Geometric integrators for stochastic rigid body dynamics

KAUST Repository

Tretyakov, Mikhail

2016-01-05

Geometric integrators play an important role in simulating dynamical systems on long time intervals with high accuracy. We will illustrate geometric integration ideas within the stochastic context, mostly on examples of stochastic thermostats for rigid body dynamics. The talk will be mainly based on joint recent work with Rusland Davidchak and Tom Ouldridge.

Geometric integrators for stochastic rigid body dynamics

KAUST Repository

Tretyakov, Mikhail

2016-01-01

Geometric integrators play an important role in simulating dynamical systems on long time intervals with high accuracy. We will illustrate geometric integration ideas within the stochastic context, mostly on examples of stochastic thermostats for rigid body dynamics. The talk will be mainly based on joint recent work with Rusland Davidchak and Tom Ouldridge.

Computing the Free Energy along a Reaction Coordinate Using Rigid Body Dynamics.

Science.gov (United States)

Tao, Peng; Sodt, Alexander J; Shao, Yihan; König, Gerhard; Brooks, Bernard R

2014-10-14

The calculations of potential of mean force along complex chemical reactions or rare events pathways are of great interest because of their importance for many areas in chemistry, molecular biology, and material science. The major difficulty for free energy calculations comes from the great computational cost for adequate sampling of the system in high-energy regions, especially close to the reaction transition state. Here, we present a method, called FEG-RBD, in which the free energy gradients were obtained from rigid body dynamics simulations. Then the free energy gradients were integrated along a reference reaction pathway to calculate free energy profiles. In a given system, the reaction coordinates defining a subset of atoms (e.g., a solute, or the quantum mechanics (QM) region of a quantum mechanics/molecular mechanics simulation) are selected to form a rigid body during the simulation. The first-order derivatives (gradients) of the free energy with respect to the reaction coordinates are obtained through the integration of constraint forces within the rigid body. Each structure along the reference reaction path is separately subjected to such a rigid body simulation. The individual free energy gradients are integrated along the reference pathway to obtain the free energy profile. Test cases provided demonstrate both the strengths and weaknesses of the FEG-RBD method. The most significant benefit of this method comes from the fast convergence rate of the free energy gradient using rigid-body constraints instead of restraints. A correction to the free energy due to approximate relaxation of the rigid-body constraint is estimated and discussed. A comparison with umbrella sampling using a simple test case revealed the improved sampling efficiency of FEG-RBD by a factor of 4 on average. The enhanced efficiency makes this method effective for calculating the free energy of complex chemical reactions when the reaction coordinate can be unambiguously defined by a

Evolution of motions of a rigid body about its center of mass

CERN Document Server

Chernousko, Felix L; Leshchenko, Dmytro D

2017-01-01

The book presents a unified and well-developed approach to the dynamics of angular motions of rigid bodies subjected to perturbation torques of different physical nature. It contains both the basic foundations of the rigid body dynamics and of the asymptotic method of averaging. The rigorous approach based on the averaging procedure is applicable to bodies with arbitrary ellopsoids of inertia. Action of various perturbation torques, both external (gravitational, aerodynamical, solar pressure) and internal (due to viscous fluid in tanks, elastic and visco-elastic properties of a body) is considered in detail. The book can be used by researchers, engineers and students working in attitude dynamics of spacecraft.

On the analysis of protein-protein interactions via knowledge-based potentials for the prediction of protein-protein docking

DEFF Research Database (Denmark)

Feliu, Elisenda; Aloy, Patrick; Oliva, Baldo

2011-01-01

Development of effective methods to screen binary interactions obtained by rigid-body protein-protein docking is key for structure prediction of complexes and for elucidating physicochemical principles of protein-protein binding. We have derived empirical knowledge-based potential functions for s...... and with independence of the partner. This information is encoded at the residue level and could be easily incorporated in the initial grid scoring for Fast Fourier Transform rigid-body docking methods.......Development of effective methods to screen binary interactions obtained by rigid-body protein-protein docking is key for structure prediction of complexes and for elucidating physicochemical principles of protein-protein binding. We have derived empirical knowledge-based potential functions...... for selecting rigid-body docking poses. These potentials include the energetic component that provides the residues with a particular secondary structure and surface accessibility. These scoring functions have been tested on a state-of-art benchmark dataset and on a decoy dataset of permanent interactions. Our...

Anti-synchronization of the rigid body exhibiting chaotic dynamics ...

African Journals Online (AJOL)

Based on a method derived from nonlinear control theory, we present a ... In this framework, the active control technique is modified and employed to design control ... state space of the two rigid bodies was verified by numerical simulations.

Student understanding of the application of Newton's second law to rotating rigid bodies

Science.gov (United States)

Close, Hunter G.; Gomez, Luanna S.; Heron, Paula R. L.

2013-06-01

We report on an investigation of student understanding of rigid body dynamics in which we asked students in introductory calculus-based physics to compare the translational motions of identical rigid bodies subject to forces that differed only in the point of contact at which they were applied. There was a widespread tendency to claim that forces that cause rotational motion have a diminished effect on translational motion. A series of related problems was developed to examine whether similar errors would be made in other contexts, and interviews were conducted to probe student thinking in greater depth. In this paper, we describe the results of our investigation and also describe a series of different interventions that culminated in the development of a tutorial that improves student ability to apply Newton's second law to rotating rigid bodies.

Modeling of a light elastic beam by a system of rigid bodies

Directory of Open Access Journals (Sweden)

Šalinić Slaviša

2004-01-01

Full Text Available This paper has shown that a light elastic beam, in the case of small elastic deformations, can be modeled by a kinematic chain without branching composed of rigid bodies which are connected by passive revolute or prismatic joints with corresponding springs in them. Elastic properties of the beam are modeled by the springs introduced. The potential energy of the elastic beam is expressed as a function of components of the vector of elastic displacement and the vector of elastic rotation calculated for the elastic centre of the beam, which results in the diagonal stiffness matrix of the beam. As the potential energy of the introduced system of bodies with springs is expressed in the function of relative joint displacements, the diagonal stiffness matrix is obtained. In addition, these two stiffness matrices are equal. The modeling process has been demonstrated on the example of an elastic beam rotating about a fixed vertical axis, with a rigid body whose mass is considerably larger than the beam mass fixed to its free end. Differential equations of motion have been formed for this mechanical system. The modeling technique described here aims at expanding of usage of well developed methods of dynamics of systems of rigid bodies to the analysis of systems with elastic bodies. .

Stabilization of Rigid Body Dynamics by Internal and External Torques

National Research Council Canada - National Science Library

Bloch, A. M; Krishnaprasad, P. S; Marsden, J. E; Sanchez de Alvarez, G

1990-01-01

...] with quadratic feedback torques for internal rotors. We show that with such torques, the equations for the rigid body with momentum wheels are Hamiltonian with respect to a Lie-Poisson bracket structure. Further...

Coupling characteristics of rigid body motion and elastic deformation of a 3-PRR parallel manipulator with flexible links

International Nuclear Information System (INIS)

Zhang Xuping; Mills, James K.; Cleghorn, William L.

2009-01-01

Modeling of multibody dynamics with flexible links is a challenging task, which not only involves the effect of rigid body motion on elastic deformations, but also includes the influence of elastic deformations on rigid body motion. This paper presents coupling characteristics of rigid body motions and elastic motions of a 3-PRR parallel manipulator with three flexible intermediate links. The intermediate links are modeled as Euler-Bernoulli beams with pinned-pinned boundary conditions based on the assumed mode method (AMM). Using Lagrange multipliers, the fully coupled equations of motions of the flexible parallel manipulator are developed by incorporating the rigid body motions with elastic motions. The mutual dependence of elastic deformations and rigid body motions are investigated from the analysis of the derived equations of motion. Open-loop simulation without joint motion controls and closed-loop simulation with joint motion controls are performed to illustrate the effect of elastic motion on rigid body motions and the coupling effect amongst flexible links. These analyses and results provide valuable insight to the design and control of the parallel manipulator with flexible intermediate links

A method for measuring the inertia properties of rigid bodies

Science.gov (United States)

Gobbi, M.; Mastinu, G.; Previati, G.

2011-01-01

A method for the measurement of the inertia properties of rigid bodies is presented. Given a rigid body and its mass, the method allows to measure (identify) the centre of gravity location and the inertia tensor during a single test. The proposed technique is based on the analysis of the free motion of a multi-cable pendulum to which the body under consideration is connected. The motion of the pendulum and the forces acting on the system are recorded and the inertia properties are identified by means of a proper mathematical procedure based on a least square estimation. After the body is positioned on the test rig, the full identification procedure takes less than 10 min. The natural frequencies of the pendulum and the accelerations involved are quite low, making this method suitable for many practical applications. In this paper, the proposed method is described and two test rigs are presented: the first is developed for bodies up to 3500 kg and the second for bodies up to 400 kg. A validation of the measurement method is performed with satisfactory results. The test rig holds a third part quality certificate according to an ISO 9001 standard and could be scaled up to measure the inertia properties of huge bodies, such as trucks, airplanes or even ships.

The theory of pseudo-rigid bodies

CERN Document Server

Cohen, Harley

1988-01-01

This monograph concerns the development, analysis, and application of the theory of pseudo-rigid bodies. It collects together our work on that subject over the last five years. While some results have appeared else­ where, much of the work is new. Our objective in writing this mono­ graph has been to present a new theory of the deformation of bodies, one that has not only a firm theoretical basis, but also the simplicity to serve as an effective tool in practical problems. Consequently, the main body of the treatise is a multifaceted development of the theory, from foundations to explicit solutions to linearizations to methods of approximation. The fact that this variety of aspects, each examined in considerable detail, can be collected together in a single, unified treat­ ment gives this theory an elegance that we feel sets it apart from many others. While our goal has always been to give a complete treatment of the theory as it now stands, the work here is not meant to be definitive. Theories are not ent...

Collisions of Constrained Rigid Body Systems with Friction

Directory of Open Access Journals (Sweden)

Haijun Shen

1998-01-01

Full Text Available A new approach is developed for the general collision problem of two rigid body systems with constraints (e.g., articulated systems, such as massy linkages in which the relative tangential velocity at the point of contact and the associated friction force can change direction during the collision. This is beyond the framework of conventional methods, which can give significant and very obvious errors for this problem, and both extends and consolidates recent work. A new parameterization and theory characterize if, when and how the relative tangential velocity changes direction during contact. Elastic and dissipative phenomena and different values for static and kinetic friction coefficients are included. The method is based on the explicitly physical analysis of events at the point of contact. Using this method, Example 1 resolves (and corrects a paradox (in the literature of the collision of a double pendulum with the ground. The method fundamentally subsumes other recent models and the collision of rigid bodies; it yields the same results as conventional methods when they would apply (Example 2. The new method reformulates and extends recent approaches in a completely physical context.

Body fixed frame, rigid gauge rotations and large N random fields in QCD

International Nuclear Information System (INIS)

Levit, S.

1995-01-01

The ''body fixed frame'' with respect to local gauge transformations is introduced. Rigid gauge ''rotations'' in QCD and their Schroedinger equation are studied for static and dynamic quarks. Possible choices of the rigid gauge field configuration corresponding to a non-vanishing static colormagnetic field in the ''body fixed'' frame are discussed. A gauge invariant variational equation is derived in this frame. For large number N of colors the rigid gauge field configuration is regarded as random with maximally random probability distribution under constraints on macroscopic-like quantities. For the uniform magnetic field the joint probability distribution of the field components is determined by maximizing the appropriate entropy under the area law constraint for the Wilson loop. In the quark sector the gauge invariance requires the rigid gauge field configuration to appear not only as a background but also as inducing an instantaneous quark-quark interaction. Both are random in the large N limit. (orig.)

Efficient time-symmetric simulation of torqued rigid bodies using Jacobi elliptic functions

International Nuclear Information System (INIS)

Celledoni, E; Saefstroem, N

2006-01-01

If the three moments of inertia are distinct, the solution to the Euler equations for the free rigid body is given in terms of Jacobi elliptic functions. Using the arithmetic-geometric mean algorithm (Abramowitz and Stegun 1992 Handbook of Mathematical Functions with Formulas, Graphs, and Mathematical Tables (New York: Dover)), these functions can be calculated efficiently and accurately. Compared to standard numerical ODE and Lie-Poisson solvers, the overall approach yields a faster and more accurate numerical solution to the Euler equations. This approach is designed for mass asymmetric rigid bodies. In the case of symmetric bodies, the exact solution is available in terms of trigonometric functions, see Dullweber et al (1997 J. Chem. Phys. 107 5840-51), Reich (1996 Fields Inst. Commun. 10 181-91) and Benettin et al (2001 SIAM J. Sci. Comp. 23 1189-203) for details. In this paper, we consider the case of asymmetric rigid bodies subject to external forces. We consider a strategy similar to the symplectic splitting method proposed in Reich (1996 Fields Inst. Commun. 10 181-91) and Dullweber et al (1997 J. Chem. Phys. 107 5840-51). The method proposed here is time-symmetric. We decompose the vector field of our problem into a free rigid body (FRB) problem and another completely integrable vector field. The FRB problem consists of the Euler equations and a differential equation for the 3 x 3 orientation matrix. The Euler equations are integrated exactly while the matrix equation is approximated using a truncated Magnus series. In our experiments, we observe that the overall numerical solution benefits greatly from the very accurate solution of the Euler equations. We apply the method to the heavy top and the simulation of artificial satellite attitude dynamics

Estimating the orientation of a rigid body moving in space using inertial sensors

Energy Technology Data Exchange (ETDEWEB)

He, Peng, E-mail: peng.he.1@ulaval.ca; Cardou, Philippe, E-mail: pcardou@gmc.ulaval.ca [Université Laval, Robotics Laboratory, Department of Mechanical Engineering (Canada); Desbiens, André, E-mail: andre.desbiens@gel.ulaval.ca [Université Laval, Department of Electrical and Computer Engineering (Canada); Gagnon, Eric, E-mail: Eric.Gagnon@drdc-rddc.gc.ca [RDDC Valcartier (Canada)

2015-09-15

This paper presents a novel method of estimating the orientation of a rigid body moving in space from inertial sensors, by discerning the gravitational and inertial components of the accelerations. In this method, both a rigid-body kinematics model and a stochastic model of the human-hand motion are formulated and combined in a nonlinear state-space system. The state equation represents the rigid body kinematics and stochastic model, and the output equation represents the inertial sensor measurements. It is necessary to mention that, since the output equation is a nonlinear function of the state, the extended Kalman filter (EKF) is applied. The absolute value of the error from the proposed method is shown to be less than 5 deg in simulation and in experiments. It is apparently stable, unlike the time-integration of gyroscope measurements, which is subjected to drift, and remains accurate under large accelerations, unlike the tilt-sensor method.

Estimating the orientation of a rigid body moving in space using inertial sensors

International Nuclear Information System (INIS)

He, Peng; Cardou, Philippe; Desbiens, André; Gagnon, Eric

2015-01-01

This paper presents a novel method of estimating the orientation of a rigid body moving in space from inertial sensors, by discerning the gravitational and inertial components of the accelerations. In this method, both a rigid-body kinematics model and a stochastic model of the human-hand motion are formulated and combined in a nonlinear state-space system. The state equation represents the rigid body kinematics and stochastic model, and the output equation represents the inertial sensor measurements. It is necessary to mention that, since the output equation is a nonlinear function of the state, the extended Kalman filter (EKF) is applied. The absolute value of the error from the proposed method is shown to be less than 5 deg in simulation and in experiments. It is apparently stable, unlike the time-integration of gyroscope measurements, which is subjected to drift, and remains accurate under large accelerations, unlike the tilt-sensor method

Topological classification of the Goryachev integrable case in rigid body dynamics

International Nuclear Information System (INIS)

Nikolaenko, S S

2016-01-01

A topological analysis of the Goryachev integrable case in rigid body dynamics is made on the basis of the Fomenko-Zieschang theory. The invariants (marked molecules) which are obtained give a complete description, from the standpoint of Liouville classification, of the systems of Goryachev type on various level sets of the energy. It turns out that on appropriate energy levels the Goryachev case is Liouville equivalent to many classical integrable systems and, in particular, the Joukowski, Clebsch, Sokolov and Kovalevskaya-Yehia cases in rigid body dynamics, as well as to some integrable billiards in plane domains bounded by confocal quadrics -- in other words, the foliations given by the closures of generic solutions of these systems have the same structure. Bibliography: 15 titles

Knowledge-In-Action: An Example with Rigid Body Motion

Science.gov (United States)

Da Costa, Sayonara Salvador Cabral; Moreira, Marco Antonio

2005-01-01

This paper reports the analysis of the resolution of a paper-and-pencil problem, by eight undergraduate students majoring in engineering (six) and physics (two) at the Pontifcia Universidade Catlica do Rio Grande do Sul, in Porto Alegre, Brazil. The problem concerns kinetics of a rigid body, and the analysis was done in the light of Johnson-Lairds…

Contact point generation for convex polytopes in interactive rigid body dynamics

DEFF Research Database (Denmark)

Silcowitz-Hansen, Morten; Abel, Sarah Maria Niebe; Erleben, Kenny

When computing contact forces in rigid body dynamics systems, most state-of-the-art solutions use iterative methods such as the projected Gauss–Seidel (PGS) method. Methods such as the PGS method are preferred for their robustness. However, the time-critical nature of interactive applications...... combined with the linear convergence rates of such methods, will often result in visual artifacts in the final simulation. With this paper, we address an issue which is of major impact on the animation quality, when using methods such as the PGS method. The issue is robust generation of contact points...... for convex polytopes. A novel contact point generation method is presented, which is based on growth distances and Gauss maps. We demonstrate improvements when using our method in the context of interactive rigid body simulation...

Matrix rigidity regulates cancer cell growth by modulating cellular metabolism and protein synthesis.

Directory of Open Access Journals (Sweden)

Robert W Tilghman

Full Text Available Tumor cells in vivo encounter diverse types of microenvironments both at the site of the primary tumor and at sites of distant metastases. Understanding how the various mechanical properties of these microenvironments affect the biology of tumor cells during disease progression is critical in identifying molecular targets for cancer therapy.This study uses flexible polyacrylamide gels as substrates for cell growth in conjunction with a novel proteomic approach to identify the properties of rigidity-dependent cancer cell lines that contribute to their differential growth on soft and rigid substrates. Compared to cells growing on more rigid/stiff substrates (>10,000 Pa, cells on soft substrates (150-300 Pa exhibited a longer cell cycle, due predominantly to an extension of the G1 phase of the cell cycle, and were metabolically less active, showing decreased levels of intracellular ATP and a marked reduction in protein synthesis. Using stable isotope labeling of amino acids in culture (SILAC and mass spectrometry, we measured the rates of protein synthesis of over 1200 cellular proteins under growth conditions on soft and rigid/stiff substrates. We identified cellular proteins whose syntheses were either preferentially inhibited or preserved on soft matrices. The former category included proteins that regulate cytoskeletal structures (e.g., tubulins and glycolysis (e.g., phosphofructokinase-1, whereas the latter category included proteins that regulate key metabolic pathways required for survival, e.g., nicotinamide phosphoribosyltransferase, a regulator of the NAD salvage pathway.The cellular properties of rigidity-dependent cancer cells growing on soft matrices are reminiscent of the properties of dormant cancer cells, e.g., slow growth rate and reduced metabolism. We suggest that the use of relatively soft gels as cell culture substrates would allow molecular pathways to be studied under conditions that reflect the different mechanical

Rigid Body Motion Calculated From Spatial Co-ordinates of Markers ...

African Journals Online (AJOL)

In this paper, we present a unified method for calculating spatial coordinates of markers for a rigid body motion such as in bones. Kinematical analysis of bone movement in cadaveric specimens or living objects had been developed. Here, we show how spatial co-ordinates of markers in or on bone can be calculated from ...

Steady fall of a rigid body in viscous fluid

Czech Academy of Sciences Publication Activity Database

Nečasová, Šárka

2005-01-01

Roč. 63, Sp. Is. (2005), s. 2113-2119 ISSN 0362-546X. [Invited Talks from the Fourth World Congress of Nonlinear Analysts (WCNA 2004). Orlando , 30.7.2004-7.8.2004] R&D Projects: GA ČR(CZ) GA201/02/0684 Institutional research plan: CEZ:AV0Z1019905 Keywords : steady fall * rigid body * viscous fluid Subject RIV: BA - General Mathematics Impact factor: 0.519, year: 2005

High-order conservative discretizations for some cases of the rigid body motion

International Nuclear Information System (INIS)

Kozlov, Roman

2008-01-01

Modified vector fields can be used to construct high-order structure-preserving numerical integrators for ordinary differential equations. In the present Letter we consider high-order integrators based on the implicit midpoint rule, which conserve quadratic first integrals. It is shown that these integrators are particularly suitable for the rigid body motion with an additional quadratic first integral. In this case high-order integrators preserve all four first integrals of motion. The approach is illustrated on the Lagrange top (a rotationally symmetric rigid body with a fixed point on the symmetry axis). The equations of motion are considered in the space fixed frame because in this frame Lagrange top admits a neat description. The Lagrange top motion includes the spherical pendulum and the planar pendulum, which swings in a vertical plane, as particular cases

Prediction of flexible/rigid regions from protein sequences using k-spaced amino acid pairs

Directory of Open Access Journals (Sweden)

Ruan Jishou

2007-04-01

Full Text Available Abstract Background Traditionally, it is believed that the native structure of a protein corresponds to a global minimum of its free energy. However, with the growing number of known tertiary (3D protein structures, researchers have discovered that some proteins can alter their structures in response to a change in their surroundings or with the help of other proteins or ligands. Such structural shifts play a crucial role with respect to the protein function. To this end, we propose a machine learning method for the prediction of the flexible/rigid regions of proteins (referred to as FlexRP; the method is based on a novel sequence representation and feature selection. Knowledge of the flexible/rigid regions may provide insights into the protein folding process and the 3D structure prediction. Results The flexible/rigid regions were defined based on a dataset, which includes protein sequences that have multiple experimental structures, and which was previously used to study the structural conservation of proteins. Sequences drawn from this dataset were represented based on feature sets that were proposed in prior research, such as PSI-BLAST profiles, composition vector and binary sequence encoding, and a newly proposed representation based on frequencies of k-spaced amino acid pairs. These representations were processed by feature selection to reduce the dimensionality. Several machine learning methods for the prediction of flexible/rigid regions and two recently proposed methods for the prediction of conformational changes and unstructured regions were compared with the proposed method. The FlexRP method, which applies Logistic Regression and collocation-based representation with 95 features, obtained 79.5% accuracy. The two runner-up methods, which apply the same sequence representation and Support Vector Machines (SVM and Naïve Bayes classifiers, obtained 79.2% and 78.4% accuracy, respectively. The remaining considered methods are

Rigid Body Time Integration by Convected Base Vectors with Implicit Constraints

DEFF Research Database (Denmark)

Krenk, Steen; Nielsen, Martin Bjerre

2013-01-01

of the kinetic energy used in the present formulation is deliberately chosen to correspond to a rigid body rotation, and the orthonormality constraints are introduced via the equivalent Green strain components of the base vectors. The particular form of the extended inertia tensor used here implies a set...

A rigid-body least-squares program with angular and translation scan facilities

CERN Document Server

Kutschabsky, L

1981-01-01

The described computer program, written in CERN Fortran, is designed to enlarge the convergence radius of the rigid-body least-squares method by allowing a stepwise change of the angular and/or translational parameters within a chosen range. (6 refs).

Nonlinear dynamics mathematical models for rigid bodies with a liquid

CERN Document Server

Lukovsky, Ivan A

2015-01-01

This book is devoted to analytically approximate methods in the nonlinear dynamics of a rigid body with cavities partly filled by liquid. It combines several methods and compares the results with experimental data. It is useful for experienced and early-stage readers interested in analytical approaches to fluid-structure interaction problems, the fundamental mathematical background and modeling the dynamics of such complex mechanical systems.

Euler-Poincare Reduction of a Rigid Body Motion

DEFF Research Database (Denmark)

Wisniewski, Rafal; Kulczycki, P.

2005-01-01

|If a mechanical system experiences symmetry, the Lagrangian becomes invariant under a certain group action. This property leads to substantial simplification of the description of movement. The standpoint in this article is a mechanical system afected by an external force of a control action....... Assuming that the system possesses symmetry and the configuration manifold corresponds to a Lie group, the Euler-Poincare reduction breaks up the motion into separate equations of dynamics and kinematics. This becomes of particular interest for modeling, estimation and control of mechanical systems......-known Euler-Poincare reduction to a rigid body motion with forcing....

Research on Rigid Body Motion Tracing in Space based on NX MCD

Science.gov (United States)

Wang, Junjie; Dai, Chunxiang; Shi, Karen; Qin, Rongkang

2018-03-01

In the use of MCD (Mechatronics Concept Designer) which is a module belong to SIEMENS Ltd industrial design software UG (Unigraphics NX), user can define rigid body and kinematic joint to make objects move according to the existing plan in simulation. At this stage, user may have the desire to see the path of some points in the moving object intuitively. In response to this requirement, this paper will compute the pose through the transformation matrix which can be available from the solver engine, and then fit these sampling points through B-spline curve. Meanwhile, combined with the actual constraints of rigid bodies, the traditional equal interval sampling strategy was optimized. The result shown that this method could satisfy the demand and make up for the deficiency in traditional sampling method. User can still edit and model on this 3D curve. Expected result has been achieved.

Lorentz Contraction, Bell's Spaceships and Rigid Body Motion in Special Relativity

Science.gov (United States)

Franklin, Jerrold

2010-01-01

The meaning of Lorentz contraction in special relativity and its connection with Bell's spaceships parable is discussed. The motion of Bell's spaceships is then compared with the accelerated motion of a rigid body. We have tried to write this in a simple form that could be used to correct students' misconceptions due to conflicting earlier…

Fast and anisotropic flexibility-rigidity index for protein flexibility and fluctuation analysis

Energy Technology Data Exchange (ETDEWEB)

Opron, Kristopher [Department of Biochemistry and Molecular Biology, Michigan State University, Michigan 48824 (United States); Xia, Kelin [Department of Mathematics, Michigan State University, Michigan 48824 (United States); Wei, Guo-Wei, E-mail: wei@math.msu.edu [Department of Biochemistry and Molecular Biology, Michigan State University, Michigan 48824 (United States); Department of Mathematics, Michigan State University, Michigan 48824 (United States); Department of Electrical and Computer Engineering, Michigan State University, Michigan 48824 (United States)

2014-06-21

Protein structural fluctuation, typically measured by Debye-Waller factors, or B-factors, is a manifestation of protein flexibility, which strongly correlates to protein function. The flexibility-rigidity index (FRI) is a newly proposed method for the construction of atomic rigidity functions required in the theory of continuum elasticity with atomic rigidity, which is a new multiscale formalism for describing excessively large biomolecular systems. The FRI method analyzes protein rigidity and flexibility and is capable of predicting protein B-factors without resorting to matrix diagonalization. A fundamental assumption used in the FRI is that protein structures are uniquely determined by various internal and external interactions, while the protein functions, such as stability and flexibility, are solely determined by the structure. As such, one can predict protein flexibility without resorting to the protein interaction Hamiltonian. Consequently, bypassing the matrix diagonalization, the original FRI has a computational complexity of O(N{sup 2}). This work introduces a fast FRI (fFRI) algorithm for the flexibility analysis of large macromolecules. The proposed fFRI further reduces the computational complexity to O(N). Additionally, we propose anisotropic FRI (aFRI) algorithms for the analysis of protein collective dynamics. The aFRI algorithms permit adaptive Hessian matrices, from a completely global 3N × 3N matrix to completely local 3 × 3 matrices. These 3 × 3 matrices, despite being calculated locally, also contain non-local correlation information. Eigenvectors obtained from the proposed aFRI algorithms are able to demonstrate collective motions. Moreover, we investigate the performance of FRI by employing four families of radial basis correlation functions. Both parameter optimized and parameter-free FRI methods are explored. Furthermore, we compare the accuracy and efficiency of FRI with some established approaches to flexibility analysis, namely

Topology Optimization of a Vibrating System of Rigid and Flexible Bodies for Maximizing Repeated Eigenfrequencies

International Nuclear Information System (INIS)

Ahn, Byungseong; Kim, Suh In; Kim, Yoon Young

2016-01-01

When a system consisting of rigid and flexible bodies is optimized to improve its dynamic characteristics, its eigenfrequencies are typically maximized. While topology optimization formulations dealing with simultaneous design of a system of rigid and flexible bodies are available, studies on eigenvalue maximization of the system are rare. In particular, no work has solved for the case when the target frequency becomes one of the repeated eigenfrequencies. The problem involving repeated eigenfrequencies is solved in this study, and a topology optimization formulation and sensitivity analysis are presented. Further, several numerical case studies are considered to demonstrate the validity of the proposed formulation

New integrable problems in a rigid body dynamics with cubic integral in velocities

Science.gov (United States)

Elmandouh, A. A.

2018-03-01

We introduce a new family of the 2D integrable mechanical system possessing an additional integral of the third degree in velocities. This system contains 20 arbitrary parameters. We also clarify that the majority of the previous systems with a cubic integral can be reconstructed from it as a special version for certain values of those parameters. The applications of this system are extended to include the problem of motion of a particle and rigid body about its fixed point. We announce new integrable problems describing the motion of a particle in the plane, pseudosphere, and surfaces of variable curvature. We also present a new integrable problem in a rigid body dynamics and this problem generalizes some of the previous results for Sokolov-Tsiganov, Yehia, Stretensky, and Goriachev.

Reconstructing rotations and rigid body motions from exact point correspondences through reflections

NARCIS (Netherlands)

Fontijne, D.; Dorst, L.; Dorst, L.; Lasenby, J.

2011-01-01

We describe a new algorithm to reconstruct a rigid body motion from point correspondences. The algorithm works by constructing a series of reflections which align the points with their correspondences one by one. This is naturally and efficiently implemented in the conformal model of geometric

On the monoaxial stabilization of a rigid body under vanishing restoring torque

Science.gov (United States)

Aleksandrov, A. Yu.; Aleksandrova, E. B.; Tikhonov, A. A.

2018-05-01

The problem of monoaxial stabilization of a rigid body is studied. It is assumed that a linear time-invariant dissipative torque and a time-varying restoring torque vanishing as time increases act on the body. Both the case of linear restoring torque and that of essentially nonlinear one are considered. With the aid of the decomposition method, conditions are obtained under which we can guarantee the asymptotic stability of an equilibrium position of the body despite the vanishing of the restoring torque. A numerical simulation is provided to demonstrate the effectiveness of our theoretical results.

Lorentz contraction, Bell's spaceships and rigid body motion in special relativity

International Nuclear Information System (INIS)

Franklin, Jerrold

2010-01-01

The meaning of Lorentz contraction in special relativity and its connection with Bell's spaceships parable is discussed. The motion of Bell's spaceships is then compared with the accelerated motion of a rigid body. We have tried to write this in a simple form that could be used to correct students' misconceptions due to conflicting earlier treatments.

Conformational Rigidity and Protein Dynamics at Distinct Timescales Regulate PTP1B Activity and Allostery.

Science.gov (United States)

Choy, Meng S; Li, Yang; Machado, Luciana E S F; Kunze, Micha B A; Connors, Christopher R; Wei, Xingyu; Lindorff-Larsen, Kresten; Page, Rebecca; Peti, Wolfgang

2017-02-16

Protein function originates from a cooperation of structural rigidity, dynamics at different timescales, and allostery. However, how these three pillars of protein function are integrated is still only poorly understood. Here we show how these pillars are connected in Protein Tyrosine Phosphatase 1B (PTP1B), a drug target for diabetes and cancer that catalyzes the dephosphorylation of numerous substrates in essential signaling pathways. By combining new experimental and computational data on WT-PTP1B and ≥10 PTP1B variants in multiple states, we discovered a fundamental and evolutionarily conserved CH/π switch that is critical for positioning the catalytically important WPD loop. Furthermore, our data show that PTP1B uses conformational and dynamic allostery to regulate its activity. This shows that both conformational rigidity and dynamics are essential for controlling protein activity. This connection between rigidity and dynamics at different timescales is likely a hallmark of all enzyme function. Copyright © 2017 Elsevier Inc. All rights reserved.

Rigid-body displacement perpendicular to a {211} twin boundary in Mo

Czech Academy of Sciences Publication Activity Database

Gemperlová, Juliana; Vystavěl, Tomáš; Gemperle, Antonín; Pénisson, J. M.

2001-01-01

Roč. 31, č. 11 (2001), s. 1767-1778 ISSN 0141-8637 R&D Projects: GA AV ČR IAA1010916; GA ČR GA202/99/1665 Institutional research plan: CEZ:AV0Z1010914 Keywords : sigma=3 Mo bicrystal * rigid-body displacement * alfa- fringe method Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.238, year: 2001

Matrix methods applied to engineering rigid body mechanics

Science.gov (United States)

Crouch, T.

The purpose of this book is to present the solution of a range of rigorous body mechanics problems using a matrix formulation of vector algebra. Essential theory concerning kinematics and dynamics is formulated in terms of matrix algebra. The solution of kinematics and dynamics problems is discussed, taking into account the velocity and acceleration of a point moving in a circular path, the velocity and acceleration determination for a linkage, the angular velocity and angular acceleration of a roller in a taper-roller thrust race, Euler's theroem on the motion of rigid bodies, an automotive differential, a rotating epicyclic, the motion of a high speed rotor mounted in gimbals, and the vibration of a spinning projectile. Attention is given to the activity of a force, the work done by a conservative force, the work and potential in a conservative system, the equilibrium of a mechanism, bearing forces due to rotor misalignment, and the frequency of vibrations of a constrained rod.

A comparative study of velocity increment generation between the rigid body and flexible models of MMET

Energy Technology Data Exchange (ETDEWEB)

Ismail, Norilmi Amilia, E-mail: aenorilmi@usm.my [School of Aerospace Engineering, Engineering Campus, Universiti Sains Malaysia, 14300 Nibong Tebal, Pulau Pinang (Malaysia)

2016-02-01

The motorized momentum exchange tether (MMET) is capable of generating useful velocity increments through spin–orbit coupling. This study presents a comparative study of the velocity increments between the rigid body and flexible models of MMET. The equations of motions of both models in the time domain are transformed into a function of true anomaly. The equations of motion are integrated, and the responses in terms of the velocity increment of the rigid body and flexible models are compared and analysed. Results show that the initial conditions, eccentricity, and flexibility of the tether have significant effects on the velocity increments of the tether.

Dynamics of parallel robots from rigid bodies to flexible elements

CERN Document Server

Briot, Sébastien

2015-01-01

This book starts with a short recapitulation on basic concepts, common to any types of robots (serial, tree structure, parallel, etc.), that are also necessary for computation of the dynamic models of parallel robots. Then, as dynamics requires the use of geometry and kinematics, the general equations of geometric and kinematic models of parallel robots are given. After, it is explained that parallel robot dynamic models can be obtained by decomposing the real robot into two virtual systems: a tree-structure robot (equivalent to the robot legs for which all joints would be actuated) plus a free body corresponding to the platform. Thus, the dynamics of rigid tree-structure robots is analyzed and algorithms to obtain their dynamic models in the most compact form are given. The dynamic model of the real rigid parallel robot is obtained by closing the loops through the use of the Lagrange multipliers. The problem of the dynamic model degeneracy near singularities is treated and optimal trajectory planning for cro...

Euler-Poincare Reduction of Externall Forced Rigid Body Motion

DEFF Research Database (Denmark)

Wisniewski, Rafal; Kulczycki, P.

2004-01-01

If a mechanical system experiences symmetry, the Lagrangian becomes invariant under a certain group action. This property leads to substantial simplification of the description of movement. The standpoint in this article is a mechanical system affected by an external force of a control action....... Assuming that the system possesses symmetry and the configuration manifold corresponds to a Lie group, the Euler-Poincaré reduction breaks up the motion into separate equations of dynamics and kinematics. This becomes of particular interest for modelling, estimation and control of mechanical systems......-known Euler-Poincaré reduction to a rigid body motion with forcing....

Euler-Poincaré Reduction of a Rigid Body Motion

DEFF Research Database (Denmark)

Wisniewski, Rafal; Kulczycki, P.

2004-01-01

If a mechanical system experiences symmetry, the Lagrangian becomes invariant under a certain group action. This property leads to substantial simplification of the description of movement. The standpoint in this article is a mechanical system affected by an external force of a control action....... Assuming that the system possesses symmetry and the configuration manifold corresponds to a Lie group, the Euler-Poincaré reduction breaks up the motion into separate equations of dynamics and kinematics. This becomes of particular interest for modelling, estimation and control of mechanical systems......-known Euler-Poincaré reduction to a rigid body motion with forcing....

Estimation of the ground shaking from the response of rigid bodies

Directory of Open Access Journals (Sweden)

Filomena de Silva

2016-12-01

Full Text Available The paper illustrates and compares simplified approaches to interpret the mechanisms of damage observed on rigid bodies in the cemetery of Amatrice, after the main shock (August 24, 2016, MW=6.0 of the Central Italy earthquake. The final goal of the work is to link the observed movements of the fallen objects to specific characteristics of the ground motion occurred at the specific site.

Effort Flow Analysis: A Methodology for Directed Product Evolution Using Rigid Body and Compliant Mechanisms

National Research Council Canada - National Science Library

Greer, James

2002-01-01

This dissertation presents a systematic design methodology for directed product evolution that uses both rigid body and compliant mechanisms to facilitate component combination in the domain of mechanical products...

Unifying Rigid and Soft Bodies Representation: The Sulfur Physics Engine

Directory of Open Access Journals (Sweden)

Dario Maggiorini

2014-01-01

Full Text Available Video games are (also real-time interactive graphic simulations: hence, providing a convincing physics simulation for each specific game environment is of paramount importance in the process of achieving a satisfying player experience. While the existing game engines appropriately address many aspects of physics simulation, some others are still in need of improvements. In particular, several specific physics properties of bodies not usually involved in the main game mechanics (e.g., properties useful to represent systems composed by soft bodies, are often poorly rendered by general-purpose engines. This issue may limit game designers when imagining innovative and compelling video games and game mechanics. For this reason, we dug into the problem of appropriately representing soft bodies. Subsequently, we have extended the approach developed for soft bodies to rigid ones, proposing and developing a unified approach in a game engine: Sulfur. To test the engine, we have also designed and developed “Escape from Quaoar,” a prototypal video game whose main game mechanic exploits an elastic rope, and a level editor for the game.

Simulating Dynamics of the System of Articulated Rigid Bodies with Joint Friction

Directory of Open Access Journals (Sweden)

M. V. Michaylyuk

2016-01-01

Full Text Available The subject of the work is to simulate dynamics of the system of articulated rigid bodies in the virtual environment complexes. The work aim is to develop algorithms and methods to simulate the multi-body system dynamics with joint friction to ensure all calculations in real time in line with visual realistic behavior of objects in a scene.The paper describes the multibody system based on a maximal set of coordinates, and to simulate the joint friction is used a Coulomb's law of dry friction. Joints are described using the holonomic constraints and their derivatives that specify the constraints on velocities of joined bodies. Based on The Coulomb’s law a correlation for the friction impulse values has been derived as an inequality. If the friction impulse performs a constraint that is a lack of relative motion of two joint-joined bodies, there is a static friction in the joint. Otherwise, there is a dynamic friction in the joint. Using a semi-implicit Euler method allows us to describe dynamics of articulated rigid bodies with joint friction as a system of linear algebraic equations and inequalities for the unknown velocities and impulse values.To solve the obtained system of equations and inequalities is used an iterative method of sequential impulses, which sequentially processes constraints for each joint with impulse calculation and its application to the joined bodies rather than considers the entire system. To improve the method convergence, at each iteration the calculated impulses are accumulated for their further using as an initial approximation at the next step of simulation.The proposed algorithms and methods have been implemented in the training complex dynamics subsystem, developed in SRISA RAS. Evaluation of these methods and algorithms has demonstrated their full adequacy to requirements for virtual environment systems and training complexes.

Elasticity of Relativistic Rigid Bodies?

Science.gov (United States)

Smarandache, Florentin

2013-10-01

In the classical Twin Paradox, according to the Special Theory of Relativity, when the traveling twin blasts off from the Earth to a relative velocity v =√{/3 } 2 c with respect to the Earth, his measuring stick and other physical objects in the direction of relative motion shrink to half their lengths. How is that possible in the real physical world to have let's say a rigid rocket shrinking to half and then later elongated back to normal as an elastic material when it stops? What is the explanation for the traveler's measuring stick and other physical objects, in effect, return to the same length to their original length in the Stay-At-Home, but there is no record of their having shrunk? If it's a rigid (not elastic) object, how can it shrink and then elongate back to normal? It might get broken in such situation.

Almost Poisson integration of rigid body systems

International Nuclear Information System (INIS)

Austin, M.A.; Krishnaprasad, P.S.; Li-Sheng Wang

1993-01-01

In this paper we discuss the numerical integration of Lie-Poisson systems using the mid-point rule. Since such systems result from the reduction of hamiltonian systems with symmetry by lie group actions, we also present examples of reconstruction rules for the full dynamics. A primary motivation is to preserve in the integration process, various conserved quantities of the original dynamics. A main result of this paper is an O(h 3 ) error estimate for the Lie-Poisson structure, where h is the integration step-size. We note that Lie-Poisson systems appear naturally in many areas of physical science and engineering, including theoretical mechanics of fluids and plasmas, satellite dynamics, and polarization dynamics. In the present paper we consider a series of progressively complicated examples related to rigid body systems. We also consider a dissipative example associated to a Lie-Poisson system. The behavior of the mid-point rule and an associated reconstruction rule is numerically explored. 24 refs., 9 figs

A conservative quaternion-based time integration algorithm for rigid body rotations with implicit constraints

DEFF Research Database (Denmark)

Nielsen, Martin Bjerre; Krenk, Steen

2012-01-01

A conservative time integration algorithm for rigid body rotations is presented in a purely algebraic form in terms of the four quaternions components and the four conjugate momentum variables via Hamilton’s equations. The introduction of an extended mass matrix leads to a symmetric set of eight...

IFACEwat: the interfacial water-implemented re-ranking algorithm to improve the discrimination of near native structures for protein rigid docking.

Science.gov (United States)

Su, Chinh; Nguyen, Thuy-Diem; Zheng, Jie; Kwoh, Chee-Keong

2014-01-01

Protein-protein docking is an in silico method to predict the formation of protein complexes. Due to limited computational resources, the protein-protein docking approach has been developed under the assumption of rigid docking, in which one of the two protein partners remains rigid during the protein associations and water contribution is ignored or implicitly presented. Despite obtaining a number of acceptable complex predictions, it seems to-date that most initial rigid docking algorithms still find it difficult or even fail to discriminate successfully the correct predictions from the other incorrect or false positive ones. To improve the rigid docking results, re-ranking is one of the effective methods that help re-locate the correct predictions in top high ranks, discriminating them from the other incorrect ones. Our results showed that the IFACEwat increased both the numbers of the near-native structures and improved their ranks as compared to the initial rigid docking ZDOCK3.0.2. In fact, the IFACEwat achieved a success rate of 83.8% for Antigen/Antibody complexes, which is 10% better than ZDOCK3.0.2. As compared to another re-ranking technique ZRANK, the IFACEwat obtains success rates of 92.3% (8% better) and 90% (5% better) respectively for medium and difficult cases. When comparing with the latest published re-ranking method F2Dock, the IFACEwat performed equivalently well or even better for several Antigen/Antibody complexes. With the inclusion of interfacial water, the IFACEwat improves mostly results of the initial rigid docking, especially for Antigen/Antibody complexes. The improvement is achieved by explicitly taking into account the contribution of water during the protein interactions, which was ignored or not fully presented by the initial rigid docking and other re-ranking techniques. In addition, the IFACEwat maintains sufficient computational efficiency of the initial docking algorithm, yet improves the ranks as well as the number of the near

On Classical Dynamics of Affinely-Rigid Bodies Subject to the Kirchhoff-Love Constraints

Directory of Open Access Journals (Sweden)

Vasyl Kovalchuk

2010-04-01

Full Text Available In this article we consider the affinely-rigid body moving in the three-dimensional physical space and subject to the Kirchhoff-Love constraints, i.e., while it deforms homogeneously in the two-dimensional central plane of the body it simultaneously performs one-dimensional oscillations orthogonal to this central plane. For the polar decomposition we obtain the stationary ellipsoids as special solutions of the general, strongly nonlinear equations of motion. It is also shown that these solutions are conceptually different from those obtained earlier for the two-polar (singular value decomposition.

Euler-Poincaré Reduction of Externally Forced Rigid Body Motion

DEFF Research Database (Denmark)

Wisniewski, Rafal; Kulczycki, P.

2004-01-01

If a mechanical system experiences symmetry, the Lagrangian becomes invariant under a certain group action. This property leads to substantial simplification of the description of movement. The standpoint in this article is a mechanical system affected by an external force of a control action....... Assuming that the system possesses symmetry and the configuration manifold corresponds to a Lie group, the Euler-Poincaré reduction breaks up the motion into separate equations of dynamics and kinematics. This becomes of particular interest for modelling, estimation and control of mechanical systems......-known Euler-Poincaré reduction to a rigid body motion with forcing....

Dynamics of Rigid Bodies and Flexible Beam Structures

DEFF Research Database (Denmark)

Nielsen, Martin Bjerre

of rigid bodies and flexible beam structures with emphasis on the rotational motion. The first part deals with motion in a rotating frame of reference. A novel approach where the equations of motion are formulated in a hybrid state-space in terms of local displacements and global velocities is presented...... quaternion parameters or nine convected base vector components. In both cases, the equations of motion are obtained via Hamilton’s equations by including the kinematic constraints associated with the redundant rotation description by means of Lagrange multipliers. A special feature of the formulation...... of the global components of the position vectors and associated convected base vectors for the element nodes. The kinematics is expressed in a homogeneous quadratic form and the constitutive stiffness is derived from complementary energy of a set of equilibrium modes, each representing a state of constant...

Case report: Inhaled foreign body mismanaged as TB, finally removed using a rigid bronchoscopy after 6 years of impaction

Directory of Open Access Journals (Sweden)

Justin Rubena Lumaya

2016-02-01

Full Text Available Foreign body aspiration is an important cause of mortality in children aged less than three years. Foreign body (FB inhalation can pose diagnostic and therapeutic challenges, especially in longstanding cases and complications such as recurrent pneumonia, lung collapse and lung abscess may develop. We report a case of an 11-year old boy with foreign body impacted in his bronchus for six years, which was mistakenly managed as pulmonary tuberculosis. Radiological evidence confirmed the diagnosis and a rigid bronchoscopy was used to remove the metallic foreign body. The standard of care for the management of a FB in a bronchus is a rigid bronchoscopy; however flexible bronchoscopy can be used, especially in adults. A thorough history with radiological evidence are essential and sometimes, followed by a diagnostic bronchoscopy.

Diagnostic-Photographic Determination of Drag/Lift/Torque Coefficients of High Speed Rigid Body in Water Column

National Research Council Canada - National Science Library

Chu, Peter C; Fan, Chenwu; Gefken, Paul R

2008-01-01

Prediction of rigid body falling through water column with a high speed (such as Mk-84 bomb) needs formulas for drag/lift and torque coefficients, which depend on various physical processes such as supercavitation and bubbles...

Flutter Instability of a Fluid-Conveying Fluid-Immersed Pipe Affixed to a Rigid Body

Science.gov (United States)

2011-01-01

rigid body, denoted by y in Fig. 4, is small. This is in addition to the Euler– Bernoulli beam assumption that the slope of the tail is small everywhere...here. These include the efficiency with which the prime mover can generate fluid momentum , pipe losses, and external drag acting on both the hull and the

On the linear problem arising from motion of a fluid around a moving rigid body

Czech Academy of Sciences Publication Activity Database

Nečasová, Šárka; Wolf, J.

2015-01-01

Roč. 140, č. 2 (2015), s. 241-259 ISSN 0862-7959 R&D Projects: GA ČR(CZ) GAP201/11/1304 Institutional support: RVO:67985840 Keywords : incompressible fluid * rotating rigid body * strong solution Subject RIV: BA - General Mathematics http://hdl.handle.net/10338.dmlcz/144329

The motion of the rigid body in viscous fluid including collisions. Global solvability result

Czech Academy of Sciences Publication Activity Database

Chemetov, N.; Nečasová, Šárka

2017-01-01

Roč. 34, April (2017), s. 416-445 ISSN 1468-1218 R&D Projects: GA ČR GA16-03230S Institutional support: RVO:67985840 Keywords : rigid body * global weak solution * collisions in finite time Subject RIV: BA - General Mathematics OBOR OECD: Pure mathematics Impact factor: 1.659, year: 2016 http://www.sciencedirect.com/science/article/pii/S1468121816301146

Rigid dietary control, flexible dietary control, and intuitive eating: Evidence for their differential relationship to disordered eating and body image concerns.

Science.gov (United States)

Linardon, Jake; Mitchell, Sarah

2017-08-01

This study aimed to replicate and extend from Tylka, Calogero, and Daníelsdóttir (2015) findings by examining the relationship between rigid control, flexible control, and intuitive eating on various indices of disordered eating (i.e., binge eating, disinhibition) and body image concerns (i.e., shape and weight over-evaluation, body checking, and weight-related exercise motivations). This study also examined whether the relationship between intuitive eating and outcomes was mediated by dichotomous thinking and body appreciation. Analysing data from a sample of 372 men and women recruited through the community, this study found that, in contrast to rigid dietary control, intuitive eating uniquely and consistently predicted lower levels of disordered eating and body image concerns. This intuitive eating-disordered eating relationship was mediated by low levels of dichotomous thinking and the intuitive eating-body image relationship was mediated by high levels of body appreciation. Flexible control predicted higher levels of body image concerns and lower levels of disordered eating only when rigid control was accounted for. Findings suggest that until the adaptive properties of flexible control are further elucidated, it may be beneficial to promote intuitive eating within public health approaches to eating disorder prevention. In addition to this, particular emphasis should also be made toward promoting body acceptance and eradicating a dichotomous thinking style around food and eating. Copyright © 2017 Elsevier Ltd. All rights reserved.

Motion of a Rigid Body Supported at One Point by a Rotating Arm

Directory of Open Access Journals (Sweden)

Jeffrey D. Stoen

1993-01-01

Full Text Available This article details a scheme for evaluating the stability of motions of a system consisting of a rigid body connected at one point to a rotating arm. The nonlinear equations of motion for the system are formulated, and a method for finding exact solutions representing motions that resemble a state of rest is presented. The equations are then linearized and roots of the eigensystem are classified and used to construct stability diagrams that facilitate the assessment of effects of varying the body's mass properties and system geometry, changing the position of the attachment joint, and adding energy dissipation in the joint.

Leonhard Euler and the mechanics of rigid bodies

Science.gov (United States)

Marquina, J. E.; Marquina, M. L.; Marquina, V.; Hernández-Gómez, J. J.

2017-01-01

In this work we present the original ideas and the construction of the rigid bodies theory realised by Leonhard Euler between 1738 and 1775. The number of treatises written by Euler on this subject is enormous, including the most notorious Scientia Navalis (1749), Decouverte d’un noveau principe de mecanique (1752), Du mouvement de rotation des corps solides autour d’un axe variable (1765), Theoria motus corporum solidorum seu rigidorum (1765) and Nova methodus motu corporum rigidorum determinandi (1776), in which he developed the ideas of the instantaneous rotation axis, the so-called Euler equations and angles, the components of what is now known as the inertia tensor, the principal axes of inertia, and, finally, the generalisation of the translation and rotation movement equations for any system. Euler, the man who ‘put most of mechanics into its modern form’ (Truesdell 1968 Essays in the History of Mechanics (Berlin: Springer) p 106).

Modelling of transport and collisions between rigid bodies to simulate the jam formation in urban flows

Directory of Open Access Journals (Sweden)

S Hadji

2008-09-01

Full Text Available This study deals with the simulation of transport and interaction betweenbodies considered as a rectangular shape particles, in urban flow. We usedan hydrodynamic two-dimensional finite elements model coupled to theparticles model based on Maxey-Riley equations, and taking into accountof contact between bodies. The finite element discretization is based onthe velocity field richer than pressure field, and the particles displacementsare computed by using a rigid body motion method. A collision strategy isalso developed to handle cases in which bodies touch.

Strongly coupled partitioned six degree-of-freedom rigid body motion solver with Aitken's dynamic under-relaxation

Directory of Open Access Journals (Sweden)

Jeng Hei Chow

2016-07-01

Full Text Available An implicit method of solving the six degree-of-freedom rigid body motion equations based on the second order Adams-Bashforth-Moulten method was utilised as an improvement over the leapfrog scheme by making modifications to the rigid body motion solver libraries directly. The implementation will depend on predictor-corrector steps still residing within the hybrid Pressure Implicit with Splitting of Operators - Semi-Implicit Method for Pressure Linked Equations (PIMPLE outer corrector loops to ensure strong coupling between fluid and motion. Aitken's under-relaxation is also introduced in this study to optimise the convergence rate and stability of the coupled solver. The resulting coupled solver ran on a free floating object tutorial test case when converged matches the original solver. It further allows a varying 70%–80% reduction in simulation times compared using a fixed under-relaxation to achieve the required stability.

Multiscale weighted colored graphs for protein flexibility and rigidity analysis

Science.gov (United States)

Bramer, David; Wei, Guo-Wei

2018-02-01

Protein structural fluctuation, measured by Debye-Waller factors or B-factors, is known to correlate to protein flexibility and function. A variety of methods has been developed for protein Debye-Waller factor prediction and related applications to domain separation, docking pose ranking, entropy calculation, hinge detection, stability analysis, etc. Nevertheless, none of the current methodologies are able to deliver an accuracy of 0.7 in terms of the Pearson correlation coefficients averaged over a large set of proteins. In this work, we introduce a paradigm-shifting geometric graph model, multiscale weighted colored graph (MWCG), to provide a new generation of computational algorithms to significantly change the current status of protein structural fluctuation analysis. Our MWCG model divides a protein graph into multiple subgraphs based on interaction types between graph nodes and represents the protein rigidity by generalized centralities of subgraphs. MWCGs not only predict the B-factors of protein residues but also accurately analyze the flexibility of all atoms in a protein. The MWCG model is validated over a number of protein test sets and compared with many standard methods. An extensive numerical study indicates that the proposed MWCG offers an accuracy of over 0.8 and thus provides perhaps the first reliable method for estimating protein flexibility and B-factors. It also simultaneously predicts all-atom flexibility in a molecule.

The general problem of the motion of coupled rigid bodies about a fixed point

CERN Document Server

Leimanis, Eugene

1965-01-01

In the theory of motion of several coupled rigid bodies about a fixed point one can distinguish three basic ramifications. 1. The first, the so-called classical direction of investigations, is concerned with particular cases of integrability ot the equations of motion of a single rigid body about a fixed point,1 and with their geo­ metrical interpretation. This path of thought was predominant until the beginning of the 20th century and its most illustrious represen­ tatives are L. EULER (1707-1783), J L. LAGRANGE (1736-1813), L. POINSOT (1777-1859), S. V. KOVALEVSKAYA (1850-1891), and others. Chapter I of the present monograph intends to reflect this branch of investigations. For collateral reading on the general questions dealt with in this chapter the reader is referred to the following textbooks and reports: A. DOMOGAROV [1J, F. KLEIN and A. SOMMERFELD [11, 1 , 1 J, A. G. 2 3 GREENHILL [10J, A. GRAY [1J, R. GRAMMEL [4 J, E. J. ROUTH [21' 2 , 1 2 31' 32J, J. B. SCARBOROUGH [1J, and V. V. GOLUBEV [1, 2J.

Collective Excitations in Protein as a Measure of Balance Between its Softness and Rigidity

International Nuclear Information System (INIS)

Shrestha, Utsab R.; Bhowmik, Debsindhu; Van Delinder, Kurt W.; Mamontov, Eugene; O’Neill, Hugh

2017-01-01

Here, we elucidate the protein activity from the perspective of protein softness and flexibility by studying the collective phonon-like excitations in a globular protein, human serum albumin (HSA), and taking advantage of the state-of-the-art inelastic X-ray scattering (IXS) technique. Such excitations demonstrate that the protein becomes softer upon thermal denaturation due to disruption of weak noncovalent bonds. On the other hand, no significant change in the local excitations is detected in ligand- (drugs) bound HSA compared to the ligand-free HSA. These results clearly suggest that the protein conformational flexibility and rigidity are balanced by the native protein structure for biological activity.

Collective Excitations in Protein as a Measure of Balance Between its Softness and Rigidity

Energy Technology Data Exchange (ETDEWEB)

Shrestha, Utsab R. [Wayne State Univ., Detroit, MI (United States). Dept. of Physics and Astronomy; Bhowmik, Debsindhu [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Computational Science and Engineering Division; Van Delinder, Kurt W. [Wayne State Univ., Detroit, MI (United States). Dept. of Physics and Astronomy; Mamontov, Eugene [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Chemical and Engineering Materials Division; O’Neill, Hugh [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biology and Soft Matter Division; Zhang, Qiu [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biology and Soft Matter Division; Alatas, Ahmet [Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source; Chu, Xiang-Qiang [Wayne State Univ., Detroit, MI (United States). Dept. of Physics and Astronomy

2017-01-12

Here, we elucidate the protein activity from the perspective of protein softness and flexibility by studying the collective phonon-like excitations in a globular protein, human serum albumin (HSA), and taking advantage of the state-of-the-art inelastic X-ray scattering (IXS) technique. Such excitations demonstrate that the protein becomes softer upon thermal denaturation due to disruption of weak noncovalent bonds. On the other hand, no significant change in the local excitations is detected in ligand- (drugs) bound HSA compared to the ligand-free HSA. These results clearly suggest that the protein conformational flexibility and rigidity are balanced by the native protein structure for biological activity.

Constrained non-rigid registration for whole body image registration: method and validation

Science.gov (United States)

Li, Xia; Yankeelov, Thomas E.; Peterson, Todd E.; Gore, John C.; Dawant, Benoit M.

2007-03-01

3D intra- and inter-subject registration of image volumes is important for tasks that include measurements and quantification of temporal/longitudinal changes, atlas-based segmentation, deriving population averages, or voxel and tensor-based morphometry. A number of methods have been proposed to tackle this problem but few of them have focused on the problem of registering whole body image volumes acquired either from humans or small animals. These image volumes typically contain a large number of articulated structures, which makes registration more difficult than the registration of head images, to which the vast majority of registration algorithms have been applied. To solve this problem, we have previously proposed an approach, which initializes an intensity-based non-rigid registration algorithm with a point based registration technique [1, 2]. In this paper, we introduce new constraints into our non-rigid registration algorithm to prevent the bones from being deformed inaccurately. Results we have obtained show that the new constrained algorithm leads to better registration results than the previous one.

A topological classification of the Chaplygin systems in the dynamics of a rigid body in a fluid

International Nuclear Information System (INIS)

Nikolaenko, S S

2014-01-01

The paper is concerned with the topological analysis of the Chaplygin integrable case in the dynamics of a rigid body in a fluid. A full list of the topological types of Chaplygin systems in their dependence on the energy level is compiled on the basis of the Fomenko-Zieschang theory. An effective description of the topology of the Liouville foliation in terms of natural coordinate variables is also presented, which opens a direct way to calculating topological invariants. It turns out that on all nonsingular energy levels Chaplygin systems are Liouville equivalent to the well-known Euler case in the dynamics of a rigid body with fixed point. Bibliography: 23 titles

Damageable contact between an elastic body and a rigid foundation

Science.gov (United States)

Campo, M.; Fernández, J. R.; Silva, A.

2009-02-01

In this work, the contact problem between an elastic body and a rigid obstacle is studied, including the development of material damage which results from internal compression or tension. The variational problem is formulated as a first-kind variational inequality for the displacements coupled with a parabolic partial differential equation for the damage field. The existence of a unique local weak solution is stated. Then, a fully discrete scheme is introduced using the finite element method to approximate the spatial variable and an Euler scheme to discretize the time derivatives. Error estimates are derived on the approximate solutions, from which the linear convergence of the algorithm is deduced under suitable regularity conditions. Finally, three two-dimensional numerical simulations are performed to demonstrate the accuracy and the behaviour of the scheme.

Digital anthropomorphic phantoms of non-rigid human respiratory and voluntary body motion for investigating motion correction in emission imaging

International Nuclear Information System (INIS)

Könik, Arda; Johnson, Karen L; Dasari, Paul; Pretorius, P H; Dey, Joyoni; King, Michael A; Connolly, Caitlin M; Segars, Paul W; Lindsay, Clifford

2014-01-01

The development of methods for correcting patient motion in emission tomography has been receiving increased attention. Often the performance of these methods is evaluated through simulations using digital anthropomorphic phantoms, such as the commonly used extended cardiac torso (XCAT) phantom, which models both respiratory and cardiac motion based on human studies. However, non-rigid body motion, which is frequently seen in clinical studies, is not present in the standard XCAT phantom. In addition, respiratory motion in the standard phantom is limited to a single generic trend. In this work, to obtain a more realistic representation of motion, we developed a series of individual-specific XCAT phantoms, modeling non-rigid respiratory and non-rigid body motions derived from the magnetic resonance imaging (MRI) acquisitions of volunteers. Acquisitions were performed in the sagittal orientation using the Navigator methodology. Baseline (no motion) acquisitions at end-expiration were obtained at the beginning of each imaging session for each volunteer. For the body motion studies, MRI was again acquired only at end-expiration for five body motion poses (shoulder stretch, shoulder twist, lateral bend, side roll, and axial slide). For the respiratory motion studies, an MRI was acquired during free/regular breathing. The magnetic resonance slices were then retrospectively sorted into 14 amplitude-binned respiratory states, end-expiration, end-inspiration, six intermediary states during inspiration, and six during expiration using the recorded Navigator signal. XCAT phantoms were then generated based on these MRI data by interactive alignment of the organ contours of the XCAT with the MRI slices using a graphical user interface. Thus far we have created five body motion and five respiratory motion XCAT phantoms from the MRI acquisitions of six healthy volunteers (three males and three females). Non-rigid motion exhibited by the volunteers was reflected in both respiratory

Digital anthropomorphic phantoms of non-rigid human respiratory and voluntary body motion for investigating motion correction in emission imaging

Science.gov (United States)

Könik, Arda; Connolly, Caitlin M.; Johnson, Karen L.; Dasari, Paul; Segars, Paul W.; Pretorius, P. H.; Lindsay, Clifford; Dey, Joyoni; King, Michael A.

2014-07-01

The development of methods for correcting patient motion in emission tomography has been receiving increased attention. Often the performance of these methods is evaluated through simulations using digital anthropomorphic phantoms, such as the commonly used extended cardiac torso (XCAT) phantom, which models both respiratory and cardiac motion based on human studies. However, non-rigid body motion, which is frequently seen in clinical studies, is not present in the standard XCAT phantom. In addition, respiratory motion in the standard phantom is limited to a single generic trend. In this work, to obtain a more realistic representation of motion, we developed a series of individual-specific XCAT phantoms, modeling non-rigid respiratory and non-rigid body motions derived from the magnetic resonance imaging (MRI) acquisitions of volunteers. Acquisitions were performed in the sagittal orientation using the Navigator methodology. Baseline (no motion) acquisitions at end-expiration were obtained at the beginning of each imaging session for each volunteer. For the body motion studies, MRI was again acquired only at end-expiration for five body motion poses (shoulder stretch, shoulder twist, lateral bend, side roll, and axial slide). For the respiratory motion studies, an MRI was acquired during free/regular breathing. The magnetic resonance slices were then retrospectively sorted into 14 amplitude-binned respiratory states, end-expiration, end-inspiration, six intermediary states during inspiration, and six during expiration using the recorded Navigator signal. XCAT phantoms were then generated based on these MRI data by interactive alignment of the organ contours of the XCAT with the MRI slices using a graphical user interface. Thus far we have created five body motion and five respiratory motion XCAT phantoms from the MRI acquisitions of six healthy volunteers (three males and three females). Non-rigid motion exhibited by the volunteers was reflected in both respiratory

In silico single-molecule manipulation of DNA with rigid body dynamics.

Directory of Open Access Journals (Sweden)

Pascal Carrivain

2014-02-01

Full Text Available We develop a new powerful method to reproduce in silico single-molecule manipulation experiments. We demonstrate that flexible polymers such as DNA can be simulated using rigid body dynamics thanks to an original implementation of Langevin dynamics in an open source library called Open Dynamics Engine. We moreover implement a global thermostat which accelerates the simulation sampling by two orders of magnitude. We reproduce force-extension as well as rotation-extension curves of reference experimental studies. Finally, we extend the model to simulations where the control parameter is no longer the torsional strain but instead the torque, and predict the expected behavior for this case which is particularly challenging theoretically and experimentally.

Dynamical analysis of an orbiting three-rigid-body system

Energy Technology Data Exchange (ETDEWEB)

Pagnozzi, Daniele, E-mail: daniele.pagnozzi@strath.ac.uk, E-mail: james.biggs@strath.ac.uk; Biggs, James D., E-mail: daniele.pagnozzi@strath.ac.uk, E-mail: james.biggs@strath.ac.uk [Department of Mechanical and Aerospace Engineering, University of Strathclyde, Glasgow, Scotland (United Kingdom)

2014-12-10

The development of multi-joint-spacecraft mission concepts calls for a deeper understanding of their nonlinear dynamics to inform and enhance system design. This paper presents a study of a three-finite-shape rigid-body system under the action of an ideal central gravitational field. The aim of this paper is to gain an insight into the natural dynamics of this system. The Hamiltonian dynamics is derived and used to identify relative attitude equilibria of the system with respect to the orbital reference frame. Then a numerical investigation of the behaviour far from the equilibria is provided using tools from modern dynamical systems theory such as energy methods, phase portraits and Poincarè maps. Results reveal a complex structure of the dynamics as well as the existence of connections between some of the equilibria. Stable equilibrium configurations appear to be surrounded by very narrow regions of regular and quasi-regular motions. Trajectories evolve on chaotic motions in the rest of the domain.

Development of Swimming Human Simulation Model Considering Rigid Body Dynamics and Unsteady Fluid Force for Whole Body

Science.gov (United States)

Nakashima, Motomu; Satou, Ken; Miura, Yasufumi

The purpose of this study is to develop a swimming human simulation model considering rigid body dynamics and unsteady fluid force for the whole body, which will be utilized to analyze various dynamical problems in human swimming. First, the modeling methods and their formulations for the human body and the fluid force are respectively described. Second, experiments to identify the coefficients of the normal drag and the added mass are conducted by use of an experimental setup, in which a limb model rotates in the water, and its rotating angle and the bending moment at the root are measured. As the result of the identification, the present model for the fluid force was found to have satisfactory performance in order to represent the unsteady fluctuations of the experimental data, although it has 10% error. Third, a simulation for the gliding position is conducted in order to identify the tangential drag coefficient. Finally, a simulation example of standard six beat front crawl swimming is shown. The swimming speed of the simulation became a reasonable value, indicating the validity of the present simulation model, although it is 7.5% lower than the actual swimming.

Generation of 3D templates of active sites of proteins with rigid prosthetic groups.

Science.gov (United States)

Nebel, Jean-Christophe

2006-05-15

With the increasing availability of protein structures, the generation of biologically meaningful 3D patterns from the simultaneous alignment of several protein structures is an exciting prospect: active sites could be better understood, protein functions and protein 3D structures could be predicted more accurately. Although patterns can already be generated at the fold and topological levels, no system produces high-resolution 3D patterns including atom and cavity positions. To address this challenge, our research focuses on generating patterns from proteins with rigid prosthetic groups. Since these groups are key elements of protein active sites, the generated 3D patterns are expected to be biologically meaningful. In this paper, we present a new approach which allows the generation of 3D patterns from proteins with rigid prosthetic groups. Using 237 protein chains representing proteins containing porphyrin rings, our method was validated by comparing 3D templates generated from homologues with the 3D structure of the proteins they model. Atom positions were predicted reliably: 93% of them had an accuracy of 1.00 A or less. Moreover, similar results were obtained regarding chemical group and cavity positions. Results also suggested our system could contribute to the validation of 3D protein models. Finally, a 3D template was generated for the active site of human cytochrome P450 CYP17, the 3D structure of which is unknown. Its analysis showed that it is biologically meaningful: our method detected the main patterns of the cytochrome P450 superfamily and the motifs linked to catalytic reactions. The 3D template also suggested the position of a residue, which could be involved in a hydrogen bond with CYP17 substrates and the shape and location of a cavity. Comparisons with independently generated 3D models comforted these hypotheses. Alignment software (Nestor3D) is available at http://www.kingston.ac.uk/~ku33185/Nestor3D.html

Structural rigidity in the capsid assembly of cowpea chlorotic mottle virus

International Nuclear Information System (INIS)

Hespenheide, B M; Jacobs, D J; Thorpe, M F

2004-01-01

The cowpea chlorotic mottle virus (CCMV) has a protein cage, or capsid, which encloses its genetic material. The structure of the capsid consists of 180 copies of a single protein that self-assemble inside a cell to form a complete capsid with icosahedral symmetry. The icosahedral surface can be naturally divided into pentagonal and hexagonal faces, and the formation of either of these faces has been proposed to be the first step in the capsid assembly process. We have used the software FIRST to analyse the rigidity of pentameric and hexameric substructures of the complete capsid to explore the viability of certain capsid assembly pathways. FIRST uses the 3D pebble game to determine structural rigidity, and a brief description of this algorithm, as applied to body-bar networks, is given here. We find that the pentameric substructure, which corresponds to a pentagonal face on the icosahedral surface, provides the best structural properties for nucleating the capsid assembly process, consistent with experimental observations

Structural rigidity in the capsid assembly of cowpea chlorotic mottle virus

Science.gov (United States)

Hespenheide, B. M.; Jacobs, D. J.; Thorpe, M. F.

2004-11-01

The cowpea chlorotic mottle virus (CCMV) has a protein cage, or capsid, which encloses its genetic material. The structure of the capsid consists of 180 copies of a single protein that self-assemble inside a cell to form a complete capsid with icosahedral symmetry. The icosahedral surface can be naturally divided into pentagonal and hexagonal faces, and the formation of either of these faces has been proposed to be the first step in the capsid assembly process. We have used the software FIRST to analyse the rigidity of pentameric and hexameric substructures of the complete capsid to explore the viability of certain capsid assembly pathways. FIRST uses the 3D pebble game to determine structural rigidity, and a brief description of this algorithm, as applied to body-bar networks, is given here. We find that the pentameric substructure, which corresponds to a pentagonal face on the icosahedral surface, provides the best structural properties for nucleating the capsid assembly process, consistent with experimental observations.

Structural rigidity in the capsid assembly of cowpea chlorotic mottle virus

Energy Technology Data Exchange (ETDEWEB)

Hespenheide, B M [Department of Physics and Astronomy, Arizona State University, PO Box 871504, Tempe, AZ 85287-1504 (United States); Jacobs, D J [Department of Physics and Astronomy, California State University, 18111 Nordhoff Street, Northridge, CA 91330-8268 (United States); Thorpe, M F [Department of Physics and Astronomy, Arizona State University, PO Box 871504, Tempe, AZ 85287-1504 (United States)

2004-11-10

The cowpea chlorotic mottle virus (CCMV) has a protein cage, or capsid, which encloses its genetic material. The structure of the capsid consists of 180 copies of a single protein that self-assemble inside a cell to form a complete capsid with icosahedral symmetry. The icosahedral surface can be naturally divided into pentagonal and hexagonal faces, and the formation of either of these faces has been proposed to be the first step in the capsid assembly process. We have used the software FIRST to analyse the rigidity of pentameric and hexameric substructures of the complete capsid to explore the viability of certain capsid assembly pathways. FIRST uses the 3D pebble game to determine structural rigidity, and a brief description of this algorithm, as applied to body-bar networks, is given here. We find that the pentameric substructure, which corresponds to a pentagonal face on the icosahedral surface, provides the best structural properties for nucleating the capsid assembly process, consistent with experimental observations.

Dynamic Behavior of Wind Turbine by a Mixed Flexible-Rigid Multi-Body Model

Science.gov (United States)

Wang, Jianhong; Qin, Datong; Ding, Yi

A mixed flexible-rigid multi-body model is presented to study the dynamic behavior of a horizontal axis wind turbine. The special attention is given to flexible body: flexible rotor is modeled by a newly developed blade finite element, support bearing elasticities, variations in the number of teeth in contact as well as contact tooth's elasticities are mainly flexible components in the power train. The couple conditions between different subsystems are established by constraint equations. The wind turbine model is generated by coupling models of rotor, power train and generator with constraint equations together. Based on this model, an eigenproblem analysis is carried out to show the mode shape of rotor and power train at a few natural frequencies. The dynamic responses and contact forces among gears under constant wind speed and fixed pitch angle are analyzed.

An iterative approach to dynamic simulation of 3D rigid body motions for real-time interactive computer animation

NARCIS (Netherlands)

Overveld, van C.W.A.M.

1991-01-01

A method is presented for approximating the motions of linked 3-dimensional rigid body systems that may be applied in the context of interactive motion specification for computer animation. The method is based on decoupling the ballistic (free) component of the motion of the points that constitute

A Compliant Bistable Mechanism Design Incorporating Elastica Buckling Beam Theory and Pseudo-Rigid-Body Model

DEFF Research Database (Denmark)

Sönmez, Ümit; Tutum, Cem Celal

2008-01-01

In this work, a new compliant bistable mechanism design is introduced. The combined use of pseudo-rigid-body model (PRBM) and the Elastica buckling theory is presented for the first time to analyze the new design. This mechanism consists of the large deflecting straight beams, buckling beams...... and the buckling Elastica solution for an original compliant mechanism kinematic analysis. New compliant mechanism designs are presented to highlight where such combined kinematic analysis is required....

How does symmetry impact the flexibility of proteins?

Science.gov (United States)

Schulze, Bernd; Sljoka, Adnan; Whiteley, Walter

2014-02-13

It is well known that (i) the flexibility and rigidity of proteins are central to their function, (ii) a number of oligomers with several copies of individual protein chains assemble with symmetry in the native state and (iii) added symmetry sometimes leads to added flexibility in structures. We observe that the most common symmetry classes of protein oligomers are also the symmetry classes that lead to increased flexibility in certain three-dimensional structures-and investigate the possible significance of this coincidence. This builds on the well-developed theory of generic rigidity of body-bar frameworks, which permits an analysis of the rigidity and flexibility of molecular structures such as proteins via fast combinatorial algorithms. In particular, we outline some very simple counting rules and possible algorithmic extensions that allow us to predict continuous symmetry-preserving motions in body-bar frameworks that possess non-trivial point-group symmetry. For simplicity, we focus on dimers, which typically assemble with twofold rotational axes, and often have allosteric function that requires motions to link distant sites on the two protein chains.

Generalized Predictive Control of Dynamic Systems with Rigid-Body Modes

Science.gov (United States)

Kvaternik, Raymond G.

2013-01-01

Numerical simulations to assess the effectiveness of Generalized Predictive Control (GPC) for active control of dynamic systems having rigid-body modes are presented. GPC is a linear, time-invariant, multi-input/multi-output predictive control method that uses an ARX model to characterize the system and to design the controller. Although the method can accommodate both embedded (implicit) and explicit feedforward paths for incorporation of disturbance effects, only the case of embedded feedforward in which the disturbances are assumed to be unknown is considered here. Results from numerical simulations using mathematical models of both a free-free three-degree-of-freedom mass-spring-dashpot system and the XV-15 tiltrotor research aircraft are presented. In regulation mode operation, which calls for zero system response in the presence of disturbances, the simulations showed reductions of nearly 100%. In tracking mode operations, where the system is commanded to follow a specified path, the GPC controllers produced the desired responses, even in the presence of disturbances.

HOW CAN DYNAMIC RIGID-BODY MODELING BE HELPFUL IN MOTOR LEARNING? - DIAGNOSING PERFORMANCE USING DYNAMIC MODELING

OpenAIRE

Shan, Gongbing; Sust, Martin; Simard, Stephane; Bohn, Christina; Nicol, Klaus

2004-01-01

There are two main problems for biomechanists in motor learning practice. One is theory vs. experience, the other is the determination of dominative information directly helpful in the practice. This project aimed at addressing these problems from a quantitative aspect by using motion capture and biomechanical rigid body modeling. The purposes were to identify differences in the description of movements amongst motion analysists (external view), athletes (internal sight) and coaches (internal...

Free Energy Landscapes of Alanine Oligopeptides in Rigid-Body and Hybrid Water Models.

Science.gov (United States)

Nayar, Divya; Chakravarty, Charusita

2015-08-27

Replica exchange molecular dynamics is used to study the effect of different rigid-body (mTIP3P, TIP4P, SPC/E) and hybrid (H1.56, H3.00) water models on the conformational free energy landscape of the alanine oligopeptides (acAnme and acA5nme), in conjunction with the CHARMM22 force field. The free energy landscape is mapped out as a function of the Ramachandran angles. In addition, various secondary structure metrics, solvation shell properties, and the number of peptide-solvent hydrogen bonds are monitored. Alanine dipeptide is found to have similar free energy landscapes in different solvent models, an insensitivity which may be due to the absence of possibilities for forming i-(i + 4) or i-(i + 3) intrapeptide hydrogen bonds. The pentapeptide, acA5nme, where there are three intrapeptide backbone hydrogen bonds, shows a conformational free energy landscape with a much greater degree of sensitivity to the choice of solvent model, though the three rigid-body water models differ only quantitatively. The pentapeptide prefers nonhelical, non-native PPII and β-sheet populations as the solvent is changed from SPC/E to the less tetrahedral liquid (H1.56) to an LJ-like liquid (H3.00). The pentapeptide conformational order metrics indicate a preference for open, solvent-exposed, non-native structures in hybrid solvent models at all temperatures of study. The possible correlations between the properties of solvent models and secondary structure preferences of alanine oligopeptides are discussed, and the competition between intrapeptide, peptide-solvent, and solvent-solvent hydrogen bonding is shown to be crucial in the relative free energies of different conformers.

Measurements of body protein for clinical investigation

International Nuclear Information System (INIS)

Mernagh, J.R.; Harrison, J.E.; McNeill, M.G.; Jeejeebhoy, K.N.; Krishnan, S.S.

1986-01-01

Body protein (nitrogen) is determined by bilaterally irradiating the body with neutrons using Pu-Be sources and measuring the resultant 10.8 MeV gamma rays from the reaction 14 N(n,8) 15 N. In the authors lab the whole body can be scanned or separate segments of the body can be measured independently. A nitrogen index has been developed based on body size and is used as a predictor of normal total body nitrogen (TBN). They have found that TBN, when normalized to body size in this way, provides a reliable index of protein status which cannot be accurately determined by body weight, anthropometry, or body potassium measurements. Changes in body composition with age were studied by measuring the composition of 56 healthy female volunteers aged 20-80. Measurements were made for K( 40 K), Ca and N. It was shown that protein and bone mineral decrease with age but that this is not reflected in K or anthropometry measurements. Results of other studies to be presented include: body protein measurements pre and post TPN (total parenteral nutrition), nutritional status of patients on long term CAPD (continuous ambulatory peritoneal dialysis) and changes in body composition as a result of TPN in patients with small cell lung cancer receiving chemotherapy. Clinical results show that indirect measurements of body protein based on weight, potassium, or anthropometry, do not give an accurate measure of body protein. For an accurate measurement, direct measurement of body protein is necessary

Modeling and experimentation with asymmetric rigid bodies: a variation on disks and inclines

International Nuclear Information System (INIS)

Raviola, Lisandro A; Zárate, Oscar; Rodríguez, Eduardo E

2014-01-01

We study the ascending motion of a disk rolling on an incline when its centre of mass lies outside the disk axis. The problem is suitable as laboratory project for a first course in mechanics at the undergraduate level and goes beyond typical textbook problems about bi-dimensional rigid body motions. We develop a theoretical model for the disk motion based on mechanical energy conservation and compare its predictions with experimental data obtained by digital video recording. Using readily available resources, a very satisfactory agreement is obtained between the model and the experimental observations. These results complement previous ones that have been reported in the literature for similar systems. (paper)

Conservative rigid body dynamics by convected base vectors with implicit constraints

DEFF Research Database (Denmark)

Krenk, Steen; Nielsen, Martin Bjerre

2014-01-01

of differential equations without additional algebraic constraints on the base vectors. A discretized form of the equations of motion is obtained by starting from a finite time increment of the Hamiltonian, and retracing the steps of the continuous formulation in discrete form in terms of increments and mean...... of the base vectors. Orthogonality and unit length of the base vectors are imposed by constraining the equivalent Green strain components, and the kinetic energy is represented corresponding to rigid body motion. The equations of motion are obtained via Hamilton’s equations including the zero...... values over each integration time increment. In this discrete form the Lagrange multipliers are given in terms of a representative value within the integration time interval, and the equations of motion are recast into a conservative mean-value and finite difference format. The Lagrange multipliers...

APPLICATION OF RIGID LINKS IN STRUCTURAL DESIGN MODELS

Directory of Open Access Journals (Sweden)

Sergey Yu. Fialko

2017-09-01

Full Text Available A special finite element modelling rigid links is proposed for the linear static and buckling analysis. Unlike the classical approach based on the theorems of rigid body kinematics, the proposed approach preserves the similarity between the adjacency graph for a sparse matrix and the adjacency graph for nodes of the finite element model, which allows applying sparse direct solvers more effectively. Besides, the proposed approach allows significantly reducing the number of nonzero entries in the factored stiffness matrix in comparison with the classical one, which greatly reduces the duration of the solution. For buckling problems of structures containing rigid bodies, this approach gives correct results. Several examples demonstrate its efficiency.

Conservative integration of rigid body motion by quaternion parameters with implicit constraints

DEFF Research Database (Denmark)

Nielsen, Martin Bjerre; Krenk, Steen

2012-01-01

An angular momentum and energy‐conserving time integration algorithm for rigid body rotation is formulated in terms of the quaternion parameters and the corresponding four‐component conjugate momentum vector via Hamilton's equations. The introduction of an extended mass matrix leads to a symmetric...... these equations via the set of momentum equations. Initially, the normalization of the quaternion array is introduced via a Lagrange multiplier. However, this Lagrange multiplier can be expressed explicitly in terms of the gradient of the external load potential, and elimination of the Lagrange multiplier from...... the final format leaves only an explicit projection applied to the external load potential gradient. An algorithm is developed by forming a finite increment of the Hamiltonian. This procedure identifies the proper selection of increments and mean values, and leads to an algorithm with conservation...

On the motion of rigid bodies in an incompressible or compressible viscous fluid under the action of gravitational forces

Czech Academy of Sciences Publication Activity Database

Ducomet, B.; Nečasová, Šárka

2013-01-01

Roč. 6, č. 5 (2013), s. 1193-1213 ISSN 1937-1632 R&D Projects: GA ČR(CZ) GAP201/11/1304 Institutional support: RVO:67985840 Keywords : motion of rigid bodies * incompressible fluid * compressible fluid Subject RIV: BA - General Mathematics https://www.aimsciences.org/journals/displayArticlesnew.jsp?paperID=8331

Governing equations of multi-component rigid body-spring discrete element models of reinforced concrete columns

International Nuclear Information System (INIS)

Guan, P B; Tingatinga, E A; Longalong, R E; Saguid, J

2016-01-01

During the past decades, the complexity of conventional methods to perform seismic performance assessment of buildings led to the development of more effective approaches. The rigid body spring-discrete element method (RBS-DEM) is one of these approaches and has recently been applied to the study of the behavior of reinforced concrete (RC) buildings subjected to strong earthquakes. In this paper, the governing equations of RBS-DEM planar elements subjected to lateral loads and horizontal ground motion are presented and used to replicate the hysteretic behavior of experimental RC columns. The RBS-DEM models of columns are made up of rigid components connected by systems of springs that simulate axial, shear, and bending behavior of an RC section. The parameters of springs were obtained using Response-2000 software and the hysteretic response of the models of select columns from the Pacific Earthquake Engineering Research (PEER) Structural Performance Database were computed numerically. Numerical examples show that one-component models were able to simulate the initial stiffness reasonably, while the displacement capacity of actual columns undergoing large displacements were underestimated. (paper)

A biomechanical testing system to determine micromotion between hip implant and femur accounting for deformation of the hip implant: Assessment of the influence of rigid body assumptions on micromotions measurements.

Science.gov (United States)

Leuridan, Steven; Goossens, Quentin; Roosen, Jorg; Pastrav, Leonard; Denis, Kathleen; Mulier, Michiel; Desmet, Wim; Vander Sloten, Jos

2017-02-01

Accurate pre-clinical evaluation of the initial stability of new cementless hip stems using in vitro micromotion measurements is an important step in the design process to assess the new stem's potential. Several measuring systems, linear variable displacement transducer-based and other, require assuming bone or implant to be rigid to obtain micromotion values or to calculate derived quantities such as relative implant tilting. An alternative linear variable displacement transducer-based measuring system not requiring a rigid body assumption was developed in this study. The system combined advantages of local unidirectional and frame-and-bracket micromotion measuring concepts. The influence and possible errors that would be made by adopting a rigid body assumption were quantified. Furthermore, as the system allowed emulating local unidirectional and frame-and-bracket systems, the influence of adopting rigid body assumptions were also analyzed for both concepts. Synthetic and embalmed bone models were tested in combination with primary and revision implants. Single-legged stance phase loading was applied to the implant - bone constructs. Adopting a rigid body assumption resulted in an overestimation of mediolateral micromotion of up to 49.7μm at more distal measuring locations. Maximal average relative rotational motion was overestimated by 0.12° around the anteroposterior axis. Frontal and sagittal tilting calculations based on a unidirectional measuring concept underestimated the true tilting by an order of magnitude. Non-rigid behavior is a factor that should not be dismissed in micromotion stability evaluations of primary and revision femoral implants. Copyright © 2017 Elsevier Ltd. All rights reserved.

Self-propulsion of a body with rigid surface and variable coefficient of lift in a perfect fluid

Science.gov (United States)

Ramodanov, Sergey M.; Tenenev, Valentin A.; Treschev, Dmitry V.

2012-11-01

We study the system of a 2D rigid body moving in an unbounded volume of incompressible, vortex-free perfect fluid which is at rest at infinity. The body is equipped with a gyrostat and a so-called Flettner rotor. Due to the latter the body is subject to a lifting force (Magnus effect). The rotational velocities of the gyrostat and the rotor are assumed to be known functions of time (control inputs). The equations of motion are presented in the form of the Kirchhoff equations. The integrals of motion are given in the case of piecewise continuous control. Using these integrals we obtain a (reduced) system of first-order differential equations on the configuration space. Then an optimal control problem for several types of the inputs is solved using genetic algorithms.

Reversible Rigidity Control Using Low Melting Temperature Alloys

Science.gov (United States)

Shan, Wanliang; Lu, Tong; Majidi, Carmel

2013-03-01

Inspired by nature, materials able to achieve rapid rigidity changes have important applications for human body protection in military and many other areas. This talk presents the fabrication and design of soft-matter technologies that exhibit rapid reversible rigidity control. Fabricated with a masked deposition technique, the soft-matter composite contains liquid-phase and phase-changing metal alloys embedded in a soft and highly stretchable elastomer. The composite material can reversibly change its rigidity by three orders of magnitude and sustain large deformation.

Higher order coupling between rigid-body and elastic motion in flexible mechanisms

International Nuclear Information System (INIS)

Esat, I.I.; Ianakiev, A.

1995-01-01

The paper presents an investigation of the influence of the higher order coupling terms between the rigid-body and elastic motion into flexible mechanism dynamics. The configuration of the mechanical system is obtained by using the so called hybrid coordinates. The kinematic description of the mechanism was obtained using the D-H 4 x 4 transformation matrices. The elastic deformation of each point of the mechanism is described by the finite element modeling (FEM) type interpolation scheme. The dynamic model of the flexible mechanism consists due to the hybrid coordinates of two groups of differential equations. The first group describes the manipulator transport motion and the second group describes the vibration. In this paper the authors evaluated the contribution of the coupling terms between the two groups of differential equations and selected only those with high contribution

Mathematical aspects of molecular replacement. III. Properties of space groups preferred by proteins in the Protein Data Bank.

Science.gov (United States)

Chirikjian, G; Sajjadi, S; Toptygin, D; Yan, Y

2015-03-01

The main goal of molecular replacement in macromolecular crystallography is to find the appropriate rigid-body transformations that situate identical copies of model proteins in the crystallographic unit cell. The search for such transformations can be thought of as taking place in the coset space Γ\\G where Γ is the Sohncke group of the macromolecular crystal and G is the continuous group of rigid-body motions in Euclidean space. This paper, the third in a series, is concerned with viewing nonsymmorphic Γ in a new way. These space groups, rather than symmorphic ones, are the most common ones for protein crystals. Moreover, their properties impact the structure of the space Γ\\G. In particular, nonsymmorphic space groups contain both Bieberbach subgroups and symmorphic subgroups. A number of new theorems focusing on these subgroups are proven, and it is shown that these concepts are related to the preferences that proteins have for crystallizing in different space groups, as observed in the Protein Data Bank.

Rigidity of Glasses and Macromolecules

Science.gov (United States)

Thorpe, M. F.

1998-03-01

The simple yet powerful ideas of percolation theory have found their way into many different areas of research. In this talk we show how RIGIDITY PERCOLATION can be studied at a similar level of sophistication, using a powerful new program THE PEBBLE GAME (D. J. Jacobs and M. F. Thorpe, Phys. Rev. E) 53, 3682 (1996). that uses an integer algorithm. This program can analyse the rigidity of two and three dimensional networks containing more than one million bars and joints. We find the total number of floppy modes, and find the critical behavior as the network goes from floppy to rigid as more bars are added. We discuss the relevance of this work to network glasses, and how it relates to experiments that involve the mechanical properties like hardness and elasticity of covalent glassy networks like Ge_xAs_ySe_1-x-y and dicuss recent experiments that suggest that the rigidity transition may be first order (Xingwei Feng, W. J.Bresser and P. Boolchand, Phys. Rev. Lett 78), 4422 (1997).. This approach is also useful in macromolecules and proteins, where detailed information about the rigid domain structure can be obtained.

Simulation of the steady-state energy transfer in rigid bodies, with convective-radiative boundary conditions, employing a minimum principle

International Nuclear Information System (INIS)

Gama, R.M.S. da.

1992-08-01

The energy transfer phenomenon in a rigid and opaque body that exchanges energy, with the environment, by convection and by diffuse thermal radiation is studied. The considered phenomenon is described by a partial differential equation, subjected to (nonlinear) boundary conditions. A minimum principle, suitable for a large class of energy transfer problems is presented. Some particular cases are simulated. (author)

iCub Whole-body Control through Force Regulation on Rigid Noncoplanar Contacts

Directory of Open Access Journals (Sweden)

Francesco eNori

2015-03-01

Full Text Available This paper details the implementation on the humanoid robot iCub of state-of-the-art algorithms for whole-body control. We regulate the forces between the robot and its surrounding environment to stabilize a desired robot posture. We assume that the forces and torques are exerted on rigid contacts. The validity of this assumption is guaranteed by constraining the contact forces and torques, e.g. the contact forces must belong to the associated friction cones. The implementation of this control strategy requires to estimate the external forces acting on the robot, and the internal joint torques. We then detail algorithms to obtain these estimations when using a robot with an iCub-like sensor set, i.e. distributed six-axis force-torque sensors and whole-body tactile sensors. A general theory for identifying the robot inertial parameters is also presented. From an actuation standpoint, we show how to implement a joint torque control in the case of DC brushless motors. In addition, the coupling mechanism of the iCub torso is investigated. The soundness of the entire control architecture is validated in a real scenario involving the robot iCub balancing and making contacts at both arms.

Quantum chemical approach for condensed-phase thermochemistry (V): Development of rigid-body type harmonic solvation model

Science.gov (United States)

Tarumi, Moto; Nakai, Hiromi

2018-05-01

This letter proposes an approximate treatment of the harmonic solvation model (HSM) assuming the solute to be a rigid body (RB-HSM). The HSM method can appropriately estimate the Gibbs free energy for condensed phases even where an ideal gas model used by standard quantum chemical programs fails. The RB-HSM method eliminates calculations for intra-molecular vibrations in order to reduce the computational costs. Numerical assessments indicated that the RB-HSM method can evaluate entropies and internal energies with the same accuracy as the HSM method but with lower calculation costs.

Analogies between the Torque-Free Motion of a Rigid Body about a Fixed Point and Light Propagation in Anisotropic Media

Science.gov (United States)

Bellver-Cebreros, Consuelo; Rodriguez-Danta, Marcelo

2009-01-01

An apparently unnoticed analogy between the torque-free motion of a rotating rigid body about a fixed point and the propagation of light in anisotropic media is stated. First, a new plane construction for visualizing this torque-free motion is proposed. This method uses an intrinsic representation alternative to angular momentum and independent of…

Dynamics on strata of trigonal Jacobians and some integrable problems of rigid body motion

International Nuclear Information System (INIS)

Braden, H W; Enolski, V Z; Fedorov, Yu N

2013-01-01

We present an algebraic geometrical and analytical description of the Goryachev case of rigid body motion. It belongs to a family of systems sharing the same properties: although completely integrable, they are not algebraically integrable, their solution is not meromorphic in the complex time and involves dynamics on the strata of the Jacobian varieties of trigonal curves. Although the strata of hyperelliptic Jacobians have already appeared in the literature in the context of some dynamical systems, the Goryachev case is the first example of an integrable system whose solution involves a more general curve. Several new features (and formulae) are encountered in the solution given in terms of sigma-functions of such a curve. (paper)

A high protein diet upregulated whole-body protein turnover during energy deficit

Science.gov (United States)

The effects of higher protein diets and sustained energy deficit (ED) on whole-body protein turnover (WBPTO) are not well described. This study examined whether dietary protein level influences whole-body protein breakdown (Ra), non-oxidative leucine disposal (NOLD), and oxidation (Ox) during ED. ...

Dynamical Behavior of a Rigid Body with One Fixed Point (Gyroscope. Basic Concepts and Results. Open Problems: a Review

Directory of Open Access Journals (Sweden)

Svetoslav Ganchev Nikolov

2015-07-01

Full Text Available The study of the dynamic behavior of a rigid body with one fixed point (gyroscope has a long history. A number of famous mathematicians and mechanical engineers have devoted enormous time and effort to clarify the role of dynamic effects on its movement (behavior – stable, periodic, quasi-periodic or chaotic. The main objectives of this review are: 1 to outline the characteristic features of the theory of dynamical systems and 2 to reveal the specific properties of the motion of a rigid body with one fixed point (gyroscope.This article consists of six sections. The first section addresses the main concepts of the theory of dynamical systems. Section two presents the main theoretical results (obtained so far concerning the dynamic behavior of a solid with one fixed point (gyroscope. Section three examines the problem of gyroscopic stabilization. Section four deals with the non-linear (chaotic dynamics of the gyroscope. Section five is a brief analysis of the gyroscope applications in engineering. The final section provides conclusions and generalizations on why the theory of dynamical systems should be used in the study of the movement of gyroscopic systems.

On potential energies and constraints in the dynamics of rigid bodies and particles

Directory of Open Access Journals (Sweden)

O'reilly Oliver M.

2002-01-01

Full Text Available A new treatment of kinematical constraints and potential energies arising in the dynamics of systems of rigid bodies and particles is presented which is suited to Newtonian and Lagrangian formulations. Its novel feature is the imposing of invariance requirements on the constraint functions and potential energy functions. These requirements are extensively used in continuum mechanics and, in the present context, one finds certain generalizations of Newton's third law of motion and an elucidation of the nature of constraint forces and moments. One motivation for such a treatment can be found by considering approaches where invariance requirements are ignored. In contrast to the treatment presented in this paper, it is shown that this may lead to a difficulty in formulating the equations governing the motion of the system.

EDF fragment relocation model based on the displacement of rigid bodies

International Nuclear Information System (INIS)

Callu, C.; Baron, D.; Ruck, J.M.

1997-01-01

In order to release the restricting conditions imposed to the reactor operations with regards to PCMI (Pellet-Cladding Mechanical Interaction), the simulation of a fuel rod thermomechanical behavior has to be improved. The computer programming has to cope with the more and more sophisticated mathematical modellings induced by the complexity and the interdependence of the phenomena. Therefore EDF is developing a new code - CYRANO3 - since 1990 putting emphasis on its evolution capacities. Concerning more precisely the PCMI simulation, the pellet fragmentation and the fragments relocation is one of the major aspect one must account for. Thanks to recent analytical experiments, EDF developed a new modelling based on the displacement of rigid bodies and on the calculation of the interaction efforts between the fragments. This paper presents the basis of the model, its introduction within the CYRANO3 code and its calibration on a specific analytical experiment. The modelling is then tested against PWR fuel rods deformations from the EDF data base. The results are presented and discussed. (author)

An Explicit Formulation of Singularity-Free Dynamic Equations of Mechanical Systems in Lagrangian Form---Part one: Single Rigid Bodies

Directory of Open Access Journals (Sweden)

Pål Johan From

2012-04-01

Full Text Available This paper presents the explicit dynamic equations of a mechanical system. The equations are presented so that they can easily be implemented in a simulation software or controller environment and are also well suited for system and controller analysis. The dynamics of a general mechanical system consisting of one or more rigid bodies can be derived from the Lagrangian. We can then use several well known properties of Lie groups to guarantee that these equations are well defined. This will, however, often lead to rather abstract formulation of the dynamic equations that cannot be implemented in a simulation software directly. In this paper we close this gap and show what the explicit dynamic equations look like. These equations can then be implemented directly in a simulation software and no background knowledge on Lie theory and differential geometry on the practitioner's side is required. This is the first of two papers on this topic. In this paper we derive the dynamics for single rigid bodies, while in the second part we study multibody systems. In addition to making the equations more accessible to practitioners, a motivation behind the papers is to correct a few errors commonly found in literature. For the first time, we show the detailed derivations and how to arrive at the correct set of equations. We also show through some simple examples that these correspond with the classical formulations found from Lagrange's equations. The dynamics is derived from the Boltzmann--Hamel equations of motion in terms of local position and velocity variables and the mapping to the corresponding quasi-velocities. Finally we present a new theorem which states that the Boltzmann--Hamel formulation of the dynamics is valid for all transformations with a Lie group topology. This has previously only been indicated through examples, but here we also present the formal proof. The main motivation of these papers is to allow practitioners not familiar with

Multiscale multiphysics and multidomain models—Flexibility and rigidity

International Nuclear Information System (INIS)

Xia, Kelin; Opron, Kristopher; Wei, Guo-Wei

2013-01-01

The emerging complexity of large macromolecules has led to challenges in their full scale theoretical description and computer simulation. Multiscale multiphysics and multidomain models have been introduced to reduce the number of degrees of freedom while maintaining modeling accuracy and achieving computational efficiency. A total energy functional is constructed to put energies for polar and nonpolar solvation, chemical potential, fluid flow, molecular mechanics, and elastic dynamics on an equal footing. The variational principle is utilized to derive coupled governing equations for the above mentioned multiphysical descriptions. Among these governing equations is the Poisson-Boltzmann equation which describes continuum electrostatics with atomic charges. The present work introduces the theory of continuum elasticity with atomic rigidity (CEWAR). The essence of CEWAR is to formulate the shear modulus as a continuous function of atomic rigidity. As a result, the dynamics complexity of a macromolecular system is separated from its static complexity so that the more time-consuming dynamics is handled with continuum elasticity theory, while the less time-consuming static analysis is pursued with atomic approaches. We propose a simple method, flexibility-rigidity index (FRI), to analyze macromolecular flexibility and rigidity in atomic detail. The construction of FRI relies on the fundamental assumption that protein functions, such as flexibility, rigidity, and energy, are entirely determined by the structure of the protein and its environment, although the structure is in turn determined by all the interactions. As such, the FRI measures the topological connectivity of protein atoms or residues and characterizes the geometric compactness of the protein structure. As a consequence, the FRI does not resort to the interaction Hamiltonian and bypasses matrix diagonalization, which underpins most other flexibility analysis methods. FRI's computational complexity is of O

On the existence of global strong solutions to the equations modeling a motion of a rigid body around a viscous fluid

Czech Academy of Sciences Publication Activity Database

Nečasová, Šárka; Wolf, J.

2016-01-01

Roč. 36, č. 3 (2016), s. 1539-1562 ISSN 1078-0947 R&D Projects: GA ČR GA13-00522S Institutional support: RVO:67985840 Keywords : incompressible fluid * motion of rigid body * strong solutions Subject RIV: BA - General Mathematics Impact factor: 1.099, year: 2016 http://www.aimsciences.org/journals/displayArticlesnew.jsp?paperID=11589

Protein characterization of protein bodies from cotyledons of Mucuna pruriens (L.) DC.

Science.gov (United States)

Bellani, Lorenza; Giglioni, Stefania; Muccifora, Simonetta

2013-03-01

Seeds of Mucuna pruriens (L.) DC. (Fabaceae) were analyzed for protein composition of protein bodies isolated from cotyledons. Protein bodies were successfully separated by Lympholyte and those of dry seeds, observed by scanning electron microscope, were elliptical or spherical in shape with a diameter of 5-12 μm. Protein content in dry seed protein bodies was 10.6 mg/g dry weight. Globulin was the largest protein fraction isolated (62.5 %), followed by albumin (18.3 %), glutelin (15.8 %) and prolamin (3.4 %). The prolamin fraction and high glutelin content are uncommon in legumes. SDS-PAGE of albumins, globulins, prolamins and glutelins provided different band numbers and molecular weights under reducing and non reducing conditions and suggested that the albumin fraction is rich in disulphide bonds.

A review of a method for dynamic load distribution, dynamical modeling, and explicit internal force control when two manipulators mutually lift and transport a rigid body object

International Nuclear Information System (INIS)

Unseren, M.A.

1997-01-01

The paper reviews a method for modeling and controlling two serial link manipulators which mutually lift and transport a rigid body object in a three dimensional workspace. A new vector variable is introduced which parameterizes the internal contact force controlled degrees of freedom. A technique for dynamically distributing the payload between the manipulators is suggested which yields a family of solutions for the contact forces and torques the manipulators impart to the object. A set of rigid body kinematic constraints which restrict the values of the joint velocities of both manipulators is derived. A rigid body dynamical model for the closed chain system is first developed in the joint space. The model is obtained by generalizing the previous methods for deriving the model. The joint velocity and acceleration variables in the model are expressed in terms of independent pseudovariables. The pseudospace model is transformed to obtain reduced order equations of motion and a separate set of equations governing the internal components of the contact forces and torques. A theoretic control architecture is suggested which explicitly decouples the two sets of equations comprising the model. The controller enables the designer to develop independent, non-interacting control laws for the position control and internal force control of the system

A review of a method for dynamic load distribution, dynamical modeling, and explicit internal force control when two manipulators mutually lift and transport a rigid body object

Energy Technology Data Exchange (ETDEWEB)

Unseren, M.A.

1997-04-20

The paper reviews a method for modeling and controlling two serial link manipulators which mutually lift and transport a rigid body object in a three dimensional workspace. A new vector variable is introduced which parameterizes the internal contact force controlled degrees of freedom. A technique for dynamically distributing the payload between the manipulators is suggested which yields a family of solutions for the contact forces and torques the manipulators impart to the object. A set of rigid body kinematic constraints which restrict the values of the joint velocities of both manipulators is derived. A rigid body dynamical model for the closed chain system is first developed in the joint space. The model is obtained by generalizing the previous methods for deriving the model. The joint velocity and acceleration variables in the model are expressed in terms of independent pseudovariables. The pseudospace model is transformed to obtain reduced order equations of motion and a separate set of equations governing the internal components of the contact forces and torques. A theoretic control architecture is suggested which explicitly decouples the two sets of equations comprising the model. The controller enables the designer to develop independent, non-interacting control laws for the position control and internal force control of the system.

CNA web server: rigidity theory-based thermal unfolding simulations of proteins for linking structure, (thermo-)stability, and function.

Science.gov (United States)

Krüger, Dennis M; Rathi, Prakash Chandra; Pfleger, Christopher; Gohlke, Holger

2013-07-01

The Constraint Network Analysis (CNA) web server provides a user-friendly interface to the CNA approach developed in our laboratory for linking results from rigidity analyses to biologically relevant characteristics of a biomolecular structure. The CNA web server provides a refined modeling of thermal unfolding simulations that considers the temperature dependence of hydrophobic tethers and computes a set of global and local indices for quantifying biomacromolecular stability. From the global indices, phase transition points are identified where the structure switches from a rigid to a floppy state; these phase transition points can be related to a protein's (thermo-)stability. Structural weak spots (unfolding nuclei) are automatically identified, too; this knowledge can be exploited in data-driven protein engineering. The local indices are useful in linking flexibility and function and to understand the impact of ligand binding on protein flexibility. The CNA web server robustly handles small-molecule ligands in general. To overcome issues of sensitivity with respect to the input structure, the CNA web server allows performing two ensemble-based variants of thermal unfolding simulations. The web server output is provided as raw data, plots and/or Jmol representations. The CNA web server, accessible at http://cpclab.uni-duesseldorf.de/cna or http://www.cnanalysis.de, is free and open to all users with no login requirement.

Thermostability in rubredoxin and its relationship to mechanical rigidity

Science.gov (United States)

Rader, A. J.

2010-03-01

The source of increased stability in proteins from organisms that thrive in extreme thermal environments is not well understood. Previous experimental and theoretical studies have suggested many different features possibly responsible for such thermostability. Many of these thermostabilizing mechanisms can be accounted for in terms of structural rigidity. Thus a plausible hypothesis accounting for this remarkable stability in thermophilic enzymes states that these enzymes have enhanced conformational rigidity at temperatures below their native, functioning temperature. Experimental evidence exists to both support and contradict this supposition. We computationally investigate the relationship between thermostability and rigidity using rubredoxin as a case study. The mechanical rigidity is calculated using atomic models of homologous rubredoxin structures from the hyperthermophile Pyrococcus furiosus and mesophile Clostridium pasteurianum using the FIRST software. A global increase in structural rigidity (equivalently a decrease in flexibility) corresponds to an increase in thermostability. Locally, rigidity differences (between mesophilic and thermophilic structures) agree with differences in protection factors.

Thermostability in rubredoxin and its relationship to mechanical rigidity

International Nuclear Information System (INIS)

Rader, A J

2010-01-01

The source of increased stability in proteins from organisms that thrive in extreme thermal environments is not well understood. Previous experimental and theoretical studies have suggested many different features possibly responsible for such thermostability. Many of these thermostabilizing mechanisms can be accounted for in terms of structural rigidity. Thus a plausible hypothesis accounting for this remarkable stability in thermophilic enzymes states that these enzymes have enhanced conformational rigidity at temperatures below their native, functioning temperature. Experimental evidence exists to both support and contradict this supposition. We computationally investigate the relationship between thermostability and rigidity using rubredoxin as a case study. The mechanical rigidity is calculated using atomic models of homologous rubredoxin structures from the hyperthermophile Pyrococcus furiosus and mesophile Clostridium pasteurianum using the FIRST software. A global increase in structural rigidity (equivalently a decrease in flexibility) corresponds to an increase in thermostability. Locally, rigidity differences (between mesophilic and thermophilic structures) agree with differences in protection factors

In vitro folding of inclusion body proteins.

Science.gov (United States)

Rudolph, R; Lilie, H

1996-01-01

Insoluble, inactive inclusion bodies are frequently formed upon recombinant protein production in transformed microorganisms. These inclusion bodies, which contain the recombinant protein in an highly enriched form, can be isolated by solid/liquid separation. After solubilization, native proteins can be generated from the inactive material by using in vitro folding techniques. New folding procedures have been developed for efficient in vitro reconstitution of complex hydrophobic, multidomain, oligomeric, or highly disulfide-bonded proteins. These protocols take into account process parameters such as protein concentration, catalysis of disulfide bond formation, temperature, pH, and ionic strength, as well as specific solvent ingredients that reduce unproductive side reactions. Modification of the protein sequence has been exploited to improve in vitro folding.

Inadequacy of Body Weight-Based Recommendations for Individual Protein Intake-Lessons from Body Composition Analysis.

Science.gov (United States)

Geisler, Corinna; Prado, Carla M; Müller, Manfred J

2016-12-31

Current body weight-based protein recommendations are ignoring the large variability in body composition, particularly lean mass (LM), which drives protein requirements. We explored and highlighted the inter-individual variability of weight versus body composition-adjusted protein intakes by secondary analysis in three cohorts of (1) 574 healthy adults (mean ± SD age: 41.4 ± 15.2 years); (2) 403 cirrhotic patients (age: 44.7 ± 12.3 years) and (3) 547 patients with lung cancer (age: 61.3 ± 8.2 years). LM was assessed using different devices (magnetic resonance imaging, dual-energy X-ray absorptiometry, computer tomography, total body potassium and bioelectrical impedance), body weight-based protein intake, its ratio (per kg LM) and mean protein requirement were calculated. Variability in protein intake in all cohorts ranged from 0.83 to 1.77 g protein per kg LM per day using (theoretical protein intake of 60 g protein per day). Calculated mean protein requirement was 1.63 g protein per kg LM per day; consequently, 95.3% of healthy subjects, 100% of cirrhotic and 97.4% of cancer patients would present with a low protein intake per kg LM. Weight-adjusted recommendations are inadequate to address the LM specific differences in protein needs of healthy subjects or clinical populations. Absolute protein intake seems to be more relevant compared to the relative proportion of protein, which in turn changes with different energy needs.

Inadequacy of Body Weight-Based Recommendations for Individual Protein Intake—Lessons from Body Composition Analysis

Directory of Open Access Journals (Sweden)

Corinna Geisler

2016-12-01

Full Text Available Current body weight-based protein recommendations are ignoring the large variability in body composition, particularly lean mass (LM, which drives protein requirements. We explored and highlighted the inter-individual variability of weight versus body composition-adjusted protein intakes by secondary analysis in three cohorts of (1 574 healthy adults (mean ± SD age: 41.4 ± 15.2 years; (2 403 cirrhotic patients (age: 44.7 ± 12.3 years and (3 547 patients with lung cancer (age: 61.3 ± 8.2 years. LM was assessed using different devices (magnetic resonance imaging, dual-energy X-ray absorptiometry, computer tomography, total body potassium and bioelectrical impedance, body weight-based protein intake, its ratio (per kg LM and mean protein requirement were calculated. Variability in protein intake in all cohorts ranged from 0.83 to 1.77 g protein per kg LM per day using (theoretical protein intake of 60 g protein per day. Calculated mean protein requirement was 1.63 g protein per kg LM per day; consequently, 95.3% of healthy subjects, 100% of cirrhotic and 97.4% of cancer patients would present with a low protein intake per kg LM. Weight-adjusted recommendations are inadequate to address the LM specific differences in protein needs of healthy subjects or clinical populations. Absolute protein intake seems to be more relevant compared to the relative proportion of protein, which in turn changes with different energy needs.

Stable and rigid DTPA-like paramagnetic tags suitable for in vitro and in situ protein NMR analysis.

Science.gov (United States)

Chen, Jia-Liang; Zhao, Yu; Gong, Yan-Jun; Pan, Bin-Bin; Wang, Xiao; Su, Xun-Cheng

2018-02-01

Organic synthesis of a ligand with high binding affinities for paramagnetic lanthanide ions is an effective way of generating paramagnetic effects on proteins. These paramagnetic effects manifested in high-resolution NMR spectroscopy are valuable dynamic and structural restraints of proteins and protein-ligand complexes. A paramagnetic tag generally contains a metal chelating moiety and a reactive group for protein modification. Herein we report two new DTPA-like tags, 4PS-PyDTTA and 4PS-6M-PyDTTA that can be site-specifically attached to a protein with a stable thioether bond. Both protein-tag adducts form stable lanthanide complexes, of which the binding affinities and paramagnetic tensors are tunable with respect to the 6-methyl group in pyridine. Paramagnetic relaxation enhancement (PRE) effects of Gd(III) complex on protein-tag adducts were evaluated in comparison with pseudocontact shift (PCS), and the results indicated that both 4PS-PyDTTA and 4PS-6M-PyDTTA tags are rigid and present high-quality PREs that are crucially important in elucidation of the dynamics and interactions of proteins and protein-ligand complexes. We also show that these two tags are suitable for in-situ protein NMR analysis.

Diffuse interface immersed boundary method for multi-fluid flows with arbitrarily moving rigid bodies

Science.gov (United States)

Patel, Jitendra Kumar; Natarajan, Ganesh

2018-05-01

We present an interpolation-free diffuse interface immersed boundary method for multiphase flows with moving bodies. A single fluid formalism using the volume-of-fluid approach is adopted to handle multiple immiscible fluids which are distinguished using the volume fractions, while the rigid bodies are tracked using an analogous volume-of-solid approach that solves for the solid fractions. The solution to the fluid flow equations are carried out using a finite volume-immersed boundary method, with the latter based on a diffuse interface philosophy. In the present work, we assume that the solids are filled with a "virtual" fluid with density and viscosity equal to the largest among all fluids in the domain. The solids are assumed to be rigid and their motion is solved using Newton's second law of motion. The immersed boundary methodology constructs a modified momentum equation that reduces to the Navier-Stokes equations in the fully fluid region and recovers the no-slip boundary condition inside the solids. An implicit incremental fractional-step methodology in conjunction with a novel hybrid staggered/non-staggered approach is employed, wherein a single equation for normal momentum at the cell faces is solved everywhere in the domain, independent of the number of spatial dimensions. The scalars are all solved for at the cell centres, with the transport equations for solid and fluid volume fractions solved using a high-resolution scheme. The pressure is determined everywhere in the domain (including inside the solids) using a variable coefficient Poisson equation. The solution to momentum, pressure, solid and fluid volume fraction equations everywhere in the domain circumvents the issue of pressure and velocity interpolation, which is a source of spurious oscillations in sharp interface immersed boundary methods. A well-balanced algorithm with consistent mass/momentum transport ensures robust simulations of high density ratio flows with strong body forces. The

Luminescent conjugated oligothiophenes for sensitive fluorescent assignment of protein inclusion bodies.

Science.gov (United States)

Klingstedt, Therése; Blechschmidt, Cristiane; Nogalska, Anna; Prokop, Stefan; Häggqvist, Bo; Danielsson, Olof; Engel, W King; Askanas, Valerie; Heppner, Frank L; Nilsson, K Peter R

2013-03-18

Small hydrophobic ligands identifying intracellular protein deposits are of great interest, as protein inclusion bodies are the pathological hallmark of several degenerative diseases. Here we report that fluorescent amyloid ligands, termed luminescent conjugated oligothiophenes (LCOs), rapidly and with high sensitivity detect protein inclusion bodies in skeletal muscle tissue from patients with sporadic inclusion body myositis (s-IBM). LCOs having a conjugated backbone of at least five thiophene units emitted strong fluorescence upon binding, and showed co-localization with proteins reported to accumulate in s-IBM protein inclusion bodies. Compared with conventional amyloid ligands, LCOs identified a larger fraction of immunopositive inclusion bodies. When the conjugated thiophene backbone was extended with terminal carboxyl groups, the LCO revealed striking spectral differences between distinct protein inclusion bodies. We conclude that 1) LCOs are sensitive, rapid and powerful tools for identifying protein inclusion bodies and 2) LCOs identify a wider range of protein inclusion bodies than conventional amyloid ligands. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A navigator-based rigid body motion correction for magnetic resonance imaging

International Nuclear Information System (INIS)

Ullisch, Marcus Goerge

2012-01-01

A novel three-dimensional navigator k-space trajectory for rigid body motion detection for Magnetic Resonance Imaging (MRI) - the Lissajous navigator - was developed and quantitatively compared to the existing spherical navigator trajectory [1]. The spherical navigator cannot sample the complete spherical surface due to slew rate limitations of the scanner hardware. By utilizing a two dimensional Lissajous figure which is projected onto the spherical surface, the Lissajous navigator overcomes this limitation. The complete sampling of the sphere consequently leads to rotation estimates with higher and more isotropic accuracy. Simulations and phantom measurements were performed for both navigators. Both simulations and measurements show a significantly higher overall accuracy of the Lissajous navigator and a higher isotropy of the rotation estimates. Measured under identical conditions with identical postprocessing, the measured mean absolute error of the rotation estimates for the Lissajous navigator was 38% lower (0.3 ) than for the spherical navigator (0.5 ). The maximum error of the Lissajous navigator was reduced by 48% relative to the spherical navigator. The Lissajous navigator delivers higher accuracy of rotation estimation and a higher degree of isotropy than the spherical navigator with no evident drawbacks; these are two decisive advantages, especially for high-resolution anatomical imaging.

A navigator-based rigid body motion correction for magnetic resonance imaging

Energy Technology Data Exchange (ETDEWEB)

Ullisch, Marcus Goerge

2012-01-24

A novel three-dimensional navigator k-space trajectory for rigid body motion detection for Magnetic Resonance Imaging (MRI) - the Lissajous navigator - was developed and quantitatively compared to the existing spherical navigator trajectory [1]. The spherical navigator cannot sample the complete spherical surface due to slew rate limitations of the scanner hardware. By utilizing a two dimensional Lissajous figure which is projected onto the spherical surface, the Lissajous navigator overcomes this limitation. The complete sampling of the sphere consequently leads to rotation estimates with higher and more isotropic accuracy. Simulations and phantom measurements were performed for both navigators. Both simulations and measurements show a significantly higher overall accuracy of the Lissajous navigator and a higher isotropy of the rotation estimates. Measured under identical conditions with identical postprocessing, the measured mean absolute error of the rotation estimates for the Lissajous navigator was 38% lower (0.3 ) than for the spherical navigator (0.5 ). The maximum error of the Lissajous navigator was reduced by 48% relative to the spherical navigator. The Lissajous navigator delivers higher accuracy of rotation estimation and a higher degree of isotropy than the spherical navigator with no evident drawbacks; these are two decisive advantages, especially for high-resolution anatomical imaging.

[In vitro renaturation of proteins from inclusion bodies].

Science.gov (United States)

Porowińska, Dorota; Marszałek, Ewelina; Wardęcka, Paulina; Komoszyński, Michał

2012-06-11

Recombinant proteins and enzymes are commonly used in many areas of our life, such as diagnostics, industry and medicine, due to heterologous synthesis in prokaryotic expression systems. However, a high expression level of foreign protein in bacteria cells results in formation of inactive and insoluble aggregates--inclusion bodies. Reactivation of aggregated proteins is a complex and time-consuming process. Every protein requires experimental optimization of the process conditions. The choice of the refolding method depends on the type of recombinant protein and its physical, chemical and biological properties. Recovery of the activity of proteins accumulated in inclusion bodies can be divided into 4 steps: 1) inclusion bodies isolation, 2) solubilization of aggregates, 3) renaturation, 4) purification of catalytically active molecules. Efficiency of the refolding process depends on many physical factors and chemical and biological agents. The above parameters determine the time of the folding and prevent protein aggregation. They also assist the folding and have an influence on the solubility and stability of native molecules. To date, dilution, dialysis and chromatography are the most often used methods for protein refolding.

A virtual pebble game to ensemble average graph rigidity.

Science.gov (United States)

González, Luis C; Wang, Hui; Livesay, Dennis R; Jacobs, Donald J

2015-01-01

The body-bar Pebble Game (PG) algorithm is commonly used to calculate network rigidity properties in proteins and polymeric materials. To account for fluctuating interactions such as hydrogen bonds, an ensemble of constraint topologies are sampled, and average network properties are obtained by averaging PG characterizations. At a simpler level of sophistication, Maxwell constraint counting (MCC) provides a rigorous lower bound for the number of internal degrees of freedom (DOF) within a body-bar network, and it is commonly employed to test if a molecular structure is globally under-constrained or over-constrained. MCC is a mean field approximation (MFA) that ignores spatial fluctuations of distance constraints by replacing the actual molecular structure by an effective medium that has distance constraints globally distributed with perfect uniform density. The Virtual Pebble Game (VPG) algorithm is a MFA that retains spatial inhomogeneity in the density of constraints on all length scales. Network fluctuations due to distance constraints that may be present or absent based on binary random dynamic variables are suppressed by replacing all possible constraint topology realizations with the probabilities that distance constraints are present. The VPG algorithm is isomorphic to the PG algorithm, where integers for counting "pebbles" placed on vertices or edges in the PG map to real numbers representing the probability to find a pebble. In the VPG, edges are assigned pebble capacities, and pebble movements become a continuous flow of probability within the network. Comparisons between the VPG and average PG results over a test set of proteins and disordered lattices demonstrate the VPG quantitatively estimates the ensemble average PG results well. The VPG performs about 20% faster than one PG, and it provides a pragmatic alternative to averaging PG rigidity characteristics over an ensemble of constraint topologies. The utility of the VPG falls in between the most

Estimating the angular velocity of a rigid body moving in the plane from tangential and centripetal acceleration measurements

International Nuclear Information System (INIS)

Cardou, Philippe; Angeles, Jorge

2008-01-01

Two methods are available for the estimation of the angular velocity of a rigid body from point-acceleration measurements: (i) the time-integration of the angular acceleration and (ii) the square-rooting of the centripetal acceleration. The inaccuracy of the first method is due mainly to the accumulation of the error on the angular acceleration throughout the time-integration process, which does not prevent that it be used successfully in crash tests with dummies, since these experiments never last more than one second. On the other hand, the error resulting from the second method is stable through time, but becomes inaccurate whenever the rigid body angular velocity approaches zero, which occurs in many applications. In order to take advantage of the complementarity of these two methods, a fusion of their estimates is proposed. To this end, the accelerometer measurements are modeled as exact signals contaminated with bias errors and Gaussian white noise. The relations between the variables at stake are written in the form of a nonlinear state-space system in which the angular velocity and the angular acceleration are state variables. Consequently, a minimum-variance-error estimate of the state vector is obtained by means of extended Kalman filtering. The performance of the proposed estimation method is assessed by means of simulation. Apparently, the resulting estimation method is more robust than the existing accelerometer-only methods and competitive with gyroscope measurements. Moreover, it allows the identification and the compensation of any bias error in the accelerometer measurements, which is a significant advantage over gyroscopes

Homogenized rigid body and spring-mass (HRBSM) model for the pushover analysis of out-of-plane loaded unreinforced and FRP reinforced walls

Science.gov (United States)

Bertolesi, Elisa; Milani, Gabriele

2017-07-01

The present paper is devoted to the discussion of a series of unreinforced and FRP retrofitted panels analyzed adopting the Rigid Body and Spring-Mass (HRBSM) model developed by the authors. To this scope, a total of four out of plane loaded masonry walls tested up to failure are considered. At a structural level, the non-linear analyses are conducted replacing the homogenized orthotropic continuum with a rigid element and non-linear spring assemblage by means of which out of plane mechanisms are allowed. FRP retrofitting is modeled adopting two noded truss elements whose mechanical properties are selected in order to describe possible debonding phenomenon or tensile rupture of the strengthening. The outcome provided numerically are compared to the experimental results showing a satisfactory agreement in terms of global pressure-deflection curves and failure mechanisms.

A review of a method for dynamic load distribution, dynamic modeling, and explicit internal force control when two serial link manipulators mutually lift and transport a rigid body object

International Nuclear Information System (INIS)

Unseren, M.A.

1997-09-01

The report reviews a method for modeling and controlling two serial link manipulators which mutually lift and transport a rigid body object in a three dimensional workspace. A new vector variable is introduced which parameterizes the internal contact force controlled degrees of freedom. A technique for dynamically distributing the payload between the manipulators is suggested which yields a family of solutions for the contact forces and torques the manipulators impart to the object. A set of rigid body kinematic constraints which restricts the values of the joint velocities of both manipulators is derived. A rigid body dynamical model for the closed chain system is first developed in the joint space. The model is obtained by generalizing the previous methods for deriving the model. The joint velocity and acceleration variables in the model are expressed in terms of independent pseudovariables. The pseudospace model is transformed to obtain reduced order equations of motion and a separate set of equations governing the internal components of the contact forces and torques. A theoretic control architecture is suggested which explicitly decouples the two sets of equations comprising the model. The controller enables the designer to develop independent, non-interacting control laws for the position control and internal force control of the system

A review of a method for dynamic load distribution, dynamic modeling, and explicit internal force control when two serial link manipulators mutually lift and transport a rigid body object

Energy Technology Data Exchange (ETDEWEB)

Unseren, M.A.

1997-09-01

The report reviews a method for modeling and controlling two serial link manipulators which mutually lift and transport a rigid body object in a three dimensional workspace. A new vector variable is introduced which parameterizes the internal contact force controlled degrees of freedom. A technique for dynamically distributing the payload between the manipulators is suggested which yields a family of solutions for the contact forces and torques the manipulators impart to the object. A set of rigid body kinematic constraints which restricts the values of the joint velocities of both manipulators is derived. A rigid body dynamical model for the closed chain system is first developed in the joint space. The model is obtained by generalizing the previous methods for deriving the model. The joint velocity and acceleration variables in the model are expressed in terms of independent pseudovariables. The pseudospace model is transformed to obtain reduced order equations of motion and a separate set of equations governing the internal components of the contact forces and torques. A theoretic control architecture is suggested which explicitly decouples the two sets of equations comprising the model. The controller enables the designer to develop independent, non-interacting control laws for the position control and internal force control of the system.

Turnover of whole body proteins and myofibrillar proteins in middle-aged active men

International Nuclear Information System (INIS)

Zackin, M.; Meredith, C.; Frontera, W.; Evans, W.

1986-01-01

Endurance-trained older men have a higher proportion of lean tissue and greater muscle cell oxidative capacity, reversing age-related trends and suggesting major changes in protein metabolism. In this study, protein turnover was determined in 6 middle-aged (52+/-1 yr) men who were well trained (VO 2 max 55.2+/-5.0 ml O 2 /kg.min) and lean (body fat 18.9+/-2.8%, muscle mass 36.6+/-0.6%). The maintained habitual exercise while consuming 0.6, 0.9 or 1.2 g protein/kg.day for 10-day periods. N flux was measured from 15 N in urea after oral 15 N-glycine administration. Myofibrillar protein breakdown was estimated from urinary 3-methyl-histidine. Dietary protein had no effect on turnover rates, even when N balance was negative. Whole body protein synthesis was 3.60+/-0.12 g/kg.day and breakdown was 3.40+/-0.14 g/kg.day for all N intakes. Whole body protein flux, synthesis and breakdown were similar to values reported for sedentary young (SY) or sedentary old (SO) men on comparable diets. 3-me-his (3.67+/-0.14 μmol/kg.day) was similar to values reported for SY but higher (p<0.01) than for SO. Myofibrillar protein breakdown per unit muscle mass (185+/-7 μmol 3-me-his/g creatinine) was higher (p<0.01) than for SY or SO. In active middle-aged men, myofibrillar proteins may account for a greater proportion of whole body protein turnover, despite an age-related reduction in muscle mass

Nuclear body formation and PML body remodeling by the human cytomegalovirus protein UL35

International Nuclear Information System (INIS)

Salsman, Jayme; Wang Xueqi; Frappier, Lori

2011-01-01

The human cytomegalovirus (HCMV) UL35 gene encodes two proteins, UL35 and UL35a. Expression of UL35 in transfected cells results in the formation of UL35 nuclear bodies that associate with promyelocytic leukemia (PML) protein. PML forms the basis for PML nuclear bodies that are important for suppressing viral lytic gene expression. Given the important relationship between PML and viral infection, we have further investigated the association of UL35 with PML bodies. We demonstrate that UL35 bodies form independently of PML and subsequently recruit PML, Sp100 and Daxx. In contrast, UL35a did not form bodies; however, it could bind UL35 and inhibit the formation of UL35 bodies. The HCMV tegument protein pp71 promoted the formation of UL35 bodies and the cytoplasmic localization of UL35a. Similarly, UL35a shifted pp71 to the cytoplasm. These results indicate that the interplay between UL35, UL35a and pp71 affects their subcellular localization and likely their functions throughout infection.

Rigid-body-spring model numerical analysis of joint performance of engineered cementitious composites and concrete

Science.gov (United States)

Khmurovska, Y.; Štemberk, P.; Křístek, V.

2017-09-01

This paper presents a numerical investigation of effectiveness of using engineered cementitious composites with polyvinyl alcohol fibers for concrete cover layer repair. A numerical model of a monolithic concaved L-shaped concrete structural detail which is strengthened with an engineered cementitious composite layer with polyvinyl alcohol fibers is created and loaded with bending moment. The numerical analysis employs nonlinear 3-D Rigid-Body-Spring Model. The proposed material model shows reliable results and can be used in further studies. The engineered cementitious composite shows extremely good performance in tension due to the strain-hardening effect. Since durability of the bond can be decreased significantly by its degradation due to the thermal loading, this effect should be also taken into account in the future work, as well as the experimental investigation, which should be performed for validation of the proposed numerical model.

Knowledge-in-action: a study on the integration of forces and energy in a rigid body

Directory of Open Access Journals (Sweden)

Consuelo Escudero

2009-03-01

Full Text Available This paper intends to go on with the study of problem solving in a compatible way with the theories of conceptual fields (TCC of Vergnaud (1990,1994,1998 and mental models of Johnson-Laird (1983,1990. Together with findings of another study (Escudero & Jaime 2007, some achievements and difficulties of freshmore engineering students when solving problems of the motion of rigid body in terms of the knowledge-in-action are analysed. The research methodology under a qualitative paradigm grouped data into categories which are not provided a priori by the theoretical framework. It can be said that the quality of the conceptual representation has been explicit in the quality of the proposed solution. Some meanings introduced by students in their problem solving activities can be characterized as operational invariants.

Prolonged bed rest decreases skeletal muscle and whole body protein synthesis

Science.gov (United States)

Ferrando, A. A.; Lane, H. W.; Stuart, C. A.; Davis-Street, J.; Wolfe, R. R.

1996-01-01

We sought to determine the extent to which the loss of lean body mass and nitrogen during inactivity was due to alterations in skeletal muscle protein metabolism. Six male subjects were studied during 7 days of diet stabilization and after 14 days of stimulated microgravity (-6 degrees bed rest). Nitrogen balance became more negative (P protein synthesis (PS; P protein also decreased by 46% (P protein breakdown and inward transport. Whole body protein synthesis determined by [15N]alanine ingestion on six subjects also revealed a 14% decrease (P protein breakdown change significantly. These results indicate that the loss of body protein with inactivity is predominantly due to a decrease in muscle PS and that this decrease is reflected in both whole body and skeletal muscle measures.

Refolding techniques for recovering biologically active recombinant proteins from inclusion bodies.

Science.gov (United States)

Yamaguchi, Hiroshi; Miyazaki, Masaya

2014-02-20

Biologically active proteins are useful for studying the biological functions of genes and for the development of therapeutic drugs and biomaterials in a biotechnology industry. Overexpression of recombinant proteins in bacteria, such as Escherichia coli, often results in the formation of inclusion bodies, which are protein aggregates with non-native conformations. As inclusion bodies contain relatively pure and intact proteins, protein refolding is an important process to obtain active recombinant proteins from inclusion bodies. However, conventional refolding methods, such as dialysis and dilution, are time consuming and, often, recovered yields of active proteins are low, and a trial-and-error process is required to achieve success. Recently, several approaches have been reported to refold these aggregated proteins into an active form. The strategies largely aim at reducing protein aggregation during the refolding procedure. This review focuses on protein refolding techniques using chemical additives and laminar flow in microfluidic chips for the efficient recovery of active proteins from inclusion bodies.

Refolding Techniques for Recovering Biologically Active Recombinant Proteins from Inclusion Bodies

Directory of Open Access Journals (Sweden)

Hiroshi Yamaguchi

2014-02-01

Full Text Available Biologically active proteins are useful for studying the biological functions of genes and for the development of therapeutic drugs and biomaterials in a biotechnology industry. Overexpression of recombinant proteins in bacteria, such as Escherichia coli, often results in the formation of inclusion bodies, which are protein aggregates with non-native conformations. As inclusion bodies contain relatively pure and intact proteins, protein refolding is an important process to obtain active recombinant proteins from inclusion bodies. However, conventional refolding methods, such as dialysis and dilution, are time consuming and, often, recovered yields of active proteins are low, and a trial-and-error process is required to achieve success. Recently, several approaches have been reported to refold these aggregated proteins into an active form. The strategies largely aim at reducing protein aggregation during the refolding procedure. This review focuses on protein refolding techniques using chemical additives and laminar flow in microfluidic chips for the efficient recovery of active proteins from inclusion bodies.

Purification and protein composition of oil bodies from Brassica napus seeds

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Jolivet Pascale

2006-11-01

Full Text Available Seed oil bodies are intracellular particles to store lipids as food reserves in oleaginous plants. Description of oil body-associated proteins of Arabidopsis thaliana has been recently reported whereas only few data are available in the case of rapeseed. Oil bodies have been prepared from two double-low varieties of Brassica napus seeds, a standard variety (Explus and an oleic variety (Cabriolet. Oil bodies have been purified using floatation technique in the successive presence of high salt concentration, detergent or urea in order to remove non-specifically trapped proteins. The integrity of the oil bodies has been verified and their size estimated. Their protein and fatty acid contents have been determined. The proteins composing these organelles were extracted, separated by denaturing gel electrophoresis, digested by trypsin and their peptides were subsequently analyzed by liquid chromatography-tandem mass spectrometry. Protein identification was performed using Arabidopsis thaliana protein sequence database and a collection of Expressed Sequence Tag (EST of Brassica napus generated from the framework of the French plant genomics programme “Genoplante”. This led to the identification of a limited number of proteins: eight oleosins showing a high similarity each other and representing up to 75% of oil body proteins, a 11 β hydroxysteroid dehydrogenase-like protein highly homologous to the same protein from A. thaliana, and only few contaminating proteins associated with myrosinase activity.

ANALYTIC EVALUATION OF RECTILINEARITY OF LOW RIGIDITY SHAFT DURING HARDENING PROCESS

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Antoni Świć

2013-03-01

Full Text Available The essential influence of the unevenness of temperature distribution while heating in the technological process on dimensions stability of low rigidity elements was shown. The new approach was applied to formulate mathematical models, which describe the elastic and inelastic behaviour of piece using transfer functions and block diagrams, allowing to use frequency method for evaluation of the behaviour of dynamic semi-finished element as the rigid body.

Protein recovery from inclusion bodies of Escherichia coli using mild solubilization process.

Science.gov (United States)

Singh, Anupam; Upadhyay, Vaibhav; Upadhyay, Arun Kumar; Singh, Surinder Mohan; Panda, Amulya Kumar

2015-03-25

Formation of inclusion bodies in bacterial hosts poses a major challenge for large scale recovery of bioactive proteins. The process of obtaining bioactive protein from inclusion bodies is labor intensive and the yields of recombinant protein are often low. Here we review the developments in the field that are targeted at improving the yield, as well as quality of the recombinant protein by optimizing the individual steps of the process, especially solubilization of the inclusion bodies and refolding of the solubilized protein. Mild solubilization methods have been discussed which are based on the understanding of the fact that protein molecules in inclusion body aggregates have native-like structure. These methods solubilize the inclusion body aggregates while preserving the native-like protein structure. Subsequent protein refolding and purification results in high recovery of bioactive protein. Other parameters which influence the overall recovery of bioactive protein from inclusion bodies have also been discussed. A schematic model describing the utility of mild solubilization methods for high throughput recovery of bioactive protein has also been presented.

Oil bodies and their associated proteins, oleosin and caleosin

DEFF Research Database (Denmark)

Frandsen, Gitte I.; Mundy, John; Tzen, Jason T. C.

2001-01-01

Oil bodies are lipid storage organelles which have been analyzed biochemically due to the economic importance of oil seeds. Although oil bodies are structurally simple, the mechanisms involved in their formation and degradation remain controversial. At present, only two proteins associated with oil....... (1999) Plant Cell Physiol 40: 1079-1086; Naested et al. (2000) Plant Mol Biol 44: 463-476]. Caleosin and caleosin-like proteins are not unique to oil bodies and are associated with an endoplasmatic reticulum subdomain in some cell types. Here we review the synthesis and degradation of oil bodies...

Dynamics of body protein deposition and changes in body composition after sudden changes in amino acid intake: I. Barrows.

Science.gov (United States)

Martínez-Ramírez, H R; Jeaurond, E A; de Lange, C F M

2008-09-01

A study was conducted to evaluate the extent and dynamics of whole body protein deposition and changes in chemical and physical body composition after a period of AA intake restriction in growing barrows with medium lean tissue growth potentials. Forty Yorkshire barrows (initial BW 14.4 +/- 1.6 kg) were scale-fed at 75% of estimated voluntary daily DE intake up to 35 kg of BW and assigned to 1 of 2 diets: AA adequate (AA+; 20% above requirements; NRC, 1998) and AA deficient (AA-; 40% below requirements; restriction phase). Thereafter (re-alimentation phase), pigs from both dietary AA levels were scale-fed or fed ad libitum diets that were not limiting in AA. Body weight gain and body composition, based on serial slaughter, were monitored during the 34-d re-alimentation phase. During the restriction phase AA intake restriction reduced BW gains (556 vs. 410 g/d; P alimentation phase (P > 0.10). Throughout the re-alimentation phase, there were no interactive effects of time, feeding level, and previous AA intake level on growth performance, body protein, and body lipid content (P > 0.10). During the re-alimentation phase, body protein deposition, derived from the linear regression analysis of body protein content vs. time, was not affected by feeding level and previous AA intake level (P > 0.10; 156 g/d for AA- vs. 157 g/d for AA+). Based on BW and body protein content, it can be concluded that no compensatory body protein deposition occurred in barrows, with medium lean tissue growth potential after AA intake restriction between 15 and 35 kg of BW. It is suggested that the upper limit to body protein deposition was the main factor that limited the extent of compensatory body protein deposition in this population of pigs. The concept of an upper limit to body protein deposition may be used to explain why compensatory growth is observed in some studies and not in others.

DNA looping by FokI: the impact of twisting and bending rigidity on protein-induced looping dynamics

Science.gov (United States)

Laurens, Niels; Rusling, David A.; Pernstich, Christian; Brouwer, Ineke; Halford, Stephen E.; Wuite, Gijs J. L.

2012-01-01

Protein-induced DNA looping is crucial for many genetic processes such as transcription, gene regulation and DNA replication. Here, we use tethered-particle motion to examine the impact of DNA bending and twisting rigidity on loop capture and release, using the restriction endonuclease FokI as a test system. To cleave DNA efficiently, FokI bridges two copies of an asymmetric sequence, invariably aligning the sites in parallel. On account of the fixed alignment, the topology of the DNA loop is set by the orientation of the sites along the DNA. We show that both the separation of the FokI sites and their orientation, altering, respectively, the twisting and the bending of the DNA needed to juxtapose the sites, have profound effects on the dynamics of the looping interaction. Surprisingly, the presence of a nick within the loop does not affect the observed rigidity of the DNA. In contrast, the introduction of a 4-nt gap fully relaxes all of the torque present in the system but does not necessarily enhance loop stability. FokI therefore employs torque to stabilise its DNA-looping interaction by acting as a ‘torsional’ catch bond. PMID:22373924

Structure and Composition of Protein Bodies from Wild-Type and High-Lysine Barley Endosperm

DEFF Research Database (Denmark)

Ingversen, J.

1975-01-01

Protein bodies were isolated from 13 and 28 day old endosperms of barley mutant 1508 and its wild type, Bomi barley. The fine structure of the isolated protein bodies was determined by electron microscopy, and the proteins present in the preparations characterized by amino-acid analysis and SDS......-polyacrylamidegel electrophoresis. Sections through pellets of isolated protein bodies from both the mutant and the wild type revealed protein body structures corresponding with those observed in sections through the intact starchy endosperms. The majority of the wild-type protein bodies was homogeneous spheres accompanied...... that the wild-type protein bodies contained large amounts of prolamines (the storage protein group which is soluble in 55 % isopropanol) and some glutelins (the storage proteins soluble in dilute alkali), whereas the mutant protein bodies have glutelin as the major component and little prolamines...

Understanding geological processes: Visualization of rigid and non-rigid transformations

Science.gov (United States)

Shipley, T. F.; Atit, K.; Manduca, C. A.; Ormand, C. J.; Resnick, I.; Tikoff, B.

2012-12-01

Visualizations are used in the geological sciences to support reasoning about structures and events. Research in cognitive sciences offers insights into the range of skills of different users, and ultimately how visualizations might support different users. To understand the range of skills needed to reason about earth processes we have developed a program of research that is grounded in the geosciences' careful description of the spatial and spatiotemporal patterns associated with earth processes. In particular, we are pursuing a research program that identifies specific spatial skills and investigates whether and how they are related to each other. For this study, we focus on a specific question: Is there an important distinction in the geosciences between rigid and non-rigid deformation? To study a general spatial thinking skill we employed displays with non-geological objects that had been altered by rigid change (rotation), and two types of non-rigid change ("brittle" (or discontinuous) and "ductile" (or continuous) deformation). Disciplinary scientists (geosciences and chemistry faculty), and novices (non-science faculty and undergraduate psychology students) answered questions that required them to visualize the appearance of the object before the change. In one study, geologists and chemists were found to be superior to non-science faculty in reasoning about rigid rotations (e.g., what an object would look like from a different perspective). Geologists were superior to chemists in reasoning about brittle deformations (e.g., what an object looked like before it was broken - here the object was a word cut into many fragments displaced in different directions). This finding is consistent with two hypotheses: 1) Experts are good at visualizing the types of changes required for their domain; and 2) Visualization of rigid and non-rigid changes are not the same skill. An additional important finding is that there was a broad range of skill in both rigid and non-rigid

Modeling meniscus rise in capillary tubes using fluid in rigid-body motion approach

Science.gov (United States)

Hamdan, Mohammad O.; Abu-Nabah, Bassam A.

2018-04-01

In this study, a new term representing net flux rate of linear momentum is introduced to Lucas-Washburn equation. Following a fluid in rigid-body motion in modeling the meniscus rise in vertical capillary tubes transforms the nonlinear Lucas-Washburn equation to a linear mass-spring-damper system. The linear nature of mass-spring-damper system with constant coefficients offers a nondimensional analytical solution where meniscus dynamics are dictated by two parameters, namely the system damping ratio and its natural frequency. This connects the numerous fluid-surface interaction physical and geometrical properties to rather two nondimensional parameters, which capture the underlying physics of meniscus dynamics in three distinct cases, namely overdamped, critically damped, and underdamped systems. Based on experimental data available in the literature and the understanding meniscus dynamics, the proposed model brings a new approach of understanding the system initial conditions. Accordingly, a closed form relation is produced for the imbibition velocity, which equals half of the Bosanquet velocity divided by the damping ratio. The proposed general analytical model is ideal for overdamped and critically damped systems. While for underdamped systems, the solution shows fair agreement with experimental measurements once the effective viscosity is determined. Moreover, the presented model shows meniscus oscillations around equilibrium height occur if the damping ratio is less than one.

A 3D, fully Eulerian, VOF-based solver to study the interaction between two fluids and moving rigid bodies using the fictitious domain method

Science.gov (United States)

Pathak, Ashish; Raessi, Mehdi

2016-04-01

We present a three-dimensional (3D) and fully Eulerian approach to capturing the interaction between two fluids and moving rigid structures by using the fictitious domain and volume-of-fluid (VOF) methods. The solid bodies can have arbitrarily complex geometry and can pierce the fluid-fluid interface, forming contact lines. The three-phase interfaces are resolved and reconstructed by using a VOF-based methodology. Then, a consistent scheme is employed for transporting mass and momentum, allowing for simulations of three-phase flows of large density ratios. The Eulerian approach significantly simplifies numerical resolution of the kinematics of rigid bodies of complex geometry and with six degrees of freedom. The fluid-structure interaction (FSI) is computed using the fictitious domain method. The methodology was developed in a message passing interface (MPI) parallel framework accelerated with graphics processing units (GPUs). The computationally intensive solution of the pressure Poisson equation is ported to GPUs, while the remaining calculations are performed on CPUs. The performance and accuracy of the methodology are assessed using an array of test cases, focusing individually on the flow solver and the FSI in surface-piercing configurations. Finally, an application of the proposed methodology in simulations of the ocean wave energy converters is presented.

Real-time motion compensated patient positioning and non-rigid deformation estimation using 4-D shape priors.

Science.gov (United States)

Wasza, Jakob; Bauer, Sebastian; Hornegger, Joachim

2012-01-01

Over the last years, range imaging (RI) techniques have been proposed for patient positioning and respiration analysis in motion compensation. Yet, current RI based approaches for patient positioning employ rigid-body transformations, thus neglecting free-form deformations induced by respiratory motion. Furthermore, RI based respiration analysis relies on non-rigid registration techniques with run-times of several seconds. In this paper we propose a real-time framework based on RI to perform respiratory motion compensated positioning and non-rigid surface deformation estimation in a joint manner. The core of our method are pre-procedurally obtained 4-D shape priors that drive the intra-procedural alignment of the patient to the reference state, simultaneously yielding a rigid-body table transformation and a free-form deformation accounting for respiratory motion. We show that our method outperforms conventional alignment strategies by a factor of 3.0 and 2.3 in the rotation and translation accuracy, respectively. Using a GPU based implementation, we achieve run-times of 40 ms.

Body Characteristics, Dietary Protein and Body Weight Regulation

DEFF Research Database (Denmark)

Ankarfeldt, Mikkel Zøllner; Ängquist, Lars; Stocks, Tanja

2014-01-01

between greater protein intake and weight gain. In both types of studies the results are based on average weight changes, and show considerable diversity in both directions. This study investigates whether the discrepancy in the evidence could be due to recruitment of overweight and obese individuals...... with greater body mass index and waist circumference were analyzed. Selecting subsets of large-scale observational cohort studies with similar characteristics as participants in clinical trials may reconcile the otherwise conflicting results....

Tidal Evolution of Asteroidal Binaries. Ruled by Viscosity. Ignorant of Rigidity.

Science.gov (United States)

Efroimsky, Michael

2015-10-01

This is a pilot paper serving as a launching pad for study of orbital and spin evolution of binary asteroids. The rate of tidal evolution of asteroidal binaries is defined by the dynamical Love numbers kl divided by quality factors Q. Common in the literature is the (oftentimes illegitimate) approximation of the dynamical Love numbers with their static counterparts. Since the static Love numbers are, approximately, proportional to the inverse rigidity, this renders a popular fallacy that the tidal evolution rate is determined by the product of the rigidity by the quality factor: {k}l/Q\\propto 1/(μ Q). In reality, the dynamical Love numbers depend on the tidal frequency and all rheological parameters of the tidally perturbed body (not just rigidity). We demonstrate that in asteroidal binaries the rigidity of their components plays virtually no role in tidal friction and tidal lagging, and thereby has almost no influence on the intensity of tidal interactions (tidal torques, tidal dissipation, tidally induced changes of the orbit). A key quantity that overwhelmingly determines the tidal evolution is a product of the effective viscosity η by the tidal frequency χ . The functional form of the torque’s dependence on this product depends on who wins in the competition between viscosity and self-gravitation. Hence a quantitative criterion, to distinguish between two regimes. For higher values of η χ , we get {k}l/Q\\propto 1/(η χ ), {while} for lower values we obtain {k}l/Q\\propto η χ . Our study rests on an assumption that asteroids can be treated as Maxwell bodies. Applicable to rigid rocks at low frequencies, this approximation is used here also for rubble piles, due to the lack of a better model. In the future, as we learn more about mechanics of granular mixtures in a weak gravity field, we may have to amend the tidal theory with other rheological parameters, ones that do not show up in the description of viscoelastic bodies. This line of study provides

Protein restriction does not affect body temperature pattern in female mice.

Science.gov (United States)

Kato, Goro A; Shichijo, Hiroki; Takahashi, Toshihiro; Shinohara, Akio; Morita, Tetsuo; Koshimoto, Chihiro

2017-10-30

Daily torpor is a physiological adaptation in mammals and birds characterized by a controlled reduction of metabolic rate and body temperature during the resting phase of circadian rhythms. In laboratory mice, daily torpor is induced by dietary caloric restriction. However, it is not known which nutrients are related to daily torpor expression. To determine whether dietary protein is a key factor in inducing daily torpor in mice, we fed mice a protein-restricted (PR) diet that included only one-quarter of the amount of protein but the same caloric level as a control (C) diet. We assigned six non-pregnant female ICR mice to each group and recorded their body weights and core body temperatures for 4 weeks. Body weights in the C group increased, but those in the PR group remained steady or decreased. Mice in both groups did not show daily torpor, but most mice in a food-restricted group (n=6) supplied with 80% of the calories given to the C group exhibited decreased body weights and frequently displayed daily torpor. This suggests that protein restriction is not a trigger of daily torpor; torpid animals can conserve their internal energy, but torpor may not play a significant role in conserving internal protein. Thus, opportunistic daily torpor in mice may function in energy conservation rather than protein saving.

Dietary protein content affects evolution for body size, body fat and viability in Drosophila melanogaster

DEFF Research Database (Denmark)

Kristensen, Torsten N; Overgaard, Johannes; Loeschcke, Volker

2011-01-01

The ability to use different food sources is likely to be under strong selection if organisms are faced with natural variation in macro-nutrient (protein, carbohydrate and lipid) availabilities. Here, we use experimental evolution to study how variable dietary protein content affects adult body...... composition and developmental success in Drosophila melanogaster. We reared flies on either a standard diet or a protein-enriched diet for 17 generations before testing them on both diet types. Flies from lines selected on protein-rich diet produced phenotypes with higher total body mass and relative lipid...... content when compared with those selected on a standard diet, irrespective of which of the two diets they were tested on. However, selection on protein-rich diet incurred a cost as flies reared on this diet had markedly lower developmental success in terms of egg-to-adult viability on both medium types...

Determining the sub-cellular localization of proteins within Caenorhabditis elegans body wall muscle.

Science.gov (United States)

Meissner, Barbara; Rogalski, Teresa; Viveiros, Ryan; Warner, Adam; Plastino, Lorena; Lorch, Adam; Granger, Laure; Segalat, Laurent; Moerman, Donald G

2011-01-01

Determining the sub-cellular localization of a protein within a cell is often an essential step towards understanding its function. In Caenorhabditis elegans, the relatively large size of the body wall muscle cells and the exquisite organization of their sarcomeres offer an opportunity to identify the precise position of proteins within cell substructures. Our goal in this study is to generate a comprehensive "localizome" for C. elegans body wall muscle by GFP-tagging proteins expressed in muscle and determining their location within the cell. For this project, we focused on proteins that we know are expressed in muscle and are orthologs or at least homologs of human proteins. To date we have analyzed the expression of about 227 GFP-tagged proteins that show localized expression in the body wall muscle of this nematode (e.g. dense bodies, M-lines, myofilaments, mitochondria, cell membrane, nucleus or nucleolus). For most proteins analyzed in this study no prior data on sub-cellular localization was available. In addition to discrete sub-cellular localization we observe overlapping patterns of localization including the presence of a protein in the dense body and the nucleus, or the dense body and the M-lines. In total we discern more than 14 sub-cellular localization patterns within nematode body wall muscle. The localization of this large set of proteins within a muscle cell will serve as an invaluable resource in our investigation of muscle sarcomere assembly and function.

Membrane and inclusion body targeting of lyssavirus matrix proteins.

Science.gov (United States)

Pollin, Reiko; Granzow, Harald; Köllner, Bernd; Conzelmann, Karl-Klaus; Finke, Stefan

2013-02-01

Lyssavirus matrix proteins (M) support virus budding and have accessory functions that may contribute to host cell manipulation and adaptation to specific hosts. Here, we show that rabies virus (RABV) and European Bat Lyssavirus Type 1 (EBLV-1) M proteins differ in targeting and accumulation at cellular membranes. In contrast to RABV M, EBLV-1 M expressed from authentic EBLV-1 or chimeric RABV accumulated at the Golgi apparatus. Chimeric M proteins revealed that Golgi association depends on the integrity of the entire EBLV-1 M protein. Since RABV and EBLV-1 M differ in the use of cellular membranes for particle formation, differential membrane targeting and transport of M might determine the site of virus production. Moreover, both RABV and EBLV-1 M were for the first time detected within the nucleus and in Negri body-like inclusions bodies. Whereas nuclear M may imply hitherto unknown functions of lyssavirus M in host cell manipulation, the presence of M in inclusion bodies may correlate with regulatory functions of M in virus RNA synthesis. The data strongly support a model in which targeting of lyssavirus M proteins to distinctintracellular sites is a key determinant of diverse features in lyssavirus replication, host adaptation and pathogenesis. © 2012 Blackwell Publishing Ltd.

Identification and characterization of a novel Chlamydia trachomatis reticulate body protein

DEFF Research Database (Denmark)

Shaw, Allan C; Larsen, Martin Røssel; Roepstorff, Peter

2002-01-01

The genome of the obligate intracellular bacterium Chlamydia trachomatis comprises 894 genes predicted by computer-based analysis. As part of a large-scale proteome analysis of C. trachomatis, a small abundant protein encoded by a previously unrecognized novel 204-bp open reading frame was identi...... cycle. The protein is rapidly degraded and is only present in reticulate or intermediate bodies, suggesting a possible function in the intracellular stage of C. trachomatis development. We have termed the protein '7-kDa reticulate body protein'....

Induction of protein body formation in plant leaves by elastin-like polypeptide fusions

Directory of Open Access Journals (Sweden)

Joensuu Jussi J

2009-08-01

Full Text Available Abstract Background Elastin-like polypeptides are synthetic biopolymers composed of a repeating pentapeptide 'VPGXG' sequence that are valuable for the simple non-chromatographic purification of recombinant proteins. In addition, elastin-like polypeptide fusions have been shown to enhance the accumulation of a range of different recombinant proteins in plants, thus addressing the major limitation of plant-based expression systems, which is a low production yield. This study's main objectives were to determine the general utility of elastin-like polypeptide protein fusions in various intracellular compartments and to elucidate elastin-like polypeptide's mechanism of action for increasing recombinant protein accumulation in the endoplasmic reticulum of plants. Results The effect of elastin-like polypeptide fusions on the accumulation of green fluorescent protein targeted to the cytoplasm, chloroplasts, apoplast, and endoplasmic reticulum was evaluated. The endoplasmic reticulum was the only intracellular compartment in which an elastin-like polypeptide tag was shown to significantly enhance recombinant protein accumulation. Interestingly, endoplasmic reticulum-targeted elastin-like polypeptide fusions induced the formation of a novel type of protein body, which may be responsible for elastin-like polypeptide's positive effect on recombinant protein accumulation by excluding the heterologous protein from normal physiological turnover. Although expressed in the leaves of plants, these novel protein bodies appeared similar in size and morphology to the prolamin-based protein bodies naturally found in plant seeds. The elastin-like polypeptide-induced protein bodies were highly mobile organelles, exhibiting various dynamic patterns of movement throughout the cells, which were dependent on intact actin microfilaments and a functional actomyosin motility system. Conclusion An endoplasmic reticulum-targeted elastin-like polypeptide fusion approach

The consequences of translational and rotational entropy lost by small molecules on binding to proteins

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Murray, Christopher W.; Verdonk, Marcel L.

2002-10-01

When a small molecule binds to a protein, it loses a significant amount of rigid body translational and rotational entropy. Estimates of the associated energy barrier vary widely in the literature yet accurate estimates are important in the interpretation of results from fragment-based drug discovery techniques. This paper describes an analysis that allows the estimation of the rigid body entropy barrier from the increase in binding affinities that results when two fragments of known affinity and known binding mode are joined together. The paper reviews the relatively rare number of examples where good quality data is available. From the analysis of this data, we estimate that the barrier to binding, due to the loss of rigid-body entropy, is 15-20 kJ/mol, i.e. around 3 orders of magnitude in affinity at 298 K. This large barrier explains why it is comparatively rare to observe multiple fragments binding to non-overlapping adjacent sites in enzymes. The barrier is also consistent with medicinal chemistry experience where small changes in the critical binding regions of ligands are often poorly tolerated by enzymes.

Steady-state structural fluctuation is a predictor of the necessity of pausing-mediated co-translational folding for small proteins.

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Huang, Wenxi; Liu, Wanting; Jin, Jingjie; Xiao, Qilan; Lu, Ruibin; Chen, Wei; Xiong, Sheng; Zhang, Gong

2018-03-25

Translational pausing coordinates protein synthesis and co-translational folding. It is a common factor that facilitates the correct folding of large, multi-domain proteins. For small proteins, pausing sites rarely occurs in the gene body, and the 3'-end pausing sites are only essential for the folding of a fraction of proteins. The determinant of the necessity of the pausings remains obscure. In this study, we demonstrated that the steady-state structural fluctuation is a predictor of the necessity of pausing-mediated co-translational folding for small proteins. Validated by experiments with 5 model proteins, we found that the rigid protein structures do not, while the flexible structures do need 3'-end pausings to fold correctly. Therefore, rational optimization of translational pausing can improve soluble expression of small proteins with flexible structures, but not the rigid ones. The rigidity of the structure can be quantitatively estimated in silico using molecular dynamic simulation. Nevertheless, we also found that the translational pausing optimization increases the fitness of the expression host, and thus benefits the recombinant protein production, independent from the soluble expression. These results shed light on the structural basis of the translational pausing and provided a practical tool for industrial protein fermentation. Copyright © 2017. Published by Elsevier Inc.

Body protein losses estimated by nitrogen balance and potassium-40 counting

International Nuclear Information System (INIS)

Belyea, R.L.; Babbitt, C.L.; Sedgwick, H.T.; Zinn, G.M.

1986-01-01

Body protein losses estimated from N balance were compared with those estimated by 40K counting. Six nonlactating dairy cows were fed an adequate N diet for 7 wk, a low N diet for 9 wk, and a replete N diet for 3 wk. The low N diet contained high cell wall grass hay plus ground corn, starch, and molasses. Soybean meal was added to the low N diet to increase N in the adequate N and replete N diets. Intake was measured daily. Digestibilities, N balance, and body composition (estimated by 40K counting) were determined during each dietary regimen. During low N treatment, hay dry matter intake declined 2 kg/d, and supplement increased about .5 kg/d. Dry matter digestibility was not altered by N treatment. Protein and acid detergent fiber digestibilities decreased from 40 and 36% during adequate N to 20 and 2%, respectively, during low N. Fecal and urinary N also declined when cows were fed the low N diet. By the end of repletion, total intake, fiber, and protein digestibilities as well as N partition were similar to or exceeded those during adequate N intake. Body protein (N) loss was estimated by N balance to be about 3 kg compared with 8 kg by 40K counting. Body fat losses (32 kg) were large because of low energy digestibility and intake. Seven kilograms of body fat were regained during repletion, but there was no change in body protein

Whole-body protein turnover response to short-term high-protein diets during weight loss: a randomized controlled trial

Science.gov (United States)

Objective: Determine whole-body protein turnover responses to high protein diets during weight loss. Design: Thirty-nine adults (age, 21 ± 1 yr; VO2peak, 48 ± 1 ml'kg-1'min-1; body mass index, 25 ± 1 kg•m2) were randomized to diets providing protein at the recommend dietary allowance (RDA), 2X-RD...

Site-specific tagging proteins with a rigid, small and stable transition metal chelator, 8-hydroxyquinoline, for paramagnetic NMR analysis

Energy Technology Data Exchange (ETDEWEB)

Yang, Yin; Huang, Feng [Nankai University, State Key Laboratory of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) (China); Huber, Thomas [Australian National University, Research School of Chemistry (Australia); Su, Xun-Cheng, E-mail: xunchengsu@nankai.edu.cn [Nankai University, State Key Laboratory of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) (China)

2016-02-15

Design of a paramagnetic metal binding motif in a protein is a valuable way for understanding the function, dynamics and interactions of a protein by paramagnetic NMR spectroscopy. Several strategies have been proposed to site-specifically tag proteins with paramagnetic lanthanide ions. Here we report a simple approach of engineering a transition metal binding motif via site-specific labelling of a protein with 2-vinyl-8-hydroxyquinoline (2V-8HQ). The protein-2V-8HQ adduct forms a stable complex with transition metal ions, Mn(II), Co(II), Ni(II), Cu(II) and Zn(II). The paramagnetic effects generated by these transition metal ions were evaluated by NMR spectroscopy. We show that 2V-8HQ is a rigid and stable transition metal binding tag. The coordination of the metal ion can be assisted by protein sidechains. More importantly, tunable paramagnetic tensors are simply obtained in an α-helix that possesses solvent exposed residues in positions i and i + 3, where i is the residue to be mutated to cysteine, i + 3 is Gln or Glu or i − 4 is His. The coordination of a sidechain carboxylate/amide or imidazole to cobalt(II) results in different structural geometries, leading to different paramagnetic tensors as shown by experimental data.

Whey Protein Supplementation Enhances Whole Body Protein Metabolism and Performance Recovery after Resistance Exercise: A Double-Blind Crossover Study.

Science.gov (United States)

West, Daniel W D; Abou Sawan, Sidney; Mazzulla, Michael; Williamson, Eric; Moore, Daniel R

2017-07-11

No study has concurrently measured changes in free-living whole body protein metabolism and exercise performance during recovery from an acute bout of resistance exercise. We aimed to determine if whey protein ingestion enhances whole body net protein balance and recovery of exercise performance during overnight (10 h) and 24 h recovery after whole body resistance exercise in trained men. In a double-blind crossover design, 12 trained men (76 ± 8 kg, 24 ± 4 years old, 14% ± 5% body fat; means ± standard deviation (SD)) performed resistance exercise in the evening prior to consuming either 25 g of whey protein (PRO; MuscleTech 100% Whey) or an energy-matched placebo (CHO) immediately post-exercise (0 h), and again the following morning (~10 h of recovery). A third randomized trial, completed by the same participants, involving no exercise and no supplement served as a rested control trial (Rest). Participants ingested [ 15 N]glycine to determine whole body protein kinetics and net protein balance over 10 and 24 h of recovery. Performance was assessed pre-exercise and at 0, 10, and 24 h of recovery using a battery of tests. Net protein balance tended to improve in PRO ( P = 0.064; effect size (ES) = 0.61, PRO vs. CHO) during overnight recovery. Over 24 h, net balance was enhanced in PRO ( P = 0.036) but not in CHO ( P = 0.84; ES = 0.69, PRO vs. CHO), which was mediated primarily by a reduction in protein breakdown (PRO protein supplementation improved MVC (ES = 0.76), REP (ES = 0.44), and peak power (ES = 0.55). In conclusion, whey protein supplementation enhances whole body anabolism, and may improve acute recovery of exercise performance after a strenuous bout of resistance exercise.

Curvilinear immersed boundary method for simulating fluid structure interaction with complex 3D rigid bodies

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Borazjani, Iman; Ge, Liang; Sotiropoulos, Fotis

2008-08-01

The sharp-interface CURVIB approach of Ge and Sotiropoulos [L. Ge, F. Sotiropoulos, A numerical method for solving the 3D unsteady incompressible Navier-Stokes equations in curvilinear domains with complex immersed boundaries, Journal of Computational Physics 225 (2007) 1782-1809] is extended to simulate fluid structure interaction (FSI) problems involving complex 3D rigid bodies undergoing large structural displacements. The FSI solver adopts the partitioned FSI solution approach and both loose and strong coupling strategies are implemented. The interfaces between immersed bodies and the fluid are discretized with a Lagrangian grid and tracked with an explicit front-tracking approach. An efficient ray-tracing algorithm is developed to quickly identify the relationship between the background grid and the moving bodies. Numerical experiments are carried out for two FSI problems: vortex induced vibration of elastically mounted cylinders and flow through a bileaflet mechanical heart valve at physiologic conditions. For both cases the computed results are in excellent agreement with benchmark simulations and experimental measurements. The numerical experiments suggest that both the properties of the structure (mass, geometry) and the local flow conditions can play an important role in determining the stability of the FSI algorithm. Under certain conditions the FSI algorithm is unconditionally unstable even when strong coupling FSI is employed. For such cases, however, combining the strong coupling iteration with under-relaxation in conjunction with the Aitken's acceleration technique is shown to effectively resolve the stability problems. A theoretical analysis is presented to explain the findings of the numerical experiments. It is shown that the ratio of the added mass to the mass of the structure as well as the sign of the local time rate of change of the force or moment imparted on the structure by the fluid determine the stability and convergence of the FSI

A soft-rigid contact model of MPM for granular flow impact on retaining structures

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Li, Xinpo; Xie, Yanfang; Gutierrez, Marte

2018-02-01

Protective measures against hazards associated with rapid debris avalanches include a variety of retaining structures such as rock/boulder fences, gabions, earthfill barriers and retaining walls. However, the development of analytical and numerical methods for the rational assessment of impact force generated by granular flows is still a challenge. In this work, a soft-rigid contact model is built under the coding framework of MPM which is a hybrid method with Eulerian-Lagrangian description. The soft bodies are discretized into particles (material points), and the rigid bodies are presented by rigid node-based surfaces. Coulomb friction model is used to implement the modeled contact mechanics, and a velocity-dependent friction coefficient is coupled into the model. Simulations of a physical experiment show that the peak and residual value of impact forces are well captured by the MPM model. An idealized scenario of debris avalanche flow down a hillslope and impacting on a retaining wall are analyzed using the MPM model. The calculated forces can provide a quantitative estimate from which mound design could proceed for practical implementation in the field.

Body macronutrient composition is predicted by lipid and not protein content of the diet.

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Moatt, Joshua P; Hambly, Catherine; Heap, Elizabeth; Kramer, Anna; Moon, Fiona; Speakman, John R; Walling, Craig A

2017-12-01

Diet is an important determinant of fitness-related traits including growth, reproduction, and survival. Recent work has suggested that variation in protein:lipid ratio and particularly the amount of protein in the diet is a key nutritional parameter. However, the traits that mediate the link between dietary macronutrient ratio and fitness-related traits are less well understood. An obvious candidate is body composition, given its well-known link to health. Here, we investigate the relationship between dietary and body macronutrient composition using a first-generation laboratory population of a freshwater fish, the three-spine stickleback ( Gasterosteus aculeatus ). Carbohydrate is relatively unimportant in the diet of predatory fish, facilitating the exploration of how dietary protein-to-lipid ratio affects their relative deposition in the body. We find a significant effect of lipid intake, rather than protein, on body protein:lipid ratio. Importantly, this was not a result of absorbing macronutrients in relation to their relative abundance in the diet, as the carcass protein:lipid ratios differed from those of the diets, with ratios usually lower in the body than in the diet. This indicates that individuals can moderate their utilization, or uptake, of ingested macronutrients to reach a target balance within the body. We found no effect of diet on swimming endurance, activity, or testes size. However, there was an effect of weight on testes size, with larger males having larger testes. Our results provide evidence for the adjustment of body protein:lipid ratio away from that of the diet. As dietary lipid intake was the key determinant of body composition, we suggest this occurs via metabolism of excess protein, which conflicts with the predictions of the protein leverage hypothesis. These results could imply that the conversion and excretion of protein is one of the causes of the survival costs associated with high-protein diets.

Effect of alcohol consumption on whole-body protein turnover in healthy adults.

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Wutzke, Klaus D; Krentz, Helga; Bruns, Gerrit

2011-03-01

The aim of the study was to investigate the whole-body protein turnover, either before or after continuous, moderate ethanol-induced oxidative stress by red wine consumption over a relatively short period in healthy volunteers. Ten healthy adults received an individual regular diet over 20 days. After 10 days, the subjects consumed 0.4 ml ethanol kg(-1) day(-1) as red wine together with dinner over a 10-day period. After 8 and 18 days, respectively, a (15)N-labelled yeast protein was administered in a dosage of 4.2 mg kg(-1) body weight. Urine and faeces were collected over 48 h, respectively. The (15)N-enrichment was measured by isotope ratio mass spectrometry, whereas the protein flux rates were calculated by a three-compartment model. The whole-body protein turnover without/with red wine consumption amounted to 3.73±0.6 and 3.49±0.6 g kg(-1) day(-1) (not significant), respectively. Moderate alcohol consumption does not induce significant short-term changes in the whole-body protein turnover of healthy adults.

P-body proteins regulate transcriptional rewiring to promote DNA replication stress resistance.

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Loll-Krippleber, Raphael; Brown, Grant W

2017-09-15

mRNA-processing (P-) bodies are cytoplasmic granules that form in eukaryotic cells in response to numerous stresses to serve as sites of degradation and storage of mRNAs. Functional P-bodies are critical for the DNA replication stress response in yeast, yet the repertoire of P-body targets and the mechanisms by which P-bodies promote replication stress resistance are unknown. In this study we identify the complete complement of mRNA targets of P-bodies during replication stress induced by hydroxyurea treatment. The key P-body protein Lsm1 controls the abundance of HHT1, ACF4, ARL3, TMA16, RRS1 and YOX1 mRNAs to prevent their toxic accumulation during replication stress. Accumulation of YOX1 mRNA causes aberrant downregulation of a network of genes critical for DNA replication stress resistance and leads to toxic acetaldehyde accumulation. Our data reveal the scope and the targets of regulation by P-body proteins during the DNA replication stress response.P-bodies form in response to stress and act as sites of mRNA storage and degradation. Here the authors identify the mRNA targets of P-bodies during DNA replication stress, and show that P-body proteins act to prevent toxic accumulation of these target transcripts.

The effect of protein and glycemic index on children's body composition

DEFF Research Database (Denmark)

Papadaki, Angeliki; Linardakis, Manolis; Larsen, Thomas Meinert

2010-01-01

To investigate the effect of protein and glycemic index (GI) on body composition among European children in the randomized, 6-month dietary intervention DiOGenes (diet, obesity, and genes) family-based study.......To investigate the effect of protein and glycemic index (GI) on body composition among European children in the randomized, 6-month dietary intervention DiOGenes (diet, obesity, and genes) family-based study....

Rigidly foldable origami gadgets and tessellations

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Evans, Thomas A.; Lang, Robert J.; Magleby, Spencer P.; Howell, Larry L.

2015-01-01

Rigidly foldable origami allows for motion where all deflection occurs at the crease lines and facilitates the application of origami in materials other than paper. In this paper, we use a recently discovered method for determining rigid foldability to identify existing flat-foldable rigidly foldable tessellations, which are also categorized. We introduce rigidly foldable origami gadgets which may be used to modify existing tessellations or to create new tessellations. Several modified and new rigidly foldable tessellations are presented. PMID:26473037

Gas-induced friction and diffusion of rigid rotors

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Martinetz, Lukas; Hornberger, Klaus; Stickler, Benjamin A.

2018-05-01

We derive the Boltzmann equation for the rotranslational dynamics of an arbitrary convex rigid body in a rarefied gas. It yields as a limiting case the Fokker-Planck equation accounting for friction, diffusion, and nonconservative drift forces and torques. We provide the rotranslational friction and diffusion tensors for specular and diffuse reflection off particles with spherical, cylindrical, and cuboidal shape, and show that the theory describes thermalization, photophoresis, and the inverse Magnus effect in the free molecular regime.

The proteins of intra-nuclear bodies: a data-driven analysis of sequence, interaction and expression

Directory of Open Access Journals (Sweden)

Bodén Mikael

2010-04-01

Full Text Available Abstract Background Cajal bodies, nucleoli, PML nuclear bodies, and nuclear speckles are morpohologically distinct intra-nuclear structures that dynamically respond to cellular cues. Such nuclear bodies are hypothesized to play important regulatory roles, e.g. by sequestering and releasing transcription factors in a timely manner. While the nucleolus and nuclear speckles have received more attention experimentally, the PML nuclear body and the Cajal body are still incompletely characterized in terms of their roles and protein complement. Results By collating recent experimentally verified data, we find that almost 1000 proteins in the mouse nuclear proteome are known to associate with one or more of the nuclear bodies. Their gene ontology terms highlight their regulatory roles: splicing is confirmed to be a core activity of speckles and PML nuclear bodies house a range of proteins involved in DNA repair. We train support-vector machines to show that nuclear proteins contain discriminative sequence features that can be used to identify their intra-nuclear body associations. Prediction accuracy is highest for nucleoli and nuclear speckles. The trained models are also used to estimate the full protein complement of each nuclear body. Protein interactions are found primarily to link proteins in the nuclear speckles with proteins from other compartments. Cell cycle expression data provide support for increased activity in nucleoli, nuclear speckles and PML nuclear bodies especially during S and G2 phases. Conclusions The large-scale analysis of the mouse nuclear proteome sheds light on the functional organization of physically embodied intra-nuclear compartments. We observe partial support for the hypothesis that the physical organization of the nucleus mirrors functional modularity. However, we are unable to unambiguously identify proteins' intra-nuclear destination, suggesting that critical drivers behind of intra-nuclear translocation are yet to

Resistance training reduces whole-body protein turnover and improves net protein retention in untrained young males.

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Hartman, Joseph W; Moore, Daniel R; Phillips, Stuart M

2006-10-01

It is thought that resistance exercise results in an increased need for dietary protein; however, data also exists to support the opposite conclusion. The purpose of this study was to determine the impact of resistance exercise training on protein metabolism in novices with the hypothesis that resistance training would reduce protein turnover and improve whole-body protein retention. Healthy males (n = 8, 22 +/- 1 y, BMI = 25.3 +/- 1.8 kg.m(-2)) participated in a progressive whole-body split routine resistance-training program 5d/week for 12 weeks. Before (PRE) and after (POST) the training, oral [15N]-glycine ingestion was used to assess nitrogen flux (Q), protein synthesis (PS), protein breakdown (PB), and net protein balance (NPB = PS-PB). Macronutrient intake was controlled over a 5d period PRE and POST, while estimates of protein turnover and urinary nitrogen balance (N(bal) = N(in) - urine N(out)) were conducted. Bench press and leg press increased 40% and 50%, respectively (p training-induced increases in both NPB (PRE = 0.22 +/- 0.13 g.kg(-1).d(-1); POST = 0.54 +/- 0.08 g.kg(-1).d(-1)) and urinary nitrogen balance (PRE = 2.8 +/- 1.7 g N.d(-1); POST = 6.5 +/- 0.9 g N.d(-1)) were observed. A program of resistance training that induced significant muscle hypertrophy resulted in reductions of both whole-body PS and PB, but an improved NPB, which favoured the accretion of skeletal muscle protein. Urinary nitrogen balance increased after training. The reduction in PS and PB and a higher NPB in combination with an increased nitrogen balance after training suggest that dietary requirements for protein in novice resistance-trained athletes are not higher, but lower, after resistance training.

Casein and soya-bean protein have different effects on whole body protein turnover at the same nitrogen balance

DEFF Research Database (Denmark)

Nielsen, K; Kondrup, J; Elsner, Petteri

1994-01-01

was recovered from urinary ammonia and urea during isotope steady state for measurement of protein synthesis and protein degradation. Compared with starvation the protein-free diet decreased N excretion by 75%, probably by increasing the rate of reutilization of amino acids from endogenous proteins for protein......The present study examined whether different proteins have different effects on whole-body protein turnover in adult rats. The rats were either starved, given a protein-free but energy-sufficient diet (1 MJ/kg body weight (BW) per d) or a diet containing intact casein, hydrolysed casein......, or hydrolysed soya-bean protein at a level of 9.1 g/kg BW per d. The diets, which were isoenergetic with the same carbohydrate: fat ratio, were given as a continuous intragastric infusion for at least 4 d. During the last 19 h 15N-glycine (a primed continuous infusion) was given intragastrically and 15N...

Serum protein concentration in low-dose total body irradiation of normal and malnourished rats

International Nuclear Information System (INIS)

Viana, W.C.M.; Lambertz, D.; Borges, E.S.; Neto, A.M.O.; Lambertz, K.M.F.T.; Amaral, A.

2016-01-01

Among the radiotherapeutics' modalities, total body irradiation (TBI) is used as treatment for certain hematological, oncological and immunological diseases. The aim of this study was to evaluate the long-term effects of low-dose TBI on plasma concentration of total protein and albumin using prematurely and undernourished rats as animal model. For this, four groups with 9 animals each were formed: Normal nourished (N); Malnourished (M); Irradiated Normal nourished (IN); Irradiated Malnourished (IM). At the age of 28 days, rats of the IN and IM groups underwent total body gamma irradiation with a source of cobalt-60. Total protein and Albumin in the blood serum was quantified by colorimetry. This research indicates that procedures involving low-dose total body irradiation in children have repercussions in the reduction in body-mass as well as in the plasma levels of total protein and albumin. Our findings reinforce the periodic monitoring of total serum protein and albumin levels as an important tool in long-term follow-up of pediatric patients in treatments associated to total body irradiation. - Highlights: • Low-dose total body irradiation (TBI) in children have repercussions in their body-mass. • Long-term total protein and albumin levels are affected by TBI. • The monitoring of total protein and albumin levels are useful in the follow-up of TBI pediatric patients.

Ramadan Fasting Decreases Body Fat but Not Protein Mass.

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Fahrial Syam, Ari; Suryani Sobur, Cecep; Abdullah, Murdani; Makmun, Dadang

2016-01-01

Many studies have shown various results regarding the effects of Ramadan fasting on weight and body composition in healthy individuals. This study aimed to evaluate the effect of Ramadan fasting on body composition in healthy Indonesian medical staff. In this study, we examined the influence of Ramadan fasting on body composition in healthy medical staff. The longitudinal study was performed during and after Ramadan fasting in 2013 (August to October). Fourty-three medical staff members (physicians, nurses and nutritionists) at the Internal Medicine Ward of the Dr. Cipto Mangunkusumo General Hospital were measured to compare their calorie intake, weight, body mass index, waist-to-hip ratio (WHR), and body composition, including body fat, protein, minerals and water, on the first and 28(th) days of Ramadan and also 4-5 weeks after Ramadan fasting. Measurements were obtained for all 43 subjects on the 28(th) day of Ramadan, but they were obtained for only 25 subjects 4 - 5 weeks after Ramadan. By the 28(th) day of Ramadan, it was found that the body weight, BMI, body fat, water and mineral measures had decreased significantly (-0.874 ± 0.859 kg, P Ramadan, body weight and composition had returned to the same levels as on the first day of Ramadan. Ramadan fasting resulted in weight loss even it was only a temporary effect, as the weight was quickly regained within one month after fasting. The catabolism catabolic state, which is related to protein loss, was not triggered during Ramadan fasting. Further research is needed to evaluate the effects of weight loss during Ramadan fasting in healthy individuals.

Explicit symplectic integrators of molecular dynamics algorithms for rigid-body molecules in the canonical, isobaric-isothermal, and related ensembles.

Science.gov (United States)

Okumura, Hisashi; Itoh, Satoru G; Okamoto, Yuko

2007-02-28

The authors propose explicit symplectic integrators of molecular dynamics (MD) algorithms for rigid-body molecules in the canonical and isobaric-isothermal ensembles. They also present a symplectic algorithm in the constant normal pressure and lateral surface area ensemble and that combined with the Parrinello-Rahman algorithm. Employing the symplectic integrators for MD algorithms, there is a conserved quantity which is close to Hamiltonian. Therefore, they can perform a MD simulation more stably than by conventional nonsymplectic algorithms. They applied this algorithm to a TIP3P pure water system at 300 K and compared the time evolution of the Hamiltonian with those by the nonsymplectic algorithms. They found that the Hamiltonian was conserved well by the symplectic algorithm even for a time step of 4 fs. This time step is longer than typical values of 0.5-2 fs which are used by the conventional nonsymplectic algorithms.

Whey Protein Supplementation Enhances Whole Body Protein Metabolism and Performance Recovery after Resistance Exercise: A Double-Blind Crossover Study

Directory of Open Access Journals (Sweden)

Daniel W. D. West

2017-07-01

Full Text Available No study has concurrently measured changes in free-living whole body protein metabolism and exercise performance during recovery from an acute bout of resistance exercise. We aimed to determine if whey protein ingestion enhances whole body net protein balance and recovery of exercise performance during overnight (10 h and 24 h recovery after whole body resistance exercise in trained men. In a double-blind crossover design, 12 trained men (76 ± 8 kg, 24 ± 4 years old, 14% ± 5% body fat; means ± standard deviation (SD performed resistance exercise in the evening prior to consuming either 25 g of whey protein (PRO; MuscleTech 100% Whey or an energy-matched placebo (CHO immediately post-exercise (0 h, and again the following morning (~10 h of recovery. A third randomized trial, completed by the same participants, involving no exercise and no supplement served as a rested control trial (Rest. Participants ingested [15N]glycine to determine whole body protein kinetics and net protein balance over 10 and 24 h of recovery. Performance was assessed pre-exercise and at 0, 10, and 24 h of recovery using a battery of tests. Net protein balance tended to improve in PRO (P = 0.064; effect size (ES = 0.61, PRO vs. CHO during overnight recovery. Over 24 h, net balance was enhanced in PRO (P = 0.036 but not in CHO (P = 0.84; ES = 0.69, PRO vs. CHO, which was mediated primarily by a reduction in protein breakdown (PRO < CHO; P < 0.01. Exercise decreased repetitions to failure (REP, maximal strength (MVC, peak and mean power, and countermovement jump performance (CMJ at 0 h (all P < 0.05 vs. Pre. At 10 h, there were small-to-moderate effects for enhanced recovery of the MVC (ES = 0.56, mean power (ES = 0.49, and CMJ variables (ES: 0.27–0.49 in PRO. At 24 h, protein supplementation improved MVC (ES = 0.76, REP (ES = 0.44, and peak power (ES = 0.55. In conclusion, whey protein supplementation enhances whole body anabolism, and may improve acute recovery of

Feed intake, live mass-gain, body composition and protein ...

African Journals Online (AJOL)

Feed intake, live mass-gain, body composition and protein deposition in pigs fed three protein levels. E.H. Kemm,* F.K. Siebrits, M.N. Ras and H.A. Badenhorst. Animal and Dairy Science Research Institute, Private Bag X2, Irene 1675, Republic of South Africa. A group of 82 genetically lean and 90 obese Landrace pigs was ...

PROTEOSE INTOXICATIONS AND INJURY OF BODY PROTEIN

Science.gov (United States)

Cooke, J. V.; Whipple, G. H.

1918-01-01

Sterile abscess formation in the dog is accompanied by a large increase in output of urinary nitrogen and also by a small but definite increase in the blood non-protein nitrogen. All this nitrogenous material of course is derived from body protein injury and autolysis. Septic inflammation in the dog (pleurisy, pneumonia, peritonitis, etc.) likewise shows a distinct rise in the blood non-protein nitrogen. This rise is not often so great as that frequently observed in the intoxication of intestinal obstruction. Many acute infections in man (septicemia, peritonitis, pneumonia, etc.) show a definite rise in the non-protein nitrogen and urea nitrogen of the blood; some cases show a very great rise above normal (over 100 mg. of non-protein nitrogen per 100 cc. of blood). There may be no anatomical change in the kidney beyond the familiar picture of cloudy swelling. This does not exclude the possibility of some transient functional derangement of the kidney epithelium. Certain obscure intoxications in man may show a considerable rise in the non-protein nitrogen of the blood, indicating a large amount of protein disintegration. These findings must be taken into account in any clinical analysis and interpretation of high non-protein nitrogen of the blood in pathological conditions. PMID:19868253

Microfluidic chips with multi-junctions: an advanced tool in recovering proteins from inclusion bodies.

Science.gov (United States)

Yamaguchi, Hiroshi; Miyazaki, Masaya

2015-01-01

Active recombinant proteins are used for studying the biological functions of genes and for the development of therapeutic drugs. Overexpression of recombinant proteins in bacteria often results in the formation of inclusion bodies, which are protein aggregates with non-native conformations. Protein refolding is an important process for obtaining active recombinant proteins from inclusion bodies. However, the conventional refolding method of dialysis or dilution is time-consuming and recovered active protein yields are often low, and a cumbersome trial-and-error process is required to achieve success. To circumvent these difficulties, we used controllable diffusion through laminar flow in microchannels to regulate the denaturant concentration. This method largely aims at reducing protein aggregation during the refolding procedure. This Commentary introduces the principles of the protein refolding method using microfluidic chips and the advantage of our results as a tool for rapid and efficient recovery of active recombinant proteins from inclusion bodies.

Tile-based rigidization surface parametric design study

Science.gov (United States)

Giner Munoz, Laura; Luntz, Jonathan; Brei, Diann; Kim, Wonhee

2018-03-01

Inflatable technologies have proven useful in consumer goods as well as in more recent applications including civil structures, aerospace, medical, and robotics. However, inflatable technologies are typically lacking in their ability to provide rigid structural support. Particle jamming improves upon this by providing structures which are normally flexible and moldable but become rigid when air is removed. Because these are based on an airtight bladder filled with loose particles, they always occupy the full volume of its rigid state, even when not rigidized. More recent developments in layer jamming have created thin, compact rigidizing surfaces replacing the loose volume of particles with thinly layered surface materials. Work in this area has been applied to several specific applications with positive results but have not generally provided the broader understanding of the rigidization performance as a function of design parameters required for directly adapting layer rigidization technology to other applications. This paper presents a parametric design study of a new layer jamming vacuum rigidization architecture: tile-based vacuum rigidization. This form of rigidization is based on layers of tiles contained within a thin vacuum bladder which can be bent, rolled, or otherwise compactly stowed, but when deployed flat, can be vacuumed and form a large, flat, rigid plate capable of supporting large forces both localized and distributed over the surface. The general architecture and operation detailing rigidization and compliance mechanisms is introduced. To quantitatively characterize the rigidization behavior, prototypes rigidization surfaces are fabricated and an experimental technique is developed based on a 3-point bending test. Performance evaluation metrics are developed to describe the stiffness, load-bearing capacity, and internal slippage of tested prototypes. A set of experimental parametric studies are performed to better understand the impact of

1H-detected MAS solid-state NMR experiments enable the simultaneous mapping of rigid and dynamic domains of membrane proteins

Science.gov (United States)

Gopinath, T.; Nelson, Sarah E. D.; Veglia, Gianluigi

2017-12-01

Magic angle spinning (MAS) solid-state NMR (ssNMR) spectroscopy is emerging as a unique method for the atomic resolution structure determination of native membrane proteins in lipid bilayers. Although 13C-detected ssNMR experiments continue to play a major role, recent technological developments have made it possible to carry out 1H-detected experiments, boosting both sensitivity and resolution. Here, we describe a new set of 1H-detected hybrid pulse sequences that combine through-bond and through-space correlation elements into single experiments, enabling the simultaneous detection of rigid and dynamic domains of membrane proteins. As proof-of-principle, we applied these new pulse sequences to the membrane protein phospholamban (PLN) reconstituted in lipid bilayers under moderate MAS conditions. The cross-polarization (CP) based elements enabled the detection of the relatively immobile residues of PLN in the transmembrane domain using through-space correlations; whereas the most dynamic region, which is in equilibrium between folded and unfolded states, was mapped by through-bond INEPT-based elements. These new 1H-detected experiments will enable one to detect not only the most populated (ground) states of biomacromolecules, but also sparsely populated high-energy (excited) states for a complete characterization of protein free energy landscapes.

Soft-Body Muscles for Evolved Virtual Creatures: The Next Step on a Bio-Mimetic Path to Meaningful Morphological Complexity

DEFF Research Database (Denmark)

Lessin, Dan; Risi, Sebastian

2015-01-01

In the past, evolved virtual creatures (EVCs) have been developed with rigid, segmented bodies, and with soft bodies, but never before with a combination of the two. In nature, however, creatures combining a rigid skeleton and non-rigid muscles are some of the most complex and successful examples...... of life on earth. Now, for the first time, creatures with fully evolved rigid-body skeletons and soft-body muscles can be developed in the virtual world, as well. By exploiting and re-purposing the capabilities of existing soft-body simulation systems, we can evolve complex and effective simulated muscles...

Effects of monohydric alcohols and polyols on the thermal stability of a protein

Energy Technology Data Exchange (ETDEWEB)

Murakami, Shota [Graduate School of Energy Science, Kyoto University, Uji, Kyoto 611-0011 (Japan); Kinoshita, Masahiro, E-mail: kinoshit@iae.kyoto-u.ac.jp [Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011 (Japan)

2016-03-28

The thermal stability of a protein is lowered by the addition of a monohydric alcohol, and this effect becomes larger as the size of hydrophobic group in an alcohol molecule increases. By contrast, it is enhanced by the addition of a polyol possessing two or more hydroxyl groups per molecule, and this effect becomes larger as the number of hydroxyl groups increases. Here, we show that all of these experimental observations can be reproduced even in a quantitative sense by rigid-body models focused on the entropic effect originating from the translational displacement of solvent molecules. The solvent is either pure water or water-cosolvent solution. Three monohydric alcohols and five polyols are considered as cosolvents. In the rigid-body models, a protein is a fused hard spheres accounting for the polyatomic structure in the atomic detail, and the solvent is formed by hard spheres or a binary mixture of hard spheres with different diameters. The effective diameter of cosolvent molecules and the packing fractions of water and cosolvent, which are crucially important parameters, are carefully estimated using the experimental data of properties such as the density of solid crystal of cosolvent, parameters in the pertinent cosolvent-cosolvent interaction potential, and density of water-cosolvent solution. We employ the morphometric approach combined with the integral equation theory, which is best suited to the physical interpretation of the calculation result. It is argued that the degree of solvent crowding in the bulk is the key factor. When it is made more serious by the cosolvent addition, the solvent-entropy gain upon protein folding is magnified, leading to the enhanced thermal stability. When it is made less serious, the opposite is true. The mechanism of the effects of monohydric alcohols and polyols is physically the same as that of sugars. However, when the rigid-body models are employed for the effect of urea, its addition is predicted to enhance the

Missed distal tracheal foreign body in consecutive bronchoscopies in a 6-year-old boy

Directory of Open Access Journals (Sweden)

Oghenevware Joel Eyekpegha

2017-01-01

Full Text Available It is unusual but not uncommon for foreign bodies to be missed at bronchoscopy. This case report highlights the importance of the clinical history in the diagnosis of aspirated foreign bodies and the usefulness of chest imaging modalities. A 6-year-old boy presented with recurrent breathlessness and cough of 2 months. He was said to have aspirated the base cap of a pen at about the time symptoms started. He had two sessions of rigid bronchoscopy and a session of flexible bronchoscopy at three different hospitals. He had an initial rigid bronchoscopy which failed to show the foreign body (FB. A chest computerized tomographic scan demonstrated the FB, which was retrieved at combined flexible/rigid bronchoscopy. Although rigid bronchoscopy is the gold standard for managing airway foreign bodies, there remains a false negative rate for this procedure and where necessary, appropriate imaging may compliment rigid bronchoscopy, especially where there is some confusion.

Casein and soy protein meals differentially affect whole-body and splanchnic protein metabolism in healthy humans.

Science.gov (United States)

Luiking, Yvette C; Deutz, Nicolaas E P; Jäkel, Martin; Soeters, Peter B

2005-05-01

Dietary protein quality is considered to be dependent on the degree and velocity with which protein is digested, absorbed as amino acids, and retained in the gut as newly synthesized protein. Metabolic animal studies suggest that the quality of soy protein is inferior to that of casein protein, but confirmatory studies in humans are lacking. The study objective was to assess the quality of casein and soy protein by comparing their metabolic effects in healthy human subjects. Whole-body protein kinetics, splanchnic leucine extraction, and urea production rates were measured in the postabsorptive state and during 8-h enteral intakes of isonitrogenous [0.42 g protein/(kg body weight . 8 h)] protein-based test meals, which contained either casein (CAPM; n = 12) or soy protein (SOPM; n = 10) in 2 separate groups. Stable isotope techniques were used to study metabolic effects. With enteral food intake, protein metabolism changed from net protein breakdown to net protein synthesis. Net protein synthesis was greater in the CAPM group than in the SOPM group [52 +/- 14 and 17 +/- 14 nmol/(kg fat-free mass (FFM) . min), respectively; P CAPM (P = 0.07). Absolute splanchnic extraction of leucine was higher in the subjects that consumed CAPM [306 +/- 31 nmol/(kg FFM . min)] vs. those that consumed SOPM [235 +/- 29 nmol/(kg FFM . min); P < 0.01]. In conclusion, a significantly larger portion of soy protein is degraded to urea, whereas casein protein likely contributes to splanchnic utilization (probably protein synthesis) to a greater extent. The biological value of soy protein must be considered inferior to that of casein protein in humans.

Modeling the Flexural Rigidity of Rod Photoreceptors

Science.gov (United States)

Haeri, Mohammad; Knox, Barry E.; Ahmadi, Aphrodite

2013-01-01

In vertebrate eyes, the rod photoreceptor has a modified cilium with an extended cylindrical structure specialized for phototransduction called the outer segment (OS). The OS has numerous stacked membrane disks and can bend or break when subjected to mechanical forces. The OS exhibits axial structural variation, with extended bands composed of a few hundred membrane disks whose thickness is diurnally modulated. Using high-resolution confocal microscopy, we have observed OS flexing and disruption in live transgenic Xenopus rods. Based on the experimental observations, we introduce a coarse-grained model of OS mechanical rigidity using elasticity theory, representing the axial OS banding explicitly via a spring-bead model. We calculate a bending stiffness of ∼105 nN⋅μm2, which is seven orders-of-magnitude larger than that of typical cilia and flagella. This bending stiffness has a quadratic relation to OS radius, so that thinner OS have lower fragility. Furthermore, we find that increasing the spatial frequency of axial OS banding decreases OS rigidity, reducing its fragility. Moreover, the model predicts a tendency for OS to break in bands with higher spring number density, analogous to the experimental observation that transgenic rods tended to break preferentially in bands of high fluorescence. We discuss how pathological alterations of disk membrane properties by mutant proteins may lead to increased OS rigidity and thus increased breakage, ultimately contributing to retinal degeneration. PMID:23442852

Esophageal Foreign Bodies

Directory of Open Access Journals (Sweden)

Ufuk Cobanoglu

2014-04-01

Full Text Available Esophageal foreign body aspiration is a common event which can cause serious morbidity and mortality in the children and adult population. For that reason, early diagnosis and treatment are crucial for preventing these life threateining complications. Children most often ingest coins and toys whereas adults commonly tend to have problems with meat and bones. Esophageal foreign bodies are located at the cricopharyngeus muscle level in 70%, the thoracic esophagus in 15% and the gastroesophageal junction in the remaining 15%. Symptoms can vary according to the shape and structure of the ingested object, type of location, patient%u2019s age and complications caused by the foreign body. Delay in treatment, esophageal perforation and an underlying esophageal disease are poor prognostic factors. In treatment, observation, foley catheter, rigid or flexible esophagoscopy and removing the foreign body with a Magill forceps, pushing the foreign body into the stomach, giving intravenous glucagon and surgical treatment methods can be used. Rigid esophagoscopy is an effective and safe procedure for foreign body diagnosis and removal. Improved endoscopic experience and clinical management of thoracic surgeons led to reduced morbidity and mortality in recent years. Most of those emergencies of childhood are preventable. Family education is very important.

Rigid-body rotation of an electron cloud in divergent magnetic fields

International Nuclear Information System (INIS)

Fruchtman, A.; Gueroult, R.; Fisch, N. J.

2013-01-01

For a given voltage across a divergent poloidal magnetic field, two electric potential distributions, each supported by a rigid-rotor electron cloud rotating with a different frequency, are found analytically. The two rotation frequencies correspond to the slow and fast rotation frequencies known in uniform plasma. Due to the centrifugal force, the equipotential surfaces, that correspond to the two electric potential distributions, diverge more than the magnetic surfaces do, the equipotential surfaces in the fast mode diverge largely in particular. The departure of the equipotential surfaces from the magnetic field surfaces may have a significant focusing effect on the ions accelerated by the electric field. The focusing effect could be important for laboratory plasma accelerators as well as for collimation of astrophysical jets

The pepATTRACT web server for blind, large-scale peptide-protein docking.

Science.gov (United States)

de Vries, Sjoerd J; Rey, Julien; Schindler, Christina E M; Zacharias, Martin; Tuffery, Pierre

2017-07-03

Peptide-protein interactions are ubiquitous in the cell and form an important part of the interactome. Computational docking methods can complement experimental characterization of these complexes, but current protocols are not applicable on the proteome scale. pepATTRACT is a novel docking protocol that is fully blind, i.e. it does not require any information about the binding site. In various stages of its development, pepATTRACT has participated in CAPRI, making successful predictions for five out of seven protein-peptide targets. Its performance is similar or better than state-of-the-art local docking protocols that do require binding site information. Here we present a novel web server that carries out the rigid-body stage of pepATTRACT. On the peptiDB benchmark, the web server generates a correct model in the top 50 in 34% of the cases. Compared to the full pepATTRACT protocol, this leads to some loss of performance, but the computation time is reduced from ∼18 h to ∼10 min. Combined with the fact that it is fully blind, this makes the web server well-suited for large-scale in silico protein-peptide docking experiments. The rigid-body pepATTRACT server is freely available at http://bioserv.rpbs.univ-paris-diderot.fr/services/pepATTRACT. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Rigidity and symmetry

CERN Document Server

Weiss, Asia; Whiteley, Walter

2014-01-01

This book contains recent contributions to the fields of rigidity and symmetry with two primary focuses: to present the mathematically rigorous treatment of rigidity of structures, and to explore the interaction of geometry, algebra, and combinatorics. Overall, the book shows how researchers from diverse backgrounds explore connections among the various discrete structures with symmetry as the unifying theme.  Contributions present recent trends and advances in discrete geometry, particularly in the theory of polytopes. The rapid development of abstract polytope theory has resulted in a rich theory featuring an attractive interplay of methods and tools from discrete geometry, group theory, classical geometry, hyperbolic geometry and topology.  The volume will also be a valuable source as an introduction to the ideas of both combinatorial and geometric rigidity theory and its applications, incorporating the surprising impact of symmetry. It will appeal to students at both the advanced undergraduate and gradu...

Body characteristics, [corrected] dietary protein and body weight regulation. Reconciling conflicting results from intervention and observational studies?

Directory of Open Access Journals (Sweden)

Mikkel Z Ankarfeldt

Full Text Available Physiological evidence indicates that high-protein diets reduce caloric intake and increase thermogenic response, which may prevent weight gain and regain after weight loss. Clinical trials have shown such effects, whereas observational cohort studies suggest an association between greater protein intake and weight gain. In both types of studies the results are based on average weight changes, and show considerable diversity in both directions. This study investigates whether the discrepancy in the evidence could be due to recruitment of overweight and obese individuals into clinical trials.Data were available from the European Diet, Obesity and Genes (DiOGenes post-weight-loss weight-maintenance trial and the Danish Diet, Cancer and Health (DCH cohort. Participants of the DCH cohort were matched with participants from the DiOGenes trial on gender, diet, and body characteristics. Different subsets of the DCH-participants, comparable with the trial participants, were analyzed for weight maintenance according to the randomization status (high or low protein of the matched trial participants.Trial participants were generally heavier, had larger waist circumference and larger fat mass than the participants in the entire DCH cohort. A better weight maintenance in the high-protein group compared to the low protein group was observed in the subgroups of the DCH cohort matching body characteristics of the trial participants.This modified observational study, minimized the differences between the RCT and observational data with regard to dietary intake, participant characteristics and statistical analysis. Compared with low protein diet the high protein diet was associated with better weight maintenance when individuals with greater body mass index and waist circumference were analyzed. Selecting subsets of large-scale observational cohort studies with similar characteristics as participants in clinical trials may reconcile the otherwise conflicting

The Role of MreB in Escherichia Coli's Cellular Rigidity

Science.gov (United States)

Shaevitz, Joshua W.

2009-03-01

Bacteria possess homologs of all three classes of eukaryotic cytoskeletal proteins. These filamentous proteins have been shown to localize proteins essential for a number of cell-biological processes in prokaryotes such as cell growth and division. However, to date, there has been no direct evidence that the cytoskeleton in bacteria bears mechanical loads or can generate physical forces than are used by the cell. I will present evidence from combined fluorescence and force microscopy measurements that MreB, an actin homolog, is responsible for half of Escherichia coli's cellular rigidity. These data support an interpretation in which the cytoskeleton, the peptidoglycan cell wall and a large turgor pressure work together to give gram-negative cells their mechanical properties.

Relatively high-protein or 'low-carb' energy-restricted diets for body weight loss and body weight maintenance?

Science.gov (United States)

Soenen, Stijn; Bonomi, Alberto G; Lemmens, Sofie G T; Scholte, Jolande; Thijssen, Myriam A M A; van Berkum, Frank; Westerterp-Plantenga, Margriet S

2012-10-10

'Low-carb' diets have been suggested to be effective in body weight (BW) management. However, these diets are relatively high in protein as well. To unravel whether body-weight loss and weight-maintenance depends on the high-protein or the 'low-carb' component of the diet. Body-weight (BW), fat mass (FM), blood- and urine-parameters of 132 participants (age=50 ± 12 yr; BW=107 ± 20 kg; BMI=37 ± 6 kg/m(2); FM=47.5 ± 11.9 kg) were compared after 3 and 12 months between four energy-restricted diets with 33% of energy requirement for the first 3 months, and 67% for the last 9 months: normal-protein normal-carbohydrate (NPNC), normal-protein low-carbohydrate (NPLC); high-protein normal-carbohydrate (HPNC), high-protein low-carbohydrate (HPLC); 24h N-analyses confirmed daily protein intakes for the normal-protein diets of 0.7 ± 0.1 and for the high-protein diets of 1.1 ± 0.2g/kg BW (pvs. NP (-11.5 ± 4 kg; -9.3 ± 0.7 kg) (pvs. NC (-12.3 ± 3 kg; -10.3 ± 1.1 kg) (ns). Diet × time interaction showed HPLC (-14.7 ± 5 kg; -11.9 ± 1.6 kg) vs. HPNC (-13.8 ± 3 kg; -11.9 ± 1.8 kg) (ns); NPLC (-12.2 ± 4 kg; -10.0 ± 0.8 kg) vs. NPNC (-10.7 ± 4 kg; -8.6 ± 0.7 kg) (ns); HPLC vs. NPLC (pvs. NPNC (pvs. NP (-8.9 ± 3 kg; -7.7 ± 0.6 kg) (pvs. NC (11.1 ± 3 kg; 9.3 ± 0.7 kg) (ns). Diet × time interaction showed HPLC (-11.6 ± 5 kg ; -8.2 ± 0.7 kg) vs. HPNC (-14.1 ± 4 kg; -10.0 ± 0.9 kg) (ns); NPNC (-8.2 ± 3 kg; -6.7 ± 0.6 kg) vs. NPLC (-9.7 ± 3 kg; -8.5 ± 0.7 kg) (ns); HPLC vs. NPLC (pvs. NPNC (pvs. all other diets reduced diastolic blood pressure more. Relationships between changes in BW, FM, FFM or metabolic parameters and energy percentage of fat in the diet were not statistically significant. Metabolic profile and fat-free-mass were improved following weight-loss. Body-weight loss and weight-maintenance depends on the high-protein, but not on the 'low-carb' component of the diet, while it is unrelated to the concomitant fat-content of the diet. Copyright �

Whole-body protein turnover of a carnivore, Felis silvestris catus.

Science.gov (United States)

Russell, K; Lobley, G E; Millward, D J

2003-01-01

The cat (Felis silvestris catus) has a higher dietary protein requirement than omnivores and herbivores, thought to be due to metabolic inflexibility. An aspect of metabolic flexibility was examined with studies of whole-body protein turnover at two levels of dietary protein energy, moderate protein (MP; 20 %) and high protein (HP; 70 %), in five adult cats in a crossover design. Following a 14 d pre-feed period, a single intravenous dose of [15N]glycine was administered and cumulative excretion of the isotope in urine and faeces determined over 48 h. N flux increased (Pwork is required to determine exactly why cats have such a high protein requirement.

Amino acid metabolism and whole-body protein turnover in lambs ...

African Journals Online (AJOL)

The effect of protein supplementation of a wheat straw diet on the metabolism of lysine, leucine, methionine and urea, and on whole-body protein turnover rate was investigated in lambs. The metabolism of lysine and leucine is reported elsewhere (Cronje et aI., 1992); in this paper methionine metabolism is discussed, and ...

Birationally rigid varieties

CERN Document Server

Pukhlikov, Aleksandr

2013-01-01

Birational rigidity is a striking and mysterious phenomenon in higher-dimensional algebraic geometry. It turns out that certain natural families of algebraic varieties (for example, three-dimensional quartics) belong to the same classification type as the projective space but have radically different birational geometric properties. In particular, they admit no non-trivial birational self-maps and cannot be fibred into rational varieties by a rational map. The origins of the theory of birational rigidity are in the work of Max Noether and Fano; however, it was only in 1970 that Iskovskikh and Manin proved birational superrigidity of quartic three-folds. This book gives a systematic exposition of, and a comprehensive introduction to, the theory of birational rigidity, presenting in a uniform way, ideas, techniques, and results that so far could only be found in journal papers. The recent rapid progress in birational geometry and the widening interaction with the neighboring areas generate the growing interest ...

Protein mobilities and P-selectin storage in Weibel–Palade bodies

OpenAIRE

Kiskin, Nikolai I.; Hellen, Nicola; Babich, Victor; Hewlett, Lindsay; Knipe, Laura; Hannah, Matthew J.; Carter, Tom

2010-01-01

Using fluorescence recovery after photobleaching (FRAP) we measured the mobilities of EGFP-tagged soluble secretory proteins in the endoplasmic reticulum (ER) and in individual Weibel–Palade bodies (WPBs) at early (immature) and late (mature) stages in their biogenesis. Membrane proteins (P-selectin, CD63, Rab27a) were also studied in individual WPBs. In the ER, soluble secretory proteins were mobile; however, following insertion into immature WPBs larger molecules (VWF, Proregion, tPA) and P...

Comparison of rigid and flexible endoscopy for removing esophageal foreign bodies in an emergency.

Science.gov (United States)

Tseng, Chia-Chen; Hsiao, Tzu-Yu; Hsu, Wei-Chung

2016-08-01

Despite the effectiveness of endoscopies in removing ingested foreign bodies (FBs) impacted in the esophagus, the merits and limitations of flexible endoscopy (FE) and rigid endoscopy (RE) remain unclear. Therefore, this study compares the advantages and disadvantages of both endoscopic procedures from a clinical perspective. A retrospective review was made of 273 patients suspected of esophageal FBs in emergency consultations of a tertiary medical referral center from March 2010 to March 2014. All patients received routine physical examinations, otolaryngological examinations, and X-rays of the neck and chest. The door-to-endoscopy time, procedure time, postendoscopic hospital stay, successful removal rates, and complications were analyzed as well. In this study, the most common esophageal FBs were fish and animal bones (76%) in adults and coins (74%) in children. The patients with existing esophageal FBs had significantly more frequent symptoms of dysphagia and signs of linear opacity as detected with lateral neck radiography than those without FB. Additionally, the door-to-endoscopy time, procedure time, and postendoscopic hospital stay was significantly shorter in FE patients than in RE patients. However, both RE and FE patients had high rates of successful FB removal (95%) and low complication rates (2%). Both FE and RE remove esophageal FBs successfully, as evidenced by their high success rates, low complication rates, and high detection rates. Although FE under local anesthesia is a less time-consuming procedure for adults, RE under general anesthesia may be preferable for children and can serve as an alternative to FE. Copyright © 2015. Published by Elsevier B.V.

Synthesis of protein in host-free reticulate bodies of Chlamydia psittaci and Chlamydia trachomatis

International Nuclear Information System (INIS)

Hatch, T.P.; Miceli, M.; Silverman, J.A.

1985-01-01

Synthesis of protein by the obligate intracellular parasitic bacteria Chlamydia psittaci (6BC) and Chlamydia trachomatis (serovar L2) isolated from host cells (host-free chlamydiae) was demonstrated for the first time. Incorporation of [ 35 S]methionine and [ 35 S]cysteine into trichloroacetic acid-precipitable material by reticulate bodies of chlamydiae persisted for 2 h and was dependent upon a exogenous source of ATP, an ATP-regenerating system, and potassium or sodium ions. Magnesium ions and amino acids stimulated synthesis; chloramphenicol, rifampin, oligomycin, and carbonyl cyanide p-trifluoromethoxyphenylhydrazone (a proton ionophore) inhibited incorporation. Ribonucleoside triphosphates (other than ATP) had little stimulatory effect. The optimum pH for host-free synthesis was between 7.0 and 7.5. The molecular weights of proteins synthesized by host-free reticulate bodies closely resembled the molecular weights of proteins synthesized by reticulate bodies in an intracellular environment, and included outer membrane proteins. Elementary bodies of chlamydiae were unable to synthesize protein even when incubated in the presence of 10 mM dithiothreitol, a reducing agent which converted the highly disulfide bond cross-linked major outer membrane protein to monomeric form

Protein flexibility: coordinate uncertainties and interpretation of structural differences

Energy Technology Data Exchange (ETDEWEB)

Rashin, Alexander A., E-mail: alexander-rashin@hotmail.com [BioChemComp Inc., 543 Sagamore Avenue, Teaneck, NJ 07666 (United States); LH Baker Center for Bioinformatics and Department of Biochemistry, Biophysics and Molecular Biology, 112 Office and Lab Building, Iowa State University, Ames, IA 50011-3020 (United States); Rashin, Abraham H. L. [BioChemComp Inc., 543 Sagamore Avenue, Teaneck, NJ 07666 (United States); Rutgers, The State University of New Jersey, 22371 BPO WAY, Piscataway, NJ 08854-8123 (United States); Jernigan, Robert L. [LH Baker Center for Bioinformatics and Department of Biochemistry, Biophysics and Molecular Biology, 112 Office and Lab Building, Iowa State University, Ames, IA 50011-3020 (United States); BioChemComp Inc., 543 Sagamore Avenue, Teaneck, NJ 07666 (United States)

2009-11-01

Criteria for the interpretability of coordinate differences and a new method for identifying rigid-body motions and nonrigid deformations in protein conformational changes are developed and applied to functionally induced and crystallization-induced conformational changes. Valid interpretations of conformational movements in protein structures determined by X-ray crystallography require that the movement magnitudes exceed their uncertainty threshold. Here, it is shown that such thresholds can be obtained from the distance difference matrices (DDMs) of 1014 pairs of independently determined structures of bovine ribonuclease A and sperm whale myoglobin, with no explanations provided for reportedly minor coordinate differences. The smallest magnitudes of reportedly functional motions are just above these thresholds. Uncertainty thresholds can provide objective criteria that distinguish between true conformational changes and apparent ‘noise’, showing that some previous interpretations of protein coordinate changes attributed to external conditions or mutations may be doubtful or erroneous. The use of uncertainty thresholds, DDMs, the newly introduced CDDMs (contact distance difference matrices) and a novel simple rotation algorithm allows a more meaningful classification and description of protein motions, distinguishing between various rigid-fragment motions and nonrigid conformational deformations. It is also shown that half of 75 pairs of identical molecules, each from the same asymmetric crystallographic cell, exhibit coordinate differences that range from just outside the coordinate uncertainty threshold to the full magnitude of large functional movements. Thus, crystallization might often induce protein conformational changes that are comparable to those related to or induced by the protein function.

Human epithelial cells increase their rigidity with ageing in vitro: direct measurements

International Nuclear Information System (INIS)

Berdyyeva, Tamara K; Woodworth, Craig D; Sokolov, Igor

2005-01-01

The decrease in elasticity of epithelial tissues with ageing contributes to many human diseases. This change was previously attributed to increased crosslinking of extracellular matrix proteins. Here we show that individual human epithelial cells also become significantly more rigid during ageing in vitro. Using atomic force microscopy (AFM), we found that the Young's modulus of viable cells was consistently increased two- to four-fold in older versus younger cells. Direct visualization of the cytoskeleton using a novel method involving the AFM suggested that increased rigidity of ageing cells was due to a higher density of cytoskeletal fibres. Our results identify a unique mechanism that might contribute to the age-related loss of elasticity in epithelial tissues

Rigidity-tuning conductive elastomer

Science.gov (United States)

Shan, Wanliang; Diller, Stuart; Tutcuoglu, Abbas; Majidi, Carmel

2015-06-01

We introduce a conductive propylene-based elastomer (cPBE) that rapidly and reversibly changes its mechanical rigidity when powered with electrical current. The elastomer is rigid in its natural state, with an elastic (Young’s) modulus of 175.5 MPa, and softens when electrically activated. By embedding the cPBE in an electrically insulating sheet of polydimethylsiloxane (PDMS), we create a cPBE-PDMS composite that can reversibly change its tensile modulus between 37 and 1.5 MPa. The rigidity change takes ˜6 s and is initiated when a 100 V voltage drop is applied across the two ends of the cPBE film. This magnitude of change in elastic rigidity is similar to that observed in natural skeletal muscle and catch connective tissue. We characterize the tunable load-bearing capability of the cPBE-PDMS composite with a motorized tensile test and deadweight experiment. Lastly, we demonstrate the ability to control the routing of internal forces by embedding several cPBE-PDMS ‘active tendons’ into a soft robotic pneumatic bending actuator. Selectively activating the artificial tendons controls the neutral axis and direction of bending during inflation.

Rigidity-tuning conductive elastomer

International Nuclear Information System (INIS)

Shan, Wanliang; Diller, Stuart; Tutcuoglu, Abbas; Majidi, Carmel

2015-01-01

We introduce a conductive propylene-based elastomer (cPBE) that rapidly and reversibly changes its mechanical rigidity when powered with electrical current. The elastomer is rigid in its natural state, with an elastic (Young’s) modulus of 175.5 MPa, and softens when electrically activated. By embedding the cPBE in an electrically insulating sheet of polydimethylsiloxane (PDMS), we create a cPBE–PDMS composite that can reversibly change its tensile modulus between 37 and 1.5 MPa. The rigidity change takes ∼6 s and is initiated when a 100 V voltage drop is applied across the two ends of the cPBE film. This magnitude of change in elastic rigidity is similar to that observed in natural skeletal muscle and catch connective tissue. We characterize the tunable load-bearing capability of the cPBE–PDMS composite with a motorized tensile test and deadweight experiment. Lastly, we demonstrate the ability to control the routing of internal forces by embedding several cPBE–PDMS ‘active tendons’ into a soft robotic pneumatic bending actuator. Selectively activating the artificial tendons controls the neutral axis and direction of bending during inflation. (paper)

Ret Finger Protein: An E3 Ubiquitin Ligase Juxtaposed to the XY Body in Meiosis

Directory of Open Access Journals (Sweden)

Isabelle Gillot

2009-01-01

Full Text Available During prophase I of male meiosis, the sex chromosomes form a compact structure called XY body that associates with the nuclear membrane of pachytene spermatocytes. Ret Finger Protein is a transcriptional repressor, able to interact with both nuclear matrix-associated proteins and double-stranded DNA. We report the precise and unique localization of Ret Finger Protein in pachytene spermatocytes, in which Ret Finger Protein takes place of lamin B1, between the XY body and the inner nuclear membrane. This localization of Ret Finger Protein does not seem to be associated with O-glycosylation or sumoylation. In addition, we demonstrate that Ret Finger Protein contains an E3 ubiquitin ligase activity. These observations lead to an attractive hypothesis in which Ret Finger Protein would be involved in the positioning and the attachment of XY body to the nuclear lamina of pachytene spermatocytes.

On flexible and rigid nouns

DEFF Research Database (Denmark)

Rijkhoff, Jan

2010-01-01

classes. Finally this article wants to claim that the distinction between rigid and flexible noun categories (a) adds a new dimension to current classifications of parts of speech systems, (b) correlates with certain grammatical phenomena (e.g. so-called number discord), and (c) helps to explain the parts......This article argues that in addition to the major flexible lexical categories in Hengeveld’s classification of parts of speech systems (Contentive, Non-Verb, Modifier), there are also flexible word classes within the rigid lexical category Noun (Set Noun, Sort Noun, General Noun). Members...... by the flexible item in the external world. I will then argue that flexible word classes constitute a proper category (i.e. they are not the result of a merger of some rigid word classes) in that members of flexible word categories display the same properties regarding category membership as members of rigid word...

Uncommon, undeclared oesophageal foreign bodies

African Journals Online (AJOL)

2011-05-11

May 11, 2011 ... presented with a sudden onset of total dysphagia and history of ingestion of foreign bodies was not volunteered by any despite direct questioning. Plain radiograph of the neck and chest in either case did not reveal presence of foreign body. Both were successfully removed through rigid oesophagoscopy.

Protein design using continuous rotamers.

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Pablo Gainza

2012-01-01

Full Text Available Optimizing amino acid conformation and identity is a central problem in computational protein design. Protein design algorithms must allow realistic protein flexibility to occur during this optimization, or they may fail to find the best sequence with the lowest energy. Most design algorithms implement side-chain flexibility by allowing the side chains to move between a small set of discrete, low-energy states, which we call rigid rotamers. In this work we show that allowing continuous side-chain flexibility (which we call continuous rotamers greatly improves protein flexibility modeling. We present a large-scale study that compares the sequences and best energy conformations in 69 protein-core redesigns using a rigid-rotamer model versus a continuous-rotamer model. We show that in nearly all of our redesigns the sequence found by the continuous-rotamer model is different and has a lower energy than the one found by the rigid-rotamer model. Moreover, the sequences found by the continuous-rotamer model are more similar to the native sequences. We then show that the seemingly easy solution of sampling more rigid rotamers within the continuous region is not a practical alternative to a continuous-rotamer model: at computationally feasible resolutions, using more rigid rotamers was never better than a continuous-rotamer model and almost always resulted in higher energies. Finally, we present a new protein design algorithm based on the dead-end elimination (DEE algorithm, which we call iMinDEE, that makes the use of continuous rotamers feasible in larger systems. iMinDEE guarantees finding the optimal answer while pruning the search space with close to the same efficiency of DEE.Software is available under the Lesser GNU Public License v3. Contact the authors for source code.

Fullrmc, a rigid body Reverse Monte Carlo modeling package enabled with machine learning and artificial intelligence.

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Aoun, Bachir

2016-05-05

A new Reverse Monte Carlo (RMC) package "fullrmc" for atomic or rigid body and molecular, amorphous, or crystalline materials is presented. fullrmc main purpose is to provide a fully modular, fast and flexible software, thoroughly documented, complex molecules enabled, written in a modern programming language (python, cython, C and C++ when performance is needed) and complying to modern programming practices. fullrmc approach in solving an atomic or molecular structure is different from existing RMC algorithms and software. In a nutshell, traditional RMC methods and software randomly adjust atom positions until the whole system has the greatest consistency with a set of experimental data. In contrast, fullrmc applies smart moves endorsed with reinforcement machine learning to groups of atoms. While fullrmc allows running traditional RMC modeling, the uniqueness of this approach resides in its ability to customize grouping atoms in any convenient way with no additional programming efforts and to apply smart and more physically meaningful moves to the defined groups of atoms. In addition, fullrmc provides a unique way with almost no additional computational cost to recur a group's selection, allowing the system to go out of local minimas by refining a group's position or exploring through and beyond not allowed positions and energy barriers the unrestricted three dimensional space around a group. © 2016 Wiley Periodicals, Inc.

Control of fluid-containing rotating rigid bodies

CERN Document Server

Gurchenkov, Anatoly A

2013-01-01

This book is devoted to the study of the dynamics of rotating bodies with cavities containing liquid. Two basic classes of motions are analyzed: rotation and libration. Cases of complete and partial filling of cavities with ideal liquid and complete filling with viscous liquid are treated. The volume presents a method for obtaining relations between angular velocities perpendicular to main rotation and external force momentums, which are treated as control. The developed models and methods of solving dynamical problems as well as numerical methods for solving problems of optimal control can be

CT-3DRA registration for radiosurgery treatments: a comparison among rigid, affine and non rigid approaches

International Nuclear Information System (INIS)

Stancanello, J.; Loeckx, D.; Francescon, P.; Calvedon, C.; Avanzo, M.; Cora, S.; Scalchi, P.; Cerveri, P.; Ferrigno, G.

2004-01-01

This work aims at comparing rigid, affine and Local Non Rigid (LNR) CT-3D Rotational Angiography (CT-3DRA) registrations based on mutual information. 10 cranial and 1 spinal cases have been registered by rigid and affine transformations; while LNR has been applied to the cases where residual deformation must be corrected. An example of CT-3DRA registration without regularization term and an example of LNR using the similarity criterion and the regularization term as well as 3D superposition of the 3DRA before and after the registration without the regularization term are presented. All the registrations performed by rigid transformation converged to an acceptable solution. The results about the robustness test in axial direction are reported. Conclusions: For cranial cases, affine transformation endowed with threshold-segmentation pre-processing can be considered the most favourable solution for almost all registrations; for some cases, LNR provides more accurate results. For the spinal case rigid transformation is the most suitable when immobilizing patient during examinations; in this case the increase of accuracy by using LNR registrations seems to be not significant

Torsional Rigidity of Minimal Submanifolds

DEFF Research Database (Denmark)

Markvorsen, Steen; Palmer, Vicente

2006-01-01

We prove explicit upper bounds for the torsional rigidity of extrinsic domains of minimal submanifolds $P^m$ in ambient Riemannian manifolds $N^n$ with a pole $p$. The upper bounds are given in terms of the torsional rigidities of corresponding Schwarz symmetrizations of the domains in warped...

A heterogeneous system based on GPU and multi-core CPU for real-time fluid and rigid body simulation

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da Silva Junior, José Ricardo; Gonzalez Clua, Esteban W.; Montenegro, Anselmo; Lage, Marcos; Dreux, Marcelo de Andrade; Joselli, Mark; Pagliosa, Paulo A.; Kuryla, Christine Lucille

2012-03-01

Computational fluid dynamics in simulation has become an important field not only for physics and engineering areas but also for simulation, computer graphics, virtual reality and even video game development. Many efficient models have been developed over the years, but when many contact interactions must be processed, most models present difficulties or cannot achieve real-time results when executed. The advent of parallel computing has enabled the development of many strategies for accelerating the simulations. Our work proposes a new system which uses some successful algorithms already proposed, as well as a data structure organisation based on a heterogeneous architecture using CPUs and GPUs, in order to process the simulation of the interaction of fluids and rigid bodies. This successfully results in a two-way interaction between them and their surrounding objects. As far as we know, this is the first work that presents a computational collaborative environment which makes use of two different paradigms of hardware architecture for this specific kind of problem. Since our method achieves real-time results, it is suitable for virtual reality, simulation and video game fluid simulation problems.

Ana3 is a conserved protein required for the structural integrity of centrioles and basal bodies.

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Stevens, Naomi R; Dobbelaere, Jeroen; Wainman, Alan; Gergely, Fanni; Raff, Jordan W

2009-11-02

Recent studies have identified a conserved "core" of proteins that are required for centriole duplication. A small number of additional proteins have recently been identified as potential duplication factors, but it is unclear whether any of these proteins are components of the core duplication machinery. In this study, we investigate the function of one of these proteins, Drosophila melanogaster Ana3. We show that Ana3 is present in centrioles and basal bodies, but its behavior is distinct from that of the core duplication proteins. Most importantly, we find that Ana3 is required for the structural integrity of both centrioles and basal bodies and for centriole cohesion, but it is not essential for centriole duplication. We show that Ana3 has a mammalian homologue, Rotatin, that also localizes to centrioles and basal bodies and appears to be essential for cilia function. Thus, Ana3 defines a conserved family of centriolar proteins and plays an important part in ensuring the structural integrity of centrioles and basal bodies.

Flexible and rigid cystoscopy in women.

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Gee, Jason R; Waterman, Bradley J; Jarrard, David F; Hedican, Sean P; Bruskewitz, Reginald C; Nakada, Stephen Y

2009-01-01

Previous studies have evaluated the tolerability of rigid versus flexible cystoscopy in men. Similar studies, however, have not been performed in women. We sought to determine whether office-based flexible cystoscopy was better tolerated than rigid cystoscopy in women. Following full IRB approval, women were prospectively randomized in a single-blind manner. Patients were randomized to flexible or rigid cystoscopy and draped in the lithotomy position to maintain blinding of the study. Questionnaires evaluated discomfort before, during, and after cystoscopy. Thirty-six women were randomized to flexible (18) or rigid (18) cystoscopy. Indications were surveillance (16), hematuria (15), recurrent UTIs (2), voiding dysfunction (1), and other (2). All questionnaires were returned by 31/36 women. Using a 10-point visual analog scale (VAS), median discomfort during the procedure for flexible and rigid cystoscopy were 1.4 and 1.8, respectively, in patients perceiving pain. Median recalled pain 1 week later was similar at 0.8 and 1.15, respectively. None of these differences were statistically significant. Flexible and rigid cystoscopy are well tolerated in women. Discomfort during and after the procedure is minimal in both groups. Urologists should perform either procedure in women based on their preference and skill level.

Epinephrine ameliorating response of serum proteins and protein fractions to whole body gamma irradiation in albino rats

International Nuclear Information System (INIS)

Mohamed, M.A.; Saada, H.N.; Roushdy, H.M.; Awad, O.M.; El-Sayed, M.M.; Azab, Kh.Sh.

1997-01-01

The present study was carried out to investigate the role of epinephrine in modifying the radiation induced effects on serum protein as presented by total protein, protein fractions and albumin/globulin (A/G) ratio in adult albino rats. Epinephrine was intraperitoneally injected at a concentration of 200 M/g body weight, 15 min, pre-9 or just after 0 whole body gamma-irradiation of rats at a dose of 6 Gy (single dose). Studies have been undertaken at periods of 1 hr, 4 hrs, 1,3 and 7 days after irradiation. Data of the present study revealed that whole body gamma-irradiation induced significant decreased in the total content of serum protein and albumin at 1,3 and 7 days post radiation exposure alpha 1-globulin significantly increased only on the 1 st hr post-irradiation, however alpha 1-globulin significantly increased along all the experimental periods. B-globulin insignificantly changed after irradiation but gamma-globulin significantly decreased during the experimental periods. These changes were associated with significant decreases in A/G ratio at 3 and 7 days post-irradiation. Administration of epinephrine pre-or after radiation exposure produced some amelioration in the radiation induced changes in the studied parameters. So, it could be concluded that epinephrine plays a beneficial radioprotective role through its pharmacologic properties

Crack identification for rigid pavements using unmanned aerial vehicles

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Bahaddin Ersoz, Ahmet; Pekcan, Onur; Teke, Turker

2017-09-01

Pavement condition assessment is an essential piece of modern pavement management systems as rehabilitation strategies are planned based upon its outcomes. For proper evaluation of existing pavements, they must be continuously and effectively monitored using practical means. Conventionally, truck-based pavement monitoring systems have been in-use in assessing the remaining life of in-service pavements. Although such systems produce accurate results, their use can be expensive and data processing can be time consuming, which make them infeasible considering the demand for quick pavement evaluation. To overcome such problems, Unmanned Aerial Vehicles (UAVs) can be used as an alternative as they are relatively cheaper and easier-to-use. In this study, we propose a UAV based pavement crack identification system for monitoring rigid pavements’ existing conditions. The system consists of recently introduced image processing algorithms used together with conventional machine learning techniques, both of which are used to perform detection of cracks on rigid pavements’ surface and their classification. Through image processing, the distinct features of labelled crack bodies are first obtained from the UAV based images and then used for training of a Support Vector Machine (SVM) model. The performance of the developed SVM model was assessed with a field study performed along a rigid pavement exposed to low traffic and serious temperature changes. Available cracks were classified using the UAV based system and obtained results indicate it ensures a good alternative solution for pavement monitoring applications.

Non-dispersive phloem-protein bodies (NPBs of Populus trichocarpa consist of a SEOR protein and do not respond to cell wounding and Ca2+

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Daniel L. Mullendore

2018-04-01

Full Text Available Differentiating sieve elements in the phloem of angiosperms produce abundant phloem-specific proteins before their protein synthesis machinery is degraded. These P-proteins initially form dense bodies, which disperse into individual filaments when the sieve element matures. In some cases, however, the dense protein agglomerations remain intact and are visible in functional sieve tubes as non-dispersive P-protein bodies, or NPBs. Species exhibiting NPBs are distributed across the entire angiosperm clade. We found that NPBs in the model tree, Populus trichocarpa, resemble the protein bodies described from other species of the order Malpighiales as they all consist of coaligned tubular fibrils bundled in hexagonal symmetry. NPBs of all Malpighiales tested proved unresponsive to sieve tube wounding and Ca2+. The P. trichocarpa NPBs consisted of a protein encoded by a gene that in the genome database of this species had been annotated as a homolog of SEOR1 (sieve element occlusion-related 1 in Arabidopsis. Sequencing of the gene in our plants corroborated this interpretation, and we named the gene PtSEOR1. Previously characterized SEOR proteins form irregular masses of P-protein slime in functional sieve tubes. We conclude that a subgroup of these proteins is involved in the formation of NPBs at least in the Malpighiales, and that these protein bodies have no role in rapid wound responses of the sieve tube network.

Estimation of the protein synthesis rates of the whole body of growing broilers

International Nuclear Information System (INIS)

Koehler, R.; Pahle, T.; Gruhn, K.; Zander, R.; Jeroch, H.; Gebhardt, G.

1988-01-01

The purpose of the investigations was to prove a method, developed for monogastric mammalians, based on a 3-compartment model and assuming a proportional growth of the pools of total N, whether it is applicable to growing poultry. The tracer, 15 N-L-lysine, was given quasi-continuously for four days. In this time and in the following period of five days without tracer intake, the 15 N excretion in the urine was measured. The average of the live weight of the broiler cockerels was 1724 g. The animals were colostomized for sampling the urine separately. Using the fluxes of lysine, the calculation of the whole-body protein synthesis rate was 64.1 g/d. The protein degradation rate was 54.4 g/d. The adequate values of the fractional rates of protein synthesis and degradation for the whole body (without feathers) were 23.3% and 19.8%, resp. Thus it is clearly shown, that the method applied gives real data of the parameters of the N metabolism for growing broilers, being in the range of values for muscle proteins and proteins of the whole body of growing poultry, published by other authors. (author)

Non-rigid registration of tomographic images with Fourier transforms

International Nuclear Information System (INIS)

Osorio, Ar; Isoardi, Ra; Mato, G

2007-01-01

Spatial image registration of deformable body parts such as thorax and abdomen has important medical applications, but at the same time, it represents an important computational challenge. In this work we propose an automatic algorithm to perform non-rigid registration of tomographic images using a non-rigid model based on Fourier transforms. As a measure of similarity, we use the correlation coefficient, finding that the optimal order of the transformation is n = 3 (36 parameters). We apply this method to a digital phantom and to 7 pairs of patient images corresponding to clinical CT scans. The preliminary results indicate a fairly good agreement according to medical experts, with an average registration error of 2 mm for the case of clinical images. For 2D images (dimensions 512x512), the average running time for the algorithm is 15 seconds using a standard personal computer. Summarizing, we find that intra-modality registration of the abdomen can be achieved with acceptable accuracy for slight deformations and can be extended to 3D with a reasonable execution time

Therapeutic rigid bronchoscopy at a tertiary care center in North India: Initial experience and systematic review of Indian literature

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Karan Madan

2014-01-01

Full Text Available Background and Aim: Rigid bronchoscopy is often an indispensable procedure in the therapeutic management of a wide variety of tracheobronchial disorders. However, it is performed at only a few centers in adult patients in India. Herein, we report our initial 1-year experience with this procedure. Materials and Methods: A prospective observational study on the indications, outcomes, and safety of various rigid bronchoscopy procedures performed between November 2009 and October 2010. Improvement in dyspnea, cough, and the overall quality of life was recorded on a visual analog scale from 0 to 100 mm. A systematic review of PubMed was performed to identify studies reporting the use of rigid bronchoscopy from India. Results: Thirty-eight rigid bronchoscopies (50 procedures were performed in 19 patients during the study period. The commonest indication was benign tracheal stenosis followed by central airway tumor, and the procedures performed were rigid bronchoplasty, tumor debulking, and stent placement. The median procedure duration was 45 (range, 30-65 min. There was significant improvement in quality of life associated with therapeutic rigid bronchoscopy. Minor procedural complications were encountered in 18 bronchoscopies, and there was no procedural mortality. The systematic review identified 15 studies, all on the role of rigid bronchoscopy in foreign body removal. Conclusions: Rigid bronchoscopy is a safe and effective modality for treatment of a variety of tracheobronchial disorders. There is a dire need of rigid bronchoscopy training at teaching hospitals in India.

Analysis of Switched-Rigid Floating Oscillator

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Prabhakar R. Marur

2009-01-01

Full Text Available In explicit finite element simulations, a technique called deformable-to-rigid (D2R switching is used routinely to reduce the computation time. Using the D2R option, the deformable parts in the model can be switched to rigid and reverted back to deformable when needed during the analysis. The time of activation of D2R however influences the overall dynamics of the system being analyzed. In this paper, a theoretical basis for the selection of time of rigid switching based on system energy is established. A floating oscillator problem is investigated for this purpose and closed-form analytical expressions are derived for different phases in rigid switching. The analytical expressions are validated by comparing the theoretical results with numerical computations.

The ultrastructure of protein bodies isolated from Pisum sativum and Iris pseudoacorus L. seeds

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Barbara Gabara

2015-01-01

Full Text Available Protein bodies of Pisum sativum and Iris pseudoacorus seeds have been isolated in sucrose gradient with addition of 50mM citrate buffer, pH 5. Their ultrastructure due to isolation procedure has been described. Two types of protein bodies are present in pea and iris seeds: simple and compex ones - with many inclusions. The method of isolation, used in this paper extracts partly proteins - probably albumins, and also substances present in globoids i.e. phytin and acid phosphatase.

Kinetics of inclusion body formation and its correlation with the characteristics of protein aggregates in Escherichia coli.

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Arun K Upadhyay

Full Text Available The objective of the research was to understand the structural determinants governing protein aggregation into inclusion bodies during expression of recombinant proteins in Escherichia coli. Recombinant human growth hormone (hGH and asparaginase were expressed as inclusion bodies in E.coli and the kinetics of aggregate formation was analyzed in details. Asparaginase inclusion bodies were of smaller size (200 nm and the size of the aggregates did not increase with induction time. In contrast, the seeding and growth behavior of hGH inclusion bodies were found to be sequential, kinetically stable and the aggregate size increased from 200 to 800 nm with induction time. Human growth hormone inclusion bodies showed higher resistance to denaturants and proteinase K degradation in comparison to those of asparaginase inclusion bodies. Asparaginase inclusion bodies were completely solubilized at 2-3 M urea concentration and could be refolded into active protein, whereas 7 M urea was required for complete solubilization of hGH inclusion bodies. Both hGH and asparaginase inclusion bodies showed binding with amyloid specific dyes. In spite of its low β-sheet content, binding with dyes was more prominent in case of hGH inclusion bodies than that of asparaginase. Arrangements of protein molecules present in the surface as well as in the core of inclusion bodies were similar. Hydrophobic interactions between partially folded amphiphillic and hydrophobic alpha-helices were found to be one of the main determinants of hGH inclusion body formation. Aggregation behavior of the protein molecules decides the nature and properties of inclusion bodies.

Kinetics of Inclusion Body Formation and Its Correlation with the Characteristics of Protein Aggregates in Escherichia coli

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Upadhyay, Arun K.; Murmu, Aruna; Singh, Anupam; Panda, Amulya K.

2012-01-01

The objective of the research was to understand the structural determinants governing protein aggregation into inclusion bodies during expression of recombinant proteins in Escherichia coli. Recombinant human growth hormone (hGH) and asparaginase were expressed as inclusion bodies in E.coli and the kinetics of aggregate formation was analyzed in details. Asparaginase inclusion bodies were of smaller size (200 nm) and the size of the aggregates did not increase with induction time. In contrast, the seeding and growth behavior of hGH inclusion bodies were found to be sequential, kinetically stable and the aggregate size increased from 200 to 800 nm with induction time. Human growth hormone inclusion bodies showed higher resistance to denaturants and proteinase K degradation in comparison to those of asparaginase inclusion bodies. Asparaginase inclusion bodies were completely solubilized at 2–3 M urea concentration and could be refolded into active protein, whereas 7 M urea was required for complete solubilization of hGH inclusion bodies. Both hGH and asparaginase inclusion bodies showed binding with amyloid specific dyes. In spite of its low β-sheet content, binding with dyes was more prominent in case of hGH inclusion bodies than that of asparaginase. Arrangements of protein molecules present in the surface as well as in the core of inclusion bodies were similar. Hydrophobic interactions between partially folded amphiphillic and hydrophobic alpha-helices were found to be one of the main determinants of hGH inclusion body formation. Aggregation behavior of the protein molecules decides the nature and properties of inclusion bodies. PMID:22479486

Higher accumulation of F1-V fusion recombinant protein in plants after induction of protein body formation.

Science.gov (United States)

Alvarez, M Lucrecia; Topal, Emel; Martin, Federico; Cardineau, Guy A

2010-01-01

Improving foreign protein accumulation is crucial for enhancing the commercial success of plant-based production systems since product yields have a major influence on process economics. Cereal grain evolved to store large amounts of proteins in tightly organized aggregates. In maize, gamma-Zein is the major storage protein synthesized by the rough endoplasmic reticulum (ER) and stored in specialized organelles called protein bodies (PB). Zera (gamma-Zein ER-accumulating domain) is the N-terminal proline-rich domain of gamma-zein that is sufficient to induce the assembly of PB formation. Fusion of the Zera domain to proteins of interest results in assembly of dense PB-like, ER-derived organelles, containing high concentration of recombinant protein. Our main goal was to increase recombinant protein accumulation in plants in order to enhance the efficiency of orally-delivered plant-made vaccines. It is well known that oral vaccination requires substantially higher doses than parental formulations. As a part of a project to develop a plant-made plague vaccine, we expressed our model antigen, the Yersinia pestis F1-V antigen fusion protein, with and without a fused Zera domain. We demonstrated that Zera-F1-V protein accumulation was at least 3x higher than F1-V alone when expressed in three different host plant systems: Ncotiana benthamiana, Medicago sativa (alfalfa) and Nicotiana tabacum NT1 cells. We confirmed the feasibility of using Zera technology to induce protein body formation in non-seed tissues. Zera expression and accumulation did not affect plant development and growth. These results confirmed the potential exploitation of Zera technology to substantially increase the accumulation of value-added proteins in plants.

Effect of beta-hydroxy-beta-methylbutyrate (HMB) on protein metabolism in whole body and in selected tissues.

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Holecek, M; Muthny, T; Kovarik, M; Sispera, L

2009-01-01

Beta-hydroxy-beta-methylbutyrate (HMB) is a leucine metabolite with protein anabolic effect. The aim of the study was to examine the role of exogenous HMB on leucine and protein metabolism in whole body and selected tissues. Rats were administered by HMB (0.1 g/kg b.w.) or by saline. The parameters of whole-body protein metabolism were evaluated 24 h later using L-[1-14C]leucine and L-[3,4,5-3H]phenylalanine. Changes in proteasome dependent proteolysis and protein synthesis were determined according the "chymotrypsin-like" enzyme activity and labeled leucine and phenylalanine incorporation into the protein. A decrease in leucine clearance and whole-body protein turnover (i.e., a decrease in whole-body proteolysis and protein synthesis) was observed in HMB treated rats. Proteasome-dependent proteolysis decreased significantly in skeletal muscle, changes in heart, liver, jejunum, colon, kidney, and spleen were insignificant. Decrease in protein synthesis was observed in the heart, colon, kidney, and spleen, while an increase was observed in the liver. There were no significant changes in leucine oxidation. We conclude that protein anabolic effect of HMB in skeletal muscle is related to inhibition of proteolysis in proteasome. Alterations in protein synthesis in visceral tissues may affect several important functions and the metabolic status of the whole body.

Investigation of protein and lipid metabolism in thyroid pathology using whole-body radiometry

International Nuclear Information System (INIS)

Gorobets, V.F.; Matveenko, E.G.

1987-01-01

Radiometry of the whole body and its organs was employed to study certain aspects of protein-aminoacid and lipid metabolism in patients with thyroid diseases. Metabolism of human serum 131 I-albumin was studied in 12 patients with neurocirculatory dystonia, in 13 patients with diffuse toxic goiter (in 10 before and after drug therapy) and in 9 controls. 75 Se-methionine aminoacid metabolism was investigated in 9 patients with toxic thyroid adenoma and in 13 controls. The body cell mass was determined in 82 patients with thyrotoxicosis by a measurable amount of 40 K. These data were compared with those of 249 healthy persons. An increase in catabolism of labeled albumin, intensification of labeled methionine metabolism at the tissue level, signs of a decrease in the total amount of metabolic albumin in the body were revealed. Intensification of protein metabolism resulted in a decrease in the body cell mass of these patients. After adequate therapy the above indices of protein metabolism in patients with thyrotoxicosis returned to normal. The assimilation of fatty acids and neutral fat was disturbed both in thyrotoxicosis and hypothyroidism

Torsional rigidity, isospectrality and quantum graphs

International Nuclear Information System (INIS)

Colladay, Don; McDonald, Patrick; Kaganovskiy, Leon

2017-01-01

We study torsional rigidity for graph and quantum graph analogs of well-known pairs of isospectral non-isometric planar domains. We prove that such isospectral pairs are distinguished by torsional rigidity. (paper)

Management of rigid post-traumatic kyphosis.

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Wu, S S; Hwa, S Y; Lin, L C; Pai, W M; Chen, P Q; Au, M K

1996-10-01

Rigid post-traumatic kyphosis after fracture of the thoracolumbar and lumbar spine represents a failure of initial management of the injury. Kyphosis moves the center of gravity anterior. The kyphosis and instability may result in pain, deformity, and increased neurologic deficits. Management for symptomatic post-traumatic kyphosis always has presented a challenge to orthopedic surgeons. To evaluate the surgical results of one stage posterior correction for rigid symptomatic post-traumatic kyphosis of the thoracolumbar and lumbar spine. The management for post-traumatic kyphosis remains controversial. Anterior, posterior, or combined anterior and posterior procedures have been advocated by different authors and show various degrees of success. One vertebra immediately above and below the level of the deformity was instrumented posteriorly by a transpedicular system (internal fixator AO). Posterior decompression was performed by excision of the spinal process and bilateral laminectomy. With the deformed vertebra through the pedicle, the vertebral body carefully is removed around the pedicle level, approximating a wedge shape. The extent to which the deformed vertebral body should be removed is determined by the attempted correction. Correction of the deformity is achieved by manipulation of the operating table and compression of the adjacent Schanz screws above and below the lesion. Thirteen patients with post-traumatic kyphosis with symptoms of fatigue and pain caused by slow progression of kyphotic deformities received posterior decompression, correction, and stabilization as a definitive treatment. The precorrection kyphosis ranged from 30-60 degrees, with a mean of 40 degrees +/- 10.8 degrees. After correction, kyphosis was reduced to an average of 1.5 degrees +/- 3.8 degrees, with a range from -5 degrees to 5 degrees. The average angle of correction was 38.8 degrees +/- 10.4 degrees, with a range from 25 degrees to 60 degrees. Significant difference was found

Protein misfolding specifies recruitment to cytoplasmic inclusion bodies.

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Bersuker, Kirill; Brandeis, Michael; Kopito, Ron R

2016-04-25

Inclusion bodies (IBs) containing aggregated disease-associated proteins and polyubiquitin (poly-Ub) conjugates are universal histopathological features of neurodegenerative diseases. Ub has been proposed to target proteins to IBs for degradation via autophagy, but the mechanisms that govern recruitment of ubiquitylated proteins to IBs are not well understood. In this paper, we use conditionally destabilized reporters that undergo misfolding and ubiquitylation upon removal of a stabilizing ligand to examine the role of Ub conjugation in targeting proteins to IBs that are composed of an N-terminal fragment of mutant huntingtin, the causative protein of Huntington's disease. We show that reporters are excluded from IBs in the presence of the stabilizing ligand but are recruited to IBs after ligand washout. However, we find that Ub conjugation is not necessary to target reporters to IBs. We also report that forced Ub conjugation by the Ub fusion degradation pathway is not sufficient for recruitment to IBs. Finally, we find that reporters and Ub conjugates are stable at IBs. These data indicate that compromised folding states, rather than conjugation to Ub, can specify recruitment to IBs. © 2016 Bersuker et al.

Sas-4 proteins are required during basal body duplication in Paramecium

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Gogendeau, Delphine; Hurbain, Ilse; Raposo, Graca; Cohen, Jean; Koll, France; Basto, Renata

2011-01-01

Centrioles and basal bodies are structurally related organelles composed of nine microtubule (MT) triplets. Studies performed in Caenorhabditis elegans embryos have shown that centriole duplication takes place in sequential way, in which different proteins are recruited in a specific order to assemble a procentriole. ZYG-1 initiates centriole duplication by triggering the recruitment of a complex of SAS-5 and SAS-6, which then recruits the final player, SAS-4, to allow the incorporation of MT singlets. It is thought that a similar mechanism (that also involves additional proteins) is present in other animal cells, but it remains to be investigated whether the same players and their ascribed functions are conserved during basal body duplication in cells that exclusively contain basal bodies. To investigate this question, we have used the multiciliated protist Paramecium tetraurelia. Here we show that in the absence of PtSas4, two types of defects in basal body duplication can be identified. In the majority of cases, the germinative disk and cartwheel, the first structures assembled during duplication, are not detected. In addition, if daughter basal bodies were formed, they invariably had defects in MT recruitment. Our results suggest that PtSas4 has a broader function than its animal orthologues. PMID:21289083

Cats during gestation and lactation fed with canned food ad libitum: energy and protein intake, development of body weight and body composition.

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Wichert, B; Signer, M; Uebelhart, D

2012-12-01

The NRC recommendations for cats for energy and protein supply during gestation and lactation are based on limited data. This study aimed to answer the question: Can the energy requirement be met with canned food or is the volume restrictive? Therefore, balance trials were conducted in 10 queens before mating, during the 4th and 7th week of gestation and during the 2nd and 6th week of lactation. The cats were fed with canned food ad libitum. Additionally, the body composition of the queens was measured by dual-energy X-ray absorptiometry (Dexa) before mating, after parturition and after weaning. Eight of 10 cats presented increased body fat content and lean body mass during gestation. The weight loss during lactation led to a loss of lean body mass, but only six cats lost body fat of widely differing amounts. It was evident that the queens' dry matter intake was consistent with that of queens fed ad libitum with dry food. The cats lost lean body mass during lactation and had negative protein balances in the 2nd week of lactation. This seems to be physiological in early lactation. Nevertheless, the protein recommendations for lactation seem to be too low. © 2011 Blackwell Verlag GmbH.

Rigidity of monodromies for Appell's hypergeometric functions

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Yoshishige Haraoka

2015-01-01

Full Text Available For monodromy representations of holonomic systems, the rigidity can be defined. We examine the rigidity of the monodromy representations for Appell's hypergeometric functions, and get the representations explicitly. The results show how the topology of the singular locus and the spectral types of the local monodromies work for the study of the rigidity.

Functional characterization of the Woronin body protein WscA of the pathogenic mold Aspergillus fumigatus.

Science.gov (United States)

Leonhardt, Yannik; Beck, Julia; Ebel, Frank

2016-05-01

Woronin bodies are fungal-specific organelles that seal damaged hyphal compartments and thereby contribute to the stress resistance and virulence of filamentous fungi. In this study, we have characterized the Aspergillus fumigatus Woronin body protein WscA. WscA is homologous to Neurospora crassa WSC, a protein that was shown to be important for biogenesis, segregation and positioning of Woronin bodies. WscA and WSC both belong to the Mpv17/PMP22 family of peroxisomal membrane proteins. An A. fumigatus ΔwscA mutant is unable to form Woronin bodies, and HexA, the protein that forms the crystal-like core of Woronin bodies, accumulates in large peroxisomes instead. The ΔwscA mutant showed no defect in segregation of HexA containing organelles, as has been reported for the corresponding N. crassa mutant. In the peroxisomes of the A. fumigatus mutant, HexA assembles into compact, donut-shaped structures. Experiments with GFP fusion proteins revealed that WscA function is highly sensitive to these modifications, in particular to an N-terminal fusion of GFP. In N. crassa, WSC was shown to be essentially required for Woronin body positioning, but the respective domain is not conserved in most other Pezizomycotina, including A. fumigatus. We have recently found evidence that HexA may have a direct role in WB positioning, since a HexA-GFP fusion protein, lacking a functional PTS1 motif, is efficiently recruited to the septal pore. In the current study we show that this targeting of HexA-GFP is independent of WscA. Copyright © 2016 Elsevier GmbH. All rights reserved.

Preparative Protein Production from Inclusion Bodies and Crystallization: A Seven-Week Biochemistry Sequence

Science.gov (United States)

Peterson, Megan J.; Snyder, W. Kalani; Westerman, Shelley; McFarland, Benjamin J.

2011-01-01

We describe how to produce and purify proteins from E. coli inclusion bodies by adapting versatile, preparative-scale techniques to the undergraduate laboratory schedule. This seven-week sequence of experiments fits into an annual cycle of research activity in biochemistry courses. Recombinant proteins are expressed as inclusion bodies, which are collected, washed, then solubilized in urea. Stepwise dialysis to dilute urea over the course of a week produces refolded protein. Column chromatography is used to purify protein into fractions, which are then analyzed with gel electrophoresis and concentration assays. Students culminate the project by designing crystallization trials in sitting-drop trays. Student evaluation of the experience has been positive, listing 5–12 new techniques learned, which are transferrable to graduate research in academia and industry. PMID:21691428

Can serum concentration of C-reactive protein, albumin and body ...

African Journals Online (AJOL)

... of acute phase proteins and a fall in CD4+T-cell counts and body weight. ... subjects (control) attending the HIV/AIDS Clinic in Nnamdi Azikiwe Teaching Hospital, ... while their weights were measured using high precision weighing balance.

Convenient method for resolving degeneracies due to symmetry of the magnetic susceptibility tensor and its application to pseudo contact shift-based protein-protein complex structure determination

Energy Technology Data Exchange (ETDEWEB)

Kobashigawa, Yoshihiro; Saio, Tomohide [Hokkaido University, Department of Structural Biology, Faculty of Advanced Life Science (Japan); Ushio, Masahiro [Hokkaido University, Graduate School of Life Science (Japan); Sekiguchi, Mitsuhiro [Astellas Pharma Inc., Analysis and Pharmacokinetics Research Labs, Department of Drug Discovery (Japan); Yokochi, Masashi; Ogura, Kenji; Inagaki, Fuyuhiko, E-mail: finagaki@pharm.hokudai.ac.jp [Hokkaido University, Department of Structural Biology, Faculty of Advanced Life Science (Japan)

2012-05-15

Pseudo contact shifts (PCSs) induced by paramagnetic lanthanide ions fixed in a protein frame provide long-range distance and angular information, and are valuable for the structure determination of protein-protein and protein-ligand complexes. We have been developing a lanthanide-binding peptide tag (hereafter LBT) anchored at two points via a peptide bond and a disulfide bond to the target proteins. However, the magnetic susceptibility tensor displays symmetry, which can cause multiple degenerated solutions in a structure calculation based solely on PCSs. Here we show a convenient method for resolving this degeneracy by changing the spacer length between the LBT and target protein. We applied this approach to PCS-based rigid body docking between the FKBP12-rapamycin complex and the mTOR FRB domain, and demonstrated that degeneracy could be resolved using the PCS restraints obtained from two-point anchored LBT with two different spacer lengths. The present strategy will markedly increase the usefulness of two-point anchored LBT for protein complex structure determination.

On Hydroelastic Body-Boundary Condition of Floating Structures

DEFF Research Database (Denmark)

Xia, Jinzhu

1996-01-01

A general linear body boundary condition of hydroelastic analysis of arbitrary shaped floating structures generalizes the classic kinematic rigid-body (Timman-Newman) boundary condition for seakeeping problems. The new boundary condition is consistent with the existing theories under certain...

Effects of protein and energy deficiency on the incorporation of 14C-Chlorella protein hydrolysate into body constituents of adult rats

International Nuclear Information System (INIS)

Yamamoto, Shigeru; Wakabayashi, Kazuo; Niiyama, Yoshiaki; Inoue, Goro

1974-01-01

The effects of protein and/or energy deficiency on 14 C incorporation into body constituents and 14 C output in expired air and urine were investigated in adult rats using 14 C-Chlorella protein hydrolysate. Rats were given a protein-free diet (PFD) for 2 weeks and conrol rats were fed ad libitum or pari-fed with the PFD group on a 12% lactalbumin diet (LA and Pair-fed, respectively). On the 15th day, animals received 14 C-Chlorella protein hydolysate with 5 g of their respective diet. One group of PFD animals was given tracer by stomach tube without food (PFD-fast). Normal control rats ate about twice as much diet as the PFD group. The respiratory 14 C output in the PFD group was identical with those in the LA and Pair-fed groups and was less than that in the PFD-fast group. The rate of protein synthesis, provisionally expressed as relative specific radioactivity, was more in the PFD group than in the normal group in the liver and less than the latter in the muscle. The LA group retained less total radioactivity in the body than the Pair-fed or PFD group, indicating high capability to hold the body protein in protein deficiency. In addition, decreased conversion of amino acids to lipids and glycogen was observed in the PFD group. All these differences are interpreted as adaptations to protein shortage. On prolonged fasting (PFD-fast group), gluconeogenesis in the liver increased to provide energy, despite the protein deficiency. The relative importances of protein and energy for tissue protein synthesis are briefly discussed. (author)

From Wage Rigidities to Labour Market Rigidities: A Turning-Point in Explaining Equilibrium Unemployment?

OpenAIRE

Marco Guerrazzi; Nicola Meccheri

2009-01-01

This paper offers a critical discussion of the concept of labour market rigidity relevant to explaining unemployment. Starting from Keynes’s own view, we discuss how the concept of labour market flexibility has changed over time, involving nominal or real wage flexibility, contract flexibility or labour market institution flexibility. We also provide a critical assessment of the factors that lead the search framework highlighting labour market rigidities (frictions) to challenge the more wide...

Why do total-body decay curves of iodine-labeled proteins begin with a delay

International Nuclear Information System (INIS)

Regoeczi, E.

1987-01-01

The initial delay that occurs in total-body radiation curves reaching their single-exponential slopes was analyzed from 106 experiments involving several mammalian species (guinea pig, mouse, rabbit, and rat) and plasma proteins (alpha 1-acid glycoprotein, antithrombin III, fibrinogen, immunoglobulin G, and transferrin) in 14 different combinations. The time interval (Td) between injection and the intercept of the slope with the full-dose value was adopted as a measure of curve nonideality. The overall mean Td was 6.6 h, but individual values showed a significant correlation to protein half-lives, whereby proteins of unequal metabolic properties exhibited different mean Td values. Targeting protein to the liver abolished delay. Choice of the isotope ( 125 I or 131 I) and size of the labeled protein had no influence on the magnitude of delay. Whole-body radiation curves of animals that received [ 125 I]iodotyrosines, Na 131 I, or 131 I-polyvinylpyrrolidone exhibited no initial delays. These results do not support the earlier notion that delay is caused by a redistribution of the labeled protein in the body to radiometrically more favorable sites. However, they are compatible with the assumption that delayed passage of a protein dose through the extracellular matrix and/or retarded transfer of proteolytic products from extravascular catabolic sites to plasma may be responsible for the phenomenon

Foreign Body Retrieval

Medline Plus

Full Text Available ... provides real-time imaging, making it a good tool for guiding removal procedures. In some cases, it is potentially more harmful to remove the ... provides real-time imaging, making it a good tool for guiding foreign body removal ... rare cases, the general anesthesia used during rigid esophagoscopy can ...

Finite-difference analysis of shells impacting rigid barriers

International Nuclear Information System (INIS)

Pirotin, S.D.; Witmer, E.A.

1977-01-01

Nuclear power plants must be protected from the adverse effects of missile impacts. A significant category of missile impact involves deformable structures (pressure vessel components, whipping pipes) striking relatively rigid targets (concrete walls, bumpers) which act as protective devices. The response and interaction of these structures is needed to assess the adequacy of these barriers for protecting vital safety related equipment. The present investigation represents an initial attempt to develop an efficient numerical procedure for predicting the deformations and impact force time-histories of shells which impact upon a rigid target. The general large-deflection equations of motion of the shell are expressed in finite-difference form in space and integrated in time through application of the central-difference temporal operator. The effect of material nonlinearities is treated by a mechanical sublayer material model which handles the strain-hardening, Bauschinger, and strain-rate effects. The general adequacy of this shell treatment has been validated by comparing predictions with the results of various experiments in which structures have been subjected to well-defined transient forcing functions (typically high-explosive impulse loading). The 'new' ingredient addressed in the present study involves an accounting for impact interaction and response of both the target structure and the attacking body. (Auth.)

Increased protein intake reduces lean body mass loss during weight loss in athletes.

Science.gov (United States)

Mettler, Samuel; Mitchell, Nigel; Tipton, Kevin D

2010-02-01

To examine the influence of dietary protein on lean body mass loss and performance during short-term hypoenergetic weight loss in athletes. In a parallel design, 20 young healthy resistance-trained athletes were examined for energy expenditure for 1 wk and fed a mixed diet (15% protein, 100% energy) in the second week followed by a hypoenergetic diet (60% of the habitual energy intake), containing either 15% (approximately 1.0 g x kg(-1)) protein (control group, n = 10; CP) or 35% (approximately 2.3 g x kg(-1)) protein (high-protein group, n = 10; HP) for 2 wk. Subjects continued their habitual training throughout the study. Total, lean body, and fat mass, performance (squat jump, maximal isometric leg extension, one-repetition maximum (1RM) bench press, muscle endurance bench press, and 30-s Wingate test) and fasting blood samples (glucose, nonesterified fatty acids (NEFA), glycerol, urea, cortisol, free testosterone, free Insulin-like growth factor-1 (IGF-1), and growth hormone), and psychologic measures were examined at the end of each of the 4 wk. Total (-3.0 +/- 0.4 and -1.5 +/- 0.3 kg for the CP and HP, respectively, P = 0.036) and lean body mass loss (-1.6 +/- 0.3 and -0.3 +/- 0.3 kg, P = 0.006) were significantly larger in the CP compared with those in the HP. Fat loss, performance, and most blood parameters were not influenced by the diet. Urea was higher in HP, and NEFA and urea showed a group x time interaction. Fatigue ratings and "worse than normal" scores on the Daily Analysis of Life Demands for Athletes were higher in HP. These results indicate that approximately 2.3 g x kg(-1) or approximately 35% protein was significantly superior to approximately 1.0 g x kg(-1) or approximately 15% energy protein for maintenance of lean body mass in young healthy athletes during short-term hypoenergetic weight loss.

Homogenization for rigid suspensions with random velocity-dependent interfacial forces

KAUST Repository

Gorb, Yuliya

2014-12-01

We study suspensions of solid particles in a viscous incompressible fluid in the presence of random velocity-dependent interfacial forces. The flow at a small Reynolds number is modeled by the Stokes equations, coupled with the motion of rigid particles arranged in a periodic array. The objective is to perform homogenization for the given suspension and obtain an equivalent description of a homogeneous (effective) medium, the macroscopic effect of the interfacial forces and the effective viscosity are determined using the analysis on a periodicity cell. In particular, the solutions uωε to a family of problems corresponding to the size of microstructure ε and describing suspensions of rigid particles with random surface forces imposed on the interface, converge H1-weakly as ε→0 a.s. to a solution of a Stokes homogenized problem, with velocity dependent body forces. A corrector to a homogenized solution that yields a strong H1-convergence is also determined. The main technical construction is built upon the Γ-convergence theory. © 2014 Elsevier Inc.

Integration of car-body flexibility into train-track coupling system dynamics analysis

Science.gov (United States)

Ling, Liang; Zhang, Qing; Xiao, Xinbiao; Wen, Zefeng; Jin, Xuesong

2018-04-01

The resonance vibration of flexible car-bodies greatly affects the dynamics performances of high-speed trains. In this paper, we report a three-dimensional train-track model to capture the flexible vibration features of high-speed train carriages based on the flexible multi-body dynamics approach. The flexible car-body is modelled using both the finite element method (FEM) and the multi-body dynamics (MBD) approach, in which the rigid motions are obtained by using the MBD theory and the structure deformation is calculated by the FEM and the modal superposition method. The proposed model is applied to investigate the influence of the flexible vibration of car-bodies on the dynamics performances of train-track systems. The dynamics performances of a high-speed train running on a slab track, including the car-body vibration behaviour, the ride comfort, and the running safety, calculated by the numerical models with rigid and flexible car-bodies are compared in detail. The results show that the car-body flexibility not only significantly affects the vibration behaviour and ride comfort of rail carriages, but also can has an important influence on the running safety of trains. The rigid car-body model underestimates the vibration level and ride comfort of rail vehicles, and ignoring carriage torsional flexibility in the curving safety evaluation of trains is conservative.

Protein synthesis in body wall and midgut during the larval moulting cycle of the silkworm, Bombyx mori

International Nuclear Information System (INIS)

Nagata, Masao

1976-01-01

14 C-leucine was injected into larvae at various points of time during the fourth moulting cycle, and four hours after the injection, dissection was carried out. The intake of radioactivity into the proteins of body wall and midgut was investigated. The specific activity of the proteins changed with the moulting of larvae, but the specific activity of the amino acid pool in tissues also changed. Accordingly, the change of specific activity in proteins was not able to be regarded as the variation of synthetic capability. The ratio of the specific activity of proteins to that of amino acid pool was determined, and it was revealed that the capability of protein synthesis of body wall and midgut was high in feeding period and lowered in moulting period, and it was different according to various stages of moulting period. As the result of investigation on the time course of the specific activity of proteins of body wall and midgut after the injection of 14 C-leucine, it was shown that the specific activity reached the maximum earlier in feeding period than in moulting period. The intake of 14 C-leucine into body wall and midgut was examined with 20 min. labeling, consequently the specific activity of proteins was high in feeding period and low in moulting period. The capability of protein synthesis was active in feeding period and dwindled in moulting period in case of the whole body of larvae. (Kako, I.)

Assessment of the distribution of protein in the human body by in-vivo neutron activation analysis

International Nuclear Information System (INIS)

Burkinshaw, L.; Hill, G.L.; Morgan, D.B.

1979-01-01

Whole-body in-vivo neutron activation analysis has been developed into a clinically acceptable technique for measuring total-body nitrogen. Since most of the nitrogen is in protein, the result gives an estimates of total-body protein, and this has proved very informative in studies of nutritional problems. It would often be useful to know how the total protein is divided between muscle and other lean tissues, and this could be determined if the body content of some other substance, distributed differently between the two types of tissue, were known. Potassium is a suitable substance. The total amount in the body is always measured in the course of the activation analysis procedure, and its concentration relative to nitrogen is more than twice as high in muscle as it is in the other lean tissues. Therefore a high proportion of muscle in the body will be reflected in a high ratio of total-body potassium to total-body nitrogen. Starting with this observation, a mathematical model has been developed which makes it possible to estimate the masses and protein contents of muscle and non-muscle lean tissues from total-body nitrogen and potassium. The errors of estimation are too large to allow conclusions to be drawn from a single measurement of an individual, but they do permit mean values for groups of subjects to be compared. This way of interpreting the results of in-vivo neutron activation analysis is expected to increase the value of the technique for studying nutritional problems. (author)

Simulation Methods in the Contact with Impact of Rigid Bodies

Directory of Open Access Journals (Sweden)

Cristina Basarabă-Opritescu

2007-10-01

Full Text Available The analysis of impacts of elastic bodies is topical and it has many applications, practical and theoretical, too. The elastic character of collision is put in evidence, especially by the velocities of some parts of a particular body, named “ring”. In the presented paper, the situation of elastic collisions is put in evidence by the simulation with the help of the program ANSYS and it refers to the particular case of the ring, with the mechanical characteristics, given in the paper

On the atmosphere of a moving body

DEFF Research Database (Denmark)

Pedersen, Johan Rønby; Aref, Hassan

2010-01-01

We explore whether a rigid body moving freely with no circulation around it in a two-dimensional ideal fluid can carry a fluid "atmosphere" with it in its motion. Somewhat surprisingly, the answer appears to be "yes." When the body is elongated and the motion is dominated by rotation, we demonstr...

On the atmosphere of a moving body

DEFF Research Database (Denmark)

Pedersen, Johan Rønby; Aref, Hassan

2010-01-01

We have explored whether a rigid body moving freely with no circulation around it in a two-dimensional ideal fluid can carry a fluid ``atmosphere'' with it in its motion. Somewhat surprisingly, the answer appears to be ``yes''. When the body is elongated and the motion is dominated by rotation, w...

Soft soils reinforced by rigid vertical inclusions

Directory of Open Access Journals (Sweden)

Iulia-Victoria NEAGOE

2013-12-01

Full Text Available Reinforcement of soft soils by rigid vertical inclusions is an increasingly used technique over the last few years. The system consists of rigid or semi-rigid vertical inclusions and a granular platform for the loads transfer from the structure to the inclusions. This technique aims to reduce the differential settlements both at ground level as below the structure. Reinforcement by rigid inclusions is mainly used for foundation works for large commercial and industrial platforms, storage tanks, wastewater treatment plants, wind farms, bridges, roads, railway embankments. The subject is one of interest as it proves the recently concerns at international level in research and design; however, most studies deal more with the static behavior and less with the dynamic one.

Protein and lipid accretion in body components of growing pigs : effects of body weight and nutrient intake

NARCIS (Netherlands)

Bikker, P.

1994-01-01

In pig production, optimization of the conversion of animal feeding-stuffs into body components, especially lean meat, requires knowledge of the response relationships between nutrient intake and animal performance. In this study, the separate effects of protein and energy intake on rate

Total proteins and protein fractions levels in pregnant rats subjected to whole-body gamma irradiation

International Nuclear Information System (INIS)

Mansour, M.A.; Roushdy, H.M.; Mazhar, F.M.; Abu-Gabal, H.A.

1986-01-01

A total number of 180 mature rats (120 females and 60 males) weighing from 120-140 g were used to study the effect of two doses (2 and 4 Gy) whole-body gamma irradiation on the level of total protein and protein fractions in serum of pregnant rats during the period of organogenesis. It was found that the levels of total protein, albumin and gamma globulins significantly decreased according to the doses of exposure. The levels of alpha and beta globulins significantly increased more in the serum of rats exposed to 2 Gy than in rats exposed to 4 Gy. The level of A/G ratio significantly decreased more in the serum of rats exposed to 2Gy than in those exposed to 4 Gy

Effects of protein and energy deficiency on the incorporation of /sup 14/C-Chlorella protein hydrolysate into body constituents of adult rats

Energy Technology Data Exchange (ETDEWEB)

Yamamoto, S; Wakabayashi, K; Niiyama, Y; Inoue, G [Tokushima Univ. (Japan). School of Medicine

1974-12-01

The effects of protein and/or energy deficiency on /sup 14/C incorporation into body constituents and /sup 14/C output in expired air and urine were investigated in adult rats using /sup 14/C-Chlorella protein hydrolysate. Rats were given a protein-free diet (PFD) for 2 weeks and conrol rats were fed ad libitum or pari-fed with the PFD group on a 12% lactalbumin diet (LA and Pair-fed, respectively). On the 15th day, animals received /sup 14/C-Chlorella protein hydolysate with 5 g of their respective diet. One group of PFD animals was given tracer by stomach tube without food (PFD-fast). Normal control rats ate about twice as much diet as the PFD group. The respiratory /sup 14/C output in the PFD group was identical with those in the LA and Pair-fed groups and was less than that in the PFD-fast group. The rate of protein synthesis, provisionally expressed as relative specific radioactivity, was more in the PFD group than in the normal group in the liver and less than the latter in the muscle. The LA group retained less total radioactivity in the body than the Pair-fed or PFD group, indicating high capability to hold the body protein in protein deficiency. In addition, decreased conversion of amino acids to lipids and glycogen was observed in the PFD group. All these differences are interpreted as adaptations to protein shortage. On prolonged fasting (PFD-fast group), gluconeogenesis in the liver increased to provide energy, despite the protein deficiency. The relative importances of protein and energy for tissue protein synthesis are briefly discussed.

A coated rigid elliptical inclusion loaded by a couple in the presence of uniform interfacial and hoop stresses

Science.gov (United States)

Wang, Xu; Schiavone, Peter

2018-06-01

We consider a confocally coated rigid elliptical inclusion, loaded by a couple and introduced into a remote uniform stress field. We show that uniform interfacial and hoop stresses along the inclusion-coating interface can be achieved when the two remote normal stresses and the remote shear stress each satisfy certain conditions. Our analysis indicates that: (i) the uniform interfacial tangential stress depends only on the area of the inclusion and the moment of the couple; (ii) the rigid-body rotation of the rigid inclusion depends only on the area of the inclusion, the coating thickness, the shear moduli of the composite and the moment of the couple; (iii) for given remote normal stresses and material parameters, the coating thickness and the aspect ratio of the inclusion are required to satisfy a particular relationship; (iv) for prescribed remote shear stress, moment and given material parameters, the coating thickness, the size and aspect ratio of the inclusion are also related. Finally, a harmonic rigid inclusion emerges as a special case if the coating and the matrix have identical elastic properties.

Low Dietary Protein Status Potentiating Risk of Health Hazard in Whole Body Gamma Irradiated Rats

International Nuclear Information System (INIS)

El-Gawish, M.A.M.; Yousri, R.M.; Roushdy, H.M.; Abdel-Reheem, K.A.; Al-Mossallamy, N.A.

1998-01-01

Investigations were planned to assess the changes in certain biochemical parameters as affected by the synergistic effect of exposure to fractionated doses of rays and / or feeding on different protein levels. The date showed that animals kept on normal or low protein diet exhibited a significant decrease in serum total protein and glucose. Also , a significant increase was recorded in insulin level in rats exposed at the radiation dose level of 20 Gy. Exposure to cumulative doses of irradiation has aggrevated the hyperglycemic effect of high protein diet with a significant and marked increase of insulin at all the applied doses. Animals fed normal high or low protein diet were found to exert significant decreases in T3, T4 while a significant increase in TSH of high protein group occurred as a result of exposure to cumulative doses of gamma-irradiation. Rats kept on low protein diet exhibited losses in body weight, hypercholesterolemia, low levels of phospholipids and triglycerides as compared with the normal protein diet group. In contrast high protein diet group showed no serious effects. Irradiation has potentiated body weight losses, hypotriglyceridemia and hypercholesterolemia in animal group fed low protein diet with a significant increase in serum phospholipids due to the higher radiation dose of 20 Gy. Protein deficiency acted synergistically with gamma irradiation and increased the susceptibility of body organs to radiation damage. Such findings contributed to the knowledge which stimulated the decrease of the internationally recognized occupational dose limits from 50 down to 20 m Sv (ICRP 1991)

CAB-Align: A Flexible Protein Structure Alignment Method Based on the Residue-Residue Contact Area.

Directory of Open Access Journals (Sweden)

Genki Terashi

Full Text Available Proteins are flexible, and this flexibility has an essential functional role. Flexibility can be observed in loop regions, rearrangements between secondary structure elements, and conformational changes between entire domains. However, most protein structure alignment methods treat protein structures as rigid bodies. Thus, these methods fail to identify the equivalences of residue pairs in regions with flexibility. In this study, we considered that the evolutionary relationship between proteins corresponds directly to the residue-residue physical contacts rather than the three-dimensional (3D coordinates of proteins. Thus, we developed a new protein structure alignment method, contact area-based alignment (CAB-align, which uses the residue-residue contact area to identify regions of similarity. The main purpose of CAB-align is to identify homologous relationships at the residue level between related protein structures. The CAB-align procedure comprises two main steps: First, a rigid-body alignment method based on local and global 3D structure superposition is employed to generate a sufficient number of initial alignments. Then, iterative dynamic programming is executed to find the optimal alignment. We evaluated the performance and advantages of CAB-align based on four main points: (1 agreement with the gold standard alignment, (2 alignment quality based on an evolutionary relationship without 3D coordinate superposition, (3 consistency of the multiple alignments, and (4 classification agreement with the gold standard classification. Comparisons of CAB-align with other state-of-the-art protein structure alignment methods (TM-align, FATCAT, and DaliLite using our benchmark dataset showed that CAB-align performed robustly in obtaining high-quality alignments and generating consistent multiple alignments with high coverage and accuracy rates, and it performed extremely well when discriminating between homologous and nonhomologous pairs of proteins

CAB-Align: A Flexible Protein Structure Alignment Method Based on the Residue-Residue Contact Area.

Science.gov (United States)

Terashi, Genki; Takeda-Shitaka, Mayuko

2015-01-01

Proteins are flexible, and this flexibility has an essential functional role. Flexibility can be observed in loop regions, rearrangements between secondary structure elements, and conformational changes between entire domains. However, most protein structure alignment methods treat protein structures as rigid bodies. Thus, these methods fail to identify the equivalences of residue pairs in regions with flexibility. In this study, we considered that the evolutionary relationship between proteins corresponds directly to the residue-residue physical contacts rather than the three-dimensional (3D) coordinates of proteins. Thus, we developed a new protein structure alignment method, contact area-based alignment (CAB-align), which uses the residue-residue contact area to identify regions of similarity. The main purpose of CAB-align is to identify homologous relationships at the residue level between related protein structures. The CAB-align procedure comprises two main steps: First, a rigid-body alignment method based on local and global 3D structure superposition is employed to generate a sufficient number of initial alignments. Then, iterative dynamic programming is executed to find the optimal alignment. We evaluated the performance and advantages of CAB-align based on four main points: (1) agreement with the gold standard alignment, (2) alignment quality based on an evolutionary relationship without 3D coordinate superposition, (3) consistency of the multiple alignments, and (4) classification agreement with the gold standard classification. Comparisons of CAB-align with other state-of-the-art protein structure alignment methods (TM-align, FATCAT, and DaliLite) using our benchmark dataset showed that CAB-align performed robustly in obtaining high-quality alignments and generating consistent multiple alignments with high coverage and accuracy rates, and it performed extremely well when discriminating between homologous and nonhomologous pairs of proteins in both

Role of the disaggregase ClpB in processing of proteins aggregated as inclusion bodies.

Science.gov (United States)

Zblewska, Kamila; Krajewska, Joanna; Zolkiewski, Michal; Kędzierska-Mieszkowska, Sabina

2014-08-01

Overproduction of heterologous proteins in bacterial systems often results in the formation of insoluble inclusion bodies (IBs), which is a major impediment in biochemical research and biotechnology. In principle, the activity of molecular chaperones could be employed to gain control over the IB formation and to improve the recombinant protein yields, but the potential of each of the major bacterial chaperones (DnaK/J, GroEL/ES, and ClpB) to process IBs has not been fully established yet. We investigated the formation of inclusion bodies (IBs) of two aggregation-prone proteins, VP1LAC and VP1GFP, overproduced in Escherichiacoli in the presence and absence of the chaperone ClpB. We found that both ClpB isoforms, ClpB95 and ClpB80 accumulated in E. coli cells during the production of IBs. The amount of IB proteins increased in the absence of ClpB. ClpB supported the resolubilization and reactivation of the aggregated VP1LAC and VP1GFP in E. coli cells. The IB disaggregation was optimal in the presence of both ClpB95 and ClpB80. Our results indicate an essential role of ClpB in controlling protein aggregation and inclusion body formation in bacteria. Copyright © 2014 Elsevier Inc. All rights reserved.

A Rigid Mid-Lift-to-Drag Ratio Approach to Human Mars Entry, Descent, and Landing

Science.gov (United States)

Cerimele, Christopher J.; Robertson, Edward A.; Sostaric, Ronald R.; Campbell, Charles H.; Robinson, Phil; Matz, Daniel A.; Johnson, Breanna J.; Stachowiak, Susan J.; Garcia, Joseph A.; Bowles, Jeffrey V.;

Foreign body in children?s airways

Directory of Open Access Journals (Sweden)

Cassol Vitor

2003-01-01

Full Text Available OBJECTIVE: To determine the clinical characteristics and the results of bronchoscopic treatment of children due to foreign body aspiration in a university hospital. METHOD: Time series of children who underwent bronchoscopies for foreign bodies aspirated into the airway between March 1993 and July 2002. Each patient was analyzed for age, sex, initial clinical diagnosis, nature and location of the foreign body, duration of symptoms between aspiration and bronchoscopy, radiological findings, results of bronchoscopic removal, complications of bronchoscopy and presence of foreign bodies in the airways. RESULTS: Thirty-four children, 20 (59% boys, ages ranging from nine months to nine years (median = 23 months. In 32 (94% children the foreign body was removed by rigid bronchoscope, and two resulted in thoracotomy. Foreign bodies were more frequent in children under three years of age (66%. A clinical history of foreign body inhalation was obtained in 27 (80% cases. Most of the foreign bodies removed were organic (65% and more frequently found in the right bronchial tree (59%. Foreign bodies were removed within 24 hours in 18 (53% cases. The most frequent radiographic findings were: unilateral air trapping, atelectasis and radiopac foreign body. Major bronchoscopy complications occurred in seven children (22%, and there were no deaths. CONCLUSIONS: More attention is necessary to the respiratory symptoms of aspirations, mainly in boys at early ages, with clinical history and compatible radiological findings. Most foreign bodies removed were of organic nature. In this case series, therapeutic rigid bronchoscopy was effective with few complications.

Matrix rigidity induces osteolytic gene expression of metastatic breast cancer cells.

Directory of Open Access Journals (Sweden)

Nazanin S Ruppender

Full Text Available Nearly 70% of breast cancer patients with advanced disease will develop bone metastases. Once established in bone, tumor cells produce factors that cause changes in normal bone remodeling, such as parathyroid hormone-related protein (PTHrP. While enhanced expression of PTHrP is known to stimulate osteoclasts to resorb bone, the environmental factors driving tumor cells to express PTHrP in the early stages of development of metastatic bone disease are unknown. In this study, we have shown that tumor cells known to metastasize to bone respond to 2D substrates with rigidities comparable to that of the bone microenvironment by increasing expression and production of PTHrP. The cellular response is regulated by Rho-dependent actomyosin contractility mediated by TGF-ß signaling. Inhibition of Rho-associated kinase (ROCK using both pharmacological and genetic approaches decreased PTHrP expression. Furthermore, cells expressing a dominant negative form of the TGF-ß receptor did not respond to substrate rigidity, and inhibition of ROCK decreased PTHrP expression induced by exogenous TGF-ß. These observations suggest a role for the differential rigidity of the mineralized bone microenvironment in early stages of tumor-induced osteolysis, which is especially important in metastatic cancer since many cancers (such as those of the breast and lung preferentially metastasize to bone.

Effectiveness of exercise and protein supplementation intervention on body composition, functional fitness, and oxidative stress among elderly Malays with sarcopenia.

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Shahar, Suzana; Kamaruddin, Norshafarina Shari; Badrasawi, Manal; Sakian, Noor Ibrahim Mohamed; Abd Manaf, Zahara; Yassin, Zaitun; Joseph, Leonard

2013-01-01

Sarcopenia, characterized as muscle loss that occurs with aging, is a major health problem in an aging population, due to its implications on mobility, quality of life, and fall risk. Protein supplementation could improve the physical fitness by increasing protein anabolism, and exercise has a documented evidence of positive effect on functional status among the elderly. However, the combined effect of both protein supplementation and exercise has not been investigated among sarcopenic elderly in the Asian population. Thus, this study aimed to determine the effectiveness of exercise intervention and protein supplementation either alone or in combination for 12 weeks, on body composition, functional fitness, and oxidative stress among elderly Malays with sarcopenia. Sixty five sarcopenic elderly Malays aged 60-74 years were assigned to the control group, exercise group (ExG), protein supplementation group (PrG), or the combination of exercise and protein supplementation group. A significant interaction effect between body weight and body mass index (BMI) was observed, with the PrG (-2.1% body weight, -1.8% BMI) showing the highest reductions. Further, there was a decrease in % body fat (-4.5%) and an increase in fat-free mass (kg) (+5.7%) in the ExG after 12 weeks (P exercise program was found to improve muscle strength and body composition, while protein supplementation reduced body weight and increased upper body strength, among sarcopenic elderly in Malaysia.

A MADS box protein interacts with a mating-type protein and is required for fruiting body development in the homothallic ascomycete Sordaria macrospora.

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Nolting, Nicole; Pöggeler, Stefanie

2006-07-01

MADS box transcription factors control diverse developmental processes in plants, metazoans, and fungi. To analyze the involvement of MADS box proteins in fruiting body development of filamentous ascomycetes, we isolated the mcm1 gene from the homothallic ascomycete Sordaria macrospora, which encodes a putative homologue of the Saccharomyces cerevisiae MADS box protein Mcm1p. Deletion of the S. macrospora mcm1 gene resulted in reduced biomass, increased hyphal branching, and reduced hyphal compartment length during vegetative growth. Furthermore, the S. macrospora Deltamcm1 strain was unable to produce fruiting bodies or ascospores during sexual development. A yeast two-hybrid analysis in conjugation with in vitro analyses demonstrated that the S. macrospora MCM1 protein can interact with the putative transcription factor SMTA-1, encoded by the S. macrospora mating-type locus. These results suggest that the S. macrospora MCM1 protein is involved in the transcriptional regulation of mating-type-specific genes as well as in fruiting body development.

A LARGE FOREIGN BODY IN THE TRACHEA (SEWING NEEDLE

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P. D. Pryanikov

2017-01-01

Full Text Available The authors present a case study: an unusual foreign body (sewing needle in the trachea. Despite the large size and unusual shape of a foreign body, we managed to remove it through the airways with rigid upper traheobronchoscopy, avoiding complications.

Thermogenic Blend Alone or in Combination with Whey Protein Supplement Stimulates Fat Metabolism and Improves Body Composition in Mice

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Vieira-Brock, Paula de Lima; Vaughan, Brent M.; Vollmer, David L.

2018-01-01

Background: Certain food ingredients promote thermogenesis and fat loss. Similarly, whey protein improves body composition. Due to this potential synergistic effect, a blend of thermogenic food ingredients containing African mango, citrus fruit extract, Coleus forskohlii, dihydrocapsiate, and red pepper was tested alone and in combination with a whey protein supplement for its effects on body composition in sedentary mice during high-fat diet. Objective: The objective of this study was to evaluate the interaction of thermogenic foods on improving body composition during consumption of an unhealthy diet. Materials and Methods: C57BL/6J young adult male mice (n = 12) were placed on a 60% high-fat diet for 4 weeks and subsequently randomly assigned to receive daily dosing by oral gavage of vehicle, the novel blend alone or with whey protein supplement for another 4 weeks. Body composition, thermal imaging of brown adipose tissue (BAT), mitochondrial BAT uncoupling protein 1 (UCP1), and plasma levels of leptin were assessed. Results: Novel blend alone and in combination with protein supplement attenuated body weight gain, fat, and increased surface BAT temperature in comparison to vehicle control and to baseline (P blend and whey protein supplement also significantly increased UCP1 protein expression in BAT mitochondria in comparison to vehicle control and novel blend alone (P blend stimulates thermogenesis and attenuates the gain in body weight and fat in response to high-fat diet in mice and these effects were improved when administered in combination with whey protein supplement. SUMMARY 30 days oral administration to mice of a novel blend containing African mango seed extract, citrus fruits extract, Coleus forskohlii root extract, dihydrocapsiate and red pepper fruit extract reduced body weight and fat gain in response to high-fat diet without impairing muscle mass.The novel blend stimulated thermogenesis as shown by the increased thermal imaging and UCP1 protein

Employment of colorimetric enzyme assay for monitoring expression and solubility of GST fusion proteins targeted to inclusion bodies.

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Mačinković, Igor S; Abughren, Mohamed; Mrkic, Ivan; Grozdanović, Milica M; Prodanović, Radivoje; Gavrović-Jankulović, Marija

2013-12-01

High levels of recombinant protein expression can lead to the formation of insoluble inclusion bodies. These complex aggregates are commonly solubilized in strong denaturants, such as 6-8M urea, although, if possible, solubilization under milder conditions could facilitate subsequent refolding and purification of bioactive proteins. Commercially available GST-tag assays are designed for quantitative measurement of GST activity under native conditions. GST fusion proteins accumulated in inclusion bodies are considered to be undetectable by such assays. In this work, solubilization of recombinantly produced proteins was performed in 4M urea. The activity of rGST was assayed in 2M urea and it was shown that rGST preserves 85% of its activity under such denaturing conditions. A colorimetric GST activity assay with 1-chloro-2, 4-dinitrobenzene (CDNB) was examined for use in rapid detection of expression targeted to inclusion bodies and for the identification of inclusion body proteins which can be solubilized in low concentrations of chaotropic agents. Applicability of the assay was evaluated by tracking protein expression of two GST-fused allergens of biopharmaceutical value in E. coli, GST-Der p 2 and GST-Mus a 5, both targeted to inclusion bodies. Copyright © 2013 Elsevier B.V. All rights reserved.

Packaging protein drugs as bacterial inclusion bodies for therapeutic applications

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Villaverde Antonio

2012-06-01

Full Text Available Abstract A growing number of insights on the biology of bacterial inclusion bodies (IBs have revealed intriguing utilities of these protein particles. Since they combine mechanical stability and protein functionality, IBs have been already exploited in biocatalysis and explored for bottom-up topographical modification in tissue engineering. Being fully biocompatible and with tuneable bio-physical properties, IBs are currently emerging as agents for protein delivery into mammalian cells in protein-replacement cell therapies. So far, IBs formed by chaperones (heat shock protein 70, Hsp70, enzymes (catalase and dihydrofolate reductase, grow factors (leukemia inhibitory factor, LIF and structural proteins (the cytoskeleton keratin 14 have been shown to rescue exposed cells from a spectrum of stresses and restore cell functions in absence of cytotoxicity. The natural penetrability of IBs into mammalian cells (reaching both cytoplasm and nucleus empowers them as an unexpected platform for the controlled delivery of essentially any therapeutic polypeptide. Production of protein drugs by biopharma has been traditionally challenged by IB formation. However, a time might have arrived in which recombinant bacteria are to be engineered for the controlled packaging of therapeutic proteins as nanoparticulate materials (nanopills, for their extra- or intra-cellular release in medicine and cosmetics.

Refolding in high hydrostatic pressure of recombinant proteins from inclusion bodies in Escherichia Coli

International Nuclear Information System (INIS)

Balduino, Keli Nunes

2009-01-01

The expression of proteins as inclusion bodies in bacteria is a widely used alternative for production of recombinant protein. However, the aggregation is a problem often encountered during refolding of these proteins. High hydrostatic pressure are able to solubilise the inclusion bodies in the presence of low concentrations of denaturant reagents, encouraging refolding protein with high efficiency and reduce costs. This work aims to refolding of recombinant proteins expressed in Escherichia coli from inclusion bodies using high hydrostatic pressure. Three toxins, all featuring five or more disulfide bonds were studied: NXH8, Natterin 2 and Bothropstoxin 1. Suspensions of inclusion bodies of the three proteins were pressurized to 2000 bars for 16 hours. The buffers were optimized for refolding of the three proteins. The buffer used in the refolding of NXH8 was 50 mM Tris HCl, pH 9.0 with proportion of 1GSH: 4GSSG at a concentration of 6 mM and 2 M GdnHCl. Inclusion bodies were used in O.D. (A600nm) of 0.5. After refolding process, dialysis was performed at pH 7.0. The final yield of obtaining soluble NXH8 was 40% (28,6 mg of soluble NXH8/L of culture medium). The refolding of Bothropstoxin 1 was obtained in refolding buffer of Tris HCl 50 mM, pH 7,5 with proportion of 2 GSH: GSSG 3 and concentration of 3 mM and 1 M GdnHCl. Use with a suspension of O.D. (A600nm) of 0.5. The final yield of recovery of Bothropstoxin 1 refolded was 32% (9,2 mg of refolded Bothropstoxin 1/L of culture medium). The refolding of Natterin 2 was performed in the refolding buffer: 20 mM Tris HCl pH 9.0 at a ratio of 2 GSH: 3GSSG and concentration of 10 mM and 1 M GdnHCl and inclusion bodies O.D. (A600nm) of 6.0. The yield of Natterin 2 refolded was 20% (3,7 mg/L of culture medium). Physico-chemical and biological analysis were performed by SDS-PAGE, western blot, scanning electron microscopy, biological tests in vivo and in vitro and structural. The analysis conducted in NXH8 did not show

Association between excess body weight and urine protein concentration in healthy dogs.

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Tefft, Karen M; Shaw, Darcy H; Ihle, Sherri L; Burton, Shelley A; Pack, LeeAnn

2014-06-01

Markedly overweight people can develop progressive proteinuria and kidney failure secondary to obesity-related glomerulopathy (ORG). Glomerular lesions in dogs with experimentally induced obesity are similar to those in people with ORG. The aim of this study was to evaluate if urine protein and albumin excretion is greater in overweight and obese dogs than in dogs of ideal body condition. Client-owned dogs were screened for underlying health conditions. These dogs were assigned a body condition score (BCS) using a 9-point scoring system. Dogs with a BCS of ≥ 6 were classified as being overweight/obese, and dogs with a BCS of 4 or 5 were classified as being of ideal body weight. The urine protein:creatinine ratio (UPC) and urine albumin:creatinine ratio (UAC) were then determined, and compared between 20 overweight/obese dogs and 22 ideal body weight control dogs. Median UPC (0.04 [range, 0.01-0.14; interquartile range, 0.07]) and UAC (0.41 [0-10.39; 3.21]) of overweight/obese dogs were not significantly different from median UPC (0.04 [0.01-0.32; 0.07]) and UAC (0.18 [0-7.04; 1.75]) in ideal body weight dogs. Clinicopathologic abnormalities consistent with ORG were absent from overweight/obese dogs in this study. © 2014 American Society for Veterinary Clinical Pathology and European Society for Veterinary Clinical Pathology.

Multivesicular Bodies in Neurons: Distribution, Protein Content, and Trafficking Functions

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VON BARTHELD, CHRISTOPHER S.; ALTICK, AMY L.

2011-01-01

Summary Multivesicular bodies (MVBs) are intracellular endosomal organelles characterized by multiple internal vesicles that are enclosed within a single outer membrane. MVBs were initially regarded as purely prelysosomal structures along the degradative endosomal pathway of internalized proteins. MVBs are now known to be involved in numerous endocytic and trafficking functions, including protein sorting, recycling, transport, storage, and release. This review of neuronal MVBs summarizes their research history, morphology, distribution, accumulation of cargo and constitutive proteins, transport, and theories of functions of MVBs in neurons and glia. Due to their complex morphologies, neurons have expanded trafficking and signaling needs, beyond those of “geometrically simpler” cells, but it is not known whether neuronal MVBs perform additional transport and signaling functions. This review examines the concept of compartment-specific MVB functions in endosomal protein trafficking and signaling within synapses, axons, dendrites and cell bodies. We critically evaluate reports of the accumulation of neuronal MVBs based on evidence of stress-induced MVB formation. Furthermore, we discuss potential functions of neuronal and glial MVBs in development, in dystrophic neuritic syndromes, injury, disease, and aging. MVBs may play a role in Alzheimer’s, Huntington’s, and Niemann-Pick diseases, some types of frontotemporal dementia, prion and virus trafficking, as well as in adaptive responses of neurons to trauma and toxin or drug exposure. Functions of MVBs in neurons have been much neglected, and major gaps in knowledge currently exist. Developing truly MVB-specific markers would help to elucidate the roles of neuronal MVBs in intra- and intercellular signaling of normal and diseased neurons. PMID:21216273

Age-associated increase of the active zone protein Bruchpilot within the honeybee mushroom body.

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Katrin B Gehring

Full Text Available In honeybees, age-associated structural modifications can be observed in the mushroom bodies. Prominent examples are the synaptic complexes (microglomeruli, MG in the mushroom body calyces, which were shown to alter their size and density with age. It is not known whether the amount of intracellular synaptic proteins in the MG is altered as well. The presynaptic protein Bruchpilot (BRP is localized at active zones and is involved in regulating the probability of neurotransmitter release in the fruit fly, Drosophila melanogaster. Here, we explored the localization of the honeybee BRP (Apis mellifera BRP, AmBRP in the bee brain and examined age-related changes in the AmBRP abundance in the central bee brain and in microglomeruli of the mushroom body calyces. We report predominant AmBRP localization near the membrane of presynaptic boutons within the mushroom body MG. The relative amount of AmBRP was increased in the central brain of two-week old bees whereas the amount of Synapsin, another presynaptic protein involved in the regulation of neurotransmitter release, shows an increase during the first two weeks followed by a decrease. In addition, we demonstrate an age-associated modulation of AmBRP located near the membrane of presynaptic boutons within MG located in mushroom body calyces where sensory input is conveyed to mushroom body intrinsic neurons. We discuss that the observed age-associated AmBRP modulation might be related to maturation processes or to homeostatic mechanisms that might help to maintain synaptic functionality in old animals.

From nonspecific DNA-protein encounter complexes to the prediction of DNA-protein interactions.

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Mu Gao

2009-03-01

Full Text Available DNA-protein interactions are involved in many essential biological activities. Because there is no simple mapping code between DNA base pairs and protein amino acids, the prediction of DNA-protein interactions is a challenging problem. Here, we present a novel computational approach for predicting DNA-binding protein residues and DNA-protein interaction modes without knowing its specific DNA target sequence. Given the structure of a DNA-binding protein, the method first generates an ensemble of complex structures obtained by rigid-body docking with a nonspecific canonical B-DNA. Representative models are subsequently selected through clustering and ranking by their DNA-protein interfacial energy. Analysis of these encounter complex models suggests that the recognition sites for specific DNA binding are usually favorable interaction sites for the nonspecific DNA probe and that nonspecific DNA-protein interaction modes exhibit some similarity to specific DNA-protein binding modes. Although the method requires as input the knowledge that the protein binds DNA, in benchmark tests, it achieves better performance in identifying DNA-binding sites than three previously established methods, which are based on sophisticated machine-learning techniques. We further apply our method to protein structures predicted through modeling and demonstrate that our method performs satisfactorily on protein models whose root-mean-square Calpha deviation from native is up to 5 A from their native structures. This study provides valuable structural insights into how a specific DNA-binding protein interacts with a nonspecific DNA sequence. The similarity between the specific DNA-protein interaction mode and nonspecific interaction modes may reflect an important sampling step in search of its specific DNA targets by a DNA-binding protein.

The adenovirus E4 11 k protein binds and relocalizes the cytoplasmic P-body component Ddx6 to aggresomes

International Nuclear Information System (INIS)

Greer, Amy E.; Hearing, Patrick; Ketner, Gary

2011-01-01

The adenovirus E4 11 k protein, product of E4 ORF3, is required in infection for processes including normal accumulation of viral late mRNAs. 11 k restructures both the nucleus and cytoplasm of infected cells by relocalizing specific host cell target proteins, most strikingly components of nuclear PML oncogenic domains. It is likely that in many cases relocalization inactivates target proteins to produce 11 k's effects, although the mechanism and targets for stimulation of late mRNA accumulation is unknown. We have identified a new set of proteins relocalized by 11 k: at least five protein components of cytoplasmic mRNA processing bodies (p-bodies) are found in 11 k-induced cytoplasmic aggresomes, sites where proteins are inactivated or destroyed. One of these p-body proteins, RNA helicase Ddx6, binds 11 k, suggesting a mechanism for relocalization. Because p-bodies are sites for mRNA degradation, their modification by 11 k may provide an explanation for the role of 11 k in viral late mRNA accumulation.

High dietary protein intake is associated with an increased body weight and total death risk.

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Hernández-Alonso, Pablo; Salas-Salvadó, Jordi; Ruiz-Canela, Miguel; Corella, Dolores; Estruch, Ramón; Fitó, Montserrat; Arós, Fernando; Gómez-Gracia, Enrique; Fiol, Miquel; Lapetra, José; Basora, Josep; Serra-Majem, Lluis; Muñoz, Miguel Ángel; Buil-Cosiales, Pilar; Saiz, Carmen; Bulló, Mònica

2016-04-01

High dietary protein diets are widely used to manage overweight and obesity. However, there is a lack of consensus about their long-term efficacy and safety. Therefore, the aim of this study was to assess the effect of long-term high-protein consumption on body weight changes and death outcomes in subjects at high cardiovascular risk. A secondary analysis of the PREDIMED trial was conducted. Dietary protein was assessed using a food-frequency questionnaire during the follow-up. Cox proportional hazard models were used to estimate the multivariate-adjusted hazard ratio (HR) and 95% confidence intervals (95%CI) for protein intake in relation to the risk of body weight and waist circumference changes, cardiovascular disease, cardiovascular death, cancer death and total death. Higher total protein intake, expressed as percentage of energy, was significantly associated with a greater risk of weight gain when protein replaced carbohydrates (HR: 1.90; 95%CI: 1.05, 3.46) but not when replaced fat (HR: 1.69; 95%CI: 0.94, 3.03). However, no association was found between protein intake and waist circumference. Contrary, higher total protein intake was associated with a greater risk of all-cause death in both carbohydrate and fat substitution models (HR: 1.59; 95%CI: 1.08, 2.35; and HR: 1.66; 95%CI: 1.13, 2.43, respectively). A higher consumption of animal protein was associated with an increased risk of fatal and non-fatal outcomes when protein substituted carbohydrates or fat. Higher dietary protein intake is associated with long-term increased risk of body weight gain and overall death in a Mediterranean population at high cardiovascular risk. Copyright © 2015 Elsevier Ltd and European Society for Clinical Nutrition and Metabolism. All rights reserved.

Impact of extraneous proteins on the gastrointestinal fate of sunflower seed (Helianthus annuus) oil bodies: a simulated gastrointestinal tract study.

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Makkhun, Sakunkhun; Khosla, Amit; Foster, Tim; McClements, David Julian; Grundy, Myriam M L; Gray, David A

2015-01-01

In this study, we examined the physicochemical nature of sunflower seed oil bodies (in the absence and presence of added protein) exposed to gastrointestinal conditions in vitro: crude oil bodies (COB); washed oil bodies (WOB); whey protein isolate-enriched oil bodies (WOB-WPI); and, sodium caseinate enriched-oil bodies (WOB-SC). All oil body emulsions were passed through an in vitro digestion model that mimicked the stomach and duodenal environments, and their physicochemical properties were measured before, during, and after digestion. Oil bodies had a positive charge under gastric conditions because the pH was below the isoelectric point of the adsorbed protein layer, but they had a negative charge under duodenal conditions which was attributed to changes in interfacial composition resulting from adsorption of bile salts. Oil bodies were highly susceptible to flocculation and coalescence in both gastric and duodenal conditions. SDS-PAGE analysis indicated degradation of oleosin proteins (ca. 18-21 kDa) to a greater or lesser extent (dependent on the emulsion) during the gastric phase in all emulsions tested; there is evidence that some oleosin remained intact in the crude oil body preparation during this phase of the digestion process. Measurements of protein displacement from the surface of COBs during direct exposure to bile salts, without inclusion of a gastric phase, indicated the removal of intact oleosin from native oil bodies.

49 CFR 587.18 - Dimensions of fixed rigid barrier.

Science.gov (United States)

2010-10-01

... TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) DEFORMABLE BARRIERS Offset Deformable Barrier § 587.18 Dimensions of fixed rigid barrier. (a) The fixed rigid barrier has a mass of not... 49 Transportation 7 2010-10-01 2010-10-01 false Dimensions of fixed rigid barrier. 587.18 Section...

RIGIDITY, SENSITIVITY AND QUALITY OF ATTACHMENT - THE ROLE OF MATERNAL RIGIDITY IN THE EARLY SOCIOEMOTIONAL DEVELOPMENT OF PREMATURE-INFANTS

NARCIS (Netherlands)

BUTCHER, PR; KALVERBOER, A; MINDERAA, RB; VANDOORMAAL, EF; TENWOLDE, Y

1993-01-01

The associations between a mother's rigidity, her sensitivity in early (3 month) interaction and the quality of her premature infant's attachment at 13 months were investigated. Rigidity as a personality characteristic was not found to be significantly associated with sensitivity or quality of

Whole-body protein turnover in malnourished patients with child class B and C cirrhosis on diets low to high in protein energy.

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Dichi, J B; Dichi, I; Maio, R; Correa, C R; Angeleli, A Y; Bicudo, M H; Rezende, T A; Burini, R C

2001-03-01

The purpose of this study was to determine the rate of whole-body protein turnover in moderately and severely alcoholic, malnourished, cirrhotic patients fed with different amounts of protein or energy. Six male patients (Child classes B and C) and four age- and sex-matched healthy control subjects were studied for 18 d in fasting and feeding states; a single oral dose of [(15)N]glycine was used as a tracer and urinary ammonia was the end product. The kinetic study showed that patients had higher protein catabolism while fasting (patients: 3.14 +/- 1.2 g of lean body mass/9 h; controls: 1.8 +/- 0.3 g of lean body mass/9 h; P hyperproteic/hyperenergetic diet when compared with fasting. Nitrogen retention was consistent with the lower protein-catabolism rate; a statistically significant increase in nitrogen balance was observed when patients were fed with the hyperproteic/hyperenergetic diet compared with fasting (4.3 +/- 3.2 g of nitrogen/d and -2.2 +/- 1.9 g of nitrogen/d, respectively; P hyperproteic/hyperenergetic diet is likely needed to improve their clinical and nutritional status.

Dissection of Molecular Mechanisms Regulating Protein Body Formation in Maize Endosperm - DE-FG03-95-ER20183

International Nuclear Information System (INIS)

Larkins, Brian A.

2003-01-01

Dissection of Molecular Mechanisms Regulating Protein Body Formation in Maize Endosperm - DE-FG03-95-ER20183 Final Technical Report and Patent Summary Dr. Brian A. Larkins, Department of Plant Sciences, University of Arizona, Tucson, AZ 85721 Endosperm texture is an important quality trait in maize, as it influences the shipping characteristics of the grain, its susceptibility to insects, the yield of grits from dry milling, energy costs during wet milling, and the baking and digestibility properties of the flour. There appears to be a causal relationship between kernel hardness and the formation of zein-containing protein bodies, as mutations affecting protein body number and structure are associated with a soft, starchy kernel. In this project we used a variety of approaches to better understand this relationship and investigate the molecular and biochemical changes associated with starchy endosperm mutants. We characterized the distribution of zein mRNAs on endosperm rough endoplasmic reticulum (RER) membranes and the interactions between zein proteins, as each of these could influence the structure of protein bodies. Based on in situ hybridization, mRNAs encoding the 22-kD alpha- and 27-kD gamma-zeins are randomly distributed on RER; hence, mRNA targeting does not appear to influence the formation of protein bodies. Investigation of the interactions between zein proteins (alpha, beta, gamma, delta) with the yeast two-hybrid system showed that interactions between the 19- and 22-alpha-zeins are relatively weak, although each of them interacted strongly with the 10-kD delta-zein. Strong interactions were detected between the alpha- and delta-zeins and the 16-kD gamma- and 15-kD beta-zeins; however, the 50-kD and 27-kD gamma-zeins did not interact detectably with the alpha- and delta-zein proteins. The NH2- and COOH-terminal domains of the 22-kD alpha-zein were found to interact most strongly with the 15-kD beta- and 16-kD gamma-zeins, suggesting the 16-kD and 15

Nutritional Status of Maintenance Dialysis Patients: Low Lean Body Mass Index and Obesity Are Common, Protein-Energy Wasting Is Uncommon.

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Mette Koefoed

Full Text Available Maintenance dialysis patients are at increased risk of abnormal nutritional status due to numerous causative factors, both nutritional and non-nutritional. The present study assessed the current prevalence of protein-energy wasting, low lean body mass index and obesity in maintenance dialysis patients, and compared different methods of nutritional assessment.In a cross-sectional study conducted in 2014 at Roskilde Hospital, Denmark, we performed anthropometry (body weight, skinfolds, mid-arm, waist, and hip circumferences, and determined plasma albumin and normalized protein catabolic rate in order to assess the prevalence of protein-energy wasting, low lean body mass index and obesity in these patients.Seventy-nine eligible maintenance dialysis patients participated. The prevalence of protein-energy wasted patients was 4% (95% CI: 2-12 as assessed by the coexistence of low lean body mass index and low fat mass index. Low lean body mass index was seen in 32% (95% CI: 22-44. Obesity prevalence as assessed from fat mass index was 43% (95% CI: 32-55. Coexistence of low lean body mass index and obesity was seen in 10% (95% CI: 5-19. The prevalence of protein-energy wasting and obesity varied considerably, depending on nutritional assessment methodology.Our data indicate that protein-energy wasting is uncommon, whereas low lean body mass index and obesity are frequent conditions among patients in maintenance dialysis. A focus on how to increase and preserve lean body mass in dialysis patients is suggested in the future. In order to clearly distinguish between shortage, sufficiency and abundance of protein and/or fat deposits in maintenance dialysis patients, we suggest the simple measurements of lean body mass index and fat mass index.

Nutritional Status of Maintenance Dialysis Patients: Low Lean Body Mass Index and Obesity Are Common, Protein-Energy Wasting Is Uncommon.

Science.gov (United States)

Koefoed, Mette; Kromann, Charles Boy; Juliussen, Sophie Ryberg; Hvidtfeldt, Danni; Ekelund, Bo; Frandsen, Niels Erik; Marckmann, Peter

2016-01-01

Maintenance dialysis patients are at increased risk of abnormal nutritional status due to numerous causative factors, both nutritional and non-nutritional. The present study assessed the current prevalence of protein-energy wasting, low lean body mass index and obesity in maintenance dialysis patients, and compared different methods of nutritional assessment. In a cross-sectional study conducted in 2014 at Roskilde Hospital, Denmark, we performed anthropometry (body weight, skinfolds, mid-arm, waist, and hip circumferences), and determined plasma albumin and normalized protein catabolic rate in order to assess the prevalence of protein-energy wasting, low lean body mass index and obesity in these patients. Seventy-nine eligible maintenance dialysis patients participated. The prevalence of protein-energy wasted patients was 4% (95% CI: 2-12) as assessed by the coexistence of low lean body mass index and low fat mass index. Low lean body mass index was seen in 32% (95% CI: 22-44). Obesity prevalence as assessed from fat mass index was 43% (95% CI: 32-55). Coexistence of low lean body mass index and obesity was seen in 10% (95% CI: 5-19). The prevalence of protein-energy wasting and obesity varied considerably, depending on nutritional assessment methodology. Our data indicate that protein-energy wasting is uncommon, whereas low lean body mass index and obesity are frequent conditions among patients in maintenance dialysis. A focus on how to increase and preserve lean body mass in dialysis patients is suggested in the future. In order to clearly distinguish between shortage, sufficiency and abundance of protein and/or fat deposits in maintenance dialysis patients, we suggest the simple measurements of lean body mass index and fat mass index.

Curating viscoelastic properties of icosahedral viruses, virus-based nanomaterials, and protein cages.

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Kant, Ravi; Rayaprolu, Vamseedhar; McDonald, Kaitlyn; Bothner, Brian

2018-06-01

The beauty, symmetry, and functionality of icosahedral virus capsids has attracted the attention of biologists, physicists, and mathematicians ever since they were first observed. Viruses and protein cages assemble into functional architectures in a range of sizes, shapes, and symmetries. To fulfill their biological roles, these structures must self-assemble, resist stress, and are often dynamic. The increasing use of icosahedral capsids and cages in materials science has driven the need to quantify them in terms of structural properties such as rigidity, stiffness, and viscoelasticity. In this study, we employed Quartz Crystal Microbalance with Dissipation technology (QCM-D) to characterize and compare the mechanical rigidity of different protein cages and viruses. We attempted to unveil the relationships between rigidity, radius, shell thickness, and triangulation number. We show that the rigidity and triangulation numbers are inversely related to each other and the comparison of rigidity and radius also follows the same trend. Our results suggest that subunit orientation, protein-protein interactions, and protein-nucleic acid interactions are important for the resistance to deformation of these complexes, however, the relationships are complex and need to be explored further. The QCM-D based viscoelastic measurements presented here help us elucidate these relationships and show the future prospect of this technique in the field of physical virology and nano-biotechnology.

Mid-Lift-to-Drag Ratio Rigid Vehicle Control System Design and Simulation for Human Mars Entry

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Johnson, Breanna J.; Cerimele, Christopher J.; Stachowiak, Susan J.; Sostaric, Ronald R.; Matz, Daniel A.; Lu, Ping

2018-01-01

The Mid-Lift-to-Drag Ratio Rigid Vehicle (MRV) is a proposed candidate in the NASA Evolvable Mars Campaign's (EMC) Pathfinder Entry, Descent, and Landing (EDL) architecture study. The purpose of the study is to design a mission and vehicle capable of transporting a 20mt payload to the surface of Mars. The MRV is unique in its rigid, asymmetrical lifting-body shape which enables a higher lift-to-drag ratio (L/D) than the typical robotic Mars entry capsule vehicles that carry much less mass. This paper presents the formulation and six-degree-of-freedom (6DOF) performance of the MRV's control system, which uses both aerosurfaces and a propulsive reaction control system (RCS) to affect longitudinal and lateral directional behavior.

Within-day protein distribution does not influence body composition responses during weight loss in resistance-training adults who are overweight.

Science.gov (United States)

Hudson, Joshua L; Kim, Jung Eun; Paddon-Jones, Douglas; Campbell, Wayne W

2017-11-01

Background: Emerging research suggests that redistributing total protein intake from 1 high-protein meal/d to multiple moderately high-protein meals improves 24-h muscle protein synthesis. Over time, this may promote positive changes in body composition. Objective: We sought to assess the effects of within-day protein intake distribution on changes in body composition during dietary energy restriction and resistance training. Design: In a randomized parallel-design study, 41 men and women [mean ± SEM age: 35 ± 2 y; body mass index (in kg/m 2 ): 31.5 ± 0.5] consumed an energy-restricted diet (750 kcal/d below the requirement) for 16 wk while performing resistance training 3 d/wk. Subjects consumed 90 g protein/d (1.0 ± 0.03 g · kg -1 · d -1 , 125% of the Recommended Dietary Allowance, at intervention week 1) in either a skewed (10 g at breakfast, 20 g at lunch, and 60 g at dinner; n = 20) or even (30 g each at breakfast, lunch, and dinner; n = 21) distribution pattern. Body composition was measured pre- and postintervention. Results: Over time, whole-body mass (least-squares mean ± SE: -7.9 ± 0.6 kg), whole-body lean mass (-1.0 ± 0.2 kg), whole-body fat mass (-6.9 ± 0.5 kg), appendicular lean mass (-0.7 ± 0.1 kg), and appendicular fat mass (-2.6 ± 0.2 kg) each decreased. The midthigh muscle area (0 ± 1 cm 2 ) did not change over time, whereas the midcalf muscle area decreased (-3 ± 1 cm 2 ). Within-day protein distribution did not differentially affect these body-composition responses. Conclusion: The effectiveness of dietary energy restriction combined with resistance training to improve body composition is not influenced by the within-day distribution of protein when adequate total protein is consumed. This trial was registered at clinicaltrials.gov as NCT02066948. © 2017 American Society for Nutrition.

Protein intake at 9 mo of age is associated with body size but not with body fat in 10-y-old Danish children

DEFF Research Database (Denmark)

Hoppe, C.; Mølgaard, C.; Thomsen, B. L.

2004-01-01

During the complementary feeding period, infants shift from a daily protein intake (PI) of approximately 1 g/kg body wt to an intake 3-4 times as high. A high PI probably has both endocrine and physiologic effects and may increase the risk of obesity.......During the complementary feeding period, infants shift from a daily protein intake (PI) of approximately 1 g/kg body wt to an intake 3-4 times as high. A high PI probably has both endocrine and physiologic effects and may increase the risk of obesity....

Refolding of proteins from inclusion bodies: rational design and recipes.

Science.gov (United States)

Basu, Anindya; Li, Xiang; Leong, Susanna Su Jan

2011-10-01

The need to develop protein biomanufacturing platforms that can deliver proteins quickly and cost-effectively is ever more pressing. The rapid rate at which genomes can now be sequenced demands efficient protein production platforms for gene function identification. There is a continued need for the biotech industry to deliver new and more effective protein-based drugs to address new diseases. Bacterial production platforms have the advantage of high expression yields, but insoluble expression of many proteins necessitates the development of diverse and optimised refolding-based processes. Strategies employed to eliminate insoluble expression are reviewed, where it is concluded that inclusion bodies are difficult to eliminate for various reasons. Rational design of refolding systems and recipes are therefore needed to expedite production of recombinant proteins. This review article discusses efforts towards rational design of refolding systems and recipes, which can be guided by the development of refolding screening platforms that yield both qualitative and quantitative information on the progression of a given refolding process. The new opportunities presented by light scattering technologies for developing rational protein refolding buffer systems which in turn can be used to develop new process designs armed with better monitoring and controlling functionalities are discussed. The coupling of dynamic and static light scattering methodologies for incorporation into future bioprocess designs to ensure delivery of high-quality refolded proteins at faster rates is also discussed.

Protein mobilities and P-selectin storage in Weibel-Palade bodies.

Science.gov (United States)

Kiskin, Nikolai I; Hellen, Nicola; Babich, Victor; Hewlett, Lindsay; Knipe, Laura; Hannah, Matthew J; Carter, Tom

2010-09-01

Using fluorescence recovery after photobleaching (FRAP) we measured the mobilities of EGFP-tagged soluble secretory proteins in the endoplasmic reticulum (ER) and in individual Weibel-Palade bodies (WPBs) at early (immature) and late (mature) stages in their biogenesis. Membrane proteins (P-selectin, CD63, Rab27a) were also studied in individual WPBs. In the ER, soluble secretory proteins were mobile; however, following insertion into immature WPBs larger molecules (VWF, Proregion, tPA) and P-selectin became immobilised, whereas small proteins (ssEGFP, eotaxin-3) became less mobile. WPB maturation led to further decreases in mobility of small proteins and CD63. Acute alkalinisation of mature WPBs selectively increased the mobilities of small soluble proteins without affecting larger molecules and the membrane proteins. Disruption of the Proregion-VWF paracrystalline core by prolonged incubation with NH(4)Cl rendered P-selectin mobile while VWF remained immobile. FRAP of P-selectin mutants revealed that immobilisation most probably involves steric entrapment of the P-selectin extracellular domain by the Proregion-VWF paracrystal. Significantly, immobilisation contributed to the enrichment of P-selectin in WPBs; a mutation of P-selectin preventing immobilisation led to a failure of enrichment. Together these data shed new light on the transitions that occur for soluble and membrane proteins following their entry and storage into post-Golgi-regulated secretory organelles.

Identification of BCAP, a new protein associated with basal bodies and centrioles.

Science.gov (United States)

Ponsard, Cecile; Seltzer, Virginie; Perret, Eric; Tournier, Frederic; Middendorp, Sandrine

2007-05-01

Cilia exert critical functions in numerous organisms, including that of cell motility, fluid transport and protozoan locomotion. Defects in this organelle can lead to lethal pathologies in humans, including primary ciliary dyskinesia. An understanding of the cilia formation process would lead to better characterization of defects involved in such pathologies. In the present study, we identified a gene encoding a novel human protein, BCAP for Basal body Centriole-Associated Protein, which shares homologies with a previously described protein, Outer Dense Fiber 2 (ODF2). ODF2, a major component of the sperm tail cytoskeleton, is required for the formation of mother centriole distal/subdistal appendages and the generation of primary cilia. Here, we show that the bcap gene contains 18 alternatively spliced exons and encodes five different isoforms, three long and two short ones. BCAP is preferentially expressed in cilia/flagella containing tissues. Moreover, its expression is correlated with cilia formation during mucociliary differentiation of human nasal epithelial cells. Using immunofluorescence analyses, BCAP was localized within basal bodies of ciliated cells and within centrioles of proliferating cells. In light of the several spliced isoforms of BCAP and the particular localization of the protein, BCAP isoforms could play distinct roles in cilia and in centrosomes.

Soy versus whey protein bars: Effects on exercise training impact on lean body mass and antioxidant status

Directory of Open Access Journals (Sweden)

Babaknia Ari

2004-12-01

Full Text Available Abstract Background Although soy protein may have many health benefits derived from its associated antioxidants, many male exercisers avoid soy protein. This is due partly to a popular, but untested notion that in males, soy is inferior to whey in promoting muscle weight gain. This study provided a direct comparison between a soy product and a whey product. Methods Lean body mass gain was examined in males from a university weight training class given daily servings of micronutrient-fortified protein bars containing soy or whey protein (33 g protein/day, 9 weeks, n = 9 for each protein treatment group. Training used workouts with fairly low repetition numbers per set. A control group from the class (N = 9 did the training, but did not consume either type protein bar. Results Both the soy and whey treatment groups showed a gain in lean body mass, but the training-only group did not. The whey and training only groups, but not the soy group, showed a potentially deleterious post-training effect on two antioxidant-related related parameters. Conclusions Soy and whey protein bar products both promoted exercise training-induced lean body mass gain, but the soy had the added benefit of preserving two aspects of antioxidant function.

Proteomic analysis of oil body membrane proteins accompanying the onset of desiccation phase during sunflower seed development

Science.gov (United States)

Thakur, Anita; Bhatla, Satish C

2015-01-01

A noteworthy metabolic signature accompanying oil body (OB) biogenesis during oilseed development is associated with the modulation of the oil body membranes proteins. Present work focuses on 2-dimensional polyacrylamide gel electrophoresis (2-D PAGE)-based analysis of the temporal changes in the OB membrane proteins analyzed by LC-MS/MS accompanying the onset of desiccation (20–30 d after anthesis; DAA) in the developing seeds of sunflower (Helianthus annuus L.). Protein spots unique to 20–30 DAA stages were picked up from 2-D gels for identification and the identified proteins were categorized into 7 functional classes. These include proteins involved in energy metabolism, reactive oxygen scavenging, proteolysis and protein turnover, signaling, oleosin and oil body biogenesis-associated proteins, desiccation and cytoskeleton. At 30 DAA stage, exclusive expressions of enzymes belonging to energy metabolism, desiccation and cytoskeleton were evident which indicated an increase in the metabolic and enzymatic activity in the cells at this stage of seed development (seed filling). Increased expression of cruciferina-like protein and dehydrin at 30 DAA stage marks the onset of desiccation. The data has been analyzed and discussed to highlight desiccation stage-associated metabolic events during oilseed development. PMID:26786011

Cracking of open traffic rigid pavement

Directory of Open Access Journals (Sweden)

Niken Chatarina

2017-01-01

Full Text Available The research is done by observing the growth of real structure cracking in Natar, Lampung, Indonesia compared to C. Niken’s et al research and literature study. The rigid pavement was done with open traffic system. There are two main crack types on Natar rigid pavement: cracks cross the road, and cracks spreads on rigid pavement surface. The observation of cracks was analyzed by analyzing material, casting, curing, loading and shrinkage mechanism. The relationship between these analysis and shrinkage mechanism was studied in concrete micro structure. Open traffic make hydration process occur under vibration; therefore, fresh concrete was compressed and tensioned alternately since beginning. High temperature together with compression, cement dissociation, the growth of Ca2+ at very early age leads abnormal swelling. No prevention from outside water movement leads hydration process occur with limited water which caused spreads fine cracks. Limited water improves shrinkage and plastic phase becomes shorter; therefore, rigid pavement can’t accommodate the abnormal swelling and shrinking alternately and creates the spread of cracks. Discontinuing casting the concrete makes both mix under different condition, the first is shrink and the second is swell and creates weak line on the border; so, the cracks appear as cracks across the road.

Supplementation with a fish protein hydrolysate (Micromesistius poutassou: effects on body weight, body composition, and CCK/GLP-1 secretion

Directory of Open Access Journals (Sweden)

Vincenzo Nobile

2016-01-01

Full Text Available Background: Fish protein hydrolysates (FPHs have been reported as a suitable source of proteins for human nutrition because of their balanced amino acid composition and positive effect on gastrointestinal absorption. Objective: Here, we investigated the effect of a FPH, Slimpro®, obtained from blue whiting (Micromesistius poutassou muscle by enzymatic hydrolysis, on body composition and on stimulating cholecystokinin (CCK and glucagon-like peptide-1 (GLP-1 secretion. Design: A randomized clinical study was carried out on 120, slightly overweight (25 kg/m2 ≤ BMI<30 kg/m2, male (25% and female (75% subjects. FPH was tested in a food supplement at two doses (1.4 and 2.8 g to establish if a dose–effect relationship exists. Product use was associated with a mild hypocaloric diet (−300 kcal/day. Body composition (body weight; fat mass; extracellular water; and circumference of waist, thighs, and hips and CCK/GLP-1 blood levels were measured at the beginning of the study and after 45 and 90 days of product use. CCK/GLP-1 levels were measured since they are involved in controlling food intake. Results: Treated subjects reported an improvement of body weight composition and an increased blood concentration of both CCK and GLP-1. No differences were found between the 1.4 and 2.8 g FPH doses, indicating a plateau effect starting from 1.4 g FPH. Conclusions: Both 1.4 and 2.8 g of FPH were effective in improving body composition and in increasing CCK and GLP-1 blood levels.

Human papillomavirus (HPV) type 16 E7 protein bodies cause tumour regression in mice

International Nuclear Information System (INIS)

Whitehead, Mark; Öhlschläger, Peter; Almajhdi, Fahad N; Alloza, Leonor; Marzábal, Pablo; Meyers, Ann E; Hitzeroth, Inga I; Rybicki, Edward P

2014-01-01

Human papillomaviruses (HPV) are the causative agents of cervical cancer in women, which results in over 250 000 deaths per year. Presently there are two prophylactic vaccines on the market, protecting against the two most common high-risk HPV types 16 and 18. These vaccines remain very expensive and are not generally affordable in developing countries where they are needed most. Additionally, there remains a need to treat women that are already infected with HPV, and who have high-grade lesions or cervical cancer. In this paper, we characterize the immunogenicity of a therapeutic vaccine that targets the E7 protein of the most prevalent high-risk HPV - type 16 – the gene which has previously been shown to be effective in DNA vaccine trials in mice. The synthetic shuffled HPV-16 E7 (16E7SH) has lost its transforming properties but retains all naturally-occurring CTL epitopes. This was genetically fused to Zera®, a self-assembly domain of the maize γ-zein able to induce the accumulation of recombinant proteins into protein bodies (PBs), within the endoplasmic reticulum in a number of expression systems. High-level expression of the HPV 16E7SH protein fused to Zera® in plants was achieved, and the protein bodies could be easily and cost-effectively purified. Immune responses comparable to the 16E7SH DNA vaccine were demonstrated in the murine model, with the protein vaccine successfully inducing a specific humoral as well as cell mediated immune response, and mediating tumour regression. The fusion of 16E7SH to the Zera® peptide was found to enhance the immune responses, presumably by means of a more efficient antigen presentation via the protein bodies. Interestingly, simply mixing the free PBs and 16E7SH also enhanced immune responses, indicating an adjuvant activity for the Zera® PBs

Sliding contact on the interface of elastic body and rigid surface using a single block Burridge-Knopoff model

Science.gov (United States)

Amireghbali, A.; Coker, D.

2018-01-01

Burridge and Knopoff proposed a mass-spring model to explore interface dynamics along a fault during an earthquake. The Burridge and Knopoff (BK) model is composed of a series of blocks of equal mass connected to each other by springs of same stiffness. The blocks also are attached to a rigid driver via another set of springs that pulls them at a constant velocity against a rigid substrate. They studied dynamics of interface for an especial case with ten blocks and a specific set of fault properties. In our study effects of Coulomb and rate-state dependent friction laws on the dynamics of a single block BK model is investigated. The model dynamics is formulated as a system of coupled nonlinear ordinary differential equations in state-space form which lends itself to numerical integration methods, e.g. Runge-Kutta procedure for solution. The results show that the rate and state dependent friction law has the potential of triggering dynamic patterns that are different from those under Coulomb law.

Determination of Weight Suspension Rigidity in the Transport-Erector Aggregates

Directory of Open Access Journals (Sweden)

V. A. Zverev

2016-01-01

Full Text Available The aim is to determine weight suspension rigidity in aggregates designed to perform technological transport-erector operations at the miscellaneous launch complexes.We consider the weight suspension comprising the following distinctive structural components: the executive weight-lowering mechanism, polyspast mechanism, rope, traverse, and rods. A created structural dynamic model of suspension allowed us to define weight suspension rigidity. Within the framework of design analysis of a dynamic model we determined the rigidity of its structural units, i.e. traverse, rope, and polyspast.Known analytical relationships were used to calculate the rope rigidity. To determine rigidity of polyspast and traverse have been created special models based on the finite element method. For each model deformation in the specific points under the test load have been defined. Data obtained were used to determine trigidity of traverses and polyspast, and also rigidity of suspension in total. The rigidity models of polispast mechanism and traverse have been developed and calculated using the software complex "Zenit-95".As the research results, the paper presents a dynamic model of the weight suspension of the transport-erector aggregate, the finite element models of the polispast mechanism and traverse, an algorithm for determining the weight suspension rigidity and relevant analytical relationships.Independent calculation of weight suspension rigidity enables us to simplify further dynamic calculation of the aggregate-weight system because it allows attaining a simpler model of the aggregate-weight system that uses the weight suspension model as an element of equivalent rigidity. Despite this simplification the model allows us to determine correctly weight movement parameters and overloads in the aggregate-weight system in the process of technical operations.

The Oncogenic Fusion Proteins SET-Nup214 and Sequestosome-1 (SQSTM1)-Nup214 Form Dynamic Nuclear Bodies and Differentially Affect Nuclear Protein and Poly(A)+ RNA Export*

Science.gov (United States)

Port, Sarah A.; Mendes, Adélia; Valkova, Christina; Spillner, Christiane; Fahrenkrog, Birthe; Kaether, Christoph; Kehlenbach, Ralph H.

2016-01-01

Genetic rearrangements are a hallmark of several forms of leukemia and can lead to oncogenic fusion proteins. One example of an affected chromosomal region is the gene coding for Nup214, a nucleoporin that localizes to the cytoplasmic side of the nuclear pore complex (NPC). We investigated two such fusion proteins, SET-Nup214 and SQSTM1 (sequestosome)-Nup214, both containing C-terminal portions of Nup214. SET-Nup214 nuclear bodies containing the nuclear export receptor CRM1 were observed in the leukemia cell lines LOUCY and MEGAL. Overexpression of SET-Nup214 in HeLa cells leads to the formation of similar nuclear bodies that recruit CRM1, export cargo proteins, and certain nucleoporins and concomitantly affect nuclear protein and poly(A)+ RNA export. SQSTM1-Nup214, although mostly cytoplasmic, also forms nuclear bodies and inhibits nuclear protein but not poly(A)+ RNA export. The interaction of the fusion proteins with CRM1 is RanGTP-dependent, as shown in co-immunoprecipitation experiments and binding assays. Further analysis revealed that the Nup214 parts mediate the inhibition of nuclear export, whereas the SET or SQSTM1 part determines the localization of the fusion protein and therefore the extent of the effect. SET-Nup214 nuclear bodies are highly mobile structures, which are in equilibrium with the nucleoplasm in interphase and disassemble during mitosis or upon treatment of cells with the CRM1-inhibitor leptomycin B. Strikingly, we found that nucleoporins can be released from nuclear bodies and reintegrated into existing NPC. Our results point to nuclear bodies as a means of preventing the formation of potentially insoluble and harmful protein aggregates that also may serve as storage compartments for nuclear transport factors. PMID:27613868

The Oncogenic Fusion Proteins SET-Nup214 and Sequestosome-1 (SQSTM1)-Nup214 Form Dynamic Nuclear Bodies and Differentially Affect Nuclear Protein and Poly(A)+ RNA Export.

Science.gov (United States)

Port, Sarah A; Mendes, Adélia; Valkova, Christina; Spillner, Christiane; Fahrenkrog, Birthe; Kaether, Christoph; Kehlenbach, Ralph H

2016-10-28

Genetic rearrangements are a hallmark of several forms of leukemia and can lead to oncogenic fusion proteins. One example of an affected chromosomal region is the gene coding for Nup214, a nucleoporin that localizes to the cytoplasmic side of the nuclear pore complex (NPC). We investigated two such fusion proteins, SET-Nup214 and SQSTM1 (sequestosome)-Nup214, both containing C-terminal portions of Nup214. SET-Nup214 nuclear bodies containing the nuclear export receptor CRM1 were observed in the leukemia cell lines LOUCY and MEGAL. Overexpression of SET-Nup214 in HeLa cells leads to the formation of similar nuclear bodies that recruit CRM1, export cargo proteins, and certain nucleoporins and concomitantly affect nuclear protein and poly(A) + RNA export. SQSTM1-Nup214, although mostly cytoplasmic, also forms nuclear bodies and inhibits nuclear protein but not poly(A) + RNA export. The interaction of the fusion proteins with CRM1 is RanGTP-dependent, as shown in co-immunoprecipitation experiments and binding assays. Further analysis revealed that the Nup214 parts mediate the inhibition of nuclear export, whereas the SET or SQSTM1 part determines the localization of the fusion protein and therefore the extent of the effect. SET-Nup214 nuclear bodies are highly mobile structures, which are in equilibrium with the nucleoplasm in interphase and disassemble during mitosis or upon treatment of cells with the CRM1-inhibitor leptomycin B. Strikingly, we found that nucleoporins can be released from nuclear bodies and reintegrated into existing NPC. Our results point to nuclear bodies as a means of preventing the formation of potentially insoluble and harmful protein aggregates that also may serve as storage compartments for nuclear transport factors. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Essential roles of protein-solvent many-body correlation in solvent-entropy effect on protein folding and denaturation: Comparison between hard-sphere solvent and water

International Nuclear Information System (INIS)

Oshima, Hiraku; Kinoshita, Masahiro

2015-01-01

In earlier works, we showed that the entropic effect originating from the translational displacement of water molecules plays the pivotal role in protein folding and denaturation. The two different solvent models, hard-sphere solvent and model water, were employed in theoretical methods wherein the entropic effect was treated as an essential factor. However, there were similarities and differences in the results obtained from the two solvent models. In the present work, to unveil the physical origins of the similarities and differences, we simultaneously consider structural transition, cold denaturation, and pressure denaturation for the same protein by employing the two solvent models and considering three different thermodynamic states for each solvent model. The solvent-entropy change upon protein folding/unfolding is decomposed into the protein-solvent pair (PA) and many-body (MB) correlation components using the integral equation theories. Each component is further decomposed into the excluded-volume (EV) and solvent-accessible surface (SAS) terms by applying the morphometric approach. The four physically insightful constituents, (PA, EV), (PA, SAS), (MB, EV), and (MB, SAS), are thus obtained. Moreover, (MB, SAS) is discussed by dividing it into two factors. This all-inclusive investigation leads to the following results: (1) the protein-water many-body correlation always plays critical roles in a variety of folding/unfolding processes; (2) the hard-sphere solvent model fails when it does not correctly reproduce the protein-water many-body correlation; (3) the hard-sphere solvent model becomes problematic when the dependence of the many-body correlation on the solvent number density and temperature is essential: it is not quite suited to studies on cold and pressure denaturating of a protein; (4) when the temperature and solvent number density are limited to the ambient values, the hard-sphere solvent model is usually successful; and (5) even at the ambient

Influence of flock coating on bending rigidity of woven fabrics

Science.gov (United States)

Ozdemir, O.; Kesimci, M. O.

2017-10-01

This work presents the preliminary results of our efforts that focused on the effect of the flock coating on the bending rigidity of woven fabrics. For this objective, a laboratory scale flocking unit is designed and flocked samples of controlled flock density are produced. Bending rigidity of the samples with different flock densities are measured on both flocked and unflocked sides. It is shown that the bending rigidity depends on both flock density and whether the side to be measured is flocked or not. Adhesive layer thickness on the bending rigidity is shown to be dramatic. And at higher basis weights, flock density gets less effective on bending rigidity.

Growth performance and certain body measurements of ostrich chicks as affected by dietary protein levels during 2-9 weeks of age.

Science.gov (United States)

Mahrose, Kh M; Attia, A I; Ismail, I E; Abou-Kassem, D E; El-Hack, M E Abd

2015-01-01

The present work was conducted to examine the effects of dietary crude protein (CP) levels (18, 21 and 24%) on growth performance (Initial and final body weight, daily body weight gain, feed consumption, feed conversion and protein efficiency ratio) during 2-9 weeks of age and certain body measurements (body height, tibiotarsus length and tibiotarsus girth) at 9 weeks of age. A total of 30 African Black unsexed ostrich chicks were used in the present study in simple randomized design. The results of the present work indicated that initial and final live body weight, body weight gain, feed consumption, feed conversion of ostrich chicks were insignificantly affected by dietary protein level used. Protein efficiency ratio was high in the group of chicks fed diet contained 18% CP. Results obtained indicated that tibiotarsus girth was decreased (P≤0.01) with the increasing dietary protein level, where the highest value of tibiotarsus girth (18.38 cm) was observed in chicks fed 18% dietary protein level. Body height and tibiotarsus length were not significantly different. In conclusion, the results of the present study indicate that ostrich chicks (during 2-9 weeks of age) could grow on diets contain lower levels of CP (18%).

An Unusual Case of Foreign Body Aspiration in an Infant

African Journals Online (AJOL)

any radio opaque foreign body. Blood gases revealed severe hypoxia with severe metabolic acidosis. Child was being planned to be taken up for emergency tracheostomy, and rigid bronchoscopic removal of foreign body, but child succumbed during resuscitation measures. During the removal of the endotracheal tube the ...

Protein bodies in leaves exchange contents through the endoplasmic reticulum

Directory of Open Access Journals (Sweden)

Reza eSaberianfar

2016-05-01

Full Text Available Protein bodies (PBs are organelles found in seeds whose main function is the storage of proteins that are used during germination for sustaining growth. PBs can also be induced to form in leaves when foreign proteins are produced at high levels in the endoplasmic reticulum (ER and when fused to one of three tags: Zera®, elastin-like polypeptides (ELP, or hydrophobin-I (HFBI. In this study, we investigate the differences between ELP, HFBI and Zera PB formation, packing, and communication. Our results confirm the ER origin of all three fusion-tag-induced PBs. We show that secretory pathway proteins can be sequestered into all types of PBs but with different patterns, and that different fusion tags can target a specific protein to different PBs. Zera PBs are mobile and dependent on actomyosin motility similar to ELP and HFBI PBs. We show in vivo trafficking of proteins between PBs using GFP photoconversion. We also show that protein trafficking between ELP or HFBI PBs is faster and proteins travel further when compared to Zera PBs. Our results indicate that fusion-tag-induced PBs do not represent terminally stored cytosolic organelles, but that they form in, and remain part of the ER, and dynamically communicate with each other via the ER. We hypothesize that the previously documented PB mobility along the actin cytoskeleton is associated with ER movement rather than independent streaming of detached organelles.

Soft-matter composites with electrically tunable elastic rigidity

International Nuclear Information System (INIS)

Shan, Wanliang; Lu, Tong; Majidi, Carmel

2013-01-01

We use a phase-changing metal alloy to reversibly tune the elastic rigidity of an elastomer composite. The elastomer is embedded with a sheet of low-melting-point Field’s metal and an electric Joule heater composed of a serpentine channel of liquid-phase gallium–indium–tin (Galinstan ® ) alloy. At room temperature, the embedded Field’s metal is solid and the composite remains elastically rigid. Joule heating causes the Field’s metal to melt and allows the surrounding elastomer to freely stretch and bend. Using a tensile testing machine, we measure that the effective elastic modulus of the composite reversibly changes by four orders of magnitude when powered on and off. This dramatic change in rigidity is accurately predicted with a model for an elastic composite. Reversible rigidity control is also accomplished by replacing the Field’s metal with shape memory polymer. In addition to demonstrating electrically tunable rigidity with an elastomer, we also introduce a new technique to rapidly produce soft-matter electronics and multifunctional materials in several minutes with laser-patterned adhesive film and masked deposition of liquid-phase metal alloy. (paper)

Soft-matter composites with electrically tunable elastic rigidity

Science.gov (United States)

Shan, Wanliang; Lu, Tong; Majidi, Carmel

2013-08-01

We use a phase-changing metal alloy to reversibly tune the elastic rigidity of an elastomer composite. The elastomer is embedded with a sheet of low-melting-point Field’s metal and an electric Joule heater composed of a serpentine channel of liquid-phase gallium-indium-tin (Galinstan®) alloy. At room temperature, the embedded Field’s metal is solid and the composite remains elastically rigid. Joule heating causes the Field’s metal to melt and allows the surrounding elastomer to freely stretch and bend. Using a tensile testing machine, we measure that the effective elastic modulus of the composite reversibly changes by four orders of magnitude when powered on and off. This dramatic change in rigidity is accurately predicted with a model for an elastic composite. Reversible rigidity control is also accomplished by replacing the Field’s metal with shape memory polymer. In addition to demonstrating electrically tunable rigidity with an elastomer, we also introduce a new technique to rapidly produce soft-matter electronics and multifunctional materials in several minutes with laser-patterned adhesive film and masked deposition of liquid-phase metal alloy.

Drosophila SMN complex proteins Gemin2, Gemin3, and Gemin5 are components of U bodies

International Nuclear Information System (INIS)

Cauchi, Ruben J.; Sanchez-Pulido, Luis; Liu, Ji-Long

2010-01-01

Uridine-rich small nuclear ribonucleoproteins (U snRNPs) play key roles in pre-mRNA processing in the nucleus. The assembly of most U snRNPs takes place in the cytoplasm and is facilitated by the survival motor neuron (SMN) complex. Discrete cytoplasmic RNA granules called U bodies have been proposed to be specific sites for snRNP assembly because they contain U snRNPs and SMN. U bodies invariably associate with P bodies, which are involved in mRNA decay and translational control. However, it remains unknown whether other SMN complex proteins also localise to U bodies. In Drosophila there are four SMN complex proteins, namely SMN, Gemin2/CG10419, Gemin3 and Gemin5/Rigor mortis. Drosophila Gemin3 was originally identified as the Drosophila orthologue of human and yeast Dhh1, a component of P bodies. Through an in silico analysis of the DEAD-box RNA helicases we confirmed that Gemin3 is the bona fide Drosophila orthologue of vertebrate Gemin3 whereas the Drosophila orthologue of Dhh1 is Me31B. We then made use of the Drosophila egg chamber as a model system to study the subcellular distribution of the Gemin proteins as well as Me31B. Our cytological investigations show that Gemin2, Gemin3 and Gemin5 colocalise with SMN in U bodies. Although they are excluded from P bodies, as components of U bodies, Gemin2, Gemin3 and Gemin5 are consistently found associated with P bodies, wherein Me31B resides. In addition to a role in snRNP biogenesis, SMN complexes residing in U bodies may also be involved in mRNP assembly and/or transport.

Drosophila SMN complex proteins Gemin2, Gemin3, and Gemin5 are components of U bodies

Energy Technology Data Exchange (ETDEWEB)

Cauchi, Ruben J.; Sanchez-Pulido, Luis [MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX (United Kingdom); Liu, Ji-Long, E-mail: jilong.liu@dpag.ox.ac.uk [MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX (United Kingdom)

2010-08-15

Uridine-rich small nuclear ribonucleoproteins (U snRNPs) play key roles in pre-mRNA processing in the nucleus. The assembly of most U snRNPs takes place in the cytoplasm and is facilitated by the survival motor neuron (SMN) complex. Discrete cytoplasmic RNA granules called U bodies have been proposed to be specific sites for snRNP assembly because they contain U snRNPs and SMN. U bodies invariably associate with P bodies, which are involved in mRNA decay and translational control. However, it remains unknown whether other SMN complex proteins also localise to U bodies. In Drosophila there are four SMN complex proteins, namely SMN, Gemin2/CG10419, Gemin3 and Gemin5/Rigor mortis. Drosophila Gemin3 was originally identified as the Drosophila orthologue of human and yeast Dhh1, a component of P bodies. Through an in silico analysis of the DEAD-box RNA helicases we confirmed that Gemin3 is the bona fide Drosophila orthologue of vertebrate Gemin3 whereas the Drosophila orthologue of Dhh1 is Me31B. We then made use of the Drosophila egg chamber as a model system to study the subcellular distribution of the Gemin proteins as well as Me31B. Our cytological investigations show that Gemin2, Gemin3 and Gemin5 colocalise with SMN in U bodies. Although they are excluded from P bodies, as components of U bodies, Gemin2, Gemin3 and Gemin5 are consistently found associated with P bodies, wherein Me31B resides. In addition to a role in snRNP biogenesis, SMN complexes residing in U bodies may also be involved in mRNP assembly and/or transport.

Effects of Ag Nanoparticles on Growth and Fat Body Proteins in Silkworms (Bombyx mori).

Science.gov (United States)

Meng, Xu; Abdlli, Nouara; Wang, Niannian; Lü, Peng; Nie, Zhichao; Dong, Xin; Lu, Shuang; Chen, Keping

2017-12-01

Ag nanoparticles (AgNPs), a widely used non-antibiotic, antibacterial material, have shown toxic and other potentially harmful effects in mammals. However, the deleterious effects of AgNPs on insects are still unknown. Here, we studied the effects of AgNPs on the model invertebrate organism Bombyx mori. After feeding silkworm larvae different concentrations of AgNPs, we evaluated the changes of B. mori body weights, survival rates, and proteomic differences. The results showed that low concentrations (mori. Although high concentrations (≥800 mg/L) of AgNPs also improved B. mori growth, they resulted in silkworm death. An analysis of fat body proteomic differences revealed 13 significant differences in fat body protein spots, nine of which exhibited significantly downregulated expression, while four showed significantly upregulated expression. Reverse transcription-polymerase chain reaction results showed that at an AgNP concentration of 1600 mg/L, the expression levels of seven proteins were similar to the transcription levels of their corresponding genes. Our results suggest that AgNPs lowered the resistance to oxidative stress, affected cell apoptosis, and induced cell necrosis by regulating related protein metabolism and metabolic pathways in B. mori.

Casein protein results in higher prandial and exercise induced whole body protein anabolism than whey protein in chronic obstructive pulmonary disease.

Science.gov (United States)

Engelen, Mariëlle P K J; Rutten, Erica P A; De Castro, Carmen L N; Wouters, Emiel F M; Schols, Annemie M W J; Deutz, Nicolaas E P

2012-09-01

Exercise is known to improve physical functioning and health status in Chronic Obstructive Pulmonary Disease (COPD). Recently, disturbances in protein turnover and amino acid kinetics have been observed after exercise in COPD. The objective was to investigate which dairy protein is able to positively influence the protein metabolic response to exercise in COPD. 8 COPD patients and 8 healthy subjects performed a cycle test on two days while ingesting casein or whey protein. Whole body protein breakdown (WbPB), synthesis (WbPS), splanchnic amino acid extraction (SPE), and NetWbPS (=WbPS-WbPB) were measured using stable isotope methodology during 20 min of exercise (at 50% peak work load of COPD group). The controls performed a second exercise test at the same relative workload. Exercise was followed by 1 h of recovery. In the healthy group, WbPS, SPE, and NetPS were higher during casein than during whey feeding (Pexercise, independent of exercise intensity (Pexercise during casein and whey feeding in COPD (Pexercise were higher in COPD (Pexercise, lower NetPS values were found independent of protein type in both groups. Casein resulted in more protein anabolism than whey protein which was maintained during and following exercise in COPD. Optimizing protein intake might be of importance for muscle maintenance during daily physical activities in COPD. Copyright © 2012 Elsevier Inc. All rights reserved.

Strongly Coupled Fluid-Body Dynamics in the Immersed Boundary Projection Method

Science.gov (United States)

Wang, Chengjie; Eldredge, Jeff D.

2014-11-01

A computational algorithm is developed to simulate dynamically coupled interaction between fluid and rigid bodies. The basic computational framework is built upon a multi-domain immersed boundary method library, whirl, developed in previous work. In this library, the Navier-Stokes equations for incompressible flow are solved on a uniform Cartesian grid by the vorticity-based immersed boundary projection method of Colonius and Taira. A solver for the dynamics of rigid-body systems is also included. The fluid and rigid-body solvers are strongly coupled with an iterative approach based on the block Gauss-Seidel method. Interfacial force, with its intimate connection with the Lagrange multipliers used in the fluid solver, is used as the primary iteration variable. Relaxation, developed from a stability analysis of the iterative scheme, is used to achieve convergence in only 2-4 iterations per time step. Several two- and three-dimensional numerical tests are conducted to validate and demonstrate the method, including flapping of flexible wings, self-excited oscillations of a system of linked plates and three-dimensional propulsion of flexible fluked tail. This work has been supported by AFOSR, under Award FA9550-11-1-0098.

Sensing of substratum rigidity and directional migration by fast-crawling cells

Science.gov (United States)

Okimura, Chika; Sakumura, Yuichi; Shimabukuro, Katsuya; Iwadate, Yoshiaki

2018-05-01

Living cells sense the mechanical properties of their surrounding environment and respond accordingly. Crawling cells detect the rigidity of their substratum and migrate in certain directions. They can be classified into two categories: slow-moving and fast-moving cell types. Slow-moving cell types, such as fibroblasts, smooth muscle cells, mesenchymal stem cells, etc., move toward rigid areas on the substratum in response to a rigidity gradient. However, there is not much information on rigidity sensing in fast-moving cell types whose size is ˜10 μ m and migration velocity is ˜10 μ m /min . In this study, we used both isotropic substrata with different rigidities and an anisotropic substratum that is rigid on the x axis but soft on the y axis to demonstrate rigidity sensing by fast-moving Dictyostelium cells and neutrophil-like differentiated HL-60 cells. Dictyostelium cells exerted larger traction forces on a more rigid isotropic substratum. Dictyostelium cells and HL-60 cells migrated in the "soft" direction on the anisotropic substratum, although myosin II-null Dictyostelium cells migrated in random directions, indicating that rigidity sensing of fast-moving cell types differs from that of slow types and is induced by a myosin II-related process.

Motion control of rigid bodies in SE(3)

Science.gov (United States)

Roza, Ashton

This thesis investigates the control of motion for a general class of vehicles that rotate and translate in three-space, and are propelled by a thrust vector which has fixed direction in body frame. The thesis addresses the problems of path following and position control. For path following, a feedback linearization controller is presented that makes the vehicle follow an arbitrary closed curve while simultaneously allowing the designer to specify the velocity profile of the vehicle on the path and its heading. For position control, a two-stage approach is presented that decouples position control from attitude control, allowing for a modular design and yielding almost global asymptotic stability of any desired hovering equilibrium. The effectiveness of the proposed method is verified both in simulation and experimentally by means of a hardware-in-the-loop setup emulating a co-axial helicopter.

Effect of high-protein or normal-protein diet on weight loss, body composition, hormone, and metabolic profile in southern Brazilian women with polycystic ovary syndrome: a randomized study.

Science.gov (United States)

Toscani, Mariana K; Mario, Fernanda M; Radavelli-Bagatini, Simone; Wiltgen, Denusa; Matos, Maria Cristina; Spritzer, Poli Maria

2011-11-01

The aim of the present study was to assess the effects of a high protein (HP) and a normal protein (NP) diet on patients with polycystic ovary syndrome (PCOS) and body mass index-matched controls in a sample of southern Brazilian women. This 8-week randomized trial was carried out at a university gynecological endocrinology clinic and included 18 patients with PCOS and 22 controls. Changes in weight, body composition, hormone, and metabolic profile were analyzed in women randomized to receive HP (30% protein, 40% carbohydrate, and 30% lipid) or NP (15% protein, 55% carbohydrate, and 30% lipid). The energy content was estimated for each participant at 20-25 kcal/kg current weight/day. Physical activity, blood pressure, homeostasis model assessment (HOMA) index, and fasting and 2-h glucose and insulin remained stable during the intervention in PCOS and controls, even in the presence of weight loss. There were no changes in lipid profile in either group. In contrast, body weight, body mass index (BMI), waist circumference, percent of body fat, and sum of trunk skinfolds decreased significantly after both diets in both groups. Total testosterone also decreased in PCOS and controls regardless of diet. In conclusion, calorie reduction, rather than protein content, seemed to affect body composition and hormonal profile in this short-term study. These findings emphasize the role of non-pharmacological interventions to reduce weight and ameliorate the anthropometric and clinical phenotype in PCOS.

Purification of inclusion bodies using PEG precipitation under denaturing conditions to produce recombinant therapeutic proteins from Escherichia coli.

Science.gov (United States)

Chen, Huanhuan; Li, Ninghuan; Xie, Yueqing; Jiang, Hua; Yang, Xiaoyi; Cagliero, Cedric; Shi, Siwei; Zhu, Chencen; Luo, Han; Chen, Junsheng; Zhang, Lei; Zhao, Menglin; Feng, Lei; Lu, Huili; Zhu, Jianwei

2017-07-01

It has been documented that the purification of inclusion bodies from Escherichia coli by size exclusion chromatography (SEC) may benefit subsequent refolding and recovery of recombinant proteins. However, loading volume and the high cost of the column limits its application in large-scale manufacturing of biopharmaceutical proteins. We report a novel process using polyethylene glycol (PEG) precipitation under denaturing conditions to replace SEC for rapid purification of inclusion bodies containing recombinant therapeutic proteins. Using recombinant human interleukin 15 (rhIL-15) as an example, inclusion bodies of rhIL-15 were solubilized in 7 M guanidine hydrochloride, and rhIL-15 was precipitated by the addition of PEG 6000. A final concentration of 5% (w/v) PEG 6000 was found to be optimal to precipitate target proteins and enhance recovery and purity. Compared to the previously reported S-200 size exclusion purification method, PEG precipitation was easier to scale up and achieved the same protein yields and quality of the product. PEG precipitation also reduced manufacturing time by about 50 and 95% of material costs. After refolding and further purification, the rhIL-15 product was highly pure and demonstrated a comparable bioactivity with a rhIL-15 reference standard. Our studies demonstrated that PEG precipitation of inclusion bodies under denaturing conditions holds significant potential as a manufacturing process for biopharmaceuticals from E. coli protein expression systems.

Proteomic characterisation of endoplasmic reticulum-derived protein bodies in tobacco leaves

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Joseph Minu

2012-03-01

Full Text Available Abstract Background The N-terminal proline-rich domain (Zera of the maize storage protein γ-zein, is able to induce the formation of endoplasmic reticulum (ER-derived protein bodies (PBs when fused to proteins of interest. This encapsulation enables a recombinant fused protein to escape from degradation and facilitates its recovery from plant biomass by gradient purification. The aim of the present work was to evaluate if induced PBs encapsulate additional proteins jointly with the recombinant protein. The exhaustive analysis of protein composition of PBs is expected to facilitate a better understanding of PB formation and the optimization of recombinant protein purification approaches from these organelles. Results We analysed the proteome of PBs induced in Nicotiana benthamiana leaves by transient transformation with Zera fused to a fluorescent marker protein (DsRed. Intact PBs with their surrounding ER-membrane were isolated on iodixanol based density gradients and their integrity verified by confocal and electron microscopy. SDS-PAGE analysis of isolated PBs showed that Zera-DsRed accounted for around 85% of PB proteins in term of abundance. Differential extraction of PBs was performed for in-depth analysis of their proteome and structure. Besides Zera-DsRed, 195 additional proteins were identified including a broad range of proteins resident or trafficking through the ER and recruited within the Zera-DsRed polymer. Conclusions This study indicates that Zera-protein fusion is still the major protein component of the new formed organelle in tobacco leaves. The analysis also reveals the presence of an unexpected diversity of proteins in PBs derived from both the insoluble Zera-DsRed polymer formation, including ER-resident and secretory proteins, and a secretory stress response induced most likely by the recombinant protein overloading. Knowledge of PBs protein composition is likely to be useful to optimize downstream purification of

Effect of rigid inclusions on sintering

International Nuclear Information System (INIS)

Rahaman, M.N.; De Jonghe, L.C.

1988-01-01

The predictions of recent theoretical studies on the effect of inert, rigid inclusions on the sintering of ceramic powder matrices are examined and compared with experimental data. The densification of glass matrix composites with inclusion volume fractions of ≤0.15 can be adequately explained by Scherer's theory for viscous sintering with rigid inclusions. Inclusions cause a vast reduction in the densification rates of polycrystalline matrix composites even at low inclusion volume fractions. Models put forward to explain the sintering of polycrystalline matrix composites are discussed

Assessment of rigid multi-modality image registration consistency using the multiple sub-volume registration (MSR) method

International Nuclear Information System (INIS)

Ceylan, C; Heide, U A van der; Bol, G H; Lagendijk, J J W; Kotte, A N T J

2005-01-01

Registration of different imaging modalities such as CT, MRI, functional MRI (fMRI), positron (PET) and single photon (SPECT) emission tomography is used in many clinical applications. Determining the quality of any automatic registration procedure has been a challenging part because no gold standard is available to evaluate the registration. In this note we present a method, called the 'multiple sub-volume registration' (MSR) method, for assessing the consistency of a rigid registration. This is done by registering sub-images of one data set on the other data set, performing a crude non-rigid registration. By analysing the deviations (local deformations) of the sub-volume registrations from the full registration we get a measure of the consistency of the rigid registration. Registration of 15 data sets which include CT, MR and PET images for brain, head and neck, cervix, prostate and lung was performed utilizing a rigid body registration with normalized mutual information as the similarity measure. The resulting registrations were classified as good or bad by visual inspection. The resulting registrations were also classified using our MSR method. The results of our MSR method agree with the classification obtained from visual inspection for all cases (p < 0.02 based on ANOVA of the good and bad groups). The proposed method is independent of the registration algorithm and similarity measure. It can be used for multi-modality image data sets and different anatomic sites of the patient. (note)

Rigid-Plastic Post-Buckling Analysis of Columns and Quadratic Plates

DEFF Research Database (Denmark)

Jönsson, Jeppe

2008-01-01

the compressive load as a function of the transverse displacement. An estimate of the magnitude of the transverse displacement prior to the forming of the collapse mechanism is introduced into the compressive load function, determined by the virtual work equation, thereby revealing a qualified estimate...... yield lines accommodate differential rotations of rigid parts and the area “collapse” yield lines accommodate local area changes of the rigid parts thereby preserving compatibility of the rigid parts of a plate. The approach will be illustrated for rigid plastic column analysis and for a quadratic plate...

Gammaherpesviral Tegument Proteins, PML-Nuclear Bodies and the Ubiquitin-Proteasome System

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Florian Full

2017-10-01

Full Text Available Gammaherpesviruses like Epstein-Barr virus (EBV and Kaposi’s sarcoma-associated herpesvirus (KSHV subvert the ubiquitin proteasome system for their own benefit in order to facilitate viral gene expression and replication. In particular, viral tegument proteins that share sequence homology to the formylglycineamide ribonucleotide amidotransferase (FGARAT, or PFAS, an enzyme in the cellular purine biosynthesis, are important for disrupting the intrinsic antiviral response associated with Promyelocytic Leukemia (PML protein-associated nuclear bodies (PML-NBs by proteasome-dependent and independent mechanisms. In addition, all herpesviruses encode for a potent ubiquitin protease that can efficiently remove ubiquitin chains from proteins and thereby interfere with several different cellular pathways. In this review, we discuss mechanisms and functional consequences of virus-induced ubiquitination and deubiquitination for early events in gammaherpesviral infection.

Association between dietary protein and change in body composition among children (EYHS)

DEFF Research Database (Denmark)

van Vught, Anneke J A H; Heitmann, Berit L; Nieuwenhuizen, Arie G

2009-01-01

BACKGROUND & AIMS: Growth hormone (GH) affects body composition by a relatively reduced fat mass and increased fat free mass. The intake of protein as well as the specific amino acids arginine and lysine potently stimulate GH secretion. This study investigated associations between intakes of prot...

Effectiveness of exercise and protein supplementation intervention on body composition, functional fitness, and oxidative stress among elderly Malays with sarcopenia

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Shahar S

2013-10-01

Full Text Available Suzana Shahar,1 Norshafarina Shari Kamaruddin,2 Manal Badrasawi,1 Noor Ibrahim Mohamed Sakian,3 Zahara Abd Manaf,1 Zaitun Yassin,4 Leonard Joseph51Dietetic Programme, 2Biomedical Programme, 3Occupational Therapy Programme, School of Healthcare Sciences, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, Kuala Lumpur, 4Department of Nutrition and Dietetics, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, 5Department of Physiotherapy, School of Healthcare Sciences, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, Kuala Lumpur, MalaysiaAbstract: Sarcopenia, characterized as muscle loss that occurs with aging, is a major health problem in an aging population, due to its implications on mobility, quality of life, and fall risk. Protein supplementation could improve the physical fitness by increasing protein anabolism, and exercise has a documented evidence of positive effect on functional status among the elderly. However, the combined effect of both protein supplementation and exercise has not been investigated among sarcopenic elderly in the Asian population. Thus, this study aimed to determine the effectiveness of exercise intervention and protein supplementation either alone or in combination for 12 weeks, on body composition, functional fitness, and oxidative stress among elderly Malays with sarcopenia. Sixty five sarcopenic elderly Malays aged 60-74 years were assigned to the control group, exercise group (ExG, protein supplementation group (PrG, or the combination of exercise and protein supplementation group. A significant interaction effect between body weight and body mass index (BMI was observed, with the PrG (-2.1% body weight, -1.8% BMI showing the highest reductions. Further, there was a decrease in % body fat (-4.5% and an increase in fat-free mass (kg (+5.7% in the ExG after 12 weeks (P < 0.05. The highest increments in lower and upper body strength were observed in the Pr

About deformation and rigidity in relativity

International Nuclear Information System (INIS)

Coll, Bartolome

2007-01-01

The notion of deformation involves that of rigidity. In relativity, starting from Born's early definition of rigidity, some other ones have been proposed, offering more or less interesting aspects but also accompanied of undesired or even pathological properties. In order to clarify the origin of these difficulties presented by the notion of rigidity in relativity, we analyze with some detail significant aspects of the unambiguous classical, Newtonian, notion. In particular, the relative character of its kinetic definition is pointed out, allowing to predict and to understand the limitations imposed by Herglotz-Noether theorem. Also, its equivalent dynamic definition is obtained and, in contrast, its absolute character is shown. But in spite of this absolute character, the dynamic definition is shown to be not extensible to relativity. The metric deformation of Minkowski space by the presence of a gravitational field is interpreted as a universal deformation, and it is shown that, under natural conditions, only a simple deformation law is possible, relating locally, but in an one-to-one way, gravitational fields and gauge classes of two-forms. We argue that fields of unit vectors associated to the internal gauge class of two-forms of every space-time (and, in particular, of Minkowski space-time) are the relativistic analogues of the classical accelerated observers, i.e. of the classical rigid motions. Some other consequences of the universal law of gravitational deformation are commented

Genus Ranges of 4-Regular Rigid Vertex Graphs.

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Buck, Dorothy; Dolzhenko, Egor; Jonoska, Nataša; Saito, Masahico; Valencia, Karin

2015-01-01

A rigid vertex of a graph is one that has a prescribed cyclic order of its incident edges. We study orientable genus ranges of 4-regular rigid vertex graphs. The (orientable) genus range is a set of genera values over all orientable surfaces into which a graph is embedded cellularly, and the embeddings of rigid vertex graphs are required to preserve the prescribed cyclic order of incident edges at every vertex. The genus ranges of 4-regular rigid vertex graphs are sets of consecutive integers, and we address two questions: which intervals of integers appear as genus ranges of such graphs, and what types of graphs realize a given genus range. For graphs with 2 n vertices ( n > 1), we prove that all intervals [ a, b ] for all a genus ranges. For graphs with 2 n - 1 vertices ( n ≥ 1), we prove that all intervals [ a, b ] for all a genus ranges. We also provide constructions of graphs that realize these ranges.

Protein content and electrophoretic profile of fat body and ovary extracts from workers of Melipona quadrifasciata anthidioides (Hymenoptera, Meliponini

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Vagner T. Paes de Oliveira

Full Text Available Workers of Melipona quadrifasciata anthidioides (Lepeletier, 1836 develop their ovaries and lay eggs, therefore the production of vitellogenin is expected. In electrophoretic profiles only fat body extracts from nurse workers and ovary extracts from newly-emerged workers show protein with molecular mass similar to vitellogenin. However, an increase in the protein content was detected in forager fat body. This increase was attributed to storage of vitellogenin or other proteins in the previous phase and not discharged into the hemolymph or to an effect of the increased titre of juvenile hormone in this phase of worker life over the fat body functioning.

Normal protein intake is required for body weight loss and weight maintenance, and elevated protein intake for additional preservation of resting energy expenditure and fat free mass.

Science.gov (United States)

Soenen, Stijn; Martens, Eveline A P; Hochstenbach-Waelen, Ananda; Lemmens, Sofie G T; Westerterp-Plantenga, Margriet S

2013-05-01

Energy-restricted high-protein diets (HPDs) have shown favorable results for body weight (BW) management, yet studies differ in their outcomes depending on the dietary protein content. Our objective was to determine the effects of dietary protein content on BW loss-related variables during a 6-mo energy restriction with the use of diets containing protein at the level of requirement [normal-protein diet (NPD), 0.8 g · kg BW(-1) (.) d(-1)] and above (HPD, 1.2 g · kg BW(-1) (.) d(-1)). In overweight and obese participants (24 men and 48 women), BW, body composition, and metabolic responses were assessed before and after subsequent energy intakes of 100, 33, and 67% of the original individual daily energy requirements. Protein intake was consistent in the NPD (0.8 ± 0.3 g · kg BW(-1) (.) d(-1)) and HPD (1.2 ± 0.3 g · kg BW(-1) (.) d(-1)) groups throughout the study (P body fat mass similarly decreased in the NPD and HPD groups (P initial sparing effect of FFM and lowering of DBP.

Comparative analysis of the protein compositions between wild type and body color mutant of helicoverpa armigera adult

International Nuclear Information System (INIS)

He Lihua; Chen Jin'e; Liu Yan; Wang Yongqiang; Liu Peigang; Meng Zhiqi

2012-01-01

To gain an in-depth understanding of the fineness and regulation mechanism of body color mutant of Helicoverpa armigera Hbner, the protein composition differences between adult of dominant mutant, recessive mutant and wild type were studied using the SDS-PAGE combined with MALDI-TOF-TOF/MS and bioinformatics analysis. The results indicated that the protein composition of the dominant mutant and wild type had little difference. However, there were obvious differences between the recessive mutant and wild-type. Three specific stripe were chosen for mass spectrometry and bioinformatics analysis, and two types of proteins related to energy metabolism and cytoskeleton were identified. These findings suggested that the two types of proteins may be associated with occurrence and regulation of body color mutant traits of H. armigera. (authors)

The Almost Periodic Rigidity of Crystallographic Bar-Joint Frameworks

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Ghada Badri

2014-04-01

Full Text Available A crystallographic bar-joint framework, C in Rd, is shown to be almost periodically infinitesimally rigid if and only if it is strictly periodically infinitesimally rigid and the rigid unit mode (RUM spectrum, Ω (C, is a singleton. Moreover, the almost periodic infinitesimal flexes of C are characterised in terms of a matrix-valued function, ΦC(z, on the d-torus, Td, determined by a full rank translation symmetry group and an associated motif of joints and bars.

Wobbling motion: A γ-rigid or γ-soft mode?

International Nuclear Information System (INIS)

Casten, R.F.; McCutchan, E.A.; Beausang, C.W.; Zamfir, N.V.; Zhang Jingye

2003-01-01

For even-even nuclei, it is shown that the predicted B(E2) values from the odd spin states of the quasi-γ band in a γ-soft nucleus to the yrast band are quite similar to those predicted for the one-phonon wobbling mode of a rigidly triaxial nucleus. This suggests that the observation of wobbling points to axial asymmetry, but not necessarily to rigid triaxiality. However, another observable that does distinguish γ-soft from γ-rigid structure is identified

Dendrimer-protein interactions versus dendrimer-based nanomedicine.

Science.gov (United States)

Shcharbin, Dzmitry; Shcharbina, Natallia; Dzmitruk, Volha; Pedziwiatr-Werbicka, Elzbieta; Ionov, Maksim; Mignani, Serge; de la Mata, F Javier; Gómez, Rafael; Muñoz-Fernández, Maria Angeles; Majoral, Jean-Pierre; Bryszewska, Maria

2017-04-01

Dendrimers are hyperbranched polymers belonging to the huge class of nanomedical devices. Their wide application in biology and medicine requires understanding of the fundamental mechanisms of their interactions with biological systems. Summarizing, electrostatic force plays the predominant role in dendrimer-protein interactions, especially with charged dendrimers. Other kinds of interactions have been proven, such as H-bonding, van der Waals forces, and even hydrophobic interactions. These interactions depend on the characteristics of both participants: flexibility and surface charge of a dendrimer, rigidity of protein structure and the localization of charged amino acids at its surface. pH and ionic strength of solutions can significantly modulate interactions. Ligands and cofactors attached to a protein can also change dendrimer-protein interactions. Binding of dendrimers to a protein can change its secondary structure, conformation, intramolecular mobility and functional activity. However, this strongly depends on rigidity versus flexibility of a protein's structure. In addition, the potential applications of dendrimers to nanomedicine are reviwed related to dendrimer-protein interactions. Copyright © 2017 Elsevier B.V. All rights reserved.

Dissection of Molecular Mechanisms Regulating Protein Body Formation in Maize Endosperm - DE-FG03-95-ER20183 B139

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Brian A. Larkins

2003-03-21

Dissection of Molecular Mechanisms Regulating Protein Body Formation in Maize Endosperm - DE-FG03-95-ER20183 Final Technical Report and Patent Summary Dr. Brian A. Larkins, Department of Plant Sciences, University of Arizona, Tucson, AZ 85721 Endosperm texture is an important quality trait in maize, as it influences the shipping characteristics of the grain, its susceptibility to insects, the yield of grits from dry milling, energy costs during wet milling, and the baking and digestibility properties of the flour. There appears to be a causal relationship between kernel hardness and the formation of zein-containing protein bodies, as mutations affecting protein body number and structure are associated with a soft, starchy kernel. In this project we used a variety of approaches to better understand this relationship and investigate the molecular and biochemical changes associated with starchy endosperm mutants. We characterized the distribution of zein mRNAs on endosperm rough endoplasmic reticulum (RER) membranes and the interactions between zein proteins, as each of these could influence the structure of protein bodies. Based on in situ hybridization, mRNAs encoding the 22-kD alpha- and 27-kD gamma-zeins are randomly distributed on RER; hence, mRNA targeting does not appear to influence the formation of protein bodies. Investigation of the interactions between zein proteins (alpha, beta, gamma, delta) with the yeast two-hybrid system showed that interactions between the 19- and 22-alpha-zeins are relatively weak, although each of them interacted strongly with the 10-kD delta-zein. Strong interactions were detected between the alpha- and delta-zeins and the 16-kD gamma- and 15-kD beta-zeins; however, the 50-kD and 27-kD gamma-zeins did not interact detectably with the alpha- and delta-zein proteins. The NH2- and COOH-terminal domains of the 22-kD alpha-zein were found to interact most strongly with the 15-kD beta- and 16-kD gamma-zeins, suggesting the 16-kD and 15

Rigid Spine Syndrome among Children in Oman

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Roshan Koul

2015-08-01

Full Text Available Objectives: Rigidity of the spine is common in adults but is rarely observed in children. The aim of this study was to report on rigid spine syndrome (RSS among children in Oman. Methods: Data on children diagnosed with RSS were collected consecutively at presentation between 1996 and 2014 at the Sultan Qaboos University Hospital (SQUH in Muscat, Oman. A diagnosis of RSS was based on the patient’s history, clinical examination, biochemical investigations, electrophysiological findings, neuro-imaging and muscle biopsy. Atrophy of the paraspinal muscles, particularly the erector spinae, was the diagnostic feature; this was noted using magnetic resonance imaging of the spine. Children with disease onset in the paraspinal muscles were labelled as having primary RSS or rigid spinal muscular dystrophy. Secondary RSS was classified as RSS due to the late involvement of other muscle diseases. Results: Over the 18-year period, 12 children were included in the study, with a maleto- female ratio of 9:3. A total of 10 children were found to have primary RSS or rigid spinal muscular dystrophy syndrome while two had secondary RSS. Onset of the disease ranged from birth to 18 months of age. A family history was noted, with two siblings from one family and three siblings from another (n = 5. On examination, children with primary RSS had typical features of severe spine rigidity at onset, with the rest of the neurological examination being normal. Conclusion: RSS is a rare disease with only 12 reported cases found at SQUH during the study period. Cases of primary RSS should be differentiated from the secondary type.

an unusual foreign body in human oesophagus – case report

African Journals Online (AJOL)

drclement

ABSTRACT. We report a case of a 65year old. Nigerian male with an unusual foreign body, a fishing hook in the oesophagus. This was confirmed with a plain radiograph of the chest done on a routine medical check-up, although patient was asymptomatic. The foreign body was removed via a rigid oesphagoscopy without ...

Online analysis of protein inclusion bodies produced in E. coli by monitoring alterations in scattered and reflected light.

Science.gov (United States)

Ude, Christian; Ben-Dov, Nadav; Jochums, André; Li, Zhaopeng; Segal, Ester; Scheper, Thomas; Beutel, Sascha

2016-05-01

The online monitoring of recombinant protein aggregate inclusion bodies during microbial cultivation is an immense challenge. Measurement of scattered and reflected light offers a versatile and non-invasive measurement technique. Therefore, we investigated two methods to detect the formation of inclusion bodies and monitor their production: (1) online 180° scattered light measurement (λ = 625 nm) using a sensor platform during cultivation in shake flask and (2) online measurement of the light reflective interference using a porous Si-based optical biosensor (SiPA). It could be shown that 180° scattered light measurement allows monitoring of alterations in the optical properties of Escherichia coli BL21 cells, associated with the formation of inclusion bodies during cultivation. A reproducible linear correlation between the inclusion body concentration of the non-fluorescent protein human leukemia inhibitory factor (hLIF) carrying a thioredoxin tag and the shift ("Δamp") in scattered light signal intensity was observed. This was also observed for the glutathione-S-transferase-tagged green fluorescent protein (GFP-GST). Continuous online monitoring of reflective interference spectra reveals a significant increase in the bacterium refractive index during hLIF production in comparison to a non-induced reference that coincide with the formation of inclusion bodies. These online monitoring techniques could be applied for fast and cost-effective screening of different protein expression systems.

Genetic parameters for energy balance, fat /protein ratio, body condition score and disease traits in German Holstein cows.

Science.gov (United States)

Buttchereit, N; Stamer, E; Junge, W; Thaller, G

2012-08-01

Various health problems in dairy cows have been related to the magnitude and duration of the energy deficit post partum. Energy balance indicator traits like fat/protein ratio in milk and body condition score could be used in selection programmes to help predicting breeding values for health traits, but currently there is a lack of appropriate genetic parameters. Therefore, genetic correlations among energy balance, fat/protein ratio, and body condition score, and mastitis, claw and leg diseases, and metabolic disorders were estimated using linear and threshold models on data from 1693 primiparous cows recorded within the first 180 days in milk. Average daily energy balance, milk fat/protein ratio and body condition score were 8 MJ NEL, 1.13 and 2.94, respectively. Disease frequencies (% cows with at least one case) were 24.6% for mastitis, 9.7% for metabolic disorders and 28.2% for claw and leg diseases. Heritability estimates were 0.06, 0.30 and 0.34 for energy balance, fat/protein ratio and body condition score, respectively. For the disease traits, heritabilities ranged between 0.04 and 0.15. The genetic correlations were, in general, associated with large standard errors, but, although not significant, the results suggest that an improvement of overall health can be expected if energy balance traits are included into future breeding programmes. A low fat/protein ratio might serve as an indicator for metabolic stability and health of claw and legs. Between body condition and mastitis, a significant negative correlation of -0.40 was estimated. The study provides a new insight into the role energy balance traits can play as auxiliary traits for robustness of dairy cows. It was concluded that both, fat/protein ratio and body condition score, are potential variables to describe how well cows can adapt to the challenge of early lactation. However, the genetic parameters should be re-estimated on a more comprehensive data set. © 2011 Blackwell Verlag GmbH.

Biomimetic model systems of rigid hair beds: Part I - Theory

Science.gov (United States)

Hood, Kaitlyn; Jammalamadaka, Mani S. S.; Hosoi, Anette

2017-11-01

Crustaceans - such as lobsters, crabs, and stomapods - have hairy appendages that they use to recognize and track odorants in the surrounding fluid. An array of rigid hairs impedes flow at different rates depending on the spacing between hairs and the Reynolds number, Re. At larger Reynolds numbers (Re >1), fluid travels through the hairs rather than around them, a phenomenon called leakiness. Crustaceans flick their appendages at different speeds in order to manipulate the leakiness between the hairs, allowing the hairs to either detect odors in a sample of fluid or collect a new sample. A single hair can be represented as a slender body attached at one end to a wall. Using both slender body theory and numerical methods, we observe that there is a region of flow around the hair that speeds up relative to the unobstructed flow. As the Reynolds number increases, this fast flow region moves closer to the hair. Using this model, we predict that an array of hairs can be engineered to have a desired leakiness profile.

Customizable rigid head fixation for infants: technical note.

Science.gov (United States)

Udayakumaran, Suhas; Onyia, Chiazor U

2016-01-01

The need and advantages of rigid fixation of the head in cranial surgeries are well documented (Berryhill et al., Otolaryngol Head Neck Surg 121:269-273, 1999). Head fixation for neurosurgical procedures in infants and in early years has been a challenge and is fraught with risk. Despite the fact that pediatric pins are designed, rigid head fixation involving direct application of pins to the head of infants and slightly older children is still generally not safe (Agrawal and Steinbok, Childs Nerv Syst 22:1473-1474, 2006). Yet, there are some surgeries in which some form of rigid fixation is required (Agrawal and Steinbok, Childs Nerv Syst 22:1473-1474, 2006). We describe a simple technique to achieve rigid fixation of the head in infants for neurosurgical procedures. This involves applying a head band made of Plaster of Paris (POP) around the head and then applying the fixation pins of the fixation frame directly on to the POP. We have used this technique of head fixation successfully for infants with no complications.

"Mind the trap": mindfulness practice reduces cognitive rigidity.

Directory of Open Access Journals (Sweden)

Jonathan Greenberg

Full Text Available Two experiments examined the relation between mindfulness practice and cognitive rigidity by using a variation of the Einstellung water jar task. Participants were required to use three hypothetical jars to obtain a specific amount of water. Initial problems were solvable by the same complex formula, but in later problems ("critical" or "trap" problems solving was possible by an additional much simpler formula. A rigidity score was compiled through perseverance of the complex formula. In Experiment 1, experienced mindfulness meditators received significantly lower rigidity scores than non-meditators who had registered for their first meditation retreat. Similar results were obtained in randomized controlled Experiment 2 comparing non-meditators who underwent an eight meeting mindfulness program with a waiting list group. The authors conclude that mindfulness meditation reduces cognitive rigidity via the tendency to be "blinded" by experience. Results are discussed in light of the benefits of mindfulness practice regarding a reduced tendency to overlook novel and adaptive ways of responding due to past experience, both in and out of the clinical setting.

Rigidity of outermost MOTS: the initial data version

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Galloway, Gregory J.

2018-03-01

In the paper Commun Anal Geom 16(1):217-229, 2008, a rigidity result was obtained for outermost marginally outer trapped surfaces (MOTSs) that do not admit metrics of positive scalar curvature. This allowed one to treat the "borderline case" in the author's work with R. Schoen concerning the topology of higher dimensional black holes (Commun Math Phys 266(2):571-576, 2006). The proof of this rigidity result involved bending the initial data manifold in the vicinity of the MOTS within the ambient spacetime. In this note we show how to circumvent this step, and thereby obtain a pure initial data version of this rigidity result and its consequence concerning the topology of black holes.

High Whey Protein Intake Delayed the Loss of Lean Body Mass in Healthy Old Rats, whereas Protein Type and Polyphenol/Antioxidant Supplementation Had No Effects

Science.gov (United States)

Mosoni, Laurent; Gatineau, Eva; Gatellier, Philippe; Migné, Carole; Savary-Auzeloux, Isabelle; Rémond, Didier; Rocher, Emilie; Dardevet, Dominique

2014-01-01

Our aim was to compare and combine 3 nutritional strategies to slow down the age-related loss of muscle mass in healthy old rats: 1) increase protein intake, which is likely to stimulate muscle protein anabolism; 2) use leucine rich, rapidly digested whey proteins as protein source (whey proteins are recognized as the most effective proteins to stimulate muscle protein anabolism). 3) Supplement animals with a mixture of chamomile extract, vitamin E, vitamin D (reducing inflammation and oxidative stress is also effective to improve muscle anabolism). Such comparisons and combinations were never tested before. Nutritional groups were: casein 12% protein, whey 12% protein, whey 18% protein and each of these groups were supplemented or not with polyphenols/antioxidants. During 6 months, we followed changes of weight, food intake, inflammation (plasma fibrinogen and alpha-2-macroglobulin) and body composition (DXA). After 6 months, we measured muscle mass, in vivo and ex-vivo fed and post-absorptive muscle protein synthesis, ex-vivo muscle proteolysis, and oxidative stress parameters (liver and muscle glutathione, SOD and total antioxidant activities, muscle carbonyls and TBARS). We showed that although micronutrient supplementation reduced inflammation and oxidative stress, the only factor that significantly reduced the loss of lean body mass was the increase in whey protein intake, with no detectable effect on muscle protein synthesis, and a tendency to reduce muscle proteolysis. We conclude that in healthy rats, increasing protein intake is an effective way to delay sarcopenia. PMID:25268515

High frequency permeameter with semi-rigid pick-up coil

International Nuclear Information System (INIS)

Shin, Sung-Yong; Shin, Kwang-Ho . E-mail : khshin@star.ks.ac.kr; Kim, Jong-sung; Kim, Young-Hak; Lim, Sang-Ho; Sa-gong, Geon

2006-01-01

In this study, we propose the application of semi-rigid cable loop as a single turn shielded loop pick-up coil for the high frequency permeameter. Since the semi-rigid cable pick-up coil has simple structure, it is very easy to make the pick-up coil with bending and conventional soldering. The permeability of cobalt base amorphous ribbon was investigated using the developed permeameter for demonstrating its performance. The permeability of the amorphous ribbon was driven from the S-parameters measured using a network analyzer and permameter having the semi-rigid pick-up coil

Folding 19 proteins to their native state and stability of large proteins from a coarse-grained model.

Science.gov (United States)

Kapoor, Abhijeet; Travesset, Alex

2014-03-01

We develop an intermediate resolution model, where the backbone is modeled with atomic resolution but the side chain with a single bead, by extending our previous model (Proteins (2013) DOI: 10.1002/prot.24269) to properly include proline, preproline residues and backbone rigidity. Starting from random configurations, the model properly folds 19 proteins (including a mutant 2A3D sequence) into native states containing β sheet, α helix, and mixed α/β. As a further test, the stability of H-RAS (a 169 residue protein, critical in many signaling pathways) is investigated: The protein is stable, with excellent agreement with experimental B-factors. Despite that proteins containing only α helices fold to their native state at lower backbone rigidity, and other limitations, which we discuss thoroughly, the model provides a reliable description of the dynamics as compared with all atom simulations, but does not constrain secondary structures as it is typically the case in more coarse-grained models. Further implications are described. Copyright © 2013 Wiley Periodicals, Inc.

Durable bistable auxetics made of rigid solids

Science.gov (United States)

Shang, Xiao; Liu, Lu; Rafsanjani, Ahmad; Pasini, Damiano

2018-02-01

Bistable Auxetic Metamaterials (BAMs) are a class of monolithic perforated periodic structures with negative Poisson's ratio. Under tension, a BAM can expand and reach a second state of equilibrium through a globally large shape transformation that is ensured by the flexibility of its elastomeric base material. However, if made from a rigid polymer, or metal, BAM ceases to function due to the inevitable rupture of its ligaments. The goal of this work is to extend the unique functionality of the original kirigami architecture of BAM to a rigid solid base material. We use experiments and numerical simulations to assess performance, bistability and durability of rigid BAMs at 10,000 cycles. Geometric maps are presented to elucidate the role of the main descriptors of BAM architecture. The proposed design enables the realization of BAM from a large palette of materials, including elastic-perfectly plastic materials and potentially brittle materials.

Utility of semi-rigid thoracoscopy in undiagnosed exudative pleural effusion.

Science.gov (United States)

Nattusamy, Loganathan; Madan, Karan; Mohan, Anant; Hadda, Vijay; Jain, Deepali; Madan, Neha Kawatra; Arava, Sudheer; Khilnani, Gopi C; Guleria, Randeep

2015-01-01

Semi-rigid thoracoscopy is a safe and efficacious procedure in patients with undiagnosed pleural effusion. Literature on its utility from developing countries is limited. We herein describe our initial experience on the utility of semi-rigid thoracoscopy from a tertiary care teaching and referral center in north India. We also perform a systematic review of studies reporting the utility of semi-rigid thoracoscopy from India. The primary objective was to evaluate the diagnostic utility of semi-rigid thoracoscopy in patients with undiagnosed exudative pleural effusion. Semi-rigid thoracoscopy was performed under local anesthesia and conscious sedation in the bronchoscopy suite. A total of 48 patients underwent semi-rigid thoracoscopy between August 2012 and December 2013 for undiagnosed pleural effusion. Mean age was 50.9 ± 14.1 years (range: 17-78 years). Pre-procedure clinico-radiological diagnoses were malignant pleural effusion [36 patients (75%)], tuberculosis (TB) [10 (20.83%) patients], and empyema [2 patients (4.17%)]. Patients with empyema underwent the procedure for pleural biopsy, optimal placement of intercostal tube and adhesiolysis. Thoracoscopic pleural biopsy diagnosed pleural malignancy in 30 (62.5%) patients and TB in 2 (4.17%) patients. Fourteen (29.17%) patients were diagnosed with non-specific pleuritis and normal pleura was diagnosed on a pleural biopsy in 2 (4.17%) patients. Overall, a definitive diagnosis of either pleural malignancy or TB was obtained in 32 (66.7%) patients. Combined overall sensitivity, specificity, positive predictive value and negative predictive value of thoracoscopic pleural biopsy for malignant pleural effusion were 96.77%, 100%, 100% and 66.67%, respectively. There was no procedure-related mortality. On performing a systematic review of literature, four studies on semi-rigid thoracoscopy from India were identified. Semi-rigid thoracoscopy is a safe and efficacious procedure in patients with undiagnosed exudative

Catalytically-active inclusion bodies-Carrier-free protein immobilizates for application in biotechnology and biomedicine.

Science.gov (United States)

Krauss, Ulrich; Jäger, Vera D; Diener, Martin; Pohl, Martina; Jaeger, Karl-Erich

2017-09-20

Bacterial inclusion bodies (IBs) consist of unfolded protein aggregates and represent inactive waste products often accumulating during heterologous overexpression of recombinant genes in Escherichia coli. This general misconception has been challenged in recent years by the discovery that IBs, apart from misfolded polypeptides, can also contain substantial amounts of active and thus correctly or native-like folded protein. The corresponding catalytically-active inclusion bodies (CatIBs) can be regarded as a biologically-active sub-micrometer sized biomaterial or naturally-produced carrier-free protein immobilizate. Fusion of polypeptide (protein) tags can induce CatIB formation paving the way towards the wider application of CatIBs in synthetic chemistry, biocatalysis and biomedicine. In the present review we summarize the history of CatIBs, present the molecular-biological tools that are available to induce CatIB formation, and highlight potential lines of application. In the second part findings regarding the formation, architecture, and structure of (Cat)IBs are summarized. Finally, an overview is presented about the available bioinformatic tools that potentially allow for the prediction of aggregation and thus (Cat)IB formation. This review aims at demonstrating the potential of CatIBs for biotechnology and hopefully contributes to a wider acceptance of this promising, yet not widely utilized, protein preparation. Copyright © 2017 Elsevier B.V. All rights reserved.

Underreporting of energy, protein and potassium intake in relation to body mass index

NARCIS (Netherlands)

Heerstrass, D W; Ocké, M C; Bueno De Mesquita, H Bas; Peeters, P.H.; Seidell, J C

BACKGROUND: Differential underreporting of dietary intake by subgroups of body mass index (BMI) will confound associations between dietary intake and BMI-related diseases. We estimated the magnitude of BMI-related underreporting for energy, protein, and potassium intake for the Dutch cohorts of the

A controlled trial of protein enrichment of meal replacements for weight reduction with retention of lean body mass

Directory of Open Access Journals (Sweden)

Bowerman Susan

2008-08-01

Full Text Available Abstract Background While high protein diets have been shown to improve satiety and retention of lean body mass (LBM, this study was designed to determine effects of a protein-enriched meal replacement (MR on weight loss and LBM retention by comparison to an isocaloric carbohydrate-enriched MR within customized diet plans utilizing MR to achieve high protein or standard protein intakes. Methods Single blind, placebo-controlled, randomized outpatient weight loss trial in 100 obese men and women comparing two isocaloric meal plans utilizing a standard MR to which was added supplementary protein or carbohydrate powder. MR was used twice daily (one meal, one snack. One additional meal was included in the meal plan designed to achieve individualized protein intakes of either 1 2.2 g protein/kg of LBM per day [high protein diet (HP] or 2 1.1 g protein/kg LBM/day standard protein diet (SP. LBM was determined using bioelectrical impedance analysis (BIA. Body weight, body composition, and lipid profiles were measured at baseline and 12 weeks. Results Eighty-five subjects completed the study. Both HP and SP MR were well tolerated, with no adverse effects. There were no differences in weight loss at 12 weeks (-4.19 ± 0.5 kg for HP group and -3.72 ± 0.7 kg for SP group, p > 0.1. Subjects in the HP group lost significantly more fat weight than the SP group (HP = -1.65 ± 0.63 kg; SP = -0.64 ± 0.79 kg, P = 0.05 as estimated by BIA. There were no significant differences in lipids nor fasting blood glucose between groups, but within the HP group a significant decrease in cholesterol and LDL cholesterol was noted at 12 weeks. This was not seen in the SP group. Conclusion Higher protein MR within a higher protein diet resulted in similar overall weight loss as the standard protein MR plan over 12 weeks. However, there was significantly more fat loss in the HP group but no significant difference in lean body mass. In this trial, subject compliance with both the

Effect of Protein Intake on Strength, Body Composition and Endocrine Changes in Strength/Power Athletes

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Kang Jie

2006-12-01

Full Text Available Abstract Comparison of protein intakes on strength, body composition and hormonal changes were examined in 23 experienced collegiate strength/power athletes participating in a 12-week resistance training program. Subjects were stratified into three groups depending upon their daily consumption of protein; below recommended levels (BL; 1.0 – 1.4 g·kg-1·day-1; n = 8, recommended levels (RL; 1.6 – 1.8 g·kg-1·day-1; n = 7 and above recommended levels (AL; > 2.0 g·kg-1·day-1; n = 8. Subjects were assessed for strength [one-repetition maximum (1-RM bench press and squat] and body composition. Resting blood samples were analyzed for total testosterone, cortisol, growth hormone, and insulin-like growth factor. No differences were seen in energy intake (3,171 ± 577 kcal between the groups, and the energy intake for all groups were also below the recommended levels for strength/power athletes. No significant changes were seen in body mass, lean body mass or fat mass in any group. Significant improvements in 1-RM bench press and 1-RM squat were seen in all three groups, however no differences between the groups were observed. Subjects in AL experienced a 22% and 42% greater change in Δ 1-RM squat and Δ 1-RM bench press than subjects in RL, however these differences were not significant. No significant changes were seen in any of the resting hormonal concentrations. The results of this study do not provide support for protein intakes greater than recommended levels in collegiate strength/power athletes for body composition improvements, or alterations in resting hormonal concentrations.

Identification and characterization of protein interactions in the mammalian mRNA processing body using a novel two-hybrid assay

Energy Technology Data Exchange (ETDEWEB)

Bloch, Donald B., E-mail: bloch@helix.mgh.harvard.edu; Nobre, Rita A.; Bernstein, Gillian A.; Yang, Wei-Hong

2011-09-10

Components of the mRNA processing body (P-body) regulate critical steps in mRNA storage, transport, translation and degradation. At the core of the P-body is the decapping complex, which removes the 5' cap from de-adenylated mRNAs and mediates an irreversible step in mRNA degradation. The assembly of P-bodies in Saccharomyces cerevisiae, Arabidopsis thaliana and Drosophila melanogaster has been previously described. Less is known about the assembly of mammalian P-bodies. To investigate the interactions that occur between components of mammalian P-bodies, we developed a fluorescence-based, two-hybrid assay system. The assay depends on the ability of one P-body component, fused to an exogenous nuclear localization sequence (NLS), to recruit other P-body components to the nucleus. The assay was used to investigate interactions between P-body components Ge-1, DCP2, DCP1, EDC3, RAP55, and RCK. The results of this study show that the modified two-hybrid assay can be used to identify protein interactions that occur in a macromolecular complex. The assay can also be used to efficiently detect protein interaction domains. The results provide important insights into mammalian P-body assembly and demonstrate similarities, and critical differences, between P-body assembly in mammalian cells compared with that of other species. -- Research highlights: {yields} A two-hybrid assay was developed to study interactions in macromolecular complexes. {yields} The assay was applied to interactions between components of mRNA P-bodies. {yields} The assay effectively and efficiently identified protein interaction domains. {yields} P-body assembly in mammalian cells differs from that in other species.

Identification and characterization of protein interactions in the mammalian mRNA processing body using a novel two-hybrid assay

International Nuclear Information System (INIS)

Bloch, Donald B.; Nobre, Rita A.; Bernstein, Gillian A.; Yang, Wei-Hong

2011-01-01

Components of the mRNA processing body (P-body) regulate critical steps in mRNA storage, transport, translation and degradation. At the core of the P-body is the decapping complex, which removes the 5' cap from de-adenylated mRNAs and mediates an irreversible step in mRNA degradation. The assembly of P-bodies in Saccharomyces cerevisiae, Arabidopsis thaliana and Drosophila melanogaster has been previously described. Less is known about the assembly of mammalian P-bodies. To investigate the interactions that occur between components of mammalian P-bodies, we developed a fluorescence-based, two-hybrid assay system. The assay depends on the ability of one P-body component, fused to an exogenous nuclear localization sequence (NLS), to recruit other P-body components to the nucleus. The assay was used to investigate interactions between P-body components Ge-1, DCP2, DCP1, EDC3, RAP55, and RCK. The results of this study show that the modified two-hybrid assay can be used to identify protein interactions that occur in a macromolecular complex. The assay can also be used to efficiently detect protein interaction domains. The results provide important insights into mammalian P-body assembly and demonstrate similarities, and critical differences, between P-body assembly in mammalian cells compared with that of other species. -- Research highlights: → A two-hybrid assay was developed to study interactions in macromolecular complexes. → The assay was applied to interactions between components of mRNA P-bodies. → The assay effectively and efficiently identified protein interaction domains. → P-body assembly in mammalian cells differs from that in other species.

Implementing a modeling software for animated protein-complex interactions using a physics simulation library.

Science.gov (United States)

Ueno, Yutaka; Ito, Shuntaro; Konagaya, Akihiko

2014-12-01

To better understand the behaviors and structural dynamics of proteins within a cell, novel software tools are being developed that can create molecular animations based on the findings of structural biology. This study proposes our method developed based on our prototypes to detect collisions and examine the soft-body dynamics of molecular models. The code was implemented with a software development toolkit for rigid-body dynamics simulation and a three-dimensional graphics library. The essential functions of the target software system included the basic molecular modeling environment, collision detection in the molecular models, and physical simulations of the movement of the model. Taking advantage of recent software technologies such as physics simulation modules and interpreted scripting language, the functions required for accurate and meaningful molecular animation were implemented efficiently.

Bug22p, a conserved centrosomal/ciliary protein also present in higher plants, is required for an effective ciliary stroke in Paramecium.

Science.gov (United States)

Laligné, C; Klotz, C; de Loubresse, N Garreau; Lemullois, M; Hori, M; Laurent, F X; Papon, J F; Louis, B; Cohen, J; Koll, F

2010-04-01

Centrioles, cilia, and flagella are ancestral conserved organelles of eukaryotic cells. Among the proteins identified in the proteomics of ciliary proteins in Paramecium, we focus here on a protein, Bug22p, previously detected by cilia and basal-body high-throughput studies but never analyzed per se. Remarkably, this protein is also present in plants, which lack centrioles and cilia. Bug22p sequence alignments revealed consensus positions that distinguish species with centrioles/cilia from plants. In Paramecium, antibody and green fluorescent protein (GFP) fusion labeling localized Bug22p in basal bodies and cilia, and electron microscopy immunolabeling refined the localization to the terminal plate of the basal bodies, the transition zone, and spots along the axoneme, preferentially between the membrane and the microtubules. RNA interference (RNAi) depletion of Bug22p provoked a strong decrease in swimming speed, followed by cell death after a few days. High-speed video microscopy and morphological analysis of Bug22p-depleted cells showed that the protein plays an important role in the efficiency of ciliary movement by participating in the stroke shape and rigidity of cilia. The defects in cell swimming and growth provoked by RNAi can be complemented by expression of human Bug22p. This is the first reported case of complementation by a human gene in a ciliate.

Algebraic Methods for Counting Euclidean Embeddings of Rigid Graphs

NARCIS (Netherlands)

I.Z. Emiris; E.P. Tsigaridas; A. Varvitsiotis (Antonios); E.R. Gasner

2009-01-01

textabstract The study of (minimally) rigid graphs is motivated by numerous applications, mostly in robotics and bioinformatics. A major open problem concerns the number of embeddings of such graphs, up to rigid motions, in Euclidean space. We capture embeddability by polynomial systems

Method of adhering bone to a rigid substrate using a graphite fiber reinforced bone cement

Science.gov (United States)

Knoell, A. C.; Maxwell, H. G. (Inventor)

1977-01-01

A method is described for adhering bone to the surface of a rigid substrate such as a metal or resin prosthesis using an improved surgical bone cement. The bone cement has mechanical properties more nearly matched to those of animal bone and thermal curing characteristics which result in less traumatization of body tissues and comprises a dispersion of short high modulus graphite fibers within a bonder composition including polymer dissolved in reactive monomer such as polymethylmethacrylate dissolved in methylmethacrylate monomer.

Poly (ADP-ribose polymerase 1 is required for protein localization to Cajal body.

Directory of Open Access Journals (Sweden)

Elena Kotova

2009-02-01

Full Text Available Recently, the nuclear protein known as Poly (ADP-ribose Polymerase1 (PARP1 was shown to play a key role in regulating transcription of a number of genes and controlling the nuclear sub-organelle nucleolus. PARP1 enzyme is known to catalyze the transfer of ADP-ribose to a variety of nuclear proteins. At present, however, while we do know that the main acceptor for pADPr in vivo is PARP1 protein itself, by PARP1 automodification, the significance of PARP1 automodification for in vivo processes is not clear. Therefore, we investigated the roles of PARP1 auto ADP-ribosylation in dynamic nuclear processes during development. Specifically, we discovered that PARP1 automodification is required for shuttling key proteins into Cajal body (CB by protein non-covalent interaction with pADPr in vivo. We hypothesize that PARP1 protein shuttling follows a chain of events whereby, first, most unmodified PARP1 protein molecules bind to chromatin and accumulate in nucleoli, but then, second, upon automodification with poly(ADP-ribose, PARP1 interacts non-covalently with a number of nuclear proteins such that the resulting protein-pADPr complex dissociates from chromatin into CB.

Human UBL5 protein interacts with coilin and meets the Cajal bodies

International Nuclear Information System (INIS)

Švéda, Martin; Častorálová, Markéta; Lipov, Jan; Ruml, Tomáš; Knejzlík, Zdeněk

2013-01-01

Highlights: •Localization of the UBL5 protein in Hela cells was determined by fluorescence microscopy and biochemical fractionation. •Colocalization of UBL5 with Cajal bodies was observed. •Interaction of UBL5 with coilin was proven by pull-down. -- Abstract: UBL5 protein, a structural homologue of ubiquitin, was shown to be involved in pre-mRNA splicing and transcription regulation in yeast and Caenorhabditis elegans, respectively. However, role of the UBL5 human orthologue is still elusive. In our study, we observed that endogenous human UBL5 that was localized in the nucleus, partially associates with Cajal bodies (CBs), nuclear domains where spliceosomal components are assembled. Simultaneous expression of exogenous UBL5 and coilin resulted in their nuclear colocalization in HeLa cells. The ability of UBL5 to interact with coilin was proved by GST pull-down assay using coilin that was either in vitro translated or extracted from HEK293T cells. Further, our results showed that the UBL5–coilin interaction was not influenced by coilin phosphorylation. These results suggest that UBL5 could be targeted to CBs via its interaction with coilin. Relation between human UBL5 protein and CBs is in the agreement with current observations about yeast orthologue Hub1 playing important role in alternative splicing

Human UBL5 protein interacts with coilin and meets the Cajal bodies

Energy Technology Data Exchange (ETDEWEB)

Švéda, Martin; Častorálová, Markéta; Lipov, Jan; Ruml, Tomáš; Knejzlík, Zdeněk, E-mail: knejzliz@vscht.cz

2013-06-28

Highlights: •Localization of the UBL5 protein in Hela cells was determined by fluorescence microscopy and biochemical fractionation. •Colocalization of UBL5 with Cajal bodies was observed. •Interaction of UBL5 with coilin was proven by pull-down. -- Abstract: UBL5 protein, a structural homologue of ubiquitin, was shown to be involved in pre-mRNA splicing and transcription regulation in yeast and Caenorhabditis elegans, respectively. However, role of the UBL5 human orthologue is still elusive. In our study, we observed that endogenous human UBL5 that was localized in the nucleus, partially associates with Cajal bodies (CBs), nuclear domains where spliceosomal components are assembled. Simultaneous expression of exogenous UBL5 and coilin resulted in their nuclear colocalization in HeLa cells. The ability of UBL5 to interact with coilin was proved by GST pull-down assay using coilin that was either in vitro translated or extracted from HEK293T cells. Further, our results showed that the UBL5–coilin interaction was not influenced by coilin phosphorylation. These results suggest that UBL5 could be targeted to CBs via its interaction with coilin. Relation between human UBL5 protein and CBs is in the agreement with current observations about yeast orthologue Hub1 playing important role in alternative splicing.

Metabolism and Whole-Body Fat Oxidation Following Post-Exercise Carbohydrate or Protein Intake

DEFF Research Database (Denmark)

Hall, Ulrika Andersson; Pettersson, Stefan; Edin, Fredrik

2018-01-01

: Protein supplementation immediately post-exercise did not affect the doubling in whole body fat oxidation seen during a subsequent exercise trial 2 hours later. Neither did it affect resting fat oxidation during the post-exercise period despite increased insulin levels and attenuated ketosis. Carbohydrate...

Role of zein proteins in structure and assembly of protein bodies and endosperm texture. Progress report and appendix 1 - preliminary data

Energy Technology Data Exchange (ETDEWEB)

Larkins, B.

1997-05-01

Although funding for this project was initiated less than two years ago, we have made significant progress with our research objectives. We have cloned the gene responsible for the fl2 mutation. In fl2, the mutant phenotype appears to result from a defective signal peptide in an alpha-zein protein. As a consequence, the signal peptide remains attached when the protein accumulates in the protein body. A mutation like fl2 could explain other semidominant and dominant opaque mutants on the basis of abnormal zein polypeptides. A manuscript describing the research that led to the cloning of fl2 is in press, and a second manuscript on the characterization of this gene has been prepared for publication. We found that increased amounts of the 27-kD gamma-zein protein enlarge the proportion of vitreous endosperm and increases the hardness of o2 mutants. This protein also enhances these properties in wild type seeds. The mechanism by which the gamma-zein protein brings about these changes is unclear, and is under investigation. We have found and characterized several mutants that reduce gamma-zein synthesis. The mutations do not significantly affect synthesis of any other type of zein protein. They appear to create an opaque phenotype by reducing the number rather than the size of protein bodies. Interestingly, the mutant seeds fail to germinate. A manuscript describing one of these mutants, o15, has been prepared for publication. We have created a number of transgenic tobacco plants that can produce alpha-, beta-, gamma(27-kD)-, or delta-zeins, as well as combinations of these proteins. Analysis of seeds from these plants and crosses of these plants has shown that tobacco endosperm can serve as a heterologous system to study zein interactions. We have obtained evidence that interactions between alpha- and gamma-zein proteins are required for stable accumulation of alpha-zeins in the endosperm. These and other preliminary results are illustrated in Appendix 1.

Nucleosome–nucleosome interactions via histone tails and linker DNA regulate nuclear rigidity

Science.gov (United States)

Shimamoto, Yuta; Tamura, Sachiko; Masumoto, Hiroshi; Maeshima, Kazuhiro

2017-01-01

Cells, as well as the nuclei inside them, experience significant mechanical stress in diverse biological processes, including contraction, migration, and adhesion. The structural stability of nuclei must therefore be maintained in order to protect genome integrity. Despite extensive knowledge on nuclear architecture and components, however, the underlying physical and molecular mechanisms remain largely unknown. We address this by subjecting isolated human cell nuclei to microneedle-based quantitative micromanipulation with a series of biochemical perturbations of the chromatin. We find that the mechanical rigidity of nuclei depends on the continuity of the nucleosomal fiber and interactions between nucleosomes. Disrupting these chromatin features by varying cation concentration, acetylating histone tails, or digesting linker DNA results in loss of nuclear rigidity. In contrast, the levels of key chromatin assembly factors, including cohesin, condensin II, and CTCF, and a major nuclear envelope protein, lamin, are unaffected. Together with in situ evidence using living cells and a simple mechanical model, our findings reveal a chromatin-based regulation of the nuclear mechanical response and provide insight into the significance of local and global chromatin structures, such as those associated with interdigitated or melted nucleosomal fibers. PMID:28428255

Equilibria of the three-body problem with rigid dumb-bell satellite

International Nuclear Information System (INIS)

Elipe, A.; Palacios, M.; Pretka-Ziomek, H.

2008-01-01

This paper is concerned with the orbital-rotational motion of an asymmetric dumb-bell (two masses with fixed distance among them) under the attraction of a central body. For this model, we find some equilibria and give sufficient conditions for their stability

Analysis of Large Flexible Body Deformation in Multibody Systems Using Absolute Coordinates

Energy Technology Data Exchange (ETDEWEB)

Dombrowski, Stefan von [Institute of Robotics and Mechatronics, German Aerospace Center (DLR) (Germany)], E-mail: stefan.von.dombrowski@dlr.de

2002-11-15

To consider large deformation problems in multibody system simulations a finite element approach, called absolute nodal coordinate.formulation,has been proposed. In this formulation absolute nodal coordinates and their material derivatives are applied to represent both deformation and rigid body motion. The choice of nodal variables allows a fully nonlinear representation of rigid body motion and can provide the exact rigid body inertia in the case of large rotations. The methodology is especially suited for but not limited to modeling of beams, cables and shells in multibody dynamics.This paper summarizes the absolute nodal coordinate formulation for a 3D Euler-Bernoulli beam model, in particular the definition of nodal variables, corresponding generalized elastic and inertia forces and equations of motion. The element stiffness matrix is a nonlinear function of the nodal variables even in the case of linearized strain/displacement relations. Nonlinear strain/displacement relations can be calculated from the global displacements using quadrature formulae.Computational examples are given which demonstrate the capabilities of the applied methodology. Consequences of the choice of shape.functions on the representation of internal forces are discussed. Linearized strain/displacement modeling is compared to the nonlinear approach and significant advantages of the latter, when using the absolute nodal coordinate formulation, are outlined.

Analysis of Large Flexible Body Deformation in Multibody Systems Using Absolute Coordinates

International Nuclear Information System (INIS)

Dombrowski, Stefan von

2002-01-01

To consider large deformation problems in multibody system simulations a finite element approach, called absolute nodal coordinate.formulation,has been proposed. In this formulation absolute nodal coordinates and their material derivatives are applied to represent both deformation and rigid body motion. The choice of nodal variables allows a fully nonlinear representation of rigid body motion and can provide the exact rigid body inertia in the case of large rotations. The methodology is especially suited for but not limited to modeling of beams, cables and shells in multibody dynamics.This paper summarizes the absolute nodal coordinate formulation for a 3D Euler-Bernoulli beam model, in particular the definition of nodal variables, corresponding generalized elastic and inertia forces and equations of motion. The element stiffness matrix is a nonlinear function of the nodal variables even in the case of linearized strain/displacement relations. Nonlinear strain/displacement relations can be calculated from the global displacements using quadrature formulae.Computational examples are given which demonstrate the capabilities of the applied methodology. Consequences of the choice of shape.functions on the representation of internal forces are discussed. Linearized strain/displacement modeling is compared to the nonlinear approach and significant advantages of the latter, when using the absolute nodal coordinate formulation, are outlined

Missed Distal Tracheal Foreign Body in Consecutive ...

African Journals Online (AJOL)

2017-05-18

May 18, 2017 ... Since invention, bronchoscopy has become the gold standard in the diagnosis and extraction of airway FB.[4]. Foreign bodies may be missed at ... Since the discovery by Gustav Killian,[9] extraction of tracheobronchial FB has been accomplished with rigid bronchoscopy which is still considered as the gold.

Simultaneous PET-MR acquisition and MR-derived motion fields for correction of non-rigid motion in PET

International Nuclear Information System (INIS)

Tsoumpas, C.; Mackewn, J.E.; Halsted, P.; King, A.P.; Buerger, C.; Totman, J.J.; Schaeffter, T.; Marsden, P.K.

2010-01-01

Positron emission tomography (PET) provides an accurate measurement of radiotracer concentration in vivo, but performance can be limited by subject motion which degrades spatial resolution and quantitative accuracy. This effect may become a limiting factor for PET studies in the body as PET scanner technology improves. In this work, we propose a new approach to address this problem by employing motion information from images measured simultaneously using a magnetic resonance (MR) scanner. The approach is demonstrated using an MR-compatible PET scanner and PET-MR acquisition with a purpose-designed phantom capable of non-rigid deformations. Measured, simultaneously acquired MR data were used to correct for motion in PET, and results were compared with those obtained using motion information from PET images alone. Motion artefacts were significantly reduced and the PET image quality and quantification was significantly improved by the use of MR motion fields, whilst the use of PET-only motion information was less successful. Combined PET-MR acquisitions potentially allow PET motion compensation in whole-body acquisitions without prolonging PET acquisition time or increasing radiation dose. This, to the best of our knowledge, is the first study to demonstrate that simultaneously acquired MR data can be used to estimate and correct for the effects of non-rigid motion in PET. (author)

Estimation of whole body protein turnover by L-[1-[sup 13]C]-leucine tracer experiment in post-viral hepatocirrhotic patients

Energy Technology Data Exchange (ETDEWEB)

Xinhua, Zhu; Zhenduo, Tang; Tengchang, Dai; Zongqin, Xia [Shanghai Second Medical Univ. (China)

1993-08-01

A constant infusion of L-[1-[sup 1]'3C]-leucine given to the subject and the plasma [sup 13]C-leucine enrichment and breath [sup 1]'3CO[sub 2] enrichment were measured with GC-MS and gas isotope ratio MS respectively. The plateau isotope enrichments reached were used to calculate the whole body protein synthesis and breakdown rates using a two pools model. 15 post-viral hepatocirrhotic patients and 6 normal adults were studied. The whole body protein synthesis and breakdown rates were both markedly increased in cirrhotic patients, with the breakdown rate higher than the synthesis rate and hence leading to a negative nitrogen balance. The changes of 7 decompensated cirrhotic patients were more severe than 8 compensated cirrhotic patients. The results suggest that the protein malnutrition and negative nitrogen balance of post-viral hepatocirrhotic patients are not simply due to low intake of protein and that the hyperactive turnover, especially the excessive breakdown of body protein might play an important role.

Effects of Dietary Protein and Lipid Levels on Growth and Body Composition of Juvenile Far Eastern Catfish

Directory of Open Access Journals (Sweden)

Kyoung-Duck Kim

2012-03-01

Full Text Available A 3×2 factorial experiment was conducted to determine the effects of dietary protein and lipid levels on the growth and body composition of juvenile far eastern catfish. Six diets were formulated to contain three levels of protein (20%, 30% and 40% and two levels of lipid (9% and 17%. Triplicate groups of fish (initial body weight of 7.6 g were hand-fed to apparent satiation for 66 days. Final mean weight was improved with increasing dietary protein and lipid levels, and the highest final mean weight was observed in fish fed the 40/17 (% protein/% lipid diet. No significant difference was observed in final mean weight for fish fed between 30/17 diet and 40/9 diet. Feed efficiency of fish fed the diets containing over 30% protein levels with 9% and 17% lipid levels were significantly higher than those of fish fed the 20% protein levels. Feed efficiency of fish fed the 30/17 diet was not significantly different from that of fish fed the 40/9 diet or 40/17 diet. Feed efficiency and protein efficiency ratio of fish fed the 20% protein diets with 17% lipid level were significantly higher than those of fish fed 9% lipid diet. Daily feed intake of fish tended to decrease with increasing dietary protein and lipid levels. Moisture content of whole body in fish fed the 9% lipid diets was significantly higher than that of fish fed the 17% lipid diets at the same protein level, but the opposite trends were found for crude lipid content. Significant effects of dietary lipid were observed for most fatty acids, according to their relative values in the diets. The results of this study suggest that the protein requirement for maximum growth of juvenile far eastern catfish may be higher than 40%, and an increase of dietary lipid level from 9% to 17% can improve growth and feed utilization.

Recovery of insulin sensitivity and optimal body composition after rapid weight loss in obese dogs fed a high-protein medium-carbohydrate diet.

Science.gov (United States)

André, A; Leriche, I; Chaix, G; Thorin, C; Burger, M; Nguyen, P

2017-06-01

This study investigated the effects of an experimental high-protein medium-carbohydrate diet (protein level, 46% metabolizable energy, ME). First, postprandial plasma glucose and insulin kinetics were determined in steady-state overweight/obese Beagle dogs (28%-41% excess body weight) for an experimental high-protein medium-carbohydrate diet (protein level, 46% ME) and a commercial high-carbohydrate medium-protein diet (protein level, 24%ME) in obese dogs. Secondly, all the dogs were included in a weight loss programme. They were fed the high-protein medium-carbohydrate diet, and the energy allocation was gradually reduced until they reached their optimal body weight. Insulin sensitivity and body composition were evaluated before and after weight loss using a euglycaemic-hyperinsulinaemic clamp and the deuterium oxide dilution technique respectively. For statistical analysis, linear mixed effect models were used with a significance level of 5%. Postprandial plasma glucose and insulin concentrations were substantially lower with the high-protein medium-carbohydrate diet than the high-carbohydrate medium-protein diet. These differences can be explained mainly by the difference in carbohydrate content between the two diets. Energy restriction (35% lower energy intake than in the obese state) resulted in a 2.23 ± 0.05% loss in body weight/week, and the dogs reached their optimal body weight in 12-16 weeks. Weight loss was associated with a significant increase in insulin sensitivity. The high-protein medium-carbohydrate diet allowed fat-free mass preservation despite a relatively high rate of weekly weight loss. The increase in insulin sensitivity indicated improved control of carbohydrate metabolism, possible due to weight loss and to the nature of the diet. Thus, a high-protein medium-carbohydrate diet is a good nutritional solution for managing the weight of overweight dogs. This diet may improve glycaemic control, which could be beneficial for preventing or

Dietary Intake of Protein from Different Sources and Weight Regain, Changes in Body Composition and Cardiometabolic Risk Factors after Weight Loss: The DIOGenes Study

Directory of Open Access Journals (Sweden)

Marleen A. van Baak

2017-12-01

Full Text Available An increase in dietary protein intake has been shown to improve weight loss maintenance in the DIOGenes trial. Here, we analysed whether the source of the dietary proteins influenced changes in body weight, body composition, and cardiometabolic risk factors during the weight maintenance period while following an energy-restricted diet. 489 overweight or obese participants of the DIOGenes trial from eight European countries were included. They successfully lost >8% of body weight and subsequently completed a six month weight maintenance period, in which they consumed an ad libitum diet varying in protein content and glycemic index. Dietary intake was estimated from three-day food diaries. A higher plant protein intake with a proportional decrease in animal protein intake did not affect body weight maintenance or cardiometabolic risk factors. A higher plant protein intake from non-cereal products instead of cereal products was associated with benefits for body weight maintenance and blood pressure. Substituting meat protein for protein from other animal sources increased insulin and HOMA-IR (homeostasis model assessment of insulin resistance. This analysis suggests that not only the amount of dietary proteins, but also the source may be important for weight and cardiometabolic risk management. However, randomized trials are needed to test the causality of these associations.

Poisson equations of rotational motion for a rigid triaxial body with application to a tumbling artificial satellite

Science.gov (United States)

Liu, J. J. F.; Fitzpatrick, P. M.

1975-01-01

A mathematical model is developed for studying the effects of gravity gradient torque on the attitude stability of a tumbling triaxial rigid satellite. Poisson equations are used to investigate the rotation of the satellite (which is in elliptical orbit about an attracting point mass) about its center of mass. An averaging method is employed to obtain an intermediate set of differential equations for the nonresonant, secular behavior of the osculating elements which describe the rotational motions of the satellite, and the averaged equations are then integrated to obtain long-term secular solutions for the osculating elements.

Associative memory through rigid origami

Science.gov (United States)

Murugan, Arvind; Brenner, Michael

2015-03-01

Mechanisms such as Miura Ori have proven useful in diverse contexts since they have only one degree of freedom that is easily controlled. We combine the theory of rigid origami and associative memory in frustrated neural networks to create structures that can ``learn'' multiple generic folding mechanisms and yet can be robustly controlled. We show that such rigid origami structures can ``recall'' a specific learned mechanism when induced by a physical impulse that only need resemble the desired mechanism (i.e. robust recall through association). Such associative memory in matter, seen before in self-assembly, arises due to a balance between local promiscuity (i.e., many local degrees of freedom) and global frustration which minimizes interference between different learned behaviors. Origami with associative memory can lead to a new class of deployable structures and kinetic architectures with multiple context-dependent behaviors.

Functionally rigid bistable [2]rotaxanes

DEFF Research Database (Denmark)

Nygaard, Sune; Leung, Ken C-F; Aprahamian, Ivan

2007-01-01

defines an unambiguous distance of 1.5 nm over which the ring moves between the MPTTF and NP units. The degenerate NP/NP [2]rotaxane was used to investigate the shuttling barrier by dynamic 1H NMR spectroscopy for the movement of the CBPQT4+ ring across the new rigid spacer. It is evident from...... better control over the position of the ring component in the ground state but also for control over the location of the CBPQT4+ ring during solution-state switching experiments, triggered either chemically (1H NMR) or electrochemically (cyclic voltammetry). In this instance, the use of the rigid spacer......Two-station [2]rotaxanes in the shape of a degenerate naphthalene (NP) shuttle and a nondegenerate monopyrrolotetrathiafulvalene (MPTTF)/NP redox-controllable switch have been synthesized and characterized in solution. Their dumbbell-shaped components are composed of polyether chains interrupted...

Rigid external maxillary distraction and rhinoplasty for pyknodysostosis.

Science.gov (United States)

Varol, Altan; Sabuncuoglu, Fidan Alakus; Sencimen, Metin; Akcam, Timur; Olmez, Hüseyin; Basa, Selçuk

2011-05-01

This article reports the treatment of an 33-year-old female patient with pyknodysostosis by rigid external distraction II midface distraction system. The patient with pyknodysostosis described in this report had severe midfacial hypoplasia. Correction of this by use of routine orthognathic surgery would require osteosynthesis and bone grafting. Risk of infection and/or nonunion after such a surgical procedure was considered too great, and therefore the possibility of treatment by distraction osteogenesis of the maxilla was evaluated. The rigid external distraction II midface distraction system was used to relocate the hypoplastic maxilla at anterior-inferior projection. Distraction osteogenesis should be considered as the primary reconstructive method for maxillofacial deformities in patients with sclerosing bone dysplasias, since this is the second reported case treated successfully with rigid external distraction.

Super rigid nature of super-deformed bands

International Nuclear Information System (INIS)

Sharma, Neha; Mittal, H.M.; Jain, A.K.

2012-01-01

The phenomenon of high-spin super-deformation represents one of the most remarkable discoveries in nuclear physics. A large number of SD bands have been observed in A = 60, 80, 130, 150, 190 mass regions. The cascades of SD bands are known to be connected by electric quadruple E2 transitions. Because of absence of linking transitions between superdeformed (SD) and normal deformed (ND) levels, the spin assignments of most of these bands carry a minimum uncertainty ≈ 1-2ħ. It was found in an analysis of SD bands in the context of semi classical approach that moment of inertia comes close to the rigid body value in most of the cases. Lack of knowledge of spins has led to an emphasis on the study of dynamical moment of inertia of SD bands and systematic of kinematic moment of inertia has not been examined so far. In this paper, we extract the band moment of inertia J 0 and softness parameter (σ) of all the SD bands corresponding to axes ratio (x) = 1.5 and present their systematic

A Class of Rigid Linker-bearing Glucosides for Membrane Protein Structural Study.

Science.gov (United States)

Sadaf, Aiman; Mortensen, Jonas S; Capaldi, Stefano; Tikhonova, Elena; Hariharan, Parameswaran; de Castro Ribeiro, Orquidea; Loland, Claus J; Guan, Lan; Byrne, Bernadette; Chae, Pil Seok

2016-03-01

Membrane proteins are amphipathic bio-macromolecules incompatible with the polar environments of aqueous media. Conventional detergents encapsulate the hydrophobic surfaces of membrane proteins allowing them to exist in aqueous solution. Membrane proteins stabilized by detergent micelles are used for structural and functional analysis. Despite the availability of a large number of detergents, only a few agents are sufficiently effective at maintaining the integrity of membrane proteins to allow successful crystallization. In the present study, we describe a novel class of synthetic amphiphiles with a branched tail group and a triglucoside head group. These head and tail groups were connected via an amide or ether linkage by using a tris(hydroxylmethyl)aminomethane (TRIS) or neopentyl glycol (NPG) linker to produce TRIS-derived triglucosides (TDTs) and NPG-derived triglucosides (NDTs), respectively. Members of this class conferred enhanced stability on target membrane proteins compared to conventional detergents. Because of straightforward synthesis of the novel agents and their favourable effects on a range of membrane proteins, these agents should be of wide applicability to membrane protein science.

The choice of label and measurement technique in tracer studies of body protein metabolism in man

International Nuclear Information System (INIS)

James, W.P.T.; Sender, P.M.; Garlick, P.J.; Waterlow, J.C.

1975-01-01

The turnover of non-serum proteins in man has had limited study despite the physiological importance of maintaining the balance between synthesis and breakdown of body proteins. Body protein is usually considered as a single pool and breakdown rates are often measured by monitoring excreted label at intervals after pulse labelling with radioactive or 15 N amino acids. No label has yet been used for measuring tissue protein breakdown in man which is free from the major problem of label re-utilization. All measurements of breakdown rates, eg. with 75 Se-selenomethionine, 15 N- or 14 C-glycine, give rate constants which are too low. The heterogeneity of body proteins also means that an estimate of the weighted average breakdown rate can only be obtained after following the excretion of isotope for a long period, perhaps of the order of 3-4 half-lives which, for man, would be 100 days after labelling. We therefore use infusions with either 14 C- or 15 N-labelled amino acids to measure breakdown and synthesis rates: these values are less affected by problems of protein heterogeneity. Single injection techniques are subject to more error than constant infusions of label because of the difficulty of defining the precursor activity. 15 N labelling need not be confined to essential amino acids if total protein rather than amino acid turnover is studied: the latter involves measurements of the labelled amino acid itself which is difficult with 15 N because of the small amounts of free amino acid nitrogen available. Carbon labelling of non-essential amino acids is unsuitable for studies of protein turnover and the choice of the position of the label on the molecule is important when labelled essential amino acids are employed. Short-term changes in protein metabolism are evaluated better with amino acids with a small pool size; the equilibration time in the excretory bicarbonate pool is also shorter than in the urea pool so that 15 N is less useful than carbon labelling. We

The diagnostic role of thoracoscope in undiagnosed pleural effusion: Rigid versus flexible

Directory of Open Access Journals (Sweden)

Mostafa Mahmoud Abdel Mageid Shaheen

2014-07-01

Conclusions: Thoracoscopy using either fibreoptic bronchoscope or rigid thoracoscope is safe and well tolerated. Rigid thoracoscope has a higher diagnostic yield, easier handling, better orientation and is less expensive. Nevertheless, fibreoptic bronchoscope is an alternative technique if rigid thoracoscopy is not available.

Mechanical Modeling and Computer Simulation of Protein Folding

Science.gov (United States)

Prigozhin, Maxim B.; Scott, Gregory E.; Denos, Sharlene

2014-01-01

In this activity, science education and modern technology are bridged to teach students at the high school and undergraduate levels about protein folding and to strengthen their model building skills. Students are guided from a textbook picture of a protein as a rigid crystal structure to a more realistic view: proteins are highly dynamic…

Rigid origami vertices: conditions and forcing sets

Directory of Open Access Journals (Sweden)

Zachary Abel

2016-04-01

Full Text Available We develop an intrinsic necessary and sufficient condition for single-vertex origami crease patterns to be able to fold rigidly.  We classify such patterns in the case where the creases are pre-assigned to be mountains and valleys as well as in the unassigned case.  We also illustrate the utility of this result by applying it to the new concept of minimal forcing sets for rigid origami models, which are the smallest collection of creases that, when folded, will force all the other creases to fold in a prescribed way.

Type number and rigidity of fibred surfaces

International Nuclear Information System (INIS)

Markov, P E

2001-01-01

Infinitesimal l-th order bendings, 1≤l≤∞, of higher-dimensional surfaces are considered in higher-dimensional flat spaces (for l=∞ an infinitesimal bending is assumed to be an analytic bending). In terms of the Allendoerfer type number, criteria are established for the (r,l)-rigidity (in the terminology of Sabitov) of such surfaces. In particular, an (r,l)-infinitesimal analogue is proved of the classical theorem of Allendoerfer on the unbendability of surfaces with type number ≥3 and the class of (r,l)-rigid fibred surfaces is distinguished

Evaluating a method for automated rigid registration

DEFF Research Database (Denmark)

Darkner, Sune; Vester-Christensen, Martin; Larsen, Rasmus

2007-01-01

to point distance. T-test for common mean are used to determine the performance of the two methods (supported by a Wilcoxon signed rank test). The performance influence of sampling density, sampling quantity, and norms is analyzed using a similar method.......We evaluate a novel method for fully automated rigid registration of 2D manifolds in 3D space based on distance maps, the Gibbs sampler and Iterated Conditional Modes (ICM). The method is tested against the ICP considered as the gold standard for automated rigid registration. Furthermore...

Bug22p, a Conserved Centrosomal/Ciliary Protein Also Present in Higher Plants, Is Required for an Effective Ciliary Stroke in Paramecium ▿ †

Science.gov (United States)

Laligné, C.; Klotz, C.; Garreau de Loubresse, N.; Lemullois, M.; Hori, M.; Laurent, F. X.; Papon, J. F.; Louis, B.; Cohen, J.; Koll, F.

2010-01-01

Centrioles, cilia, and flagella are ancestral conserved organelles of eukaryotic cells. Among the proteins identified in the proteomics of ciliary proteins in Paramecium, we focus here on a protein, Bug22p, previously detected by cilia and basal-body high-throughput studies but never analyzed per se. Remarkably, this protein is also present in plants, which lack centrioles and cilia. Bug22p sequence alignments revealed consensus positions that distinguish species with centrioles/cilia from plants. In Paramecium, antibody and green fluorescent protein (GFP) fusion labeling localized Bug22p in basal bodies and cilia, and electron microscopy immunolabeling refined the localization to the terminal plate of the basal bodies, the transition zone, and spots along the axoneme, preferentially between the membrane and the microtubules. RNA interference (RNAi) depletion of Bug22p provoked a strong decrease in swimming speed, followed by cell death after a few days. High-speed video microscopy and morphological analysis of Bug22p-depleted cells showed that the protein plays an important role in the efficiency of ciliary movement by participating in the stroke shape and rigidity of cilia. The defects in cell swimming and growth provoked by RNAi can be complemented by expression of human Bug22p. This is the first reported case of complementation by a human gene in a ciliate. PMID:20118210

Multibody Dynamic Stress Simulation of Rigid-Flexible Shovel Crawler Shoes

Directory of Open Access Journals (Sweden)

Samuel Frimpong

2016-06-01

Full Text Available Electric shovels are used in surface mining operations to achieve economic production capacities. The capital investments and operating costs associated with the shovels deployed in the Athabasca oil sands formation are high due to the abrasive conditions. The shovel crawler shoes interact with sharp and abrasive sand particles, and, thus, are subjected to high transient dynamic stresses. These high stresses cause wear and tear leading to crack initiation, propagation and premature fatigue failure. The objective of this paper is to develop a model to characterize the crawler stresses and deformation for the P&H 4100C BOSS during propel and loading using rigid-flexible multi-body dynamic theory. A 3-D virtual prototype model of the rigid-flexible crawler track assembly and its interactions with oil sand formation is simulated to capture the model dynamics within multibody dynamics software MSC ADAMS. The modal and stress shapes and modal loads due to machine weight for each flexible crawler shoes are generated from finite element analysis (FEA. The modal coordinates from the simulation are combined with mode and stress shapes using modal superposition method to calculate real-time stresses and deformation of flexible crawler shoes. The results show a maximum von Mises stress value of 170 MPa occurring in the driving crawler shoe during the propel motion. This study provides a foundation for the subsequent fatigue life analysis of crawler shoes for extending crawler service life.