelA with 5-aspartate tag at the N-terminal end of GH9 domain – an 82% increase over wild type CelA. In addition, Expression of CelA with N-terminal repeated aspartate residues in C. bescii results in a dramatic increase in its ability to grow on Avicel.« less

Enhancement of branching efficiency by the actin filament-binding activity of N-WASP/WAVE2.

PubMed

Suetsugu, S; Miki, H; Yamaguchi, H; Obinata, T; Takenawa, T

2001-12-01

The actin-related protein (Arp) 2/3 complex is an essential regulator of de novo actin filament formation. Arp2/3 nucleates the polymerization of actin and creates branched actin filaments when activated by Arp2/3-complex activating domain (VCA) of Wiskott-Aldrich syndrome proteins (WASP family proteins). We found that the branching of actin filaments on pre-existing ADP filaments mediated by the Arp2/3 complex is twice as efficient when Arp2/3 was activated by wild-type neural WASP (N-WASP) or WASP-family verprolin-homologous protein (WAVE) 2 than when activated by the VCA domain alone. By contrast, there was no difference between wild-type N-WASP or WAVE2 and VCA in the branching efficiency on de novo filaments, which are thought to consist mainly of ADP-phosphate filaments. This increased branching efficiency on ADP filaments is due to the basic region located in the center of N-WASP and WAVE2, which was found to associate with ADP actin filaments. Actin filaments and phosphatidylinositol bisphosphate (PIP2) associate with N-WASP at different sites. This association of N-WASP and WAVE2 with actin filaments enhanced recruitment of Arp2/3 to the pre-existing filaments, presumably leading to efficient nucleation and branch formation on pre-existing filaments. These data together suggest that the actin filament binding activity of N-WASP and WAVE2 in the basic region increases the number of barbed ends created on pre-existing filaments. Efficient branching on ADP filaments may be important for initiation of actin-based motility.

Efficient HIV-1 inhibition by a 16 nt-long RNA aptamer designed by combining in vitro selection and in silico optimisation strategies

PubMed Central

Sánchez-Luque, Francisco J.; Stich, Michael; Manrubia, Susanna; Briones, Carlos; Berzal-Herranz, Alfredo

2014-01-01

The human immunodeficiency virus type-1 (HIV-1) genome contains multiple, highly conserved structural RNA domains that play key roles in essential viral processes. Interference with the function of these RNA domains either by disrupting their structures or by blocking their interaction with viral or cellular factors may seriously compromise HIV-1 viability. RNA aptamers are amongst the most promising synthetic molecules able to interact with structural domains of viral genomes. However, aptamer shortening up to their minimal active domain is usually necessary for scaling up production, what requires very time-consuming, trial-and-error approaches. Here we report on the in vitro selection of 64 nt-long specific aptamers against the complete 5′-untranslated region of HIV-1 genome, which inhibit more than 75% of HIV-1 production in a human cell line. The analysis of the selected sequences and structures allowed for the identification of a highly conserved 16 nt-long stem-loop motif containing a common 8 nt-long apical loop. Based on this result, an in silico designed 16 nt-long RNA aptamer, termed RNApt16, was synthesized, with sequence 5′-CCCCGGCAAGGAGGGG-3′. The HIV-1 inhibition efficiency of such an aptamer was close to 85%, thus constituting the shortest RNA molecule so far described that efficiently interferes with HIV-1 replication. PMID:25175101

Towards automated processing of clinical Finnish: sublanguage analysis and a rule-based parser.

PubMed

Laippala, Veronika; Ginter, Filip; Pyysalo, Sampo; Salakoski, Tapio

2009-12-01

In this paper, we present steps taken towards more efficient automated processing of clinical Finnish, focusing on daily nursing notes in a Finnish Intensive Care Unit (ICU). First, we analyze ICU Finnish as a sublanguage, identifying its specific features facilitating, for example, the development of a specialized syntactic analyser. The identified features include frequent omission of finite verbs, limitations in allowed syntactic structures, and domain-specific vocabulary. Second, we develop a formal grammar and a parser for ICU Finnish, thus providing better tools for the development of further applications in the clinical domain. The grammar is implemented in the LKB system in a typed feature structure formalism. The lexicon is automatically generated based on the output of the FinTWOL morphological analyzer adapted to the clinical domain. As an additional experiment, we study the effect of using Finnish constraint grammar to reduce the size of the lexicon. The parser construction thus makes efficient use of existing resources for Finnish. The grammar currently covers 76.6% of ICU Finnish sentences, producing highly accurate best-parse analyzes with F-score of 91.1%. We find that building a parser for the highly specialized domain sublanguage is not only feasible, but also surprisingly efficient, given an existing morphological analyzer with broad vocabulary coverage. The resulting parser enables a deeper analysis of the text than was previously possible.

Stackfile Database

NASA Technical Reports Server (NTRS)

deVarvalho, Robert; Desai, Shailen D.; Haines, Bruce J.; Kruizinga, Gerhard L.; Gilmer, Christopher

2013-01-01

This software provides storage retrieval and analysis functionality for managing satellite altimetry data. It improves the efficiency and analysis capabilities of existing database software with improved flexibility and documentation. It offers flexibility in the type of data that can be stored. There is efficient retrieval either across the spatial domain or the time domain. Built-in analysis tools are provided for frequently performed altimetry tasks. This software package is used for storing and manipulating satellite measurement data. It was developed with a focus on handling the requirements of repeat-track altimetry missions such as Topex and Jason. It was, however, designed to work with a wide variety of satellite measurement data [e.g., Gravity Recovery And Climate Experiment -- GRACE). The software consists of several command-line tools for importing, retrieving, and analyzing satellite measurement data.

An approximate solution to improve computational efficiency of impedance-type payload load prediction

NASA Technical Reports Server (NTRS)

White, C. W.

1981-01-01

The computational efficiency of the impedance type loads prediction method was studied. Three goals were addressed: devise a method to make the impedance method operate more efficiently in the computer; assess the accuracy and convenience of the method for determining the effect of design changes; and investigate the use of the method to identify design changes for reduction of payload loads. The method is suitable for calculation of dynamic response in either the frequency or time domain. It is concluded that: the choice of an orthogonal coordinate system will allow the impedance method to operate more efficiently in the computer; the approximate mode impedance technique is adequate for determining the effect of design changes, and is applicable for both statically determinate and statically indeterminate payload attachments; and beneficial design changes to reduce payload loads can be identified by the combined application of impedance techniques and energy distribution review techniques.

Structural features of the KPI domain control APP dimerization, trafficking, and processing.

PubMed

Ben Khalifa, Naouel; Tyteca, Donatienne; Marinangeli, Claudia; Depuydt, Mathieu; Collet, Jean-François; Courtoy, Pierre J; Renauld, Jean-Christophe; Constantinescu, Stefan; Octave, Jean-Noël; Kienlen-Campard, Pascal

2012-02-01

The two major isoforms of human APP, APP695 and APP751, differ by the presence of a Kunitz-type protease inhibitor (KPI) domain in the extracellular region. APP processing and function is thought to be regulated by homodimerization. We used bimolecular fluorescence complementation (BiFC) to study dimerization of different APP isoforms and mutants. APP751 was found to form significantly more homodimers than APP695. Mutation of dimerization motifs in the TM domain did not affect fluorescence complementation, but native folding of KPI is critical for APP751 homodimerization. APP751 and APP695 dimers were mostly localized at steady state in the Golgi region, suggesting that most of the APP751 and 695 dimers are in the secretory pathway. Mutation of the KPI led to the retention of the APP homodimers in the endoplasmic reticulum. We finally showed that APP751 is more efficiently processed through the nonamyloidogenic pathway than APP695. These findings provide new insight on the particular role of KPI domain in APP dimerization. The correlation observed between dimerization, subcellular localization, and processing suggests that dimerization acts as an efficient regulator of APP trafficking in the secretory compartments that has major consequences on its processing.

Comparison of temporal and spectral scattering methods using acoustically large breast models derived from magnetic resonance images.

PubMed

Hesford, Andrew J; Tillett, Jason C; Astheimer, Jeffrey P; Waag, Robert C

2014-08-01

Accurate and efficient modeling of ultrasound propagation through realistic tissue models is important to many aspects of clinical ultrasound imaging. Simplified problems with known solutions are often used to study and validate numerical methods. Greater confidence in a time-domain k-space method and a frequency-domain fast multipole method is established in this paper by analyzing results for realistic models of the human breast. Models of breast tissue were produced by segmenting magnetic resonance images of ex vivo specimens into seven distinct tissue types. After confirming with histologic analysis by pathologists that the model structures mimicked in vivo breast, the tissue types were mapped to variations in sound speed and acoustic absorption. Calculations of acoustic scattering by the resulting model were performed on massively parallel supercomputer clusters using parallel implementations of the k-space method and the fast multipole method. The efficient use of these resources was confirmed by parallel efficiency and scalability studies using large-scale, realistic tissue models. Comparisons between the temporal and spectral results were performed in representative planes by Fourier transforming the temporal results. An RMS field error less than 3% throughout the model volume confirms the accuracy of the methods for modeling ultrasound propagation through human breast.

Selective, Embedded, Just-In-Time Specialization (SEJITS): Portable Parallel Performance from Sequential, Productive, Embedded Domain-Specific Languages

DTIC Science & Technology

2012-12-01

identity operation SIMD Single instruction, multiple datastream parallel computing Scala A byte-compiled programming language featuring dynamic type...Specific Languages 5a. CONTRACT NUMBER FA8750-10-1-0191 5b. GRANT NUMBER N/A 5c. PROGRAM ELEMENT NUMBER 61101E 6. AUTHOR(S) Armando Fox 5d...application performance, but usually must rely on efficiency programmers who are experts in explicit parallel programming to achieve it. Since such efficiency

Importance of the short cytoplasmic domain of the feline immunodeficiency virus transmembrane glycoprotein for fusion activity and envelope glycoprotein incorporation into virions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Celma, Cristina C.P.; Paladino, Monica G.; Gonzalez, Silvia A.

2007-09-30

The mature form of the envelope (Env) glycoprotein of lentiviruses is a heterodimer composed of the surface (SU) and transmembrane (TM) subunits. Feline immunodeficiency virus (FIV) possesses a TM glycoprotein with a cytoplasmic tail of approximately 53 amino acids which is unusually short compared with that of the other lentiviral glycoproteins (more than 100 residues). To investigate the relevance of the FIV TM cytoplasmic domain to Env-mediated viral functions, we characterized the biological properties of a series of Env glycoproteins progressively shortened from the carboxyl terminus. All the mutant Env proteins were efficiently expressed in feline cells and processed intomore » the SU and TM subunits. Deletion of 5 or 11 amino acids from the TM C-terminus did not significantly affect Env surface expression, fusogenic activity or Env incorporation into virions, whereas removal of 17 or 23 residues impaired Env-mediated cell-to-cell fusion. Further truncation of the FIV TM by 29 residues resulted in an Env glycoprotein that was poorly expressed at the cell surface, exhibited only 20% of the wild-type Env fusogenic capacity and was inefficiently incorporated into virions. Remarkably, deletion of the TM C-terminal 35 or 41 amino acids restored or even enhanced Env biological functions. Indeed, these mutant Env glycoproteins bearing cytoplasmic domains of 18 or 12 amino acids were found to be significantly more fusogenic than the wild-type Env and were efficiently incorporated into virions. Interestingly, truncation of the TM cytoplasmic domain to only 6 amino acids did not affect Env incorporation into virions but abrogated Env fusogenicity. Finally, removal of the entire TM cytoplasmic tail or deletion of as many as 6 amino acids into the membrane-spanning domain led to a complete loss of Env functions. Our results demonstrate that despite its relatively short length, the FIV TM cytoplasmic domain plays an important role in modulating Env-mediated viral functions.« less

Topological domain walls in helimagnets

NASA Astrophysics Data System (ADS)

Schoenherr, P.; Müller, J.; Köhler, L.; Rosch, A.; Kanazawa, N.; Tokura, Y.; Garst, M.; Meier, D.

2018-05-01

Domain walls naturally arise whenever a symmetry is spontaneously broken. They interconnect regions with different realizations of the broken symmetry, promoting structure formation from cosmological length scales to the atomic level1,2. In ferroelectric and ferromagnetic materials, domain walls with unique functionalities emerge, holding great promise for nanoelectronics and spintronics applications3-5. These walls are usually of Ising, Bloch or Néel type and separate homogeneously ordered domains. Here we demonstrate that a wide variety of new domain walls occurs in the presence of spatially modulated domain states. Using magnetic force microscopy and micromagnetic simulations, we show three fundamental classes of domain walls to arise in the near-room-temperature helimagnet iron germanium. In contrast to conventional ferroics, the domain walls exhibit a well-defined inner structure, which—analogous to cholesteric liquid crystals—consists of topological disclination and dislocation defects. Similar to the magnetic skyrmions that form in the same material6,7, the domain walls can carry a finite topological charge, permitting an efficient coupling to spin currents and contributions to a topological Hall effect. Our study establishes a new family of magnetic nano-objects with non-trivial topology, opening the door to innovative device concepts based on helimagnetic domain walls.

Oligomerization triggered by foldon: a simple method to enhance the catalytic efficiency of lichenase and xylanase.

PubMed

Wang, Xinzhe; Ge, Huihua; Zhang, Dandan; Wu, Shuyu; Zhang, Guangya

2017-07-03

Effective and simple methods that lead to higher enzymatic efficiencies are highly sough. Here we proposed a foldon-triggered trimerization of the target enzymes with significantly improved catalytic performances by fusing a foldon domain at the C-terminus of the enzymes via elastin-like polypeptides (ELPs). The foldon domain comprises 27 residues and can forms trimers with high stability. Lichenase and xylanase can hydrolyze lichenan and xylan to produce value added products and biofuels, and they have great potentials as biotechnological tools in various industrial applications. We took them as the examples and compared the kinetic parameters of the engineered trimeric enzymes to those of the monomeric and wild type ones. When compared with the monomeric ones, the catalytic efficiency (k cat /K m ) of the trimeric lichenase and xylanase increased 4.2- and 3.9- fold. The catalytic constant (k cat ) of the trimeric lichenase and xylanase increased 1.8- fold and 5.0- fold than their corresponding wild-type counterparts. Also, the specific activities of trimeric lichenase and xylanase increased by 149% and 94% than those of the monomeric ones. Besides, the recovery of the lichenase and xylanase activities increased by 12.4% and 6.1% during the purification process using ELPs as the non-chromatographic tag. The possible reason is the foldon domain can reduce the transition temperature of the ELPs. The trimeric lichenase and xylanase induced by foldon have advantages in the catalytic performances. Besides, they were easier to purify with increased purification fold and decreased the loss of activities compared to their corresponding monomeric ones. Trimerizing of the target enzymes triggered by the foldon domain could improve their activities and facilitate the purification, which represents a simple and effective enzyme-engineering tool. It should have exciting potentials both in industrial and laboratory scales.

Disrupted White Matter Network and Cognitive Decline in Type 2 Diabetes Patients.

PubMed

Zhang, Junying; Liu, Zhen; Li, Zixiao; Wang, Yunxia; Chen, Yaojing; Li, Xin; Chen, Kewei; Shu, Ni; Zhang, Zhanjun

2016-05-06

Type 2 diabetes mellitus is accompanied by cognitive impairment and is associated with an increased risk of dementia. Damage to brain structures such as white matter network disruption may underlie this cognitive disturbance. In the present study, 886 non-diabetic and 163 type 2 diabetic participants completed a battery of neuropsychological tests. Among them, 38 diabetic patients and 34 non-diabetic participants that matched the patients for age/sex/education received a magnetic resonance imaging-based diffusion tensor imaging. Then we calculated the topological properties of the white matter network using a graph theoretical method to investigate network efficiency differences between groups. We found that type 2 diabetic patients had inferior performances compared to the non-diabetic controls, in several cognitive domains involving executive function, spatial processing, memory, and attention. We also found that diabetic patients exhibited a disrupted topological organization of the white matter network (including the global network properties, i.e., network strength, global efficiency, local efficiency and shortest path length, and the nodal efficiency of the right rolandic operculum) in the brain. Moreover, those global network properties and the nodal efficiency of the right rolandic operculum both had positive correlations with executive function in the patient group. The results suggest that type 2 diabetes mellitus leads to an alteration in the topological organization of the cortical white matter network and this alteration may account for the observed cognitive decline.

Moment equations for chromatography using superficially porous spherical particles.

PubMed

Miyabe, Kanji

2011-01-01

New moment equations were developed for chromatography using superficially porous (shell-type) spherical particles, which have recently attracted much attention as one of separation media for fast separation with high efficiency. At first, the moment equations of the first absolute and second central moments in the real time domain were derived from the analytical solution in the Laplace domain of a set of basic equations of the general rate model of chromatography, which represent the mass balance, mass-transfer rate, and reaction kinetics in the column packed with shell-type particles. Then, the moment equations were used for analyzing the experimental data of chromatography of kallidin in a Halo column, which were published in a previous paper written by other researchers. It was tried to predict the chromatographic behavior of shell-type particles having different shell thicknesses. The new moment equations are useful for a detailed analysis of the chromatographic behavior of shell-type spherical particles. It is also concluded that they can be used for the preliminarily optimization of their structural characteristics.

Performance advantages of CPML over UPML absorbing boundary conditions in FDTD algorithm

NASA Astrophysics Data System (ADS)

Gvozdic, Branko D.; Djurdjevic, Dusan Z.

2017-01-01

Implementation of absorbing boundary condition (ABC) has a very important role in simulation performance and accuracy in finite difference time domain (FDTD) method. The perfectly matched layer (PML) is the most efficient type of ABC. The aim of this paper is to give detailed insight in and discussion of boundary conditions and hence to simplify the choice of PML used for termination of computational domain in FDTD method. In particular, we demonstrate that using the convolutional PML (CPML) has significant advantages in terms of implementation in FDTD method and reducing computer resources than using uniaxial PML (UPML). An extensive number of numerical experiments has been performed and results have shown that CPML is more efficient in electromagnetic waves absorption. Numerical code is prepared, several problems are analyzed and relative error is calculated and presented.

Certifying Domain-Specific Policies

NASA Technical Reports Server (NTRS)

Lowry, Michael; Pressburger, Thomas; Rosu, Grigore; Koga, Dennis (Technical Monitor)

2001-01-01

Proof-checking code for compliance to safety policies potentially enables a product-oriented approach to certain aspects of software certification. To date, previous research has focused on generic, low-level programming-language properties such as memory type safety. In this paper we consider proof-checking higher-level domain -specific properties for compliance to safety policies. The paper first describes a framework related to abstract interpretation in which compliance to a class of certification policies can be efficiently calculated Membership equational logic is shown to provide a rich logic for carrying out such calculations, including partiality, for certification. The architecture for a domain-specific certifier is described, followed by an implemented case study. The case study considers consistency of abstract variable attributes in code that performs geometric calculations in Aerospace systems.

The retinal specific CD147 Ig0 domain: from molecular structure to biological activity

PubMed Central

Redzic, Jasmina S.; Armstrong, Geoffrey S.; Isern, Nancy. G.; Jones, David N.M.; Kieft, Jeffrey S.; Eisenmesser, Elan Zohar

2011-01-01

CD147 is a type I transmembrane protein that is involved in inflammatory diseases, cancer progression, and multiple human pathogens utilize CD147 for efficient infection. In several cancers, CD147 expression is so high that it is now used as a prognostic marker. The two primary isoforms of CD147 that are related to cancer progression have been identified, differing in their number of immunoglobulin (Ig)-like domains. These include CD147 Ig1-Ig2 that is ubiquitously expressed in most tissues and CD147 Ig0-Ig1-Ig2 that is retinal specific and implicated in retinoblastoma. However, little is known in regard to the retinal specific CD147 Ig0 domain despite its potential role in retinoblastoma. We present the first crystal structure of the human CD147 Ig0 domain and show that the CD147 Ig0 domain is a crystallographic dimer with an I-type domain structure, which is maintained in solution. Furthermore, we have utilized our structural data together with mutagenesis to probe the biological activity of CD147-containing proteins both with and without the CD147 Ig0 domain within several model cell lines. Our findings reveal that the CD147 Ig0 domain is a potent stimulator of interleukin-6 and suggest that the CD147 Ig0 domain has its own receptor distinct from that of the other CD147 Ig-like domains, CD147 Ig1-Ig2. Finally, we show that the CD147 Ig0 dimer is the functional unit required for activity and can be disrupted by a single point mutation. PMID:21620857

Assessment of tropism and effectiveness of new primate-derived hybrid recombinant AAV serotypes in the mouse and primate retina.

PubMed

Charbel Issa, Peter; De Silva, Samantha R; Lipinski, Daniel M; Singh, Mandeep S; Mouravlev, Alexandre; You, Qisheng; Barnard, Alun R; Hankins, Mark W; During, Matthew J; Maclaren, Robert E

2013-01-01

Adeno-associated viral vectors (AAV) have been shown to be safe in the treatment of retinal degenerations in clinical trials. Thus, improving the efficiency of viral gene delivery has become increasingly important to increase the success of clinical trials. In this study, structural domains of different rAAV serotypes isolated from primate brain were combined to create novel hybrid recombinant AAV serotypes, rAAV2/rec2 and rAAV2/rec3. The efficacy of these novel serotypes were assessed in wild type mice and in two models of retinal degeneration (the Abca4(-/-) mouse which is a model for Stargardt disease and in the Pde6b(rd1/rd1) mouse) in vivo, in primate tissue ex-vivo, and in the human-derived SH-SY5Y cell line, using an identical AAV2 expression cassette. We show that these novel hybrid serotypes can transduce retinal tissue in mice and primates efficiently, although no more than AAV2/2 and rAAV2/5 serotypes. Transduction efficiency appeared lower in the Abca4(-/-) mouse compared to wild type with all vectors tested, suggesting an effect of specific retinal diseases on the efficiency of gene delivery. Shuffling of AAV capsid domains may have clinical applications for patients who develop T-cell immune responses following AAV gene therapy, as specific peptide antigen sequences could be substituted using this technique prior to vector re-treatments.

CLUMPY DISKS AS A TESTBED FOR FEEDBACK-REGULATED GALAXY FORMATION

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mayer, Lucio; Tamburello, Valentina; Lupi, Alessandro

2016-10-10

We study the dependence of fragmentation in massive gas-rich galaxy disks at z >1 on stellar feedback schemes and hydrodynamical solvers, employing the GASOLINE2 SPH code and the lagrangian mesh-less code GIZMO in finite mass mode. Non-cosmological galaxy disk runs with the standard delayed-cooling blastwave feedback are compared with runs adopting a new superbubble feedback, which produces winds by modeling the detailed physics of supernova-driven bubbles and leads to efficient self-regulation of star formation. We find that, with blastwave feedback, massive star-forming clumps form in comparable number and with very similar masses in GASOLINE2 and GIZMO. Typical clump masses aremore » in the range 10{sup 7}–10{sup 8} M {sub ⊙}, lower than in most previous works, while giant clumps with masses above 10{sup 9} M {sub ⊙} are exceedingly rare. By contrast, superbubble feedback does not produce massive star-forming bound clumps as galaxies never undergo a phase of violent disk instability. In this scheme, only sporadic, unbound star-forming overdensities lasting a few tens of Myr can arise, triggered by non-linear perturbations from massive satellite companions. We conclude that there is severe tension between explaining massive star-forming clumps observed at z >1 primarily as the result of disk fragmentation driven by gravitational instability and the prevailing view of feedback-regulated galaxy formation. The link between disk stability and star formation efficiency should thus be regarded as a key testing ground for galaxy formation theory.« less

Insights into the conformational switching mechanism of the human vascular endothelial growth factor receptor type 2 kinase domain.

PubMed

Chioccioli, Matteo; Marsili, Simone; Bonaccini, Claudia; Procacci, Piero; Gratteri, Paola

2012-02-27

Human vascular endothelial growth factor receptor type 2 (h-VEFGR2) is a receptor tyrosine kinase involved in the angiogenesis process and regarded as an interesting target for the design of anticancer drugs. Its activation/inactivation mechanism is related to conformational changes in its cytoplasmatic kinase domain, involving first among all the αC-helix in N-lobe and the A-loop in C-lobe. Affinity of inhibitors for the active or inactive kinase form could dictate the open or closed conformation of the A-loop, thus making the different conformations of the kinase domain receptor (KDR) domain different drug targets in drug discovery. In this view, a detailed knowledge of the conformational landscape of KDR domain is of central relevance to rationalize the efficiency and selectivity of kinase inhibitors. Here, molecular dynamics simulations were used to gain insight into the conformational switching activity of the KDR domain and to identify intermediate conformations between the two limiting active and inactive conformations. Specific energy barriers have been selectively removed to induce, and hence highlight at the atomistic level, the regulation mechanism of the A-loop opening. The proposed strategy allowed to repeatedly observe the escape of the KDR domain from the DFG-out free energy basin and to identify rare intermediate conformations between the DFG-out and the DFG-in structures to be employed in a structure-based drug discovery process.

Discrete and continuum modelling of soil cutting

NASA Astrophysics Data System (ADS)

Coetzee, C. J.

2014-12-01

Both continuum and discrete methods are used to investigate the soil cutting process. The Discrete Element Method ( dem) is used for the discrete modelling and the Material-Point Method ( mpm) is used for continuum modelling. M pmis a so-called particle method or meshless finite element method. Standard finite element methods have difficulty in modelling the entire cutting process due to large displacements and deformation of the mesh. The use of meshless methods overcomes this problem. M pm can model large deformations, frictional contact at the soil-tool interface, and dynamic effects (inertia forces). In granular materials the discreteness of the system is often important and rotational degrees of freedom are active, which might require enhanced theoretical approaches like polar continua. In polar continuum theories, the material points are considered to possess orientations. A material point has three degrees-of-freedom for rigid rotations, in addition to the three classic translational degrees-of-freedom. The Cosserat continuum is the most transparent and straightforward extension of the nonpolar (classic) continuum. Two-dimensional dem and mpm (polar and nonpolar) simulations of the cutting problem are compared to experiments. The drag force and flow patterns are compared using cohesionless corn grains as material. The corn macro (continuum) and micro ( dem) properties were obtained from shear and oedometer tests. Results show that the dilatancy angle plays a significant role in the flow of material but has less of an influence on the draft force. Nonpolar mpm is the most accurate in predicting blade forces, blade-soil interface stresses and the position and orientation of shear bands. Polar mpm fails in predicting the orientation of the shear band, but is less sensitive to mesh size and mesh orientation compared to nonpolar mpm. dem simulations show less material dilation than observed during experiments.

Crystal Structure of Chitinase ChiW from Paenibacillus sp. str. FPU-7 Reveals a Novel Type of Bacterial Cell-Surface-Expressed Multi-Modular Enzyme Machinery

PubMed Central

Itoh, Takafumi; Hibi, Takao; Suzuki, Fumiko; Sugimoto, Ikumi; Fujiwara, Akihiro; Inaka, Koji; Tanaka, Hiroaki; Ohta, Kazunori; Fujii, Yutaka; Taketo, Akira; Kimoto, Hisashi

2016-01-01

The Gram-positive bacterium Paenibacillus sp. str. FPU-7 effectively hydrolyzes chitin by using a number of chitinases. A unique chitinase with two catalytic domains, ChiW, is expressed on the cell surface of this bacterium and has high activity towards various chitins, even crystalline chitin. Here, the crystal structure of ChiW at 2.1 Å resolution is presented and describes how the enzyme degrades chitin on the bacterial cell surface. The crystal structure revealed a unique multi-modular architecture composed of six domains to function efficiently on the cell surface: a right-handed β-helix domain (carbohydrate-binding module family 54, CBM-54), a Gly-Ser-rich loop, 1st immunoglobulin-like (Ig-like) fold domain, 1st β/α-barrel catalytic domain (glycoside hydrolase family 18, GH-18), 2nd Ig-like fold domain and 2nd β/α-barrel catalytic domain (GH-18). The structure of the CBM-54, flexibly linked to the catalytic region of ChiW, is described here for the first time. It is similar to those of carbohydrate lyases but displayed no detectable carbohydrate degradation activities. The CBM-54 of ChiW bound to cell wall polysaccharides, such as chin, chitosan, β-1,3-glucan, xylan and cellulose. The structural and biochemical data obtained here also indicated that the enzyme has deep and short active site clefts with endo-acting character. The affinity of CBM-54 towards cell wall polysaccharides and the degradation pattern of the catalytic domains may help to efficiently decompose the cell wall chitin through the contact surface. Furthermore, we clarify that other Gram-positive bacteria possess similar cell-surface-expressed multi-modular enzymes for cell wall polysaccharide degradation. PMID:27907169

Comparative Genomic Analyses of the Bacterial Phosphotransferase System

PubMed Central

Barabote, Ravi D.; Saier, Milton H.

2005-01-01

We report analyses of 202 fully sequenced genomes for homologues of known protein constituents of the bacterial phosphoenolpyruvate-dependent phosphotransferase system (PTS). These included 174 bacterial, 19 archaeal, and 9 eukaryotic genomes. Homologues of PTS proteins were not identified in archaea or eukaryotes, showing that the horizontal transfer of genes encoding PTS proteins has not occurred between the three domains of life. Of the 174 bacterial genomes (136 bacterial species) analyzed, 30 diverse species have no PTS homologues, and 29 species have cytoplasmic PTS phosphoryl transfer protein homologues but lack recognizable PTS permeases. These soluble homologues presumably function in regulation. The remaining 77 species possess all PTS proteins required for the transport and phosphorylation of at least one sugar via the PTS. Up to 3.2% of the genes in a bacterium encode PTS proteins. These homologues were analyzed for family association, range of protein types, domain organization, and organismal distribution. Different strains of a single bacterial species often possess strikingly different complements of PTS proteins. Types of PTS protein domain fusions were analyzed, showing that certain types of domain fusions are common, while others are rare or prohibited. Select PTS proteins were analyzed from different phylogenetic standpoints, showing that PTS protein phylogeny often differs from organismal phylogeny. The results document the frequent gain and loss of PTS protein-encoding genes and suggest that the lateral transfer of these genes within the bacterial domain has played an important role in bacterial evolution. Our studies provide insight into the development of complex multicomponent enzyme systems and lead to predictions regarding the types of protein-protein interactions that promote efficient PTS-mediated phosphoryl transfer. PMID:16339738

Engineering the N-terminal end of CelA results in improved performance and growth of Caldicellulosiruptor bescii on crystalline cellulose

DOE PAGES

Kim, Sun -Ki; Chung, Daehwan; Himmel, Michael E.; ...

2016-12-26

Here, CelA is the most abundant enzyme secreted by Caldicellulosiruptor bescii and has been shown to outperform mixtures of commercially available exo- and endoglucanases in vitro. CelA contains both a glycoside hydrolase family 9 endoglucanase and a glycoside hydrolase family 48 exoglucanase known to be synergistic in their activity, connected by three cellulose-binding domains via linker peptides. Here, repeated aspartate residues were introduced into the N-terminal ends of CelA GH9 and GH48 domains to improve secretion efficiency and/or catalytic efficiency of CelA. Among several constructs, the highest activity on carboxymethylcellulose (CMC), 0.81 ± 0.03 mg/mL was observed for the C.more » bescii strain containing CelA with 5-aspartate tag at the N-terminal end of GH9 domain – an 82% increase over wild type CelA. In addition, Expression of CelA with N-terminal repeated aspartate residues in C. bescii results in a dramatic increase in its ability to grow on Avicel.« less

A novel multiphysic model for simulation of swelling equilibrium of ionized thermal-stimulus responsive hydrogels

NASA Astrophysics Data System (ADS)

Li, Hua; Wang, Xiaogui; Yan, Guoping; Lam, K. Y.; Cheng, Sixue; Zou, Tao; Zhuo, Renxi

2005-03-01

In this paper, a novel multiphysic mathematical model is developed for simulation of swelling equilibrium of ionized temperature sensitive hydrogels with the volume phase transition, and it is termed the multi-effect-coupling thermal-stimulus (MECtherm) model. This model consists of the steady-state Nernst-Planck equation, Poisson equation and swelling equilibrium governing equation based on the Flory's mean field theory, in which two types of polymer-solvent interaction parameters, as the functions of temperature and polymer-network volume fraction, are specified with or without consideration of the hydrogen bond interaction. In order to examine the MECtherm model consisting of nonlinear partial differential equations, a meshless Hermite-Cloud method is used for numerical solution of one-dimensional swelling equilibrium of thermal-stimulus responsive hydrogels immersed in a bathing solution. The computed results are in very good agreements with experimental data for the variation of volume swelling ratio with temperature. The influences of the salt concentration and initial fixed-charge density are discussed in detail on the variations of volume swelling ratio of hydrogels, mobile ion concentrations and electric potential of both interior hydrogels and exterior bathing solution.

Effect of Dialkyl Ammonium Cationic Surfactants on the Microfluidity of Membranes Containing Raft Domains.

PubMed

Uyama, Makoto; Inoue, Kaori; Kinoshita, Koichi; Miyahara, Reiji; Yokoyama, Hirokazu; Nakano, Minoru

2018-01-01

It has been reported that a lot of receptors localize in lipid raft domains and that the microfluidity of these domains regulates the activation of these receptors. In this study, we focused on the lipid raft and in order to evaluate the physicochemical effects of surfactants on microfluidity of lipid membranes, we used liposomes comprising of egg-yolk L-α-phosphatidylcholine, egg-yolk sphingomyelin, and cholesterol as a model of cell membranes containing raft domains. The microfluidity of the domains was characterized by fluorescence spectrometry using 1,6-diphenyl-1,3,5-hexatriene and 2-dimethylamino-6-lauroylnaphthalene. Among several surfactants, dialkylammonium-type cationic surfactants most efficiently increased the microfluidity. It is therefore concluded that (1) the electrostatic interaction between the cationic surfactant and eggPC/eggSM/cholesterol liposome could be important, (2) surfactants with alkyl chains more effectively inserted into membranes than those with acyl chains, and (3) cationic surfactants with lower T m values have a greater ability to increase the fluidity.

Tunable short-wavelength spin wave excitation from pinned magnetic domain walls

PubMed Central

Van de Wiele, Ben; Hämäläinen, Sampo J.; Baláž, Pavel; Montoncello, Federico; van Dijken, Sebastiaan

2016-01-01

Miniaturization of magnonic devices for wave-like computing requires emission of short-wavelength spin waves, a key feature that cannot be achieved with microwave antennas. In this paper, we propose a tunable source of short-wavelength spin waves based on highly localized and strongly pinned magnetic domain walls in ferroelectric-ferromagnetic bilayers. When driven into oscillation by a microwave spin-polarized current, the magnetic domain walls emit spin waves with the same frequency as the excitation current. The amplitude of the emitted spin waves and the range of attainable excitation frequencies depend on the availability of domain wall resonance modes. In this respect, pinned domain walls in magnetic nanowires are particularly attractive. In this geometry, spin wave confinement perpendicular to the nanowire axis produces a multitude of domain wall resonances enabling efficient spin wave emission at frequencies up to 100 GHz and wavelengths down to 20 nm. At high frequency, the emission of spin waves in magnetic nanowires becomes monochromatic. Moreover, pinning of magnetic domain wall oscillators onto the same ferroelectric domain boundary in parallel nanowires guarantees good coherency between spin wave sources, which opens perspectives towards the realization of Mach-Zehnder type logic devices and sensors. PMID:26883893

Mutations in type 3 reovirus that determine binding to sialic acid are contained in the fibrous tail domain of viral attachment protein sigma1.

PubMed

Chappell, J D; Gunn, V L; Wetzel, J D; Baer, G S; Dermody, T S

1997-03-01

The reovirus attachment protein, sigma1, determines numerous aspects of reovirus-induced disease, including viral virulence, pathways of spread, and tropism for certain types of cells in the central nervous system. The sigma1 protein projects from the virion surface and consists of two distinct morphologic domains, a virion-distal globular domain known as the head and an elongated fibrous domain, termed the tail, which is anchored into the virion capsid. To better understand structure-function relationships of sigma1 protein, we conducted experiments to identify sequences in sigma1 important for viral binding to sialic acid, a component of the receptor for type 3 reovirus. Three serotype 3 reovirus strains incapable of binding sialylated receptors were adapted to growth in murine erythroleukemia (MEL) cells, in which sialic acid is essential for reovirus infectivity. MEL-adapted (MA) mutant viruses isolated by serial passage in MEL cells acquired the capacity to bind sialic acid-containing receptors and demonstrated a dependence on sialic acid for infection of MEL cells. Analysis of reassortant viruses isolated from crosses of an MA mutant virus and a reovirus strain that does not bind sialic acid indicated that the sigma1 protein is solely responsible for efficient growth of MA mutant viruses in MEL cells. The deduced sigma1 amino acid sequences of the MA mutant viruses revealed that each strain contains a substitution within a short region of sequence in the sigma1 tail predicted to form beta-sheet. These studies identify specific sequences that determine the capacity of reovirus to bind sialylated receptors and suggest a location for a sialic acid-binding domain. Furthermore, the results support a model in which type 3 sigma1 protein contains discrete receptor binding domains, one in the head and another in the tail that binds sialic acid.

Multitrace/singletrace formulations and Domain Decomposition Methods for the solution of Helmholtz transmission problems for bounded composite scatterers

NASA Astrophysics Data System (ADS)

Jerez-Hanckes, Carlos; Pérez-Arancibia, Carlos; Turc, Catalin

2017-12-01

We present Nyström discretizations of multitrace/singletrace formulations and non-overlapping Domain Decomposition Methods (DDM) for the solution of Helmholtz transmission problems for bounded composite scatterers with piecewise constant material properties. We investigate the performance of DDM with both classical Robin and optimized transmission boundary conditions. The optimized transmission boundary conditions incorporate square root Fourier multiplier approximations of Dirichlet to Neumann operators. While the multitrace/singletrace formulations as well as the DDM that use classical Robin transmission conditions are not particularly well suited for Krylov subspace iterative solutions of high-contrast high-frequency Helmholtz transmission problems, we provide ample numerical evidence that DDM with optimized transmission conditions constitute efficient computational alternatives for these type of applications. In the case of large numbers of subdomains with different material properties, we show that the associated DDM linear system can be efficiently solved via hierarchical Schur complements elimination.

No evidence for adaptation of current egg drop syndrome 1976 viruses to chickens.

PubMed

Tsukamoto, K; Kuwabara, M; Kaneko, M; Mase, M; Imai, K

2004-01-01

In order to determine whether the current field strains of egg drop syndrome (EDS) 1976 viruses adapt to chickens, we compared the growth efficiency of three Japanese field strains (PA-1/79, AWI/98, Gifu/01) in chicken and duck embryo liver cells. The growth efficiency in chicken or duck embryo liver cells was almost similar in these strains. The fiber protein may carry the type-specific antigen and the hemagglutination activity, and hexon protein may contain the subgroup-specific antigenic determinants. Therefore, the fiber head and hexon loop 1 DNA domain sequences of the six Japanese field strains UPA-1/79, ME/80, 44/81, Kyoto/91, AWI/98, Gifu/01) were compared, but these DNA domains were identical among the six field strains. Our data suggested that the EDS virus was maintained without discernible changes for the last two decades in the field.

Effects of mutations within the SV40 large T antigen ATPase/p53 binding domain on viral replication and transformation.

PubMed

Peden, K W; Srinivasan, A; Vartikar, J V; Pipas, J M

1998-01-01

The simian virus 40 (SV40) large T antigen is a 708 amino-acid protein possessing multiple biochemical activities that play distinct roles in productive infection or virus-induced cell transformation. The carboxy-terminal portion of T antigen includes a domain that carries the nucleotide binding and ATPase activities of the protein, as well as sequences required for T antigen to associate with the cellular tumor suppressor p53. Consequently this domain functions both in viral DNA replication and cellular transformation. We have generated a collection of SV40 mutants with amino-acid deletions, insertions or substitutions in specific domains of the protein. Here we report the properties of nine mutants with single or multiple substitutions between amino acids 402 and 430, a region thought to be important for both the p53 binding and ATPase functions. The mutants were examined for the ability to produce infectious progeny virions, replicate viral DNA in vivo, perform in trans complementation tests, and transform established cell lines. Two of the mutants exhibited a wild-type phenotype in all these tests. The remaining seven mutants were defective for plaque formation and viral DNA replication, but in each case these defects could be complemented by a wild-type T antigen supplied in trans. One of these replication-defective mutants efficiently transformed the REF52 and C3H10T1/2 cell lines as assessed by the dense-focus assay. The remaining six mutants were defective for transforming REF52 cells and transformed the C3H10T1/2 line with a reduced efficiency. The ability of mutant T antigen to transform REF52 cells correlated with their ability to induce increased levels of p53.

A-posteriori error estimation for the finite point method with applications to compressible flow

NASA Astrophysics Data System (ADS)

Ortega, Enrique; Flores, Roberto; Oñate, Eugenio; Idelsohn, Sergio

2017-08-01

An a-posteriori error estimate with application to inviscid compressible flow problems is presented. The estimate is a surrogate measure of the discretization error, obtained from an approximation to the truncation terms of the governing equations. This approximation is calculated from the discrete nodal differential residuals using a reconstructed solution field on a modified stencil of points. Both the error estimation methodology and the flow solution scheme are implemented using the Finite Point Method, a meshless technique enabling higher-order approximations and reconstruction procedures on general unstructured discretizations. The performance of the proposed error indicator is studied and applications to adaptive grid refinement are presented.

Novel two-way artificial boundary condition for 2D vertical water wave propagation modelled with Radial-Basis-Function Collocation Method

NASA Astrophysics Data System (ADS)

Mueller, A.

2018-04-01

A new transparent artificial boundary condition for the two-dimensional (vertical) (2DV) free surface water wave propagation modelled using the meshless Radial-Basis-Function Collocation Method (RBFCM) as boundary-only solution is derived. The two-way artificial boundary condition (2wABC) works as pure incidence, pure radiation and as combined incidence/radiation BC. In this work the 2wABC is applied to harmonic linear water waves; its performance is tested against the analytical solution for wave propagation over horizontal sea bottom, standing and partially standing wave as well as wave interference of waves with different periods.

Modeling of heterogeneous elastic materials by the multiscale hp-adaptive finite element method

NASA Astrophysics Data System (ADS)

Klimczak, Marek; Cecot, Witold

2018-01-01

We present an enhancement of the multiscale finite element method (MsFEM) by combining it with the hp-adaptive FEM. Such a discretization-based homogenization technique is a versatile tool for modeling heterogeneous materials with fast oscillating elasticity coefficients. No assumption on periodicity of the domain is required. In order to avoid direct, so-called overkill mesh computations, a coarse mesh with effective stiffness matrices is used and special shape functions are constructed to account for the local heterogeneities at the micro resolution. The automatic adaptivity (hp-type at the macro resolution and h-type at the micro resolution) increases efficiency of computation. In this paper details of the modified MsFEM are presented and a numerical test performed on a Fichera corner domain is presented in order to validate the proposed approach.

A path-oriented matrix-based knowledge representation system

NASA Technical Reports Server (NTRS)

Feyock, Stefan; Karamouzis, Stamos T.

1993-01-01

Experience has shown that designing a good representation is often the key to turning hard problems into simple ones. Most AI (Artificial Intelligence) search/representation techniques are oriented toward an infinite domain of objects and arbitrary relations among them. In reality much of what needs to be represented in AI can be expressed using a finite domain and unary or binary predicates. Well-known vector- and matrix-based representations can efficiently represent finite domains and unary/binary predicates, and allow effective extraction of path information by generalized transitive closure/path matrix computations. In order to avoid space limitations a set of abstract sparse matrix data types was developed along with a set of operations on them. This representation forms the basis of an intelligent information system for representing and manipulating relational data.

Coupling compositional liquid gas Darcy and free gas flows at porous and free-flow domains interface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Masson, R., E-mail: roland.masson@unice.fr; Team COFFEE INRIA Sophia Antipolis Méditerranée; Trenty, L., E-mail: laurent.trenty@andra.fr

This paper proposes an efficient splitting algorithm to solve coupled liquid gas Darcy and free gas flows at the interface between a porous medium and a free-flow domain. This model is compared to the reduced model introduced in [6] using a 1D approximation of the gas free flow. For that purpose, the gas molar fraction diffusive flux at the interface in the free-flow domain is approximated by a two point flux approximation based on a low-frequency diagonal approximation of a Steklov–Poincaré type operator. The splitting algorithm and the reduced model are applied in particular to the modelling of the massmore » exchanges at the interface between the storage and the ventilation galleries in radioactive waste deposits.« less

Cytochrome P450BM-3 reduces aldehydes to alcohols through a direct hydride transfer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kaspera, Ruediger; Sahele, Tariku; Lakatos, Kyle

Highlights: Black-Right-Pointing-Pointer Cytochrome P450BM-3 reduced aldehydes to alcohols efficiently (k{sub cat} {approx} 25 min{sup -1}). Black-Right-Pointing-Pointer Reduction is a direct hydride transfer from R-NADP{sup 2}H to the carbonyl moiety. Black-Right-Pointing-Pointer P450 domain variants enhance reduction through potential allosteric/redox interactions. Black-Right-Pointing-Pointer Novel reaction will have implications for metabolism of xenobiotics. -- Abstract: Cytochrome P450BM-3 catalyzed the reduction of lipophilic aldehydes to alcohols efficiently. A k{sub cat} of {approx}25 min{sup -1} was obtained for the reduction of methoxy benzaldehyde with wild type P450BM-3 protein which was higher than in the isolated reductase domain (BMR) alone and increased in specific P450-domain variants. Themore » reduction was caused by a direct hydride transfer from preferentially R-NADP{sup 2}H to the carbonyl moiety of the substrate. Weak substrate-P450-binding of the aldehyde, turnover with the reductase domain alone, a deuterium incorporation in the product from NADP{sup 2}H but not D{sub 2}O, and no inhibition by imidazole suggests the reductase domain of P450BM-3 as the potential catalytic site. However, increased aldehyde reduction by P450 domain variants (P450BM-3 F87A T268A) may involve allosteric or redox mechanistic interactions between heme and reductase domains. This is a novel reduction of aldehydes by P450BM-3 involving a direct hydride transfer and could have implications for the metabolism of endogenous substrates or xenobiotics.« less

Self-Taught Low-Rank Coding for Visual Learning.

PubMed

Li, Sheng; Li, Kang; Fu, Yun

2018-03-01

The lack of labeled data presents a common challenge in many computer vision and machine learning tasks. Semisupervised learning and transfer learning methods have been developed to tackle this challenge by utilizing auxiliary samples from the same domain or from a different domain, respectively. Self-taught learning, which is a special type of transfer learning, has fewer restrictions on the choice of auxiliary data. It has shown promising performance in visual learning. However, existing self-taught learning methods usually ignore the structure information in data. In this paper, we focus on building a self-taught coding framework, which can effectively utilize the rich low-level pattern information abstracted from the auxiliary domain, in order to characterize the high-level structural information in the target domain. By leveraging a high quality dictionary learned across auxiliary and target domains, the proposed approach learns expressive codings for the samples in the target domain. Since many types of visual data have been proven to contain subspace structures, a low-rank constraint is introduced into the coding objective to better characterize the structure of the given target set. The proposed representation learning framework is called self-taught low-rank (S-Low) coding, which can be formulated as a nonconvex rank-minimization and dictionary learning problem. We devise an efficient majorization-minimization augmented Lagrange multiplier algorithm to solve it. Based on the proposed S-Low coding mechanism, both unsupervised and supervised visual learning algorithms are derived. Extensive experiments on five benchmark data sets demonstrate the effectiveness of our approach.

Grooved nanowires from self-assembling hairpin molecules for solar cells.

PubMed

Tevis, Ian D; Tsai, Wei-Wen; Palmer, Liam C; Aytun, Taner; Stupp, Samuel I

2012-03-27

One of the challenges facing bulk heterojunction organic solar cells is obtaining organized films during the phase separation of intimately mixed donor and acceptor components. We report here on the use of hairpin-shaped sexithiophene molecules to generate by self-assembly grooved nanowires as the donor component in bulk heterojunction solar cells. Photovoltaic devices were fabricated via spin-casting to produce by solvent evaporation a percolating network of self-assembled nanowires and fullerene acceptors. Thermal annealing was found to increase power conversion efficiencies by promoting domain growth while still maintaining this percolating network of nanostructures. The benefits of self-assembly and grooved nanowires were examined by building devices from a soluble sexithiophene derivative that does not form one-dimensional structures. In these systems, excessive phase separation caused by thermal annealing leads to the formation of defects and lower device efficiencies. We propose that the unique hairpin shape of the self-assembling molecules allows the nanowires as they form to interact well with the fullerenes in receptor-ligand type configurations at the heterojunction of the two domains, thus enhancing device efficiencies by 23%. © 2012 American Chemical Society

Improving the reversibility of thermal denaturation and catalytic efficiency of Bacillus licheniformis α-amylase through stabilizing a long loop in domain B.

PubMed

Li, Zhu; Duan, Xuguo; Chen, Sheng; Wu, Jing

2017-01-01

The reversibility of thermal denaturation and catalytic efficiency of Bacillus licheniformis α-amylase were improved through site-directed mutagenesis. By using multiple sequence alignment and PoPMuSiC algorithm, Ser187 and Asn188, which located within a long loop in Domain B of Bacillus licheniformis α-amylase, were selected for mutation. In addition, Ala269, which is adjacent to Ser187 and Asn188, was also investigated. Seven mutants carrying the mutations S187D, N188T, N188S, A269K, A269K/S187D, S187D/N188T, and A269K/S187D/N188T were generated and characterized. The most thermostable mutant, A269K/S187D/N188T, exhibited a 9-fold improvement in half-life at 95°C and pH 5.5, compared with that of the wild-type enzyme. Mutant A269K/S187D/N188T also exhibited improved catalytic efficiency. The catalytic efficiency of mutant A269K/S187D/N188T reached 5.87×103±0.17 g·L-1·s-1 at pH 5.5, which is 1.84-fold larger than the corresponding value determined for the wild-type enzyme. Furthermore, the structure analysis showed that immobilization of the loop containing Ser187 and Asn188 plays a significant role in developing the properties of Bacillus licheniformis α-amylase.

Improving the reversibility of thermal denaturation and catalytic efficiency of Bacillus licheniformis α-amylase through stabilizing a long loop in domain B

PubMed Central

Li, Zhu; Duan, Xuguo; Chen, Sheng; Wu, Jing

2017-01-01

The reversibility of thermal denaturation and catalytic efficiency of Bacillus licheniformis α-amylase were improved through site-directed mutagenesis. By using multiple sequence alignment and PoPMuSiC algorithm, Ser187 and Asn188, which located within a long loop in Domain B of Bacillus licheniformis α-amylase, were selected for mutation. In addition, Ala269, which is adjacent to Ser187 and Asn188, was also investigated. Seven mutants carrying the mutations S187D, N188T, N188S, A269K, A269K/S187D, S187D/N188T, and A269K/S187D/N188T were generated and characterized. The most thermostable mutant, A269K/S187D/N188T, exhibited a 9-fold improvement in half-life at 95°C and pH 5.5, compared with that of the wild-type enzyme. Mutant A269K/S187D/N188T also exhibited improved catalytic efficiency. The catalytic efficiency of mutant A269K/S187D/N188T reached 5.87×103±0.17 g·L-1·s-1 at pH 5.5, which is 1.84-fold larger than the corresponding value determined for the wild-type enzyme. Furthermore, the structure analysis showed that immobilization of the loop containing Ser187 and Asn188 plays a significant role in developing the properties of Bacillus licheniformis α-amylase. PMID:28253342

Complex Stoichiometry reordering of PTCDA on Ag(111) upon K Intercalation

NASA Astrophysics Data System (ADS)

Brivio, G. P.; Baby, A.; Zwick, C.; Gruenewald, M.; Forker, R.; Fritz, T.; Fratesi, G.; Hofmann, O. T.; Zojer, E.

Alkali metal atoms are a simple yet efficient n-type dopant of organic semiconductors. However, the molecular crystal structures need be controlled and well understood in order to optimize the electronic properties (charge carrier density and mobility) of the target material. Here, we report that potassium intercalation into PTCDA monolayer domains on a Ag(111) substrate induces distinct stoichiometry-dependent structural reordering processes, resulting in highly ordered and large KxPTCDA domains. The emerging structures are analyzed by low temperature scanning tunneling microscopy (STM), scanning tunneling hydrogen microscopy (STHM), and low-energy electron diffraction (LEED) as a function of the stoichiometry and by density functional theory (DFT) calculations. Large stable monolayer domains are found for x=2,4. The epitaxy types for all intercalated stages are determined as point-on-line. The K atoms adsorb in the vicinity of the oxygen atoms of the PTCDA molecules, and their positions are determined with sub-Angstrom precision. This is a crucial prerequisite for the prospective assessment of the electronic properties of such composite films, as they depend on the mutual alignment between donor atoms and acceptor molecules.

Facile Affinity Maturation of Antibody Variable Domains Using Natural Diversity Mutagenesis

PubMed Central

Tiller, Kathryn E.; Chowdhury, Ratul; Li, Tong; Ludwig, Seth D.; Sen, Sabyasachi; Maranas, Costas D.; Tessier, Peter M.

2017-01-01

The identification of mutations that enhance antibody affinity while maintaining high antibody specificity and stability is a time-consuming and laborious process. Here, we report an efficient methodology for systematically and rapidly enhancing the affinity of antibody variable domains while maximizing specificity and stability using novel synthetic antibody libraries. Our approach first uses computational and experimental alanine scanning mutagenesis to identify sites in the complementarity-determining regions (CDRs) that are permissive to mutagenesis while maintaining antigen binding. Next, we mutagenize the most permissive CDR positions using degenerate codons to encode wild-type residues and a small number of the most frequently occurring residues at each CDR position based on natural antibody diversity. This mutagenesis approach results in antibody libraries with variants that have a wide range of numbers of CDR mutations, including antibody domains with single mutations and others with tens of mutations. Finally, we sort the modest size libraries (~10 million variants) displayed on the surface of yeast to identify CDR mutations with the greatest increases in affinity. Importantly, we find that single-domain (VHH) antibodies specific for the α-synuclein protein (whose aggregation is associated with Parkinson’s disease) with the greatest gains in affinity (>5-fold) have several (four to six) CDR mutations. This finding highlights the importance of sampling combinations of CDR mutations during the first step of affinity maturation to maximize the efficiency of the process. Interestingly, we find that some natural diversity mutations simultaneously enhance all three key antibody properties (affinity, specificity, and stability) while other mutations enhance some of these properties (e.g., increased specificity) and display trade-offs in others (e.g., reduced affinity and/or stability). Computational modeling reveals that improvements in affinity are generally not due to direct interactions involving CDR mutations but rather due to indirect effects that enhance existing interactions and/or promote new interactions between the antigen and wild-type CDR residues. We expect that natural diversity mutagenesis will be useful for efficient affinity maturation of a wide range of antibody fragments and full-length antibodies. PMID:28928732

Tag-KEM from Set Partial Domain One-Way Permutations

NASA Astrophysics Data System (ADS)

Abe, Masayuki; Cui, Yang; Imai, Hideki; Kurosawa, Kaoru

Recently a framework called Tag-KEM/DEM was introduced to construct efficient hybrid encryption schemes. Although it is known that generic encode-then-encrypt construction of chosen ciphertext secure public-key encryption also applies to secure Tag-KEM construction and some known encoding method like OAEP can be used for this purpose, it is worth pursuing more efficient encoding method dedicated for Tag-KEM construction. This paper proposes an encoding method that yields efficient Tag-KEM schemes when combined with set partial one-way permutations such as RSA and Rabin's encryption scheme. To our knowledge, this leads to the most practical hybrid encryption scheme of this type. We also present an efficient Tag-KEM which is CCA-secure under general factoring assumption rather than Blum factoring assumption.

Adaptive eigenspace method for inverse scattering problems in the frequency domain

NASA Astrophysics Data System (ADS)

Grote, Marcus J.; Kray, Marie; Nahum, Uri

2017-02-01

A nonlinear optimization method is proposed for the solution of inverse scattering problems in the frequency domain, when the scattered field is governed by the Helmholtz equation. The time-harmonic inverse medium problem is formulated as a PDE-constrained optimization problem and solved by an inexact truncated Newton-type iteration. Instead of a grid-based discrete representation, the unknown wave speed is projected to a particular finite-dimensional basis of eigenfunctions, which is iteratively adapted during the optimization. Truncating the adaptive eigenspace (AE) basis at a (small and slowly increasing) finite number of eigenfunctions effectively introduces regularization into the inversion and thus avoids the need for standard Tikhonov-type regularization. Both analytical and numerical evidence underpins the accuracy of the AE representation. Numerical experiments demonstrate the efficiency and robustness to missing or noisy data of the resulting adaptive eigenspace inversion method.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bodenheimer, Annette M.; Meilleur, Flora

Trichoderma reesei Cel7A efficiently hydrolyses cellulose. We report here the crystallographic structures of the wild-type TrCel7A catalytic domain (CD) in an open state and, for the first time, in a closed state. Molecular dynamics (MD) simulations indicate that the loops along the CD tunnel move in concerted motions. Together, the crystallographic and MD data suggest that the CD cycles between the tense and relaxed forms that are characteristic of work producing enzymes. Analysis of the interactions formed by R251 provides a structural rationale for the concurrent decrease in product inhibition and catalytic efficiency measured for product-binding site mutants.

FRET-based binding assay between a fluorescent cAMP analogue and a cyclic nucleotide-binding domain tagged with a CFP.

PubMed

Romero, Francisco; Santana-Calvo, Carmen; Sánchez-Guevara, Yoloxochitl; Nishigaki, Takuya

2017-09-01

The cyclic nucleotide-binding domain (CNBD) functions as a regulatory domain of many proteins involved in cyclic nucleotide signalling. We developed a straightforward and reliable binding assay based on intermolecular fluorescence resonance energy transfer (FRET) between an adenosine-3', 5'-cyclic monophosphate analogue labelled with fluorescein and a recombinant CNBD of human EPAC1 tagged with a cyan fluorescence protein (CFP). The high FRET efficiency of this method (~ 80%) allowed us to perform several types of binding experiments with nanomolar range of sample using conventional equipment. In addition, the CFP tag on the CNBD enabled us to perform a specific binding experiment using an unpurified protein. Considering these advantages, this technique is useful to study poorly characterized CNBDs. © 2017 Federation of European Biochemical Societies.

The C-terminal domain of glyceraldehyde 3-phosphate dehydrogenase plays an important role in suppression of tRNALys3 packaging into human immunodeficiency virus type-1 particles.

PubMed

Kishimoto, Naoki; Onitsuka-Kishimoto, Ayano; Iga, Nozomi; Takamune, Nobutoki; Shoji, Shozo; Misumi, Shogo

2016-12-01

Human immunodeficiency virus type-1 (HIV-1) requires the packaging of human tRNA Lys3 as a primer for effective viral reverse transcription. Previously, we reported that glyceraldehyde 3-phosphate dehydrogenase (GAPDH) suppresses the packaging efficiency of tRNA Lys3 . Although the binding of GAPDH to Pr55 gag is important for the suppression mechanism, it remains unclear which domain of GAPDH is responsible for the interaction with Pr55 gag . In this study, we show that Asp 256 , Lys 260 , Lys 263 and Glu 267 of GAPDH are important for the suppression of tRNA Lys3 packaging. Yeast two-hybrid analysis demonstrated that the C -terminal domain of GAPDH (151-335) interacts with both the matrix region (MA; 1-132) and capsid N -terminal domain (CA-NTD; 133-282). The D256R, K263E or E267R mutation of GAPDH led to the loss of the ability to bind to wild-type (WT) MA, and the D256R/K260E double mutation of GAPDH resulted in the loss of detectable binding activity to WT CA-NTD. In contrast, R58E, Q59A or Q63A of MA, and E76R or R82E of CA-NTD abrogated the interaction with the C -terminal domain of GAPDH. Multiple-substituted GAPDH mutant (D256R/K260E/K263E/E267R) retained the oligomeric formation with WT GAPDH in HIV-1 producing cells, but the incorporation level of the hetero-oligomer was decreased in viral particles. Furthermore, the viruses produced from cells expressing the D256R/K260E/K263E/E267R mutant restored tRNA Lys3 packaging efficiency because the mutant exerted a dominant negative effect by preventing WT GAPDH from binding to MA and CA-NTD and improved the reverse transcription. These findings indicate that the amino acids Asp 256 , Lys 260 , Lys 263 and Glu 267 of GAPDH is essential for the mechanism of tRNA Lys3 -packaging suppression and the D256R/K260E/K263E/E267R mutant of GAPDH acts in a dominant negative manner to suppress tRNA Lys3 packaging.

H4 replication-dependent diacetylation and Hat1 promote S-phase chromatin assembly in vivo

PubMed Central

Ejlassi-Lassallette, Aïda; Mocquard, Eloïse; Arnaud, Marie-Claire; Thiriet, Christophe

2011-01-01

While specific posttranslational modification patterns within the H3 and H4 tail domains are associated with the S-phase, their actual functions in replication-dependent chromatin assembly have not yet been defined. Here we used incorporation of trace amounts of recombinant proteins into naturally synchronous macroplasmodia of Physarum polycephalum to examine the function of H3 and H4 tail domains in replication-coupled chromatin assembly. We found that the H3/H4 complex lacking the H4 tail domain was not efficiently recovered in nuclei, whereas depletion of the H3 tail domain did not impede nuclear import but chromatin assembly failed. Furthermore, our results revealed that the proper pattern of acetylation on the H4 tail domain is required for nuclear import and chromatin assembly. This is most likely due to binding of Hat1, as coimmunoprecipitation experiments showed Hat1 associated with predeposition histones in the cytoplasm and with replicating chromatin. These results suggest that the type B histone acetyltransferase assists in shuttling the H3/H4 complex from cytoplasm to the replication forks. PMID:21118997

The conserved glycine residues in the transmembrane domain of the Semliki Forest virus fusion protein are not required for assembly and fusion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liao Maofu; Kielian, Margaret

2005-02-05

The alphavirus Semliki Forest virus (SFV) infects cells via a low pH-triggered fusion reaction mediated by the viral E1 protein. Both the E1 fusion peptide and transmembrane (TM) domain are essential for membrane fusion, but the functional requirements for the TM domain are poorly understood. Here we explored the role of the five TM domain glycine residues, including the highly conserved glycine pair at E1 residues 415/416. SFV mutants with alanine substitutions for individual or all five glycine residues (5G/A) showed growth kinetics and fusion pH dependence similar to those of wild-type SFV. Mutants with increasing substitution of glycine residuesmore » showed an increasingly more stringent requirement for cholesterol during fusion. The 5G/A mutant showed decreased fusion kinetics and extent in fluorescent lipid mixing assays. TM domain glycine residues thus are not required for efficient SFV fusion or assembly but can cause subtle effects on the properties of membrane fusion.« less

Synthetic mRNA is a more reliable tool for the delivery of DNA-targeting proteins into the cell nucleus than fusion with a protein transduction domain.

PubMed

Leontovyc, Ivan; Habart, David; Loukotova, Sarka; Kosinova, Lucie; Kriz, Jan; Saudek, Frantisek; Koblas, Tomas

2017-01-01

Cell reprogramming requires efficient delivery of reprogramming transcription factors into the cell nucleus. Here, we compared the robustness and workload of two protein delivery methods that avoid the risk of genomic integration. The first method is based on fusion of the protein of interest to a protein transduction domain (PTD) for delivery across the membranes of target cells. The second method relies on de novo synthesis of the protein of interest inside the target cells utilizing synthetic mRNA (syn-mRNA) as a template. We established a Cre/lox reporter system in three different cell types derived from human (PANC-1, HEK293) and rat (BRIN-BD11) tissues and used Cre recombinase to model a protein of interest. The system allowed constitutive expression of red fluorescence protein (RFP), while green fluorescence protein (GFP) was expressed only after the genomic action of Cre recombinase. The efficiency of protein delivery into cell nuclei was quantified as the frequency of GFP+ cells in the total cell number. The PTD method showed good efficiency only in BRIN-BD11 cells (68%), whereas it failed in PANC-1 and HEK293 cells. By contrast, the syn-mRNA method was highly effective in all three cell types (29-71%). We conclude that using synthetic mRNA is a more robust and less labor-intensive approach than using the PTD-fusion alternative.

The crystal structure of human GlnRS provides basis for the development of neurological disorders

DOE PAGES

Ognjenovic, Jana; Wu, Jiang; Matthies, Doreen; ...

2016-02-10

Cytosolic glutaminyl-tRNA synthetase (GlnRS) is the singular enzyme responsible for translation of glutamine codons. Compound heterozygous mutations in GlnRS cause severe brain disorders by a poorly understood mechanism. Herein, we present crystal structures of the wild type and two pathological mutants of human GlnRS, which reveal, for the first time, the domain organization of the intact enzyme and the structure of the functionally important N-terminal domain (NTD). Pathological mutations mapping in the NTD alter the domain structure, and decrease catalytic activity and stability of GlnRS, whereas missense mutations in the catalytic domain induce misfolding of the enzyme. Our results suggestmore » that the reduced catalytic efficiency and a propensity of GlnRS mutants to misfold trigger the disease development. As a result, this report broadens the spectrum of brain pathologies elicited by protein misfolding and provides a paradigm for understanding the role of mutations in aminoacyl-tRNA synthetases in neurological diseases. Keywords« less

Controlled motion of domain walls in submicron amorphous wires

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ţibu, Mihai; Lostun, Mihaela; Rotărescu, Cristian

Results on the control of the domain wall displacement in cylindrical Fe{sub 77.5}Si{sub 7.5}B{sub 15} amorphous glass-coated submicron wires prepared by rapid quenching from the melt are reported. The control methods have relied on conical notches with various depths, up to a few tens of nm, made in the glass coating and in the metallic nucleus using a focused ion beam (FIB) system, and on the use of small nucleation coils at one of the sample ends in order to apply magnetic field pulses aimed to enhance the nucleation of reverse domains. The notch-based method is used for the firstmore » time in the case of cylindrical ultrathin wires. The results show that the most efficient technique of controlling the domain wall motion in this type of samples is the simultaneous use of notches and nucleation coils. Their effect depends on wire diameter, notch depth, its position on the wire length, and characteristics of the applied pulse.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Becker, Verena; Sengupta, D; Ketteler, Robin

The formation of signal-promoting dimeric or oligomeric receptor complexes at the cell surface is modulated by self-interaction of their transmembrane (TM) domains. To address the importance of TM domain packing density for receptor functionality, we examined a set of asparagine mutants in the TM domain of the erythropoietin receptor (EpoR). We identified EpoR-T242N as a receptor variant that is present at the cell surface similar to wild-type EpoR but lacks visible localization in vesicle-like structures and is impaired in efficient activation of specific signaling cascades. Analysis by a molecular modeling approach indicated an increased interhelical distance for the EpoR-T242N TMmore » dimer. By employing the model, we designed additional mutants with increased or decreased packing volume and confirmed a correlation between packing volume and biological responsiveness. These results propose that the packing density of the TM domain provides a novel layer for fine-tuned regulation of signal transduction and cellular decisions.« less

The crystal structure of human GlnRS provides basis for the development of neurological disorders

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ognjenovic, Jana; Wu, Jiang; Matthies, Doreen

Cytosolic glutaminyl-tRNA synthetase (GlnRS) is the singular enzyme responsible for translation of glutamine codons. Compound heterozygous mutations in GlnRS cause severe brain disorders by a poorly understood mechanism. Herein, we present crystal structures of the wild type and two pathological mutants of human GlnRS, which reveal, for the first time, the domain organization of the intact enzyme and the structure of the functionally important N-terminal domain (NTD). Pathological mutations mapping in the NTD alter the domain structure, and decrease catalytic activity and stability of GlnRS, whereas missense mutations in the catalytic domain induce misfolding of the enzyme. Our results suggestmore » that the reduced catalytic efficiency and a propensity of GlnRS mutants to misfold trigger the disease development. As a result, this report broadens the spectrum of brain pathologies elicited by protein misfolding and provides a paradigm for understanding the role of mutations in aminoacyl-tRNA synthetases in neurological diseases. Keywords« less

Expression, purification, and characterization of recombinant human and murine milk fat globule-epidermal growth factor-factor 8.

PubMed

Castellanos, Erick R; Ciferri, Claudio; Phung, Wilson; Sandoval, Wendy; Matsumoto, Marissa L

2016-08-01

Milk fat globule-epidermal growth factor-factor 8 (MFG-E8), as its name suggests, is a major glycoprotein component of milk fat globules secreted by the mammary epithelium. Although its role in milk fat production is unclear, MFG-E8 has been shown to act as a bridge linking apoptotic cells to phagocytes for removal of these dying cells. MFG-E8 is capable of bridging these two very different cell types via interactions through both its epidermal growth factor (EGF)-like domain(s) and its lectin-type C domains. The EGF-like domain interacts with αVβ3 and αVβ5 integrins on the surface of phagocytes, whereas the C domains bind phosphatidylserine found on the surface of apoptotic cells. In an attempt to purify full-length, recombinant MFG-E8 expressed in either insect cells or CHO cells, we find that it is highly aggregated. Systematic truncation of the domain architecture of MFG-E8 indicates that the C domains are mainly responsible for the aggregation propensity. Addition of Triton X-100 to the conditioned cell culture media allowed partial recovery of non-aggregated, full-length MFG-E8. A more comprehensive detergent screen identified CHAPS as a stabilizer of MFG-E8 and allowed purification of a significant portion of non-aggregated, full-length protein. The CHAPS-stabilized recombinant MFG-E8 retained its natural ability to bind both αVβ3 and αVβ5 integrins and phosphatidylserine suggesting that it is properly folded and active. Herein we describe an efficient purification method for production of non-aggregated, full-length MFG-E8. Copyright © 2016 Elsevier Inc. All rights reserved.

The Thioredoxin Domain of Neisseria Gonorrhoeae PilB can use Electrons from DsbD to Reduce Downstream Methionine Sulfoxide Reductases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brot,N.; Collet, J.; Johnson, L.

2006-01-01

The PilB protein from Neisseria gonorrhoeae is located in the periplasm and made up of three domains. The N-terminal, thioredoxin-like domain (NT domain) is fused to tandem methionine sulfoxide reductase A and B domains (MsrA/B). We show that the {alpha} domain of Escherichia coli DsbD is able to reduce the oxidized NT domain, which suggests that DsbD in Neisseria can transfer electrons from the cytoplasmic thioredoxin to the periplasm for the reduction of the MsrA/B domains. An analysis of the available complete genomes provides further evidence for this proposition in other bacteria where DsbD/CcdA, Trx, MsrA, and MsrB gene homologsmore » are all located in a gene cluster with a common transcriptional direction. An examination of wild-type PilB and a panel of Cys to Ser mutants of the full-length protein and the individually expressed domains have also shown that the NT domain more efficiently reduces the MsrA/B domains when in the polyprotein context. Within this framework there does not appear to be a preference for the NT domain to reduce the proximal MsrA domain over MsrB domain. Finally, we report the 1.6 {angstrom} crystal structure of the NT domain. This structure confirms the presence of a surface loop that makes it different from other membrane-tethered, Trx-like molecules including TlpA, CcmG and ResA. Subtle differences are observed in this loop when compared to the N. meningitidis NT domain structure. The data taken together supports the formation of specific NT domain interactions with the MsrA/B domains and its in vivo recycling partner, DsbD.« less

Design and isolation of ribozyme-substrate pairs using RNase P-based ribozymes containing altered substrate binding sites.

PubMed Central

Mobley, E M; Pan, T

1999-01-01

Substrate recognition and cleavage by the bacterial RNase P RNA requires two domains, a specificity domain, or S-domain, and a catalytic domain, or C-domain. The S-domain binds the T stem-loop region in a pre-tRNA substrate to confer specificity for tRNA substrates. In this work, the entire S-domain of the Bacillus subtilis RNase P RNA is replaced with an artificial substrate binding module. New RNA substrates are isolated by in vitro selection using two libraries containing random regions of 60 nt. At the end of the selection, the cleavage rates of the substrate library are approximately 0.7 min(-1)in 10 mM MgCl(2)at 37 degrees C, approximately 4-fold better than the cleavage of a pre-tRNA substrate by the wild-type RNase P RNA under the same conditions. The contribution of the S-domain replacement to the catalytic efficiency is from 6- to 22 000-fold. Chemical and nuclease mapping of two ribozyme-product complexes shows that this contribution correlates with direct interactions between the S-domain replacement and the selected substrate. These results demonstrate the feasibility of design and isolation of RNase P-based, matching ribozyme-substrate pairs without prior knowledge of the sequence or structure of the interactive modules in the ribozyme or substrate. PMID:10518624

The clathrin-binding and J-domains of GAK support the uncoating and chaperoning of clathrin by Hsc70 in the brain

PubMed Central

Park, Bum-Chan; Yim, Yang-In; Zhao, Xiaohong; Olszewski, Maciej B.; Eisenberg, Evan; Greene, Lois E.

2015-01-01

ABSTRACT Cyclin-G-associated kinase (GAK), the ubiquitously expressed J-domain protein, is essential for the chaperoning and uncoating of clathrin that is mediated by Hsc70 (also known as HSPA8). Adjacent to the C-terminal J-domain that binds to Hsc70, GAK has a clathrin-binding domain that is linked to an N-terminal kinase domain through a PTEN-like domain. Knocking out GAK in fibroblasts caused inhibition of clathrin-dependent trafficking, which was rescued by expressing a 62-kDa fragment of GAK, comprising just the clathrin-binding and J-domains. Expressing this fragment as a transgene in mice rescued the lethality and the histological defects caused by knocking out GAK in the liver or in the brain. Furthermore, when both GAK and auxilin (also known as DNAJC6), the neuronal-specific homolog of GAK, were knocked out in the brain, mice expressing the 62-kDa GAK fragment were viable, lived a normal life-span and had no major behavior abnormalities. However, these mice were about half the size of wild-type mice. Therefore, the PTEN-like domains of GAK and auxilin are not essential for Hsc70-dependent chaperoning and uncoating of clathrin, but depending on the tissue, these domains appear to increase the efficiency of these co-chaperones. PMID:26345367

Enhanced external quantum efficiency in GaN-based vertical-type light-emitting diodes by localized surface plasmons

PubMed Central

Yao, Yung-Chi; Hwang, Jung-Min; Yang, Zu-Po; Haung, Jing-Yu; Lin, Chia-Ching; Shen, Wei-Chen; Chou, Chun-Yang; Wang, Mei-Tan; Huang, Chun-Ying; Chen, Ching-Yu; Tsai, Meng-Tsan; Lin, Tzu-Neng; Shen, Ji-Lin; Lee, Ya-Ju

2016-01-01

Enhancement of the external quantum efficiency of a GaN-based vertical-type light emitting diode (VLED) through the coupling of localized surface plasmon (LSP) resonance with the wave-guided mode light is studied. To achieve this experimentally, Ag nanoparticles (NPs), as the LSP resonant source, are drop-casted on the most top layer of waveguide channel, which is composed of hydrothermally synthesized ZnO nanorods capped on the top of GaN-based VLED. Enhanced light-output power and external quantum efficiency are observed, and the amount of enhancement remains steady with the increase of the injected currents. To understand the observations theoretically, the absorption spectra and the electric field distributions of the VLED with and without Ag NPs decorated on ZnO NRs are determined using the finite-difference time-domain (FDTD) method. The results prove that the observation of enhancement of the external quantum efficiency can be attributed to the creation of an extra escape channel for trapped light due to the coupling of the LSP with wave-guided mode light, by which the energy of wave-guided mode light can be transferred to the efficient light scattering center of the LSP. PMID:26935648

Origin of effects of additive solvent on film-morphology in solution-processed nonfullerene solar cells.

PubMed

Chen, Yuxia; Zhang, Xin; Zhan, Chuanlang; Yao, Jiannian

2015-04-01

In this paper, we report an efficient nonfullerene solar cell based on small molecules of p-DTS(FBTTh2)2 and bis-PDI-T. Characterization data indicate that the nature of the acceptor aggregate is a key factor that affects the photocurrent. There is a good relationship between the short-circuit current density (J(SC)) and the phase size of the acceptor-rich domains. The phase size of the acceptor-rich domains is tuned by both the additive types and additive content. As the kind of additive goes from 1-chloronaphthalene (CN) to 1,8-octanedithiol (ODT) and 1,8-diiodooctane (DIO), by this order the solubility of the acceptor in the additive is down, the phase size significantly decreases from over 400 nm down to 30 nm. Also, the acceptor's domain size decreases from 80 to 30 nm as the DIO content ([DIO]) is down from 1% to 0.15%. Following this trend, less DIO remains in the wet film as residue after the host chloroform evaporates, and thus less acceptor can be dissolved in the residue DIO. This decreasing of DIO content acts on the film-morphology similarly as the additive changes down to the one having a lower solubility. Accordingly, our results indicate that it is the dissolved amount of the organic component in the residue additive solvent of the wet film that plays a role in turning the phase size. The efficiency from this small molecule system is significantly raised from 0.02% up to 3.7% by selecting the additive type and fine-tuning the additive content.

Inhibition of ice recrystallization and cryoprotective activity of wheat proteins in liver and pancreatic cells

PubMed Central

Chow‐Shi‐Yée, Mélanie; Briard, Jennie G.; Grondin, Mélanie; Averill‐Bates, Diana A.

2016-01-01

Abstract Efficient cryopreservation of cells at ultralow temperatures requires the use of substances that help maintain viability and metabolic functions post‐thaw. We are developing new technology where plant proteins are used to substitute the commonly‐used, but relatively toxic chemical dimethyl sulfoxide. Recombinant forms of four structurally diverse wheat proteins, TaIRI‐2 (ice recrystallization inhibition), TaBAS1 (2‐Cys peroxiredoxin), WCS120 (dehydrin), and TaENO (enolase) can efficiently cryopreserve hepatocytes and insulin‐secreting INS832/13 cells. This study shows that TaIRI‐2 and TaENO are internalized during the freeze–thaw process, while TaBAS1 and WCS120 remain at the extracellular level. Possible antifreeze activity of the four proteins was assessed. The “splat cooling” method for quantifying ice recrystallization inhibition activity (a property that characterizes antifreeze proteins) revealed that TaIRI‐2 and TaENO are more potent than TaBAS1 and WCS120. Because of their ability to inhibit ice recrystallization, the wheat recombinant proteins TaIRI‐2 and TaENO are promising candidates and could prove useful to improve cryopreservation protocols for hepatocytes and insulin‐secreting cells, and possibly other cell types. TaENO does not have typical ice‐binding domains, and the TargetFreeze tool did not predict an antifreeze capacity, suggesting the existence of nontypical antifreeze domains. The fact that TaBAS1 is an efficient cryoprotectant but does not show antifreeze activity indicates a different mechanism of action. The cryoprotective properties conferred by WCS120 depend on biochemical properties that remain to be determined. Overall, our results show that the proteins' efficiencies vary between cell types, and confirm that a combination of different protection mechanisms is needed to successfully cryopreserve mammalian cells. PMID:26889747

Inhibition of ice recrystallization and cryoprotective activity of wheat proteins in liver and pancreatic cells.

PubMed

Chow-Shi-Yée, Mélanie; Briard, Jennie G; Grondin, Mélanie; Averill-Bates, Diana A; Ben, Robert N; Ouellet, François

2016-05-01

Efficient cryopreservation of cells at ultralow temperatures requires the use of substances that help maintain viability and metabolic functions post-thaw. We are developing new technology where plant proteins are used to substitute the commonly-used, but relatively toxic chemical dimethyl sulfoxide. Recombinant forms of four structurally diverse wheat proteins, TaIRI-2 (ice recrystallization inhibition), TaBAS1 (2-Cys peroxiredoxin), WCS120 (dehydrin), and TaENO (enolase) can efficiently cryopreserve hepatocytes and insulin-secreting INS832/13 cells. This study shows that TaIRI-2 and TaENO are internalized during the freeze-thaw process, while TaBAS1 and WCS120 remain at the extracellular level. Possible antifreeze activity of the four proteins was assessed. The "splat cooling" method for quantifying ice recrystallization inhibition activity (a property that characterizes antifreeze proteins) revealed that TaIRI-2 and TaENO are more potent than TaBAS1 and WCS120. Because of their ability to inhibit ice recrystallization, the wheat recombinant proteins TaIRI-2 and TaENO are promising candidates and could prove useful to improve cryopreservation protocols for hepatocytes and insulin-secreting cells, and possibly other cell types. TaENO does not have typical ice-binding domains, and the TargetFreeze tool did not predict an antifreeze capacity, suggesting the existence of nontypical antifreeze domains. The fact that TaBAS1 is an efficient cryoprotectant but does not show antifreeze activity indicates a different mechanism of action. The cryoprotective properties conferred by WCS120 depend on biochemical properties that remain to be determined. Overall, our results show that the proteins' efficiencies vary between cell types, and confirm that a combination of different protection mechanisms is needed to successfully cryopreserve mammalian cells. © 2016 The Protein Society.

Technical efficiency of Shiraz school of medicine in research and education domains: a data envelopment analysis.

PubMed

Delavari, Somayeh; Rezaee, Rita; Hatam, Nahid; Delavari, Sajad

2016-01-01

Efficiency evaluation of universities and faculties is one of the tools that help managers to identify the departments' strengths and weakness. The main objective of the present research was to measure and compare the technical efficiency of Shiraz school of medicine departments using Data Envelopment Analysis (DEA) technique. This cross-sectional and retrospective study was performed on clinical and non-clinical departments in research and education domains over the period of 2006 to 2011. Different inputs and outputs were considered for research and educational domain separately. Efficiency was measured based on the observed optimal performance. Findings showed that pathology and anatomy departments achieved the score of 100 in technical efficiency in education during 2006 to 2011. During this period, parasitology, psychiatric and pediatrics department's achieved the score of 100 for technical efficiency in research domain. The lowest mean of relative educational efficiency belonged to orthopedic department; as to relative research efficiency, the lowest mean was shown in orthopedics and genetics departments. The mean technical efficiency of non-medical departments in education and research domain was 91.93 and 76.08, respectively, while the mean technical efficiency of the clinical department in educational and research fields was 91.02 and 82.23, respectively. Using multiple input and output in DEA technique provided a comprehensive evaluation of efficiency in Shiraz school of medicine departments. The DEA could successfully estimate the technical efficiency of the departments in research and educational fields. Moreover, the deficiency in each department was found; this could help them to plan for improvement.

Compressed-domain video indexing techniques using DCT and motion vector information in MPEG video

NASA Astrophysics Data System (ADS)

Kobla, Vikrant; Doermann, David S.; Lin, King-Ip; Faloutsos, Christos

1997-01-01

Development of various multimedia applications hinges on the availability of fast and efficient storage, browsing, indexing, and retrieval techniques. Given that video is typically stored efficiently in a compressed format, if we can analyze the compressed representation directly, we can avoid the costly overhead of decompressing and operating at the pixel level. Compressed domain parsing of video has been presented in earlier work where a video clip is divided into shots, subshots, and scenes. In this paper, we describe key frame selection, feature extraction, and indexing and retrieval techniques that are directly applicable to MPEG compressed video. We develop a frame-type independent representation of the various types of frames present in an MPEG video in which al frames can be considered equivalent. Features are derived from the available DCT, macroblock, and motion vector information and mapped to a low-dimensional space where they can be accessed with standard database techniques. The spatial information is used as primary index while the temporal information is used to enhance the robustness of the system during the retrieval process. The techniques presented enable fast archiving, indexing, and retrieval of video. Our operational prototype typically takes a fraction of a second to retrieve similar video scenes from our database, with over 95% success.

A taxonomy and comparison of parallel block multi-level preconditioners for the incompressible Navier-Stokes equations.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shadid, John Nicolas; Elman, Howard; Shuttleworth, Robert R.

2007-04-01

In recent years, considerable effort has been placed on developing efficient and robust solution algorithms for the incompressible Navier-Stokes equations based on preconditioned Krylov methods. These include physics-based methods, such as SIMPLE, and purely algebraic preconditioners based on the approximation of the Schur complement. All these techniques can be represented as approximate block factorization (ABF) type preconditioners. The goal is to decompose the application of the preconditioner into simplified sub-systems in which scalable multi-level type solvers can be applied. In this paper we develop a taxonomy of these ideas based on an adaptation of a generalized approximate factorization of themore » Navier-Stokes system first presented in [25]. This taxonomy illuminates the similarities and differences among these preconditioners and the central role played by efficient approximation of certain Schur complement operators. We then present a parallel computational study that examines the performance of these methods and compares them to an additive Schwarz domain decomposition (DD) algorithm. Results are presented for two and three-dimensional steady state problems for enclosed domains and inflow/outflow systems on both structured and unstructured meshes. The numerical experiments are performed using MPSalsa, a stabilized finite element code.« less

Design considerations for quasi-phase-matching in doubly resonant lithium niobate hexagonal micro-resonators

NASA Astrophysics Data System (ADS)

Sono, Tleyane J.; Riziotis, Christos; Mailis, Sakellaris; Eason, Robert W.

2017-09-01

Fabrication capabilities of high optical quality hexagonal superstructures by chemical etching of inverted ferroelectric domains in lithium niobate platform suggests a route for efficient implementation of compact hexagonal microcavities. Such nonlinear optical hexagonal micro-resonators are proposed as a platform for second harmonic generation (SHG) by the combined mechanisms of total internal reflection (TIR) and quasi-phase-matching (QPM). The proposed scheme for SHG via TIR-QPM in a hexagonal microcavity can improve the efficiency and also the compactness of SHG devices compared to traditional linear-type based devices. A simple theoretical model based on six-bounce trajectory and phase matching conditions was capable for obtaining the optimal cavity size. Furthermore numerical simulation results based on finite difference time domain beam propagation method analysis confirmed the solutions obtained by demonstrating resonant operation of the microcavity for the second harmonic wave produced by TIR-QPM. Design aspects, optimization issues and characteristics of the proposed nonlinear device are presented.

Using maximum entropy modeling for optimal selection of sampling sites for monitoring networks

USGS Publications Warehouse

Stohlgren, Thomas J.; Kumar, Sunil; Barnett, David T.; Evangelista, Paul H.

2011-01-01

Environmental monitoring programs must efficiently describe state shifts. We propose using maximum entropy modeling to select dissimilar sampling sites to capture environmental variability at low cost, and demonstrate a specific application: sample site selection for the Central Plains domain (453,490 km2) of the National Ecological Observatory Network (NEON). We relied on four environmental factors: mean annual temperature and precipitation, elevation, and vegetation type. A “sample site” was defined as a 20 km × 20 km area (equal to NEON’s airborne observation platform [AOP] footprint), within which each 1 km2 cell was evaluated for each environmental factor. After each model run, the most environmentally dissimilar site was selected from all potential sample sites. The iterative selection of eight sites captured approximately 80% of the environmental envelope of the domain, an improvement over stratified random sampling and simple random designs for sample site selection. This approach can be widely used for cost-efficient selection of survey and monitoring sites.

An Efficient Implementation For Real Time Applications Of The Wigner-Ville Distribution

NASA Astrophysics Data System (ADS)

Boashash, Boualem; Black, Peter; Whitehouse, Harper J.

1986-03-01

The Wigner-Ville Distribution (WVD) is a valuable tool for time-frequency signal analysis. In order to implement the WVD in real time an efficient algorithm and architecture have been developed which may be implemented with commercial components. This algorithm successively computes the analytic signal corresponding to the input signal, forms a weighted kernel function and analyses the kernel via a Discrete Fourier Transform (DFT). To evaluate the analytic signal required by the algorithm it is shown that the time domain definition implemented as a finite impulse response (FIR) filter is practical and more efficient than the frequency domain definition of the analytic signal. The windowed resolution of the WVD in the frequency domain is shown to be similar to the resolution of a windowed Fourier Transform. A real time signal processsor has been designed for evaluation of the WVD analysis system. The system is easily paralleled and can be configured to meet a variety of frequency and time resolutions. The arithmetic unit is based on a pair of high speed VLSI floating-point multiplier and adder chips. Dual operand buses and an independent result bus maximize data transfer rates. The system is horizontally microprogrammed and utilizes a full instruction pipeline. Each microinstruction specifies two operand addresses, a result location, the type of arithmetic and the memory configuration. input and output is via shared memory blocks with front-end processors to handle data transfers during the non access periods of the analyzer.

Oligomeric structure and chaperone-like activity of Drosophila melanogaster mitochondrial small heat shock protein Hsp22 and arginine mutants in the alpha-crystallin domain.

PubMed

Dabbaghizadeh, Afrooz; Finet, Stéphanie; Morrow, Genevieve; Moutaoufik, Mohamed Taha; Tanguay, Robert M

2017-07-01

The structure and chaperone function of DmHsp22WT, a small Hsp of Drosophila melanogaster localized within mitochondria were examined. Mutations of conserved arginine mutants within the alpha-crystallin domain (ACD) domain (R105G, R109G, and R110G) were introduced, and their effects on oligomerization and chaperone function were assessed. Arginine to glycine mutations do not induce significant changes in tryptophan fluorescence, and the mutated proteins form oligomers that are of equal or smaller size than the wild-type protein. They all form oligomer with one single peak as determined by size exclusion chromatography. While all mutants demonstrate the same efficiency as the DmHsp22WT in a DTT-induced insulin aggregation assay, all are more efficient chaperones to prevent aggregation of malate dehydrogenase. Arginine mutants of DmHsp22 are efficient chaperones to retard aggregation of CS and Luc. In summary, this study shows that mutations of arginine to glycine in DmHsp22 ACD induce a number of structural changes, some of which differ from those described in mammalian sHsps. Interestingly, only the R110G-DmHsp22 mutant, and not the expected R109G equivalent to human R140-HspB1, R116-HspB4, and R120-HspB5, showed different structural properties compared with the DmHsp22WT.

Reflective type objective based spectral-domain phase-sensitive optical coherence tomography for high-sensitive structural and functional imaging of cochlear microstructures through intact bone of an excised guinea pig cochlea

NASA Astrophysics Data System (ADS)

Subhash, Hrebesh M.; Wang, Ruikang K.; Chen, Fangyi; Nuttall, Alfred L.

2013-03-01

Most of the optical coherence tomographic (OCT) systems for high resolution imaging of biological specimens are based on refractive type microscope objectives, which are optimized for specific wave length of the optical source. In this study, we present the feasibility of using commercially available reflective type objective for high sensitive and high resolution structural and functional imaging of cochlear microstructures of an excised guinea pig through intact temporal bone. Unlike conventional refractive type microscopic objective, reflective objective are free from chromatic aberrations due to their all-reflecting nature and can support a broadband of spectrum with very high light collection efficiency.

Trust Model to Enhance Security and Interoperability of Cloud Environment

NASA Astrophysics Data System (ADS)

Li, Wenjuan; Ping, Lingdi

Trust is one of the most important means to improve security and enable interoperability of current heterogeneous independent cloud platforms. This paper first analyzed several trust models used in large and distributed environment and then introduced a novel cloud trust model to solve security issues in cross-clouds environment in which cloud customer can choose different providers' services and resources in heterogeneous domains can cooperate. The model is domain-based. It divides one cloud provider's resource nodes into the same domain and sets trust agent. It distinguishes two different roles cloud customer and cloud server and designs different strategies for them. In our model, trust recommendation is treated as one type of cloud services just like computation or storage. The model achieves both identity authentication and behavior authentication. The results of emulation experiments show that the proposed model can efficiently and safely construct trust relationship in cross-clouds environment.

Magnetic minerals' classification for sources of magnetic anomalies

NASA Astrophysics Data System (ADS)

Kletetschka, G.; Wieczorek, M. A.

2016-12-01

Our analysis allows interpretation of magnetic anomalies detected in meteorites, on Mars and Moon, and other bodies where the sources of magnetic field can be assumed to be thermoremanent magnetization (Mtr). We show how the specific approach allows reconsideration of the major magnetic carriers on Moon and Mars. Furthermore we are deriving a generalized equation for iron concentration estimate from magnetizations derived from crustal magnetic anomalies on the Moon. There is fundamental linear relation between the magnetic efficiency of thermoremanent magnetization Mtr measured at room temperature and level of the ambient field present at the time of acquisition. We used experimental data for derivation of the empirical constants for paleofield estimate equations. Specific magnetic mineral carriers from single domain (SD) through pseudosingle domain (PSD) to multidomain (MD) states include iron, meteoritic iron, magnetite, maghemite, pyrrhotite, and hematite. The Mtr/Msr is linearly proportional to the product of the magnetizing field and saturation remanence, while the proportionality constant is independent of magnetic mineralogy, domain state, or composition. We show that the level of magnetic paleofield record relates to two types of demagnetizing field that act as a barrier against the domain wall pinning during the magnetic acquisition. The first type of demagnetizing field relates to saturation magnetization constant derived from the distribution of Bohr's magnetons within the crystal lattice. The second type of demagnetizing field originates from the effect of shape of the magnetic minerals. Knowledge of the character of these demagnetizing fields is a prerequisite for paleofield estimates from rocks containing known magnetic mineralogy and magnetic shape anisotropy.

Clinical assessment of organizational strategy: An examination of healthy adults.

PubMed

Banerjee, Pia; White, Desirée A

2015-06-01

During the assessment of patients with cognitive difficulties, clinicians often examine strategic processing, particularly the ability to use organization-based strategies to efficiently complete various tasks. Several commonly used neuropsychological tasks are currently thought to provide measures of organizational strategic processing, but empirical evidence for the construct validity of these strategic measures is needed before interpreting them as measuring the same underlying ability. This is particularly important for the assessment of organizational strategic processing because the measures span cognitive domains (e.g., memory strategy, language strategy) as well as types of organization. In the present study, 200 adults were administered cognitive tasks commonly used in clinical practice to assess organizational strategic processing. Factor analysis was used to examine whether these measures of organizational strategic processing, which involved different cognitive domains and types of organization, could be operationalized as measuring a unitary construct. A very good-fitting model of the data demonstrated no significant shared variance among any of the strategic variables from different tasks (root mean square error of approximation < .0001, standardized root-mean-square residual = .045, comparative fit index = 1.000). These findings suggest that organizational strategic processing is highly specific to the demands and goals of individual tasks even when tasks share commonalities such as involving the same cognitive domain. In the design of neuropsychological batteries involving the assessment of organizational strategic processing, it is recommended that various strategic measures across cognitive domains and types of organizational processing are selected as guided by each patient's individual cognitive difficulties. (c) 2015 APA, all rights reserved).

The N domain of somatic angiotensin-converting enzyme negatively regulates ectodomain shedding and catalytic activity.

PubMed

Woodman, Zenda L; Schwager, Sylva L U; Redelinghuys, Pierre; Carmona, Adriana K; Ehlers, Mario R W; Sturrock, Edward D

2005-08-01

sACE (somatic angiotensin-converting enzyme) consists of two homologous, N and C domains, whereas the testis isoenzyme [tACE (testis ACE)] consists of a single C domain. Both isoenzymes are shed from the cell surface by a sheddase activity, although sACE is shed much less efficiently than tACE. We hypothesize that the N domain of sACE plays a regulatory role, by occluding a recognition motif on the C domain required for ectodomain shedding and by influencing the catalytic efficiency. To test this, we constructed two mutants: CNdom-ACE and CCdom-ACE. CNdom-ACE was shed less efficiently than sACE, whereas CCdom-ACE was shed as efficiently as tACE. Notably, cleavage occurred both within the stalk and the interdomain bridge in both mutants, suggesting that a sheddase recognition motif resides within the C domain and is capable of directly cleaving at both positions. Analysis of the catalytic properties of the mutants and comparison with sACE and tACE revealed that the k(cat) for sACE and CNdom-ACE was less than or equal to the sum of the kcat values for tACE and the N-domain, suggesting negative co-operativity, whereas the kcat value for the CCdom-ACE suggested positive co-operativity between the two domains. Taken together, the results provide support for (i) the existence of a sheddase recognition motif in the C domain and (ii) molecular flexibility of the N and C domains in sACE, resulting in occlusion of the C-domain recognition motif by the N domain as well as close contact of the two domains during hydrolysis of peptide substrates.

The N domain of somatic angiotensin-converting enzyme negatively regulates ectodomain shedding and catalytic activity

PubMed Central

Woodman, Zenda L.; Schwager, Sylva L. U.; Redelinghuys, Pierre; Carmona, Adriana K.; Ehlers, Mario R. W.; Sturrock, Edward D.

2005-01-01

sACE (somatic angiotensin-converting enzyme) consists of two homologous, N and C domains, whereas the testis isoenzyme [tACE (testis ACE)] consists of a single C domain. Both isoenzymes are shed from the cell surface by a sheddase activity, although sACE is shed much less efficiently than tACE. We hypothesize that the N domain of sACE plays a regulatory role, by occluding a recognition motif on the C domain required for ectodomain shedding and by influencing the catalytic efficiency. To test this, we constructed two mutants: CNdom-ACE and CCdom-ACE. CNdom-ACE was shed less efficiently than sACE, whereas CCdom-ACE was shed as efficiently as tACE. Notably, cleavage occurred both within the stalk and the interdomain bridge in both mutants, suggesting that a sheddase recognition motif resides within the C domain and is capable of directly cleaving at both positions. Analysis of the catalytic properties of the mutants and comparison with sACE and tACE revealed that the kcat for sACE and CNdom-ACE was less than or equal to the sum of the kcat values for tACE and the N-domain, suggesting negative co-operativity, whereas the kcat value for the CCdom-ACE suggested positive co-operativity between the two domains. Taken together, the results provide support for (i) the existence of a sheddase recognition motif in the C domain and (ii) molecular flexibility of the N and C domains in sACE, resulting in occlusion of the C-domain recognition motif by the N domain as well as close contact of the two domains during hydrolysis of peptide substrates. PMID:15813703

The effect of expert knowledge on medical search: medical experts have specialized abilities for detecting serious lesions.

PubMed

Nakashima, Ryoichi; Watanabe, Chisaki; Maeda, Eriko; Yoshikawa, Takeharu; Matsuda, Izuru; Miki, Soichiro; Yokosawa, Kazuhiko

2015-09-01

How does domain-specific knowledge influence the experts' performance in their domain of expertise? Specifically, can visual search experts find, with uniform efficiency, any type of target in their domain of expertise? We examined whether acquired knowledge of target importance influences an expert's visual search performance. In some professional searches (e.g., medical screenings), certain targets are rare; one aim of this study was to examine the extent to which experts miss such targets in their searches. In one experiment, radiologists (medical experts) engaged in a medical lesion search task in which both the importance (i.e., seriousness/gravity) and the prevalence of targets varied. Results showed decreased target detection rates in the low prevalence conditions (i.e., the prevalence effect). Also, experts were better at detecting important (versus unimportant) lesions. Results of an experiment using novices ruled out the possibility that decreased performance with unimportant targets was due to low target noticeability/visibility. Overall, the findings suggest that radiologists do not have a generalized ability to detect any type of lesion; instead, they have acquired a specialized ability to detect only those important lesions relevant for effective medical practices.

[Current Status of Home Visit Programs: Activities and Barriers of Home Care Nursing Services].

PubMed

Oh, Eui Geum; Lee, Hyun Joo; Kim, Yukyung; Sung, Ji Hyun; Park, Young Su; Yoo, Jae Yong; Woo, Soohee

2015-10-01

The purpose of this study was to examine the current status of home care nursing services provided by community health nurses and to identify barriers to the services. A cross-sectional survey was conducted with three types of community health care nurses. Participants were 257 nurses, 46 of whom were hospital based home care nurses, 176 were community based visiting nurses, and 35 were long term care insurance based visiting nurses. A structured questionnaire on 7 domains of home care nursing services with a 4-point Likert scale was used to measure activities and barriers to care. Data were analyzed using SPSS WIN 21.0 program. Hospital based home care nurses showed a high level of service performance activity in the domain of clinical laboratory tests, medications and injections, therapeutic nursing, and education. Community based visiting nurses had a high level of service performance in the reference domain. Long term care insurance based visiting nurses showed a high level of performance in the service domains of fundamental nursing and counseling. The results show that although health care service provided by the three types of community health nurse overlapped, the focus of the service is differentiated. Therefore, these results suggest that existing home care services will need to be utilized efficiently in the development of a new nursing care service for patients living in the community after hospital discharge.

Evidence of reduced recombination rate in human regulatory domains.

PubMed

Liu, Yaping; Sarkar, Abhishek; Kheradpour, Pouya; Ernst, Jason; Kellis, Manolis

2017-10-20

Recombination rate is non-uniformly distributed across the human genome. The variation of recombination rate at both fine and large scales cannot be fully explained by DNA sequences alone. Epigenetic factors, particularly DNA methylation, have recently been proposed to influence the variation in recombination rate. We study the relationship between recombination rate and gene regulatory domains, defined by a gene and its linked control elements. We define these links using expression quantitative trait loci (eQTLs), methylation quantitative trait loci (meQTLs), chromatin conformation from publicly available datasets (Hi-C and ChIA-PET), and correlated activity links that we infer across cell types. Each link type shows a "recombination rate valley" of significantly reduced recombination rate compared to matched control regions. This recombination rate valley is most pronounced for gene regulatory domains of early embryonic development genes, housekeeping genes, and constitutive regulatory elements, which are known to show increased evolutionary constraint across species. Recombination rate valleys show increased DNA methylation, reduced doublestranded break initiation, and increased repair efficiency, specifically in the lineage leading to the germ line. Moreover, by using only the overlap of functional links and DNA methylation in germ cells, we are able to predict the recombination rate with high accuracy. Our results suggest the existence of a recombination rate valley at regulatory domains and provide a potential molecular mechanism to interpret the interplay between genetic and epigenetic variations.

Efficient subgroup C avian sarcoma and leukosis virus receptor activity requires the IgV domain of the Tvc receptor and proper display on the cell membrane.

PubMed

Munguia, Audelia; Federspiel, Mark J

2008-11-01

We recently identified and cloned the receptor for subgroup C avian sarcoma and leukosis viruses [ASLV(C)], i.e., Tvc, a protein most closely related to mammalian butyrophilins, which are members of the immunoglobulin protein family. The extracellular domain of Tvc contains two immunoglobulin-like domains, IgV and IgC, which presumably each contain a disulfide bond important for native function of the protein. In this study, we have begun to identify the functional determinants of Tvc responsible for ASLV(C) receptor activity. We found that the IgV domain of the Tvc receptor is responsible for interacting with the glycoprotein of ASLV(C). Additional experiments demonstrated that a domain was necessary as a spacer between the IgV domain and the membrane-spanning domain for efficient Tvc receptor activity, most likely to orient the IgV domain a proper distance from the cell membrane. The effects on ASLV(C) glycoprotein binding and infection efficiency were also studied by site-directed mutagenesis of the cysteine residues of Tvc as well as conserved amino acid residues of the IgV Tvc domain compared to other IgV domains. In this initial analysis of Tvc determinants important for interacting with ASLV(C) glycoproteins, at least two aromatic amino acid residues in the IgV domain of Tvc, Trp-48 and Tyr-105, were identified as critical for efficient ASLV(C) infection. Interestingly, one or more aromatic amino acid residues have been identified as critical determinants in the other ASLV(A-E) receptors for a proper interaction with ASLV glycoproteins. This suggests that the ASLV glycoproteins may share a common mechanism of receptor interaction with an aromatic residue(s) on the receptor critical for triggering conformational changes in SU that initiate the fusion process required for efficient virus infection.

Efficient Subgroup C Avian Sarcoma and Leukosis Virus Receptor Activity Requires the IgV Domain of the Tvc Receptor and Proper Display on the Cell Membrane▿

PubMed Central

Munguia, Audelia; Federspiel, Mark J.

2008-01-01

We recently identified and cloned the receptor for subgroup C avian sarcoma and leukosis viruses [ASLV(C)], i.e., Tvc, a protein most closely related to mammalian butyrophilins, which are members of the immunoglobulin protein family. The extracellular domain of Tvc contains two immunoglobulin-like domains, IgV and IgC, which presumably each contain a disulfide bond important for native function of the protein. In this study, we have begun to identify the functional determinants of Tvc responsible for ASLV(C) receptor activity. We found that the IgV domain of the Tvc receptor is responsible for interacting with the glycoprotein of ASLV(C). Additional experiments demonstrated that a domain was necessary as a spacer between the IgV domain and the membrane-spanning domain for efficient Tvc receptor activity, most likely to orient the IgV domain a proper distance from the cell membrane. The effects on ASLV(C) glycoprotein binding and infection efficiency were also studied by site-directed mutagenesis of the cysteine residues of Tvc as well as conserved amino acid residues of the IgV Tvc domain compared to other IgV domains. In this initial analysis of Tvc determinants important for interacting with ASLV(C) glycoproteins, at least two aromatic amino acid residues in the IgV domain of Tvc, Trp-48 and Tyr-105, were identified as critical for efficient ASLV(C) infection. Interestingly, one or more aromatic amino acid residues have been identified as critical determinants in the other ASLV(A-E) receptors for a proper interaction with ASLV glycoproteins. This suggests that the ASLV glycoproteins may share a common mechanism of receptor interaction with an aromatic residue(s) on the receptor critical for triggering conformational changes in SU that initiate the fusion process required for efficient virus infection. PMID:18768966

A conserved OmpA-like protein in Legionella pneumophila required for efficient intracellular replication.

PubMed

Goodwin, Ian P; Kumova, Ogan K; Ninio, Shira

2016-08-01

The OmpA-like protein domain has been associated with peptidoglycan-binding proteins, and is often found in virulence factors of bacterial pathogens. The intracellular pathogen Legionella pneumophila encodes for six proteins that contain the OmpA-like domain, among them the highly conserved uncharacterized protein we named CmpA. Here we set out to characterize the CmpA protein and determine its contribution to intracellular survival of L. pneumophila Secondary structure analysis suggests that CmpA is an inner membrane protein with a peptidoglycan-binding domain at the C-teminus. A cmpA mutant was able to replicate normally in broth, but failed to compete with an isogenic wild-type strain in an intracellular growth competition assay. The cmpA mutant also displayed significant intracellular growth defects in both the protozoan host Acanthamoeba castellanii and in primary bone marrow-derived macrophages, where uptake into the cells was also impaired. The cmpA phenotypes were completely restored upon expression of CmpA in trans The data presented here establish CmpA as a novel virulence factor of L. pneumophila that is required for efficient intracellular replication in both mammalian and protozoan hosts. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Energy-efficient writing scheme for magnetic domain-wall motion memory

NASA Astrophysics Data System (ADS)

Kim, Kab-Jin; Yoshimura, Yoko; Ham, Woo Seung; Ernst, Rick; Hirata, Yuushou; Li, Tian; Kim, Sanghoon; Moriyama, Takahiro; Nakatani, Yoshinobu; Ono, Teruo

2017-04-01

We present an energy-efficient magnetic domain-writing scheme for domain wall (DW) motion-based memory devices. A cross-shaped nanowire is employed to inject a domain into the nanowire through current-induced DW propagation. The energy required for injecting the magnetic domain is more than one order of magnitude lower than that for the conventional field-based writing scheme. The proposed scheme is beneficial for device miniaturization because the threshold current for DW propagation scales with the device size, which cannot be achieved in the conventional field-based technique.

Diverse C-Terminal Sequences Involved in Flavobacterium johnsoniae Protein Secretion

PubMed Central

Kulkarni, Surashree S.; Zhu, Yongtao; Brendel, Colton J.

2017-01-01

ABSTRACT Flavobacterium johnsoniae and many related bacteria secrete proteins across the outer membrane using the type IX secretion system (T9SS). Proteins secreted by T9SSs have amino-terminal signal peptides for export across the cytoplasmic membrane by the Sec system and carboxy-terminal domains (CTDs) targeting them for secretion across the outer membrane by the T9SS. Most but not all T9SS CTDs belong to the family TIGR04183 (type A CTDs). We functionally characterized diverse CTDs for secretion by the F. johnsoniae T9SS. Attachment of the CTDs from F. johnsoniae RemA, AmyB, and ChiA to the foreign superfolder green fluorescent protein (sfGFP) that had a signal peptide at the amino terminus resulted in secretion across the outer membrane. In each case, approximately 80 to 100 amino acids from the extreme carboxy termini were needed for efficient secretion. Several type A CTDs from distantly related members of the phylum Bacteroidetes functioned in F. johnsoniae, supporting the secretion of sfGFP by the F. johnsoniae T9SS. F. johnsoniae SprB requires the T9SS for secretion but lacks a type A CTD. It has a conserved C-terminal domain belonging to the family TIGR04131, which we refer to as a type B CTD. The CTD of SprB was required for its secretion, but attachment of C-terminal regions of SprB of up to 1,182 amino acids to sfGFP failed to result in secretion. Additional features outside the C-terminal region of SprB may be required for its secretion. IMPORTANCE Type IX protein secretion systems (T9SSs) are common in but limited to members of the phylum Bacteroidetes. Most proteins that are secreted by T9SSs have conserved carboxy-terminal domains that belong to the protein domain family TIGR04183 (type A CTDs) or TIGR04131 (type B CTDs). Here, we identify features of T9SS CTDs of F. johnsoniae that are required for protein secretion and demonstrate that type A CTDs from distantly related members of the phylum function with the F. johnsoniae T9SS to secrete the foreign protein sfGFP. In contrast, type B CTDs failed to target sfGFP for secretion, suggesting a more complex association with the T9SS. PMID:28396348

Cellobiohydrolase I enzymes

DOEpatents

Adney, William S; Himmel, Michael E; Decker, Stephen R; Knoshaug, Eric P; Nimlos, Mark R; Crowley, Michael F; Jeoh, Tina

2014-01-28

Provided herein is an isolated Cel7A polypeptide comprising mutations in the catalytic domain of the polypeptide relative to the catalytic domain of a wild type Cel7A polypeptide, wherein the mutations reduce N-linked glycosylation of the isolated polypeptide relative to the wild type polypeptide. Also provided herein is an isolated Cel7A polypeptide comprising increased O-linked glycosylation of the linker domain relative to a linker domain of a wild type Cel7A polypeptide. The increased O-linked glycosylation is a result of the addition of and/or substitution of one or more serine and/or threonine residues to the linker domain relative to the linker domain of the wild type polypeptide. In some embodiments, the isolated Cel7A polypeptide comprising mutations in the catalytic domain of the polypeptide relative to the catalytic domain of a wild type Cel7A polypeptide further comprises increased O-linked glycosylation of the linker domain relative to a linker domain of a wild type Cel7A polypeptide. The mutations in the catalytic domain reduce N-linked glycosylation of the isolated polypeptide relative to the wild type polypeptide. The addition of and/or substitution of one or more serine and/or threonine residues to the linker domain relative to the linker domain of the wild type polypeptide increases O-linked glycosylation of the isolated polypeptide. Further provided are compositions comprising such polypeptides and nucleic acids encoding such polypeptides. Still further provided are methods for making such polypeptides.

Interoperable cross-domain semantic and geospatial framework for automatic change detection

NASA Astrophysics Data System (ADS)

Kuo, Chiao-Ling; Hong, Jung-Hong

2016-01-01

With the increasingly diverse types of geospatial data established over the last few decades, semantic interoperability in integrated applications has attracted much interest in the field of Geographic Information System (GIS). This paper proposes a new strategy and framework to process cross-domain geodata at the semantic level. This framework leverages the semantic equivalence of concepts between domains through bridge ontology and facilitates the integrated use of different domain data, which has been long considered as an essential superiority of GIS, but is impeded by the lack of understanding about the semantics implicitly hidden in the data. We choose the task of change detection to demonstrate how the introduction of ontology concept can effectively make the integration possible. We analyze the common properties of geodata and change detection factors, then construct rules and summarize possible change scenario for making final decisions. The use of topographic map data to detect changes in land use shows promising success, as far as the improvement of efficiency and level of automation is concerned. We believe the ontology-oriented approach will enable a new way for data integration across different domains from the perspective of semantic interoperability, and even open a new dimensionality for the future GIS.

Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression

PubMed Central

Libbrecht, Maxwell W.; Ay, Ferhat; Hoffman, Michael M.; Gilbert, David M.; Bilmes, Jeffrey A.; Noble, William Stafford

2015-01-01

The genomic neighborhood of a gene influences its activity, a behavior that is attributable in part to domain-scale regulation. Previous genomic studies have identified many types of regulatory domains. However, due to the difficulty of integrating genomics data sets, the relationships among these domain types are poorly understood. Semi-automated genome annotation (SAGA) algorithms facilitate human interpretation of heterogeneous collections of genomics data by simultaneously partitioning the human genome and assigning labels to the resulting genomic segments. However, existing SAGA methods cannot integrate inherently pairwise chromatin conformation data. We developed a new computational method, called graph-based regularization (GBR), for expressing a pairwise prior that encourages certain pairs of genomic loci to receive the same label in a genome annotation. We used GBR to exploit chromatin conformation information during genome annotation by encouraging positions that are close in 3D to occupy the same type of domain. Using this approach, we produced a model of chromatin domains in eight human cell types, thereby revealing the relationships among known domain types. Through this model, we identified clusters of tightly regulated genes expressed in only a small number of cell types, which we term “specific expression domains.” We found that domain boundaries marked by promoters and CTCF motifs are consistent between cell types even when domain activity changes. Finally, we showed that GBR can be used to transfer information from well-studied cell types to less well-characterized cell types during genome annotation, making it possible to produce high-quality annotations of the hundreds of cell types with limited available data. PMID:25677182

Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression.

PubMed

Libbrecht, Maxwell W; Ay, Ferhat; Hoffman, Michael M; Gilbert, David M; Bilmes, Jeffrey A; Noble, William Stafford

2015-04-01

The genomic neighborhood of a gene influences its activity, a behavior that is attributable in part to domain-scale regulation. Previous genomic studies have identified many types of regulatory domains. However, due to the difficulty of integrating genomics data sets, the relationships among these domain types are poorly understood. Semi-automated genome annotation (SAGA) algorithms facilitate human interpretation of heterogeneous collections of genomics data by simultaneously partitioning the human genome and assigning labels to the resulting genomic segments. However, existing SAGA methods cannot integrate inherently pairwise chromatin conformation data. We developed a new computational method, called graph-based regularization (GBR), for expressing a pairwise prior that encourages certain pairs of genomic loci to receive the same label in a genome annotation. We used GBR to exploit chromatin conformation information during genome annotation by encouraging positions that are close in 3D to occupy the same type of domain. Using this approach, we produced a model of chromatin domains in eight human cell types, thereby revealing the relationships among known domain types. Through this model, we identified clusters of tightly regulated genes expressed in only a small number of cell types, which we term "specific expression domains." We found that domain boundaries marked by promoters and CTCF motifs are consistent between cell types even when domain activity changes. Finally, we showed that GBR can be used to transfer information from well-studied cell types to less well-characterized cell types during genome annotation, making it possible to produce high-quality annotations of the hundreds of cell types with limited available data. © 2015 Libbrecht et al.; Published by Cold Spring Harbor Laboratory Press.

Antibody-mediated targeting of replication-competent retroviral vectors.

PubMed

Tai, Chien-Kuo; Logg, Christopher R; Park, Jinha M; Anderson, W French; Press, Michael F; Kasahara, Noriyuki

2003-05-20

Replication-competent murine leukemia virus (MLV) vectors can be engineered to achieve high efficiency gene transfer to solid tumors in vivo and tumor-restricted replication, however their safety can be further enhanced by redirecting tropism of the virus envelope. We have therefore tested the targeting capability and replicative stability of ecotropic and amphotropic replication-competent retrovirus (RCR) vectors containing two tandem repeats from the immunoglobulin G-binding domain of Staphylococcal protein A inserted into the proline-rich "hinge" region of the envelope, which enables modular use of antibodies of various specificities for vector targeting. The modified envelopes were efficiently expressed and incorporated into virions, were capable of capturing monoclonal anti-HER2 antibodies, and mediated efficient binding of the virus-antibody complex to HER2-positive target cells. While infectivity was markedly reduced by pseudotyping with targeted envelopes alone, coexpression of wild-type envelope rescued efficient cellular entry. Both ecotropic and amphotropic RCR vector/anti-HER2 antibody complexes achieved significant enhancement of transduction on murine target cells overexpressing HER2, which could be competed by preincubation with excess free antibodies. Interestingly, HER2-expressing human breast cancer cells did not show enhancement of transduction despite efficient antibody-mediated cell surface binding, suggesting that target cell-specific parameters markedly affect the efficiency of post-binding entry processes. Serial replication of targeted vectors resulted in selection of Z domain deletion variants, but reduction of the overall size of the vector genome enhanced its stability. Application of antibody-mediated targeting to the initial localization of replication-competent virus vectors to tumor sites will thus require optimized target selection and vector design.

Critical Role of Interdomain Interactions in the Conformational Change and Catalytic Mechanism of Endoplasmic Reticulum Aminopeptidase 1.

PubMed

Stamogiannos, Athanasios; Maben, Zachary; Papakyriakou, Athanasios; Mpakali, Anastasia; Kokkala, Paraskevi; Georgiadis, Dimitris; Stern, Lawrence J; Stratikos, Efstratios

2017-03-14

Endoplasmic reticulum aminopeptidase 1 (ERAP1) is an intracellular enzyme that is important for the generation of antigenic epitopes and major histocompatibility class I-restricted adaptive immune responses. ERAP1 processes a vast variety of different peptides but still shows length and sequence selectivity, although the mechanism behind these properties is poorly understood. X-ray crystallographic analysis has revealed that ERAP1 can assume at least two distinct conformations in which C-terminal domain IV is either proximal or distal to active site domain II. To improve our understanding of the role of this conformational change in the catalytic mechanism of ERAP1, we used site-directed mutagenesis to perturb key salt bridges between domains II and IV. Enzymatic analysis revealed that these mutations, although located away from the catalytic site, greatly reduce the catalytic efficiency and change the allosteric kinetic behavior. The variants were more efficiently activated by small peptides and bound a competitive inhibitor with weaker affinity and faster dissociation kinetics. Molecular dynamics analysis suggested that the mutations affect the conformational distribution of ERAP1, reducing the population of closed states. Small-angle X-ray scattering indicated that both the wild type and the ERAP1 variants are predominantly in an open conformational state in solution. Overall, our findings suggest that electrostatic interactions between domains II and IV in ERAP1 are crucial for driving a conformational change that regulates the structural integrity of the catalytic site. The extent of domain opening in ERAP1 probably underlies its specialization for antigenic peptide precursors and should be taken into account in inhibitor development efforts.

Distinct functional domains within the acidic cluster of tegument protein pp28 required for trafficking and cytoplasmic envelopment of human cytomegalovirus.

PubMed

Seo, Jun-Young; Jeon, Hyejin; Hong, Sookyung; Britt, William J

2016-10-01

Human cytomegalovirus UL99-encoded tegument protein pp28 contains a 16 aa acidic cluster that is required for pp28 trafficking to the assembly compartment (AC) and the virus assembly. However, functional signals within the acidic cluster of pp28 remain undefined. Here, we demonstrated that an acidic cluster rather than specific sorting signals was required for trafficking to the AC. Recombinant viruses with chimeric pp28 proteins expressing non-native acidic clusters exhibited delayed viral growth kinetics and decreased production of infectious virus, indicating that the native acidic cluster of pp28 was essential for wild-type virus assembly. These results suggested that the acidic cluster of pp28 has distinct functional domains required for trafficking and for efficient virus assembly. The first half (aa 44-50) of the acidic cluster was sufficient for pp28 trafficking, whereas the native acidic cluster consisting of aa 51-59 was required for the assembly of wild-type levels of infectious virus.

Band-gap analysis of a novel lattice with a hierarchical periodicity using the spectral element method

NASA Astrophysics Data System (ADS)

Wu, Zhijing; Li, Fengming; Zhang, Chuanzeng

2018-05-01

Inspired by the hierarchical structures of butterfly wing surfaces, a new kind of lattice structures with a two-order hierarchical periodicity is proposed and designed, and the band-gap properties are investigated by the spectral element method (SEM). The equations of motion of the whole structure are established considering the macro and micro periodicities of the system. The efficiency of the SEM is exploited in the modeling process and validated by comparing the results with that of the finite element method (FEM). Based on the highly accurate results in the frequency domain, the dynamic behaviors of the proposed two-order hierarchical structures are analyzed. An original and interesting finding is the existence of the distinct macro and micro stop-bands in the given frequency domain. The mechanisms for these two types of band-gaps are also explored. Finally, the relations between the hierarchical periodicities and the different types of the stop-bands are investigated by analyzing the parametrical influences.

Peroxisomal multifunctional enzyme type 2 from the fruitfly: dehydrogenase and hydratase act as separate entities, as revealed by structure and kinetics.

PubMed

Haataja, Tatu J K; Koski, M Kristian; Hiltunen, J Kalervo; Glumoff, Tuomo

2011-05-01

All of the peroxisomal β-oxidation pathways characterized thus far house at least one MFE (multifunctional enzyme) catalysing two out of four reactions of the spiral. MFE type 2 proteins from various species display great variation in domain composition and predicted substrate preference. The gene CG3415 encodes for Drosophila melanogaster MFE-2 (DmMFE-2), complements the Saccharomyces cerevisiae MFE-2 deletion strain, and the recombinant protein displays both MFE-2 enzymatic activities in vitro. The resolved crystal structure is the first one for a full-length MFE-2 revealing the assembly of domains, and the data can also be transferred to structure-function studies for other MFE-2 proteins. The structure explains the necessity of dimerization. The lack of substrate channelling is proposed based on both the structural features, as well as by the fact that hydration and dehydrogenation activities of MFE-2, if produced as separate enzymes, are equally efficient in catalysis as the full-length MFE-2.

Domain decomposition methods for the parallel computation of reacting flows

NASA Technical Reports Server (NTRS)

Keyes, David E.

1988-01-01

Domain decomposition is a natural route to parallel computing for partial differential equation solvers. Subdomains of which the original domain of definition is comprised are assigned to independent processors at the price of periodic coordination between processors to compute global parameters and maintain the requisite degree of continuity of the solution at the subdomain interfaces. In the domain-decomposed solution of steady multidimensional systems of PDEs by finite difference methods using a pseudo-transient version of Newton iteration, the only portion of the computation which generally stands in the way of efficient parallelization is the solution of the large, sparse linear systems arising at each Newton step. For some Jacobian matrices drawn from an actual two-dimensional reacting flow problem, comparisons are made between relaxation-based linear solvers and also preconditioned iterative methods of Conjugate Gradient and Chebyshev type, focusing attention on both iteration count and global inner product count. The generalized minimum residual method with block-ILU preconditioning is judged the best serial method among those considered, and parallel numerical experiments on the Encore Multimax demonstrate for it approximately 10-fold speedup on 16 processors.

Chimeric TALE recombinases with programmable DNA sequence specificity.

PubMed

Mercer, Andrew C; Gaj, Thomas; Fuller, Roberta P; Barbas, Carlos F

2012-11-01

Site-specific recombinases are powerful tools for genome engineering. Hyperactivated variants of the resolvase/invertase family of serine recombinases function without accessory factors, and thus can be re-targeted to sequences of interest by replacing native DNA-binding domains (DBDs) with engineered zinc-finger proteins (ZFPs). However, imperfect modularity with particular domains, lack of high-affinity binding to all DNA triplets, and difficulty in construction has hindered the widespread adoption of ZFPs in unspecialized laboratories. The discovery of a novel type of DBD in transcription activator-like effector (TALE) proteins from Xanthomonas provides an alternative to ZFPs. Here we describe chimeric TALE recombinases (TALERs): engineered fusions between a hyperactivated catalytic domain from the DNA invertase Gin and an optimized TALE architecture. We use a library of incrementally truncated TALE variants to identify TALER fusions that modify DNA with efficiency and specificity comparable to zinc-finger recombinases in bacterial cells. We also show that TALERs recombine DNA in mammalian cells. The TALER architecture described herein provides a platform for insertion of customized TALE domains, thus significantly expanding the targeting capacity of engineered recombinases and their potential applications in biotechnology and medicine.

The TFIIH subunit Tfb3 regulates cullin neddylation

PubMed Central

Rabut, Gwenaël; Le Dez, Gaëlle; Verma, Rati; Makhnevych, Taras; Knebel, Axel; Kurz, Thimo; Boone, Charles; Deshaies, Raymond J.; Peter, Matthias

2011-01-01

Summary Cullin proteins are scaffolds for the assembly of multi-subunit ubiquitin ligases, which ubiquitylate a large number of proteins involved in widely-varying cellular functions. Multiple mechanisms cooperate to regulate cullin activity, including neddylation of their C-terminal domain. Interestingly, we found that the yeast Cul4-type cullin Rtt101 is not only neddylated but also ubiquitylated, and both modifications promote Rtt101 function in vivo. Surprisingly, proper modification of Rtt101 neither correlated with catalytic activity of the RING-domain of Hrt1 nor did it require the Nedd8 ligase Dcn1. Instead, ubiquitylation of Rtt101 was dependent on the ubiquitin-conjugating enzyme Ubc4, while efficient neddylation involves the RING-domain protein Tfb3, a subunit of the transcription factor TFIIH. Tfb3 also controls Cul3 neddylation and activity in vivo, and physically interacts with Ubc4 and the Nedd8-conjugating enzyme Ubc12 as well as the Hrt1/Rtt101 complex. Together, these results suggest that the conserved RING-domain protein Tfb3 controls activation of a subset of cullins. PMID:21816351

Arrhythmia Classification Based on Multi-Domain Feature Extraction for an ECG Recognition System.

PubMed

Li, Hongqiang; Yuan, Danyang; Wang, Youxi; Cui, Dianyin; Cao, Lu

2016-10-20

Automatic recognition of arrhythmias is particularly important in the diagnosis of heart diseases. This study presents an electrocardiogram (ECG) recognition system based on multi-domain feature extraction to classify ECG beats. An improved wavelet threshold method for ECG signal pre-processing is applied to remove noise interference. A novel multi-domain feature extraction method is proposed; this method employs kernel-independent component analysis in nonlinear feature extraction and uses discrete wavelet transform to extract frequency domain features. The proposed system utilises a support vector machine classifier optimized with a genetic algorithm to recognize different types of heartbeats. An ECG acquisition experimental platform, in which ECG beats are collected as ECG data for classification, is constructed to demonstrate the effectiveness of the system in ECG beat classification. The presented system, when applied to the MIT-BIH arrhythmia database, achieves a high classification accuracy of 98.8%. Experimental results based on the ECG acquisition experimental platform show that the system obtains a satisfactory classification accuracy of 97.3% and is able to classify ECG beats efficiently for the automatic identification of cardiac arrhythmias.

Arrhythmia Classification Based on Multi-Domain Feature Extraction for an ECG Recognition System

PubMed Central

Li, Hongqiang; Yuan, Danyang; Wang, Youxi; Cui, Dianyin; Cao, Lu

2016-01-01

Automatic recognition of arrhythmias is particularly important in the diagnosis of heart diseases. This study presents an electrocardiogram (ECG) recognition system based on multi-domain feature extraction to classify ECG beats. An improved wavelet threshold method for ECG signal pre-processing is applied to remove noise interference. A novel multi-domain feature extraction method is proposed; this method employs kernel-independent component analysis in nonlinear feature extraction and uses discrete wavelet transform to extract frequency domain features. The proposed system utilises a support vector machine classifier optimized with a genetic algorithm to recognize different types of heartbeats. An ECG acquisition experimental platform, in which ECG beats are collected as ECG data for classification, is constructed to demonstrate the effectiveness of the system in ECG beat classification. The presented system, when applied to the MIT-BIH arrhythmia database, achieves a high classification accuracy of 98.8%. Experimental results based on the ECG acquisition experimental platform show that the system obtains a satisfactory classification accuracy of 97.3% and is able to classify ECG beats efficiently for the automatic identification of cardiac arrhythmias. PMID:27775596

PLATSIM: A Simulation and Analysis Package for Large-Order Flexible Systems. Version 2.0

NASA Technical Reports Server (NTRS)

Maghami, Peiman G.; Kenny, Sean P.; Giesy, Daniel P.

1997-01-01

The software package PLATSIM provides efficient time and frequency domain analysis of large-order generic space platforms. PLATSIM can perform open-loop analysis or closed-loop analysis with linear or nonlinear control system models. PLATSIM exploits the particular form of sparsity of the plant matrices for very efficient linear and nonlinear time domain analysis, as well as frequency domain analysis. A new, original algorithm for the efficient computation of open-loop and closed-loop frequency response functions for large-order systems has been developed and is implemented within the package. Furthermore, a novel and efficient jitter analysis routine which determines jitter and stability values from time simulations in a very efficient manner has been developed and is incorporated in the PLATSIM package. In the time domain analysis, PLATSIM simulates the response of the space platform to disturbances and calculates the jitter and stability values from the response time histories. In the frequency domain analysis, PLATSIM calculates frequency response function matrices and provides the corresponding Bode plots. The PLATSIM software package is written in MATLAB script language. A graphical user interface is developed in the package to provide convenient access to its various features.

Efficient learning mechanisms hold in the social domain and are implemented in the medial prefrontal cortex

PubMed Central

Tobler, Philippe N.

2015-01-01

When we are learning to associate novel cues with outcomes, learning is more efficient if we take advantage of previously learned associations and thereby avoid redundant learning. The blocking effect represents this sort of efficiency mechanism and refers to the phenomenon in which a novel stimulus is blocked from learning when it is associated with a fully predicted outcome. Although there is sufficient evidence that this effect manifests itself when individuals learn about their own rewards, it remains unclear whether it also does when they learn about others’ rewards. We employed behavioral and neuroimaging methods to address this question. We demonstrate that blocking does indeed occur in the social domain and it does so to a similar degree as observed in the individual domain. On the neural level, activations in the medial prefrontal cortex (mPFC) show a specific contribution to blocking and learning-related prediction errors in the social domain. These findings suggest that the efficiency principle that applies to reward learning in the individual domain also applies to that in the social domain, with the mPFC playing a central role in implementing it. PMID:25326037

Efficient computation of turbulent flow in ribbed passages using a non-overlapping near-wall domain decomposition method

NASA Astrophysics Data System (ADS)

Jones, Adam; Utyuzhnikov, Sergey

2017-08-01

Turbulent flow in a ribbed channel is studied using an efficient near-wall domain decomposition (NDD) method. The NDD approach is formulated by splitting the computational domain into an inner and outer region, with an interface boundary between the two. The computational mesh covers the outer region, and the flow in this region is solved using the open-source CFD code Code_Saturne with special boundary conditions on the interface boundary, called interface boundary conditions (IBCs). The IBCs are of Robin type and incorporate the effect of the inner region on the flow in the outer region. IBCs are formulated in terms of the distance from the interface boundary to the wall in the inner region. It is demonstrated that up to 90% of the region between the ribs in the ribbed passage can be removed from the computational mesh with an error on the friction factor within 2.5%. In addition, computations with NDD are faster than computations based on low Reynolds number (LRN) models by a factor of five. Different rib heights can be studied with the same mesh in the outer region without affecting the accuracy of the friction factor. This is tested with six different rib heights in an example of a design optimisation study. It is found that the friction factors computed with NDD are almost identical to the fully-resolved results. When used for inverse problems, NDD is considerably more efficient than LRN computations because only one computation needs to be performed and only one mesh needs to be generated.

Automatic topic identification of health-related messages in online health community using text classification.

PubMed

Lu, Yingjie

2013-01-01

To facilitate patient involvement in online health community and obtain informative support and emotional support they need, a topic identification approach was proposed in this paper for identifying automatically topics of the health-related messages in online health community, thus assisting patients in reaching the most relevant messages for their queries efficiently. Feature-based classification framework was presented for automatic topic identification in our study. We first collected the messages related to some predefined topics in a online health community. Then we combined three different types of features, n-gram-based features, domain-specific features and sentiment features to build four feature sets for health-related text representation. Finally, three different text classification techniques, C4.5, Naïve Bayes and SVM were adopted to evaluate our topic classification model. By comparing different feature sets and different classification techniques, we found that n-gram-based features, domain-specific features and sentiment features were all considered to be effective in distinguishing different types of health-related topics. In addition, feature reduction technique based on information gain was also effective to improve the topic classification performance. In terms of classification techniques, SVM outperformed C4.5 and Naïve Bayes significantly. The experimental results demonstrated that the proposed approach could identify the topics of online health-related messages efficiently.

Cancerouspdomains: comprehensive analysis of cancer type-specific recurrent somatic mutations in proteins and domains.

PubMed

Hashemi, Seirana; Nowzari Dalini, Abbas; Jalali, Adrin; Banaei-Moghaddam, Ali Mohammad; Razaghi-Moghadam, Zahra

2017-08-16

Discriminating driver mutations from the ones that play no role in cancer is a severe bottleneck in elucidating molecular mechanisms underlying cancer development. Since protein domains are representatives of functional regions within proteins, mutations on them may disturb the protein functionality. Therefore, studying mutations at domain level may point researchers to more accurate assessment of the functional impact of the mutations. This article presents a comprehensive study to map mutations from 29 cancer types to both sequence- and structure-based domains. Statistical analysis was performed to identify candidate domains in which mutations occur with high statistical significance. For each cancer type, the corresponding type-specific domains were distinguished among all candidate domains. Subsequently, cancer type-specific domains facilitated the identification of specific proteins for each cancer type. Besides, performing interactome analysis on specific proteins of each cancer type showed high levels of interconnectivity among them, which implies their functional relationship. To evaluate the role of mitochondrial genes, stem cell-specific genes and DNA repair genes in cancer development, their mutation frequency was determined via further analysis. This study has provided researchers with a publicly available data repository for studying both CATH and Pfam domain regions on protein-coding genes. Moreover, the associations between different groups of genes/domains and various cancer types have been clarified. The work is available at http://www.cancerouspdomains.ir .

Multigrid treatment of implicit continuum diffusion

NASA Astrophysics Data System (ADS)

Francisquez, Manaure; Zhu, Ben; Rogers, Barrett

2017-10-01

Implicit treatment of diffusive terms of various differential orders common in continuum mechanics modeling, such as computational fluid dynamics, is investigated with spectral and multigrid algorithms in non-periodic 2D domains. In doubly periodic time dependent problems these terms can be efficiently and implicitly handled by spectral methods, but in non-periodic systems solved with distributed memory parallel computing and 2D domain decomposition, this efficiency is lost for large numbers of processors. We built and present here a multigrid algorithm for these types of problems which outperforms a spectral solution that employs the highly optimized FFTW library. This multigrid algorithm is not only suitable for high performance computing but may also be able to efficiently treat implicit diffusion of arbitrary order by introducing auxiliary equations of lower order. We test these solvers for fourth and sixth order diffusion with idealized harmonic test functions as well as a turbulent 2D magnetohydrodynamic simulation. It is also shown that an anisotropic operator without cross-terms can improve model accuracy and speed, and we examine the impact that the various diffusion operators have on the energy, the enstrophy, and the qualitative aspect of a simulation. This work was supported by DOE-SC-0010508. This research used resources of the National Energy Research Scientific Computing Center (NERSC).

Efficient integration method for fictitious domain approaches

NASA Astrophysics Data System (ADS)

Duczek, Sascha; Gabbert, Ulrich

2015-10-01

In the current article, we present an efficient and accurate numerical method for the integration of the system matrices in fictitious domain approaches such as the finite cell method (FCM). In the framework of the FCM, the physical domain is embedded in a geometrically larger domain of simple shape which is discretized using a regular Cartesian grid of cells. Therefore, a spacetree-based adaptive quadrature technique is normally deployed to resolve the geometry of the structure. Depending on the complexity of the structure under investigation this method accounts for most of the computational effort. To reduce the computational costs for computing the system matrices an efficient quadrature scheme based on the divergence theorem (Gauß-Ostrogradsky theorem) is proposed. Using this theorem the dimension of the integral is reduced by one, i.e. instead of solving the integral for the whole domain only its contour needs to be considered. In the current paper, we present the general principles of the integration method and its implementation. The results to several two-dimensional benchmark problems highlight its properties. The efficiency of the proposed method is compared to conventional spacetree-based integration techniques.

Structural and evolutionary relationships of "AT-less" type I polyketide synthase ketosynthases.

PubMed

Lohman, Jeremy R; Ma, Ming; Osipiuk, Jerzy; Nocek, Boguslaw; Kim, Youngchang; Chang, Changsoo; Cuff, Marianne; Mack, Jamey; Bigelow, Lance; Li, Hui; Endres, Michael; Babnigg, Gyorgy; Joachimiak, Andrzej; Phillips, George N; Shen, Ben

2015-10-13

Acyltransferase (AT)-less type I polyketide synthases (PKSs) break the type I PKS paradigm. They lack the integrated AT domains within their modules and instead use a discrete AT that acts in trans, whereas a type I PKS module minimally contains AT, acyl carrier protein (ACP), and ketosynthase (KS) domains. Structures of canonical type I PKS KS-AT didomains reveal structured linkers that connect the two domains. AT-less type I PKS KSs have remnants of these linkers, which have been hypothesized to be AT docking domains. Natural products produced by AT-less type I PKSs are very complex because of an increased representation of unique modifying domains. AT-less type I PKS KSs possess substrate specificity and fall into phylogenetic clades that correlate with their substrates, whereas canonical type I PKS KSs are monophyletic. We have solved crystal structures of seven AT-less type I PKS KS domains that represent various sequence clusters, revealing insight into the large structural and subtle amino acid residue differences that lead to unique active site topologies and substrate specificities. One set of structures represents a larger group of KS domains from both canonical and AT-less type I PKSs that accept amino acid-containing substrates. One structure has a partial AT-domain, revealing the structural consequences of a type I PKS KS evolving into an AT-less type I PKS KS. These structures highlight the structural diversity within the AT-less type I PKS KS family, and most important, provide a unique opportunity to study the molecular evolution of substrate specificity within the type I PKSs.

Structural and evolutionary relationships of “AT-less” type I polyketide synthase ketosynthases

PubMed Central

Lohman, Jeremy R.; Ma, Ming; Osipiuk, Jerzy; Nocek, Boguslaw; Kim, Youngchang; Chang, Changsoo; Cuff, Marianne; Mack, Jamey; Bigelow, Lance; Li, Hui; Endres, Michael; Babnigg, Gyorgy; Joachimiak, Andrzej; Phillips, George N.; Shen, Ben

2015-01-01

Acyltransferase (AT)-less type I polyketide synthases (PKSs) break the type I PKS paradigm. They lack the integrated AT domains within their modules and instead use a discrete AT that acts in trans, whereas a type I PKS module minimally contains AT, acyl carrier protein (ACP), and ketosynthase (KS) domains. Structures of canonical type I PKS KS-AT didomains reveal structured linkers that connect the two domains. AT-less type I PKS KSs have remnants of these linkers, which have been hypothesized to be AT docking domains. Natural products produced by AT-less type I PKSs are very complex because of an increased representation of unique modifying domains. AT-less type I PKS KSs possess substrate specificity and fall into phylogenetic clades that correlate with their substrates, whereas canonical type I PKS KSs are monophyletic. We have solved crystal structures of seven AT-less type I PKS KS domains that represent various sequence clusters, revealing insight into the large structural and subtle amino acid residue differences that lead to unique active site topologies and substrate specificities. One set of structures represents a larger group of KS domains from both canonical and AT-less type I PKSs that accept amino acid-containing substrates. One structure has a partial AT-domain, revealing the structural consequences of a type I PKS KS evolving into an AT-less type I PKS KS. These structures highlight the structural diversity within the AT-less type I PKS KS family, and most important, provide a unique opportunity to study the molecular evolution of substrate specificity within the type I PKSs. PMID:26420866

The Dimer Interfaces of Protease and Extra-Protease Domains Influence the Activation of Protease and the Specificity of GagPol Cleavage

PubMed Central

Pettit, Steven C.; Gulnik, Sergei; Everitt, Lori; Kaplan, Andrew H.

2003-01-01

Activation of the human immunodeficiency virus type 1 (HIV-1) protease is an essential step in viral replication. As is the case for all retroviral proteases, enzyme activation requires the formation of protease homodimers. However, little is known about the mechanisms by which retroviral proteases become active within their precursors. Using an in vitro expression system, we have examined the determinants of activation efficiency and the order of cleavage site processing for the protease of HIV-1 within the full-length GagPol precursor. Following activation, initial cleavage occurs between the viral p2 and nucleocapsid proteins. This is followed by cleavage of a novel site located in the transframe domain. Mutational analysis of the dimer interface of the protease produced differential effects on activation and specificity. A subset of mutations produced enhanced cleavage at the amino terminus of the protease, suggesting that, in the wild-type precursor, cleavages that liberate the protease are a relatively late event. Replacement of the proline residue at position 1 of the protease dimer interface resulted in altered cleavage of distal sites and suggests that this residue functions as a cis-directed specificity determinant. In summary, our studies indicate that interactions within the protease dimer interface help determine the order of precursor cleavage and contribute to the formation of extended-protease intermediates. Assembly domains within GagPol outside the protease domain also influence enzyme activation. PMID:12477841

The dimer interfaces of protease and extra-protease domains influence the activation of protease and the specificity of GagPol cleavage.

PubMed

Pettit, Steven C; Gulnik, Sergei; Everitt, Lori; Kaplan, Andrew H

2003-01-01

Activation of the human immunodeficiency virus type 1 (HIV-1) protease is an essential step in viral replication. As is the case for all retroviral proteases, enzyme activation requires the formation of protease homodimers. However, little is known about the mechanisms by which retroviral proteases become active within their precursors. Using an in vitro expression system, we have examined the determinants of activation efficiency and the order of cleavage site processing for the protease of HIV-1 within the full-length GagPol precursor. Following activation, initial cleavage occurs between the viral p2 and nucleocapsid proteins. This is followed by cleavage of a novel site located in the transframe domain. Mutational analysis of the dimer interface of the protease produced differential effects on activation and specificity. A subset of mutations produced enhanced cleavage at the amino terminus of the protease, suggesting that, in the wild-type precursor, cleavages that liberate the protease are a relatively late event. Replacement of the proline residue at position 1 of the protease dimer interface resulted in altered cleavage of distal sites and suggests that this residue functions as a cis-directed specificity determinant. In summary, our studies indicate that interactions within the protease dimer interface help determine the order of precursor cleavage and contribute to the formation of extended-protease intermediates. Assembly domains within GagPol outside the protease domain also influence enzyme activation.

Action Algebras and Model Algebras in Denotational Semantics

NASA Astrophysics Data System (ADS)

Guedes, Luiz Carlos Castro; Haeusler, Edward Hermann

This article describes some results concerning the conceptual separation of model dependent and language inherent aspects in a denotational semantics of a programming language. Before going into the technical explanation, the authors wish to relate a story that illustrates how correctly and precisely posed questions can influence the direction of research. By means of his questions, Professor Mosses aided the PhD research of one of the authors of this article and taught the other, who at the time was a novice supervisor, the real meaning of careful PhD supervision. The student’s research had been partially developed towards the implementation of programming languages through denotational semantics specification, and the student had developed a prototype [12] that compared relatively well to some industrial compilers of the PASCAL language. During a visit to the BRICS lab in Aarhus, the student’s supervisor gave Professor Mosses a draft of an article describing the prototype and its implementation experiments. The next day, Professor Mosses asked the supervisor, “Why is the generated code so efficient when compared to that generated by an industrial compiler?” and “You claim that the efficiency is simply a consequence of the Object- Orientation mechanisms used by the prototype programming language (C++); this should be better investigated. Pay more attention to the class of programs that might have this good comparison profile.” As a result of these aptly chosen questions and comments, the student and supervisor made great strides in the subsequent research; the advice provided by Professor Mosses made them perceive that the code generated for certain semantic domains was efficient because it mapped to the “right aspect” of the language semantics. (Certain functional types, used to represent mappings such as Stores and Environments, were pushed to the level of the object language (as in gcc). This had the side-effect of generating code for arrays in the same way as that for functional denotational types. For example, PASCAL arrays belong to the “language inherent” aspect, while the Store domain seems to belong to the “model dependent” aspect. This distinction was important because it focussed attention on optimizing the model dependent semantic domains to obtain a more efficient implementation.) The research led to a nice conclusion: The guidelines of Action Semantics induce a clear separation of the model and language inherent aspects of a language’s semantics. A good implementation of facets, particularly the model dependent ones, leads to generation of an efficient compiler. In this article we discuss the separation of the language inherent and model-inherent domains at the theoretical and conceptual level. In doing so, the authors hope to show how Professor Mosses’s influence extended beyond his technical advice to his professional and personal examples on the supervision of PhD research.

A cross-disciplinary response to improve test activities: The corporate memory capitalization in Ariane4 test domain

NASA Technical Reports Server (NTRS)

Vo, Dinh Phuoc; Soler, Christian; Aussenac, N.; Macchion, D.

1993-01-01

The Assembly, Integration, Test, and Validation (AIT/AIV) of the Ariane4 Vehicle Equipment Bay was held at Matra Marconi Space (MMS) site of Toulouse for several years. For this activity, incident interpretation necessitates a great deal of different knowledge. When complex faults occur, particularly those appearing during overall control tests, experts of various domains (EGSE, software, on-board equipment) have to join for investigation sessions. Thus, an assistance tool for the identification of faulty equipment will improve the efficiency of diagnosis and the overall productivity of test activities. As a solution, the Aramiihs laboratory proposed considering the opportunity of a knowledge based system intended to assist the tester in diagnosis. This knowledge based system is, in fact, a short-term achievement of a long-term goal which is the capitalization of corporate memory in the Ariane4 test domain. Aramiihs is a research unit where engineers from MMS and researchers from the IRIT-CNRS cooperate on problems concerning new types of man-system interaction.

Designed Transcriptional Regulation in Mammalian Cells Based on TALE- and CRISPR/dCas9.

PubMed

Lebar, Tina; Jerala, Roman

2018-01-01

Transcriptional regulation lies at the center of many cellular processes and is the result of cellular response to different external and internal signals. Control of transcription of selected genes enables an unprecedented access to shape the cellular response. While orthogonal transcription factors from bacteria, yeast, plants, or other cells have been used to introduce new cellular logic into mammalian cells, the discovery of designable modular DNA binding domains, such as Transcription Activator-Like Effectors (TALEs) and the CRISPR system, enable targeting of almost any selected DNA sequence. Fusion or conditional association of DNA targeting domain with transcriptional effector domains enables controlled regulation of almost any endogenous or ectopic gene. Moreover, the designed regulators can be linked into genetic circuits to implement complex responses, such as different types of Boolean functions and switches. In this chapter, we describe the protocols for achieving efficient transcriptional regulation with TALE- and CRISPR-based designed transcription factors in mammalian cells.

Crustal-Scale Fault Interaction at Rifted Margins and the Formation of Domain-Bounding Breakaway Complexes: Insights From Offshore Norway

NASA Astrophysics Data System (ADS)

Osmundsen, P. T.; Péron-Pinvidic, G.

2018-03-01

The large-magnitude faults that control crustal thinning and excision at rifted margins combine into laterally persistent structural boundaries that separate margin domains of contrasting morphology and structure. We term them breakaway complexes. At the Mid-Norwegian margin, we identify five principal breakaway complexes that separate the proximal, necking, distal, and outer margin domains. Downdip and lateral interactions between the faults that constitute breakaway complexes became fundamental to the evolution of the 3-D margin architecture. Different types of fault interaction are observed along and between these faults, but simple models for fault growth will not fully describe their evolution. These structures operate on the crustal scale, cut large thicknesses of heterogeneously layered lithosphere, and facilitate fundamental margin processes such as deformation coupling and exhumation. Variations in large-magnitude fault geometry, erosional footwall incision, and subsequent differential subsidence along the main breakaway complexes likely record the variable efficiency of these processes.

HIV-1 matrix domain removal ameliorates virus assembly and processing defects incurred by positive nucleocapsid charge elimination.

PubMed

Ko, Li-Jung; Yu, Fu-Hsien; Huang, Kuo-Jung; Wang, Chin-Tien

2015-01-01

Human immunodeficiency virus type 1 nucleocapsid (NC) basic residues presumably contribute to virus assembly via RNA, which serves as a scaffold for Gag-Gag interaction during particle assembly. To determine whether NC basic residues play a role in Gag cleavage (thereby impacting virus assembly), Gag processing efficiency and virus particle production were analyzed for an HIV-1 mutant NC15A, with alanine serving as a substitute for all NC basic residues. Results indicate that NC15A significantly impaired virus maturation in addition to significantly affecting Gag membrane binding and assembly. Interestingly, removal of the matrix (MA) central globular domain ameliorated the NC15A assembly and processing defects, likely through enhancement of Gag multimerization and membrane binding capacities.

Repartitioning Strategies for Massively Parallel Simulation of Reacting Flow

NASA Astrophysics Data System (ADS)

Pisciuneri, Patrick; Zheng, Angen; Givi, Peyman; Labrinidis, Alexandros; Chrysanthis, Panos

2015-11-01

The majority of parallel CFD simulators partition the domain into equal regions and assign the calculations for a particular region to a unique processor. This type of domain decomposition is vital to the efficiency of the solver. However, as the simulation develops, the workload among the partitions often become uneven (e.g. by adaptive mesh refinement, or chemically reacting regions) and a new partition should be considered. The process of repartitioning adjusts the current partition to evenly distribute the load again. We compare two repartitioning tools: Zoltan, an architecture-agnostic graph repartitioner developed at the Sandia National Laboratories; and Paragon, an architecture-aware graph repartitioner developed at the University of Pittsburgh. The comparative assessment is conducted via simulation of the Taylor-Green vortex flow with chemical reaction.

Efficient learning mechanisms hold in the social domain and are implemented in the medial prefrontal cortex.

PubMed

Seid-Fatemi, Azade; Tobler, Philippe N

2015-05-01

When we are learning to associate novel cues with outcomes, learning is more efficient if we take advantage of previously learned associations and thereby avoid redundant learning. The blocking effect represents this sort of efficiency mechanism and refers to the phenomenon in which a novel stimulus is blocked from learning when it is associated with a fully predicted outcome. Although there is sufficient evidence that this effect manifests itself when individuals learn about their own rewards, it remains unclear whether it also does when they learn about others' rewards. We employed behavioral and neuroimaging methods to address this question. We demonstrate that blocking does indeed occur in the social domain and it does so to a similar degree as observed in the individual domain. On the neural level, activations in the medial prefrontal cortex (mPFC) show a specific contribution to blocking and learning-related prediction errors in the social domain. These findings suggest that the efficiency principle that applies to reward learning in the individual domain also applies to that in the social domain, with the mPFC playing a central role in implementing it. © The Author (2014). Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

Topology and boundary shape optimization as an integrated design tool

NASA Technical Reports Server (NTRS)

Bendsoe, Martin Philip; Rodrigues, Helder Carrico

1990-01-01

The optimal topology of a two dimensional linear elastic body can be computed by regarding the body as a domain of the plane with a high density of material. Such an optimal topology can then be used as the basis for a shape optimization method that computes the optimal form of the boundary curves of the body. This results in an efficient and reliable design tool, which can be implemented via common FEM mesh generator and CAD type input-output facilities.

Computational performance of Free Mesh Method applied to continuum mechanics problems

PubMed Central

YAGAWA, Genki

2011-01-01

The free mesh method (FMM) is a kind of the meshless methods intended for particle-like finite element analysis of problems that are difficult to handle using global mesh generation, or a node-based finite element method that employs a local mesh generation technique and a node-by-node algorithm. The aim of the present paper is to review some unique numerical solutions of fluid and solid mechanics by employing FMM as well as the Enriched Free Mesh Method (EFMM), which is a new version of FMM, including compressible flow and sounding mechanism in air-reed instruments as applications to fluid mechanics, and automatic remeshing for slow crack growth, dynamic behavior of solid as well as large-scale Eigen-frequency of engine block as applications to solid mechanics. PMID:21558753

3D SPH numerical simulation of the wave generated by the Vajont rockslide

NASA Astrophysics Data System (ADS)

Vacondio, R.; Mignosa, P.; Pagani, S.

2013-09-01

A 3D numerical modeling of the wave generated by the Vajont slide, one of the most destructive ever occurred, is presented in this paper. A meshless Lagrangian Smoothed Particle Hydrodynamics (SPH) technique was adopted to simulate the highly fragmented violent flow generated by the falling slide in the artificial reservoir. The speed-up achievable via General Purpose Graphic Processing Units (GP-GPU) allowed to adopt the adequate resolution to describe the phenomenon. The comparison with the data available in literature showed that the results of the numerical simulation reproduce satisfactorily the maximum run-up, also the water surface elevation in the residual lake after the event. Moreover, the 3D velocity field of the flow during the event and the discharge hydrograph which overtopped the dam, were obtained.

Structural and evolutionary relationships of "AT-less" type I polyketide synthase ketosynthases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lohman, Jeremy; Ma, Ming; Osipiuk, Jerzy

2015-10-13

Acyltransferase (AT)-less type I polyketide synthases (PKSs) break the type I PKS paradigm. They lack the integrated AT domains within their modules and instead use a discrete AT that acts in trans, whereas a type I PKS module minimally contains AT, acyl carrier protein (ACP), and ketosynthase (KS) domains. Structures of canonical type I PKS KS-AT didomains reveal structured linkers that connect the two domains. AT-less type I PKS KSs have remnants of these linkers, which have been hypothesized to be AT docking domains. Natural products produced by AT-less type I PKSs are very complex because of an increased representationmore » of unique modifying domains. AT-less type I PKS KSs possess substrate specificity and fall into phylogenetic clades that correlate with their substrates, whereas canonical type I PKS KSs are monophyletic. We have solved crystal structures of seven AT-less type I PKS KS domains that represent various sequence clusters, revealing insight into the large structural and subtle amino acid residue differences that lead to unique active site topologies and substrate specificities. One set of structures represents a larger group of KS domains from both canonical and AT-less type I PKSs that accept amino acid-containing substrates. One structure has a partial AT-domain, revealing the structural consequences of a type I PKS KS evolving into an AT-less type I PKS KS. These structures highlight the structural diversity within the AT-less type I PKS KS family, and most important, provide a unique opportunity to study the molecular evolution of substrate specificity within the type I PKSs.« less

A hybrid fault diagnosis approach based on mixed-domain state features for rotating machinery.

PubMed

Xue, Xiaoming; Zhou, Jianzhong

2017-01-01

To make further improvement in the diagnosis accuracy and efficiency, a mixed-domain state features data based hybrid fault diagnosis approach, which systematically blends both the statistical analysis approach and the artificial intelligence technology, is proposed in this work for rolling element bearings. For simplifying the fault diagnosis problems, the execution of the proposed method is divided into three steps, i.e., fault preliminary detection, fault type recognition and fault degree identification. In the first step, a preliminary judgment about the health status of the equipment can be evaluated by the statistical analysis method based on the permutation entropy theory. If fault exists, the following two processes based on the artificial intelligence approach are performed to further recognize the fault type and then identify the fault degree. For the two subsequent steps, mixed-domain state features containing time-domain, frequency-domain and multi-scale features are extracted to represent the fault peculiarity under different working conditions. As a powerful time-frequency analysis method, the fast EEMD method was employed to obtain multi-scale features. Furthermore, due to the information redundancy and the submergence of original feature space, a novel manifold learning method (modified LGPCA) is introduced to realize the low-dimensional representations for high-dimensional feature space. Finally, two cases with 12 working conditions respectively have been employed to evaluate the performance of the proposed method, where vibration signals were measured from an experimental bench of rolling element bearing. The analysis results showed the effectiveness and the superiority of the proposed method of which the diagnosis thought is more suitable for practical application. Copyright © 2016 ISA. Published by Elsevier Ltd. All rights reserved.

Modulating the Effects of the Bacterial Chaperonin GroEL on Fibrillogenic Polypeptides through Modification of Domain Hinge Architecture.

PubMed

Fukui, Naoya; Araki, Kiho; Hongo, Kunihiro; Mizobata, Tomohiro; Kawata, Yasushi

2016-11-25

The isolated apical domain of the Escherichia coli GroEL subunit displays the ability to suppress the irreversible fibrillation of numerous amyloid-forming polypeptides. In previous experiments, we have shown that mutating Gly-192 (located at hinge II that connects the apical domain and the intermediate domain) to a tryptophan results in an inactive chaperonin whose apical domain is disoriented. In this study, we have utilized this disruptive effect of Gly-192 mutation to our advantage, by substituting this residue with amino acid residues of varying van der Waals volumes with the intent to modulate the affinity of GroEL toward fibrillogenic peptides. The affinities of GroEL toward fibrillogenic polypeptides such as Aβ(1-40) (amyloid-β(1-40)) peptide and α-synuclein increased in accordance to the larger van der Waals volume of the substituent amino acid side chain in the G192X mutants. When we compared the effects of wild-type GroEL and selected GroEL G192X mutants on α-synuclein fibril formation, we found that the effects of the chaperonin on α-synuclein fibrillation were different; the wild-type chaperonin caused changes in both the initial lag phase and the rate of fibril extension, whereas the effects of the G192X mutants were more specific toward the nucleus-forming lag phase. The chaperonins also displayed differential effects on α-synuclein fibril morphology, suggesting that through mutation of Gly-192, we may induce changes to the intermolecular affinities between GroEL and α-synuclein, leading to more efficient fibril suppression, and in specific cases, modulation of fibril morphology. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Structural and Functional Adaptation of Vancomycin Resistance VanT Serine Racemases

PubMed Central

Meziane-Cherif, Djalal; Stogios, Peter J.; Evdokimova, Elena; Egorova, Olga

2015-01-01

ABSTRACT Vancomycin resistance in Gram-positive bacteria results from the replacement of the d-alanyl–d-alanine target of peptidoglycan precursors with d-alanyl–d-lactate or d-alanyl–d-serine (d-Ala-d-Ser), to which vancomycin has low binding affinity. VanT is one of the proteins required for the production of d-Ala-d-Ser-terminating precursors by converting l-Ser to d-Ser. VanT is composed of two domains, an N-terminal membrane-bound domain, likely involved in l-Ser uptake, and a C-terminal cytoplasmic catalytic domain which is related to bacterial alanine racemases. To gain insight into the molecular function of VanT, the crystal structure of the catalytic domain of VanTG from VanG-type resistant Enterococcus faecalis BM4518 was determined. The structure showed significant similarity to type III pyridoxal 5′-phosphate (PLP)-dependent alanine racemases, which are essential for peptidoglycan synthesis. Comparative structural analysis between VanTG and alanine racemases as well as site-directed mutagenesis identified three specific active site positions centered around Asn696 which are responsible for the l-amino acid specificity. This analysis also suggested that VanT racemases evolved from regular alanine racemases by acquiring additional selectivity toward serine while preserving that for alanine. The 4-fold-lower relative catalytic efficiency of VanTG against l-Ser versus l-Ala implied that this enzyme relies on its membrane-bound domain for l-Ser transport to increase the overall rate of d-Ser production. These findings illustrate how vancomycin pressure selected for molecular adaptation of a housekeeping enzyme to a bifunctional enzyme to allow for peptidoglycan remodeling, a strategy increasingly observed in antibiotic-resistant bacteria. PMID:26265719

Structural and functional adaptation of vancomycin resistance VanT serine racemases

DOE PAGES

Meziane-Cherif, Djalal; Stogios, Peter J.; Evdokimova, Elena; ...

2015-08-11

Vancomycin resistance in Gram-positive bacteria results from the replacement of the D-alanyl–D-alanine target of peptidoglycan precursors with D-alanyl–D-lactate or D-alanyl–D-serine (D-Ala-D-Ser), to which vancomycin has low binding affinity. VanT is one of the proteins required for the production of D-Ala-D-Ser-terminating precursors by converting L-Ser to D-Ser. VanT is composed of two domains, an N-terminal membrane-bound domain, likely involved in L-Ser uptake, and a C-terminal cytoplasmic catalytic domain which is related to bacterial alanine racemases. To gain insight into the molecular function of VanT, the crystal structure of the catalytic domain of VanT G from VanG-type resistant Enterococcus faecalis BM4518more » was determined. The structure showed significant similarity to type III pyridoxal 5'-phosphate (PLP)-dependent alanine racemases, which are essential for peptidoglycan synthesis. Comparative structural analysis between VanT G and alanine racemases as well as site-directed mutagenesis identified three specific active site positions centered around Asn 696 which are responsible for theL-amino acid specificity. This analysis also suggested that VanT racemases evolved from regular alanine racemases by acquiring additional selectivity toward serine while preserving that for alanine. The 4-fold-lower relative catalytic efficiency of VanT G against L-Ser versus L-Ala implied that this enzyme relies on its membrane-bound domain for L-Ser transport to increase the overall rate of D-Ser production. These findings illustrate how vancomycin pressure selected for molecular adaptation of a housekeeping enzyme to a bifunctional enzyme to allow for peptidoglycan remodeling, a strategy increasingly observed in antibiotic-resistant bacteria.« less

The Bcr Kinase Downregulates Ras Signaling by Phosphorylating AF-6 and Binding to Its PDZ Domain

PubMed Central

Radziwill, G.; Erdmann, R. A.; Margelisch, U.; Moelling, K.

2003-01-01

The protein kinase Bcr is a negative regulator of cell proliferation and oncogenic transformation. We identified Bcr as a ligand for the PDZ domain of the cell junction and Ras-interacting protein AF-6. The Bcr kinase phosphorylates AF-6, which subsequently allows efficient binding of Bcr to AF-6, showing that the Bcr kinase is a regulator of the PDZ domain-ligand interaction. Bcr and AF-6 colocalize in epithelial cells at the plasma membrane. In addition, Bcr, AF-6, and Ras form a trimeric complex. Bcr increases the affinity of AF-6 to Ras, and a mutant of AF-6 that lacks a specific phosphorylation site for Bcr shows a reduced binding to Ras. Wild-type Bcr, but not Bcr mutants defective in binding to AF-6, interferes with the Ras-dependent stimulation of the Raf/MEK/ERK pathway. Since AF-6 binds to Bcr via its PDZ domain and to Ras via its Ras-binding domain, we propose that AF-6 functions as a scaffold-like protein that links Bcr and Ras to cellular junctions. We suggest that this trimeric complex is involved in downregulation of Ras-mediated signaling at sites of cell-cell contact to maintain cells in a nonproliferating state. PMID:12808105

Oligosaccharide Binding in Escherichia coli Glycogen Synthase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sheng, Fang; Yep, Alejandra; Feng, Lei

2010-11-17

Glycogen/starch synthase elongates glucan chains and is the key enzyme in the synthesis of glycogen in bacteria and starch in plants. Cocrystallization of Escherichia coli wild-type glycogen synthase (GS) with substrate ADPGlc and the glucan acceptor mimic HEPPSO produced a closed form of GS and suggests that domain-domain closure accompanies glycogen synthesis. Cocrystallization of the inactive GS mutant E377A with substrate ADPGlc and oligosaccharide results in the first oligosaccharide-bound glycogen synthase structure. Four bound oligosaccharides are observed, one in the interdomain cleft (G6a) and three on the N-terminal domain surface (G6b, G6c, and G6d). Extending from the center of themore » enzyme to the interdomain cleft opening, G6a mostly interacts with the highly conserved N-terminal domain residues lining the cleft of GS. The surface-bound oligosaccharides G6c and G6d have less interaction with enzyme and exhibit a more curled, helixlike structural arrangement. The observation that oligosaccharides bind only to the N-terminal domain of GS suggests that glycogen in vivo probably binds to only one side of the enzyme to ensure unencumbered interdomain movement, which is required for efficient, continuous glucan-chain synthesis.« less

Secretion of the Intimin Passenger Domain Is Driven by Protein Folding*

PubMed Central

Leo, Jack C.; Oberhettinger, Philipp; Yoshimoto, Shogo; Udatha, D. B. R. K. Gupta; Morth, J. Preben; Schütz, Monika; Hori, Katsutoshi

2016-01-01

Intimin is an essential adhesin of attaching and effacing organisms such as entropathogenic Escherichia coli. It is also the prototype of type Ve secretion or inverse autotransport, where the extracellular C-terminal region or passenger is exported with the help of an N-terminal transmembrane β-barrel domain. We recently reported a stalled secretion intermediate of intimin, where the passenger is located in the periplasm but the β-barrel is already inserted into the membrane. Stalling of this mutant is due to the insertion of an epitope tag at the very N terminus of the passenger. Here, we examined how this insertion disrupts autotransport and found that it causes misfolding of the N-terminal immunoglobulin (Ig)-like domain D00. We could also stall the secretion by making an internal deletion in D00, and introducing the epitope tag into the second Ig-like domain, D0, also resulted in reduced passenger secretion. In contrast to many classical autotransporters, where a proximal folding core in the passenger is required for secretion, the D00 domain is dispensable, as the passenger of an intimin mutant lacking D00 entirely is efficiently exported. Furthermore, the D00 domain is slightly less stable than the D0 and D1 domains, unfolding at ∼200 piconewtons (pN) compared with ∼250 pN for D0 and D1 domains as measured by atomic force microscopy. Our results support a model where the secretion of the passenger is driven by sequential folding of the extracellular Ig-like domains, leading to vectorial transport of the passenger domain across the outer membrane in an N to C direction. PMID:27466361

Structure-guided systems-level engineering of oxidation-prone methionine residues in catalytic domain of an alkaline α-amylase from Alkalimonas amylolytica for significant improvement of both oxidative stability and catalytic efficiency.

PubMed

Yang, Haiquan; Liu, Long; Shin, Hyun-dong; Li, Jianghua; Du, Guocheng; Chen, Jian

2013-01-01

High oxidative stability and catalytic efficiency are required for the alkaline α-amylases to keep the enzymatic performance under the harsh conditions in detergent industries. In this work, we attempted to significantly improve both the oxidative stability and catalytic efficiency of an alkaline α-amylase from Alkalimonas amylolytica by engineering the five oxidation-prone methionine residues around the catalytic domain via a systematic approach. Specifically, based on the tertiary structure analysis, five methionines (Met 145, Met 214, Met 229, Met 247 and Met 317) were individually substituted with oxidation-resistant threonine, isoleucine and alaline, respectively. Among the created 15 mutants, 7 mutants M145A, M145I, M214A, M229A, M229T, M247T and M317I showed significantly enhanced oxidative stability or catalytic efficiency. In previous work, we found that the replacement of M247 with leucine could significantly improve the oxidative stability. Thus, these 8 positive mutants (M145A, M145I, M214A, M229A, M229T, M247T, M247L and M317I) were used to conduct the second round of combinational mutations. Among the constructed 85 mutants (25 two-point mutants, 36 three-point mutants, 16 four-point mutants and 8 five-point mutants), the mutant M145I-214A-229T-247T-317I showed a 5.4-fold increase in oxidative stability and a 3.0-fold increase in catalytic efficiency. Interestingly, the specific activity, alkaline stability and thermal stability of this mutant were also increased. The increase of salt bridge and hydrogen bonds around the catalytic domain contributed to the significantly improved catalytic efficiency and stability, as revealed by the three-dimensional structure model of wild-type alkaline α-amylase and its mutant M145I-214A-229T-247T-317I. With the significantly improved oxidative stability and catalytic efficiency, the mutant M145I-214A-229T-247T-317I has a great potential as a detergent additive, and this structure-guided systems engineering strategy may be useful for the protein engineering of the other microbial enzymes to fulfill industrial requirements.

Automatic domain updating technique for improving computational efficiency of 2-D flood-inundation simulation

NASA Astrophysics Data System (ADS)

Tanaka, T.; Tachikawa, Y.; Ichikawa, Y.; Yorozu, K.

2017-12-01

Flood is one of the most hazardous disasters and causes serious damage to people and property around the world. To prevent/mitigate flood damage through early warning system and/or river management planning, numerical modelling of flood-inundation processes is essential. In a literature, flood-inundation models have been extensively developed and improved to achieve flood flow simulation with complex topography at high resolution. With increasing demands on flood-inundation modelling, its computational burden is now one of the key issues. Improvements of computational efficiency of full shallow water equations are made from various perspectives such as approximations of the momentum equations, parallelization technique, and coarsening approaches. To support these techniques and more improve the computational efficiency of flood-inundation simulations, this study proposes an Automatic Domain Updating (ADU) method of 2-D flood-inundation simulation. The ADU method traces the wet and dry interface and automatically updates the simulation domain in response to the progress and recession of flood propagation. The updating algorithm is as follow: first, to register the simulation cells potentially flooded at initial stage (such as floodplains nearby river channels), and then if a registered cell is flooded, to register its surrounding cells. The time for this additional process is saved by checking only cells at wet and dry interface. The computation time is reduced by skipping the processing time of non-flooded area. This algorithm is easily applied to any types of 2-D flood inundation models. The proposed ADU method is implemented to 2-D local inertial equations for the Yodo River basin, Japan. Case studies for two flood events show that the simulation is finished within two to 10 times smaller time showing the same result as that without the ADU method.

PLATSIM: An efficient linear simulation and analysis package for large-order flexible systems

NASA Technical Reports Server (NTRS)

Maghami, Periman; Kenny, Sean P.; Giesy, Daniel P.

1995-01-01

PLATSIM is a software package designed to provide efficient time and frequency domain analysis of large-order generic space platforms implemented with any linear time-invariant control system. Time domain analysis provides simulations of the overall spacecraft response levels due to either onboard or external disturbances. The time domain results can then be processed by the jitter analysis module to assess the spacecraft's pointing performance in a computationally efficient manner. The resulting jitter analysis algorithms have produced an increase in speed of several orders of magnitude over the brute force approach of sweeping minima and maxima. Frequency domain analysis produces frequency response functions for uncontrolled and controlled platform configurations. The latter represents an enabling technology for large-order flexible systems. PLATSIM uses a sparse matrix formulation for the spacecraft dynamics model which makes both the time and frequency domain operations quite efficient, particularly when a large number of modes are required to capture the true dynamics of the spacecraft. The package is written in MATLAB script language. A graphical user interface (GUI) is included in the PLATSIM software package. This GUI uses MATLAB's Handle graphics to provide a convenient way for setting simulation and analysis parameters.

Health Systems Science Curricula in Undergraduate Medical Education: Identifying and Defining a Potential Curricular Framework.

PubMed

Gonzalo, Jed D; Dekhtyar, Michael; Starr, Stephanie R; Borkan, Jeffrey; Brunett, Patrick; Fancher, Tonya; Green, Jennifer; Grethlein, Sara Jo; Lai, Cindy; Lawson, Luan; Monrad, Seetha; O'Sullivan, Patricia; Schwartz, Mark D; Skochelak, Susan

2017-01-01

The authors performed a review of 30 Accelerating Change in Medical Education full grant submissions and an analysis of the health systems science (HSS)-related curricula at the 11 grant recipient schools to develop a potential comprehensive HSS curricular framework with domains and subcategories. In phase 1, to identify domains, grant submissions were analyzed and coded using constant comparative analysis. In phase 2, a detailed review of all existing and planned syllabi and curriculum documents at the grantee schools was performed, and content in the core curricular domains was coded into subcategories. The lead investigators reviewed and discussed drafts of the categorization scheme, collapsed and combined domains and subcategories, and resolved disagreements via group discussion. Analysis yielded three types of domains: core, cross-cutting, and linking. Core domains included health care structures and processes; health care policy, economics, and management; clinical informatics and health information technology; population and public health; value-based care; and health system improvement. Cross-cutting domains included leadership and change agency; teamwork and interprofessional education; evidence-based medicine and practice; professionalism and ethics; and scholarship. One linking domain was identified: systems thinking. This broad framework aims to build on the traditional definition of systems-based practice and highlight the need for medical and other health professions schools to better align education programs with the anticipated needs of the systems in which students will practice. HSS will require a critical investigation into existing curricula to determine the most efficient methods for integration with the basic and clinical sciences.

Golgi retention of a trans-Golgi membrane protein, galactosyltransferase, requires cysteine and histidine residues within the membrane-anchoring domain.

PubMed

Aoki, D; Lee, N; Yamaguchi, N; Dubois, C; Fukuda, M N

1992-05-15

Galactosyltransferase (GT; UDPgalactose:beta-D-N-acetylglucosaminide beta-1,4-galactosyltransferase, EC 2.4.1.22) is a type II membrane-anchored protein composed of a short N-terminal cytoplasmic tail, a signal/membrane-anchoring domain, and a stem region followed by a large catalytic domain including the C terminus. To identify the peptide segment and key amino acid residues that are critical for Golgi localization of GT, the expression vector pGT-hCG was designed to encode the entire GT molecule fused to the C-terminal region of human chorionic gonadotropin alpha subunit (hCG alpha) as a reporter. COS-1 cells transfected with pGT-hCG expressed the chimera in the Golgi region, as detected by immunofluorescence microscopy using anti-hCG antibodies. Two deletion mutants, delta tail and delta stem, which are lacking most of the N-terminal cytoplasmic tail or 10 amino acids immediately after the membrane-anchoring domain, were localized in the Golgi. Replacement mutations of the membrane-anchoring domain of GT showed that the second quarter of the transmembrane domain or Cys29-Ala30-Leu31-His32-Leu33 is necessary for GT to be retained in the Golgi. Furthermore, the point mutants Cys29----Ser29 and His32----Leu32 were partially transported to the plasma membrane, whereas an Ala30-Leu31----Phe30-Gly31 mutant was localized in the Golgi. Finally, a double mutant, Cys29/His32----Ser29/Leu32, was found to be transported efficiently to the plasma membrane. The signal-anchoring domain of the transferrin receptor, a type II plasma membrane protein, was then replaced by portions of the GT transmembrane domain. Although the Cys-Xaa-Xaa-His sequence by itself cannot retain the transferrin receptor in the Golgi, the cytoplasmic half of the transmembrane domain of GT was partially capable of retaining the transferrin receptor in the Golgi. These results suggest that the cytoplasmic (or N-terminal) half of the transmembrane domain of GT contributes to the Golgi retention signal and that particularly Cys29 and His32 in this region are critical for GT to be retained in the Golgi.

Golgi retention of a trans-Golgi membrane protein, galactosyltransferase, requires cysteine and histidine residues within the membrane-anchoring domain.

PubMed Central

Aoki, D; Lee, N; Yamaguchi, N; Dubois, C; Fukuda, M N

1992-01-01

Galactosyltransferase (GT; UDPgalactose:beta-D-N-acetylglucosaminide beta-1,4-galactosyltransferase, EC 2.4.1.22) is a type II membrane-anchored protein composed of a short N-terminal cytoplasmic tail, a signal/membrane-anchoring domain, and a stem region followed by a large catalytic domain including the C terminus. To identify the peptide segment and key amino acid residues that are critical for Golgi localization of GT, the expression vector pGT-hCG was designed to encode the entire GT molecule fused to the C-terminal region of human chorionic gonadotropin alpha subunit (hCG alpha) as a reporter. COS-1 cells transfected with pGT-hCG expressed the chimera in the Golgi region, as detected by immunofluorescence microscopy using anti-hCG antibodies. Two deletion mutants, delta tail and delta stem, which are lacking most of the N-terminal cytoplasmic tail or 10 amino acids immediately after the membrane-anchoring domain, were localized in the Golgi. Replacement mutations of the membrane-anchoring domain of GT showed that the second quarter of the transmembrane domain or Cys29-Ala30-Leu31-His32-Leu33 is necessary for GT to be retained in the Golgi. Furthermore, the point mutants Cys29----Ser29 and His32----Leu32 were partially transported to the plasma membrane, whereas an Ala30-Leu31----Phe30-Gly31 mutant was localized in the Golgi. Finally, a double mutant, Cys29/His32----Ser29/Leu32, was found to be transported efficiently to the plasma membrane. The signal-anchoring domain of the transferrin receptor, a type II plasma membrane protein, was then replaced by portions of the GT transmembrane domain. Although the Cys-Xaa-Xaa-His sequence by itself cannot retain the transferrin receptor in the Golgi, the cytoplasmic half of the transmembrane domain of GT was partially capable of retaining the transferrin receptor in the Golgi. These results suggest that the cytoplasmic (or N-terminal) half of the transmembrane domain of GT contributes to the Golgi retention signal and that particularly Cys29 and His32 in this region are critical for GT to be retained in the Golgi. Images PMID:1584766

Independent regulation of reovirus membrane penetration and apoptosis by the mu1 phi domain.

PubMed

Danthi, Pranav; Coffey, Caroline M; Parker, John S L; Abel, Ty W; Dermody, Terence S

2008-12-01

Apoptosis plays an important role in the pathogenesis of reovirus encephalitis. Reovirus outer-capsid protein mu1, which functions to penetrate host cell membranes during viral entry, is the primary regulator of apoptosis following reovirus infection. Ectopic expression of full-length and truncated forms of mu1 indicates that the mu1 phi domain is sufficient to elicit a cell death response. To evaluate the contribution of the mu1 phi domain to the induction of apoptosis following reovirus infection, phi mutant viruses were generated by reverse genetics and analyzed for the capacity to penetrate cell membranes and elicit apoptosis. We found that mutations in phi diminish reovirus membrane penetration efficiency by preventing conformational changes that lead to generation of key reovirus entry intermediates. Independent of effects on membrane penetration, amino acid substitutions in phi affect the apoptotic potential of reovirus, suggesting that phi initiates apoptosis subsequent to cytosolic delivery. In comparison to wild-type virus, apoptosis-defective phi mutant viruses display diminished neurovirulence following intracranial inoculation of newborn mice. These results indicate that the phi domain of mu1 plays an important regulatory role in reovirus-induced apoptosis and disease.

Public-domain-software solution to data-access problems for numerical modelers

USGS Publications Warehouse

Jenter, Harry; Signell, Richard

1992-01-01

Unidata's network Common Data Form, netCDF, provides users with an efficient set of software for scientific-data-storage, retrieval, and manipulation. The netCDF file format is machine-independent, direct-access, self-describing, and in the public domain, thereby alleviating many problems associated with accessing output from large hydrodynamic models. NetCDF has programming interfaces in both the Fortran and C computer language with an interface to C++ planned for release in the future. NetCDF also has an abstract data type that relieves users from understanding details of the binary file structure; data are written and retrieved by an intuitive, user-supplied name rather than by file position. Users are aided further by Unidata's inclusion of the Common Data Language, CDL, a printable text-equivalent of the contents of a netCDF file. Unidata provides numerous operators and utilities for processing netCDF files. In addition, a number of public-domain and proprietary netCDF utilities from other sources are available at this time or will be available later this year. The U.S. Geological Survey has produced and is producing a number of public-domain netCDF utilities.

Oxygen reduction reaction on highly-durable Pt/nanographene fuel cell catalyst synthesized employing in-liquid plasma

NASA Astrophysics Data System (ADS)

Amano, Tomoki; Kondo, Hiroki; Takeda, Keigo; Ishikawa, Kenji; Kano, Hiroyuki; Hiramatsu, Mineo; Sekine, Makoto; Hori, Masaru

2016-09-01

We recently have established ultrahigh-speed synthesis method of nanographene materials employing in-liquid plasma, and reported high durability of Pt/nanographene composites as a fuel cell catalyst. Crystallinity and domain size of nanographene materials were essential to their durability. However, their mechanism is not clarified yet. In this study, we investigated the oxygen reduction reaction using three-types of nanographene materials with different crystallinity and domain sizes, which were synthesized using ethanol, 1-propanol and 1-butanol, respectively. According to our previous studies, the nanographene material synthesized using the lower molecular weight alcohol has the higher crystallinity and larger domain size. Pt nanoparticles were supported on the nanographene surfaces by reducing 8 wt% H2PtCl6 diluted with H2O. Oxygen reduction current densities at a potential of 0.2 V vs. RHE were 5.43, 5.19 and 3.69 mA/cm2 for the samples synthesized using ethanol, 1-propanol and 1-butanol, respectively. This means that the higher crystallinity nanographene showed the larger oxygen reduction current density. The controls of crystallinity and domain size of nanographene materials are essential to not only their durability but also highly efficiency as catalyst electrodes.

Low performance on mathematical tasks in preschoolers: the importance of domain-general and domain-specific abilities.

PubMed

Costa, H M; Nicholson, B; Donlan, C; Van Herwegen, J

2018-04-01

Different domain-specific and domain-general cognitive precursors play a key role in the development of mathematical abilities. The contribution of these domains to mathematical ability changes during development. Primary school-aged children who show mathematical difficulties form a heterogeneous group, but it is not clear whether this also holds for preschool low achievers (LAs) and how domain-specific and domain-general abilities contribute to mathematical difficulties at a young age. The aim of this study was to explore the cognitive characteristics of a sample of preschool LAs and identify sub-types of LAs. 81 children were identified as LAs from 283 preschoolers aged 3 to 5 years old and were assessed on a number of domain-general and domain-specific tasks. Cluster analysis revealed four subgroups of LAs in mathematics: (1) a weak processing sub-type; (2) a general mathematical LAs sub-type; (3) a mixed abilities sub-type; and (4) a visuo-spatial deficit sub-type. Whilst two of the groups showed specific domain-general difficulties, none showed only domain-specific difficulties. Current findings suggest that preschool LAs constitute a heterogeneous group and stress the importance of domain-general factors for the development of mathematical abilities during the preschool years. © 2018 MENCAP and International Association of the Scientific Study of Intellectual and Developmental Disabilities and John Wiley & Sons Ltd.

Adenovirus Type 5 Viral Particles Pseudotyped with Mutagenized Fiber Proteins Show Diminished Infectivity of Coxsackie B-Adenovirus Receptor-Bearing Cells

PubMed Central

Jakubczak, John L.; Rollence, Michele L.; Stewart, David A.; Jafari, Jonathon D.; Von Seggern, Dan J.; Nemerow, Glen R.; Stevenson, Susan C.; Hallenbeck, Paul L.

2001-01-01

A major limitation of adenovirus type 5 (Ad5)-based gene therapy, the inability to target therapeutic genes to selected cell types, is attributable to the natural tropism of the virus for the widely expressed coxsackievirus-adenovirus receptor (CAR) protein. Modifications of the Ad5 fiber knob domain have been shown to alter the tropism of the virus. We have developed a novel system to rapidly evaluate the function of modified fiber proteins in their most relevant context, the adenoviral capsid. This transient transfection/infection system combines transfection of cells with plasmids that express high levels of the modified fiber protein and infection with Ad5.βgal.ΔF, an E1-, E3-, and fiber-deleted adenoviral vector encoding β-galactosidase. We have used this system to test the adenoviral transduction efficiency mediated by a panel of fiber protein mutants that were proposed to influence CAR interaction. A series of amino acid modifications were incorporated via mutagenesis into the fiber expression plasmid, and the resulting fiber proteins were subsequently incorporated onto adenoviral particles. Mutations located in the fiber knob AB and CD loops demonstrated the greatest reduction in fiber-mediated gene transfer in HeLa cells. We also observed effects on transduction efficiency with mutations in the FG loop, indicating that the binding site may extend to the adjacent monomer in the fiber trimer and in the HI loop. These studies support the concept that modification of the fiber knob domain to diminish or ablate CAR interaction should result in a detargeted adenoviral vector that can be combined simultaneously with novel ligands for the development of a systemically administered, targeted adenoviral vector. PMID:11222722

A subthreshold aVLSI implementation of the Izhikevich simple neuron model.

PubMed

Rangan, Venkat; Ghosh, Abhishek; Aparin, Vladimir; Cauwenberghs, Gert

2010-01-01

We present a circuit architecture for compact analog VLSI implementation of the Izhikevich neuron model, which efficiently describes a wide variety of neuron spiking and bursting dynamics using two state variables and four adjustable parameters. Log-domain circuit design utilizing MOS transistors in subthreshold results in high energy efficiency, with less than 1pJ of energy consumed per spike. We also discuss the effects of parameter variations on the dynamics of the equations, and present simulation results that replicate several types of neural dynamics. The low power operation and compact analog VLSI realization make the architecture suitable for human-machine interface applications in neural prostheses and implantable bioelectronics, as well as large-scale neural emulation tools for computational neuroscience.

Characteristics of microstrip muscle-loaded single-arm Archimedean spiral antennas as investigated by FDTD numerical computations.

PubMed

Jacobsen, Svein; Rolfsnes, Hans Olav; Stauffer, Paul R

2005-02-01

The radiation characteristics and mode of operation of single-arm, groundplane backed, Archimedean spiral antennas are investigated by means of conformal finite difference time domain numerical analysis. It is shown that this antenna type may be categorized as a well-matched, broadband, circularly polarized traveling wave structure that can be fed directly by nonbalanced coaxial networks. The study further concentrates on relevant design and description features parameterized in terms of measures like radiation efficiency, sensing depth, directivity, and axial ratio of complementary polarizations. We document that an antenna of only 30-mm transverse size produces circularly polarized waves in a two-octave frequency span (2-8 GHz) with acceptable radiation efficiency (76%-94%) when loaded by muscle-like tissue.

CCOMP: An efficient algorithm for complex roots computation of determinantal equations

NASA Astrophysics Data System (ADS)

Zouros, Grigorios P.

2018-01-01

In this paper a free Python algorithm, entitled CCOMP (Complex roots COMPutation), is developed for the efficient computation of complex roots of determinantal equations inside a prescribed complex domain. The key to the method presented is the efficient determination of the candidate points inside the domain which, in their close neighborhood, a complex root may lie. Once these points are detected, the algorithm proceeds to a two-dimensional minimization problem with respect to the minimum modulus eigenvalue of the system matrix. In the core of CCOMP exist three sub-algorithms whose tasks are the efficient estimation of the minimum modulus eigenvalues of the system matrix inside the prescribed domain, the efficient computation of candidate points which guarantee the existence of minima, and finally, the computation of minima via bound constrained minimization algorithms. Theoretical results and heuristics support the development and the performance of the algorithm, which is discussed in detail. CCOMP supports general complex matrices, and its efficiency, applicability and validity is demonstrated to a variety of microwave applications.

Paired D10A Cas9 nickases are sometimes more efficient than individual nucleases for gene disruption.

PubMed

Gopalappa, Ramu; Suresh, Bharathi; Ramakrishna, Suresh; Kim, Hyongbum Henry

2018-03-23

The use of paired Cas9 nickases instead of Cas9 nuclease drastically reduces off-target effects. Because both nickases must function for a nickase pair to make a double-strand break, the efficiency of paired nickases can intuitively be expected to be lower than that of either corresponding nuclease alone. Here, we carefully compared the gene-disrupting efficiency of Cas9 paired nickases with that of nucleases. Interestingly, the T7E1 assay and deep sequencing showed that on-target efficiency of paired D10A Cas9 nickases was frequently comparable, but sometimes higher than that of either corresponding nucleases in mammalian cells. As the underlying mechanism, we found that the HNH domain, which is preserved in the D10A Cas9 nickase, has higher activity than the RuvC domain in mammalian cells. In this study, we showed: (i) the in vivo cleavage efficiency of the HNH domain of Cas9 in mammalian cells is higher than that of the RuvC domain, (ii) paired Cas9 nickases are sometimes more efficient than individual nucleases for gene disruption. We envision that our findings which were overlooked in previous reports will serve as a new potential guideline for tool selection for CRISPR-Cas9-mediated gene disruption, facilitating efficient and precise genome editing.

Use of a near-field optical probe to locally launch surface plasmon polaritons on plasmonic waveguides: a study by the finite difference time domain method.

PubMed

Hwang, B S; Kwon, M H; Kim, Jeongyong

2004-08-01

We used the finite difference time domain (FDTD) method to study the use of scanning near field optical microscopy (SNOM) to locally excite the nanometric plasmonic waveguides. In our calculation, the light is funneled through a SNOM probe with a sub-wavelength optical aperture and is irradiated on one end of two types of plasmonic waveguides made of 50 nm Au sphere arrays and Au nanowires. The incident light was well localized at one end of the waveguides and consequently propagated toward the other end, due to the excitation of surface plasmon polaritons. We found that the propagation length of the nanosphere array type waveguide varies from 100 to 130 nm depending on the light wavelength, the size of the probe aperture, and the launching heights. Our result shows that reducing the aperture size and using the light of the plasmon resonance wavelength of the nanosphere array could increase the propagation length and, thus, the efficiency of electromagnetic energy transportation through nanosphere arrays. 2004 Wiley-Liss, Inc.

Identification of an Essential Region for Translocation of Clostridium difficile Toxin B.

PubMed

Chen, Shuyi; Wang, Haiying; Gu, Huawei; Sun, Chunli; Li, Shan; Feng, Hanping; Wang, Jufang

2016-08-15

Clostridium difficile toxin A (TcdA) and toxin B (TcdB) are the major virulence factors involved in C. difficile-associated diarrhea and pseudomembranous colitis. TcdA and TcdB both contain at least four distinct domains: the glucosyltransferase domain, cysteine protease domain, receptor binding domain, and translocation domain. Few studies have investigated the translocation domain and its mechanism of action. Recently, it was demonstrated that a segment of 97 amino acids (AA 1756-1852, designated D97) within the translocation domain of TcdB is essential for the in vitro and in vivo toxicity of TcdB. However, the mechanism by which D97 regulates the action of TcdB in host cells and the important amino acids within this region are unknown. In this study, we discovered that a smaller fragment, amino acids 1756-1780, located in the N-terminus of the D97 fragment, is essential for translocation of the effector glucosyltransferase domain into the host cytosol. A sequence of 25AA within D97 is predicted to form an alpha helical structure and is the critical part of D97. The deletion mutant TcdB∆1756-1780 showed similar glucosyltransferase and cysteine protease activity, cellular binding, and pore formation to wild type TcdB, but it failed to induce the glucosylation of Rho GTPase Rac1 of host cells. Moreover, we found that TcdB∆1756-1780 was rapidly degraded in the endosome of target cells, and therefore its intact glucosyltransferase domain was unable to translocate efficiently into host cytosol. Our finding provides an insight into the molecular mechanisms of action of TcdB in the intoxication of host cells.

The interdomain interface in bifunctional enzyme protein 3/4A (NS3/4A) regulates protease and helicase activities.

PubMed

Aydin, Cihan; Mukherjee, Sourav; Hanson, Alicia M; Frick, David N; Schiffer, Celia A

2013-12-01

Hepatitis C (HCV) protein 3/4A (NS3/4A) is a bifunctional enzyme comprising two separate domains with protease and helicase activities, which are essential for viral propagation. Both domains are stable and have enzymatic activity separately, and the relevance and implications of having protease and helicase together as a single protein remains to be explored. Altered in vitro activities of isolated domains compared with the full-length NS3/4A protein suggest the existence of interdomain communication. The molecular mechanism and extent of this communication was investigated by probing the domain-domain interface observed in HCV NS3/4A crystal structures. We found in molecular dynamics simulations that the two domains of NS3/4A are dynamically coupled through the interface. Interestingly, mutations designed to disrupt this interface did not hinder the catalytic activities of either domain. In contrast, substrate cleavage and DNA unwinding by these mutants were mostly enhanced compared with the wild-type protein. Disrupting the interface did not significantly alter RNA unwinding activity; however, the full-length protein was more efficient in RNA unwinding than the isolated protease domain, suggesting a more direct role in RNA processing independent of the interface. Our findings suggest that HCV NS3/4A adopts an "extended" catalytically active conformation, and interface formation acts as a switch to regulate activity. We propose a unifying model connecting HCV NS3/4A conformational states and protease and helicase function, where interface formation and the dynamic interplay between the two enzymatic domains of HCV NS3/4A potentially modulate the protease and helicase activities in vivo. © 2013 The Protein Society.

Murine Coronavirus Ubiquitin-Like Domain Is Important for Papain-Like Protease Stability and Viral Pathogenesis

PubMed Central

Mielech, Anna M.; Deng, Xufang; Chen, Yafang; Kindler, Eveline; Wheeler, Dorthea L.; Mesecar, Andrew D.; Thiel, Volker; Perlman, Stanley

2015-01-01

ABSTRACT Ubiquitin-like domains (Ubls) now are recognized as common elements adjacent to viral and cellular proteases; however, their function is unclear. Structural studies of the papain-like protease (PLP) domains of coronaviruses (CoVs) revealed an adjacent Ubl domain in severe acute respiratory syndrome CoV, Middle East respiratory syndrome CoV, and the murine CoV, mouse hepatitis virus (MHV). Here, we tested the effect of altering the Ubl adjacent to PLP2 of MHV on enzyme activity, viral replication, and pathogenesis. Using deletion and substitution approaches, we identified sites within the Ubl domain, residues 785 to 787 of nonstructural protein 3, which negatively affect protease activity, and valine residues 785 and 787, which negatively affect deubiquitinating activity. Using reverse genetics, we engineered Ubl mutant viruses and found that AM2 (V787S) and AM3 (V785S) viruses replicate efficiently at 37°C but generate smaller plaques than wild-type (WT) virus, and AM2 is defective for replication at higher temperatures. To evaluate the effect of the mutation on protease activity, we purified WT and Ubl mutant PLP2 and found that the proteases exhibit similar specific activities at 25°C. However, the thermal stability of the Ubl mutant PLP2 was significantly reduced at 30°C, thereby reducing the total enzymatic activity. To determine if the destabilizing mutation affects viral pathogenesis, we infected C57BL/6 mice with WT or AM2 virus and found that the mutant virus is highly attenuated, yet it replicates sufficiently to elicit protective immunity. These studies revealed that modulating the Ubl domain adjacent to the PLP reduces protease stability and viral pathogenesis, revealing a novel approach to coronavirus attenuation. IMPORTANCE Introducing mutations into a protein or virus can have either direct or indirect effects on function. We asked if changes in the Ubl domain, a conserved domain adjacent to the coronavirus papain-like protease, altered the viral protease activity or affected viral replication or pathogenesis. Our studies using purified wild-type and Ubl mutant proteases revealed that mutations in the viral Ubl domain destabilize and inactivate the adjacent viral protease. Furthermore, we show that a CoV encoding the mutant Ubl domain is unable to replicate at high temperature or cause lethal disease in mice. Our results identify the coronavirus Ubl domain as a novel modulator of viral protease stability and reveal manipulating the Ubl domain as a new approach for attenuating coronavirus replication and pathogenesis. PMID:25694594

Histone Code Modulation by Oncogenic PWWP-Domain Protein in Breast Cancers

DTIC Science & Technology

2010-06-01

athanogene 4 * DDHD2 DDHD domain containing 2 * PPAPDC1B phosphatidic acid phosphatase type 2 domain containing 1B * WHSC1L1 Wolf-Hirschhorn syndrome...from alternative splicing of exon 10. The WHSC1L1 long isoform encodes a 1437 amino acid protein containing 2 PWWP domains, 2 PHD-type zinc finger...motifs, a TANG2 domain, an AWS domain and a SET domain. The short isoform encodes a 645 amino acid protein containing a PWWP domain only. Our western

Photo dynamics of BLUF domain mutant H44R of AppA from Rhodobacter sphaeroides

NASA Astrophysics Data System (ADS)

Zirak, P.; Penzkofer, A.; Hegemann, P.; Mathes, T.

2007-05-01

The photo-cycle dynamics of the H44R mutant of the BLUF domain of the transcriptional anti-repressor protein AppA (AppA-H44R) from the non-sulfur anoxyphototropic purple bacterium Rhodobacter sphaeroides is studied in order to gain information on the involvement of His44 in the photo-cyclic mechanism of the AppA BLUF domain and to add information to the involved processes. The amino acid residue histidine at position 44 is replaced by arginine. A 12 nm red-shifted signalling state is formed upon blue-light excitation, while in wild-type AppA (AppA-wt) the red-shift is 16 nm. The recovery to the receptor dark state is approximately a factor of 2.5 faster ( τrec ≈ 6.5 min) than the recovery of the wild-type counterpart. Extended light exposure of the mutant causes photo-degradation of flavin (mainly free flavin conversion to lumichrome and re-equilibration between free and non-covalently bound flavin) and protein aggregation (showing up as light scattering). No photo-degradation was observed for AppA-wt. The quantum efficiency of signalling-state formation determined by intensity dependent absorption measurements is found to be ϕs ≈ 0.3 (for AppA-wt: ϕs ≈ 0.24). A two-component single-exponential fluorescence relaxation was observed, which is interpreted as fast fluorescence quenching to an equilibrium value by photo-induced electron transfer followed by slower fluorescence decay due to charge recombination. Based on the experimental findings, an extended photo-cycle model for BLUF domains is proposed.

Domain wall in a quantum anomalous Hall insulator as a magnetoelectric piston

NASA Astrophysics Data System (ADS)

Upadhyaya, Pramey; Tserkovnyak, Yaroslav

2016-07-01

We theoretically study the magnetoelectric coupling in a quantum anomalous Hall insulator state induced by interfacing a dynamic magnetization texture to a topological insulator. In particular, we propose that the quantum anomalous Hall insulator with a magnetic configuration of a domain wall, when contacted by electrical reservoirs, acts as a magnetoelectric piston. A moving domain wall pumps charge current between electrical leads in a closed circuit, while applying an electrical bias induces reciprocal domain-wall motion. This pistonlike action is enabled by a finite reflection of charge carriers via chiral modes imprinted by the domain wall. Moreover, we find that, when compared with the recently discovered spin-orbit torque-induced domain-wall motion in heavy metals, the reflection coefficient plays the role of an effective spin-Hall angle governing the efficiency of the proposed electrical control of domain walls. Quantitatively, this effective spin-Hall angle is found to approach a universal value of 2, providing an efficient scheme to reconfigure the domain-wall chiral interconnects for possible memory and logic applications.

A Domain Decomposition Parallelization of the Fast Marching Method

NASA Technical Reports Server (NTRS)

Herrmann, M.

2003-01-01

In this paper, the first domain decomposition parallelization of the Fast Marching Method for level sets has been presented. Parallel speedup has been demonstrated in both the optimal and non-optimal domain decomposition case. The parallel performance of the proposed method is strongly dependent on load balancing separately the number of nodes on each side of the interface. A load imbalance of nodes on either side of the domain leads to an increase in communication and rollback operations. Furthermore, the amount of inter-domain communication can be reduced by aligning the inter-domain boundaries with the interface normal vectors. In the case of optimal load balancing and aligned inter-domain boundaries, the proposed parallel FMM algorithm is highly efficient, reaching efficiency factors of up to 0.98. Future work will focus on the extension of the proposed parallel algorithm to higher order accuracy. Also, to further enhance parallel performance, the coupling of the domain decomposition parallelization to the G(sub 0)-based parallelization will be investigated.

Finite size effects in ferroelectric-semiconductor thin films under open-circuit electric boundary conditions

DOE PAGES

Eliseev, Eugene A.; Kalinin, Sergei V.; Morozovska, Anna N.

2015-01-21

General features of finite size effects in the ferroelectric-semiconductor film under open-circuit electric boundary conditions are analyzed using Landau-Ginzburg-Devonshire theory and continuum media electrostatics. The temperature dependence of the film critical thickness, spontaneous polarization and depolarization field profiles of the open-circuited films are found to be significantly different from the characteristics of short-circuited ones. In particular, we predict the re-entrant type transition boundary between the mono-domain and poly-domain ferroelectric states due to reduced internal screening efficiency and analyzed possible experimental scenarios created by this mechanism. Performed analysis is relevant for the quantitative description of free-standing ferroelectric films phase diagrams andmore » polar properties. Also our results can be useful for the explanation of the scanning-probe microscopy experiments on free ferroelectric surfaces.« less

Substructure coupling in the frequency domain

NASA Technical Reports Server (NTRS)

1985-01-01

Frequency domain analysis was found to be a suitable method for determining the transient response of systems subjected to a wide variety of loads. However, since a large number of calculations are performed within the discrete frequency loop, the method loses it computational efficiency if the loads must be represented by a large number of discrete frequencies. It was also discovered that substructure coupling in the frequency domain work particularly well for analyzing structural system with a small number of interface and loaded degrees of freedom. It was discovered that substructure coupling in the frequency domain can lead to an efficient method of obtaining natural frequencies of undamped structures. It was also found that the damped natural frequencies of a system may be determined using frequency domain techniques.

Tetravalent dengue DIIIC protein together with alum and ODN elicits a Th1 response and neutralizing antibodies in mice.

PubMed

Zuest, Roland; Valdes, Iris; Skibinski, David; Lin, Yufang; Toh, Ying Xiu; Chan, Katherine; Hermida, Lisset; Connolly, John; Guillen, Gerardo; Fink, Katja

2015-03-17

Dengue disease is a global challenge for healthcare systems particularly during outbreaks, and millions of dollars are spent every year for vector control. An efficient and safe vaccine that is cost-effective could resolve the burden that dengue virus imposes on affected countries. We describe here the immunogenicity of a tetravalent formulation of a recombinant fusion protein consisting of E domain III and the capsid protein of dengue serotypes 1-4 (Tetra DIIIC). E domain III is an epitope for efficient neutralizing antibodies while the capsid protein contains T cell epitopes. Besides combining B and T cell epitopes, Tetra DIIIC is highly immunogenic due to its aggregate form and a two-component adjuvant. Following previous studies assessing the monovalent DIIIC formulations, we addressed here the quality and breadth of the T cell- and antibody response of Tetra DIIIC in mice. Tetra DIIIC induced a Th1-type response against all four DENV serotypes and dengue-specific antibodies were predominantly IgG1 and IgG2a and neutralizing, while the induction of neutralizing antibodies was dependent on IFN signaling. Importantly, the Th1 and IgG1/IgG2a profile of the DIIIC vaccine approach is similar to an efficient natural anti-dengue response. Copyright © 2015 Elsevier Ltd. All rights reserved.

Turning Potential Flexibility Into Flexible Performance: Moderating Effect of Self-Efficacy and Use of Flexible Cognition

PubMed Central

Liu, Ru-De; Wang, Jia; Star, Jon R.; Zhen, Rui; Jiang, Rong-Huan; Fu, Xin-Chen

2018-01-01

This study examined the relationship between two types of mathematical flexibility – potential flexibility, which indicates individuals’ knowledge of multiple strategies and strategy efficiency, and practical flexibility, which refers to individuals’ flexible performances when solving math problems. Both types of flexibility were assessed in the domain of linear equation solving. Furthermore, two types of beliefs – self-efficacy and use of flexible cognition (UFC) – were investigated as potential moderators between potential and practical flexibility. 121 8th grade students from China took part in this study. Results indicate that potential flexibility positively predicted practical flexibility. Additionally, self-efficacy and UFC might moderate the relationship between these two types of flexibility, suggesting that potential flexibility may lead to different degrees of practical flexibility depending on different levels of beliefs. Implications of these findings for research on mathematical flexibility and for educational practice are discussed. PMID:29780344

RGAugury: a pipeline for genome-wide prediction of resistance gene analogs (RGAs) in plants.

PubMed

Li, Pingchuan; Quan, Xiande; Jia, Gaofeng; Xiao, Jin; Cloutier, Sylvie; You, Frank M

2016-11-02

Resistance gene analogs (RGAs), such as NBS-encoding proteins, receptor-like protein kinases (RLKs) and receptor-like proteins (RLPs), are potential R-genes that contain specific conserved domains and motifs. Thus, RGAs can be predicted based on their conserved structural features using bioinformatics tools. Computer programs have been developed for the identification of individual domains and motifs from the protein sequences of RGAs but none offer a systematic assessment of the different types of RGAs. A user-friendly and efficient pipeline is needed for large-scale genome-wide RGA predictions of the growing number of sequenced plant genomes. An integrative pipeline, named RGAugury, was developed to automate RGA prediction. The pipeline first identifies RGA-related protein domains and motifs, namely nucleotide binding site (NB-ARC), leucine rich repeat (LRR), transmembrane (TM), serine/threonine and tyrosine kinase (STTK), lysin motif (LysM), coiled-coil (CC) and Toll/Interleukin-1 receptor (TIR). RGA candidates are identified and classified into four major families based on the presence of combinations of these RGA domains and motifs: NBS-encoding, TM-CC, and membrane associated RLP and RLK. All time-consuming analyses of the pipeline are paralleled to improve performance. The pipeline was evaluated using the well-annotated Arabidopsis genome. A total of 98.5, 85.2, and 100 % of the reported NBS-encoding genes, membrane associated RLPs and RLKs were validated, respectively. The pipeline was also successfully applied to predict RGAs for 50 sequenced plant genomes. A user-friendly web interface was implemented to ease command line operations, facilitate visualization and simplify result management for multiple datasets. RGAugury is an efficiently integrative bioinformatics tool for large scale genome-wide identification of RGAs. It is freely available at Bitbucket: https://bitbucket.org/yaanlpc/rgaugury .

3D Structure and Interaction of p24β and p24δ Golgi Dynamics Domains: Implication for p24 Complex Formation and Cargo Transport.

PubMed

Nagae, Masamichi; Hirata, Tetsuya; Morita-Matsumoto, Kana; Theiler, Romina; Fujita, Morihisa; Kinoshita, Taroh; Yamaguchi, Yoshiki

2016-10-09

The p24 family consists of four subfamilies (p24α, p24β, p24γ, and p24δ), and the proteins are thought to form hetero-oligomeric complexes for efficient transport of cargo proteins from the endoplasmic reticulum to the Golgi apparatus. The proteins possess a conserved luminal Golgi dynamics (GOLD) domain, whose functions are largely unknown. Here, we present structural and biochemical studies of p24β1 and p24δ1 GOLD domains. Use of GOLD domain-deleted mutants revealed that the GOLD domain of p24δ1 is required for proper p24 hetero-oligomeric complex formation and efficient transport of GPI-anchored proteins. The p24β1 and p24δ1 GOLD domains share a common β-sandwich fold with a characteristic intrasheet disulfide bond. The GOLD domain of p24δ1 crystallized as dimers, allowing the analysis of a homophilic interaction site. Surface plasmon resonance and solution NMR analyses revealed that p24β1 and p24δ1 GOLD domains interact weakly (K d = ~10 -4 M). Bi-protein titration provided interaction site maps. We propose that the heterophilic interaction of p24 GOLD domains contributes to the formation of the p24 hetero-oligomeric complex and to efficient cargo transport. Copyright © 2016 Elsevier Ltd. All rights reserved.

Transformation-specific interaction of the bovine papillomavirus E5 oncoprotein with the platelet-derived growth factor receptor transmembrane domain and the epidermal growth factor receptor cytoplasmic domain.

PubMed Central

Cohen, B D; Goldstein, D J; Rutledge, L; Vass, W C; Lowy, D R; Schlegel, R; Schiller, J T

1993-01-01

The bovine papillomavirus E5 transforming protein appears to activate both the epidermal growth factor receptor (EGF-R) and the platelet-derived growth factor receptor (PDGF-R) by a ligand-independent mechanism. To further investigate the ability of E5 to activate receptors of different classes and to determine whether this stimulation occurs through the extracellular domain required for ligand activation, we constructed chimeric genes encoding PDGF-R and EGF-R by interchanging the extracellular, membrane, and cytoplasmic coding domains. Chimeras were transfected into NIH 3T3 and CHO(LR73) cells. All chimeras expressed stable protein which, upon addition of the appropriate ligand, could be activated as assayed by tyrosine autophosphorylation and biological transformation. Cotransfection of E5 with the wild-type and chimeric receptors resulted in the ligand-independent activation of receptors, provided that a receptor contained either the transmembrane domain of the PDGF-R or the cytoplasmic domain of the EGF-R. Chimeric receptors that contained both of these domains exhibited the highest level of E5-induced biochemical and biological stimulation. These results imply that E5 activates the PDGF-R and EGR-R by two distinct mechanisms, neither of which specifically involves the extracellular domain of the receptor. Consistent with the biochemical and biological activation data, coimmunoprecipitation studies demonstrated that E5 formed a complex with any chimera that contained a PDGF-R transmembrane domain or an EGF-R cytoplasmic domain, with those chimeras containing both domains demonstrating the greatest efficiency of complex formation. These results suggest that although different domains of the PDGF-R and EGF-R are required for E5 activation, both receptors are activated directly by formation of an E5-containing complex. Images PMID:8394451

Uniform rotating field network structure to efficiently package a magnetic bubble domain memory

NASA Technical Reports Server (NTRS)

Murray, Glen W. (Inventor); Chen, Thomas T. (Inventor); Wolfshagen, Ronald G. (Inventor); Ypma, John E. (Inventor)

1978-01-01

A unique and compact open coil rotating magnetic field network structure to efficiently package an array of bubble domain devices is disclosed. The field network has a configuration which effectively enables selected bubble domain devices from the array to be driven in a vertical magnetic field and in an independent and uniform horizontal rotating magnetic field. The field network is suitably adapted to minimize undesirable inductance effects, improve capabilities of heat dissipation, and facilitate repair or replacement of a bubble device.

Structure of the cytoplasmic domain of Yersinia pestis YscD, an essential component of the type III secretion system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lountos, George T.; Tropea, Joseph E.; Waugh, David S.

2012-09-17

The Yersinia pestis YscD protein is an essential component of the type III secretion system. YscD consists of an N-terminal cytoplasmic domain (residues 1-121), a transmembrane linker (122-142) and a large periplasmic domain (143-419). Both the cytoplasmic and the periplasmic domains are required for the assembly of the type III secretion system. Here, the structure of the YscD cytoplasmic domain solved by SAD phasing is presented. Although the three-dimensional structure is similar to those of forkhead-associated (FHA) domains, comparison with the structures of canonical FHA domains revealed that the cytoplasmic domain of YscD lacks the conserved residues that are requiredmore » for binding phosphothreonine and is therefore unlikely to function as a true FHA domain.« less

Myasthenia Gravis Impairment Index: Responsiveness, meaningful change, and relative efficiency.

PubMed

Barnett, Carolina; Bril, Vera; Kapral, Moira; Kulkarni, Abhaya V; Davis, Aileen M

2017-12-05

To study responsiveness and meaningful change of the Myasthenia Gravis Impairment Index (MGII) and its relative efficiency compared to other measures. We enrolled 95 patients receiving prednisone, IV immunoglobulin (IVIg), or plasma exchange (PLEX) and 54 controls. Patients were assessed with the MGII and other measures-including the Quantitative Myasthenia Gravis Score, Myasthenia Gravis Composite, and Myasthenia Gravis Activities of Daily Living-at baseline and 3-4 weeks after treatment. Statistical markers of responsiveness included between-groups and within-group differences, and we estimated the relative efficiency of the MGII compared to other measures. Patient-meaningful change was assessed with an anchor-based method, using the patient's impression of change. We determined the minimal detectable change (MDC) and the minimal important difference (MID) at the group and individual level. Treated patients had a higher change in MGII scores than controls (analysis of covariance p < 0.001). The ocular domain changed more with prednisone than with IVIg/PLEX (effect size 0.67 and 0.13, analysis of covariance p = 0.001). The generalized domain changed more with IVIg/PLEX than with prednisone (effect size 0.50 and 0.22, analysis of covariance p = 0.07). For the total MGII score, the individual MDC95 was 9.1 and the MID was 5.5 for individuals and 8.1 for groups. Relative efficiency ratios were >1 favoring the MGII. The MGII demonstrated responsiveness to prednisone, IVIg, and PLEX in patients with myasthenia. There is a differential response in ocular and generalized symptoms to type of therapy. The MGII has higher relative efficiency than comparison measures and is viable for use in clinical trials. Copyright © 2017 The Author(s). Published by Wolters Kluwer Health, Inc. on behalf of the American Academy of Neurology.

Assembly line termination in cylindrocyclophane biosynthesis: discovery of an editing type II thioesterase domain in a type I polyketide synthase† †Electronic supplementary information (ESI) available: Fig. S1–S12; Tables S1–S8, full experimental details and procedures, 1H and 13C NMR spectral data and HRMS data of compounds 10 and 11 and the internal standards. See DOI: 10.1039/c4sc03132f Click here for additional data file.

PubMed Central

Nakamura, H.; Wang, J. X.

2015-01-01

The termination step is an important source of structural diversity in polyketide biosynthesis. Most type I polyketide synthase (PKS) assembly lines are terminated by a thioesterase (TE) domain located at the C-terminus of the final module, while other PKS assembly lines lack a terminal TE domain and are instead terminated by a separate enzyme in trans. In cylindrocyclophane biosynthesis, the type I modular PKS assembly line is terminated by a freestanding type III PKS (CylI). Unexpectedly, the final module of the type I PKS (CylH) also possesses a C-terminal TE domain. Unlike typical type I PKSs, the CylH TE domain does not influence assembly line termination by CylI in vitro. Instead, this domain phylogenetically resembles a type II TE and possesses activity consistent with an editing function. This finding may shed light on the evolution of unusual PKS termination logic. In addition, the presence of related type II TE domains in many cryptic type I PKS and nonribosomal peptide synthetase (NRPS) assembly lines has implications for pathway annotation, product prediction, and engineering. PMID:29218151

Comparison between spin-orbit torques measured by domain-wall motions and harmonic measurements

NASA Astrophysics Data System (ADS)

Kim, Joo-Sung; Nam, Yune-Seok; Kim, Dae-Yun; Park, Yong-Keun; Park, Min-Ho; Choe, Sug-Bong

2018-05-01

Here we report the comparison of the spin torque efficiencies measured by three different experimental schemes for Pt/Co/X stacks with material X (= Pt, Ta, Ti, Al, Au, Pd, and Ru. 7 materials). The first two spin torque efficiencies ɛDW (1 ) and ɛDW (2 ) are quantified by the measurement of spin-torque-induced effective field for domain-wall depinning and creeping motions, respectively. The last one—longitudinal spin torque efficiency ɛL—is measured by harmonic signal measurement of the magnetization rotation with uniform magnetization configuration. The results confirm that, for all measured Pt/Co/X stacks, ɛDW (1 ) and ɛDW (2 ) are exactly consistent to each other and these two efficiencies are roughly proportional to ɛL with proportionality constant π/2, which comes from the integration over the domain-wall configuration.

A Fast Solver for Implicit Integration of the Vlasov--Poisson System in the Eulerian Framework

DOE Office of Scientific and Technical Information (OSTI.GOV)

Garrett, C. Kristopher; Hauck, Cory D.

In this paper, we present a domain decomposition algorithm to accelerate the solution of Eulerian-type discretizations of the linear, steady-state Vlasov equation. The steady-state solver then forms a key component in the implementation of fully implicit or nearly fully implicit temporal integrators for the nonlinear Vlasov--Poisson system. The solver relies on a particular decomposition of phase space that enables the use of sweeping techniques commonly used in radiation transport applications. The original linear system for the phase space unknowns is then replaced by a smaller linear system involving only unknowns on the boundary between subdomains, which can then be solvedmore » efficiently with Krylov methods such as GMRES. Steady-state solves are combined to form an implicit Runge--Kutta time integrator, and the Vlasov equation is coupled self-consistently to the Poisson equation via a linearized procedure or a nonlinear fixed-point method for the electric field. Finally, numerical results for standard test problems demonstrate the efficiency of the domain decomposition approach when compared to the direct application of an iterative solver to the original linear system.« less

Damage Detection in Composite Structures with Wavenumber Array Data Processing

NASA Technical Reports Server (NTRS)

Tian, Zhenhua; Leckey, Cara; Yu, Lingyu

2013-01-01

Guided ultrasonic waves (GUW) have the potential to be an efficient and cost-effective method for rapid damage detection and quantification of large structures. Attractive features include sensitivity to a variety of damage types and the capability of traveling relatively long distances. They have proven to be an efficient approach for crack detection and localization in isotropic materials. However, techniques must be pushed beyond isotropic materials in order to be valid for composite aircraft components. This paper presents our study on GUW propagation and interaction with delamination damage in composite structures using wavenumber array data processing, together with advanced wave propagation simulations. Parallel elastodynamic finite integration technique (EFIT) is used for the example simulations. Multi-dimensional Fourier transform is used to convert time-space wavefield data into frequency-wavenumber domain. Wave propagation in the wavenumber-frequency domain shows clear distinction among the guided wave modes that are present. This allows for extracting a guided wave mode through filtering and reconstruction techniques. Presence of delamination causes spectral change accordingly. Results from 3D CFRP guided wave simulations with delamination damage in flat-plate specimens are used for wave interaction with structural defect study.

DASS: efficient discovery and p-value calculation of substructures in unordered data.

PubMed

Hollunder, Jens; Friedel, Maik; Beyer, Andreas; Workman, Christopher T; Wilhelm, Thomas

2007-01-01

Pattern identification in biological sequence data is one of the main objectives of bioinformatics research. However, few methods are available for detecting patterns (substructures) in unordered datasets. Data mining algorithms mainly developed outside the realm of bioinformatics have been adapted for that purpose, but typically do not determine the statistical significance of the identified patterns. Moreover, these algorithms do not exploit the often modular structure of biological data. We present the algorithm DASS (Discovery of All Significant Substructures) that first identifies all substructures in unordered data (DASS(Sub)) in a manner that is especially efficient for modular data. In addition, DASS calculates the statistical significance of the identified substructures, for sets with at most one element of each type (DASS(P(set))), or for sets with multiple occurrence of elements (DASS(P(mset))). The power and versatility of DASS is demonstrated by four examples: combinations of protein domains in multi-domain proteins, combinations of proteins in protein complexes (protein subcomplexes), combinations of transcription factor target sites in promoter regions and evolutionarily conserved protein interaction subnetworks. The program code and additional data are available at http://www.fli-leibniz.de/tsb/DASS

F1174V mutation alters the ALK active conformation in response to Crizotinib in NSCLC: Insight from molecular simulations.

PubMed

Dehghanian, Fariba; Kay, Maryam; Vallian, Sadeq

2017-08-01

Crizotinib is an efficient antineoplastic drug for treatment of non-small cell lung carcinoma (NSCLC), which is identified as an anaplastic lymphoma kinase (ALK) inhibitor. F1174V is a recently identified acquired point mutation relating to the Crizotinib resistance in NSCLC patients. The mechanism of Crizotinib resistance relating to F1174V mutation as a non-active site mutation remains unclear. In this study, the molecular dynamic simulation was used to investigate the possible mechanisms by which F1174V mutation may affect the structure and activity of ALK kinase domain. The results suggested that F1174V mutation could cause two important secondary structure alterations, which led to the local conformational change in ALK kinase domain. This causes more positive free energy in the mutant complex in comparison with the wild-type one. In addition, our structural analyses illustrated that F1174V mutation could result in some important interactions, which represent the key characteristics of the ALK active conformation. This study provided a molecular mechanism for ALK Crizotinib resistance caused by F1174V mutation,which could facilitate designing more efficient drugs. Copyright © 2017 Elsevier Inc. All rights reserved.

A Fast Solver for Implicit Integration of the Vlasov--Poisson System in the Eulerian Framework

DOE PAGES

Garrett, C. Kristopher; Hauck, Cory D.

2018-04-05

In this paper, we present a domain decomposition algorithm to accelerate the solution of Eulerian-type discretizations of the linear, steady-state Vlasov equation. The steady-state solver then forms a key component in the implementation of fully implicit or nearly fully implicit temporal integrators for the nonlinear Vlasov--Poisson system. The solver relies on a particular decomposition of phase space that enables the use of sweeping techniques commonly used in radiation transport applications. The original linear system for the phase space unknowns is then replaced by a smaller linear system involving only unknowns on the boundary between subdomains, which can then be solvedmore » efficiently with Krylov methods such as GMRES. Steady-state solves are combined to form an implicit Runge--Kutta time integrator, and the Vlasov equation is coupled self-consistently to the Poisson equation via a linearized procedure or a nonlinear fixed-point method for the electric field. Finally, numerical results for standard test problems demonstrate the efficiency of the domain decomposition approach when compared to the direct application of an iterative solver to the original linear system.« less

Chimeric antigen receptor containing ICOS signaling domain mediates specific and efficient antitumor effect of T cells against EGFRvIII expressing glioma

PubMed Central

2013-01-01

Background Adoptive transfer of chimeric antigen receptor (CAR)-modified T cells appears to be a promising immunotherapeutic strategy. CAR combines the specificity of antibody and cytotoxicity of cytotoxic T lymphocytes, enhancing T cells’ ability to specifically target antigens and to effectively kill cancer cells. Recent efforts have been made to integrate the costimulatory signals in the CAR to improve the antitumor efficacy. Epidermal growth factor receptor variant III (EGFRvIII) is an attractive therapeutic target as it frequently expresses in glioma and many other types of cancers. Our current study aimed to investigate the specific and efficient antitumor effect of T cells modified with CAR containing inducible costimulator (ICOS) signaling domain. Methods A second generation of EGFRvIII/CAR was generated and it contained the EGFRvIII single chain variable fragment, ICOS signaling domain and CD3ζ chain. Lentiviral EGFRvIII/CAR was prepared and human CD3+ T cells were infected by lentivirus encoding EGFRvIII/CAR. The expression of EGFRvIII/CAR on CD3+ T cells was confirmed by flow cytometry and Western blot. The functions of EGFRvIII/CAR+ T cells were evaluated using in vitro and in vivo methods including cytotoxicity assay, cytokine release assay and xenograft tumor mouse model. Results Chimeric EGFRvIIIscFv-ICOS-CD3ζ (EGFRvIII/CAR) was constructed and lentiviral EGFRvIII/CAR were made to titer of 106 TU/ml. The transduction efficiency of lentiviral EGFRvIII/CAR on T cells reached around 70% and expression of EGFRvIII/CAR protein was verified by immunoblotting as a band of about 57 kDa. Four hour 51Cr release assays demonstrated specific and efficient cytotoxicity of EGFRvIII/CAR+ T cells against EGFRvIII expressing U87 cells. A robust increase in the IFN-γ secretion was detected in the co-culture supernatant of the EGFRvIII/CAR+ T cells and the EGFRvIII expressing U87 cells. Intravenous and intratumor injection of EGFRvIII/CAR+ T cells inhibited the in vivo growth of the EGFRvIII expressing glioma cells. Conclusions Our study demonstrates that the EGFRvIII/CAR-modified T cells can destroy glioma cells efficiently in an EGFRvIII specific manner and release IFN-γ in an antigen dependent manner. The specific recognition and effective killing activity of the EGFRvIII-directed T cells with ICOS signaling domain lays a foundation for us to employ such approach in future cancer treatment. PMID:23656794

Chimeric antigen receptor containing ICOS signaling domain mediates specific and efficient antitumor effect of T cells against EGFRvIII expressing glioma.

PubMed

Shen, Chan-Juan; Yang, Yu-Xiu; Han, Ethan Q; Cao, Na; Wang, Yun-Fei; Wang, Yi; Zhao, Ying-Ying; Zhao, Li-Ming; Cui, Jian; Gupta, Puja; Wong, Albert J; Han, Shuang-Yin

2013-05-09

Adoptive transfer of chimeric antigen receptor (CAR)-modified T cells appears to be a promising immunotherapeutic strategy. CAR combines the specificity of antibody and cytotoxicity of cytotoxic T lymphocytes, enhancing T cells' ability to specifically target antigens and to effectively kill cancer cells. Recent efforts have been made to integrate the costimulatory signals in the CAR to improve the antitumor efficacy. Epidermal growth factor receptor variant III (EGFRvIII) is an attractive therapeutic target as it frequently expresses in glioma and many other types of cancers. Our current study aimed to investigate the specific and efficient antitumor effect of T cells modified with CAR containing inducible costimulator (ICOS) signaling domain. A second generation of EGFRvIII/CAR was generated and it contained the EGFRvIII single chain variable fragment, ICOS signaling domain and CD3ζ chain. Lentiviral EGFRvIII/CAR was prepared and human CD3+ T cells were infected by lentivirus encoding EGFRvIII/CAR. The expression of EGFRvIII/CAR on CD3+ T cells was confirmed by flow cytometry and Western blot. The functions of EGFRvIII/CAR+ T cells were evaluated using in vitro and in vivo methods including cytotoxicity assay, cytokine release assay and xenograft tumor mouse model. Chimeric EGFRvIIIscFv-ICOS-CD3ζ (EGFRvIII/CAR) was constructed and lentiviral EGFRvIII/CAR were made to titer of 106 TU/ml. The transduction efficiency of lentiviral EGFRvIII/CAR on T cells reached around 70% and expression of EGFRvIII/CAR protein was verified by immunoblotting as a band of about 57 kDa. Four hour 51Cr release assays demonstrated specific and efficient cytotoxicity of EGFRvIII/CAR+ T cells against EGFRvIII expressing U87 cells. A robust increase in the IFN-γ secretion was detected in the co-culture supernatant of the EGFRvIII/CAR+ T cells and the EGFRvIII expressing U87 cells. Intravenous and intratumor injection of EGFRvIII/CAR+ T cells inhibited the in vivo growth of the EGFRvIII expressing glioma cells. Our study demonstrates that the EGFRvIII/CAR-modified T cells can destroy glioma cells efficiently in an EGFRvIII specific manner and release IFN-γ in an antigen dependent manner. The specific recognition and effective killing activity of the EGFRvIII-directed T cells with ICOS signaling domain lays a foundation for us to employ such approach in future cancer treatment.

The ubiquitin ligase Cbl-b limits Pseudomonas aeruginosa exotoxin T-mediated virulence.

PubMed

Balachandran, Priya; Dragone, Leonard; Garrity-Ryan, Lynne; Lemus, Armando; Weiss, Arthur; Engel, Joanne

2007-02-01

Pseudomonas aeruginosa, an important cause of opportunistic infections in humans, delivers bacterial cytotoxins by type III secretion directly into the host cell cytoplasm, resulting in disruption of host cell signaling and host innate immunity. However, little is known about the fate of the toxins themselves following injection into the host cytosol. Here, we show by both in vitro and in vivo studies that the host ubiquitin ligase Cbl-b interacts with the type III-secreted effector exotoxin T (ExoT) and plays a key role in vivo in limiting bacterial dissemination mediated by ExoT. We demonstrate that, following polyubiquitination, ExoT undergoes regulated proteasomal degradation in the host cell cytosol. ExoT interacts with the E3 ubiquitin ligase Cbl-b and Crk, the substrate for the ExoT ADP ribosyltransferase (ADPRT) domain. The efficiency of degradation is dependent upon the activity of the ADPRT domain. In mouse models of acute pneumonia and systemic infection, Cbl-b is specifically required to limit the dissemination of ExoT-producing bacteria whereas c-Cbl plays no detectable role. To the best of our knowledge, this represents the first identification of a mammalian gene product that is specifically required for in vivo resistance to disease mediated by a type III-secreted effector.

The ubiquitin ligase Cbl-b limits Pseudomonas aeruginosa exotoxin T–mediated virulence

PubMed Central

Balachandran, Priya; Dragone, Leonard; Garrity-Ryan, Lynne; Lemus, Armando; Weiss, Arthur; Engel, Joanne

2007-01-01

Pseudomonas aeruginosa, an important cause of opportunistic infections in humans, delivers bacterial cytotoxins by type III secretion directly into the host cell cytoplasm, resulting in disruption of host cell signaling and host innate immunity. However, little is known about the fate of the toxins themselves following injection into the host cytosol. Here, we show by both in vitro and in vivo studies that the host ubiquitin ligase Cbl-b interacts with the type III–secreted effector exotoxin T (ExoT) and plays a key role in vivo in limiting bacterial dissemination mediated by ExoT. We demonstrate that, following polyubiquitination, ExoT undergoes regulated proteasomal degradation in the host cell cytosol. ExoT interacts with the E3 ubiquitin ligase Cbl-b and Crk, the substrate for the ExoT ADP ribosyltransferase (ADPRT) domain. The efficiency of degradation is dependent upon the activity of the ADPRT domain. In mouse models of acute pneumonia and systemic infection, Cbl-b is specifically required to limit the dissemination of ExoT-producing bacteria whereas c-Cbl plays no detectable role. To the best of our knowledge, this represents the first identification of a mammalian gene product that is specifically required for in vivo resistance to disease mediated by a type III–secreted effector. PMID:17235393

Cellular receptor traffic is essential for productive duck hepatitis B virus infection.

PubMed

Breiner, K M; Schaller, H

2000-03-01

We have investigated the mechanism of duck hepatitis B virus (DHBV) entry into susceptible primary duck hepatocytes (PDHs), using mutants of carboxypeptidase D (gp180), a transmembrane protein shown to act as the primary cellular receptor for avian hepatitis B virus uptake. The variant proteins were abundantly produced from recombinant adenoviruses and tested for the potential to functionally outcompete the endogenous wild-type receptor. Overexpression of wild-type gp180 significantly enhanced the efficiency of DHBV infection in PDHs but did not affect ongoing DHBV replication, an observation further supporting gp180 receptor function. A gp180 mutant deficient for endocytosis abolished DHBV infection, indicating endocytosis to be the route of hepadnaviral entry. With further gp180 variants, carrying mutations in the cytoplasmic domain and characterized by an accelerated turnover, the ability of gp180 to function as a DHBV receptor was found to depend on a wild-type-like sorting phenotype which largely avoids transport toward the endolysosomal compartment. Based on these data, we propose a model in which a distinct intracellular DHBV traffic to the endosome, but not beyond, is a prerequisite for completion of viral entry, i.e., for fusion and capsid release. Furthermore, the deletion of the two enzymatically active carboxypeptidase domains of gp180 did not lead to a loss of receptor function.

Hydrodynamic Simulations of Protoplanetary Disks with GIZMO

NASA Astrophysics Data System (ADS)

Rice, Malena; Laughlin, Greg

2018-01-01

Over the past several decades, the field of computational fluid dynamics has rapidly advanced as the range of available numerical algorithms and computationally feasible physical problems has expanded. The development of modern numerical solvers has provided a compelling opportunity to reconsider previously obtained results in search for yet undiscovered effects that may be revealed through longer integration times and more precise numerical approaches. In this study, we compare the results of past hydrodynamic disk simulations with those obtained from modern analytical resources. We focus our study on the GIZMO code (Hopkins 2015), which uses meshless methods to solve the homogeneous Euler equations of hydrodynamics while eliminating problems arising as a result of advection between grid cells. By comparing modern simulations with prior results, we hope to provide an improved understanding of the impact of fluid mechanics upon the evolution of protoplanetary disks.

Smoothed particle hydrodynamics method from a large eddy simulation perspective

NASA Astrophysics Data System (ADS)

Di Mascio, A.; Antuono, M.; Colagrossi, A.; Marrone, S.

2017-03-01

The Smoothed Particle Hydrodynamics (SPH) method, often used for the modelling of the Navier-Stokes equations by a meshless Lagrangian approach, is revisited from the point of view of Large Eddy Simulation (LES). To this aim, the LES filtering procedure is recast in a Lagrangian framework by defining a filter that moves with the positions of the fluid particles at the filtered velocity. It is shown that the SPH smoothing procedure can be reinterpreted as a sort of LES Lagrangian filtering, and that, besides the terms coming from the LES convolution, additional contributions (never accounted for in the SPH literature) appear in the equations when formulated in a filtered fashion. Appropriate closure formulas are derived for the additional terms and a preliminary numerical test is provided to show the main features of the proposed LES-SPH model.

Meshless modelling of dynamic behaviour of glasses under intense shock loadings: Application to matter ejection during high velocity impacts on thin brittle targets

NASA Astrophysics Data System (ADS)

Michel, Y.; Chevalier, J.-M.; Durin, C.; Espinosa, C.; Malaise, F.; Barrau, J.-J.

2006-08-01

The purpose of this study is to present a new material model adapted to SPH modelling of dynamic behaviour of glasses under shock loadings. This model has the ability to reproduce fragmentation and densification of glasses under compression as well as brittle tensile failure. It has been implemented in Ls-Dyna software and coupled with a SPH code. By comparison with CEA-CESTA experimental data the model has been validated for fused silica and Pyrex glass for stress level up to 35GPa. For Laser MegaJoule applications, the present material model was applied to 3D high velocity impacts on thin brittle targets with good agreement with experimental data obtained using CESTA's double stage light gas gun in term of damages and matter ejection.

Fast switching and signature of efficient domain wall motion driven by spin-orbit torques in a perpendicular anisotropy magnetic insulator/Pt bilayer

NASA Astrophysics Data System (ADS)

Avci, Can Onur; Rosenberg, Ethan; Baumgartner, Manuel; Beran, Lukáš; Quindeau, Andy; Gambardella, Pietro; Ross, Caroline A.; Beach, Geoffrey S. D.

2017-08-01

We report fast and efficient current-induced switching of a perpendicular anisotropy magnetic insulator thulium iron garnet by using spin-orbit torques (SOT) from the Pt overlayer. We first show that, with quasi-DC (10 ms) current pulses, SOT-induced switching can be achieved with an external field as low as 2 Oe, making TmIG an outstanding candidate to realize efficient switching in heterostructures that produce moderate stray fields without requiring an external field. We then demonstrate deterministic switching with fast current pulses (≤20 ns) with an amplitude of ˜1012 A/m2, similar to all-metallic structures. We reveal that, in the presence of an initially nucleated domain, the critical switching current is reduced by up to a factor of five with respect to the fully saturated initial state, implying efficient current-driven domain wall motion in this system. Based on measurements with 2 ns-long pulses, we estimate the domain wall velocity of the order of ˜400 m/s per j = 1012 A/m2.

Direct recognition of superparamagnetic nanocrystals by macrophage scavenger receptor SR-AI.

PubMed

Chao, Ying; Karmali, Priya P; Mukthavaram, Rajesh; Kesari, Santosh; Kouznetsova, Valentina L; Tsigelny, Igor F; Simberg, Dmitri

2013-05-28

Scavenger receptors (SRs) are molecular pattern recognition receptors that have been shown to mediate opsonin-independent uptake of therapeutic and imaging nanoparticles, underlying the importance of SRs in nanomedicine. Unlike pathogens, engineered nanomaterials offer great flexibility in control of surface properties, allowing addressing specific questions regarding the molecular mechanisms of nanoparticle recognition. Recently, we showed that SR-type AI/II mediates opsonin-independent internalization of dextran superparamagnetic iron oxide (SPIO) nanoparticles via positively charged extracellular collagen-like domain. To understand the mechanism of opsonin-independent SPIO recognition, we tested the binding and uptake of nanoparticles with different surface coatings by SR-AI. SPIO coated with 10 kDa dextran was efficiently recognized and taken up by SR-AI transfected cells and J774 macrophages, while SPIO with 20 kDa dextran coating or cross-linked dextran hydrogel avoided the binding and uptake. Nanoparticle negative charge density and zeta-potential did not correlate with SR-AI binding/uptake efficiency. Additional experiments and computer modeling revealed that recognition of the iron oxide crystalline core by the positively charged collagen-like domain of SR-AI is sterically hindered by surface polymer coating. Importantly, the modeling revealed a strong complementarity between the surface Fe-OH groups of the magnetite crystal and the charged lysines of the collagen-like domain of SR-AI, suggesting a specific recognition of SPIO crystalline surface. These data provide an insight into the molecular recognition of nanocrystals by innate immunity receptors and the mechanisms whereby polymer coatings promote immune evasion.

Functional dissection of the Hox protein Abdominal-B in Drosophila cell culture

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhai, Zongzhao; CellNetworks - Cluster of Excellence, Centre for Organismal Studies; Graduate School of Chinese Academy of Sciences, Beijing 100039

2011-11-04

Highlights: Black-Right-Pointing-Pointer ct340 CRM was identified to be the posterior spiracle enhancer of gene cut. Black-Right-Pointing-Pointer ct340 is under the direct transcriptional control of Hox protein Abd-B. Black-Right-Pointing-Pointer An efficient cloning system was developed to assay protein-DNA interaction. Black-Right-Pointing-Pointer New features of Abd-B dependent target gene regulation were detected. -- Abstract: Hox transcription factors regulate the morphogenesis along the anterior-posterior (A/P) body axis through the interaction with small cis-regulatory modules (CRMs) of their target gene, however so far very few Hox CRMs are known and have been analyzed in detail. In this study we have identified a new Hox CRM,more » ct340, which guides the expression of the cell type specification gene cut (ct) in the posterior spiracle under the direct control of the Hox protein Abdominal-B (Abd-B). Using the ct340 enhancer activity as readout, an efficient cloning system to generate VP16 activation domain fusion protein was developed to unambiguously test protein-DNA interaction in Drosophila cell culture. By functionally dissecting the Abd-B protein, new features of Abd-B dependent target gene regulation were detected. Due to its easy adaptability, this system can be generally used to map functional domains within sequence-specific transcriptional factors in Drosophila cell culture, and thus provide preliminary knowledge of the protein functional domain structure for further in vivo analysis.« less

The Natural Neighbour Radial Point Interpolation Meshless Method Applied to the Non-Linear Analysis

NASA Astrophysics Data System (ADS)

Dinis, L. M. J. S.; Jorge, R. M. Natal; Belinha, J.

2011-05-01

In this work the Natural Neighbour Radial Point Interpolation Method (NNRPIM), is extended to large deformation analysis of elastic and elasto-plastic structures. The NNPRIM uses the Natural Neighbour concept in order to enforce the nodal connectivity and to create a node-depending background mesh, used in the numerical integration of the NNRPIM interpolation functions. Unlike the FEM, where geometrical restrictions on elements are imposed for the convergence of the method, in the NNRPIM there are no such restrictions, which permits a random node distribution for the discretized problem. The NNRPIM interpolation functions, used in the Galerkin weak form, are constructed using the Radial Point Interpolators, with some differences that modify the method performance. In the construction of the NNRPIM interpolation functions no polynomial base is required and the used Radial Basis Function (RBF) is the Multiquadric RBF. The NNRPIM interpolation functions posses the delta Kronecker property, which simplify the imposition of the natural and essential boundary conditions. One of the scopes of this work is to present the validation the NNRPIM in the large-deformation elasto-plastic analysis, thus the used non-linear solution algorithm is the Newton-Rapson initial stiffness method and the efficient "forward-Euler" procedure is used in order to return the stress state to the yield surface. Several non-linear examples, exhibiting elastic and elasto-plastic material properties, are studied to demonstrate the effectiveness of the method. The numerical results indicated that NNRPIM handles large material distortion effectively and provides an accurate solution under large deformation.

Minimum Free Energy Path of Ligand-Induced Transition in Adenylate Kinase

PubMed Central

Matsunaga, Yasuhiro; Fujisaki, Hiroshi; Terada, Tohru; Furuta, Tadaomi; Moritsugu, Kei; Kidera, Akinori

2012-01-01

Large-scale conformational changes in proteins involve barrier-crossing transitions on the complex free energy surfaces of high-dimensional space. Such rare events cannot be efficiently captured by conventional molecular dynamics simulations. Here we show that, by combining the on-the-fly string method and the multi-state Bennett acceptance ratio (MBAR) method, the free energy profile of a conformational transition pathway in Escherichia coli adenylate kinase can be characterized in a high-dimensional space. The minimum free energy paths of the conformational transitions in adenylate kinase were explored by the on-the-fly string method in 20-dimensional space spanned by the 20 largest-amplitude principal modes, and the free energy and various kinds of average physical quantities along the pathways were successfully evaluated by the MBAR method. The influence of ligand binding on the pathways was characterized in terms of rigid-body motions of the lid-shaped ATP-binding domain (LID) and the AMP-binding (AMPbd) domains. It was found that the LID domain was able to partially close without the ligand, while the closure of the AMPbd domain required the ligand binding. The transition state ensemble of the ligand bound form was identified as those structures characterized by highly specific binding of the ligand to the AMPbd domain, and was validated by unrestrained MD simulations. It was also found that complete closure of the LID domain required the dehydration of solvents around the P-loop. These findings suggest that the interplay of the two different types of domain motion is an essential feature in the conformational transition of the enzyme. PMID:22685395

Probing the potential of CnaB-type domains for the design of tag/catcher systems

PubMed Central

Pröschel, Marlene; Kraner, Max E.; Horn, Anselm H. C.; Schäfer, Lena; Sonnewald, Uwe

2017-01-01

Building proteins into larger, post-translational assemblies in a defined and stable way is still a challenging task. A promising approach relies on so-called tag/catcher systems that are fused to the proteins of interest and allow a durable linkage via covalent intermolecular bonds. Tags and catchers are generated by splitting protein domains that contain intramolecular isopeptide or ester bonds that form autocatalytically under physiological conditions. There are already numerous biotechnological and medical applications that demonstrate the usefulness of covalent linkages mediated by these systems. Additional covalent tag/catcher systems would allow creating more complex and ultra-stable protein architectures and networks. Two of the presently available tag/catcher systems were derived from closely related CnaB-domains of Streptococcus pyogenes and Streptococcus dysgalactiae proteins. However, it is unclear whether domain splitting is generally tolerated within the CnaB-family or only by a small subset of these domains. To address this point, we have selected a set of four CnaB domains of low sequence similarity and characterized the resulting tag/catcher systems by computational and experimental methods. Experimental testing for intermolecular isopeptide bond formation demonstrated two of the four systems to be functional. For these two systems length and sequence variations of the peptide tags were investigated revealing only a relatively small effect on the efficiency of the reaction. Our study suggests that splitting into tag and catcher moieties is tolerated by a significant portion of the naturally occurring CnaB-domains, thus providing a large reservoir for the design of novel tag/catcher systems. PMID:28654665

Protein Domain-Level Landscape of Cancer-Type-Specific Somatic Mutations

PubMed Central

Yang, Fan; Petsalaki, Evangelia; Rolland, Thomas; Hill, David E.; Vidal, Marc; Roth, Frederick P.

2015-01-01

Identifying driver mutations and their functional consequences is critical to our understanding of cancer. Towards this goal, and because domains are the functional units of a protein, we explored the protein domain-level landscape of cancer-type-specific somatic mutations. Specifically, we systematically examined tumor genomes from 21 cancer types to identify domains with high mutational density in specific tissues, the positions of mutational hotspots within these domains, and the functional and structural context where possible. While hotspots corresponding to specific gain-of-function mutations are expected for oncoproteins, we found that tumor suppressor proteins also exhibit strong biases toward being mutated in particular domains. Within domains, however, we observed the expected patterns of mutation, with recurrently mutated positions for oncogenes and evenly distributed mutations for tumor suppressors. For example, we identified both known and new endometrial cancer hotspots in the tyrosine kinase domain of the FGFR2 protein, one of which is also a hotspot in breast cancer, and found new two hotspots in the Immunoglobulin I-set domain in colon cancer. Thus, to prioritize cancer mutations for further functional studies aimed at more precise cancer treatments, we have systematically correlated mutations and cancer types at the protein domain level. PMID:25794154

Application of augmented-Lagrangian methods in meteorology: Comparison of different conjugate-gradient codes for large-scale minimization

NASA Technical Reports Server (NTRS)

Navon, I. M.

1984-01-01

A Lagrange multiplier method using techniques developed by Bertsekas (1982) was applied to solving the problem of enforcing simultaneous conservation of the nonlinear integral invariants of the shallow water equations on a limited area domain. This application of nonlinear constrained optimization is of the large dimensional type and the conjugate gradient method was found to be the only computationally viable method for the unconstrained minimization. Several conjugate-gradient codes were tested and compared for increasing accuracy requirements. Robustness and computational efficiency were the principal criteria.

Representation of the Characteristics of Piezoelectric Fiber Composites with Neural Networks

NASA Astrophysics Data System (ADS)

Yapici, A.; Bickraj, K.; Yenilmez, A.; Li, M.; Tansel, I. N.; Martin, S. A.; Pereira, C. M.; Roth, L. E.

2007-03-01

Ideal sensors for the future should be economical, efficient, highly intelligent, and capable of obtaining their operation power from the environment. The use of piezoelectric fiber composites coupled with a low power microprocessor and backpropagation type neural networks is proposed for the development of a simple sensor to estimate the characteristics of harmonic forces. Three neural networks were used for the estimation of amplitude, gain and variation of the load in the time domain. The average estimation errors of the neural networks were less than 8% in all of the studied cases.

CARIBIAM: constrained Association Rules using Interactive Biological IncrementAl Mining.

PubMed

Rahal, Imad; Rahhal, Riad; Wang, Baoying; Perrizo, William

2008-01-01

This paper analyses annotated genome data by applying a very central data-mining technique known as Association Rule Mining (ARM) with the aim of discovering rules and hypotheses capable of yielding deeper insights into this type of data. In the literature, ARM has been noted for producing an overwhelming number of rules. This work proposes a new technique capable of using domain knowledge in the form of queries in order to efficiently mine only the subset of the associations that are of interest to investigators in an incremental and interactive manner.

Latent myostatin has significant activity and this activity is controlled more efficiently by WFIKKN1 than by WFIKKN2

PubMed Central

Szláma, György; Trexler, Mária; Patthy, László

2013-01-01

Myostatin, a negative regulator of skeletal muscle growth, is produced from myostatin precursor by multiple steps of proteolytic processing. After cleavage by a furin-type protease, the propeptide and growth factor domains remain associated, forming a noncovalent complex, the latent myostatin complex. Mature myostatin is liberated from latent myostatin by bone morphogenetic protein 1/tolloid proteases. Here, we show that, in reporter assays, latent myostatin preparations have significant myostatin activity, as the noncovalent complex dissociates at an appreciable rate, and both mature and semilatent myostatin (a complex in which the dimeric growth factor domain interacts with only one molecule of myostatin propeptide) bind to myostatin receptor. The interaction of myostatin receptor with semilatent myostatin is efficiently blocked by WAP, Kazal, immunoglobulin, Kunitz and NTR domain-containing protein 1 or growth and differentiation factor-associated serum protein 2 (WFIKKN1), a large extracellular multidomain protein that binds both mature myostatin and myostatin propeptide [Kondás et al. (2008) J Biol Chem 283, 23677–23684]. Interestingly, the paralogous protein WAP, Kazal, immunoglobulin, Kunitz and NTR domain-containing protein 2 or growth and differentiation factor-associated serum protein 1 (WFIKKN2) was less efficient than WFIKKN1 as an antagonist of the interactions of myostatin receptor with semilatent myostatin. Our studies have shown that this difference is attributable to the fact that only WFIKKN1 has affinity for the propeptide domain, and this interaction increases its potency in suppressing the receptor-binding activity of semilatent myostatin. As the interaction of WFIKKN1 with various forms of myostatin permits tighter control of myostatin activity until myostatin is liberated from latent myostatin by bone morphogenetic protein 1/tolloid proteases, WFIKKN1 may have greater potential as an antimyostatic agent than WFIKKN2. Structured digital abstract Furin cleaves Promyostatin by protease assay (View interaction) myostatin binds to PRO by surface plasmon resonance (View interaction) BMP-1 cleaves Promyostatin by protease assay (View interaction) ACR IIB physically interacts with Latent Myostatin by surface plasmon resonance (View interaction) Promyostatin and Promyostatin bind by comigration in gel electrophoresis (View interaction) WFIKKN1 binds to Latent Myostatin by pull down (View interaction) ACR IIB binds to Mature Myostatin by surface plasmon resonance (View Interaction: 1, 2, 3) WFIKKN1 binds to Myostatin Prodomain by surface plasmon resonance (View Interaction: 1, 2, 3) PMID:23829672

Detecting atypical examples of known domain types by sequence similarity searching: the SBASE domain library approach.

PubMed

Dhir, Somdutta; Pacurar, Mircea; Franklin, Dino; Gáspári, Zoltán; Kertész-Farkas, Attila; Kocsor, András; Eisenhaber, Frank; Pongor, Sándor

2010-11-01

SBASE is a project initiated to detect known domain types and predicting domain architectures using sequence similarity searching (Simon et al., Protein Seq Data Anal, 5: 39-42, 1992, Pongor et al, Nucl. Acids. Res. 21:3111-3115, 1992). The current approach uses a curated collection of domain sequences - the SBASE domain library - and standard similarity search algorithms, followed by postprocessing which is based on a simple statistics of the domain similarity network (http://hydra.icgeb.trieste.it/sbase/). It is especially useful in detecting rare, atypical examples of known domain types which are sometimes missed even by more sophisticated methodologies. This approach does not require multiple alignment or machine learning techniques, and can be a useful complement to other domain detection methodologies. This article gives an overview of the project history as well as of the concepts and principles developed within this the project.

Identification of multiple nuclear localization signals in murine Elf3, an ETS transcription factor.

PubMed

Do, Hyun-Jin; Song, Hyuk; Yang, Heung-Mo; Kim, Dong-Ku; Kim, Nam-Hyung; Kim, Jin-Hoi; Cha, Kwang-Yul; Chung, Hyung-Min; Kim, Jae-Hwan

2006-03-20

We investigated nuclear localization signal (NLS) determinants within the AT-hook and ETS DNA-binding domains of murine Elf3 (mElf3), a member of the subfamily of epithelium-specific ETS transcription factors. Deletion mutants containing the AT-hook, ETS domain or both localized strictly in the nucleus, suggesting that these individual domains contain independent NLS motif(s). Within the AT-hook domain, four basic residues (244KRKR247) were critical for strong NLS activity, and two potent bipartite NLS motifs (236-252 and 249-267) were sufficient for nuclear import of mElf3, although less efficient than the full domain. In addition, one stretch of basic residues (318KKK320) within the ETS domain appears to be essential for mElf3 nuclear localization. Taken together, mElf3 contains multiple NLS motifs, which may function cooperatively to effect efficient nuclear transport.

The DUSP–Ubl domain of USP4 enhances its catalytic efficiency by promoting ubiquitin exchange

PubMed Central

Clerici, Marcello; Luna-Vargas, Mark P. A.; Faesen, Alex C.; Sixma, Titia K.

2014-01-01

Ubiquitin-specific protease USP4 is emerging as an important regulator of cellular pathways, including the TGF-β response, NF-κB signalling and splicing, with possible roles in cancer. Here we show that USP4 has its catalytic triad arranged in a productive conformation. Nevertheless, it requires its N-terminal DUSP–Ubl domain to achieve full catalytic turnover. Pre-steady-state kinetics measurements reveal that USP4 catalytic domain activity is strongly inhibited by slow dissociation of ubiquitin after substrate hydrolysis. The DUSP–Ubl domain is able to enhance ubiquitin dissociation, hence promoting efficient turnover. In a mechanism that requires all USP4 domains, binding of the DUSP–Ubl domain promotes a change of a switching loop near the active site. This ‘allosteric regulation of product discharge’ provides a novel way of regulating deubiquitinating enzymes that may have relevance for other enzyme classes. PMID:25404403

Spectral identification of topological domains

PubMed Central

Chen, Jie; Hero, Alfred O.; Rajapakse, Indika

2016-01-01

Motivation: Topological domains have been proposed as the backbone of interphase chromosome structure. They are regions of high local contact frequency separated by sharp boundaries. Genes within a domain often have correlated transcription. In this paper, we present a computational efficient spectral algorithm to identify topological domains from chromosome conformation data (Hi-C data). We consider the genome as a weighted graph with vertices defined by loci on a chromosome and the edge weights given by interaction frequency between two loci. Laplacian-based graph segmentation is then applied iteratively to obtain the domains at the given compactness level. Comparison with algorithms in the literature shows the advantage of the proposed strategy. Results: An efficient algorithm is presented to identify topological domains from the Hi-C matrix. Availability and Implementation: The Matlab source code and illustrative examples are available at http://bionetworks.ccmb.med.umich.edu/ Contact: indikar@med.umich.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27153657

The retinal specific CD147 Ig0 domain: from molecular structure to biological activity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Redzic, Jasmina S.; Armstrong, Geoffrey S.; Isern, Nancy G.

2011-06-18

CD147 is a type I transmembrane protein that is involved in inflammatory diseases, cancer progression, and multiple human pathogens utilize CD147 for efficient infection. In several cancers, CD147 expression is so high that it is now used as a prognostic marker. The two primary isoforms of CD147 that are related to cancer progression have been identified, differing in their number of immunoglobulin (Ig)-like domains. These include CD147 Ig1-Ig2 that is ubiquitously expressed in most tissues and CD147 Ig0-Ig1-Ig2 that is retinal specific and implicated in retinoblastoma. However, little is known in regard to the retinal specific CD147 Ig0 domain despitemore » its potential role in retinoblastoma. Thus, here we have extensively characterized the CD147 Ig0 domain by elucidating its three-dimensional structure through crystallography and its solution behavior through several biophysical methods that include nuclear magnetic resonance. Furthermore, we have utilized this data together with mutagenesis to probe the biological activity of CD147-containing proteins both with and without the CD147 Ig0 domain within several model cell lines. Our findings reveal that the CD147 Ig0 domain is a potent stimulator of interleukin-6, which is a well-known contributor to retinoblastoma and suggest that the CD147 Ig0 domain has its own receptor distinct from that of the other CD147 Ig-like domains, CD147 Ig1-Ig2. Furthermore, we show that the CD147 Ig0 dimer is the functional unit required for activity and can be disrupted by a single point mutation.« less

Mining Metatranscriptomic Data of a Cyanobacterial Bloom for Patterns of Secondary Metabolism Gene Expression

NASA Astrophysics Data System (ADS)

Penn, K.; Wang, J.; Thompson, J. R.

2012-12-01

The secondary metabolism of bacterial cells produces small molecules that can have both medicinal properties and toxigenic effects. This study focuses on mining metatranscriptomes from a tropical eutrophic water reservoir in Singapore experiencing a cyanobacterial Harmful Algal Bloom dominated by Microcystis, to identify the types of secondary metabolites genes being expressed and by what taxa. A phylogenomic approach as implemented in the online tool Natural Product Domain Seeker (NaPDoS) was used. NaPDoS was recently developed to classify ketosynthase and condensation domains from polyketide synthases and non-ribosomal peptide synthetases, respectively, to provide insight into potential types of pathway products. Water samples from the reservoir were collected six times over a day/night cycle. Total RNA was extracted and subjected to ribosomal depletion followed by cDNA synthesis and next-generation Illumina DNA sequencing, generating 493,468 to 678,064 95-101 base pairs post-quality control reads per sample. Evidence for expression of PKS and NRPS type genes based on identification of a ketosynthase and condensation domains are present in all time points. KS domains fall into to two main phylogenetic groups, type I and type II, within the type II group of domains are domains for fatty acid biosynthesis (fab), which is considered a part of primary metabolism. Type I KS domains are part of the classic PKS natural product biosynthetic genes that make things such as antibiotics and other toxins such as microcystin. 2849 KS domains were detected in the combined reservoir samples, of these 1141 were likely from fatty acid biosynthesis and 1708 were related to secondary metabolism type KS domains. The most abundant KS domains (485) besides the fab genes are closely related to a KS domain that is not currently experimentally linked to a known secondary metabolite but the domain is found in four Microcystis genomes along with two other species of cyanobacteria. The three KS domains from the microcystin pathway make up 238 of the KS domains. The third most abundant KS domain is related to a protein annotated as a heterocyst glycolipid protein from the Microcystis aeruginosa genome sequence, as Microcystis is not known to produce heterocysts the gene is likely a part of an undescribed type of glycolipid biosynthetic pathway. In relation to NRPS pathways there were 899 reads classified as condensation domains. The most abundant one is closely related to the C domains from an uncharacterized NRPS pathway. The next most abundant domains are from microcystin (178), aeruginosin (84) and micropeptin (47) all are NRPS pathways from Microcystis. Although it is unsurprising that most of the KS and C domains are from Microcystis it is clear that there are still uncharacterized secondary metabolites produced by this well studied bacterial genus. Unexpectedly, there are more KS domains related to secondary metabolism then fabs. This study provides unique insight into the production of secondary metabolites in a natural setting and supports that these have an important ecological function because of the significant transcription levels at all time points. A clear understanding of the ecological function of secondary metabolites will undoubtedly be crucial to future efforts to control cyanoHABs.

LBM-EP: Lattice-Boltzmann method for fast cardiac electrophysiology simulation from 3D images.

PubMed

Rapaka, S; Mansi, T; Georgescu, B; Pop, M; Wright, G A; Kamen, A; Comaniciu, Dorin

2012-01-01

Current treatments of heart rhythm troubles require careful planning and guidance for optimal outcomes. Computational models of cardiac electrophysiology are being proposed for therapy planning but current approaches are either too simplified or too computationally intensive for patient-specific simulations in clinical practice. This paper presents a novel approach, LBM-EP, to solve any type of mono-domain cardiac electrophysiology models at near real-time that is especially tailored for patient-specific simulations. The domain is discretized on a Cartesian grid with a level-set representation of patient's heart geometry, previously estimated from images automatically. The cell model is calculated node-wise, while the transmembrane potential is diffused using Lattice-Boltzmann method within the domain defined by the level-set. Experiments on synthetic cases, on a data set from CESC'10 and on one patient with myocardium scar showed that LBM-EP provides results comparable to an FEM implementation, while being 10 - 45 times faster. Fast, accurate, scalable and requiring no specific meshing, LBM-EP paves the way to efficient and detailed models of cardiac electrophysiology for therapy planning.

Anchoring in Numeric Judgments of Visual Stimuli

PubMed Central

Langeborg, Linda; Eriksson, Mårten

2016-01-01

This article investigates effects of anchoring in age estimation and estimation of quantities, two tasks which to different extents are based on visual stimuli. The results are compared to anchoring in answers to classic general knowledge questions that rely on semantic knowledge. Cognitive load was manipulated to explore possible differences between domains. Effects of source credibility, manipulated by differing instructions regarding the selection of anchor values (no information regarding anchor selection, information that the anchors are randomly generated or information that the anchors are answers from an expert) on anchoring were also investigated. Effects of anchoring were large for all types of judgments but were not affected by cognitive load or by source credibility in either one of the researched domains. A main effect of cognitive load on quantity estimations and main effects of source credibility in the two visually based domains indicate that the manipulations were efficient. Implications for theoretical explanations of anchoring are discussed. In particular, because anchoring did not interact with cognitive load, the results imply that the process behind anchoring in visual tasks is predominantly automatic and unconscious. PMID:26941684

A nucleolar targeting signal in PML-I addresses PML to nucleolar caps in stressed or senescent cells.

PubMed

Condemine, Wilfried; Takahashi, Yuki; Le Bras, Morgane; de Thé, Hugues

2007-09-15

The promyelocytic leukemia (PML) tumour suppressor is the organiser of PML nuclear bodies, which are domains the precise functions of which are still disputed. We show that upon several types of stress, endogenous PML proteins form nucleolar caps and eventually engulf nucleolar components. Only two specific PML splice variants (PML-I and PML-IV) are efficiently targeted to the nucleolus and the abundant PML-I isoform is required for the targeting of endogenous PML proteins to this organelle. We identified a nucleolar targeting domain within the evolutionarily conserved C-terminus of PML-I. This domain contains a predicted exonuclease III fold essential for the targeting of the PML-I C-terminus to nucleolar fibrillar centres. Furthermore, spontaneous or oncogene retrieval-induced senescence is associated with the formation of very large PML nuclear bodies that initially contain nucleolar components. Later, poly-ubiquitin conjugates are found on the outer shell or within most of these senescence-associated PML bodies. Thus, unexpectedly, the scarcely studied PML-I isoform links PML bodies, nucleolus, senescence and proteolysis.

Crystal structure of tandem type III fibronectin domains from Drosophila neuroglian at 2.0 A.

PubMed

Huber, A H; Wang, Y M; Bieber, A J; Bjorkman, P J

1994-04-01

We report the crystal structure of two adjacent fibronectin type III repeats from the Drosophila neural cell adhesion molecule neuroglian. Each domain consists of two antiparallel beta sheets and is folded topologically identically to single fibronectin type III domains from the extracellular matrix proteins tenascin and fibronectin. beta bulges and left-handed polyproline II helices disrupt the regular beta sheet structure of both neuroglian domains. The hydrophobic interdomain interface includes a metal-binding site, presumably involved in stabilizing the relative orientation between domains and predicted by sequence comparision to be present in the vertebrate homolog molecule L1. The neuroglian domains are related by a near perfect 2-fold screw axis along the longest molecular dimension. Using this relationship, a model for arrays of tandem fibronectin type III repeats in neuroglian and other molecules is proposed.

Restriction digest screening facilitates efficient detection of site-directed mutations introduced by CRISPR in C. albicans UME6.

PubMed

Evans, Ben A; Smith, Olivia L; Pickerill, Ethan S; York, Mary K; Buenconsejo, Kristen J P; Chambers, Antonio E; Bernstein, Douglas A

2018-01-01

Introduction of point mutations to a gene of interest is a powerful tool when determining protein function. CRISPR-mediated genome editing allows for more efficient transfer of a desired mutation into a wide range of model organisms. Traditionally, PCR amplification and DNA sequencing is used to determine if isolates contain the intended mutation. However, mutation efficiency is highly variable, potentially making sequencing costly and time consuming. To more efficiently screen for correct transformants, we have identified restriction enzymes sites that encode for two identical amino acids or one or two stop codons. We used CRISPR to introduce these restriction sites directly upstream of the Candida albicans UME6 Zn 2+ -binding domain, a known regulator of C. albicans filamentation. While repair templates coding for different restriction sites were not equally successful at introducing mutations, restriction digest screening enabled us to rapidly identify isolates with the intended mutation in a cost-efficient manner. In addition, mutated isolates have clear defects in filamentation and virulence compared to wild type C. albicans . Our data suggest restriction digestion screening efficiently identifies point mutations introduced by CRISPR and streamlines the process of identifying residues important for a phenotype of interest.

An approach in building a chemical compound search engine in oracle database.

PubMed

Wang, H; Volarath, P; Harrison, R

2005-01-01

A searching or identifying of chemical compounds is an important process in drug design and in chemistry research. An efficient search engine involves a close coupling of the search algorithm and database implementation. The database must process chemical structures, which demands the approaches to represent, store, and retrieve structures in a database system. In this paper, a general database framework for working as a chemical compound search engine in Oracle database is described. The framework is devoted to eliminate data type constrains for potential search algorithms, which is a crucial step toward building a domain specific query language on top of SQL. A search engine implementation based on the database framework is also demonstrated. The convenience of the implementation emphasizes the efficiency and simplicity of the framework.

Topologically associating domains are stable units of replication-timing regulation.

PubMed

Pope, Benjamin D; Ryba, Tyrone; Dileep, Vishnu; Yue, Feng; Wu, Weisheng; Denas, Olgert; Vera, Daniel L; Wang, Yanli; Hansen, R Scott; Canfield, Theresa K; Thurman, Robert E; Cheng, Yong; Gülsoy, Günhan; Dennis, Jonathan H; Snyder, Michael P; Stamatoyannopoulos, John A; Taylor, James; Hardison, Ross C; Kahveci, Tamer; Ren, Bing; Gilbert, David M

2014-11-20

Eukaryotic chromosomes replicate in a temporal order known as the replication-timing program. In mammals, replication timing is cell-type-specific with at least half the genome switching replication timing during development, primarily in units of 400-800 kilobases ('replication domains'), whose positions are preserved in different cell types, conserved between species, and appear to confine long-range effects of chromosome rearrangements. Early and late replication correlate, respectively, with open and closed three-dimensional chromatin compartments identified by high-resolution chromosome conformation capture (Hi-C), and, to a lesser extent, late replication correlates with lamina-associated domains (LADs). Recent Hi-C mapping has unveiled substructure within chromatin compartments called topologically associating domains (TADs) that are largely conserved in their positions between cell types and are similar in size to replication domains. However, TADs can be further sub-stratified into smaller domains, challenging the significance of structures at any particular scale. Moreover, attempts to reconcile TADs and LADs to replication-timing data have not revealed a common, underlying domain structure. Here we localize boundaries of replication domains to the early-replicating border of replication-timing transitions and map their positions in 18 human and 13 mouse cell types. We demonstrate that, collectively, replication domain boundaries share a near one-to-one correlation with TAD boundaries, whereas within a cell type, adjacent TADs that replicate at similar times obscure replication domain boundaries, largely accounting for the previously reported lack of alignment. Moreover, cell-type-specific replication timing of TADs partitions the genome into two large-scale sub-nuclear compartments revealing that replication-timing transitions are indistinguishable from late-replicating regions in chromatin composition and lamina association and accounting for the reduced correlation of replication timing to LADs and heterochromatin. Our results reconcile cell-type-specific sub-nuclear compartmentalization and replication timing with developmentally stable structural domains and offer a unified model for large-scale chromosome structure and function.

Mdt1 Facilitates Efficient Repair of Blocked DNA Double-Strand Breaks and Recombinational Maintenance of Telomeres▿

PubMed Central

Pike, Brietta L.; Heierhorst, Jörg

2007-01-01

DNA recombination plays critical roles in DNA repair and alternative telomere maintenance. Here we show that absence of the SQ/TQ cluster domain-containing protein Mdt1 (Ybl051c) renders Saccharomyces cerevisiae particularly hypersensitive to bleomycin, a drug that causes 3′-phospho-glycolate-blocked DNA double-strand breaks (DSBs). mdt1Δ also hypersensitizes partially recombination-defective cells to camptothecin-induced 3′-phospho-tyrosyl protein-blocked DSBs. Remarkably, whereas mdt1Δ cells are unable to restore broken chromosomes after bleomycin treatment, they efficiently repair “clean” endonuclease-generated DSBs. Epistasis analyses indicate that MDT1 acts in the repair of bleomycin-induced DSBs by regulating the efficiency of the homologous recombination pathway as well as telomere-related functions of the KU complex. Moreover, mdt1Δ leads to severe synthetic growth defects with a deletion of the recombination facilitator and telomere-positioning factor gene CTF18 already in the absence of exogenous DNA damage. Importantly, mdt1Δ causes a dramatic shift from the usually prevalent type II to the less-efficient type I pathway of recombinational telomere maintenance in the absence of telomerase in liquid senescence assays. As telomeres resemble protein-blocked DSBs, the results indicate that Mdt1 acts in a novel blocked-end-specific recombination pathway that is required for the efficiency of both drug-induced DSB repair and telomerase-independent telomere maintenance. PMID:17636027

Parallel Domain Decomposition Formulation and Software for Large-Scale Sparse Symmetrical/Unsymmetrical Aeroacoustic Applications

NASA Technical Reports Server (NTRS)

Nguyen, D. T.; Watson, Willie R. (Technical Monitor)

2005-01-01

The overall objectives of this research work are to formulate and validate efficient parallel algorithms, and to efficiently design/implement computer software for solving large-scale acoustic problems, arised from the unified frameworks of the finite element procedures. The adopted parallel Finite Element (FE) Domain Decomposition (DD) procedures should fully take advantages of multiple processing capabilities offered by most modern high performance computing platforms for efficient parallel computation. To achieve this objective. the formulation needs to integrate efficient sparse (and dense) assembly techniques, hybrid (or mixed) direct and iterative equation solvers, proper pre-conditioned strategies, unrolling strategies, and effective processors' communicating schemes. Finally, the numerical performance of the developed parallel finite element procedures will be evaluated by solving series of structural, and acoustic (symmetrical and un-symmetrical) problems (in different computing platforms). Comparisons with existing "commercialized" and/or "public domain" software are also included, whenever possible.

Interaction with Tsg101 is necessary for the efficient transport and release of nucleocapsids in marburg virus-infected cells.

PubMed

Dolnik, Olga; Kolesnikova, Larissa; Welsch, Sonja; Strecker, Thomas; Schudt, Gordian; Becker, Stephan

2014-10-01

Endosomal sorting complex required for transport (ESCRT) machinery supports the efficient budding of Marburg virus (MARV) and many other enveloped viruses. Interaction between components of the ESCRT machinery and viral proteins is predominantly mediated by short tetrapeptide motifs, known as late domains. MARV contains late domain motifs in the matrix protein VP40 and in the genome-encapsidating nucleoprotein (NP). The PSAP late domain motif of NP recruits the ESCRT-I protein tumor susceptibility gene 101 (Tsg101). Here, we generated a recombinant MARV encoding NP with a mutated PSAP late domain (rMARV(PSAPmut)). rMARV(PSAPmut) was attenuated by up to one log compared with recombinant wild-type MARV (rMARV(wt)), formed smaller plaques and exhibited delayed virus release. Nucleocapsids in rMARV(PSAPmut)-infected cells were more densely packed inside viral inclusions and more abundant in the cytoplasm than in rMARV(wt)-infected cells. A similar phenotype was detected when MARV-infected cells were depleted of Tsg101. Live-cell imaging analyses revealed that Tsg101 accumulated in inclusions of rMARV(wt)-infected cells and was co-transported together with nucleocapsids. In contrast, rMARV(PSAPmut) nucleocapsids did not display co-localization with Tsg101, had significantly shorter transport trajectories, and migration close to the plasma membrane was severely impaired, resulting in reduced recruitment into filopodia, the major budding sites of MARV. We further show that the Tsg101 interacting protein IQGAP1, an actin cytoskeleton regulator, was recruited into inclusions and to individual nucleocapsids together with Tsg101. Moreover, IQGAP1 was detected in a contrail-like structure at the rear end of migrating nucleocapsids. Down regulation of IQGAP1 impaired release of MARV. These results indicate that the PSAP motif in NP, which enables binding to Tsg101, is important for the efficient actin-dependent transport of nucleocapsids to the sites of budding. Thus, the interaction between NP and Tsg101 supports several steps of MARV assembly before virus fission.

Spectral Collocation Time-Domain Modeling of Diffractive Optical Elements

NASA Astrophysics Data System (ADS)

Hesthaven, J. S.; Dinesen, P. G.; Lynov, J. P.

1999-11-01

A spectral collocation multi-domain scheme is developed for the accurate and efficient time-domain solution of Maxwell's equations within multi-layered diffractive optical elements. Special attention is being paid to the modeling of out-of-plane waveguide couplers. Emphasis is given to the proper construction of high-order schemes with the ability to handle very general problems of considerable geometric and material complexity. Central questions regarding efficient absorbing boundary conditions and time-stepping issues are also addressed. The efficacy of the overall scheme for the time-domain modeling of electrically large, and computationally challenging, problems is illustrated by solving a number of plane as well as non-plane waveguide problems.

Using Online Algorithms to Solve NP-Hard Problems More Efficiently in Practice

DTIC Science & Technology

2007-12-01

bounds. For the openstacks , TPP, and pipesworld domains, our results were qualitatively different: most instances in these domains were either easy...between our results in these two sets of domains. For most in- stances in the openstacks domain we found no k values that elicited a “yes” answer in

Indexing and retrieval of MPEG compressed video

NASA Astrophysics Data System (ADS)

Kobla, Vikrant; Doermann, David S.

1998-04-01

To keep pace with the increased popularity of digital video as an archival medium, the development of techniques for fast and efficient analysis of ideo streams is essential. In particular, solutions to the problems of storing, indexing, browsing, and retrieving video data from large multimedia databases are necessary to a low access to these collections. Given that video is often stored efficiently in a compressed format, the costly overhead of decompression can be reduced by analyzing the compressed representation directly. In earlier work, we presented compressed domain parsing techniques which identified shots, subshots, and scenes. In this article, we present efficient key frame selection, feature extraction, indexing, and retrieval techniques that are directly applicable to MPEG compressed video. We develop a frame type independent representation which normalizes spatial and temporal features including frame type, frame size, macroblock encoding, and motion compensation vectors. Features for indexing are derived directly from this representation and mapped to a low- dimensional space where they can be accessed using standard database techniques. Spatial information is used as primary index into the database and temporal information is used to rank retrieved clips and enhance the robustness of the system. The techniques presented enable efficient indexing, querying, and retrieval of compressed video as demonstrated by our system which typically takes a fraction of a second to retrieve similar video scenes from a database, with over 95 percent recall.

Age Differences in the Effects of Domain Knowledge on Reading Efficiency

PubMed Central

Miller, Lisa M. Soederberg

2009-01-01

The present study investigated age differences in the effects of knowledge on the efficiency with which information is processed while reading. Individuals between 18 and 85 years of age, with varying levels of cooking knowledge, read and recalled a series of short passages within the domain of cooking. Reading efficiency was operationalized as time spent reading divided by the amount recalled for each passage. Results showed that reading efficiency increased with increasing levels of knowledge among older but not younger adults. Similarly, those with smaller working memory capacities showed increasing efficiency with increasing knowledge. These findings suggest that knowledge promotes a more efficient allocation policy which is particularly helpful in later life, perhaps due to age-related declines in working memory capacity. PMID:19290738

Site-specific photoconjugation of antibodies using chemically synthesized IgG-binding domains.

PubMed

Perols, Anna; Karlström, Amelie Eriksson

2014-03-19

Site-specific labeling of antibodies can be performed using the immunoglobulin-binding Z domain, derived from staphylococcal protein A (SpA), which has a well-characterized binding site in the Fc region of antibodies. By introducing a photoactivable probe in the Z domain, a covalent bond can be formed between the Z domain and the antibody by irradiation with UV light. The aim of this study was to improve the conjugation yield for labeling of different subclasses of IgG having different sequence composition, using a photoactivated Z domain variant. Four different variants of the Z domain (Z5BPA, Z5BBA, Z32BPA, and Z32BBA) were synthesized to investigate the influence of the position of the photoactivable probe and the presence of a flexible linker between the probe and the protein. For two of the variants, the photoreactive benzophenone group was introduced as part of an amino acid side chain by incorporation of the unnatural amino acid benzoylphenylalanine (BPA) during peptide synthesis. For the other two variants, the photoreactive benzophenone group was attached via a flexible linker by coupling of benzoylbenzoic acid (BBA) to the ε-amino group of a selectively deprotected lysine residue. Photoconjugation experiments using human IgG1, mouse IgG1, and mouse IgG2A demonstrated efficient conjugation for all antibodies. It was shown that differences in linker length had a large impact on the conjugation efficiency for labeling of mouse IgG1, whereas the positioning of the photoactivable probe in the sequence of the protein had a larger effect for mouse IgG2A. Conjugation to human IgG1 was only to a minor extent affected by position or linker length. For each subclass of antibody, the best variant tested using a standard conjugation protocol resulted in conjugation efficiencies of 41-66%, which corresponds to on average approximately one Z domain attached to each antibody. As a combination of the two best performing variants, Z5BBA and Z32BPA, a Z domain variant with two photoactivable probes (Z5BBA32BPA) was also synthesized with the aim of targeting a wider panel of antibody subclasses and species. This new reagent could efficiently couple to all antibody subclasses that were targeted by the single benzophenone-labeled Z domain variants, with conjugation efficiencies of 26-41%.

Spin-wave diode

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lan, Jin; Yu, Weichao; Wu, Ruqian

A diode, a device allowing unidirectional signal transmission, is a fundamental element of logic structures, and it lies at the heart of modern information systems. The spin wave or magnon, representing a collective quasiparticle excitation of the magnetic order in magnetic materials, is a promising candidate for an information carrier for the next-generation energy-saving technologies. Here, we propose a scalable and reprogrammable pure spin-wave logic hardware architecture using domain walls and surface anisotropy stripes as waveguides on a single magnetic wafer. We demonstrate theoretically the design principle of the simplest logic component, a spin-wave diode, utilizing the chiral bound statesmore » in a magnetic domain wall with a Dzyaloshinskii-Moriya interaction, and confirm its performance through micromagnetic simulations. As a result, these findings open a new vista for realizing different types of pure spin-wave logic components and finally achieving an energy-efficient and hardware-reprogrammable spin-wave computer.« less

Efficient Sample Tracking With OpenLabFramework

PubMed Central

List, Markus; Schmidt, Steffen; Trojnar, Jakub; Thomas, Jochen; Thomassen, Mads; Kruse, Torben A.; Tan, Qihua; Baumbach, Jan; Mollenhauer, Jan

2014-01-01

The advance of new technologies in biomedical research has led to a dramatic growth in experimental throughput. Projects therefore steadily grow in size and involve a larger number of researchers. Spreadsheets traditionally used are thus no longer suitable for keeping track of the vast amounts of samples created and need to be replaced with state-of-the-art laboratory information management systems. Such systems have been developed in large numbers, but they are often limited to specific research domains and types of data. One domain so far neglected is the management of libraries of vector clones and genetically engineered cell lines. OpenLabFramework is a newly developed web-application for sample tracking, particularly laid out to fill this gap, but with an open architecture allowing it to be extended for other biological materials and functional data. Its sample tracking mechanism is fully customizable and aids productivity further through support for mobile devices and barcoded labels. PMID:24589879

Spin-wave diode

DOE PAGES

Lan, Jin; Yu, Weichao; Wu, Ruqian; ...

2015-12-28

A diode, a device allowing unidirectional signal transmission, is a fundamental element of logic structures, and it lies at the heart of modern information systems. The spin wave or magnon, representing a collective quasiparticle excitation of the magnetic order in magnetic materials, is a promising candidate for an information carrier for the next-generation energy-saving technologies. Here, we propose a scalable and reprogrammable pure spin-wave logic hardware architecture using domain walls and surface anisotropy stripes as waveguides on a single magnetic wafer. We demonstrate theoretically the design principle of the simplest logic component, a spin-wave diode, utilizing the chiral bound statesmore » in a magnetic domain wall with a Dzyaloshinskii-Moriya interaction, and confirm its performance through micromagnetic simulations. As a result, these findings open a new vista for realizing different types of pure spin-wave logic components and finally achieving an energy-efficient and hardware-reprogrammable spin-wave computer.« less

Fast frequency domain method to detect skew in a document image

NASA Astrophysics Data System (ADS)

Mehta, Sunita; Walia, Ekta; Dutta, Maitreyee

2015-12-01

In this paper, a new fast frequency domain method based on Discrete Wavelet Transform and Fast Fourier Transform has been implemented for the determination of the skew angle in a document image. Firstly, image size reduction is done by using two-dimensional Discrete Wavelet Transform and then skew angle is computed using Fast Fourier Transform. Skew angle error is almost negligible. The proposed method is experimented using a large number of documents having skew between -90° and +90° and results are compared with Moments with Discrete Wavelet Transform method and other commonly used existing methods. It has been determined that this method works more efficiently than the existing methods. Also, it works with typed, picture documents having different fonts and resolutions. It overcomes the drawback of the recently proposed method of Moments with Discrete Wavelet Transform that does not work with picture documents.

Linear finite-difference bond graph model of an ionic polymer actuator

NASA Astrophysics Data System (ADS)

Bentefrit, M.; Grondel, S.; Soyer, C.; Fannir, A.; Cattan, E.; Madden, J. D.; Nguyen, T. M. G.; Plesse, C.; Vidal, F.

2017-09-01

With the recent growing interest for soft actuation, many new types of ionic polymers working in air have been developed. Due to the interrelated mechanical, electrical, and chemical properties which greatly influence the characteristics of such actuators, their behavior is complex and difficult to understand, predict and optimize. In light of this challenge, an original linear multiphysics finite difference bond graph model was derived to characterize this ionic actuation. This finite difference scheme was divided into two coupled subparts, each related to a specific physical, electrochemical or mechanical domain, and then converted into a bond graph model as this language is particularly suited for systems from multiple energy domains. Simulations were then conducted and a good agreement with the experimental results was obtained. Furthermore, an analysis of the power efficiency of such actuators as a function of space and time was proposed and allowed to evaluate their performance.

Neuroglian activates Echinoid to antagonize the Drosophila EGF receptor signaling pathway.

PubMed

Islam, Rafique; Wei, Shu-Yi; Chiu, Wei-Hsin; Hortsch, Michael; Hsu, Jui-Chou

2003-05-01

echinoid (ed) encodes an cell-adhesion molecule (CAM) that contains immunoglobulin domains and regulates the EGFR signaling pathway during Drosophila eye development. Based on our previous genetic mosaic and epistatic analysis, we proposed that Ed, via homotypic interactions, activates a novel, as yet unknown pathway that antagonizes EGFR signaling. In this report, we demonstrate that Ed functions as a homophilic adhesion molecule and also engages in a heterophilic trans-interaction with Drosophila Neuroglian (Nrg), an L1-type CAM. Co-expression of ed and nrg in the eye exhibits a strong genetic synergy in inhibiting EGFR signaling. This synergistic effect requires the intracellular domain of Ed, but not that of Nrg. In addition, Ed and Nrg colocalize in the Drosophila eye and are efficiently co-immunoprecipitated. Together, our results suggest a model in which Nrg acts as a heterophilic ligand and activator of Ed, which in turn antagonizes EGFR signaling.

Spatial frequency domain spectroscopy of two layer media

NASA Astrophysics Data System (ADS)

Yudovsky, Dmitry; Durkin, Anthony J.

2011-10-01

Monitoring of tissue blood volume and oxygen saturation using biomedical optics techniques has the potential to inform the assessment of tissue health, healing, and dysfunction. These quantities are typically estimated from the contribution of oxyhemoglobin and deoxyhemoglobin to the absorption spectrum of the dermis. However, estimation of blood related absorption in superficial tissue such as the skin can be confounded by the strong absorption of melanin in the epidermis. Furthermore, epidermal thickness and pigmentation varies with anatomic location, race, gender, and degree of disease progression. This study describes a technique for decoupling the effect of melanin absorption in the epidermis from blood absorption in the dermis for a large range of skin types and thicknesses. An artificial neural network was used to map input optical properties to spatial frequency domain diffuse reflectance of two layer media. Then, iterative fitting was used to determine the optical properties from simulated spatial frequency domain diffuse reflectance. Additionally, an artificial neural network was trained to directly map spatial frequency domain reflectance to sets of optical properties of a two layer medium, thus bypassing the need for iteration. In both cases, the optical thickness of the epidermis and absorption and reduced scattering coefficients of the dermis were determined independently. The accuracy and efficiency of the iterative fitting approach was compared with the direct neural network inversion.

HD domain of SAMHD1 influences Vpx-induced degradation at a post-interaction step.

PubMed

Kang, Jian; Hou, Jingwei; Zhao, Ke; Yu, Xiao-Fang; Du, Juan

2016-02-12

Primate SAMHD1 proteins are potent inhibitors of viruses, including retroviruses such as HIV-1, HIV-2, and SIV. Vpx, a distinctive viral protein expressed by HIV-2 and some SIVs, induces SAMHD1 degradation by forming a Vpx-DCAF1-based ubiquitin ligase complex. Either the N- or the C-terminus of SAMHD1 is critical for Vpx-induced degradation, depending on the types of SAMHD1 and Vpx proteins. However, it was not fully understood whether other regions of SAMHD1 also contribute to its depletion by Vpx. In the present study, we report that SAMHD1 from chicken (SAMHD1GG) was not degraded by SIVmac Vpx, in contrast with results for human SAMHD1 (SAMHD1HS). Results regarding to SAMHD1HS and SAMHD1GG fusion proteins supported previous findings that the C-terminus of SAMHD1HS is essential for Vpx-induced degradation. Internal domain substitution, however, revealed that the HD domain also contributes to Vpx-mediated SAMHD1 degradation. Interestingly, the HD domain influenced Vpx-mediated SAMHD1 degradation without affecting Vpx-SAMHD1 interaction. Therefore, our findings revealed that factors in addition to Vpx-SAMHD1 binding influence the efficiency of Vpx-mediated SAMHD1 degradation. Copyright © 2016 Elsevier Inc. All rights reserved.

PDZ Binding Domains, Structural Disorder and Phosphorylation: A Menage-a-trois Tailing Dcp2 mRNA Decapping Enzymes.

PubMed

Gunawardana, Dilantha

2016-01-01

Diverse cellular activities are mediated through the interaction of protein domains and their binding partners. One such protein domain widely distributed in the higher metazoan world is the PDZ domain, which facilitates abundant protein-protein interactions. The PDZ domain-PDZ binding domain interaction has been implicated in several pathologies including Alzheimer's disease, Parkinson's disease and Down syndrome. PDZ domains bind to C-terminal peptides/proteins which have either of the following combinations: S/T-X-hydrophobic-COOH for type I, hydrophobic-Xhydrophobic- COOH for type II, and D/E-X-hydrophobic-COOH for type III, although hydrophobicity in the termini form the key characteristic of the PDZ-binding domains. We identified and characterized a Dcp2 type mRNA decapping enzyme from Arabidopsis thaliana, a protein containing a putative PDZ-binding domain using mutagenesis and protein biochemistry. Now we are using bioinformatics to study the Cterminal end of mRNA decapping enzymes from complex metazoans with the aim of (1) identifying putative PDZ-binding domains (2) Correlating structural disorder with PDZ binding domains and (3) Demonstrating the presence of phosphorylation sites in C-terminal extremities of Dcp2 type mRNA decapping enzymes. It is proposed here that the trinity of PDZbinding domains, structural disorder and phosphorylation-susceptible sites are a feature of the Dcp2 family of decapping enzymes and perhaps is a wider trick in protein evolution where scaffolding/tethering is a requirement for localization and function. It is critical though laboratory-based supporting evidence is sought to back-up this bioinformatics exploration into tail regions of mRNA decapping enzymes.

Three-dimensional inverse modelling of damped elastic wave propagation in the Fourier domain

NASA Astrophysics Data System (ADS)

Petrov, Petr V.; Newman, Gregory A.

2014-09-01

3-D full waveform inversion (FWI) of seismic wavefields is routinely implemented with explicit time-stepping simulators. A clear advantage of explicit time stepping is the avoidance of solving large-scale implicit linear systems that arise with frequency domain formulations. However, FWI using explicit time stepping may require a very fine time step and (as a consequence) significant computational resources and run times. If the computational challenges of wavefield simulation can be effectively handled, an FWI scheme implemented within the frequency domain utilizing only a few frequencies, offers a cost effective alternative to FWI in the time domain. We have therefore implemented a 3-D FWI scheme for elastic wave propagation in the Fourier domain. To overcome the computational bottleneck in wavefield simulation, we have exploited an efficient Krylov iterative solver for the elastic wave equations approximated with second and fourth order finite differences. The solver does not exploit multilevel preconditioning for wavefield simulation, but is coupled efficiently to the inversion iteration workflow to reduce computational cost. The workflow is best described as a series of sequential inversion experiments, where in the case of seismic reflection acquisition geometries, the data has been laddered such that we first image highly damped data, followed by data where damping is systemically reduced. The key to our modelling approach is its ability to take advantage of solver efficiency when the elastic wavefields are damped. As the inversion experiment progresses, damping is significantly reduced, effectively simulating non-damped wavefields in the Fourier domain. While the cost of the forward simulation increases as damping is reduced, this is counterbalanced by the cost of the outer inversion iteration, which is reduced because of a better starting model obtained from the larger damped wavefield used in the previous inversion experiment. For cross-well data, it is also possible to launch a successful inversion experiment without laddering the damping constants. With this type of acquisition geometry, the solver is still quite effective using a small fixed damping constant. To avoid cycle skipping, we also employ a multiscale imaging approach, in which frequency content of the data is also laddered (with the data now including both reflection and cross-well data acquisition geometries). Thus the inversion process is launched using low frequency data to first recover the long spatial wavelength of the image. With this image as a new starting model, adding higher frequency data refines and enhances the resolution of the image. FWI using laddered frequencies with an efficient damping schemed enables reconstructing elastic attributes of the subsurface at a resolution that approaches half the smallest wavelength utilized to image the subsurface. We show the possibility of effectively carrying out such reconstructions using two to six frequencies, depending upon the application. Using the proposed FWI scheme, massively parallel computing resources are essential for reasonable execution times.

Parallel deterministic transport sweeps of structured and unstructured meshes with overloaded mesh decompositions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pautz, Shawn D.; Bailey, Teresa S.

Here, the efficiency of discrete ordinates transport sweeps depends on the scheduling algorithm, the domain decomposition, the problem to be solved, and the computational platform. Sweep scheduling algorithms may be categorized by their approach to several issues. In this paper we examine the strategy of domain overloading for mesh partitioning as one of the components of such algorithms. In particular, we extend the domain overloading strategy, previously defined and analyzed for structured meshes, to the general case of unstructured meshes. We also present computational results for both the structured and unstructured domain overloading cases. We find that an appropriate amountmore » of domain overloading can greatly improve the efficiency of parallel sweeps for both structured and unstructured partitionings of the test problems examined on up to 10 5 processor cores.« less

Parallel deterministic transport sweeps of structured and unstructured meshes with overloaded mesh decompositions

DOE PAGES

Pautz, Shawn D.; Bailey, Teresa S.

2016-11-29

Here, the efficiency of discrete ordinates transport sweeps depends on the scheduling algorithm, the domain decomposition, the problem to be solved, and the computational platform. Sweep scheduling algorithms may be categorized by their approach to several issues. In this paper we examine the strategy of domain overloading for mesh partitioning as one of the components of such algorithms. In particular, we extend the domain overloading strategy, previously defined and analyzed for structured meshes, to the general case of unstructured meshes. We also present computational results for both the structured and unstructured domain overloading cases. We find that an appropriate amountmore » of domain overloading can greatly improve the efficiency of parallel sweeps for both structured and unstructured partitionings of the test problems examined on up to 10 5 processor cores.« less

When the CA-TIMS therapy fails: the over-enthusiastic, the mixed-up, and the stubborn zircon

NASA Astrophysics Data System (ADS)

Corfu, F.

2009-12-01

Mattinson’s CA-TIMS technique has proven to be highly successful in efficiently removing disturbed domains of zircon, thus enabling the determination of precise and accurate ages in a variety of geological situations. The method generally produces equal or better results than mechanical abrasion. There are, however, cases where CA-TIMS fails to achieve perfect concordance, and occasionally actually increases the degree of discordance. Such a behaviour (the over-reaction) is observed for example in U-rich (>1000 ppm) but texturally homogeneous zircon, a type quite common in highly differentiated portions of mafic intrusions, in granitic pegmatites, and in some metamorphic rocks. Because of their internal uniformity, such zircons do not exhibit large contrasts in crystallinity and solubility and after the baking stage of the CA-TIMS procedure they will either totally dissolve in the first HF attack, or produce discordant results. By contrast, mechanical abrasion of this type of zircon can isolate alteration-free zircon domains that yield concordant and reproducible data. This is due to the homogeneity of the crystals, the lack of zoning limiting contrasts in the degrees of metamictization and brittleness and preventing fracturing. The absence of fractures helps to confine alteration of zircon to the marginal domains, and these can be removed very efficiently by mechanical abrasion. This behaviour is exemplified by zircon populations from 252.0 Ma and 182.5 Ma mafic sills in Siberia and the Karoo basin. Another class of zircons that in general does not, or only partially comply with CA-TIMS includes populations from metamorphic and poly-orogenic rocks, typical of many Proterozoic orogens. The metamorphic reprocessing of zircon into low-U domains can freeze-in old Pb-loss patterns that cannot be undone by any technique. New metamorphic zircon growth can also create mixtures of different aged domains that cannot be resolved by CA-TIMS. In favourable circumstances, however, CA-TIMS could provide elegant ways to isolate the metamorphic components. A third category includes zircon populations that fail to achieve consistent ages, or concordant plateaus in multi-step partial dissolutions, even though they may have all the attributes of ideal CA-TIMS objects. The category is exemplified by a 62 Ma magmatic suite with a simple geological history and good quality zircon populations. The zircons have moderate U contents, regular growth zoning and few visible imperfections, yet the data reveal very extensive Pb loss requiring the almost total dissolution of the zircon before reaching the concordant residues. Baking of some of these zircon populations turns the colourless crystals brick-red (but still transparent), the red colour persisting long into the partial dissolution procedure. These features suggest that Pb loss may be related to a submicroscopic network of impurities and primary defects in the crystal structures which form pathways for the diffusion of Pb. Subsequent annealing appears to make the discordant domains impervious to partial dissolution. In conclusion, it is evident that CA-TIMS is a very helpful new technique for U-Pb geochronology, but some limitations must be considered that require case-by-case judgment and good Krogh-type abraders in reserve.

Crystal structure of the second fibronectin type III (FN3) domain from human collagen α1 type XX.

PubMed

Zhao, Jingfeng; Ren, Jixia; Wang, Nan; Cheng, Zhong; Yang, Runmei; Lin, Gen; Guo, Yi; Cai, Dayong; Xie, Yong; Zhao, Xiaohong

2017-12-01

Collagen α1 type XX, which contains fibronectin type III (FN3) repeats involving six FN3 domains (referred to as the FN#1-FN#6 domains), is an unusual member of the fibril-associated collagens with interrupted triple helices (FACIT) subfamily of collagens. The results of standard protein BLAST suggest that the FN3 repeats might contribute to collagen α1 type XX acting as a cytokine receptor. To date, solution NMR structures of the FN#3, FN#4 and FN#6 domains have been determined. To obtain further structural evidence to understand the relationship between the structure and function of the FN3 repeats from collagen α1 type XX, the crystal structure of the FN#2 domain from human collagen α1 type XX (residues Pro386-Pro466; referred to as FN2-HCXX) was solved at 2.5 Å resolution. The crystal structure of FN2-HCXX shows an immunoglobulin-like fold containing a β-sandwich structure, which is formed by a three-stranded β-sheet (β1, β2 and β5) packed onto a four-stranded β-sheet (β3, β4, β6 and β7). Two consensus domains, tencon and fibcon, are structural analogues of FN2-HCXX. Fn8, an FN3 domain from human oncofoetal fibronectin, is the closest structural analogue of FN2-HCXX derived from a naturally occurring sequence. Based solely on the structural similarity of FN2-HCXX to other FN3 domains, the detailed functions of FN2-HCXX and the FN3 repeats in collagen α1 type XX cannot be identified.

Folding and conformational consequences of glycine to alanine replacements at different positions in a collagen model peptide.

PubMed

Bhate, Manjiri; Wang, Xin; Baum, Jean; Brodsky, Barbara

2002-05-21

The collagen model peptide T1-892 includes a C-terminal nucleation domain, (Gly-Pro-Hyp)(4), and an N-terminal (Gly-X-Y)(6) sequence taken from type I collagen. In osteogenesis imperfecta (OI) and other collagen diseases, single base mutations often convert one Gly to a larger residue, and T1-892 homologues modeling such mutations were synthesized with Gly to Ala substitutions in either the (Gly-Pro-Hyp)(4) domain, Gly25Ala, or the (Gly-X-Y)(6) domain, Gly10Ala. CD and NMR studies show the Gly10Ala peptide forms a normal triple-helix at the C-terminal end and propagates from the C- to the N-terminus until the Gly --> Ala substitution is encountered. At this point, triple-helix folding is terminated and cannot be reinitiated, leaving a nonhelical N-terminus. A decreased thermal stability is observed as a result of the shorter length of the triple-helix. In contrast, introduction of the Gly to Ala replacement at position 25, in the nucleation domain, shifts the monomer/trimer equilibrium toward the monomer form. The increased monomer and lower trimer populations are reflected in the dramatic decrease in triple-helix content and stability. Unlike the Ala replacement at position 10, the Ala substitution in the (Gly-Pro-Hyp)(4) region can still be incorporated into a triple-helix, but at a greatly decreased rate of folding, since the original efficient nucleation site is no longer operative. The specific consequences of Gly to Ala replacements in two distinctive sequences in this triple-helical peptide may help clarify the variability in OI clinical severity resulting from mutations at different sites along type I collagen chains.

Analysis on the time and frequency domains of the acceleration in front crawl stroke.

PubMed

Gil, Joaquín Madera; Moreno, Luis-Millán González; Mahiques, Juan Benavent; Muñoz, Víctor Tella

2012-05-01

The swimming involves accelerations and decelerations in the swimmer's body. Thus, the main objective of this study is to make a temporal and frequency analysis of the acceleration in front crawl swimming, regarding the gender and the performance. The sample was composed by 31 male swimmers (15 of high-level and 16 of low-level) and 20 female swimmers (11 of high-level and 9 of low-level). The acceleration was registered from the third complete cycle during eight seconds in a 25 meters maximum velocity test. A position transducer (200Hz) was used to collect the data, and it was synchronized to an aquatic camera (25Hz). The acceleration in the temporal (root mean square, minimum and maximum of the acceleration) and frequency (power peak, power peak frequency and spectral area) domains was calculated with Fourier analysis, as well as the velocity and the spectrums distribution in function to present one or more main peaks (type 1 and type 2). A one-way ANOVA was used to establish differences between gender and performance. Results show differences between genders in all the temporal domain variables (p<0.05) and only the Spectral Area (SA) in the frequency domain (p<0.05). Between gender and performance, only the Root Mean Square (RMS) showed differences in the performance of the male swimmers (p<0.05) and in the higher level swimmers, the Maximum (Max) and the Power Peak (PP) of the acceleration showed differences between both genders (p<0.05). These results confirms the importance of knowing the RMS to determine the efficiency of the swimmers regarding gender and performance level.

Reciprocal voltage sensor-to-pore coupling leads to potassium channel C-type inactivation

PubMed Central

Conti, Luca; Renhorn, Jakob; Gabrielsson, Anders; Turesson, Fredrik; Liin, Sara I; Lindahl, Erik; Elinder, Fredrik

2016-01-01

Voltage-gated potassium channels open at depolarized membrane voltages. A prolonged depolarization causes a rearrangement of the selectivity filter which terminates the conduction of ions – a process called slow or C-type inactivation. How structural rearrangements in the voltage-sensor domain (VSD) cause alteration in the selectivity filter, and vice versa, are not fully understood. We show that pulling the pore domain of the Shaker potassium channel towards the VSD by a Cd2+ bridge accelerates C-type inactivation. Molecular dynamics simulations show that such pulling widens the selectivity filter and disrupts the K+ coordination, a hallmark for C-type inactivation. An engineered Cd2+ bridge within the VSD also affect C-type inactivation. Conversely, a pore domain mutation affects VSD gating-charge movement. Finally, C-type inactivation is caused by the concerted action of distant amino acid residues in the pore domain. All together, these data suggest a reciprocal communication between the pore domain and the VSD in the extracellular portion of the channel. PMID:27278891

Reciprocal voltage sensor-to-pore coupling leads to potassium channel C-type inactivation

NASA Astrophysics Data System (ADS)

Conti, Luca; Renhorn, Jakob; Gabrielsson, Anders; Turesson, Fredrik; Liin, Sara I.; Lindahl, Erik; Elinder, Fredrik

2016-06-01

Voltage-gated potassium channels open at depolarized membrane voltages. A prolonged depolarization causes a rearrangement of the selectivity filter which terminates the conduction of ions - a process called slow or C-type inactivation. How structural rearrangements in the voltage-sensor domain (VSD) cause alteration in the selectivity filter, and vice versa, are not fully understood. We show that pulling the pore domain of the Shaker potassium channel towards the VSD by a Cd2+ bridge accelerates C-type inactivation. Molecular dynamics simulations show that such pulling widens the selectivity filter and disrupts the K+ coordination, a hallmark for C-type inactivation. An engineered Cd2+ bridge within the VSD also affect C-type inactivation. Conversely, a pore domain mutation affects VSD gating-charge movement. Finally, C-type inactivation is caused by the concerted action of distant amino acid residues in the pore domain. All together, these data suggest a reciprocal communication between the pore domain and the VSD in the extracellular portion of the channel.

Functional Characterisation of the WW Minimal Domain for Delivering Therapeutic Proteins by Adenovirus Dodecahedron

PubMed Central

Villegas-Méndez, Ana; Fender, Pascal; Garin, Marina I.; Rothe, Romy; Liguori, Lavinia; Marques, Bruno; Lenormand, Jean-Luc

2012-01-01

Protein transduction offers a great therapeutic potential by efficient delivery of biologically active cargo into cells. The Adenovirus Dd (Dodecahedron) has recently been shown to deliver proteins fused to the tandem WW2-3-4 structural domains from the E3 ubiquitin ligase Nedd4. In this study, we conclusively show that Dd is able to efficiently deliver cargo inside living cells, which mainly localize in fast moving endocytic vesicles, supporting active transport along the cytoskeleton. We further improve this delivery system by expressing a panel of 13 WW-GFP mutant forms to characterize their binding properties towards Dd. We identified the domain WW3 and its mutant form WW3_10_13 to be sufficient for optimal binding to Dd. We greatly minimise the interacting WW modules from 20 to 6 kDa without compromising its efficient delivery by Dd. Using these minimal WW domains fused to the tumor suppressor p53 protein, we show efficient cellular uptake and distribution into cancer cells, leading to specific induction of apoptosis in these cells. Taken together, these findings represent a step further towards the development of a Dd-based delivery system for future therapeutic application. PMID:23028993

Giant energy density and high efficiency achieved in bismuth ferrite-based film capacitors via domain engineering.

PubMed

Pan, Hao; Ma, Jing; Ma, Ji; Zhang, Qinghua; Liu, Xiaozhi; Guan, Bo; Gu, Lin; Zhang, Xin; Zhang, Yu-Jun; Li, Liangliang; Shen, Yang; Lin, Yuan-Hua; Nan, Ce-Wen

2018-05-08

Developing high-performance film dielectrics for capacitive energy storage has been a great challenge for modern electrical devices. Despite good results obtained in lead titanate-based dielectrics, lead-free alternatives are strongly desirable due to environmental concerns. Here we demonstrate that giant energy densities of ~70 J cm -3 , together with high efficiency as well as excellent cycling and thermal stability, can be achieved in lead-free bismuth ferrite-strontium titanate solid-solution films through domain engineering. It is revealed that the incorporation of strontium titanate transforms the ferroelectric micro-domains of bismuth ferrite into highly-dynamic polar nano-regions, resulting in a ferroelectric to relaxor-ferroelectric transition with concurrently improved energy density and efficiency. Additionally, the introduction of strontium titanate greatly improves the electrical insulation and breakdown strength of the films by suppressing the formation of oxygen vacancies. This work opens up a feasible and propagable route, i.e., domain engineering, to systematically develop new lead-free dielectrics for energy storage.

The Pseudokinase Domain of Saccharomyces cerevisiae Tra1 Is Required for Nuclear Localization and Incorporation into the SAGA and NuA4 Complexes.

PubMed

Berg, Matthew D; Genereaux, Julie; Karagiannis, Jim; Brandl, Christopher J

2018-05-31

Tra1 is an essential component of the SAGA/SLIK and NuA4 complexes in S. cerevisiae , recruiting these co-activator complexes to specific promoters. As a PIKK family member, Tra1 is characterized by a C-terminal phosphoinositide 3-kinase (PI3K) domain. Unlike other PIKK family members ( e.g. , Tor1, Tor2, Mec1, Tel1), Tra1 has no demonstrable kinase activity. We identified three conserved arginine residues in Tra1 that reside proximal or within the cleft between the N- and C-terminal subdomains of the PI3K domain. To establish a function for Tra1's PI3K domain and specifically the cleft region, we characterized a tra1 allele where these three arginine residues are mutated to glutamine. The half-life of the Tra1[Formula: see text] protein is reduced but its steady state level is maintained at near wild-type levels by a transcriptional feedback mechanism. The tra1 [Formula: see text] allele results in slow growth under stress and alters the expression of genes also regulated by other components of the SAGA complex. Tra1[Formula: see text] is less efficiently transported to the nucleus than the wild-type protein. Likely related to this, Tra1[Formula: see text] associates poorly with SAGA/SLIK and NuA4. The ratio of Spt7 SLIK to Spt7 SAGA increases in the tra1 [Formula: see text] strain and truncated forms of Spt20 become apparent upon isolation of SAGA/SLIK. Intragenic suppressor mutations of tra1 [Formula: see text] map to the cleft region further emphasizing its importance. We propose that the PI3K domain of Tra1 is directly or indirectly important for incorporating Tra1 into SAGA and NuA4 and thus the biosynthesis and/or stability of the intact complexes. Copyright © 2018 Berg et al.

Changes in myonuclear domain size do not precede muscle hypertrophy during prolonged resistance-type exercise training.

PubMed

Snijders, T; Smeets, J S J; van Kranenburg, J; Kies, A K; van Loon, L J C; Verdijk, L B

2016-02-01

Muscle fibre hypertrophy is accompanied by an increase in myonuclear number, an increase in myonuclear domain size or both. It has been suggested that increases in myonuclear domain size precede myonuclear accretion and subsequent muscle fibre hypertrophy during prolonged exercise training. In this study, we assessed the changes in muscle fibre size, myonuclear and satellite cell content throughout 12 weeks of resistance-type exercise training in young men. Twenty-two young men (23 ± 1 year) were assigned to a progressive, 12-weeks resistance-type exercise training programme (3 sessions per week). Muscle biopsies from the vastus lateralis muscle were taken before and after 2, 4, 8 and 12 weeks of exercise training. Muscle fibre size, myonuclear content, myonuclear domain size and satellite cell content were assessed by immunohistochemistry. Type I and type II muscle fibre size increased gradually throughout the 12 weeks of training (type I: 18 ± 5%, type II: 41 ± 6%, P < 0.01). Myonuclear content increased significantly over time in both the type I (P < 0.01) and type II (P < 0.001) muscle fibres. No changes in type I and type II myonuclear domain size were observed at any time point throughout the intervention. Satellite cell content increased significantly over time in both type I and type II muscle fibres (P < 0.001). Increases in myonuclear domain size do not appear to drive myonuclear accretion and muscle fibre hypertrophy during prolonged resistance-type exercise training in vivo in humans. © 2015 Scandinavian Physiological Society. Published by John Wiley & Sons Ltd.

A new mode of regulation of N-type inactivation in a Caenorhabditis elegans voltage-gated potassium channel.

PubMed

Cai, Shi-Qing; Sesti, Federico

2007-06-22

N-type inactivation in voltage-gated K+ (Kv) channels is a widespread means to modulate neuronal excitability and signaling. Here we have shown a novel mechanism of N-type inactivation in a Caenorhabditis elegans Kv channel. The N-terminal sequence of KVS-1 contains a domain of 22 amino acids that resembles the inactivation ball in A-type channels, which is preceded by a domain of eighteen amino acids. Wild type KVS-1 currents can be described as A-type; however, their kinetics are significantly (approximately 5-fold) slower. When the putative inactivation ball is deleted, the current becomes non-inactivating. Inactivation is restored in non-inactivating channels by diffusion of the missing inactivation domain in the cytoplasm. Deletion of the domain in front of the ball speeds inactivation kinetics approximately 5-fold. We conclude that KVS-1 is the first example of a novel type of Kv channel simultaneously possessing an N-inactivating ball preceded by an N inactivation regulatory domain (NIRD) that acts to slow down inactivation through steric mechanisms.

Mesenchymal Stem Cells Sense Three Dimensional Type I Collagen through Discoidin Domain Receptor 1.

PubMed

Lund, A W; Stegemann, J P; Plopper, G E

2009-01-01

The extracellular matrix provides structural and organizational cues for tissue development and defines and maintains cellular phenotype during cell fate determination. Multipotent mesenchymal stem cells use this matrix to tightly regulate the balance between their differentiation potential and self-renewal in the native niche. When understood, the mechanisms that govern cell-matrix crosstalk during differentiation will allow for efficient engineering of natural and synthetic matrices to specifically direct and maintain stem cell phenotype. This work identifies the discoidin domain receptor 1 (DDR1), a collagen activated receptor tyrosine kinase, as a potential link through which stem cells sense and respond to the 3D organization of their extracellular matrix microenvironment. DDR1 is dependent upon both the structure and proteolytic state of its collagen ligand and is specifically expressed and localized in three dimensional type I collagen culture. Inhibition of DDR1 expression results in decreased osteogenic potential, increased cell spreading, stress fiber formation and ERK1/2 phosphorylation. Additionally, loss of DDR1 activity alters the cell-mediated organization of the naïve type I collagen matrix. Taken together, these results demonstrate a role for DDR1 in the stem cell response to and interaction with three dimensional type I collagen. Dynamic changes in cell shape in 3D culture and the tuning of the local ECM microstructure, directs crosstalk between DDR1 and two dimensional mechanisms of osteogenesis that can alter their traditional roles.

Earthquake Declustering via a Nearest-Neighbor Approach in Space-Time-Magnitude Domain

NASA Astrophysics Data System (ADS)

Zaliapin, I. V.; Ben-Zion, Y.

2016-12-01

We propose a new method for earthquake declustering based on nearest-neighbor analysis of earthquakes in space-time-magnitude domain. The nearest-neighbor approach was recently applied to a variety of seismological problems that validate the general utility of the technique and reveal the existence of several different robust types of earthquake clusters. Notably, it was demonstrated that clustering associated with the largest earthquakes is statistically different from that of small-to-medium events. In particular, the characteristic bimodality of the nearest-neighbor distances that helps separating clustered and background events is often violated after the largest earthquakes in their vicinity, which is dominated by triggered events. This prevents using a simple threshold between the two modes of the nearest-neighbor distance distribution for declustering. The current study resolves this problem hence extending the nearest-neighbor approach to the problem of earthquake declustering. The proposed technique is applied to seismicity of different areas in California (San Jacinto, Coso, Salton Sea, Parkfield, Ventura, Mojave, etc.), as well as to the global seismicity, to demonstrate its stability and efficiency in treating various clustering types. The results are compared with those of alternative declustering methods.

Norovirus P particle efficiently elicits innate, humoral and cellular immunity.

PubMed

Fang, Hao; Tan, Ming; Xia, Ming; Wang, Leyi; Jiang, Xi

2013-01-01

Norovirus (NoV) P domain complexes, the 24 mer P particles and the P dimers, induced effective humoral immunity, but their role in the cellular immune responses remained unclear. We reported here a study on cellular immune responses of the two P domain complexes in comparison with the virus-like particle (VLP) of a GII.4 NoV (VA387) in mice. The P domain complexes induced significant central memory CD4(+) T cell phenotypes (CD4(+) CD44(+) CD62L(+) CCR7(+)) and activated polyclonal CD4(+) T cells as shown by production of Interleukin (IL)-2, Interferon (IFN)-γ, and Tumor Necrosis Factor (TNF)-α. Most importantly, VA387-specific CD4(+) T cell epitope induced a production of IFN-γ, indicating an antigen-specific CD4(+) T cell response in P domain complex-immunized mice. Furthermore, P domain complexes efficiently induced bone marrow-derived dendritic cell (BMDC) maturation, evidenced by up-regulation of co-stimulatory and MHC class II molecules, as well as production of IL-12 and IL-1β. Finally, P domain complex-induced mature dendritic cells (DCs) elicited proliferation of specific CD4(+) T cells targeting VA387 P domain. Overall, we conclude that the NoV P domain complexes are efficiently presented by DCs to elicit not only humoral but also cellular immune responses against NoVs. Since the P particle is highly effective for both humoral and cellular immune responses and easily produced in Escherichia coli (E. coli), it is a good choice of vaccine against NoVs and a vaccine platform against other diseases.

Malfunctions in radioactivity sensors' networks

NASA Astrophysics Data System (ADS)

Khalipova, Veronika; Damart, Guillaume; Beauzamy, Bernard; Bruna, Giovanni

2018-01-01

The capacity to promptly and efficiently detect any source of contamination of the environment (a radioactive cloud) at a local and a country scale is mandatory to a safe and secure exploitation of civil nuclear energy. It must rely upon a robust network of measurement devices, to be optimized vs. several parameters, including the overall reliability, the investment, the operation and maintenance costs. We show that a network can be arranged in different ways, but many of them are inadequate. Through simulations, we test the efficiency of several configurations of sensors, in the same domain. The denser arrangement turns out to be the more efficient, but the efficiency is increased when sensors are non-uniformly distributed over the country, with accumulation at the borders. In the case of France, as radioactive threats are most likely to come from the East, the best solution is densifying the sensors close to the eastern border. Our approach differs from previous work because it is "failure oriented": we determine the laws of probability for all types of failures and deduce in this respect the best organization of the network.

Parallelization of PANDA discrete ordinates code using spatial decomposition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Humbert, P.

2006-07-01

We present the parallel method, based on spatial domain decomposition, implemented in the 2D and 3D versions of the discrete Ordinates code PANDA. The spatial mesh is orthogonal and the spatial domain decomposition is Cartesian. For 3D problems a 3D Cartesian domain topology is created and the parallel method is based on a domain diagonal plane ordered sweep algorithm. The parallel efficiency of the method is improved by directions and octants pipelining. The implementation of the algorithm is straightforward using MPI blocking point to point communications. The efficiency of the method is illustrated by an application to the 3D-Ext C5G7more » benchmark of the OECD/NEA. (authors)« less

Tunable resonance-domain diffraction gratings based on electrostrictive polymers.

PubMed

Axelrod, Ramon; Shacham-Diamand, Yosi; Golub, Michael A

2017-03-01

Critical combination of high diffraction efficiency and large diffraction angles can be delivered by resonance-domain diffractive optics with high aspect ratio and wavelength-scale grating periods. To advance from static to electrically tunable resonance-domain diffraction grating, we resorted to its replication onto 2-5 μm thick P(VDF-TrFE-CFE) electrostrictive ter-polymer membranes. Electromechanical and optical computer simulations provided higher than 90% diffraction efficiency, a large continuous deflection range exceeding 20°, and capabilities for adiabatic spatial modulation of the grating period and slant. A prototype of the tunable resonance-domain diffraction grating was fabricated in a soft-stamp thermal nanoimprinting process, characterized, optically tested, and provided experimental feasibility proof for the tunable sub-micron-period gratings on electrostrictive polymers.

A 170kDa multi-domain cystatin of Fasciola gigantica is active in the male reproductive system.

PubMed

Geadkaew, Amornrat; Kosa, Nanthawat; Siricoon, Sinee; Grams, Suksiri Vichasri; Grams, Rudi

2014-09-01

Cystatins are functional as intra- and extracellular inhibitors of cysteine proteases and are expressed as single or multi-domain proteins. We have previously described two single domain type 1 cystatins in the trematode Fasciola gigantica that are released into the parasite's intestinal tract and exhibit inhibitory activity against endogenous and host cathepsin L and B proteases. In contrast, the here presented 170kDa multi-domain cystatin (FgMDC) comprises signal peptide and 12 tandem repeated cystatin-like domains with similarity to type 2 single domain cystatins. The domains show high sequence divergence with identity values often <20% and at only 26.8% between the highest matching domains 6 and 10. Several domains contain degenerated QVVAG core motifs and/or lack other important residues of active type 2 cystatins. Domain-specific antisera detected multiple forms of FgMDC ranging from <10 to >120kDa molecular mass in immunoblots of parasite crude extracts and ES product with different banding patterns for each antiserum demonstrating complex processing of the proprotein. The four domains with the highest conserved QVVAG motifs were expressed in Escherichia coli and the refolded recombinant proteins blocked cysteine protease activity in the parasite's ES product. Strikingly, immunohistochemical analysis using seven domain-specific antisera localized FgMDC in testis lobes and sperm. It is speculated that the processed cystatin-like domains have function analogous to the mammalian group of male reproductive tissue-specific type 2 cystatins and are functional in spermiogenesis and fertilization. Copyright © 2014 Elsevier B.V. All rights reserved.

The β-Prism Lectin Domain of Vibrio cholerae Hemolysin Promotes Self-assembly of the β-Pore-forming Toxin by a Carbohydrate-independent Mechanism*

PubMed Central

Ganguly, Sreerupa; Mukherjee, Amarshi; Mazumdar, Budhaditya; Ghosh, Amar N.; Banerjee, Kalyan K.

2014-01-01

Vibrio cholerae cytolysin/hemolysin (VCC) is an amphipathic 65-kDa β-pore-forming toxin with a C-terminal β-prism lectin domain. Because deletion or point mutation of the lectin domain seriously compromises hemolytic activity, it is thought that carbohydrate-dependent interactions play a critical role in membrane targeting of VCC. To delineate the contributions of the cytolysin and lectin domains in pore formation, we used wild-type VCC, 50-kDa VCC (VCC50) without the lectin domain, and mutant VCCD617A with no carbohydrate-binding activity. VCC and its two variants with no carbohydrate-binding activity moved to the erythrocyte stroma with apparent association constants on the order of 107 m−1. However, loss of the lectin domain severely reduced the efficiency of self-association of the VCC monomer with the β-barrel heptamer in the synthetic lipid bilayer from ∼83 to 27%. Notably, inactivation of the carbohydrate-binding activity by the D617A mutation marginally reduced oligomerization to ∼77%. Oligomerization of VCC50 was temperature-insensitive; by contrast, VCC self-assembly increased with increasing temperature, suggesting that the process is driven by entropy and opposed by enthalpy. Asialofetuin, the β1-galactosyl-terminated glycoprotein inhibitor of VCC-induced hemolysis, promoted oligomerization of 65-kDa VCC to a species that resembled the membrane-inserted heptamer in stoichiometry and morphology but had reduced global amphipathicity. In conclusion, we propose (i) that the β-prism lectin domain facilitated toxin assembly by producing entropy during relocation in the heptamer and (ii) that glycoconjugates inhibited VCC by promoting its assembly to a water-soluble, less amphipathic oligomer variant with reduced ability to penetrate the bilayer. PMID:24356964

Ketide Synthase (KS) Domain Prediction and Analysis of Iterative Type II PKS Gene in Marine Sponge-Associated Actinobacteria Producing Biosurfactants and Antimicrobial Agents

PubMed Central

Selvin, Joseph; Sathiyanarayanan, Ganesan; Lipton, Anuj N.; Al-Dhabi, Naif Abdullah; Valan Arasu, Mariadhas; Kiran, George S.

2016-01-01

The important biological macromolecules, such as lipopeptide and glycolipid biosurfactant producing marine actinobacteria were analyzed and their potential linkage between type II polyketide synthase (PKS) genes was explored. A unique feature of type II PKS genes is their high amino acid (AA) sequence homology and conserved gene organization. These enzymes mediate the biosynthesis of polyketide natural products with enormous structural complexity and chemical nature by combinatorial use of various domains. Therefore, deciphering the order of AA sequence encoded by PKS domains tailored the chemical structure of polyketide analogs still remains a great challenge. The present work deals with an in vitro and in silico analysis of PKS type II genes from five actinobacterial species to correlate KS domain architecture and structural features. Our present analysis reveals the unique protein domain organization of iterative type II PKS and KS domain of marine actinobacteria. The findings of this study would have implications in metabolic pathway reconstruction and design of semi-synthetic genomes to achieve rational design of novel natural products. PMID:26903957

No-Reference Video Quality Assessment Based on Statistical Analysis in 3D-DCT Domain.

PubMed

Li, Xuelong; Guo, Qun; Lu, Xiaoqiang

2016-05-13

It is an important task to design models for universal no-reference video quality assessment (NR-VQA) in multiple video processing and computer vision applications. However, most existing NR-VQA metrics are designed for specific distortion types which are not often aware in practical applications. A further deficiency is that the spatial and temporal information of videos is hardly considered simultaneously. In this paper, we propose a new NR-VQA metric based on the spatiotemporal natural video statistics (NVS) in 3D discrete cosine transform (3D-DCT) domain. In the proposed method, a set of features are firstly extracted based on the statistical analysis of 3D-DCT coefficients to characterize the spatiotemporal statistics of videos in different views. These features are used to predict the perceived video quality via the efficient linear support vector regression (SVR) model afterwards. The contributions of this paper are: 1) we explore the spatiotemporal statistics of videos in 3DDCT domain which has the inherent spatiotemporal encoding advantage over other widely used 2D transformations; 2) we extract a small set of simple but effective statistical features for video visual quality prediction; 3) the proposed method is universal for multiple types of distortions and robust to different databases. The proposed method is tested on four widely used video databases. Extensive experimental results demonstrate that the proposed method is competitive with the state-of-art NR-VQA metrics and the top-performing FR-VQA and RR-VQA metrics.

Modified Finite Particle Methods for Stokes problems

NASA Astrophysics Data System (ADS)

Montanino, A.; Asprone, D.; Reali, A.; Auricchio, F.

2018-04-01

The Modified Finite Particle Method (MFPM) is a numerical method belonging to the class of meshless methods, nowadays widely investigated due to their characteristic of being capable to easily model large deformation and fluid-dynamic problems. Here we use the MFPM to approximate the Stokes problem. Since the classical formulation of the Stokes problem may lead to pressure spurious oscillations, we investigate alternative formulations and focus on how MFPM discretization behaves in those situations. Some of the investigated formulations, in fact, do not enforce strongly the incompressibility constraint, and therefore an important issue of the present work is to verify if the MFPM is able to correctly reproduce the incompressibility in those cases. The numerical results show that for the formulations in which the incompressibility constraint is properly satisfied from a numerical point of view, the expected second-order is achieved, both in static and in dynamic problems.

GANDALF - Graphical Astrophysics code for N-body Dynamics And Lagrangian Fluids

NASA Astrophysics Data System (ADS)

Hubber, D. A.; Rosotti, G. P.; Booth, R. A.

2018-01-01

GANDALF is a new hydrodynamics and N-body dynamics code designed for investigating planet formation, star formation and star cluster problems. GANDALF is written in C++, parallelized with both OPENMP and MPI and contains a PYTHON library for analysis and visualization. The code has been written with a fully object-oriented approach to easily allow user-defined implementations of physics modules or other algorithms. The code currently contains implementations of smoothed particle hydrodynamics, meshless finite-volume and collisional N-body schemes, but can easily be adapted to include additional particle schemes. We present in this paper the details of its implementation, results from the test suite, serial and parallel performance results and discuss the planned future development. The code is freely available as an open source project on the code-hosting website github at https://github.com/gandalfcode/gandalf and is available under the GPLv2 license.

A new method for solving the quantum hydrodynamic equations of motion: application to two-dimensional reactive scattering.

PubMed

Pauler, Denise K; Kendrick, Brian K

2004-01-08

The de Broglie-Bohm hydrodynamic equations of motion are solved using a meshless method based on a moving least squares approach and an arbitrary Lagrangian-Eulerian frame of reference. A regridding algorithm adds and deletes computational points as needed in order to maintain a uniform interparticle spacing, and unitary time evolution is obtained by propagating the wave packet using averaged fields. The numerical instabilities associated with the formation of nodes in the reflected portion of the wave packet are avoided by adding artificial viscosity to the equations of motion. The methodology is applied to a two-dimensional model collinear reaction with an activation barrier. Reaction probabilities are computed as a function of both time and energy, and are in excellent agreement with those based on the quantum trajectory method. (c) 2004 American Institute of Physics

Functional properties and structural requirements of the plasmid pMV158-encoded MobM relaxase domain.

PubMed

Fernández-López, Cris; Pluta, Radoslaw; Pérez-Luque, Rosa; Rodríguez-González, Lorena; Espinosa, Manuel; Coll, Miquel; Lorenzo-Díaz, Fabián; Boer, D Roeland

2013-07-01

A crucial element in the horizontal transfer of mobilizable and conjugative plasmids is the relaxase, a single-stranded endonuclease that nicks the origin of transfer (oriT) of the plasmid DNA. The relaxase of the pMV158 mobilizable plasmid is MobM (494 residues). In solution, MobM forms a dimer through its C-terminal domain, which is proposed to anchor the protein to the cell membrane and to participate in type 4 secretion system (T4SS) protein-protein interactions. In order to gain a deeper insight into the structural MobM requirements for efficient DNA catalysis, we studied two endonuclease domain variants that include the first 199 or 243 amino acid residues (MobMN199 and MobMN243, respectively). Our results confirmed that the two proteins behaved as monomers in solution. Interestingly, MobMN243 relaxed supercoiled DNA and cleaved single-stranded oligonucleotides harboring oriTpMV158, whereas MobMN199 was active only on supercoiled DNA. Protein stability studies using gel electrophoresis and mass spectrometry showed increased susceptibility to degradation at the domain boundary between the N- and C-terminal domains, suggesting that the domains change their relative orientation upon DNA binding. Overall, these results demonstrate that MobMN243 is capable of nicking the DNA substrate independently of its topology and that the amino acids 200 to 243 modulate substrate specificity but not the nicking activity per se. These findings suggest that these amino acids are involved in positioning the DNA for the nuclease reaction rather than in the nicking mechanism itself.

User’s Manual for a Prototype Binding of ANSI-Standard SQL to Ada Supporting the SAME Methodology for the Software Technology for Adaptable, Reliable Systems (STARS) Program

DTIC Science & Technology

1990-06-30

declaring all of the valid enumeration values for a domain of type enumeration. Example-> In type color_vals is (red, blue , green), color_vals is the name...Color Vals is (red, white, blue ); package Fifth is new domainl.generateenum domain (ColorVals, Colors, enumeration, nullandnotnull); Resulting...generated domain definition-> type colorsnotnull is (red, white, blue ); package colors_ops is new sqlenumeration_pkg(colors notnull); type colors_type is

Relationships between major epitopes of the IA-2 autoantigen in Type 1 diabetes: Implications for determinant spreading.

PubMed

McLaughlin, Kerry A; Richardson, Carolyn C; Williams, Stefan; Bonifacio, Ezio; Morgan, Diana; Feltbower, Richard G; Powell, Michael; Rees Smith, Bernard; Furmaniak, Jadwiga; Christie, Michael R

2015-10-01

Diversification of autoimmunity to islet autoantigens is critical for progression to Type 1 diabetes. B-cells participate in diversification by modifying antigen processing, thereby influencing which peptides are presented to T-cells. In Type 1 diabetes, JM antibodies are associated with T-cell responses to PTP domain peptides. We investigated whether this is the consequence of close structural alignment of JM and PTP domain determinants on IA-2. Fab fragments of IA-2 antibodies with epitopes mapped to the JM domain blocked IA-2 binding of antibodies that recognise epitopes in the IA-2 PTP domain. Peptides from both the JM and PTP domains were protected from degradation during proteolysis of JM antibody:IA-2 complexes and included those representing major T-cell determinants in Type 1 diabetes. The results demonstrate close structural relationships between JM and PTP domain epitopes on IA-2. Stabilisation of PTP domain peptides during proteolysis in JM-specific B-cells may explain determinant spreading in IA-2 autoimmunity. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Simulation study on improving efficiencies of perovskite solar cell: Introducing nano textures on it

NASA Astrophysics Data System (ADS)

Xie, Ziang; Sun, Shuren; Wang, Wei; Qin, Laixiang; Yan, Yu; Hou, Ruixiang; Qin, G. G.

2018-03-01

We report that the power conversion efficiencies (PCEs) of the planar CH3NH3PbI3 solar cells (SCs) can be largely improved by fabricating nano textures on the SC surface. With the finite difference time domain (FDTD) method, the ultimate efficiencies of the planar CH3NH3PbI3 SCs with two types of nano textures are investigated: the column-shaped nano hollow (CLNH) array and the cone-shaped nano hollow (CNNH) array. For the nano textured CH3NH3PbI3 SCs with photovoltaic layer depth in the range of 125 nm ∼ 500 nm, when the array period and filling fraction of the nano textures are optimized, in comparison with the planar ones, their PCE increased 42% ∼ 84% for the CLNH textured ones, and 52% ∼ 63% for the CNNH textured ones. As a conclusion, introduction of nano textures on the SC surface is a promising route for improving the PCEs of the perovskite SCs.

Efficient Implementations of the Quadrature-Free Discontinuous Galerkin Method

NASA Technical Reports Server (NTRS)

Lockard, David P.; Atkins, Harold L.

1999-01-01

The efficiency of the quadrature-free form of the dis- continuous Galerkin method in two dimensions, and briefly in three dimensions, is examined. Most of the work for constant-coefficient, linear problems involves the volume and edge integrations, and the transformation of information from the volume to the edges. These operations can be viewed as matrix-vector multiplications. Many of the matrices are sparse as a result of symmetry, and blocking and specialized multiplication routines are used to account for the sparsity. By optimizing these operations, a 35% reduction in total CPU time is achieved. For nonlinear problems, the calculation of the flux becomes dominant because of the cost associated with polynomial products and inversion. This component of the work can be reduced by up to 75% when the products are approximated by truncating terms. Because the cost is high for nonlinear problems on general elements, it is suggested that simplified physics and the most efficient element types be used over most of the domain.

Optimization of imprintable nanostructured a-Si solar cells: FDTD study.

PubMed

Fisker, Christian; Pedersen, Thomas Garm

2013-03-11

We present a finite-difference time-domain (FDTD) study of an amorphous silicon (a-Si) thin film solar cell, with nano scale patterns on the substrate surface. The patterns, based on the geometry of anisotropically etched silicon gratings, are optimized with respect to the period and anti-reflection (AR) coating thickness for maximal absorption in the range of the solar spectrum. The structure is shown to increase the cell efficiency by 10.2% compared to a similar flat solar cell with an optimized AR coating thickness. An increased back reflection can be obtained with a 50 nm zinc oxide layer on the back reflector, which gives an additional efficiency increase, leading to a total of 14.9%. In addition, the patterned cells are shown to be up to 3.8% more efficient than an optimized textured reference cell based on the Asahi U-type glass surface. The effects of variations of the optimized solar cell structure due to the manufacturing process are investigated, and shown to be negligible for variations below ±10%.

Diagnostic efficiency of an ability-focused battery.

PubMed

Miller, Justin B; Fichtenberg, Norman L; Millis, Scott R

2010-05-01

An ability-focused battery (AFB) is a selected group of well-validated neuropsychological measures that assess the conventional range of cognitive domains. This study examined the diagnostic efficiency of an AFB for use in clinical decision making with a mixed sample composed of individuals with neurological brain dysfunction and individuals referred for cognitive assessment without evidence of neurological disorders. Using logistic regression analyses and ROC curve analysis, a five-domain model composed of attention, processing speed, visual-spatial reasoning, language/verbal reasoning, and memory domain scores was fitted that had an AUC of.89 (95% CI =.84-.95). A more parsimonious two-domain model using processing speed and memory was also fitted that had an AUC of.90 (95% confidence interval =.84-.95). A model composed of a global ability score calculated from the mean of the individual domain scores was also fitted with an AUC of.88 (95% CI =.82-.94).

Characteristics of ferroelectric-ferroelastic domains in Néel-type skyrmion host GaV4S8

NASA Astrophysics Data System (ADS)

Butykai, Ádám; Bordács, Sándor; Kézsmárki, István; Tsurkan, Vladimir; Loidl, Alois; Döring, Jonathan; Neuber, Erik; Milde, Peter; Kehr, Susanne C.; Eng, Lukas M.

2017-03-01

GaV4S8 is a multiferroic semiconductor hosting Néel-type magnetic skyrmions dressed with electric polarization. At Ts = 42 K, the compound undergoes a structural phase transition of weakly first-order, from a non-centrosymmetric cubic phase at high temperatures to a polar rhombohedral structure at low temperatures. Below Ts, ferroelectric domains are formed with the electric polarization pointing along any of the four <111> axes. Although in this material the size and the shape of the ferroelectric-ferroelastic domains may act as important limiting factors in the formation of the Néel-type skyrmion lattice emerging below TC = 13 K, the characteristics of polar domains in GaV4S8 have not been studied yet. Here, we report on the inspection of the local-scale ferroelectric domain distribution in rhombohedral GaV4S8 using low-temperature piezoresponse force microscopy. We observed mechanically and electrically compatible lamellar domain patterns, where the lamellae are aligned parallel to the (100)-type planes with a typical spacing between 100 nm-1.2 μm. Since the magnetic pattern, imaged by atomic force microscopy using a magnetically coated tip, abruptly changes at the domain boundaries, we expect that the control of ferroelectric domain size in polar skyrmion hosts can be exploited for the spatial confinement and manipulation of Néel-type skyrmions.

Three-Dimensional Smoothed Particle Hydrodynamics Modeling of Preferential Flow Dynamics at Fracture Intersections on a High-Performance Computing Platform

NASA Astrophysics Data System (ADS)

Kordilla, J.; Bresinsky, L. T.

2017-12-01

The physical mechanisms that govern preferential flow dynamics in unsaturated fractured rock formations are complex and not well understood. Fracture intersections may act as an integrator of unsaturated flow, leading to temporal delay, intermittent flow and partitioning dynamics. In this work, a three-dimensional Pairwise-Force Smoothed Particle Hydrodynamics (PF-SPH) model is being applied in order to simulate gravity-driven multiphase flow at synthetic fracture intersections. SPH, as a meshless Lagrangian method, is particularly suitable for modeling deformable interfaces, such as three-phase contact dynamics of droplets, rivulets and free-surface films. The static and dynamic contact angle can be recognized as the most important parameter of gravity-driven free-surface flow. In SPH, surface tension and adhesion naturally emerges from the implemented pairwise fluid-fluid (sff) and solid-fluid (ssf) interaction force. The model was calibrated to a contact angle of 65°, which corresponds to the wetting properties of water on Poly(methyl methacrylate). The accuracy of the SPH simulations were validated against an analytical solution of Poiseuille flow between two parallel plates and against laboratory experiments. Using the SPH model, the complex flow mode transitions from droplet to rivulet flow of an experimental study were reproduced. Additionally, laboratory dimensionless scaling experiments of water droplets were successfully replicated in SPH. Finally, SPH simulations were used to investigate the partitioning dynamics of single droplets into synthetic horizontal fractures with various apertures (Δdf = 0, 0.5, 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0 mm) and offsets (Δdoff = -1.5, -1.0, -0.5, 0, 1.0, 2.0, 3.0 mm). Fluid masses were measured in the domains R1, R2 and R3. The perfect conditions of ideally smooth surfaces and the SPH inherent advantage of particle tracking allow the recognition of small scale partitioning mechanisms and its importance for bulk flow behavior.

Parallel CE/SE Computations via Domain Decomposition

NASA Technical Reports Server (NTRS)

Himansu, Ananda; Jorgenson, Philip C. E.; Wang, Xiao-Yen; Chang, Sin-Chung

2000-01-01

This paper describes the parallelization strategy and achieved parallel efficiency of an explicit time-marching algorithm for solving conservation laws. The Space-Time Conservation Element and Solution Element (CE/SE) algorithm for solving the 2D and 3D Euler equations is parallelized with the aid of domain decomposition. The parallel efficiency of the resultant algorithm on a Silicon Graphics Origin 2000 parallel computer is checked.

Effect of female genital mutilation/cutting; types I and II on sexual function: case-controlled study.

PubMed

Ismail, Sahar A; Abbas, Ahmad M; Habib, Dina; Morsy, Hanan; Saleh, Medhat A; Bahloul, Mustafa

2017-08-30

The existing literature is contradictory regarding effects of female genital mutilation/cutting (FGM/C) on sexual functions. The aim of this study was to explore the impact of type I and II FGM/C on sexual function of Egyptian women. We recruited 197 cut women and 197 control women from those visiting Assiut University hospitals for different reasons. We asked each woman to fill the Arabic female sexual function index (FSFI) (a self reported 19-item questionnaire assessing the main domains of female sexual function). Genital Examination was done to confirm the type of FGM. Female sexual dysfunction (FSD) was found in 83.8% of FGM/C cases in contrast to 64.5% of the control. The total FSFI score in the FGM/C group (19.82 ± 7.1) was significantly lower than in the control group (23.34 ± 8.1). Concerning the types of FGM/C, type 73.6% of cases had type I and 26.4% had type II. Type I FGM/C was performed mainly by physicians (62.1%) while type II was performed mainly by midwives (44.4%). FSD was found in 83.4% of FGM/C I cases and in 84.6% of FGM/C II cases. There was no statistically significant difference between the two types of FGM/C as regards total and individual domain scores except for the pain domain. There were significantly lower total and individual domain scores in both FGM/C types except for the desire domain compared to control. In this study, FGM/C was associated with reduced scores of FSFI on all domains scores, and among both types I and II, both were associated with sexual dysfunction.

Role of the DELSEED Loop in Torque Transmission of F1-ATPase

PubMed Central

Tanigawara, Mizue; Tabata, Kazuhito V.; Ito, Yuko; Ito, Jotaro; Watanabe, Rikiya; Ueno, Hiroshi; Ikeguchi, Mitsunori; Noji, Hiroyuki

2012-01-01

F1-ATPase is an ATP-driven rotary motor that generates torque at the interface between the catalytic β-subunits and the rotor γ-subunit. The β-subunit inwardly rotates the C-terminal domain upon nucleotide binding/dissociation; hence, the region of the C-terminal domain that is in direct contact with γ—termed the DELSEED loop—is thought to play a critical role in torque transmission. We substituted all the DELSEED loop residues with alanine to diminish specific DELSEED loop-γ interactions and with glycine to disrupt the loop structure. All the mutants rotated unidirectionally with kinetic parameters comparable to those of the wild-type F1, suggesting that the specific interactions between DELSEED loop and γ is not involved in cooperative interplays between the catalytic β-subunits. Glycine substitution mutants generated half the torque of the wild-type F1, whereas the alanine mutant generated comparable torque. Fluctuation analyses of the glycine/alanine mutants revealed that the γ-subunit was less tightly held in the α3β3-stator ring of the glycine mutant than in the wild-type F1 and the alanine mutant. Molecular dynamics simulation showed that the DELSEED loop was disordered by the glycine substitution, whereas it formed an α-helix in the alanine mutant. Our results emphasize the importance of loop rigidity for efficient torque transmissions. PMID:23009846

Roles of the active site residues and metal cofactors in noncanonical base-pairing during catalysis by human DNA polymerase iota.

PubMed

Makarova, Alena V; Ignatov, Artem; Miropolskaya, Nataliya; Kulbachinskiy, Andrey

2014-10-01

Human DNA polymerase iota (Pol ι) is a Y-family polymerase that can bypass various DNA lesions but possesses very low fidelity of DNA synthesis in vitro. Structural analysis of Pol ι revealed a narrow active site that promotes noncanonical base-pairing during catalysis. To better understand the structure-function relationships in the active site of Pol ι we investigated substitutions of individual amino acid residues in its fingers domain that contact either the templating or the incoming nucleotide. Two of the substitutions, Y39A and Q59A, significantly decreased the catalytic activity but improved the fidelity of Pol ι. Surprisingly, in the presence of Mn(2+) ions, the wild-type and mutant Pol ι variants efficiently incorporated nucleotides opposite template purines containing modifications that disrupted either Hoogsteen or Watson-Crick base-pairing, suggesting that Pol ι may use various types of interactions during nucleotide addition. In contrast, in Mg(2+) reactions, wild-type Pol ι was dependent on Hoogsteen base-pairing, the Y39A mutant was essentially inactive, and the Q59A mutant promoted Watson-Crick interactions with template purines. The results suggest that Pol ι utilizes distinct mechanisms of nucleotide incorporation depending on the metal cofactor and reveal important roles of specific residues from the fingers domain in base-pairing and catalysis. Copyright © 2014 Elsevier B.V. All rights reserved.

The Research on Automatic Construction of Domain Model Based on Deep Web Query Interfaces

NASA Astrophysics Data System (ADS)

JianPing, Gu

The integration of services is transparent, meaning that users no longer face the millions of Web services, do not care about the required data stored, but do not need to learn how to obtain these data. In this paper, we analyze the uncertainty of schema matching, and then propose a series of similarity measures. To reduce the cost of execution, we propose the type-based optimization method and schema matching pruning method of numeric data. Based on above analysis, we propose the uncertain schema matching method. The experiments prove the effectiveness and efficiency of our method.

Critical Role of the HTLV-1 Capsid N-Terminal Domain for Gag-Gag Interactions and Virus Particle Assembly.

PubMed

Martin, Jessica L; Mendonça, Luiza; Marusinec, Rachel; Zuczek, Jennifer; Angert, Isaac; Blower, Ruth J; Mueller, Joachim D; Perilla, Juan R; Zhang, Wei; Mansky, Louis M

2018-04-25

The retroviral Gag protein is the main structural protein responsible for virus particle assembly and release. Like human immunodeficiency virus type 1 (HIV-1) Gag, human T-cell leukemia virus type 1 (HTLV-1) has a structurally conserved capsid (CA) domain, including a β-hairpin turn and a centralized coiled-coil-like structure of six α helices in the CA amino-terminal domain (NTD) as well as four α-helices in the CA carboxy-terminal domain (CTD). CA drives Gag oligomerization, which is critical for both immature Gag lattice formation and particle production. The HIV-1 CA CTD has previously been shown to be a primary determinant for CA-CA interactions, and while both the HTLV-1 CA NTD and CTD have been implicated in Gag-Gag interactions, our recent observations have implicated the HTLV-1 CA NTD as encoding key determinants that dictate particle morphology. Here, we have conducted alanine-scanning mutagenesis in the HTLV-1 CA NTD nucleotide-encoding sequences spanning the loop regions and amino acids at the beginning and ends of α-helices due to their structural dissimilarity from the HIV-1 CA NTD structure. We analyzed both Gag subcellular distribution and efficiency of particle production for these mutants. We discovered several important residues (i.e., M17, Q47/F48, and Y61). Modeling implicated that these residues reside at the dimer interface (i.e., M17 and Y61) or at the trimer interface (i.e., Q47/F48). Taken together, these observations highlight the critical role of the HTLV-1 CA NTD in Gag-Gag interactions and particle assembly, which is, to the best of our knowledge, in contrast to HIV-1 and other retroviruses. Importance Retrovirus particle assembly and release from infected cells is driven by the Gag structural protein. Gag-Gag interactions, which form an oligomeric lattice structure at a particle budding site, are essential to the biogenesis of an infectious virus particle. The capsid (CA) domain of Gag is generally thought to possess the key determinants for Gag-Gag interactions, and the present study has discovered several critical amino acid residues in the CA domain of human T-cell leukemia virus type 1 (HTLV-1) Gag, an important cancer-causing human retrovirus, which are distinct from that of human immunodeficiency virus type 1 (HIV-1) as well as other retroviruses studied to date. Altogether, our results provide important new insights into a poorly understood aspect of HTLV-1 replication, which significantly enhances our understanding of the molecular nature of Gag-Gag interaction determinants crucial for virus particle assembly. Copyright © 2018 American Society for Microbiology.

The Roles and Regulation of Polycomb Complexes in Neural Development

PubMed Central

Corley, Matthew; Kroll, Kristen L.

2014-01-01

In the developing mammalian nervous system, common progenitors integrate both cell extrinsic and intrinsic regulatory programs to produce distinct neuronal and glial cell types as development proceeds. This spatiotemporal restriction of neural progenitor differentiation is enforced, in part, by the dynamic reorganization of chromatin into repressive domains by Polycomb Repressive Complexes, effectively limiting the expression of fate-determining genes. Here, we review distinct roles that the Polycomb Repressive Complexes play during neurogenesis and gliogenesis, while also highlighting recent work describing the molecular mechanisms that govern their dynamic activity in neural development. Further investigation of how Polycomb complexes are regulated in neural development will enable more precise manipulation of neural progenitor differentiation, facilitating the efficient generation of specific neuronal and glial cell types for many biological applications. PMID:25367430

Interaction of von Willebrand factor domains with collagen investigated by single molecule force spectroscopy

NASA Astrophysics Data System (ADS)

Posch, Sandra; Obser, Tobias; König, Gesa; Schneppenheim, Reinhard; Tampé, Robert; Hinterdorfer, Peter

2018-03-01

von Willebrand factor (VWF) is a huge multimeric protein that plays a key role in primary hemostasis. Sites for collagen binding, an initial event of hemostasis, are located in the VWF-domains A1 and A3. In this study, we investigated single molecule interactions between collagen surfaces and wild type VWF A1A2A3 domain constructs, as well as clinically relevant VWF A3 domain point mutations, such as p.Ser1731Thr, p.Gln1734His, and p.His1786Arg. For this, we utilized atomic force microscopy based single molecular force spectroscopy. The p.Ser1731Thr mutant had no impact on the VWF-collagen type III and VI interactions, while the p.Gln1734His and p.His1786Arg mutants showed a slight increase in bond stability to collagen type III. This effect probably arises from additional hydrogen bonds that come along with the introduction of these mutations. Using the same mutants, but collagen type VI as a binding partner, resulted in a significant increase in bond stability. VWF domain A1 was reported to be essential for the interaction with collagen type VI and thus our findings strengthen the hypothesis that the VWF A1 domain can compensate for mutations in the VWF A3 domain. Additionally, our data suggest that the mutations could even stabilize the interaction between VWF and collagen without shear. VWF-collagen interactions seem to be an important system in which defective interactions between one VWF domain and one type of collagen can be compensated by alternative binding events.

Simple and Efficient Numerical Evaluation of Near-Hypersingular Integrals

NASA Technical Reports Server (NTRS)

Fink, Patrick W.; Wilton, Donald R.; Khayat, Michael A.

2007-01-01

Recently, significant progress has been made in the handling of singular and nearly-singular potential integrals that commonly arise in the Boundary Element Method (BEM). To facilitate object-oriented programming and handling of higher order basis functions, cancellation techniques are favored over techniques involving singularity subtraction. However, gradients of the Newton-type potentials, which produce hypersingular kernels, are also frequently required in BEM formulations. As is the case with the potentials, treatment of the near-hypersingular integrals has proven more challenging than treating the limiting case in which the observation point approaches the surface. Historically, numerical evaluation of these near-hypersingularities has often involved a two-step procedure: a singularity subtraction to reduce the order of the singularity, followed by a boundary contour integral evaluation of the extracted part. Since this evaluation necessarily links basis function, Green s function, and the integration domain (element shape), the approach ill fits object-oriented programming concepts. Thus, there is a need for cancellation-type techniques for efficient numerical evaluation of the gradient of the potential. Progress in the development of efficient cancellation-type procedures for the gradient potentials was recently presented. To the extent possible, a change of variables is chosen such that the Jacobian of the transformation cancels the singularity. However, since the gradient kernel involves singularities of different orders, we also require that the transformation leaves remaining terms that are analytic. The terms "normal" and "tangential" are used herein with reference to the source element. Also, since computational formulations often involve the numerical evaluation of both potentials and their gradients, it is highly desirable that a single integration procedure efficiently handles both.

The JH2 domain and SH2-JH2 linker regulate JAK2 activity: A detailed kinetic analysis of wild type and V617F mutant kinase domains.

PubMed

Sanz Sanz, Arturo; Niranjan, Yashavanthi; Hammarén, Henrik; Ungureanu, Daniela; Ruijtenbeek, Rob; Touw, Ivo P; Silvennoinen, Olli; Hilhorst, Riet

2014-10-01

JAK2 tyrosine kinase regulates many cellular functions. Its activity is controlled by the pseudokinase (JH2) domain by still poorly understood mechanisms. The V617F mutation in the pseudokinase domain activates JAK2 and causes myeloproliferative neoplasms. We conducted a detailed kinetic analysis of recombinant JAK2 tyrosine kinase domain (JH1) and wild-type and V617F tandem kinase (JH1JH2) domains using peptide microarrays to define the functions of the kinase domains. The results show that i) JAK2 follows a random Bi-Bi reaction mechanism ii) JH2 domain restrains the activity of the JH1 domain by reducing the affinity for ATP and ATP competitive inhibitors iii) V617F decreases affinity for ATP but increases catalytic activity compared to wild-type and iv) the SH2-JH2 linker region participates in controlling activity by reducing the affinity for ATP. Copyright © 2014 Elsevier B.V. All rights reserved.

Computational methods for efficient structural reliability and reliability sensitivity analysis

NASA Technical Reports Server (NTRS)

Wu, Y.-T.

1993-01-01

This paper presents recent developments in efficient structural reliability analysis methods. The paper proposes an efficient, adaptive importance sampling (AIS) method that can be used to compute reliability and reliability sensitivities. The AIS approach uses a sampling density that is proportional to the joint PDF of the random variables. Starting from an initial approximate failure domain, sampling proceeds adaptively and incrementally with the goal of reaching a sampling domain that is slightly greater than the failure domain to minimize over-sampling in the safe region. Several reliability sensitivity coefficients are proposed that can be computed directly and easily from the above AIS-based failure points. These probability sensitivities can be used for identifying key random variables and for adjusting design to achieve reliability-based objectives. The proposed AIS methodology is demonstrated using a turbine blade reliability analysis problem.

Evidence for an extensive collagen type III/VI proximal domain in the rat femur. I. Diminution with ovariectomy.

PubMed

Luther, F; Saino, H; Carter, D H; Aaron, J E

2003-06-01

Collagenous proteins other than Type I have received little attention in hypogonadal bone loss. Using femora from 25 young (2.5 months) and older (11 months) control and ovariectomized adult rats killed 1-4 months postoperation, cancellous atrophy was histologically confirmed, and the immunolocalization of collagen Type III was examined. This occurred as numerous immunofluorescent Sharpey-like fibers, 5-25 microm thick, regularly associated with collagen Type VI, which ramified the femoral cortex. Sequential transverse cryosections enabled the mapping of the fibers in three-dimensions, demonstrating that they constituted an extensive subperiosteal domain which may be a lasting legacy of early skeletal development. Fiber density was greatest in the trochanters and femoral neck. The domain tapered distally and was apparently anchored into the mid-shaft by intracortical cartilaginous islands, staining for collagen Type VI (as well as Type II and fibronectin). Ovariectomy caused disconnection of the fibers and reduced the proximal domain of both young and older animals, previously positive areas of the cortex becoming negative. It is concluded that collagen Type III/VI occupies a substantial, discrete domain in the rat proximal femur as a complex extension of the periosteum. Diminution of this cortical domain with trabecular atrophy suggests that it has a proactive or reactive role in determining bone mass and strength by facilitating musculoskeletal exchange in a form that is disengaged by ovariectomy.

Restriction digest screening facilitates efficient detection of site-directed mutations introduced by CRISPR in C. albicans UME6

PubMed Central

Evans, Ben A.; Smith, Olivia L.; Pickerill, Ethan S.; York, Mary K.; Buenconsejo, Kristen J.P.; Chambers, Antonio E.

2018-01-01

Introduction of point mutations to a gene of interest is a powerful tool when determining protein function. CRISPR-mediated genome editing allows for more efficient transfer of a desired mutation into a wide range of model organisms. Traditionally, PCR amplification and DNA sequencing is used to determine if isolates contain the intended mutation. However, mutation efficiency is highly variable, potentially making sequencing costly and time consuming. To more efficiently screen for correct transformants, we have identified restriction enzymes sites that encode for two identical amino acids or one or two stop codons. We used CRISPR to introduce these restriction sites directly upstream of the Candida albicans UME6 Zn2+-binding domain, a known regulator of C. albicans filamentation. While repair templates coding for different restriction sites were not equally successful at introducing mutations, restriction digest screening enabled us to rapidly identify isolates with the intended mutation in a cost-efficient manner. In addition, mutated isolates have clear defects in filamentation and virulence compared to wild type C. albicans. Our data suggest restriction digestion screening efficiently identifies point mutations introduced by CRISPR and streamlines the process of identifying residues important for a phenotype of interest. PMID:29892505

N-terminal domains of human DNA polymerase lambda promote primer realignment during translesion DNA synthesis

PubMed Central

Taggart, David J.; Dayeh, Daniel M.; Fredrickson, Saul W.; Suo, Zucai

2014-01-01

The X-family DNA polymerases λ (Polλ) and β (Polβ) possess similar 5′-2-deoxyribose-5-phosphatelyase (dRPase) and polymerase domains. Besides these domains, Polλ also possesses a BRCA1 C-terminal (BRCT) domain and a proline-rich domain at its N terminus. However, it is unclear how these non-enzymatic domains contribute to the unique biological functions of Polλ. Here, we used primer extension assays and a newly developed high-throughput short oligonucleotide sequencing assay (HT-SOSA) to compare the efficiency of lesion bypass and fidelity of human Polβ, Polλ and two N-terminal deletion constructs of Polλ during the bypass of either an abasic site or a 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxodG) lesion. We demonstrate that the BRCT domain of Polλ enhances the efficiency of abasic site bypass by approximately 1.6-fold. In contrast, deletion of the N-terminal domains of Polλ did not affect the efficiency of 8-oxodG bypass relative to nucleotide incorporations opposite undamaged dG. HT-SOSA analysis demonstrated that Polλ and Polβ preferentially generated −1 or −2 frameshift mutations when bypassing an abasic site and the single or double base deletion frequency was highly sequence dependent. Interestingly, the BRCT and proline-rich domains of Polλ cooperatively promoted the generation of −2 frameshift mutations when the abasic site was situated within a sequence context that was susceptible to homology-driven primer realignment. Furthermore, both N-terminal domains of Polλ increased the generation of −1 frameshift mutations during 8-oxodG bypass and influenced the frequency of substitution mutations produced by Polλ opposite the 8-oxodG lesion. Overall, our data support a model wherein the BRCT and proline-rich domains of Polλ act cooperatively to promote primer/template realignment between DNA strands of limited sequence homology. This function of the N-terminal domains may facilitate the role of Polλ as a gap-filling polymerase within the non-homologous end joining pathway. PMID:25108835

Improving solubility and refolding efficiency of human V(H)s by a novel mutational approach.

PubMed

Tanha, Jamshid; Nguyen, Thanh-Dung; Ng, Andy; Ryan, Shannon; Ni, Feng; Mackenzie, Roger

2006-11-01

The antibody V(H) domains of camelids tend to be soluble and to resist aggregation, in contrast to human V(H) domains. For immunotherapy, attempts have therefore been made to improve the properties of human V(H)s by camelization of a small set of framework residues. Here, we have identified through sequence comparison of well-folded llama V(H) domains an alternative set of residues (not typically camelid) for mutation. Thus, the solubility and thermal refolding efficiency of a typical human V(H), derived from the human antibody BT32/A6, were improved by introduction of two mutations in framework region (FR) 1 and 4 to generate BT32/A6.L1. Three more mutations in FR3 of BT32/A6.L1 further improved the thermal refolding efficiency while retaining solubility and cooperative melting profiles. To demonstrate practical utility, BT32/A6.L1 was used to construct a phage display library from which were isolated human V(H)s with good antigen binding activity and solubility. The engineered human V(H) domains described here may be useful for immunotherapy, due to their expected low immunogenicity, and in applications involving transient high temperatures, due to their efficient refolding after thermal denaturation.

TALE-mediated epigenetic suppression of CDKN2A increases replication in human fibroblasts.

PubMed

Bernstein, Diana L; Le Lay, John E; Ruano, Elena G; Kaestner, Klaus H

2015-05-01

Current strategies to alter disease-associated epigenetic modifications target ubiquitously expressed epigenetic regulators. This approach does not allow specific genes to be controlled in specific cell types; therefore, tools to selectively target epigenetic modifications in the desired cell type and strategies to more efficiently correct aberrant gene expression in disease are needed. Here, we have developed a method for directing DNA methylation to specific gene loci by conjugating catalytic domains of DNA methyltransferases (DNMTs) to engineered transcription activator-like effectors (TALEs). We demonstrated that these TALE-DNMTs direct DNA methylation specifically to the targeted gene locus in human cells. Further, we determined that minimizing direct nucleotide sequence repeats within the TALE moiety permits efficient lentivirus transduction, allowing easy targeting of primary cell types. Finally, we demonstrated that directed DNA methylation with a TALE-DNMT targeting the CDKN2A locus, which encodes the cyclin-dependent kinase inhibitor p16, decreased CDKN2A expression and increased replication of primary human fibroblasts, as intended. Moreover, overexpression of p16 in these cells reversed the proliferative phenotype, demonstrating the specificity of our epigenetic targeting. Together, our results demonstrate that TALE-DNMTs can selectively target specific genes and suggest that this strategy has potential application for the development of locus-specific epigenetic therapeutics.

TALE-mediated epigenetic suppression of CDKN2A increases replication in human fibroblasts

PubMed Central

Bernstein, Diana L.; Le Lay, John E.; Ruano, Elena G.; Kaestner, Klaus H.

2015-01-01

Current strategies to alter disease-associated epigenetic modifications target ubiquitously expressed epigenetic regulators. This approach does not allow specific genes to be controlled in specific cell types; therefore, tools to selectively target epigenetic modifications in the desired cell type and strategies to more efficiently correct aberrant gene expression in disease are needed. Here, we have developed a method for directing DNA methylation to specific gene loci by conjugating catalytic domains of DNA methyltransferases (DNMTs) to engineered transcription activator–like effectors (TALEs). We demonstrated that these TALE-DNMTs direct DNA methylation specifically to the targeted gene locus in human cells. Further, we determined that minimizing direct nucleotide sequence repeats within the TALE moiety permits efficient lentivirus transduction, allowing easy targeting of primary cell types. Finally, we demonstrated that directed DNA methylation with a TALE-DNMT targeting the CDKN2A locus, which encodes the cyclin-dependent kinase inhibitor p16, decreased CDKN2A expression and increased replication of primary human fibroblasts, as intended. Moreover, overexpression of p16 in these cells reversed the proliferative phenotype, demonstrating the specificity of our epigenetic targeting. Together, our results demonstrate that TALE-DNMTs can selectively target specific genes and suggest that this strategy has potential application for the development of locus-specific epigenetic therapeutics. PMID:25866970

Adaptive model reduction for continuous systems via recursive rational interpolation

NASA Technical Reports Server (NTRS)

Lilly, John H.

1994-01-01

A method for adaptive identification of reduced-order models for continuous stable SISO and MIMO plants is presented. The method recursively finds a model whose transfer function (matrix) matches that of the plant on a set of frequencies chosen by the designer. The algorithm utilizes the Moving Discrete Fourier Transform (MDFT) to continuously monitor the frequency-domain profile of the system input and output signals. The MDFT is an efficient method of monitoring discrete points in the frequency domain of an evolving function of time. The model parameters are estimated from MDFT data using standard recursive parameter estimation techniques. The algorithm has been shown in simulations to be quite robust to additive noise in the inputs and outputs. A significant advantage of the method is that it enables a type of on-line model validation. This is accomplished by simultaneously identifying a number of models and comparing each with the plant in the frequency domain. Simulations of the method applied to an 8th-order SISO plant and a 10-state 2-input 2-output plant are presented. An example of on-line model validation applied to the SISO plant is also presented.

Iterative load-balancing method with multigrid level relaxation for particle simulation with short-range interactions

NASA Astrophysics Data System (ADS)

Furuichi, Mikito; Nishiura, Daisuke

2017-10-01

We developed dynamic load-balancing algorithms for Particle Simulation Methods (PSM) involving short-range interactions, such as Smoothed Particle Hydrodynamics (SPH), Moving Particle Semi-implicit method (MPS), and Discrete Element method (DEM). These are needed to handle billions of particles modeled in large distributed-memory computer systems. Our method utilizes flexible orthogonal domain decomposition, allowing the sub-domain boundaries in the column to be different for each row. The imbalances in the execution time between parallel logical processes are treated as a nonlinear residual. Load-balancing is achieved by minimizing the residual within the framework of an iterative nonlinear solver, combined with a multigrid technique in the local smoother. Our iterative method is suitable for adjusting the sub-domain frequently by monitoring the performance of each computational process because it is computationally cheaper in terms of communication and memory costs than non-iterative methods. Numerical tests demonstrated the ability of our approach to handle workload imbalances arising from a non-uniform particle distribution, differences in particle types, or heterogeneous computer architecture which was difficult with previously proposed methods. We analyzed the parallel efficiency and scalability of our method using Earth simulator and K-computer supercomputer systems.

A subregion-based burden test for simultaneous identification of susceptibility loci and subregions within.

PubMed

Zhu, Bin; Mirabello, Lisa; Chatterjee, Nilanjan

2018-06-22

In rare variant association studies, aggregating rare and/or low frequency variants, may increase statistical power for detection of the underlying susceptibility gene or region. However, it is unclear which variants, or class of them, in a gene contribute most to the association. We proposed a subregion-based burden test (REBET) to simultaneously select susceptibility genes and identify important underlying subregions. The subregions are predefined by shared common biologic characteristics, such as the protein domain or functional impact. Based on a subset-based approach considering local correlations between combinations of test statistics of subregions, REBET is able to properly control the type I error rate while adjusting for multiple comparisons in a computationally efficient manner. Simulation studies show that REBET can achieve power competitive to alternative methods when rare variants cluster within subregions. In two case studies, REBET is able to identify known disease susceptibility genes, and more importantly pinpoint the unreported most susceptible subregions, which represent protein domains essential for gene function. R package REBET is available at https://dceg.cancer.gov/tools/analysis/rebet. Published 2018. This article is a U.S. Government work and is in the public domain in the USA.

Antiferromagnetic domain wall as spin wave polarizer and retarder.

PubMed

Lan, Jin; Yu, Weichao; Xiao, Jiang

2017-08-02

As a collective quasiparticle excitation of the magnetic order in magnetic materials, spin wave, or magnon when quantized, can propagate in both conducting and insulating materials. Like the manipulation of its optical counterpart, the ability to manipulate spin wave polarization is not only important but also fundamental for magnonics. With only one type of magnetic lattice, ferromagnets can only accommodate the right-handed circularly polarized spin wave modes, which leaves no freedom for polarization manipulation. In contrast, antiferromagnets, with two opposite magnetic sublattices, have both left and right-circular polarizations, and all linear and elliptical polarizations. Here we demonstrate theoretically and confirm by micromagnetic simulations that, in the presence of Dzyaloshinskii-Moriya interaction, an antiferromagnetic domain wall acts naturally as a spin wave polarizer or a spin wave retarder (waveplate). Our findings provide extremely simple yet flexible routes toward magnonic information processing by harnessing the polarization degree of freedom of spin wave.Spin waves are promising candidates as carriers for energy-efficient information processing, but they have not yet been fully explored application wise. Here the authors theoretically demonstrate that antiferromagnetic domain walls are naturally spin wave polarizers and retarders, two key components of magnonic devices.

Final Report from The University of Texas at Austin for DEGAS: Dynamic Global Address Space programming environments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Erez, Mattan; Yelick, Katherine; Sarkar, Vivek

The Dynamic, Exascale Global Address Space programming environment (DEGAS) project will develop the next generation of programming models and runtime systems to meet the challenges of Exascale computing. Our approach is to provide an efficient and scalable programming model that can be adapted to application needs through the use of dynamic runtime features and domain-specific languages for computational kernels. We address the following technical challenges: Programmability: Rich set of programming constructs based on a Hierarchical Partitioned Global Address Space (HPGAS) model, demonstrated in UPC++. Scalability: Hierarchical locality control, lightweight communication (extended GASNet), and ef- ficient synchronization mechanisms (Phasers). Performance Portability:more » Just-in-time specialization (SEJITS) for generating hardware-specific code and scheduling libraries for domain-specific adaptive runtimes (Habanero). Energy Efficiency: Communication-optimal code generation to optimize energy efficiency by re- ducing data movement. Resilience: Containment Domains for flexible, domain-specific resilience, using state capture mechanisms and lightweight, asynchronous recovery mechanisms. Interoperability: Runtime and language interoperability with MPI and OpenMP to encourage broad adoption.« less

An enhanced chemoenzymatic method for loading substrates onto carrier protein domains.

PubMed

Kittilä, Tiia; Cryle, Max J

2018-06-01

Non-ribosomal peptide synthetase (NRPS) machineries produce many medically relevant peptides that cannot be easily accessed by chemical synthesis. Thus, understanding NRPS mechanism is of crucial importance to allow efficient redesign of these machineries to produce new compounds. During NRPS-mediated synthesis, substrates are covalently attached to peptidyl carrier proteins (PCPs), and studies of NRPSs are impeded by difficulties in producing PCPs loaded with substrates. Different approaches to load substrates onto PCP domains have been described, but all suffer from difficulties in either the complexity of chemical synthesis or low enzymatic efficiency. Here, we describe an enhanced chemoenzymatic loading method that combines 2 approaches into a single, highly efficient one-pot loading reaction. First, d-pantetheine and ATP are converted into dephospho-coenzyme A via the actions of 2 enzymes from coenzyme A (CoA) biosynthesis. Next, phosphoadenylates are dephosphorylated using alkaline phosphatase to allow linker attachment to PCP domain by Sfp mutant R4-4, which is inhibited by phosphoadenylates. This route does not depend on activity of the commonly problematic dephospho-CoA kinase and, therefore, offers an improved method for substrate loading onto PCP domains.

Spatio-temporal variations in climate, primary productivity and efficiency of water and carbon use of the land cover types in Sudan and Ethiopia.

PubMed

Khalifa, Muhammad; Elagib, Nadir Ahmed; Ribbe, Lars; Schneider, Karl

2018-05-15

The impact of climate variability on the Net Primary Productivity (NPP) of different land cover types and the reaction of NPP to drought conditions are still unclear, especially in Sub-Saharan Africa. This research utilizes public-domain data for the period 2000 through 2013 to analyze these aspects for several land cover types in Sudan and Ethiopia, as examples of data-scarce countries. Spatio-temporal variation in NPP, water use efficiency (WUE) and carbon use efficiency (CUE) for several land covers were correlated with variations in precipitation, temperature and drought at different time scales, i.e. 1, 3, 6 and 12months using Standardized Precipitation Evapotranspiration Index (SPEI) datasets. WUE and CUE were estimated as the ratios of NPP to actual evapotranspiration and NPP to Gross Primary Productivity (GPP), respectively. Results of this study revealed that NPP, WUE and CUE of the different land cover types in Ethiopia have higher magnitudes than their counterparts in Sudan. Moreover, they exhibit higher sensitivity to drought and variation in precipitation. Whereas savannah represents the most sensitive land cover to drought, croplands and permanent wetlands are the least sensitive ones. The inter-annual variation in NPP, WUE and CUE in Ethiopia is likely to be driven by a drought of time scale of three months. No statistically significant correlation was found for Sudan between the inter-annual variations in these indicators with drought at any of the time scales considered in the study. Our findings are useful from the view point of both food security for a growing population and mitigation to climate change as discussed in the present study. Copyright © 2017 Elsevier B.V. All rights reserved.

The influenza virus neuraminidase protein transmembrane and head domains have coevolved.

PubMed

da Silva, Diogo V; Nordholm, Johan; Dou, Dan; Wang, Hao; Rossman, Jeremy S; Daniels, Robert

2015-01-15

Transmembrane domains (TMDs) from single-spanning membrane proteins are commonly viewed as membrane anchors for functional domains. Influenza virus neuraminidase (NA) exemplifies this concept, as it retains enzymatic function upon proteolytic release from the membrane. However, the subtype 1 NA TMDs have become increasingly more polar in human strains since 1918, which suggests that selection pressure exists on this domain. Here, we investigated the N1 TMD-head domain relationship by exchanging a prototypical "old" TMD (1933) with a "recent" (2009), more polar TMD and an engineered hydrophobic TMD. Each exchange altered the TMD association, decreased the NA folding efficiency, and significantly reduced viral budding and replication at 37°C compared to at 33°C, at which NA folds more efficiently. Passaging the chimera viruses at 37°C restored the NA folding efficiency, viral budding, and infectivity by selecting for NA TMD mutations that correspond with their polar or hydrophobic assembly properties. These results demonstrate that single-spanning membrane protein TMDs can influence distal domain folding, as well as membrane-related processes, and suggest the NA TMD in H1N1 viruses has become more polar to maintain compatibility with the evolving enzymatic head domain. The neuraminidase (NA) protein from influenza A viruses (IAVs) functions to promote viral release and is one of the major surface antigens. The receptor-destroying activity in NA resides in the distal head domain that is linked to the viral membrane by an N-terminal hydrophobic transmembrane domain (TMD). Over the last century, the subtype 1 NA TMDs (N1) in human H1N1 viruses have become increasingly more polar, and the head domains have changed to alter their antigenicity. Here, we provide the first evidence that an "old" N1 head domain from 1933 is incompatible with a "recent" (2009), more polar N1 TMD sequence and that, during viral replication, the head domain drives the selection of TMD mutations. These mutations modify the intrinsic TMD assembly to restore the head domain folding compatibility and the resultant budding deficiency. This likely explains why the N1 TMDs have become more polar and suggests the N1 TMD and head domain have coevolved. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Hypoxia-inducible vascular endothelial growth factor gene therapy using the oxygen-dependent degradation domain in myocardial ischemia.

PubMed

Kim, Hyun Ah; Lim, Soyeon; Moon, Hyung-Ho; Kim, Sung Wan; Hwang, Ki-Chul; Lee, Minhyung; Kim, Sun Hwa; Choi, Donghoon

2010-10-01

A hypoxia-inducible VEGF expression system with the oxygen-dependent degradation (ODD) domain was constructed and tested to be used in gene therapy for ischemic myocardial disease. Luciferase and VEGF expression vector systems were constructed with or without the ODD domain: pEpo-SV-Luc (or pEpo-SV-VEGF) and pEpo-SV-Luc-ODD (or pEpo-SV-VEGF-ODD). In vitro gene expression efficiency of each vector type was evaluated in HEK 293 cells under both hypoxic and normoxic conditions. The amount of VEGF protein was estimated by ELISA. The VEGF expression vectors with or without the ODD domain were injected into ischemic rat myocardium. Fibrosis, neovascularization, and cardiomyocyte apoptosis were assessed using Masson's trichrome staining, α-smooth muscle actin (α-SMA) immunostaining, and the TUNEL assay, respectively. The plasmid vectors containing ODD significantly improved the expression level of VEGF protein in hypoxic conditions. The enhancement of VEGF protein production was attributed to increased protein stability due to oxygen deficiency. In a rat model of myocardial ischemia, the pEpo-SV-VEGF-ODD group exhibited less myocardial fibrosis, higher microvessel density, and less cardiomyocyte apoptosis compared to the control groups (saline and pEpo-SV-VEGF treatments). An ODD-mediated VEGF expression system that facilitates VEGF-production under hypoxia may be useful in the treatment of ischemic heart disease.

Current induced domain wall motion and tilting in Pt/Co/Ta structures with perpendicular magnetic anisotropy in the presence of the Dyzaloshinskii–Moriya interaction

NASA Astrophysics Data System (ADS)

Yun, Jijun; Li, Dong; Cui, Baoshan; Guo, Xiaobin; Wu, Kai; Zhang, Xu; Wang, Yupei; Mao, Jian; Zuo, Yalu; Xi, Li

2018-04-01

Current induced domain wall motion (CIDWM) was studied in Pt/Co/Ta structures with perpendicular magnetic anisotropy and the Dyzaloshinskii–Moriya interaction (DMI) by the spin-orbit torque (SOT). We measured the strength of DMI and SOT efficiency in Pt/Co/Ta with the variation of the thickness of Ta using a current induced hysteresis loop shift method. The results indicate that the DMI stabilizes a chiral Néel-type domain wall (DW), and the DW motion can be driven by the enhanced large SOT generated from Pt and Ta with opposite signs of spin Hall angle in Pt/Co/Ta stacks. The CIDWM velocity, which is 104 times larger than the field driven DW velocity, obeys a creep law, and reaches around tens of meters per second with current density of ~106 A cm‑2. We also found that the Joule heating accompanied with current also accelerates the DW motion. Meanwhile, a domain wall tilting was observed, which increases with current density increasing. These results can be explained by the spin Hall effect generated from both heavy metals Pt and Ta, inherent DMI, and the current accompanying Joule heating effect. Our results could provide some new designing prospects to move multiple DWs by SOT for achieving racetrack memories.

DNA Polymerase α Subunit Residues and Interactions Required for Efficient Initiation Complex Formation Identified by a Genetic Selection.

PubMed

Lindow, Janet C; Dohrmann, Paul R; McHenry, Charles S

2015-07-03

Biophysical and structural studies have defined many of the interactions that occur between individual components or subassemblies of the bacterial replicase, DNA polymerase III holoenzyme (Pol III HE). Here, we extended our knowledge of residues and interactions that are important for the first step of the replicase reaction: the ATP-dependent formation of an initiation complex between the Pol III HE and primed DNA. We exploited a genetic selection using a dominant negative variant of the polymerase catalytic subunit that can effectively compete with wild-type Pol III α and form initiation complexes, but cannot elongate. Suppression of the dominant negative phenotype was achieved by secondary mutations that were ineffective in initiation complex formation. The corresponding proteins were purified and characterized. One class of mutant mapped to the PHP domain of Pol III α, ablating interaction with the ϵ proofreading subunit and distorting the polymerase active site in the adjacent polymerase domain. Another class of mutation, found near the C terminus, interfered with τ binding. A third class mapped within the known β-binding domain, decreasing interaction with the β2 processivity factor. Surprisingly, mutations within the β binding domain also ablated interaction with τ, suggesting a larger τ binding site than previously recognized. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Construction of an anti-programmed death-ligand 1 chimeric antigen receptor and determination of its antitumor function with transduced cells

PubMed Central

Xie, Jiasen; Zhou, Zishan; Jiao, Shunchang; Li, Xiaokun

2018-01-01

A chimeric antigen receptor (CAR) is a type of fusion protein that comprises an antigen-recognition domain and signaling domains. In the present study, a programmed death-ligand 1 (PD-L1)-specific CAR, comprised of a single-chain variable fragment (scFv) derived from a monoclonal antibody, co-stimulatory domains of cluster of differentiation (CD) 28 and 4-1BB and a T-cell-activation domain derived from CD3ζ, was designed. The construction was cloned and packaged into the lentiviral vector pLVX. Flow cytometry confirmed that peripheral blood mononuclear cells were efficiently transduced and that the CAR was successfully expressed on T cells. The cytotoxicity of transduced T cells was detected using PD-L1-positive NCI-H358 bronchioalveolar carcinoma cells and A549 lung adenocarcinoma cells (with a low expression of PD-L1, only in the A549 cells). The results demonstrated mild cytotoxicity at an effector-to-target ratio of 10:1. An ELISA revealed a significant increase in the level of interferon-γ released from T cells transduced with scFv-28Bz when the cells were co-cultured with PD-L1-positive NCI-H358 cells, while interkeukin-2 and tumor necrosis factor-α levels remained unchanged. These data indicated a potential method for the treatment of solid tumors. PMID:29928397

Comparative studies on the properties of glycyrrhetinic acid-loaded PLGA microparticles prepared by emulsion and template methods.

PubMed

Wang, Hong; Zhang, Guangxing; Sui, Hong; Liu, Yanhua; Park, Kinam; Wang, Wenping

2015-12-30

The O/W emulsion method has been widely used for the production of poly (lactide-co-glycolide) (PLGA) microparticles. Recently, a template method has been used to make homogeneous microparticles with predefined size and shape, and shown to be useful in encapsulating different types of active compounds. However, differences between the template method and emulsion method have not been examined. In the current study, PLGA microparticles were prepared by the two methods using glycyrrhetinic acid (GA) as a model drug. The properties of obtained microparticles were characterized and compared on drug distribution, in vitro release, and degradation. An encapsulation efficiency of over 70% and a mean particle size of about 40μm were found for both methods. DSC thermograms and XRPD diffractograms indicated that GA was highly dispersed or in the amorphous state in the matrix of microparticles. The emulsion method produced microparticles of a broad size distribution with a core-shell type structure and many drug-rich domains inside each microparticle. Its drug release and matrix degradation was slow before Day 50 and then accelerated. In contrast, the template method formed microparticles with narrow size distribution and drug distribution without apparent drug-rich domains. The template microparticles with a loading efficiency of 85% exhibited a zero-order release profile for 3 months after the initial burst release of 26.7%, and a steady surface erosion process as well. The same microparticles made by two different methods showed two distinguished drug release profiles. The two different methods can be supplementary with each other in optimization of drug formulation for achieving predetermined drug release patterns. Copyright © 2015 Elsevier B.V. All rights reserved.

Domain Motion Enhanced (DoME) Model for Efficient Conformational Sampling of Multidomain Proteins.

PubMed

Kobayashi, Chigusa; Matsunaga, Yasuhiro; Koike, Ryotaro; Ota, Motonori; Sugita, Yuji

2015-11-19

Large conformational changes of multidomain proteins are difficult to simulate using all-atom molecular dynamics (MD) due to the slow time scale. We show that a simple modification of the structure-based coarse-grained (CG) model enables a stable and efficient MD simulation of those proteins. "Motion Tree", a tree diagram that describes conformational changes between two structures in a protein, provides information on rigid structural units (domains) and the magnitudes of domain motions. In our new CG model, which we call the DoME (domain motion enhanced) model, interdomain interactions are defined as being inversely proportional to the magnitude of the domain motions in the diagram, whereas intradomain interactions are kept constant. We applied the DoME model in combination with the Go model to simulations of adenylate kinase (AdK). The results of the DoME-Go simulation are consistent with an all-atom MD simulation for 10 μs as well as known experimental data. Unlike the conventional Go model, the DoME-Go model yields stable simulation trajectories against temperature changes and conformational transitions are easily sampled despite domain rigidity. Evidently, identification of domains and their interfaces is useful approach for CG modeling of multidomain proteins.

An Efficient Semi-supervised Learning Approach to Predict SH2 Domain Mediated Interactions.

PubMed

Kundu, Kousik; Backofen, Rolf

2017-01-01

Src homology 2 (SH2) domain is an important subclass of modular protein domains that plays an indispensable role in several biological processes in eukaryotes. SH2 domains specifically bind to the phosphotyrosine residue of their binding peptides to facilitate various molecular functions. For determining the subtle binding specificities of SH2 domains, it is very important to understand the intriguing mechanisms by which these domains recognize their target peptides in a complex cellular environment. There are several attempts have been made to predict SH2-peptide interactions using high-throughput data. However, these high-throughput data are often affected by a low signal to noise ratio. Furthermore, the prediction methods have several additional shortcomings, such as linearity problem, high computational complexity, etc. Thus, computational identification of SH2-peptide interactions using high-throughput data remains challenging. Here, we propose a machine learning approach based on an efficient semi-supervised learning technique for the prediction of 51 SH2 domain mediated interactions in the human proteome. In our study, we have successfully employed several strategies to tackle the major problems in computational identification of SH2-peptide interactions.

Central catalytic domain of BRAP (RNF52) recognizes the types of ubiquitin chains and utilizes oligo-ubiquitin for ubiquitylation

PubMed Central

Hanada, Kazuharu; Ohsawa, Noboru

2017-01-01

Really interesting new gene (RING)-finger protein 52 (RNF52), an E3 ubiquitin ligase, is found in eukaryotes from yeast to humans. Human RNF52 is known as breast cancer type 1 susceptibility protein (BRCA1)-associated protein 2 (BRAP or BRAP2). The central catalytic domain of BRAP comprises four subdomains: nucleotide-binding α/β plait (NBP), really interesting new gene (RING) zinc finger, ubiquitin-specific protease (UBP)-like zinc finger (ZfUBP), and coiled-coil (CC). This domain architecture is conserved in RNF52 orthologs; however, the domain's function in the ubiquitin system has not been delineated. In the present study, we discovered that the RNF52 domain, comprising NBP–RING–ZfUBP–CC, binds to ubiquitin chains (oligo-ubiquitin) but not to the ubiquitin monomers, and can utilize various ubiquitin chains for ubiquitylation and auto-ubiquitylation. The RNF52 domain preferentially bound to M1- and K63-linked di-ubiquitin chains, weakly to K27-linked chains, but not to K6-, K11-, or K48-linked chains. The binding preferences of the RNF52 domain for ubiquitin-linkage types corresponded to ubiquitin usage in the ubiquitylation reaction, except for K11-, K29-, and K33-linked chains. Additionally, the RNF52 domain directly ligated the intact M1-linked, tri-, and tetra-ubiquitin chains and recognized the structural alterations caused by the phosphomimetic mutation of these ubiquitin chains. Full-length BRAP had nearly the same specificity for the ubiquitin-chain types as the RNF52 domain alone. Mass spectrometry analysis of oligomeric ubiquitylation products, mediated by the RNF52 domain, revealed that the ubiquitin-linkage types and auto-ubiquitylation sites depend on the length of ubiquitin chains. Here, we propose a model for the oligomeric ubiquitylation process, controlled by the RNF52 domain, which is not a sequential assembly process involving monomers. PMID:28768733

Field driven magnetic racetrack memory accompanied with the interfacial Dzyaloshinskii-Moriya interaction

NASA Astrophysics Data System (ADS)

Kim, June-Seo; Lee, Hyeon-Jun; Hong, Jung-Il; You, Chun-Yeol

2018-06-01

The in-plane magnetic field pulse driven domain wall motion on a perpendicularly magnetized nanowire is numerically investigated by performing micromagnetic simulations and magnetic domain wall dynamics are evaluated analytically with one-dimensional collective coordinate models including the interfacial Dzyaloshinskii-Moriya interaction. With the action of the precession torque, the chirality and the magnetic field direction dependent displacements of the magnetic domain walls are clearly observed. In order to move Bloch type and Neel type domain walls, a longitudinal and a transverse in-plane magnetic field pulse are required, respectively. The domain wall type (Bloch or Neel) can easily be determined by the dynamic motion of the domain walls under the applied pulse fields. By applying a temporally asymmetric in-plane field pulse and successive notches in the perpendicularly magnetized nanowire strip line with a proper interval, the concept of racetrack memory based on the synchronous displacements of the chirality dependent multiple domain walls is verified to be feasible. Requirement of multiple domain walls with homogeneous chirality is achieved with the help of Dzyaloshinskii-Moriya interaction.

Frequency domain finite-element and spectral-element acoustic wave modeling using absorbing boundaries and perfectly matched layer

NASA Astrophysics Data System (ADS)

Rahimi Dalkhani, Amin; Javaherian, Abdolrahim; Mahdavi Basir, Hadi

2018-04-01

Wave propagation modeling as a vital tool in seismology can be done via several different numerical methods among them are finite-difference, finite-element, and spectral-element methods (FDM, FEM and SEM). Some advanced applications in seismic exploration benefit the frequency domain modeling. Regarding flexibility in complex geological models and dealing with the free surface boundary condition, we studied the frequency domain acoustic wave equation using FEM and SEM. The results demonstrated that the frequency domain FEM and SEM have a good accuracy and numerical efficiency with the second order interpolation polynomials. Furthermore, we developed the second order Clayton and Engquist absorbing boundary condition (CE-ABC2) and compared it with the perfectly matched layer (PML) for the frequency domain FEM and SEM. In spite of PML method, CE-ABC2 does not add any additional computational cost to the modeling except assembling boundary matrices. As a result, considering CE-ABC2 is more efficient than PML for the frequency domain acoustic wave propagation modeling especially when computational cost is high and high-level absorbing performance is unnecessary.

The Antitumor Effect of Single-domain Antibodies Directed Towards Membrane-associated Catalase and Superoxide Dismutase.

PubMed

Bauer, Georg; Motz, Manfred

2016-11-01

Neutralizing single-domain antibodies directed towards catalase or superoxide dismutase (SOD) caused efficient reactivation of intercellular reactive oxygen species/reactive nitrogen species (ROS/RNS)-dependent apoptosis-inducing signaling specifically in human tumor cells. Single-domain antibodies targeted tumor cell-specific membrane-associated SOD and catalase, but not the corresponding intracellular enzymes. They were shown to be about 200-fold more effective than corresponding classical recombinant antigen-binding fragments and more than four log steps more efficient than monoclonal antibodies. Combined addition of single-domain antibodies against catalase and SOD caused a remarkable synergistic effect. Proof-of-concept experiments in immunocompromised mice using human tumor xenografts and single-domain antibodies directed towards SOD showed an inhibition of tumor growth. Neutralizing single-domain antibodies directed to catalase and SOD also caused a very strong synergistic effect with the established chemotherapeutic agent taxol, indicating an overlap of signaling pathways. This effect might also be useful in order to avoid unwanted side-effects and to drastically lower the costs for taxol-based therapy. Copyright© 2016 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

Deblending using an improved apex-shifted hyperbolic radon transform based on the Stolt migration operator

NASA Astrophysics Data System (ADS)

Gong, Xiangbo; Feng, Fei; Jiao, Xuming; Wang, Shengchao

2017-10-01

Simultaneous seismic source separation, also known as deblending, is an essential process for blended acquisition. With the assumption that the blending noise is coherent in the common shot domain but is incoherent in other domains, traditional deblending methods are commonly performed in the common receiver, common midpoint or common offset domain. In this paper, we propose an improved apex-shifted hyperbolic radon transform (ASHRT) to deblend directly in the common shot domain. A time-axis stretch strategy named Stolt-stretch is introduced to overcome the limitation of the constant velocity assumption of Stolt-based operators. To improve the sparsity in the transform domain, a total variation (TV) norm inversion is implemented to enhance the energy convergence in the radon panel. Because of highly efficient Stolt migration and the demigration operator in the frequency-wavenumber domain, as well as the flexible geometry condition of the source-receiver, this approach is quite suitable for quality control (QC) during streamer acquisition. The synthetic and field examples demonstrate that our proposition is robust and efficient.

Contribution of trimeric autotransporter C-terminal domains of oligomeric coiled-coil adhesin (Oca) family members YadA, UspA1, EibA, and Hia to translocation of the YadA passenger domain and virulence of Yersinia enterocolitica.

PubMed

Ackermann, Nikolaus; Tiller, Maximilian; Anding, Gisela; Roggenkamp, Andreas; Heesemann, Jürgen

2008-07-01

The Oca family is a novel class of autotransporter-adhesins with highest structural similarity in their C-terminal transmembrane region, which supposedly builds a beta-barrel pore in the outer membrane (OM). The prototype of the Oca family is YadA, an adhesin of Yersinia enterocolitica and Yersinia pseudotuberculosis. YadA forms a homotrimeric lollipop-like structure on the bacterial surface. The C-terminal regions of three YadA monomers form a barrel in the OM and translocate the trimeric N-terminal passenger domain, consisting of stalk, neck, and head region to the exterior. To elucidate the structural and functional role of the C-terminal translocator domain (TLD) and to assess its promiscuous capability with respect to transport of related passenger domains, we constructed chimeric YadA proteins, which consist of the N-terminal YadA passenger domain and C-terminal TLDs of Oca family members UspA1 (Moraxella catarrhalis), EibA (Escherichia coli), and Hia (Haemophilus influenzae). These constructs were expressed in Y. enterocolitica and compared for OM localization, surface exposure, oligomerization, adhesion properties, serum resistance, and mouse virulence. We demonstrate that all chimeric YadA proteins translocated the YadA passenger domain across the OM. Y. enterocolitica strains producing YadA chimeras or wild-type YadA showed comparable binding to collagen and epithelial cells. However, strains producing YadA chimeras were attenuated in serum resistance and mouse virulence. These results demonstrate for the first time that TLDs of Oca proteins of different origin are efficient translocators of the YadA passenger domain and that the cognate TLD of YadA is essential for bacterial survival in human serum and mouse virulence.

Efficient T-cell receptor signaling requires a high-affinity interaction between the Gads C-SH3 domain and the SLP-76 RxxK motif.

PubMed

Seet, Bruce T; Berry, Donna M; Maltzman, Jonathan S; Shabason, Jacob; Raina, Monica; Koretzky, Gary A; McGlade, C Jane; Pawson, Tony

2007-02-07

The relationship between the binding affinity and specificity of modular interaction domains is potentially important in determining biological signaling responses. In signaling from the T-cell receptor (TCR), the Gads C-terminal SH3 domain binds a core RxxK sequence motif in the SLP-76 scaffold. We show that residues surrounding this motif are largely optimized for binding the Gads C-SH3 domain resulting in a high-affinity interaction (K(D)=8-20 nM) that is essential for efficient TCR signaling in Jurkat T cells, since Gads-mediated signaling declines with decreasing affinity. Furthermore, the SLP-76 RxxK motif has evolved a very high specificity for the Gads C-SH3 domain. However, TCR signaling in Jurkat cells is tolerant of potential SLP-76 crossreactivity, provided that very high-affinity binding to the Gads C-SH3 domain is maintained. These data provide a quantitative argument that the affinity of the Gads C-SH3 domain for SLP-76 is physiologically important and suggest that the integrity of TCR signaling in vivo is sustained both by strong selection of SLP-76 for the Gads C-SH3 domain and by a capacity to buffer intrinsic crossreactivity.

The dual exo/endo-type mode and the effect of ionic strength on the mode of catalysis of chitinase 60 (CHI60) from Serratia sp. TU09 and its mutants.

PubMed

Kuttiyawong, K; Nakapong, S; Pichyangkura, R

2008-11-03

Mutations of the tryptophan residues in the tryptophan-track of the N-terminal domain (W33F/Y and W69F/Y) and in the catalytic domain (W245F/Y) of Serratia sp. TU09 Chitinase 60 (CHI60) were constructed, as single and double point substitutions to either phenylalanine or tyrosine. The enzyme-substrate interaction and mode of catalysis, exo/endo-type, of wild type CHI60 and mutant enzymes on soluble (partially N-acetylated chitin), amorphous (colloidal chitin), and crystalline (β-chitin) substrates were studied. All CHI60 mutants exhibited a reduced substrate binding activity on colloidal chitin. CHI60 possesses a dual mode of catalysis with both exo- and endo-type activities allowing the enzyme to work efficiently on various substrate types. CHI60 preferentially uses the endo-type mode on soluble and amorphous substrates and the exo-type mode on crystalline substrate. However, the prevalent mode of hydrolysis mediated by CHI60 is regulated by ionic strength. Slightly elevated ionic strength, 0.1-0.2M NaCl, which promotes enzyme-substrate interactions, enhances CHI60 hydrolytic activity on amorphous substrate and, interestingly, on partially N-acetylated chitin. High ionic strength, 0.5-2.0M NaCl, prevents the enzyme from dissociating from amorphous substrate, occupying the enzyme in an enzyme-substrate non-productive complex. However, on crystalline substrates, the activity of CHI60 was only inhibited approximately 50% at high ionic strength, suggesting that the enzyme hydrolyzes crystalline substrates with an exo-type mode processively while remaining tightly bound to the substrate. Moreover, substitution of Trp-33 to either phenylalanine or tyrosine reduced the activity of the enzyme at high ionic strength, suggesting an important role of Trp-33 on enzyme processivity.

Resolved simulations of a granular-fluid flow through a check dam with a SPH-DCDEM model

NASA Astrophysics Data System (ADS)

Birjukovs Canelas, Ricardo; Domínguez, Jose; Crespo, Alejandro; Gómez-Gesteira, Moncho; Ferreira, Rui M. L.

2017-04-01

Debris flows represent some of the most relevant phenomena in geomorphological events. Due to the potential destructiveness of such flows, they are the target of a vast amount of research. Experimental research in laboratory facilities or in the field is fundamental to characterize the fundamental rheological properties of these flows and to provide insights on its structure. However, characterizing interparticle contacts and the structure of the motion of the granular phase is difficult, even in controlled laboratory conditions, and possible only for simple geometries. This work addresses the need for a numerical simulation tool applicable to granular-fluid mixtures featuring high spatial and temporal resolution, thus capable of resolving the motion of individual particles, including all interparticle contacts and susceptible to complement laboratory research. The DualSPHysics meshless numerical implementation based on Smoothed Particle Hydrodynamics (SPH) is expanded with a Distributed Contact Discrete Element Method (DCDEM) in order to explicitly solve the fluid and the solid phase. The specific objective is to test the SPH-DCDEM approach by comparing its results with experimental data. An experimental set-up for stony debris flows in a slit check dam is reproduced numerically, where solid material is introduced through a hopper assuring a constant solid discharge for the considered time interval. With each sediment particle possibly undergoing several simultaneous contacts, thousands of time-evolving interactions are efficiently treated due to the model's algorithmic structure and the HPC implementation of DualSPHysics. The results, comprising mainly of retention curves, are in good agreement with the measurements, correctly reproducing the changes in efficiency with slit spacing and density. The encouraging results, coupled with the prospect of so far unique insights into the internal dynamics of a debris flow show the potential of high-performance resolved approaches to the description of the flow and the study of its mitigation strategies. This research as partially supported by Portuguese and European funds, within programs COMPETE2020 and PORL-FEDER, through project PTDC/ECM-HID/6387/2014 granted by the National Foundation for Science and Technology (FCT).

Molecular basis of usher pore gating in Escherichia coli pilus biogenesis.

PubMed

Volkan, Ender; Kalas, Vasilios; Pinkner, Jerome S; Dodson, Karen W; Henderson, Nadine S; Pham, Thieng; Waksman, Gabriel; Delcour, Anne H; Thanassi, David G; Hultgren, Scott J

2013-12-17

Extracellular fibers called chaperone-usher pathway pili are critical virulence factors in a wide range of Gram-negative pathogenic bacteria that facilitate binding and invasion into host tissues and mediate biofilm formation. Chaperone-usher pathway ushers, which catalyze pilus assembly, contain five functional domains: a 24-stranded transmembrane β-barrel translocation domain (TD), a β-sandwich plug domain (PLUG), an N-terminal periplasmic domain, and two C-terminal periplasmic domains (CTD1 and 2). Pore gating occurs by a mechanism whereby the PLUG resides stably within the TD pore when the usher is inactive and then upon activation is translocated into the periplasmic space, where it functions in pilus assembly. Using antibiotic sensitivity and electrophysiology experiments, a single salt bridge was shown to function in maintaining the PLUG in the TD channel of the P pilus usher PapC, and a loop between the 12th and 13th beta strands of the TD (β12-13 loop) was found to facilitate pore opening. Mutation of the β12-13 loop resulted in a closed PapC pore, which was unable to efficiently mediate pilus assembly. Deletion of the PapH terminator/anchor resulted in increased OM permeability, suggesting a role for the proper anchoring of pili in retaining OM integrity. Further, we introduced cysteine residues in the PLUG and N-terminal periplasmic domains that resulted in a FimD usher with a greater propensity to exist in an open conformation, resulting in increased OM permeability but no loss in type 1 pilus assembly. These studies provide insights into the molecular basis of usher pore gating and its roles in pilus biogenesis and OM permeability.

Functional Analysis of Vaccinia Virus B5R Protein: Essential Role in Virus Envelopment Is Independent of a Large Portion of the Extracellular Domain

PubMed Central

Herrera, Elizabeth; del Mar Lorenzo, María; Blasco, Rafael; Isaacs, Stuart N.

1998-01-01

Vaccinia virus has two forms of infectious virions: the intracellular mature virus and the extracellular enveloped virus (EEV). EEV is critical for cell-to-cell and long-range spread of the virus. The B5R open reading frame (ORF) encodes a membrane protein that is essential for EEV formation. Deletion of the B5R ORF results in a dramatic reduction of EEV, and as a consequence, the virus produces small plaques in vitro and is highly attenuated in vivo. The extracellular portion of B5R is composed mainly of four domains that are similar to the short consensus repeats (SCRs) present in complement regulatory proteins. To determine the contribution of these putative SCR domains to EEV formation, we constructed recombinant vaccinia viruses that replaced the wild-type B5R gene with a mutated gene encoding a B5R protein lacking the SCRs. The resulting recombinant viruses produced large plaques, indicating efficient cell-to-cell spread in vitro, and gradient centrifugation of supernatants from infected cells confirmed that EEV was formed. In contrast, phalloidin staining of infected cells showed that the virus lacking the SCR domains was deficient in the induction of thick actin bundles. Thus, the highly conserved SCR domains present in the extracellular portion of the B5R protein are dispensable for EEV formation. This indicates that the B5R protein is a key viral protein with multiple functions in the process of virus envelopment and release. In addition, given the similarity of the extracellular domain to complement control proteins, the B5R protein may be involved in viral evasion from host immune responses. PMID:9420227

HD domain of SAMHD1 influences Vpx-induced degradation at a post-interaction step

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kang, Jian; Hou, Jingwei; Zhao, Ke

Primate SAMHD1 proteins are potent inhibitors of viruses, including retroviruses such as HIV-1, HIV-2, and SIV. Vpx, a distinctive viral protein expressed by HIV-2 and some SIVs, induces SAMHD1 degradation by forming a Vpx-DCAF1-based ubiquitin ligase complex. Either the N- or the C-terminus of SAMHD1 is critical for Vpx-induced degradation, depending on the types of SAMHD1 and Vpx proteins. However, it was not fully understood whether other regions of SAMHD1 also contribute to its depletion by Vpx. In the present study, we report that SAMHD1 from chicken (SAMHD1{sub GG}) was not degraded by SIVmac Vpx, in contrast with results formore » human SAMHD1 (SAMHD1{sub HS}). Results regarding to SAMHD1{sub HS} and SAMHD1{sub GG} fusion proteins supported previous findings that the C-terminus of SAMHD1{sub HS} is essential for Vpx-induced degradation. Internal domain substitution, however, revealed that the HD domain also contributes to Vpx-mediated SAMHD1 degradation. Interestingly, the HD domain influenced Vpx-mediated SAMHD1 degradation without affecting Vpx-SAMHD1 interaction. Therefore, our findings revealed that factors in addition to Vpx-SAMHD1 binding influence the efficiency of Vpx-mediated SAMHD1 degradation. - Highlights: • SAMHD1{sub GG} from chicken could not be depleted by SIVmac Vpx. • The C-terminus of human SAMHD1{sub HS} is critical for its degradation by Vpx. • The HD domain is essential for Vpx-induced degradation of SAMHD1{sub HS}. • Altering the HD domain does not affect Vpx-SAMHD1 interaction.« less

Polymerisation of fibrin αC-domains promotes endothelial cell migration and proliferation.

PubMed

Yakovlev, S; Mikhailenko, I; Tsurupa, G; Belkin, A M; Medved, L

2014-12-01

Upon conversion of fibrinogen into fibrin, fibrinogen αC-domains containing the RGD recognition motif form ordered αC polymers. Our previous study revealed that polymerisation of these domains promotes integrin-dependent adhesion and spreading of endothelial cells, as well as integrin-mediated activation of the FAK and ERK1/2 signalling pathways. The major goal of this study was to test the impact of αC-domain polymerisation on endothelial cell migration and proliferation during wound healing, and to clarify the mechanism underlying superior activity of αC polymers toward endothelial cells. In an in vitro wound healing assay, confluent endothelial cell monolayers on tissue culture plates coated with the αC monomer or αC polymers were wounded by scratching and wound closure was monitored by time-lapse videomicroscopy. Although the plates were coated with equal amounts of αC species, as confirmed by ELISA, wound closure by the cells occurred much faster on αC polymers, indicating that αC-domain polymerisation promotes cell migration and proliferation. In agreement, endothelial cell proliferation was also more efficient on αC polymers, as revealed by cell proliferation assay. Wound closure on both types of substrates was equally inhibited by the integrin-blocking GRGDSP peptide and a specific antagonist of the ERK1/2 signalling pathway. In contrast, blocking the FAK signaling pathway by a specific antagonist decreased wound closure only on αC polymers. These results indicate that polymerisation of the αC-domains enhances integrin-dependent endothelial cell migration and proliferation mainly through the FAK signalling pathway. Furthermore, clustering of integrin-binding RGD motifs in αC polymers is the major mechanism triggering these events.

Isolation and characterization of an IgNAR variable domain specific for the human mitochondrial translocase receptor Tom70.

PubMed

Nuttall, Stewart D; Krishnan, Usha V; Doughty, Larissa; Pearson, Kylie; Ryan, Michael T; Hoogenraad, Nicholas J; Hattarki, Meghan; Carmichael, Jennifer A; Irving, Robert A; Hudson, Peter J

2003-09-01

The new antigen receptor (IgNAR) from sharks is a disulphide bonded dimer of two protein chains, each containing one variable and five constant domains, and functions as an antibody. In order to assess the antigen-binding capabilities of isolated IgNAR variable domains (VNAR), we have constructed an in vitro library incorporating synthetic CDR3 regions of 15-18 residues in length. Screening of this library against the 60 kDa cytosolic domain of the 70 kDa outer membrane translocase receptor from human mitochondria (Tom70) resulted in one dominant antigen-specific clone (VNAR 12F-11) after four rounds of in vitro selection. VNAR 12F-11 was expressed into the Escherichia coli periplasm and purified by anti-FLAG affinity chromatography at yields of 3 mg x L(-1). Purified protein eluted from gel filtration columns as a single monomeric protein and CD spectrum analysis indicated correct folding into the expected beta-sheet conformation. Specific binding to Tom70 was demonstrated by ELISA and BIAcore (Kd = 2.2 +/- 0.31 x 10(-9) m-1) indicating that these VNAR domains can be efficiently displayed as bacteriophage libraries, and selected against target antigens with an affinity and stability equivalent to that obtained for other single domain antibodies. As an initial step in producing 'intrabody' variants of 12F-11, the impact of modifying or removing the conserved immunoglobulin intradomain disulphide bond was assessed. High affinity binding was only retained in the wild-type protein, which combined with our inability to affinity mature 12F-11, suggests that this particular VNAR is critically dependent upon precise CDR loop conformations for its binding affinity.

Intramembranous valine linked to schizophrenia is required for neuregulin 1 regulation of the morphological development of cortical neurons

PubMed Central

Chen, Yachi; Hancock, Melissa L.; Role, Lorna W.; Talmage, David A.

2010-01-01

Neuregulin 1 (NRG1) signaling is critical to various aspects of neuronal development and function. Among different NRG1 isoforms, the Type III isoforms of NRG1 are unique in their ability to signal via the intracellular domain following γ-secretase-dependent intramembranous processing. However, the functional consequences of Type III NRG1 signaling via its intracellular domain are largely unknown. In this study, we have identified mutations within Type III NRG1 that disrupt intramembranous proteolytic processing and abolish intracellular domain signaling. In particular, substitutions at valine 321, previously linked to schizophrenia risks, result in NRG1 proteins that fail to undergo γ-secretase-mediated nuclear localization and transcriptional activation. Using processing-defective mutants of Type III NRG1, we demonstrate that the intracellular domain signaling is specifically required for NRG1 regulation of the growth and branching of cortical dendrites but not axons. Consistent with the role of Type III NRG1 signaling via the intracellular domain in the initial patterning of cortical dendrites, our findings from pharmacological and genetic studies indicate that Type III NRG1 functions in dendritic development independent of ERBB kinase activity. Taken together, these results support the proposal that aberrant intracellular processing and defective signaling via the intracellular domain of Type III NRG1 impair a subset of NRG1 functions in cortical development and contribute to abnormal neuroconnectivity implicated in schizophrenia. PMID:20610754

Stress induced modulation of magnetic domain diffraction of single crystalline yttrium iron garnet

NASA Astrophysics Data System (ADS)

Mito, Shinichiro; Yoshihara, Yuki; Takagi, Hiroyuki; Inoue, Mitsuteru

2018-05-01

Stress induced modulation of the diffraction angle and efficiency of the light reflected from a stripe-domain magnetic garnet was demonstrated. The spacing of the magnetic domain was changed using the inverse magnetostriction effect. The sample structure was a piezo actuator/Al reflection layer/magnetic garnet substrate. A diffraction angle between the 0th and 1st ordered light was changed from 9.12 deg. to 10.20 deg. This result indicates that the domain spacing was changed from 3.3 μm to 3.0 μm. The change of the diffraction angle was irreversible for the voltage. However, reversible, linear and continuous change of the diffraction efficiency was observed. These results could be applicable for a voltage-driven optical solid state light deflector with low power consumption and high switching speed.

An oligodeoxyribonucleotide that supports catalytic activity in the hammerhead ribozyme domain.

PubMed Central

Chartrand, P; Harvey, S C; Ferbeyre, G; Usman, N; Cedergren, R

1995-01-01

A study of the activity of deoxyribonucleotide-substituted analogs of the hammerhead domain of RNA catalysis has led to the design of a 14mer oligomer composed entirely of deoxyribonucleotides that promotes the cleavage of an RNA substrate. Characterization of this reaction with sequence variants and mixed DNA/RNA oligomers shows that, although the all-deoxyribonucleotide oligomer is less efficient in catalysis, the DNA/substrate complex shares many of the properties of the all-RNA hammerhead domain such as multiple turnover kinetics and dependence on Mg2+ concentration. On the other hand, the values of kinetic parameters distinguish the DNA oligomer from the all-RNA oligomer. In addition, an analog of the oligomer having a single ribonucleotide in a strongly conserved position of the hammerhead domain is associated with more efficient catalysis than the all-RNA oligomer. Images PMID:7479070

DOE Office of Scientific and Technical Information (OSTI.GOV)

Petit, Chad M.; Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803; Chouljenko, Vladimir N.

The SARS-coronavirus (SARS-CoV) is the etiological agent of the severe acute respiratory syndrome (SARS). The SARS-CoV spike (S) glycoprotein mediates membrane fusion events during virus entry and virus-induced cell-to-cell fusion. The cytoplasmic portion of the S glycoprotein contains four cysteine-rich amino acid clusters. Individual cysteine clusters were altered via cysteine-to-alanine amino acid replacement and the modified S glycoproteins were tested for their transport to cell-surfaces and ability to cause cell fusion in transient transfection assays. Mutagenesis of the cysteine cluster I, located immediately proximal to the predicted transmembrane, domain did not appreciably reduce cell-surface expression, although S-mediated cell fusion wasmore » reduced by more than 50% in comparison to the wild-type S. Similarly, mutagenesis of the cysteine cluster II located adjacent to cluster I reduced S-mediated cell fusion by more than 60% compared to the wild-type S, while cell-surface expression was reduced by less than 20%. Mutagenesis of cysteine clusters III and IV did not appreciably affect S cell-surface expression or S-mediated cell fusion. The wild-type S was palmitoylated as evidenced by the efficient incorporation of {sup 3}H-palmitic acid in wild-type S molecules. S glycoprotein palmitoylation was significantly reduced for mutant glycoproteins having cluster I and II cysteine changes, but was largely unaffected for cysteine cluster III and IV mutants. These results show that the S cytoplasmic domain is palmitoylated and that palmitoylation of the membrane proximal cysteine clusters I and II may be important for S-mediated cell fusion.« less

Human exposure assessment in the near field of GSM base-station antennas using a hybrid finite element/method of moments technique.

PubMed

Meyer, Frans J C; Davidson, David B; Jakobus, Ulrich; Stuchly, Maria A

2003-02-01

A hybrid finite-element method (FEM)/method of moments (MoM) technique is employed for specific absorption rate (SAR) calculations in a human phantom in the near field of a typical group special mobile (GSM) base-station antenna. The MoM is used to model the metallic surfaces and wires of the base-station antenna, and the FEM is used to model the heterogeneous human phantom. The advantages of each of these frequency domain techniques are, thus, exploited, leading to a highly efficient and robust numerical method for addressing this type of bioelectromagnetic problem. The basic mathematical formulation of the hybrid technique is presented. This is followed by a discussion of important implementation details-in particular, the linear algebra routines for sparse, complex FEM matrices combined with dense MoM matrices. The implementation is validated by comparing results to MoM (surface equivalence principle implementation) and finite-difference time-domain (FDTD) solutions of human exposure problems. A comparison of the computational efficiency of the different techniques is presented. The FEM/MoM implementation is then used for whole-body and critical-organ SAR calculations in a phantom at different positions in the near field of a base-station antenna. This problem cannot, in general, be solved using the MoM or FDTD due to computational limitations. This paper shows that the specific hybrid FEM/MoM implementation is an efficient numerical tool for accurate assessment of human exposure in the near field of base-station antennas.

Crystal Structure of a Two-domain Fragment of Hepatocyte Growth Factor Activator Inhibitor-1: FUNCTIONAL INTERACTIONS BETWEEN THE KUNITZ-TYPE INHIBITOR DOMAIN-1 AND THE NEIGHBORING POLYCYSTIC KIDNEY DISEASE-LIKE DOMAIN.

PubMed

Hong, Zebin; De Meulemeester, Laura; Jacobi, Annemarie; Pedersen, Jan Skov; Morth, J Preben; Andreasen, Peter A; Jensen, Jan K

2016-07-01

Hepatocyte growth factor activator inhibitor-1 (HAI-1) is a type I transmembrane protein and inhibitor of several serine proteases, including hepatocyte growth factor activator and matriptase. The protein is essential for development as knock-out mice die in utero due to placental defects caused by misregulated extracellular proteolysis. HAI-1 contains two Kunitz-type inhibitor domains (Kunitz), which are generally thought of as a functionally self-contained protease inhibitor unit. This is not the case for HAI-1, where our results reveal how interdomain interactions have evolved to stimulate the inhibitory activity of an integrated Kunitz. Here we present an x-ray crystal structure of an HAI-1 fragment covering the internal domain and Kunitz-1. The structure reveals not only that the previously uncharacterized internal domain is a member of the polycystic kidney disease domain family but also how the two domains engage in interdomain interactions. Supported by solution small angle x-ray scattering and a combination of site-directed mutagenesis and functional assays, we show that interdomain interactions not only stabilize the fold of the internal domain but also stimulate the inhibitory activity of Kunitz-1. By completing our structural characterization of the previously unknown N-terminal region of HAI-1, we provide new insight into the interplay between tertiary structure and the inhibitory activity of a multidomain protease inhibitor. We propose a previously unseen mechanism by which the association of an auxiliary domain stimulates the inhibitory activity of a Kunitz-type inhibitor (i.e. the first structure of an intramolecular interaction between a Kunitz and another domain). © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Prevalence of the F-type lectin domain.

PubMed

Bishnoi, Ritika; Khatri, Indu; Subramanian, Srikrishna; Ramya, T N C

2015-08-01

F-type lectins are fucolectins with characteristic fucose and calcium-binding sequence motifs and a unique lectin fold (the "F-type" fold). F-type lectins are phylogenetically widespread with selective distribution. Several eukaryotic F-type lectins have been biochemically and structurally characterized, and the F-type lectin domain (FLD) has also been studied in the bacterial proteins, Streptococcus mitis lectinolysin and Streptococcus pneumoniae SP2159. However, there is little knowledge about the extent of occurrence of FLDs and their domain organization, especially, in bacteria. We have now mined the extensive genomic sequence information available in the public databases with sensitive sequence search techniques in order to exhaustively survey prokaryotic and eukaryotic FLDs. We report 437 FLD sequence clusters (clustered at 80% sequence identity) from eukaryotic, eubacterial and viral proteins. Domain architectures are diverse but mostly conserved in closely related organisms, and domain organizations of bacterial FLD-containing proteins are very different from their eukaryotic counterparts, suggesting unique specialization of FLDs to suit different requirements. Several atypical phylogenetic associations hint at lateral transfer. Among eukaryotes, we observe an expansion of FLDs in terms of occurrence and domain organization diversity in the taxa Mollusca, Hemichordata and Branchiostomi, perhaps coinciding with greater emphasis on innate immune strategies in these organisms. The naturally occurring FLDs with diverse domain organizations that we have identified here will be useful for future studies aimed at creating designer molecular platforms for directing desired biological activities to fucosylated glycoconjugates in target niches. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

High affinity receptor labeling based on basic leucine zipper domain peptides conjugated with pH-sensitive fluorescent dye: Visualization of AMPA-type glutamate receptor endocytosis in living neurons.

PubMed

Hayashi, Ayako; Asanuma, Daisuke; Kamiya, Mako; Urano, Yasuteru; Okabe, Shigeo

2016-01-01

Techniques to visualize receptor trafficking in living neurons are important, but currently available methods are limited in their labeling efficiency, specificity and reliability. Here we report a method for receptor labeling with a basic leucine zipper domain peptide (ZIP) and a binding cassette specific to ZIP. Receptors are tagged with a ZIP-binding cassette at their extracellular domain. Tagged receptors expressed in cultured cells were labeled with exogenously applied fluorescently labeled ZIP with low background and high affinity. To test if ZIP labeling is useful in monitoring endocytosis and intracellular trafficking, we next conjugated ZIP with a pH-sensitive dye RhP-M (ZIP-RhP-M). ZIP binding to its binding cassette was pH-resistant and RhP-M fluorescence dramatically increased in acidic environment. Thus AMPA-type glutamate receptors (AMPARs) labeled by ZIP-RhP-M can report receptor endocytosis and subsequent intracellular trafficking. Application of ZIP-RhP-M to cultured hippocampal neurons expressing AMPARs tagged with a ZIP-binding cassette resulted in appearance of fluorescent puncta in PSD-95-positive large spines, suggesting local endocytosis and acidification of AMPARs in individual mature spines. This spine pool of AMPARs in acidic environment was distinct from the early endosomes labeled by transferrin uptake. These results suggest that receptor labeling by ZIP-RhP-M is a useful technique for monitoring endocytosis and intracellular trafficking. This article is part of the Special Issue entitled 'Synaptopathy--from Biology to Therapy'. Copyright © 2015 Elsevier Ltd. All rights reserved.

Rapid and highly efficient construction of TALE-based transcriptional regulators and nucleases for genome modification.

PubMed

Li, Lixin; Piatek, Marek J; Atef, Ahmed; Piatek, Agnieszka; Wibowo, Anjar; Fang, Xiaoyun; Sabir, J S M; Zhu, Jian-Kang; Mahfouz, Magdy M

2012-03-01

Transcription activator-like effectors (TALEs) can be used as DNA-targeting modules by engineering their repeat domains to dictate user-selected sequence specificity. TALEs have been shown to function as site-specific transcriptional activators in a variety of cell types and organisms. TALE nucleases (TALENs), generated by fusing the FokI cleavage domain to TALE, have been used to create genomic double-strand breaks. The identity of the TALE repeat variable di-residues, their number, and their order dictate the DNA sequence specificity. Because TALE repeats are nearly identical, their assembly by cloning or even by synthesis is challenging and time consuming. Here, we report the development and use of a rapid and straightforward approach for the construction of designer TALE (dTALE) activators and nucleases with user-selected DNA target specificity. Using our plasmid set of 100 repeat modules, researchers can assemble repeat domains for any 14-nucleotide target sequence in one sequential restriction-ligation cloning step and in only 24 h. We generated several custom dTALEs and dTALENs with new target sequence specificities and validated their function by transient expression in tobacco leaves and in vitro DNA cleavage assays, respectively. Moreover, we developed a web tool, called idTALE, to facilitate the design of dTALENs and the identification of their genomic targets and potential off-targets in the genomes of several model species. Our dTALE repeat assembly approach along with the web tool idTALE will expedite genome-engineering applications in a variety of cell types and organisms including plants.

The neural cell adhesion molecule promotes FGFR-dependent phosphorylation and membrane targeting of the exocyst complex to induce exocytosis in growth cones.

PubMed

Chernyshova, Yana; Leshchyns'ka, Iryna; Hsu, Shu-Chan; Schachner, Melitta; Sytnyk, Vladimir

2011-03-09

The exocyst complex is an essential regulator of polarized exocytosis involved in morphogenesis of neurons. We show that this complex binds to the intracellular domain of the neural cell adhesion molecule (NCAM). NCAM promotes FGF receptor-mediated phosphorylation of two tyrosine residues in the sec8 subunit of the exocyst complex and is required for efficient recruitment of the exocyst complex to growth cones. NCAM at the surface of growth cones induces Ca(2+)-dependent vesicle exocytosis, which is blocked by an inhibitor of L-type voltage-dependent Ca(2+) channels and tetanus toxin. Preferential exocytosis in growth cones underlying neurite outgrowth is inhibited in NCAM-deficient neurons as well as in neurons transfected with phosphorylation-deficient sec8 and dominant-negative peptides derived from the intracellular domain of NCAM. Thus, we reveal a novel role for a cell adhesion molecule in that it regulates addition of the new membrane to the cell surface of growth cones in developing neurons.

Residues in the membrane-spanning domain core modulate conformation and fusogenicity of the HIV-1 envelope glycoprotein

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shang Liang; Hunter, Eric, E-mail: eric.hunter2@emory.ed

2010-09-01

The membrane-spanning domain (MSD) of human immunodeficiency virus type I (HIV-1) envelope glycoprotein (Env) is critical for its biological activity. Initial studies have defined an almost invariant 'core' structure in the MSD and demonstrated that it is crucial for anchoring Env in the membrane and virus entry. We show here that amino acid substitutions in the MSD 'core' do not influence specific virus-cell attachment, nor CD4 receptor and CXCR4 coreceptor recognition by Env. However, substitutions within the MSD 'core' delayed the kinetics and reduced the efficiency of cell-cell fusion mediated by Env. Although we observed no evidence that membrane fusionmore » mediated by the MSD core mutants was arrested at a hemifusion stage, impaired Env fusogenicity was correlated with minor conformational changes in the V2, C1, and C5 regions in gp120 and the immunodominant loop in gp41. These changes could delay initiation of the conformational changes required in the fusion process.« less

N-Glycosylation of Human R-Spondin 1 Is Required for Efficient Secretion and Stability but Not for Its Heparin Binding Ability.

PubMed

Chang, Chiung-Fang; Hsu, Li-Sung; Weng, Chieh-Yu; Chen, Chih-Kai; Wang, Shu-Ying; Chou, Yi-Hwa; Liu, Yan-Yu; Yuan, Zi-Xiu; Huang, Wen-Ying; Lin, Ho; Chen, Yau-Hung; Tsai, Jen-Ning

2016-06-14

R-spondin 1 (Rspo1) plays an essential role in stem cell biology by potentiating Wnt signaling activity. Despite the fact that Rspo1 holds therapeutic potential for a number of diseases, its biogenesis is not fully elucidated. All Rspo proteins feature two amino-terminal furin-like repeats, which are responsible for Wnt signal potentiation, and a thrombospondin type 1 (TSR1) domain that can provide affinity towards heparan sulfate proteoglycans. Using chemical inhibitors, deglycosylase and site-directed mutagenesis, we found that human Rspo1 and Rspo3 are both N-glycosylated at N137, a site near the C-terminus of the furin repeat 2 domain, and Rspo2 is N-glycosylated at N160, a position near the N-terminus of TSR1 domain. Elimination of N-glycosylation at these sites affects their accumulation in media but have no effect on the ability towards heparin. Introduction of the N-glycosylation site to Rspo2 mutant at the position homologous to N137 in Rspo1 restored full glycosylation and rescued the accumulation defect of nonglycosylated Rspo2 mutant in media. Similar effect can be observed in the N137 Rspo1 or Rspo3 mutant engineered with Rspo2 N-glycosylation site. The results highlight the importance of N-glycosylation at these two positions in efficient folding and secretion of Rspo family. Finally, we further showed that human Rspo1 is subjected to endoplasmic reticulum (ER) quality control in N-glycan-dependent manner. While N-glycan of Rspo1 plays a role in its intracellular stability, it had little effect on secreted Rspo1. Our findings provide evidence for the critical role of N-glycosylation in the biogenesis of Rspo1.

N-Glycosylation of Human R-Spondin 1 Is Required for Efficient Secretion and Stability but Not for Its Heparin Binding Ability

PubMed Central

Chang, Chiung-Fang; Hsu, Li-Sung; Weng, Chieh-Yu; Chen, Chih-Kai; Wang, Shu-Ying; Chou, Yi-Hwa; Liu, Yan-Yu; Yuan, Zi-Xiu; Huang, Wen-Ying; Lin, Ho; Chen, Yau-Hung; Tsai, Jen-Ning

2016-01-01

R-spondin 1 (Rspo1) plays an essential role in stem cell biology by potentiating Wnt signaling activity. Despite the fact that Rspo1 holds therapeutic potential for a number of diseases, its biogenesis is not fully elucidated. All Rspo proteins feature two amino-terminal furin-like repeats, which are responsible for Wnt signal potentiation, and a thrombospondin type 1 (TSR1) domain that can provide affinity towards heparan sulfate proteoglycans. Using chemical inhibitors, deglycosylase and site-directed mutagenesis, we found that human Rspo1 and Rspo3 are both N-glycosylated at N137, a site near the C-terminus of the furin repeat 2 domain, and Rspo2 is N-glycosylated at N160, a position near the N-terminus of TSR1 domain. Elimination of N-glycosylation at these sites affects their accumulation in media but have no effect on the ability towards heparin. Introduction of the N-glycosylation site to Rspo2 mutant at the position homologous to N137 in Rspo1 restored full glycosylation and rescued the accumulation defect of nonglycosylated Rspo2 mutant in media. Similar effect can be observed in the N137 Rspo1 or Rspo3 mutant engineered with Rspo2 N-glycosylation site. The results highlight the importance of N-glycosylation at these two positions in efficient folding and secretion of Rspo family. Finally, we further showed that human Rspo1 is subjected to endoplasmic reticulum (ER) quality control in N-glycan-dependent manner. While N-glycan of Rspo1 plays a role in its intracellular stability, it had little effect on secreted Rspo1. Our findings provide evidence for the critical role of N-glycosylation in the biogenesis of Rspo1. PMID:27314333

A Surface Groove Essential for Viral Bcl-2 Function During Chronic Infection In Vivo

PubMed Central

Petros, Andrew M; Nettesheim, David; van Dyk, Linda F.; Labrada, Lucia; Speck, Samuel H; Levine, Beth

2005-01-01

Antiapoptotic Bcl-2 family proteins inhibit apoptosis in cultured cells by binding BH3 domains of proapoptotic Bcl-2 family members via a hydrophobic BH3 binding groove on the protein surface. We investigated the physiological importance of the BH3 binding groove of an antiapoptotic Bcl-2 protein in mammals in vivo by analyzing a viral Bcl-2 family protein. We show that the γ-herpesvirus 68 (γHV68) Bcl-2 family protein (γHV68 v-Bcl-2), which is known to inhibit apoptosis in cultured cells, inhibits both apoptosis in primary lymphocytes and Bax toxicity in yeast. Nuclear magnetic resonance determination of the γHV68 v-Bcl-2 structure revealed a BH3 binding groove that binds BH3 domain peptides from proapoptotic Bcl-2 family members Bax and Bak via a molecular mechanism shared with host Bcl-2 family proteins, involving a conserved arginine in the BH3 peptide binding groove. Mutations of this conserved arginine and two adjacent amino acids to alanine (SGR to AAA) within the BH3 binding groove resulted in a properly folded protein that lacked the capacity of the wild-type γHV68 v-Bcl-2 to bind Bax BH3 peptide and to block Bax toxicity in yeast. We tested the physiological importance of this v-Bcl-2 domain during viral infection by engineering viral mutants encoding a v-Bcl-2 containing the SGR to AAA mutation. This mutation resulted in a virus defective for both efficient reactivation of γHV68 from latency and efficient persistent γHV68 replication. These studies demonstrate an essential functional role for amino acids in the BH3 peptide binding groove of a viral Bcl-2 family member during chronic infection. PMID:16201011

Mutations to essential orphan response regulator HP1043 of Helicobacter pylori result in growth-stage regulatory defects.

PubMed

Olekhnovich, Igor N; Vitko, Serhiy; Chertihin, Olga; Hontecillas, Raquel; Viladomiu, Monica; Bassaganya-Riera, Josep; Hoffman, Paul S

2013-05-01

Helicobacter pylori establishes lifelong infections of the gastric mucosa, a niche considered hostile to most microbes. While responses to gastric acidity and local inflammation are understood, little is known as to how they are integrated into homeostatic control of cell division and growth-stage gene expression. Here we investigate the essential orphan response regulator HP1043, a member of the OmpR/PhoB subfamily of transcriptional regulators that is unique to the Epsilonproteobacteria and that lacks phosphorylation domains. To test the hypothesis that conformational changes in the homodimer might lead to defects in gene expression, we sought mutations that might alter DNA-binding efficiency. Two introduced mutations (C215S, C221S) C terminal to the DNA-binding domain of HP1043 (HP1043CC11) resulted in a 2-fold higher affinity for its own promoter by footprinting. Modeling studies with the crystal structure of HP1043 suggested that C215S might affect the helix-turn-helix domain. Genomic replacement of the hp1043 allele with the hp1043CC11 mutant allele resulted in a 2-fold decrease in protein levels, despite a dramatic increase in mRNA. The mutations did not affect in vitro growth rates or colonization efficiency in a mouse model. Proteomic profiling (CC11 mutant strain versus wild type) identified many expression differences, and quantitative PCR further revealed that 11 out of 12 examined genes had lost growth-stage regulation and that 6 of the genes contained HP1043 binding consensus sequences within the promoter regions (fur, cagA, cag23, flhA, flip, and napA). Our studies show that mutations that affect DNA-binding affinity can be used to identify new members of the HP1043 regulon.

A Conserved START Domain Coenzyme Q-binding Polypeptide is Required for Efficient Q Biosynthesis, Respiratory Electron Transport, and Antioxidant Function in Saccharomyces cerevisiae

PubMed Central

Morvaridi, Susan; Saiki, Ryoichi; Johnson, Jarrett S.; Liau, Wei-Siang; Hirano, Kathleen; Kawashima, Tadashi; Ji, Ziming; Loo, Joseph A.; Shepherd, Jennifer N.; Clarke, Catherine F.

2014-01-01

Coenzyme Qn (ubiquinone or Qn) is a redox active lipid composed of a fully substituted benzoquinone ring and a polyisoprenoid tail of n isoprene units. Saccharomyces cerevisiae coq1-coq9 mutants have defects in Q biosynthesis, lack Q6, are respiratory defective, and sensitive to stress imposed by polyunsaturated fatty acids. The hallmark phenotype of the Q-less yeast coq mutants is that respiration in isolated mitochondria can be rescued by the addition of Q2, a soluble Q analog. Yeast coq10 mutants share each of these phenotypes, with the surprising exception that they continue to produce Q6. Structure determination of the Caulobacter crescentus Coq10 homolog (CC1736) revealed a steroidogenic acute regulatory protein-related lipid transfer (START) domain, a hydrophobic tunnel known to bind specific lipids in other START domain family members. Here we show that purified CC1736 binds Q2, Q3, Q10, or demethoxy-Q3 in an equimolar ratio, but fails to bind 3-farnesyl-4-hydroxybenzoic acid, a farnesylated analog of an early Q-intermediate. Over-expression of C. crescentus CC1736 or COQ8 restores respiratory electron transport and antioxidant function of Q6 in the yeast coq10 null mutant. Studies with stable isotope ring precursors of Q reveal that early Q-biosynthetic intermediates accumulate in the coq10 mutant and de novo Q-biosynthesis is less efficient than in the wild-type yeast or rescued coq10 mutant. The results suggest that the Coq10 polypeptide:Q (protein:ligand) complex may serve essential functions in facilitating de novo Q biosynthesis and in delivering newly synthesized Q to one or more complexes of the respiratory electron transport chain. PMID:23270816

Gene Transduction and Cell Entry Pathway of Fiber-Modified Adenovirus Type 5 Vectors Carrying Novel Endocytic Peptide Ligands Selected on Human Tracheal Glandular Cells

PubMed Central

Gaden, Florence; Franqueville, Laure; Magnusson, Maria K.; Hong, Saw See; Merten, Marc D.; Lindholm, Leif; Boulanger, Pierre

2004-01-01

Monolayers of cystic fibrosis transmembrane conductance regulator (CFTR)-deficient human tracheal glandular cells (CF-KM4) were subjected to phage biopanning, and cell-internalized phages were isolated and sequenced, in order to identify CF-KM4-specific peptide ligands that would confer upon adenovirus type 5 (Ad5) vector a novel cell target specificity and/or higher efficiency of gene delivery into airway cells of patients with cystic fibrosis (CF). Three different ligands, corresponding to prototypes of the most represented families of phagotopes recovered from intracellular phages, were designed and individually inserted into Ad5-green fluorescent protein (GFP) (AdGFP) vectors at the extremities of short fiber shafts (seven repeats [R7]) terminated by scissile knobs. Only one vector, carrying the decapeptide GHPRQMSHVY (abbreviated as QM10), showed an enhanced gene transduction of CF-KM4 cells compared to control nonliganded vector with fibers of the same length (AdGFP-R7-knob). The enhancement in gene transfer efficiency was not specific to CF-KM4 cells but was observed in other mammalian cell lines tested. The QM10-liganded vector was referred to as AdGFP-QM10-knob in its knobbed version and as AdGFP-QM10 in its proteolytically deknobbed version. AdGFP-QM10 was found to transduce cells with a higher efficiency than its knob-bearing version, AdGFP-QM10-knob. Consistent with this, competition experiments indicated that the presence of knob domains was not an absolute requirement for cell attachment of the QM10-liganded vector and that the knobless AdGFP-QM10 used alternative cell-binding domains on its capsid, including penton base capsomer, via a site(s) different from its RGD motifs. The QM10-mediated effect on gene transduction seemed to take place at the step of endocytosis in both quantitative and qualitative manners. Virions of AdGFP-QM10 were endocytosed in higher numbers than virions of the control vector and were directed to a compartment different from the early endosomes targeted by members of species C Ad. AdGFP-QM10 was found to accumulate in late endosomal and low-pH compartments, suggesting that QM10 acted as an endocytic ligand of the lysosomal pathway. These results validated the concept of detargeting and retargeting Ad vectors via our deknobbing system and redirecting Ad vectors to an alternative endocytic pathway via a peptide ligand inserted in the fiber shaft domain. PMID:15194799

TRIM25 RING-finger E3 ubiquitin ligase is essential for RIG-I-mediated antiviral activity.

PubMed

Gack, Michaela U; Shin, Young C; Joo, Chul-Hyun; Urano, Tomohiko; Liang, Chengyu; Sun, Lijun; Takeuchi, Osamu; Akira, Shizuo; Chen, Zhijian; Inoue, Satoshi; Jung, Jae U

2007-04-19

Retinoic-acid-inducible gene-I (RIG-I; also called DDX58) is a cytosolic viral RNA receptor that interacts with MAVS (also called VISA, IPS-1 or Cardif) to induce type I interferon-mediated host protective innate immunity against viral infection. Furthermore, members of the tripartite motif (TRIM) protein family, which contain a cluster of a RING-finger domain, a B box/coiled-coil domain and a SPRY domain, are involved in various cellular processes, including cell proliferation and antiviral activity. Here we report that the amino-terminal caspase recruitment domains (CARDs) of RIG-I undergo robust ubiquitination induced by TRIM25 in mammalian cells. The carboxy-terminal SPRY domain of TRIM25 interacts with the N-terminal CARDs of RIG-I; this interaction effectively delivers the Lys 63-linked ubiquitin moiety to the N-terminal CARDs of RIG-I, resulting in a marked increase in RIG-I downstream signalling activity. The Lys 172 residue of RIG-I is critical for efficient TRIM25-mediated ubiquitination and for MAVS binding, as well as the ability of RIG-I to induce antiviral signal transduction. Furthermore, gene targeting demonstrates that TRIM25 is essential not only for RIG-I ubiquitination but also for RIG-I-mediated interferon- production and antiviral activity in response to RNA virus infection. Thus, we demonstrate that TRIM25 E3 ubiquitin ligase induces the Lys 63-linked ubiquitination of RIG-I, which is crucial for the cytosolic RIG-I signalling pathway to elicit host antiviral innate immunity.

Domain-Adapted Convolutional Networks for Satellite Image Classification: A Large-Scale Interactive Learning Workflow

DOE PAGES

Lunga, Dalton D.; Yang, Hsiuhan Lexie; Reith, Andrew E.; ...

2018-02-06

Satellite imagery often exhibits large spatial extent areas that encompass object classes with considerable variability. This often limits large-scale model generalization with machine learning algorithms. Notably, acquisition conditions, including dates, sensor position, lighting condition, and sensor types, often translate into class distribution shifts introducing complex nonlinear factors and hamper the potential impact of machine learning classifiers. Here, this article investigates the challenge of exploiting satellite images using convolutional neural networks (CNN) for settlement classification where the class distribution shifts are significant. We present a large-scale human settlement mapping workflow based-off multiple modules to adapt a pretrained CNN to address themore » negative impact of distribution shift on classification performance. To extend a locally trained classifier onto large spatial extents areas we introduce several submodules: First, a human-in-the-loop element for relabeling of misclassified target domain samples to generate representative examples for model adaptation; second, an efficient hashing module to minimize redundancy and noisy samples from the mass-selected examples; and third, a novel relevance ranking module to minimize the dominance of source example on the target domain. The workflow presents a novel and practical approach to achieve large-scale domain adaptation with binary classifiers that are based-off CNN features. Experimental evaluations are conducted on areas of interest that encompass various image characteristics, including multisensors, multitemporal, and multiangular conditions. Domain adaptation is assessed on source–target pairs through the transfer loss and transfer ratio metrics to illustrate the utility of the workflow.« less

Domain-Adapted Convolutional Networks for Satellite Image Classification: A Large-Scale Interactive Learning Workflow

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lunga, Dalton D.; Yang, Hsiuhan Lexie; Reith, Andrew E.

Satellite imagery often exhibits large spatial extent areas that encompass object classes with considerable variability. This often limits large-scale model generalization with machine learning algorithms. Notably, acquisition conditions, including dates, sensor position, lighting condition, and sensor types, often translate into class distribution shifts introducing complex nonlinear factors and hamper the potential impact of machine learning classifiers. Here, this article investigates the challenge of exploiting satellite images using convolutional neural networks (CNN) for settlement classification where the class distribution shifts are significant. We present a large-scale human settlement mapping workflow based-off multiple modules to adapt a pretrained CNN to address themore » negative impact of distribution shift on classification performance. To extend a locally trained classifier onto large spatial extents areas we introduce several submodules: First, a human-in-the-loop element for relabeling of misclassified target domain samples to generate representative examples for model adaptation; second, an efficient hashing module to minimize redundancy and noisy samples from the mass-selected examples; and third, a novel relevance ranking module to minimize the dominance of source example on the target domain. The workflow presents a novel and practical approach to achieve large-scale domain adaptation with binary classifiers that are based-off CNN features. Experimental evaluations are conducted on areas of interest that encompass various image characteristics, including multisensors, multitemporal, and multiangular conditions. Domain adaptation is assessed on source–target pairs through the transfer loss and transfer ratio metrics to illustrate the utility of the workflow.« less

Nebo: An efficient, parallel, and portable domain-specific language for numerically solving partial differential equations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Earl, Christopher; Might, Matthew; Bagusetty, Abhishek

This study presents Nebo, a declarative domain-specific language embedded in C++ for discretizing partial differential equations for transport phenomena on multiple architectures. Application programmers use Nebo to write code that appears sequential but can be run in parallel, without editing the code. Currently Nebo supports single-thread execution, multi-thread execution, and many-core (GPU-based) execution. With single-thread execution, Nebo performs on par with code written by domain experts. With multi-thread execution, Nebo can linearly scale (with roughly 90% efficiency) up to 12 cores, compared to its single-thread execution. Moreover, Nebo’s many-core execution can be over 140x faster than its single-thread execution.

Nebo: An efficient, parallel, and portable domain-specific language for numerically solving partial differential equations

DOE PAGES

Earl, Christopher; Might, Matthew; Bagusetty, Abhishek; ...

2016-01-26

This study presents Nebo, a declarative domain-specific language embedded in C++ for discretizing partial differential equations for transport phenomena on multiple architectures. Application programmers use Nebo to write code that appears sequential but can be run in parallel, without editing the code. Currently Nebo supports single-thread execution, multi-thread execution, and many-core (GPU-based) execution. With single-thread execution, Nebo performs on par with code written by domain experts. With multi-thread execution, Nebo can linearly scale (with roughly 90% efficiency) up to 12 cores, compared to its single-thread execution. Moreover, Nebo’s many-core execution can be over 140x faster than its single-thread execution.

Protein Kinase LegK2 Is a Type IV Secretion System Effector Involved in Endoplasmic Reticulum Recruitment and Intracellular Replication of Legionella pneumophila ▿

PubMed Central

Hervet, Eva; Charpentier, Xavier; Vianney, Anne; Lazzaroni, Jean-Claude; Gilbert, Christophe; Atlan, Danièle; Doublet, Patricia

2011-01-01

Legionella pneumophila is the etiological agent of Legionnaires' disease. Crucial to the pathogenesis of this intracellular pathogen is its ability to subvert host cell defenses, permitting intracellular replication in specialized vacuoles within host cells. The Dot/Icm type IV secretion system (T4SS), which translocates a large number of bacterial effectors into host cell, is absolutely required for rerouting the Legionella phagosome. Many Legionella effectors display distinctive eukaryotic domains, among which are protein kinase domains. In silico analysis and in vitro phosphorylation assays identified five functional protein kinases, LegK1 to LegK5, encoded by the epidemic L. pneumophila Lens strain. Except for LegK5, the Legionella protein kinases are all T4SS effectors. LegK2 plays a key role in bacterial virulence, as demonstrated by gene inactivation. The legK2 mutant containing vacuoles displays less-efficient recruitment of endoplasmic reticulum markers, which results in delayed intracellular replication. Considering that a kinase-dead substitution mutant of legK2 exhibits the same virulence defects, we highlight here a new molecular mechanism, namely, protein phosphorylation, developed by L. pneumophila to establish a replicative niche and evade host cell defenses. PMID:21321072

Vegetation sensitivity to global anthropogenic carbon dioxide emissions in a topographically complex region

USGS Publications Warehouse

Diffenbaugh, N.S.; Sloan, L.C.; Snyder, M.A.; Bell, J.L.; Kaplan, J.; Shafer, S.L.; Bartlein, P.J.

2003-01-01

Anthropogenic increases in atmospheric carbon dioxide (CO2) concentrations may affect vegetation distribution both directly through changes in photosynthesis and water-use efficiency, and indirectly through CO2-induced climate change. Using an equilibrium vegetation model (BIOME4) driven by a regional climate model (RegCM2.5), we tested the sensitivity of vegetation in the western United States, a topographically complex region, to the direct, indirect, and combined effects of doubled preindustrial atmospheric CO2 concentrations. Those sensitivities were quantified using the kappa statistic. Simulated vegetation in the western United States was sensitive to changes in atmospheric CO2 concentrations, with woody biome types replacing less woody types throughout the domain. The simulated vegetation was also sensitive to climatic effects, particularly at high elevations, due to both warming throughout the domain and decreased precipitation in key mountain regions such as the Sierra Nevada of California and the Cascade and Blue Mountains of Oregon. Significantly, when the direct effects of CO2 on vegetation were tested in combination with the indirect effects of CO2-induced climate change, new vegetation patterns were created that were not seen in either of the individual cases. This result indicates that climatic and nonclimatic effects must be considered in tandem when assessing the potential impacts of elevated CO2 levels.

West Nile virus discriminates between DC-SIGN and DC-SIGNR for cellular attachment and infection.

PubMed

Davis, Carl W; Nguyen, Hai-Yen; Hanna, Sheri L; Sánchez, Melissa D; Doms, Robert W; Pierson, Theodore C

2006-02-01

The C-type lectins DC-SIGN and DC-SIGNR bind mannose-rich glycans with high affinity. In vitro, cells expressing these attachment factors efficiently capture, and are infected by, a diverse array of appropriately glycosylated pathogens, including dengue virus. In this study, we investigated whether these lectins could enhance cellular infection by West Nile virus (WNV), a mosquito-borne flavivirus related to dengue virus. We discovered that DC-SIGNR promoted WNV infection much more efficiently than did DC-SIGN, particularly when the virus was grown in human cell types. The presence of a single N-linked glycosylation site on either the prM or E glycoprotein of WNV was sufficient to allow DC-SIGNR-mediated infection, demonstrating that uncleaved prM protein present on a flavivirus virion can influence viral tropism under certain circumstances. Preferential utilization of DC-SIGNR was a specific property conferred by the WNV envelope glycoproteins. Chimeras between DC-SIGN and DC-SIGNR demonstrated that the ability of DC-SIGNR to promote WNV infection maps to its carbohydrate recognition domain. WNV virions and subviral particles bound to DC-SIGNR with much greater affinity than DC-SIGN. We believe this is the first report of a pathogen interacting more efficiently with DC-SIGNR than with DC-SIGN. Our results should lead to the discovery of new mechanisms by which these well-studied lectins discriminate among ligands.

A constrained-gradient method to control divergence errors in numerical MHD

NASA Astrophysics Data System (ADS)

Hopkins, Philip F.

2016-10-01

In numerical magnetohydrodynamics (MHD), a major challenge is maintaining nabla \\cdot {B}=0. Constrained transport (CT) schemes achieve this but have been restricted to specific methods. For more general (meshless, moving-mesh, ALE) methods, `divergence-cleaning' schemes reduce the nabla \\cdot {B} errors; however they can still be significant and can lead to systematic errors which converge away slowly. We propose a new constrained gradient (CG) scheme which augments these with a projection step, and can be applied to any numerical scheme with a reconstruction. This iteratively approximates the least-squares minimizing, globally divergence-free reconstruction of the fluid. Unlike `locally divergence free' methods, this actually minimizes the numerically unstable nabla \\cdot {B} terms, without affecting the convergence order of the method. We implement this in the mesh-free code GIZMO and compare various test problems. Compared to cleaning schemes, our CG method reduces the maximum nabla \\cdot {B} errors by ˜1-3 orders of magnitude (˜2-5 dex below typical errors if no nabla \\cdot {B} cleaning is used). By preventing large nabla \\cdot {B} at discontinuities, this eliminates systematic errors at jumps. Our CG results are comparable to CT methods; for practical purposes, the nabla \\cdot {B} errors are eliminated. The cost is modest, ˜30 per cent of the hydro algorithm, and the CG correction can be implemented in a range of numerical MHD methods. While for many problems, we find Dedner-type cleaning schemes are sufficient for good results, we identify a range of problems where using only Powell or `8-wave' cleaning can produce order-of-magnitude errors.

The Formation of a Milky Way-sized Disk Galaxy. I. A Comparison of Numerical Methods

NASA Astrophysics Data System (ADS)

Zhu, Qirong; Li, Yuexing

2016-11-01

The long-standing challenge of creating a Milky Way- (MW-) like disk galaxy from cosmological simulations has motivated significant developments in both numerical methods and physical models. We investigate these two fundamental aspects in a new comparison project using a set of cosmological hydrodynamic simulations of an MW-sized galaxy. In this study, we focus on the comparison of two particle-based hydrodynamics methods: an improved smoothed particle hydrodynamics (SPH) code Gadget, and a Lagrangian Meshless Finite-Mass (MFM) code Gizmo. All the simulations in this paper use the same initial conditions and physical models, which include star formation, “energy-driven” outflows, metal-dependent cooling, stellar evolution, and metal enrichment. We find that both numerical schemes produce a late-type galaxy with extended gaseous and stellar disks. However, notable differences are present in a wide range of galaxy properties and their evolution, including star-formation history, gas content, disk structure, and kinematics. Compared to Gizmo, the Gadget simulation produced a larger fraction of cold, dense gas at high redshift which fuels rapid star formation and results in a higher stellar mass by 20% and a lower gas fraction by 10% at z = 0, and the resulting gas disk is smoother and more coherent in rotation due to damping of turbulent motion by the numerical viscosity in SPH, in contrast to the Gizmo simulation, which shows a more prominent spiral structure. Given its better convergence properties and lower computational cost, we argue that the MFM method is a promising alternative to SPH in cosmological hydrodynamic simulations.

THE FORMATION OF A MILKY WAY-SIZED DISK GALAXY. I. A COMPARISON OF NUMERICAL METHODS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhu, Qirong; Li, Yuexing, E-mail: qxz125@psu.edu

The long-standing challenge of creating a Milky Way- (MW-) like disk galaxy from cosmological simulations has motivated significant developments in both numerical methods and physical models. We investigate these two fundamental aspects in a new comparison project using a set of cosmological hydrodynamic simulations of an MW-sized galaxy. In this study, we focus on the comparison of two particle-based hydrodynamics methods: an improved smoothed particle hydrodynamics (SPH) code Gadget, and a Lagrangian Meshless Finite-Mass (MFM) code Gizmo. All the simulations in this paper use the same initial conditions and physical models, which include star formation, “energy-driven” outflows, metal-dependent cooling, stellarmore » evolution, and metal enrichment. We find that both numerical schemes produce a late-type galaxy with extended gaseous and stellar disks. However, notable differences are present in a wide range of galaxy properties and their evolution, including star-formation history, gas content, disk structure, and kinematics. Compared to Gizmo, the Gadget simulation produced a larger fraction of cold, dense gas at high redshift which fuels rapid star formation and results in a higher stellar mass by 20% and a lower gas fraction by 10% at z = 0, and the resulting gas disk is smoother and more coherent in rotation due to damping of turbulent motion by the numerical viscosity in SPH, in contrast to the Gizmo simulation, which shows a more prominent spiral structure. Given its better convergence properties and lower computational cost, we argue that the MFM method is a promising alternative to SPH in cosmological hydrodynamic simulations.« less

LOOPREF: A Fluid Code for the Simulation of Coronal Loops

NASA Technical Reports Server (NTRS)

deFainchtein, Rosalinda; Antiochos, Spiro; Spicer, Daniel

1998-01-01

This report documents the code LOOPREF. LOOPREF is a semi-one dimensional finite element code that is especially well suited to simulate coronal-loop phenomena. It has a full implementation of adaptive mesh refinement (AMR), which is crucial for this type of simulation. The AMR routines are an improved version of AMR1D. LOOPREF's versatility makes is suitable to simulate a wide variety of problems. In addition to efficiently providing very high resolution in rapidly changing regions of the domain, it is equipped to treat loops of variable cross section, any non-linear form of heat conduction, shocks, gravitational effects, and radiative loss.

Multiple Loops of the Dihydropyridine Receptor Pore Subunit Are Required for Full-Scale Excitation-Contraction Coupling in Skeletal Muscle

PubMed Central

Carbonneau, Leah; Bhattacharya, Dipankar; Sheridan, David C.; Coronado, Roberto

2005-01-01

Understanding which cytosolic domains of the dihydropyridine receptor participate in excitation-contraction (EC) coupling is critical to validate current structural models. Here we quantified the contribution to skeletal-type EC coupling of the α1S (CaV1.1) II-III loop when alone or in combination with the rest of the cytosolic domains of α1S. Chimeras consisting of α1C (CaV1.2) with α1S substitutions at each of the interrepeat loops (I-II, II-III, and III-IV loops) and N- and C-terminal domains were evaluated in dysgenic (α1S-null) myotubes for phenotypic expression of skeletal-type EC coupling. Myotubes were voltage-clamped, and Ca2+ transients were measured by confocal line-scan imaging of fluo-4 fluorescence. In agreement with previous results, the α1C/α1S II-III loop chimera, but none of the other single-loop chimeras, recovered a sigmoidal fluorescence-voltage curve indicative of skeletal-type EC coupling. To quantify Ca2+ transients in the absence of inward Ca2+ current, but without changing the external solution, a mutation, E736K, was introduced into the P-loop of repeat II of α1C. The Ca2+ transients expressed by the α1C(E736K)/α1S II-III loop chimera were ∼70% smaller than those expressed by the Ca2+-conducting α1C/α1S II-III variant. The low skeletal-type EC coupling expressed by the α1C/α1S II-III loop chimera was confirmed in the Ca2+-conducting α1C/α1S II-III loop variant using Cd2+ (10−4 M) as the Ca2+ current blocker. In contrast to the behavior of the II-III loop chimera, Ca2+ transients expressed by an α1C/α1S chimera carrying all tested skeletal α1S domains (all α1S interrepeat loops, N- and C-terminus) were similar in shape and amplitude to wild-type α1S, and did not change in the presence of the E736K mutation or in the presence of 10−4 M Cd2+. Controls indicated that similar dihydropyridine receptor charge movements were expressed by the non-Ca2+ permeant α1S(E1014K) variant, the α1C(E736K)/α1S II-III loop chimera, and the α1C(E736K)/α1S chimera carrying all tested α1S domains. The data indicate that the functional recovery produced by the α1S II-III loop is incomplete and that multiple cytosolic domains of α1S are necessary for a quantitative recovery of the EC-coupling phenotype of skeletal myotubes. Thus, despite the importance of the II-III loop there may be other critical determinants in α1S that influence the efficiency of EC coupling. PMID:15849247

Domain architecture conservation in orthologs

PubMed Central

2011-01-01

Background As orthologous proteins are expected to retain function more often than other homologs, they are often used for functional annotation transfer between species. However, ortholog identification methods do not take into account changes in domain architecture, which are likely to modify a protein's function. By domain architecture we refer to the sequential arrangement of domains along a protein sequence. To assess the level of domain architecture conservation among orthologs, we carried out a large-scale study of such events between human and 40 other species spanning the entire evolutionary range. We designed a score to measure domain architecture similarity and used it to analyze differences in domain architecture conservation between orthologs and paralogs relative to the conservation of primary sequence. We also statistically characterized the extents of different types of domain swapping events across pairs of orthologs and paralogs. Results The analysis shows that orthologs exhibit greater domain architecture conservation than paralogous homologs, even when differences in average sequence divergence are compensated for, for homologs that have diverged beyond a certain threshold. We interpret this as an indication of a stronger selective pressure on orthologs than paralogs to retain the domain architecture required for the proteins to perform a specific function. In general, orthologs as well as the closest paralogous homologs have very similar domain architectures, even at large evolutionary separation. The most common domain architecture changes observed in both ortholog and paralog pairs involved insertion/deletion of new domains, while domain shuffling and segment duplication/deletion were very infrequent. Conclusions On the whole, our results support the hypothesis that function conservation between orthologs demands higher domain architecture conservation than other types of homologs, relative to primary sequence conservation. This supports the notion that orthologs are functionally more similar than other types of homologs at the same evolutionary distance. PMID:21819573

High-level expression of a novel recombinant human plasminogen activator (rhPA) in the milk of transgenic rabbits and its thrombolytic bioactivity in vitro.

PubMed

Song, Shaozheng; Ge, Xin; Cheng, Yaobin; Lu, Rui; Zhang, Ting; Yu, Baoli; Ji, Xueqiao; Qi, Zhengqiang; Rong, Yao; Yuan, Yuguo; Cheng, Yong

2016-08-01

The human tissue-type plasminogen activator (tPA) is a key kinase of fibrinolysis that plays an important role in dissolving fibrin clots to promote thrombolysis. The recombinant human plasminogen activator (rhPA) has more thrombolytic advantages than the wild type tPA. To increase the half-life and thrombolytic activity of tPA, a mutant containing only the essential K2 fibrin-binding and P activating plasminogen domains of the wild type tPA was cloned. This fragment was then inserted into goat β-casein regulatory sequences. Then, a mammary gland-specific expression vector, PCL25/rhPA, was constructed, and the transgenic rabbits were generated. In this study, 18 live transgenic founders (12♀, 6♂) were generated using pronuclear microinjection. Six transgenic rabbits were obtained, and the expression levels of rhPA in the milk had a range of 15.2-630 µg/ml. A fibrin agarose plate assay of rhPA showed that it had strong thrombolytic bioactivity in vitro, and the highest specific activity was >360 (360 times more than that of alteplase). The results indicated that the rhPA containing only the K2 and P domains is efficiently expressed with higher thrombolytic bioactivity in the milk of transgenic rabbits. Our study also demonstrated a new method for the large-scale production of clinically relevant recombinant pharmaceutical proteins in the mammary glands of transgenic rabbits.

Load- and polysaccharide-dependent activation of the Na+-type MotPS stator in the Bacillus subtilis flagellar motor.

PubMed

Terahara, Naoya; Noguchi, Yukina; Nakamura, Shuichi; Kami-Ike, Nobunori; Ito, Masahiro; Namba, Keiichi; Minamino, Tohru

2017-04-05

The flagellar motor of Bacillus subtilis possesses two distinct H + -type MotAB and Na + -type MotPS stators. In contrast to the MotAB motor, the MotPS motor functions efficiently at elevated viscosity in the presence of 200 mM NaCl. Here, we analyzed the torque-speed relationship of the Bacillus MotAB and MotPS motors over a wide range of external loads. The stall torque of the MotAB and MotPS motors at high load was about 2,200 pN nm and 220 pN nm, respectively. The number of active stators in the MotAB and MotPS motors was estimated to be about ten and one, respectively. However, the number of functional stators in the MotPS motor was increased up to ten with an increase in the concentration of a polysaccharide, Ficoll 400, as well as in the load. The maximum speeds of the MotAB and MotPS motors at low load were about 200 Hz and 50 Hz, respectively, indicating that the rate of the torque-generation cycle of the MotPS motor is 4-fold slower than that of the MotAB motor. Domain exchange experiments showed that the C-terminal periplasmic domain of MotS directly controls the assembly and disassembly dynamics of the MotPS stator in a load- and polysaccharide-dependent manner.

Load- and polysaccharide-dependent activation of the Na+-type MotPS stator in the Bacillus subtilis flagellar motor

PubMed Central

Terahara, Naoya; Noguchi, Yukina; Nakamura, Shuichi; Kami-ike, Nobunori; Ito, Masahiro; Namba, Keiichi; Minamino, Tohru

2017-01-01

The flagellar motor of Bacillus subtilis possesses two distinct H+-type MotAB and Na+-type MotPS stators. In contrast to the MotAB motor, the MotPS motor functions efficiently at elevated viscosity in the presence of 200 mM NaCl. Here, we analyzed the torque-speed relationship of the Bacillus MotAB and MotPS motors over a wide range of external loads. The stall torque of the MotAB and MotPS motors at high load was about 2,200 pN nm and 220 pN nm, respectively. The number of active stators in the MotAB and MotPS motors was estimated to be about ten and one, respectively. However, the number of functional stators in the MotPS motor was increased up to ten with an increase in the concentration of a polysaccharide, Ficoll 400, as well as in the load. The maximum speeds of the MotAB and MotPS motors at low load were about 200 Hz and 50 Hz, respectively, indicating that the rate of the torque-generation cycle of the MotPS motor is 4-fold slower than that of the MotAB motor. Domain exchange experiments showed that the C-terminal periplasmic domain of MotS directly controls the assembly and disassembly dynamics of the MotPS stator in a load- and polysaccharide-dependent manner. PMID:28378843

Molecular Dynamics Simulation of Rap1 Myb-type domain in Saccharomyces cerevisiae

PubMed Central

Mukherjee, Koel; Pandey, Dev Mani; Vidyarthi, Ambarish Saran

2012-01-01

Telomere is a nucleoprotein complex that plays important role in stability and their maintenance and consists of random repeats of species specific motifs. In budding Saccharomyces cerevisiae, Repressor Activator Protein 1 (Rap1) is a sequence specific protein that involved in transcriptional regulation. Rap1 consist of three active domains like N-terminal BRCT-domain, DNA-binding domain and C-terminal RCT-domain. In this study the unknown 3D structure of Myb-type domain (having 61 residues) within DNAbinding domain was modeled by Modeller7, and verified using different online bioinformatics tools (ProCheck, WhatIf, Verify3D). Dynamics of Myb-type domain of Rap1was carried out through simulation studies using GROMACS software. Time dependent interactions among the molecules were analyzed by Root Mean Square Deviation (RMSD), Radius of Gyration (Rg) and Root Mean Square Fluctuation (RMSF) plots. Motional properties in reduced dimension were also performed by Principal Component Analysis (PCA). Result indicated that Rap1 interacts with DNA major groove through its Helix Turn Helix motifs. Helix 3 was rigid, less amount of fluctuation was found as it interacts with DNA major groove. Helix2 and N-terminal having considerable fluctuation in the time scale. PMID:23144544

Molecular Dynamics Simulation of Rap1 Myb-type domain in Saccharomyces cerevisiae.

PubMed

Mukherjee, Koel; Pandey, Dev Mani; Vidyarthi, Ambarish Saran

2012-01-01

Telomere is a nucleoprotein complex that plays important role in stability and their maintenance and consists of random repeats of species specific motifs. In budding Saccharomyces cerevisiae, Repressor Activator Protein 1 (Rap1) is a sequence specific protein that involved in transcriptional regulation. Rap1 consist of three active domains like N-terminal BRCT-domain, DNA-binding domain and C-terminal RCT-domain. In this study the unknown 3D structure of Myb-type domain (having 61 residues) within DNAbinding domain was modeled by Modeller7, and verified using different online bioinformatics tools (ProCheck, WhatIf, Verify3D). Dynamics of Myb-type domain of Rap1was carried out through simulation studies using GROMACS software. Time dependent interactions among the molecules were analyzed by Root Mean Square Deviation (RMSD), Radius of Gyration (Rg) and Root Mean Square Fluctuation (RMSF) plots. Motional properties in reduced dimension were also performed by Principal Component Analysis (PCA). Result indicated that Rap1 interacts with DNA major groove through its Helix Turn Helix motifs. Helix 3 was rigid, less amount of fluctuation was found as it interacts with DNA major groove. Helix2 and N-terminal having considerable fluctuation in the time scale.

Evolution of Src Homology 2 (SH2) Domain to Recognize Sulfotyrosine.

PubMed

Ju, Tong; Niu, Wei; Guo, Jiantao

2016-09-16

Protein tyrosine O-sulfation is considered as the most common type of post-translational tyrosine modification in nature and plays important roles in extracellular biomolecular interactions. To facilitate the mapping, biological study, and medicinal application of this type of post-translational modification, we seek to evolve a small protein scaffold that recognizes sulfotyrosine with high affinity. We focused our efforts on the engineering of the Src Homology 2 (SH2) domain, which represents the largest class of known phosphotyrosine-recognition domain in nature and has a highly evolvable binding pocket. By using phage display, we successfully engineered the SH2 domain to recognize sulfotyrosine with high affinity. The best mutant, SH2-60.1, displayed more than 1700 fold higher sulfotyrosine-binding affinity than that of the wild-type SH2 domain. We also demonstrated that the evolved SH2 domain mutants could be used to detect sulfoprotein levels on the cell surface. These evolved SH2 domain mutants can be potentially applied to the study of protein tyrosine O-sulfation with proper experimental designs.

Efficient Power Network Analysis with Modeling of Inductive Effects

NASA Astrophysics Data System (ADS)

Zeng, Shan; Yu, Wenjian; Hong, Xianlong; Cheng, Chung-Kuan

In this paper, an efficient method is proposed to accurately analyze large-scale power/ground (P/G) networks, where inductive parasitics are modeled with the partial reluctance. The method is based on frequency-domain circuit analysis and the technique of vector fitting [14], and obtains the time-domain voltage response at given P/G nodes. The frequency-domain circuit equation including partial reluctances is derived, and then solved with the GMRES algorithm with rescaling, preconditioning and recycling techniques. With the merit of sparsified reluctance matrix and iterative solving techniques for the frequency-domain circuit equations, the proposed method is able to handle large-scale P/G networks with complete inductive modeling. Numerical results show that the proposed method is orders of magnitude faster than HSPICE, several times faster than INDUCTWISE [4], and capable of handling the inductive P/G structures with more than 100, 000 wire segments.

Advanced EMT and Phasor-Domain Hybrid Simulation with Simulation Mode Switching Capability for Transmission and Distribution Systems

DOE PAGES

Huang, Qiuhua; Vittal, Vijay

2018-05-09

Conventional electromagnetic transient (EMT) and phasor-domain hybrid simulation approaches presently exist for trans-mission system level studies. Their simulation efficiency is generally constrained by the EMT simulation. With an increasing number of distributed energy resources and non-conventional loads being installed in distribution systems, it is imperative to extend the hybrid simulation application to include distribution systems and integrated transmission and distribution systems. Meanwhile, it is equally important to improve the simulation efficiency as the modeling scope and complexity of the detailed system in the EMT simulation increases. To meet both requirements, this paper introduces an advanced EMT and phasor-domain hybrid simulationmore » approach. This approach has two main features: 1) a comprehensive phasor-domain modeling framework which supports positive-sequence, three-sequence, three-phase and mixed three-sequence/three-phase representations and 2) a robust and flexible simulation mode switching scheme. The developed scheme enables simulation switching from hybrid simulation mode back to pure phasor-domain dynamic simulation mode to achieve significantly improved simulation efficiency. The proposed method has been tested on integrated transmission and distribution systems. In conclusion, the results show that with the developed simulation switching feature, the total computational time is significantly reduced compared to running the hybrid simulation for the whole simulation period, while maintaining good simulation accuracy.« less

Advanced EMT and Phasor-Domain Hybrid Simulation with Simulation Mode Switching Capability for Transmission and Distribution Systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Qiuhua; Vittal, Vijay

Conventional electromagnetic transient (EMT) and phasor-domain hybrid simulation approaches presently exist for trans-mission system level studies. Their simulation efficiency is generally constrained by the EMT simulation. With an increasing number of distributed energy resources and non-conventional loads being installed in distribution systems, it is imperative to extend the hybrid simulation application to include distribution systems and integrated transmission and distribution systems. Meanwhile, it is equally important to improve the simulation efficiency as the modeling scope and complexity of the detailed system in the EMT simulation increases. To meet both requirements, this paper introduces an advanced EMT and phasor-domain hybrid simulationmore » approach. This approach has two main features: 1) a comprehensive phasor-domain modeling framework which supports positive-sequence, three-sequence, three-phase and mixed three-sequence/three-phase representations and 2) a robust and flexible simulation mode switching scheme. The developed scheme enables simulation switching from hybrid simulation mode back to pure phasor-domain dynamic simulation mode to achieve significantly improved simulation efficiency. The proposed method has been tested on integrated transmission and distribution systems. In conclusion, the results show that with the developed simulation switching feature, the total computational time is significantly reduced compared to running the hybrid simulation for the whole simulation period, while maintaining good simulation accuracy.« less

Accurate and efficient seismic data interpolation in the principal frequency wavenumber domain

NASA Astrophysics Data System (ADS)

Wang, Benfeng; Lu, Wenkai

2017-12-01

Seismic data irregularity caused by economic limitations, acquisition environmental constraints or bad trace elimination, can decrease the performance of the below multi-channel algorithms, such as surface-related multiple elimination (SRME), though some can overcome the irregularity defects. Therefore, accurate interpolation to provide the necessary complete data is a pre-requisite, but its wide applications are constrained because of its large computational burden for huge data volume, especially in 3D explorations. For accurate and efficient interpolation, the curvelet transform- (CT) based projection onto convex sets (POCS) method in the principal frequency wavenumber (PFK) domain is introduced. The complex-valued PF components can characterize their original signal with a high accuracy, but are at least half the size, which can help provide a reasonable efficiency improvement. The irregularity of the observed data is transformed into incoherent noise in the PFK domain, and curvelet coefficients may be sparser when CT is performed on the PFK domain data, enhancing the interpolation accuracy. The performance of the POCS-based algorithms using complex-valued CT in the time space (TX), principal frequency space, and PFK domains are compared. Numerical examples on synthetic and field data demonstrate the validity and effectiveness of the proposed method. With less computational burden, the proposed method can achieve a better interpolation result, and it can be easily extended into higher dimensions.

Effects of synthetic cohesin-containing scaffold protein architecture on binding dockerin-enzyme fusions on the surface of Lactococcus lactis.

PubMed

Wieczorek, Andrew S; Martin, Vincent J J

2012-12-15

The microbial synthesis of fuels, commodity chemicals, and bioactive compounds necessitates the assemblage of multiple enzyme activities to carry out sequential chemical reactions, often via substrate channeling by means of multi-domain or multi-enzyme complexes. Engineering the controlled incorporation of enzymes in recombinant protein complexes is therefore of interest. The cellulosome of Clostridium thermocellum is an extracellular enzyme complex that efficiently hydrolyzes crystalline cellulose. Enzymes interact with protein scaffolds via type 1 dockerin/cohesin interactions, while scaffolds in turn bind surface anchor proteins by means of type 2 dockerin/cohesin interactions, which demonstrate a different binding specificity than their type 1 counterparts. Recombinant chimeric scaffold proteins containing cohesins of different specificity allow binding of multiple enzymes to specific sites within an engineered complex. We report the successful display of engineered chimeric scaffold proteins containing both type 1 and type 2 cohesins on the surface of Lactococcus lactis cells. The chimeric scaffold proteins were able to form complexes with the Escherichia coli β-glucuronidase fused to either type 1 or type 2 dockerin, and differences in binding efficiencies were correlated with scaffold architecture. We used E. coli β-galactosidase, also fused to type 1 or type 2 dockerins, to demonstrate the targeted incorporation of two enzymes into the complexes. The simultaneous binding of enzyme pairs each containing a different dockerin resulted in bi-enzymatic complexes tethered to the cell surface. The sequential binding of the two enzymes yielded insights into parameters affecting assembly of the complex such as protein size and position within the scaffold. The spatial organization of enzymes into complexes is an important strategy for increasing the efficiency of biochemical pathways. In this study, chimeric protein scaffolds consisting of type 1 and type 2 cohesins anchored on the surface of L. lactis allowed for the controlled positioning of dockerin-fused reporter enzymes onto the scaffolds. By binding single enzymes or enzyme pairs to the scaffolds, our data also suggest that the size and relative positions of enzymes can affect the catalytic profiles of the resulting complexes. These insights will be of great value as we engineer more advanced scaffold-guided protein complexes to optimize biochemical pathways.

Multi-Layer Approach for the Detection of Selective Forwarding Attacks

PubMed Central

Alajmi, Naser; Elleithy, Khaled

2015-01-01

Security breaches are a major threat in wireless sensor networks (WSNs). WSNs are increasingly used due to their broad range of important applications in both military and civilian domains. WSNs are prone to several types of security attacks. Sensor nodes have limited capacities and are often deployed in dangerous locations; therefore, they are vulnerable to different types of attacks, including wormhole, sinkhole, and selective forwarding attacks. Security attacks are classified as data traffic and routing attacks. These security attacks could affect the most significant applications of WSNs, namely, military surveillance, traffic monitoring, and healthcare. Therefore, there are different approaches to detecting security attacks on the network layer in WSNs. Reliability, energy efficiency, and scalability are strong constraints on sensor nodes that affect the security of WSNs. Because sensor nodes have limited capabilities in most of these areas, selective forwarding attacks cannot be easily detected in networks. In this paper, we propose an approach to selective forwarding detection (SFD). The approach has three layers: MAC pool IDs, rule-based processing, and anomaly detection. It maintains the safety of data transmission between a source node and base station while detecting selective forwarding attacks. Furthermore, the approach is reliable, energy efficient, and scalable. PMID:26610499

Quantum efficiency investigations of type-II InAs/GaSb midwave infrared superlattice photodetectors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Giard, E., E-mail: edouard.giard@onera.fr; Ribet-Mohamed, I.; Jaeck, J.

2014-07-28

We present in this paper a comparison between different type-II InAs/GaSb superlattice (T2SL) photodiodes and focal plane array (FPA) in the mid-wavelength infrared domain to understand which phenomenon drives the performances of the T2SL structure in terms of quantum efficiency (QE). Our measurements on test photodiodes suggest low minority carrier diffusion length in the “InAs-rich” design, which penalizes carriers' collection in this structure for low bias voltage and front side illumination. This analysis is completed by a comparison of the experimental data with a fully analytic model, which allows to infer a hole diffusion length shorter than 100 nm. In addition,more » measurements on a FPA with backside illumination are finally presented. Results show an average QE in the 3–4.7 μm window equal to 42% for U{sub bias} = −0.1 V, 77 K operating temperature and no anti-reflection coating. These measurements, completed by modulation transfer function and noise measurements, reveal that the InAs-rich design, despite a low hole diffusion length, is promising for high performance infrared imaging applications.« less

Multi-Layer Approach for the Detection of Selective Forwarding Attacks.

PubMed

Alajmi, Naser; Elleithy, Khaled

2015-11-19

Security breaches are a major threat in wireless sensor networks (WSNs). WSNs are increasingly used due to their broad range of important applications in both military and civilian domains. WSNs are prone to several types of security attacks. Sensor nodes have limited capacities and are often deployed in dangerous locations; therefore, they are vulnerable to different types of attacks, including wormhole, sinkhole, and selective forwarding attacks. Security attacks are classified as data traffic and routing attacks. These security attacks could affect the most significant applications of WSNs, namely, military surveillance, traffic monitoring, and healthcare. Therefore, there are different approaches to detecting security attacks on the network layer in WSNs. Reliability, energy efficiency, and scalability are strong constraints on sensor nodes that affect the security of WSNs. Because sensor nodes have limited capabilities in most of these areas, selective forwarding attacks cannot be easily detected in networks. In this paper, we propose an approach to selective forwarding detection (SFD). The approach has three layers: MAC pool IDs, rule-based processing, and anomaly detection. It maintains the safety of data transmission between a source node and base station while detecting selective forwarding attacks. Furthermore, the approach is reliable, energy efficient, and scalable.

1H and 15N NMR resonance assignments and secondary structure of titin type I domains.

PubMed

Muhle-Goll, C; Nilges, M; Pastore, A

1997-01-01

Titin/connectin is a giant muscle protein with a highly modular architecture consisting of multiple repeats of two sequence motifs, named type I and type II. Type I modules have been suggested to be intracellular members of the fibronectin type III (Fn3) domain family. Along the titin sequence they are exclusively present in the region of the molecule located in the sarcomere A-band. This region has been shown to interact with myosin and C-protein. One of the most noticeable features of type I modules is that they are particularly rich in semiconserved prolines, since these residues account for about 8% of their sequence. We have determined the secondary structure of a representative type I domain (A71) by 15N and 1H NMR. We show that the type I domains of titin have the Fn3 fold as proposed, consisting of a three- and a four-stranded beta-sheet. When the two sheets are placed on top of each other to form the beta-sandwich characteristic of the Fn3 fold, 8 out of 10 prolines are found on the same side of the molecule and form an exposed hydrophobic patch. This suggests that the semiconserved prolines might be relevant for the function of type I modules, providing a surface for binding to other A-band proteins. The secondary structure of A71 was structurally aligned to other extracellular Fn3 modules of known 3D structure. The alignment shows that titin type I modules have closest similarity to the first Fn3 domain of Drosophila neuroglian.

Rational Design of Mini-Cas9 for Transcriptional Activation.

PubMed

Ma, Dacheng; Peng, Shuguang; Huang, Weiren; Cai, Zhiming; Xie, Zhen

2018-04-20

Nuclease dead Cas9 (dCas9) has been widely used for modulating gene expression by fusing with different activation or repression domains. However, delivery of the CRISPR/Cas system fused with various effector domains in a single adeno-associated virus (AAV) remains challenging due to the payload limit. Here, we engineered a set of downsized variants of Cas9 including Staphylococcus aureus Cas9 (SaCas9) that retained DNA binding activity by deleting conserved functional domains. We demonstrated that fusing FokI nuclease domain to the N-terminal of the minimal SaCas9 (mini-SaCas9) or to the middle of the split mini-SaCas9 can trigger efficient DNA cleavage. In addition, we constructed a set of compact transactivation domains based on the tripartite VPR activation domain and self-assembled arrays of split SpyTag:SpyCatch peptides, which are suitable for fusing to the mini-SaCas9. Lastly, we produced a single AAV containing the mini-SaCas9 fused with a downsized transactivation domain along with an optimized gRNA expression cassette, which showed efficient transactivation activity. Our results highlighted a practical approach to generate down-sized CRISPR/Cas9 and gene activation systems for in vivo applications.

Engineering and improvement of the efficiency of a chimeric [P450cam-RhFRed reductase domain] enzyme.

PubMed

Robin, Aélig; Roberts, Gareth A; Kisch, Johannes; Sabbadin, Federico; Grogan, Gideon; Bruce, Neil; Turner, Nicholas J; Flitsch, Sabine L

2009-05-14

A chimeric oxygenase, in which the P450cam domain was fused to the reductase host domains of a P450RhF from Rhodococcus sp. strain NCIMB 9784 was optimised to allow for a biotransformation at 30 mM substrate in 80% overall yield, with the linker region between P450 and FMN domain proving to be important for the effective biotransformation of (+)-camphor to 5-exo-hydroxycamphor.

Structures of class A macrophage scavenger receptors. Electron microscopic study of flexible, multidomain, fibrous proteins and determination of the disulfide bond pattern of the scavenger receptor cysteine-rich domain.

PubMed

Resnick, D; Chatterton, J E; Schwartz, K; Slayter, H; Krieger, M

1996-10-25

Structures of secreted forms of the human type I and II class A macrophage scavenger receptors were studied using biochemical and biophysical methods. Proteolytic analysis was used to determine the intramolecular disulfide bonds in the type I-specific scavenger receptor cysteine-rich (SRCR) domain: Cys2-Cys7, Cys3-Cys8, and Cys5-Cys6. This pattern is likely to be shared by the highly homologous domains in the many other members of the SRCR domain superfamily. Electron microscopy using rotary shadowing and negative staining showed that the type I and II receptors are extended molecules whose contour lengths are approximately 440 A. They comprised two adjacent fibrous segments, an alpha-helical coiled-coil ( approximately 230 A, including a contribution from the N-terminal spacer domain) and a collagenous triple helix ( approximately 210 A). The type I molecules also contained a C-terminal globular structure ( approximately 58 x 76 A) composed of three SRCR domains. The fibrous domains were joined by an extremely flexible hinge. The angle between these domains varied from 0 to 180 degrees and depended on the conditions of sample preparation. Unexpectedly, at physiologic pH, the prevalent angle seen using rotary shadowing was 0 degrees , resulting in a structure that is significantly more compact than previously suggested. The apparent juxtaposition of the fibrous domains at neutral pH provides a framework for future structure-function studies of these unusual multiligand receptors.

A novel endolysin disrupts Streptococcus suis with high efficiency.

PubMed

Ji, Wenhui; Huang, Qingqing; Sun, Liang; Wang, Hengan; Yan, Yaxian; Sun, Jianhe

2015-12-01

Streptococcus suis serotype 2 (S. suis 2) is a zoonotic pathogen that exhibits high-level resistance and multi-drug resistance to classic antibiotics and causes serious human casualties and heavy economic losses in the swine industry worldwide. Therefore, alternative therapies or novel antibacterial agents need to be developed to combat this pathogen. A novel endolysin derived from the S. suis temperate phage phi7917, termed Ly7917, was identified, which had broad lytic activity against S. suis type 1, 2, 7 and 9. Ly7917 consisted of an N-terminal cysteine, histidine-dependent amidohydrolases/peptidase catalytic domain and C-terminal SH3b cell wall binding domain. The endolysin maintained activity at high pH and its catalytic activity could be improved by addition of 10 μM 1.5 mM Ca(2+). In animal studies, 90% of BALB/c mice challenged with typical virulent strain HA9801 of S. suis 2 were protected by Ly7917 treatment. The bacterial load in the blood of HA9801-challenged mice was efficiently reduced almost 50% by Ly7917 while that of penicillin-G-treated mice kept almost unchanged. Our data suggest that Ly7917 may be an alternative therapeutic agent for infections caused by virulent S. suis strains. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

The function of the inner nuclear envelope protein SUN1 in mRNA export is regulated by phosphorylation.

PubMed

Li, Ping; Stumpf, Maria; Müller, Rolf; Eichinger, Ludwig; Glöckner, Gernot; Noegel, Angelika A

2017-08-22

SUN1, a component of the LINC (Linker of Nucleoskeleton and Cytoskeleton) complex, functions in mammalian mRNA export through the NXF1-dependent pathway. It associates with mRNP complexes by direct interaction with NXF1. It also binds to the NPC through association with the nuclear pore component Nup153, which is involved in mRNA export. The SUN1-NXF1 association is at least partly regulated by a protein kinase C (PKC) which phosphorylates serine 113 (S113) in the N-terminal domain leading to reduced interaction. The phosphorylation appears to be important for the SUN1 function in nuclear mRNA export since GFP-SUN1 carrying a S113A mutation was less efficient in restoring mRNA export after SUN1 knockdown as compared to the wild type protein. By contrast, GFP-SUN1-S113D resembling the phosphorylated state allowed very efficient export of poly(A)+RNA. Furthermore, probing a possible role of the LINC complex component Nesprin-2 in this process we observed impaired mRNA export in Nesprin-2 knockdown cells. This effect might be independent of SUN1 as expression of a GFP tagged SUN-domain deficient SUN1, which no longer can interact with Nesprin-2, did not affect mRNA export.

Platelet glycoprotein Ibalpha forms catch bonds with human WT vWF but not with type 2B von Willebrand disease vWF.

PubMed

Yago, Tadayuki; Lou, Jizhong; Wu, Tao; Yang, Jun; Miner, Jonathan J; Coburn, Leslie; López, José A; Cruz, Miguel A; Dong, Jing-Fei; McIntire, Larry V; McEver, Rodger P; Zhu, Cheng

2008-09-01

Arterial blood flow enhances glycoprotein Ibalpha (GPIbalpha) binding to vWF, which initiates platelet adhesion to injured vessels. Mutations in the vWF A1 domain that cause type 2B von Willebrand disease (vWD) reduce the flow requirement for adhesion. Here we show that increasing force on GPIbalpha/vWF bonds first prolonged ("catch") and then shortened ("slip") bond lifetimes. Two type 2B vWD A1 domain mutants, R1306Q and R1450E, converted catch bonds to slip bonds by prolonging bond lifetimes at low forces. Steered molecular dynamics simulations of GPIbalpha dissociating from the A1 domain suggested mechanisms for catch bonds and their conversion by the A1 domain mutations. Catch bonds caused platelets and GPIbalpha-coated microspheres to roll more slowly on WT vWF and WT A1 domains as flow increased from suboptimal levels, explaining flow-enhanced rolling. Longer bond lifetimes at low forces eliminated the flow requirement for rolling on R1306Q and R1450E mutant A1 domains. Flowing platelets agglutinated with microspheres bearing R1306Q or R1450E mutant A1 domains, but not WT A1 domains. Therefore, catch bonds may prevent vWF multimers from agglutinating platelets. A disintegrin and metalloproteinase with a thrombospondin type 1 motif-13 (ADAMTS-13) reduced platelet agglutination with microspheres bearing a tridomain A1A2A3 vWF fragment with the R1450E mutation in a shear-dependent manner. We conclude that in type 2B vWD, prolonged lifetimes of vWF bonds with GPIbalpha on circulating platelets may allow ADAMTS-13 to deplete large vWF multimers, causing bleeding.

Efficient Time-Domain Imaging Processing for One-Stationary Bistatic Forward-Looking SAR Including Motion Errors

PubMed Central

Xie, Hongtu; Shi, Shaoying; Xiao, Hui; Xie, Chao; Wang, Feng; Fang, Qunle

2016-01-01

With the rapid development of the one-stationary bistatic forward-looking synthetic aperture radar (OS-BFSAR) technology, the huge amount of the remote sensing data presents challenges for real-time imaging processing. In this paper, an efficient time-domain algorithm (ETDA) considering the motion errors for the OS-BFSAR imaging processing, is presented. This method can not only precisely handle the large spatial variances, serious range-azimuth coupling and motion errors, but can also greatly improve the imaging efficiency compared with the direct time-domain algorithm (DTDA). Besides, it represents the subimages on polar grids in the ground plane instead of the slant-range plane, and derives the sampling requirements considering motion errors for the polar grids to offer a near-optimum tradeoff between the imaging precision and efficiency. First, OS-BFSAR imaging geometry is built, and the DTDA for the OS-BFSAR imaging is provided. Second, the polar grids of subimages are defined, and the subaperture imaging in the ETDA is derived. The sampling requirements for polar grids are derived from the point of view of the bandwidth. Finally, the implementation and computational load of the proposed ETDA are analyzed. Experimental results based on simulated and measured data validate that the proposed ETDA outperforms the DTDA in terms of the efficiency improvement. PMID:27845757

Blockade of a key region in the extracellular domain inhibits HER2 dimerization and signaling.

PubMed

Menendez, Javier A; Schroeder, Barbara; Peirce, Susan K; Vellon, Luciano; Papadimitropoulou, Adriana; Espinoza, Ingrid; Lupu, Ruth

2015-06-01

Several treatment strategies target the human epidermal growth factor receptor 2 (HER2) in breast carcinomas, including monoclonal antibodies directed against HER2's extracellular domain (ECD) and small molecule inhibitors of its tyrosine kinase activity. Yet, novel therapies are needed that prevent HER2 dimerization with other HER family members, because current treatments are only partially effective. To test the hypothesis that HER2 activation requires a protein sequence in the HER2-ECD that mediates HER2 homo- and heterodimerization, we introduced a series of deletion mutations in the third subdomain of HER2-ECD. These deletion mutants were retrovirally expressed in breast cancer (BC) cells that naturally overexpress HER2 and in noncancerous, HER2-negative breast epithelial cells. One-factor analysis of variance or Student's t test were used to analyze differences. All statistical tests were two-sided. The smallest deletion in the ECD domain of HER2, which removed only 16 amino acids (HER2-ECDΔ451-466), completely disrupted the oncogenic potential of HER2. In contrast to wild-type HER2, the mutant-inhibited anchorage-independent growth (mean number of colonies: mutant, 70, 95% confidence interval [CI] = 55 to 85; wild-type, 400, 95% CI = 320 to 480, P < .001) increased sensitivity to paclitaxel treatment in both transformed and nontransformed cells. Overexpression of HER2Δ451-466 efficiently inhibited activation of HER1, HER2, and HER3 in all cell lines tested. These findings reveal that an essential "activating" sequence exists in the extracellular domain of HER2. Disruption of this sequence disables the HER2 dimerization loop, blocks subsequent activation of HER2-driven oncogenic signaling, and generates a dominant-negative form of HER2. Reagents specifically against this molecular activation switch may represent a novel targeted approach for the management of HER2-overexpressing carcinomas. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Central catalytic domain of BRAP (RNF52) recognizes the types of ubiquitin chains and utilizes oligo-ubiquitin for ubiquitylation.

PubMed

Shoji, Shisako; Hanada, Kazuharu; Ohsawa, Noboru; Shirouzu, Mikako

2017-09-07

Really interesting new gene (RING)-finger protein 52 (RNF52), an E3 ubiquitin ligase, is found in eukaryotes from yeast to humans. Human RNF52 is known as breast cancer type 1 susceptibility protein (BRCA1)-associated protein 2 (BRAP or BRAP2). The central catalytic domain of BRAP comprises four subdomains: nucleotide-binding α/β plait (NBP), really interesting new gene (RING) zinc finger, ubiquitin-specific protease (UBP)-like zinc finger (ZfUBP), and coiled-coil (CC). This domain architecture is conserved in RNF52 orthologs; however, the domain's function in the ubiquitin system has not been delineated. In the present study, we discovered that the RNF52 domain, comprising NBP-RING-ZfUBP-CC, binds to ubiquitin chains (oligo-ubiquitin) but not to the ubiquitin monomers, and can utilize various ubiquitin chains for ubiquitylation and auto-ubiquitylation. The RNF52 domain preferentially bound to M1- and K63-linked di-ubiquitin chains, weakly to K27-linked chains, but not to K6-, K11-, or K48-linked chains. The binding preferences of the RNF52 domain for ubiquitin-linkage types corresponded to ubiquitin usage in the ubiquitylation reaction, except for K11-, K29-, and K33-linked chains. Additionally, the RNF52 domain directly ligated the intact M1-linked, tri-, and tetra-ubiquitin chains and recognized the structural alterations caused by the phosphomimetic mutation of these ubiquitin chains. Full-length BRAP had nearly the same specificity for the ubiquitin-chain types as the RNF52 domain alone. Mass spectrometry analysis of oligomeric ubiquitylation products, mediated by the RNF52 domain, revealed that the ubiquitin-linkage types and auto-ubiquitylation sites depend on the length of ubiquitin chains. Here, we propose a model for the oligomeric ubiquitylation process, controlled by the RNF52 domain, which is not a sequential assembly process involving monomers. © 2017 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

Deletion and site-specific mutagenesis of nucleolin's carboxy GAR domain.

PubMed

Pellar, Gregory J; DiMario, Patrick J

2003-04-01

Vertebrate nucleolin is an abundant RNA-binding protein in the dense fibrillar component of active nucleoli. Nucleolin is modular in composition. Its amino-terminal third contains alternating acidic and basic domains, its middle section contains four consensus RNA-binding domains (cRBDs), and its carboxy-terminus contains a distinctive glycine/arginine-rich (GAR) domain with several RGG motifs. The arginines within these motifs are asymmetrically dimethylated. Several laboratories have shown that the GAR domain is necessary but not sufficient for the efficient localization of nucleolin to nucleoli. We examined the distribution of endogenous fibrillarin, Nopp140, and B23 when full-length and DeltaGAR nucleolin were expressed exogenously as enhanced green fluorescent protein (EGFP)-tagged fusions. Only B23 redistributed when DeltaGAR-EGFP was expressed at moderate to high levels, suggesting an in vivo interaction between nucleolin and B23. Next we substituted all ten arginines within the GAR domain of Chinese hamster ovary (CHO) nucleolin with lysines to test the hypothesis that methylation of the carboxy GAR domain is necessary for the nucleolar association of nucleolin. The lysine-substituted mutant was not an in vitro substrate for the yeast protein methyltransferase, Hmt1p/Rmt1. It was, however, able to associate properly with interphase nucleoli and with interphase pre-nucleolar bodies upon recovery from hypotonic shock. We conclude, therefore, that although the GAR domain is necessary for the efficient localization of nucleolin to nucleoli, methylation of this domain is not required for proper nucleolar localization.

A Simple and Efficient Computational Approach to Chafed Cable Time-Domain Reflectometry Signature Prediction

NASA Technical Reports Server (NTRS)

Kowalski, Marc Edward

2009-01-01

A method for the prediction of time-domain signatures of chafed coaxial cables is presented. The method is quasi-static in nature, and is thus efficient enough to be included in inference and inversion routines. Unlike previous models proposed, no restriction on the geometry or size of the chafe is required in the present approach. The model is validated and its speed is illustrated via comparison to simulations from a commercial, three-dimensional electromagnetic simulator.

Geometrical control of pure spin current induced domain wall depinning.

PubMed

Pfeiffer, A; Reeve, R M; Voto, M; Savero-Torres, W; Richter, N; Vila, L; Attané, J P; Lopez-Diaz, L; Kläui, Mathias

2017-03-01

We investigate the pure spin-current assisted depinning of magnetic domain walls in half ring based Py/Al lateral spin valve structures. Our optimized geometry incorporating a patterned notch in the detector electrode, directly below the Al spin conduit, provides a tailored pinning potential for a transverse domain wall and allows for a precise control over the magnetization configuration and as a result the domain wall pinning. Due to the patterned notch, we are able to study the depinning field as a function of the applied external field for certain applied current densities and observe a clear asymmetry for the two opposite field directions. Micromagnetic simulations show that this can be explained by the asymmetry of the pinning potential. By direct comparison of the calculated efficiencies for different external field and spin current directions, we are able to disentangle the different contributions from the spin transfer torque, Joule heating and the Oersted field. The observed high efficiency of the pure spin current induced spin transfer torque allows for a complete depinning of the domain wall at zero external field for a charge current density of [Formula: see text] A m -2 , which is attributed to the optimal control of the position of the domain wall.

Multi Agent Reward Analysis for Learning in Noisy Domains

NASA Technical Reports Server (NTRS)

Tumer, Kagan; Agogino, Adrian K.

2005-01-01

In many multi agent learning problems, it is difficult to determine, a priori, the agent reward structure that will lead to good performance. This problem is particularly pronounced in continuous, noisy domains ill-suited to simple table backup schemes commonly used in TD(lambda)/Q-learning. In this paper, we present a new reward evaluation method that allows the tradeoff between coordination among the agents and the difficulty of the learning problem each agent faces to be visualized. This method is independent of the learning algorithm and is only a function of the problem domain and the agents reward structure. We then use this reward efficiency visualization method to determine an effective reward without performing extensive simulations. We test this method in both a static and a dynamic multi-rover learning domain where the agents have continuous state spaces and where their actions are noisy (e.g., the agents movement decisions are not always carried out properly). Our results show that in the more difficult dynamic domain, the reward efficiency visualization method provides a two order of magnitude speedup in selecting a good reward. Most importantly it allows one to quickly create and verify rewards tailored to the observational limitations of the domain.

The Diaphanous-related Formin FHOD1 associates with ROCK1 and promotes Src-dependent plasma membrane blebbing.

PubMed

Hannemann, Sebastian; Madrid, Ricardo; Stastna, Jana; Kitzing, Thomas; Gasteier, Judith; Schönichen, André; Bouchet, Jerome; Jimenez, Alberto; Geyer, Matthias; Grosse, Robert; Benichou, Serge; Fackler, Oliver T

2008-10-10

Diaphanous-related formins (DRFs) mediate GTPase-triggered actin rearrangements to regulate central cellular processes, such as cell motility and cytokinesis. The DRF FHOD1 interacts with the Rho-GTPase Rac1 and mediates formation of actin stress fibers in its deregulated form; the physiologically relevant activities and molecular mechanisms of endogenous FHOD1, however, are still unknown. Here we report that FHOD1 physically associates via the N-terminal part of its FH2 domain with the central domain of ROCK1. Although FHOD1 does not affect the kinase activity of ROCK1, the DRF is an efficient substrate for phosphorylation by ROCK1. Co-expression of FHOD1 and ROCK1 results in the generation of nonapoptotic plasma membrane (PM) blebs, to which the DRF is efficiently recruited. Blebbing induced by FHOD1 and ROCK1 depends on F-actin integrity, the Rho-ROCK cascade, and Src activity and is reminiscent of the recently described PM blebs triggered by expression of Src homology 4 (SH4) domain PM targeting signals. Consistently, endogenous FHOD1 is required in SH4 domain expressing cells for efficient PM blebbing and rounded cell morphology in two-dimensional cultures or three-dimensional matrices, respectively. Efficient association of FHOD1 with ROCK1, as well as recruitment of the DRF to blebs, depends on Src activity, suggesting that the functional interaction between both proteins is regulated by Src. These results define a role for endogenous FHOD1 in SH4 domain-induced blebbing and suggest that its activity is regulated by ROCK1 in a Src-dependent manner.

Steric Pressure among Membrane-Bound Polymers Opposes Lipid Phase Separation.

PubMed

Imam, Zachary I; Kenyon, Laura E; Carrillo, Adelita; Espinoza, Isai; Nagib, Fatema; Stachowiak, Jeanne C

2016-04-19

Lipid rafts are thought to be key organizers of membrane-protein complexes in cells. Many proteins that interact with rafts have bulky polymeric components such as intrinsically disordered protein domains and polysaccharide chains. Therefore, understanding the interaction between membrane domains and membrane-bound polymers provides insights into the roles rafts play in cells. Multiple studies have demonstrated that high concentrations of membrane-bound polymeric domains create significant lateral steric pressure at membrane surfaces. Furthermore, our recent work has shown that lateral steric pressure at membrane surfaces opposes the assembly of membrane domains. Building on these findings, here we report that membrane-bound polymers are potent suppressors of membrane phase separation, which can destabilize lipid domains with substantially greater efficiency than globular domains such as membrane-bound proteins. Specifically, we created giant vesicles with a ternary lipid composition, which separated into coexisting liquid ordered and disordered phases. Lipids with saturated tails and poly(ethylene glycol) (PEG) chains conjugated to their head groups were included at increasing molar concentrations. When these lipids were sparse on the membrane surface they partitioned to the liquid ordered phase. However, as they became more concentrated, the fraction of GUVs that were phase-separated decreased dramatically, ultimately yielding a population of homogeneous membrane vesicles. Experiments and physical modeling using compositions of increasing PEG molecular weight and lipid miscibility phase transition temperature demonstrate that longer polymers are the most efficient suppressors of membrane phase separation when the energetic barrier to lipid mixing is low. In contrast, as the miscibility transition temperature increases, longer polymers are more readily driven out of domains by the increased steric pressure. Therefore, the concentration of shorter polymers required to suppress phase separation decreases relative to longer polymers. Collectively, our results demonstrate that crowded, membrane-bound polymers are highly efficient suppressors of phase separation and suggest that the ability of lipid domains to resist steric pressure depends on both their lipid composition and the size and concentration of the membrane-bound polymers they incorporate.

Horizontal Transmission of Cytosolic Sup35 Prions by Extracellular Vesicles.

PubMed

Liu, Shu; Hossinger, André; Hofmann, Julia P; Denner, Philip; Vorberg, Ina M

2016-07-12

Prions are infectious protein particles that replicate by templating their aggregated state onto soluble protein of the same type. Originally identified as the causative agent of transmissible spongiform encephalopathies, prions in yeast (Saccharomyces cerevisiae) are epigenetic elements of inheritance that induce phenotypic changes of their host cells. The prototype yeast prion is the translation termination factor Sup35. Prions composed of Sup35 or its modular prion domain NM are heritable and are transmitted vertically to progeny or horizontally during mating. Interestingly, in mammalian cells, protein aggregates derived from yeast Sup35 NM behave as true infectious entities that employ dissemination strategies similar to those of mammalian prions. While transmission is most efficient when cells are in direct contact, we demonstrate here that cytosolic Sup35 NM prions are also released into the extracellular space in association with nanometer-sized membrane vesicles. Importantly, extracellular vesicles are biologically active and are taken up by recipient cells, where they induce self-sustained Sup35 NM protein aggregation. Thus, in mammalian cells, extracellular vesicles can serve as dissemination vehicles for protein-based epigenetic information transfer. Prions are proteinaceous infectious particles that propagate by templating their quaternary structure onto nascent proteins of the same kind. Prions in yeast act as heritable epigenetic elements that can alter the phenotype when transmitted to daughter cells or during mating. Prion activity is conferred by so-called prion domains often enriched in glutamine and asparagine residues. Interestingly, many mammalian proteins also contain domains with compositional similarity to yeast prion domains. We have recently provided a proof-of-principle demonstration that a yeast prion domain also retains its prion activity in mammalian cells. We demonstrate here that cytosolic prions composed of a yeast prion domain are also packaged into extracellular vesicles that transmit the prion phenotype to bystander cells. Thus, proteins with prion-like domains can behave as proteinaceous information molecules that exploit the cellular vesicle trafficking machinery for intercellular long-distance dissemination. Copyright © 2016 Liu et al.

Solution Structure of Homology Region (HR) Domain of Type II Secretion System*

PubMed Central

Gu, Shuang; Kelly, Geoff; Wang, Xiaohui; Frenkiel, Tom; Shevchik, Vladimir E.; Pickersgill, Richard W.

2012-01-01

The type II secretion system of Gram-negative bacteria is important for bacterial pathogenesis and survival; it is composed of 12 mostly multimeric core proteins, which build a sophisticated secretion machine spanning both bacterial membranes. OutC is the core component of the inner membrane subcomplex thought to be involved in both recognition of substrate and interaction with the outer membrane secretin OutD. Here, we report the solution structure of the HR domain of OutC and explore its interaction with the secretin. The HR domain adopts a β-sandwich-like fold consisting of two β-sheets each composed of three anti-parallel β-strands. This structure is strikingly similar to the periplasmic region of PilP, an inner membrane lipoprotein from the type IV pilus system highlighting the common evolutionary origin of these two systems and showing that all the core components of the type II secretion system have a structural or sequence ortholog within the type IV pili system. The HR domain is shown to interact with the N0 domain of the secretin. The importance of this interaction is explored in the context of the functional secretion system. PMID:22253442

Inhibition of master transcription factors in pluripotent cells induces early stage differentiation

PubMed Central

De, Debojyoti; Jeong, Myong-Ho; Leem, Young-Eun; Svergun, Dmitri I.; Wemmer, David E.; Kang, Jong-Sun; Kim, Kyeong Kyu; Kim, Sung-Hou

2014-01-01

The potential for pluripotent cells to differentiate into diverse specialized cell types has given much hope to the field of regenerative medicine. Nevertheless, the low efficiency of cell commitment has been a major bottleneck in this field. Here we provide a strategy to enhance the efficiency of early differentiation of pluripotent cells. We hypothesized that the initial phase of differentiation can be enhanced if the transcriptional activity of master regulators of stemness is suppressed, blocking the formation of functional transcriptomes. However, an obstacle is the lack of an efficient strategy to block protein–protein interactions. In this work, we take advantage of the biochemical property of seventeen kilodalton protein (Skp), a bacterial molecular chaperone that binds directly to sex determining region Y-box 2 (Sox2). The small angle X-ray scattering analyses provided a low resolution model of the complex and suggested that the transactivation domain of Sox2 is probably wrapped in a cleft on Skp trimer. Upon the transduction of Skp into pluripotent cells, the transcriptional activity of Sox2 was inhibited and the expression of Sox2 and octamer-binding transcription factor 4 was reduced, which resulted in the expression of early differentiation markers and appearance of early neuronal and cardiac progenitors. These results suggest that the initial stage of differentiation can be accelerated by inhibiting master transcription factors of stemness. This strategy can possibly be applied to increase the efficiency of stem cell differentiation into various cell types and also provides a clue to understanding the mechanism of early differentiation. PMID:24434556

Insight into dementia care management using social-behavioral theory and mixed methods.

PubMed

Connor, Karen; McNeese-Smith, Donna; van Servellen, Gwen; Chang, Betty; Lee, Martin; Cheng, Eric; Hajar, Abdulrahman; Vickrey, Barbara G

2009-01-01

For health organizations (private and public) to advance their care-management programs, to use resources effectively and efficiently, and to improve patient outcomes, it is germane to isolate and quantify care-management activities and to identify overarching domains. The aims of this study were to identify and report on an application of mixed methods of qualitative statistical techniques, based on a theoretical framework, and to construct variables for factor analysis and exploratory factor analytic steps for identifying domains of dementia care management. Care-management activity data were extracted from the care plans of 181 pairs of individuals (with dementia and their informal caregivers) who had participated in the intervention arm of a randomized controlled trial of a dementia care-management program. Activities were organized into types, using card-sorting methods, influenced by published theoretical constructs on self-efficacy and general strain theory. These activity types were mapped in the initial data set to construct variables for exploratory factor analysis. Principal components extraction with varimax and promax rotations was used to estimate the number of factors. Cronbach's alpha was calculated for the items in each factor to assess internal consistency reliability. The two-phase card-sorting technique yielded 45 activity types out of 450 unique activities. Exploratory factor analysis produced four care-management domains (factors): behavior management, clinical strategies and caregiver support, community agency, and safety. Internal consistency reliability (Cronbach's alpha) of items for each factor ranged from.63 for the factor "safety" to.89 for the factor "behavior management" (Factor 1). Applying a systematic method to a large set of care-management activities can identify a parsimonious number of higher order categories of variables and factors to guide the understanding of dementia care-management processes. Further application of this methodology in outcome analyses and to other data sets is necessary to test its practicality.