Enroute NASA/FAA low-frequency propfan test in Alabama (October 1987): A versatile atmospheric aircraft long-range noise prediction system

NASA Astrophysics Data System (ADS)

Tsouka, Despina G.

In order to obtain a flight-to-static noise prediction of an advanced Turboprop (propfan) Aircraft, FAA went on an elaboration of the data that were measured during a full scale measuring program that was conducted by NASA and FAA/DOT/TSC on October 1987 in Alabama. The elaboration process was based on aircraft simulation to a point source, on an atmospheric two dimensional noise model, on the American National Standard algorithm for the calculation of atmospheric absortion, and on the DOT/TSC convention for ground reflection effects. Using the data of the Alabama measurements, the present paper examines the development of a generalized, flexible and more accurate process for the evaluation of the static and flight low-frequency long-range noise data. This paper also examines the applicability of the assumptions made by the Integrated Noise Model about linear propagation, of the three dimensional Hamiltonian Rays Tracing model and of the Weyl-Van der Pol model. The model proposes some assumptions in order to increase the calculations flexibility without significant loss of accuracy. In addition, it proposes the usage of the three dimensional Hamiltonian Rays Tracing model and the Weyl-Van der Pol model in order to increase the accuracy and to ensure the generalization of noise propagation prediction over grounds with variable impedance.

Amplitude and phase fluctuations of Van der Pol oscillator under external random forcing

NASA Astrophysics Data System (ADS)

Singh, Aman K.; Yadava, R. D. S.

2018-05-01

The paper presents an analytical study of noise in Van der Pol oscillator output subjected to an external force noise assumed to be characterized by delta function (white noise). The external fluctuations are assumed to be small in comparison to the average response of the noise free system. The autocorrelation function and power spectrum are calculated under the condition of weak nonlinearity. The latter ensures limit cycle oscillations. The total spectral power density is dominated by the contributions from the phase fluctuations. The amplitude fluctuations are at least two orders of magnitude smaller. The analysis is shown to be useful to interpretation microcantilever based biosensing data.

Synchronization between two coupled direct current glow discharge plasma sources

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

Chaubey, Neeraj; Mukherjee, S.; Sen, A.

2015-02-15

Experimental results on the nonlinear dynamics of two coupled glow discharge plasma sources are presented. A variety of nonlinear phenomena including frequency synchronization and frequency pulling are observed as the coupling strength is varied. Numerical solutions of a model representation of the experiment consisting of two coupled asymmetric Van der Pol type equations are found to be in good agreement with the observed results.

Emergent global oscillations in heterogeneous excitable media: The example of pancreatic β cells

NASA Astrophysics Data System (ADS)

Cartwright, Julyan H. E.

2000-07-01

Using the standard van der Pol-FitzHugh-Nagumo excitable medium model, I demonstrate a generic mechanism, diversity, that provokes the emergence of global oscillations from individually quiescent elements in heterogeneous excitable media. This mechanism may be operating in the mammalian pancreas, where excitable β cells, quiescent when isolated, are found to oscillate when coupled, despite the absence of a pacemaker region.

Wavelets, non-linearity and turbulence in fusion plasmas

NASA Astrophysics Data System (ADS)

van Milligen, B. Ph.

Introduction Linear spectral analysis tools Wavelet analysis Wavelet spectra and coherence Joint wavelet phase-frequency spectra Non-linear spectral analysis tools Wavelet bispectra and bicoherence Interpretation of the bicoherence Analysis of computer-generated data Coupled van der Pol oscillators A large eddy simulation model for two-fluid plasma turbulence A long wavelength plasma drift wave model Analysis of plasma edge turbulence from Langmuir probe data Radial coherence observed on the TJ-IU torsatron Bicoherence profile at the L/H transition on CCT Conclusions

Direction of Coupling from Phases of Interacting Oscillators: A Permutation Information Approach

NASA Astrophysics Data System (ADS)

Bahraminasab, A.; Ghasemi, F.; Stefanovska, A.; McClintock, P. V. E.; Kantz, H.

2008-02-01

We introduce a directionality index for a time series based on a comparison of neighboring values. It can distinguish unidirectional from bidirectional coupling, as well as reveal and quantify asymmetry in bidirectional coupling. It is tested on a numerical model of coupled van der Pol oscillators, and applied to cardiorespiratory data from healthy subjects. There is no need for preprocessing and fine-tuning the parameters, which makes the method very simple, computationally fast and robust.

Compilation of Abstracts of Theses Submitted By Candidates for Degrees

DTIC Science & Technology

1990-09-30

based on a relationship between the Chaos methods ( the Poincare section and Van der Pol plane ) and the vibration amplitude and phase was discovered... half subsampled fields scored well and the one-eighth fields were poor. Even in the latter case, the model filled data gaps and areas of cyclonic and...flight test of a half scale unmanned air vehicle was conducted for the purpose of predicting the londgitudinal and laternal-directional behavior of

Dynamics of multi-frequency oscillator ensembles with resonant coupling

NASA Astrophysics Data System (ADS)

Lück, S.; Pikovsky, A.

2011-07-01

We study dynamics of populations of resonantly coupled oscillators having different frequencies. Starting from the coupled van der Pol equations we derive the Kuramoto-type phase model for the situation, where the natural frequencies of two interacting subpopulations are in relation 2:1. Depending on the parameter of coupling, ensembles can demonstrate fully synchronous clusters, partial synchrony (only one subpopulation synchronizes), or asynchrony in both subpopulations. Theoretical description of the dynamics based on the Watanabe-Strogatz approach is developed.

A model for predicting aortic dynamic response to -G sub z impact acceleration.

NASA Technical Reports Server (NTRS)

Advani, S. H.; Tarnay, T. J.; Byars, E. F.; Love, J. S.

1972-01-01

A steady state dynamic response model for the radial motion of the aorta is developed from in vivo pressure-displacement and nerve stimulation experiments on canines. The model represented by a modified Van der Pol wave motion oscillator closely predicts steady state and perturbed response results. The applicability of the steady state canine aortic model to tailward acting impact forces is studied by means of the perturbed phase plane of the oscillator. The backflow through the aortic arch resulting from a specified acceleration-time profile is computed and an analysis for predicting the forced motion aortic response is presented.

Chaotic Oscillations of Second Order Linear Hyperbolic Equations with Nonlinear Boundary Conditions: A Factorizable but Noncommutative Case

NASA Astrophysics Data System (ADS)

Li, Liangliang; Huang, Yu; Chen, Goong; Huang, Tingwen

If a second order linear hyperbolic partial differential equation in one-space dimension can be factorized as a product of two first order operators and if the two first order operators commute, with one boundary condition being the van der Pol type and the other being linear, one can establish the occurrence of chaos when the parameters enter a certain regime [Chen et al., 2014]. However, if the commutativity of the two first order operators fails to hold, then the treatment in [Chen et al., 2014] no longer works and significant new challenges arise in determining nonlinear boundary conditions that engenders chaos. In this paper, we show that by incorporating a linear memory effect, a nonlinear van der Pol boundary condition can cause chaotic oscillations when the parameter enters a certain regime. Numerical simulations illustrating chaotic oscillations are also presented.

Torus Breakdown and Homoclinic Chaos in a Glow Discharge Tube

NASA Astrophysics Data System (ADS)

Ginoux, Jean-Marc; Meucci, Riccardo; Euzzor, Stefano

2017-12-01

Starting from historical researches, we used, like Van der Pol and Le Corbeiller, a cubic function for modeling the current-voltage characteristic of a direct current low-pressure plasma discharge tube, i.e. a neon tube. This led us to propose a new four-dimensional autonomous dynamical system allowing to describe the experimentally observed phenomenon. Then, mathematical analysis and detailed numerical investigations of such a fourth-order torus circuit enabled to highlight bifurcation routes from torus breakdown to homoclinic chaos following the Newhouse-Ruelle-Takens scenario.

Synchronous Oscillations in Van Der Pol Generator with Modulated Natural Frequency

NASA Astrophysics Data System (ADS)

Nimets, A. Yu.; Vavriv, D. M.

2015-12-01

The synchronous operation of Van Der Pole generator with the low-frequency modulated natural frequency has been investigated. The presence of low-frequency modulation is shown to lead to formation of additional synchronization regions. The appearance of such regions is found to be caused by threefrequency resonances resulted from the interaction between oscillations of the generator natural frequency, modulation frequency and synchronized signal frequency. Characteristics of synchronous oscillations due to the below mentioned three-frequency interaction are obtained and comparison with the case of synchronization of oscillator on the main mode made.

Explosive death of conjugate coupled Van der Pol oscillators on networks

NASA Astrophysics Data System (ADS)

Zhao, Nannan; Sun, Zhongkui; Yang, Xiaoli; Xu, Wei

2018-06-01

Explosive death phenomenon has been gradually gaining attention of researchers due to the research boom of explosive synchronization, and it has been observed recently for the identical or nonidentical coupled systems in all-to-all network. In this work, we investigate the emergence of explosive death in networked Van der Pol (VdP) oscillators with conjugate variables coupling. It is demonstrated that the network structures play a crucial role in identifying the types of explosive death behaviors. We also observe that the damping coefficient of the VdP system not only can determine whether the explosive death state is generated but also can adjust the forward transition point. We further show that the backward transition point is independent of the network topologies and the damping coefficient, which is well confirmed by theoretical analysis. Our results reveal the generality of explosive death phenomenon in different network topologies and are propitious to promote a better comprehension for the oscillation quenching behaviors.

Duffing's Equation and Nonlinear Resonance

ERIC Educational Resources Information Center

Fay, Temple H.

2003-01-01

The phenomenon of nonlinear resonance (sometimes called the "jump phenomenon") is examined and second-order van der Pol plane analysis is employed to indicate that this phenomenon is not a feature of the equation, but rather the result of accumulated round-off error, truncation error and algorithm error that distorts the true bounded solution onto…

Stochastic responses of Van der Pol vibro-impact system with fractional derivative damping excited by Gaussian white noise.

PubMed

Xiao, Yanwen; Xu, Wei; Wang, Liang

2016-03-01

This paper focuses on the study of the stochastic Van der Pol vibro-impact system with fractional derivative damping under Gaussian white noise excitation. The equations of the original system are simplified by non-smooth transformation. For the simplified equation, the stochastic averaging approach is applied to solve it. Then, the fractional derivative damping term is facilitated by a numerical scheme, therewith the fourth-order Runge-Kutta method is used to obtain the numerical results. And the numerical simulation results fit the analytical solutions. Therefore, the proposed analytical means to study this system are proved to be feasible. In this context, the effects on the response stationary probability density functions (PDFs) caused by noise excitation, restitution condition, and fractional derivative damping are considered, in addition the stochastic P-bifurcation is also explored in this paper through varying the value of the coefficient of fractional derivative damping and the restitution coefficient. These system parameters not only influence the response PDFs of this system but also can cause the stochastic P-bifurcation.

Stochastic responses of Van der Pol vibro-impact system with fractional derivative damping excited by Gaussian white noise

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

Xiao, Yanwen; Xu, Wei, E-mail: weixu@nwpu.edu.cn; Wang, Liang

2016-03-15

This paper focuses on the study of the stochastic Van der Pol vibro-impact system with fractional derivative damping under Gaussian white noise excitation. The equations of the original system are simplified by non-smooth transformation. For the simplified equation, the stochastic averaging approach is applied to solve it. Then, the fractional derivative damping term is facilitated by a numerical scheme, therewith the fourth-order Runge-Kutta method is used to obtain the numerical results. And the numerical simulation results fit the analytical solutions. Therefore, the proposed analytical means to study this system are proved to be feasible. In this context, the effects onmore » the response stationary probability density functions (PDFs) caused by noise excitation, restitution condition, and fractional derivative damping are considered, in addition the stochastic P-bifurcation is also explored in this paper through varying the value of the coefficient of fractional derivative damping and the restitution coefficient. These system parameters not only influence the response PDFs of this system but also can cause the stochastic P-bifurcation.« less

Fitting Nonlinear Ordinary Differential Equation Models with Random Effects and Unknown Initial Conditions Using the Stochastic Approximation Expectation-Maximization (SAEM) Algorithm.

PubMed

Chow, Sy-Miin; Lu, Zhaohua; Sherwood, Andrew; Zhu, Hongtu

2016-03-01

The past decade has evidenced the increased prevalence of irregularly spaced longitudinal data in social sciences. Clearly lacking, however, are modeling tools that allow researchers to fit dynamic models to irregularly spaced data, particularly data that show nonlinearity and heterogeneity in dynamical structures. We consider the issue of fitting multivariate nonlinear differential equation models with random effects and unknown initial conditions to irregularly spaced data. A stochastic approximation expectation-maximization algorithm is proposed and its performance is evaluated using a benchmark nonlinear dynamical systems model, namely, the Van der Pol oscillator equations. The empirical utility of the proposed technique is illustrated using a set of 24-h ambulatory cardiovascular data from 168 men and women. Pertinent methodological challenges and unresolved issues are discussed.

FITTING NONLINEAR ORDINARY DIFFERENTIAL EQUATION MODELS WITH RANDOM EFFECTS AND UNKNOWN INITIAL CONDITIONS USING THE STOCHASTIC APPROXIMATION EXPECTATION–MAXIMIZATION (SAEM) ALGORITHM

PubMed Central

Chow, Sy- Miin; Lu, Zhaohua; Zhu, Hongtu; Sherwood, Andrew

2014-01-01

The past decade has evidenced the increased prevalence of irregularly spaced longitudinal data in social sciences. Clearly lacking, however, are modeling tools that allow researchers to fit dynamic models to irregularly spaced data, particularly data that show nonlinearity and heterogeneity in dynamical structures. We consider the issue of fitting multivariate nonlinear differential equation models with random effects and unknown initial conditions to irregularly spaced data. A stochastic approximation expectation–maximization algorithm is proposed and its performance is evaluated using a benchmark nonlinear dynamical systems model, namely, the Van der Pol oscillator equations. The empirical utility of the proposed technique is illustrated using a set of 24-h ambulatory cardiovascular data from 168 men and women. Pertinent methodological challenges and unresolved issues are discussed. PMID:25416456

Analysis of structural patterns in the brain with the complex network approach

NASA Astrophysics Data System (ADS)

Maksimenko, Vladimir A.; Makarov, Vladimir V.; Kharchenko, Alexander A.; Pavlov, Alexey N.; Khramova, Marina V.; Koronovskii, Alexey A.; Hramov, Alexander E.

2015-03-01

In this paper we study mechanisms of the phase synchronization in a model network of Van der Pol oscillators and in the neural network of the brain by consideration of macroscopic parameters of these networks. As the macroscopic characteristics of the model network we consider a summary signal produced by oscillators. Similar to the model simulations, we study EEG signals reflecting the macroscopic dynamics of neural network. We show that the appearance of the phase synchronization leads to an increased peak in the wavelet spectrum related to the dynamics of synchronized oscillators. The observed correlation between the phase relations of individual elements and the macroscopic characteristics of the whole network provides a way to detect phase synchronization in the neural networks in the cases of normal and pathological activity.

Simulation of noisy dynamical system by Deep Learning

NASA Astrophysics Data System (ADS)

Yeo, Kyongmin

2017-11-01

Deep learning has attracted huge attention due to its powerful representation capability. However, most of the studies on deep learning have been focused on visual analytics or language modeling and the capability of the deep learning in modeling dynamical systems is not well understood. In this study, we use a recurrent neural network to model noisy nonlinear dynamical systems. In particular, we use a long short-term memory (LSTM) network, which constructs internal nonlinear dynamics systems. We propose a cross-entropy loss with spatial ridge regularization to learn a non-stationary conditional probability distribution from a noisy nonlinear dynamical system. A Monte Carlo procedure to perform time-marching simulations by using the LSTM is presented. The behavior of the LSTM is studied by using noisy, forced Van der Pol oscillator and Ikeda equation.

Chaos control applied to cardiac rhythms represented by ECG signals

NASA Astrophysics Data System (ADS)

Borem Ferreira, Bianca; Amorim Savi, Marcelo; Souza de Paula, Aline

2014-10-01

The control of irregular or chaotic heartbeats is a key issue in cardiology. In this regard, chaos control techniques represent a good alternative since they suggest treatments different from those traditionally used. This paper deals with the application of the extended time-delayed feedback control method to stabilize pathological chaotic heart rhythms. Electrocardiogram (ECG) signals are employed to represent the cardiovascular behavior. A mathematical model is employed to generate ECG signals using three modified Van der Pol oscillators connected with time delay couplings. This model provides results that qualitatively capture the general behavior of the heart. Controlled ECG signals show the ability of the strategy either to control or to suppress the chaotic heart dynamics generating less-critical behaviors.

Heuristics for the Hodgkin-Huxley system.

PubMed

Hoppensteadt, Frank

2013-09-01

Hodgkin and Huxley (HH) discovered that voltages control ionic currents in nerve membranes. This led them to describe electrical activity in a neuronal membrane patch in terms of an electronic circuit whose characteristics were determined using empirical data. Due to the complexity of this model, a variety of heuristics, including relaxation oscillator circuits and integrate-and-fire models, have been used to investigate activity in neurons, and these simpler models have been successful in suggesting experiments and explaining observations. Connections between most of the simpler models had not been made clear until recently. Shown here are connections between these heuristics and the full HH model. In particular, we study a new model (Type III circuit): It includes the van der Pol-based models; it can be approximated by a simple integrate-and-fire model; and it creates voltages and currents that correspond, respectively, to the h and V components of the HH system. Copyright © 2012 Elsevier Inc. All rights reserved.

Unfolding an electronic integrate-and-fire circuit.

PubMed

Carrillo, Humberto; Hoppensteadt, Frank

2010-01-01

Many physical and biological phenomena involve accumulation and discharge processes that can occur on significantly different time scales. Models of these processes have contributed to understand excitability self-sustained oscillations and synchronization in arrays of oscillators. Integrate-and-fire (I+F) models are popular minimal fill-and-flush mathematical models. They are used in neuroscience to study spiking and phase locking in single neuron membranes, large scale neural networks, and in a variety of applications in physics and electrical engineering. We show here how the classical first-order I+F model fits into the theory of nonlinear oscillators of van der Pol type by demonstrating that a particular second-order oscillator having small parameters converges in a singular perturbation limit to the I+F model. In this sense, our study provides a novel unfolding of such models and it identifies a constructible electronic circuit that is closely related to I+F.

Modelling vertical human walking forces using self-sustained oscillator

NASA Astrophysics Data System (ADS)

Kumar, Prakash; Kumar, Anil; Racic, Vitomir; Erlicher, Silvano

2018-01-01

This paper proposes a model of a self-sustained oscillator which can generate reliably the vertical contact force between the feet of a healthy pedestrian and the supporting flat rigid surface. The model is motivated by the self-sustained nature of the walking process, i.e. a pedestrian generates the required inner energy to sustain its repetitive body motion. The derived model is a fusion of the well-known Rayleigh, Van der Pol and Duffing oscillators. Some additional nonlinear terms are added to produce both the odd and even harmonics observed in the experimentally measured force data. The model parameters were derived from force records due to twelve pedestrians walking on an instrumented treadmill at ten speeds using a linear least square technique. The stability analysis was performed using the energy balance method and perturbation method. The results obtained from the model show a good agreement with the experimental results.

Evaluation of dynamical models: dissipative synchronization and other techniques.

PubMed

Aguirre, Luis Antonio; Furtado, Edgar Campos; Tôrres, Leonardo A B

2006-12-01

Some recent developments for the validation of nonlinear models built from data are reviewed. Besides giving an overall view of the field, a procedure is proposed and investigated based on the concept of dissipative synchronization between the data and the model, which is very useful in validating models that should reproduce dominant dynamical features, like bifurcations, of the original system. In order to assess the discriminating power of the procedure, four well-known benchmarks have been used: namely, Duffing-Ueda, Duffing-Holmes, and van der Pol oscillators, plus the Hénon map. The procedure, developed for discrete-time systems, is focused on the dynamical properties of the model, rather than on statistical issues. For all the systems investigated, it is shown that the discriminating power of the procedure is similar to that of bifurcation diagrams--which in turn is much greater than, say, that of correlation dimension--but at a much lower computational cost.

Mikrobielle Kurzzeitteste zur Bestimmung der mutagenen Potenz chemischer Substanzen

NASA Astrophysics Data System (ADS)

Gericke, Dietmar

1983-04-01

During the last 20 years it became much more interesting to test new chemicals as fast as possible for their carcinogenic potency. Therefore new test models were developed. Mutagenicity seems to be one sign for carcinogenicity. Therefore test systems using microorganisms were studied which are influenced by mutagenic substances. These systems are described, first of all the Ames-Test, using revertants of Salmonella typhimurium, secondly the Escherichia coli system deficient of DNA-polymerase A (DNA-Pol A-). The yeast Saccharomyces cerevisiae was introduced some years ago and finally the Neurospora crassa system serves as an additional test to define exactly the localisation of mutations. The tests and their problems are discussed.

Stability diagram for the forced Kuramoto model.

PubMed

Childs, Lauren M; Strogatz, Steven H

2008-12-01

We analyze the periodically forced Kuramoto model. This system consists of an infinite population of phase oscillators with random intrinsic frequencies, global sinusoidal coupling, and external sinusoidal forcing. It represents an idealization of many phenomena in physics, chemistry, and biology in which mutual synchronization competes with forced synchronization. In other words, the oscillators in the population try to synchronize with one another while also trying to lock onto an external drive. Previous work on the forced Kuramoto model uncovered two main types of attractors, called forced entrainment and mutual entrainment, but the details of the bifurcations between them were unclear. Here we present a complete bifurcation analysis of the model for a special case in which the infinite-dimensional dynamics collapse to a two-dimensional system. Exact results are obtained for the locations of Hopf, saddle-node, and Takens-Bogdanov bifurcations. The resulting stability diagram bears a striking resemblance to that for the weakly nonlinear forced van der Pol oscillator.

Lyapunov stability and its application to systems of ordinary differential equations

NASA Technical Reports Server (NTRS)

Kennedy, E. W.

1979-01-01

An outline and a brief introduction to some of the concepts and implications of Lyapunov stability theory are presented. Various aspects of the theory are illustrated by the inclusion of eight examples, including the Cartesian coordinate equations of the two-body problem, linear and nonlinear (Van der Pol's equation) oscillatory systems, and the linearized Kustaanheimo-Stiefel element equations for the unperturbed two-body problem.

Dynamics of Relaxation Processes of Spontaneous Otoacoustic Emissions

NASA Astrophysics Data System (ADS)

Murphy, William James

The dynamical response of spontaneous otoacoustic emissions (SOAEs) to suppression by ipsilateral pulsed external tones of different frequencies and levels is investigated in nine female subjects under normal conditions and in four female subjects during periods when aspirin is being administered. A simple Van der Pol limit-cycle oscillator driven by an external tone is used as an interpretive model. Typical results for both the onset of, and recovery from suppression yield 1/r_1 (where -r_1 is the negative linear component of the damping function) in the range of 2-25 msec. In accordance with the predictions of the model: (a) the relaxation time for the onset of suppression increases with the amount of suppression induced by the external tone, (b) the values of r _1 and the amplitudes of the unsuppressed emissions exhibit an inverse correlation, (c) the values inferred for r_1 are not significantly dependent on the frequency of the pulsed suppressor tone and (d) the inferred r_1 values are not significantly dependent upon the amount of suppression. In investigations involving subjects under aspirin administration, the changes in the relaxation time constants indicate that the main effect of aspirin administration is to reduce the negative damping parameter r_1. The salicylate is apparently not metabolized in some subjects whose emissions are negligibly affected by aspirin administration. A modification of the single-oscillator model is used to describe pulsed suppression data obtained from a primary SOAE (2545 Hz) which is suppressed by a neighboring secondary emission (2895 Hz). The response of the SOAE amplitude during pulsed suppression is modeled by a pair of Van der Pol limit-cycle oscillators with the primary oscillator linearly coupled to the displacement of the secondary higher-frequency one. The relaxation time constants for the onset of, and recovery from, suppression are 4.5 and 4.8 msec, respectively, for the primary SOAE and 7.5 and 10.5 msec for the secondary one. Aspirin administration reduces the magnitude of the overshoot by reducing the level of the higher frequency SOAE and thereby eliminating the suppression of the lower frequency one.

Mode suppression of a two-dimensional potential relaxation instability in a weakly magnetized discharge plasma

NASA Astrophysics Data System (ADS)

Gyergyek, T.; Čerček, M.; Jelić, N.; Stanojević, M.

1993-05-01

A potential relaxation instability (PRI) is modulated by an external signal using an additional grid to modulate the radial plasma potential profile in a magnetized plasma column in a linear magnetized discharge plasma device. It is observed that the electrode current oscillations follow the van der Pol equation with an external forcing term, and the linear growth rate of the instability is measured.

Perturbation analysis of the limit cycle of the free van der Pol equation

NASA Technical Reports Server (NTRS)

Dadfar, M. B.; Geer, J.; Anderson, C. M.

1983-01-01

A power series expansion in the damping parameter, epsilon, of the limit cycle of the free van der Pol equation is constructed and analyzed. Coefficients in the expansion are computed in exact rational arithmetic using the symbolic manipulation system MACSYMA and using a FORTRAN program. The series is analyzed using Pade approximants. The convergence of the series for the maximum amplitude of the limit cycle is limited by two pair of complex conjugate singularities in the complex epsilon-plane. A new expansion parameter is introduced which maps these singularities to infinity and leads to a new expansion for the amplitude which converges for all real values of epsilon. Amplitudes computed from this transformed series agree very well with reported numerical and asymptotic results. For the limit cycle itself, convergence of the series expansion is limited by three pair of complex conjugate branch point singularities. Two pair remain fixed throughout the cycle, and correspond to the singularities found in the maximum amplitude series, while the third pair moves in the epsilon-plane as a function of t from one of the fixed pairs to the other. The limit cycle series is transformed using a new expansion parameter, which leads to a new series that converges for larger values of epsilon.

Cooperative Adaptive Output Regulation for Second-Order Nonlinear Multiagent Systems With Jointly Connected Switching Networks.

PubMed

Liu, Wei; Huang, Jie

2018-03-01

This paper studies the cooperative global robust output regulation problem for a class of heterogeneous second-order nonlinear uncertain multiagent systems with jointly connected switching networks. The main contributions consist of the following three aspects. First, we generalize the result of the adaptive distributed observer from undirected jointly connected switching networks to directed jointly connected switching networks. Second, by performing a new coordinate and input transformation, we convert our problem into the cooperative global robust stabilization problem of a more complex augmented system via the distributed internal model principle. Third, we solve the stabilization problem by a distributed state feedback control law. Our result is illustrated by the leader-following consensus problem for a group of Van der Pol oscillators.

Genuine Quantum Signatures in Synchronization of Anharmonic Self-Oscillators.

PubMed

Lörch, Niels; Amitai, Ehud; Nunnenkamp, Andreas; Bruder, Christoph

2016-08-12

We study the synchronization of a Van der Pol self-oscillator with Kerr anharmonicity to an external drive. We demonstrate that the anharmonic, discrete energy spectrum of the quantum oscillator leads to multiple resonances in both phase locking and frequency entrainment not present in the corresponding classical system. Strong driving close to these resonances leads to nonclassical steady-state Wigner distributions. Experimental realizations of these genuine quantum signatures can be implemented with current technology.

Polynomial law for controlling the generation of n-scroll chaotic attractors in an optoelectronic delayed oscillator

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

Márquez, Bicky A., E-mail: bmarquez@ivic.gob.ve; Suárez-Vargas, José J., E-mail: jjsuarez@ivic.gob.ve; Ramírez, Javier A.

2014-09-01

Controlled transitions between a hierarchy of n-scroll attractors are investigated in a nonlinear optoelectronic oscillator. Using the system's feedback strength as a control parameter, it is shown experimentally the transition from Van der Pol-like attractors to 6-scroll, but in general, this scheme can produce an arbitrary number of scrolls. The complexity of every state is characterized by Lyapunov exponents and autocorrelation coefficients.

Arm motion coupling during locomotion-like actions: An experimental study and a dynamic model

PubMed Central

Shapkova, E.Yu; Terekhov, A.V.; Latash, M.L.

2010-01-01

We studied the coordination of arm movements in standing persons who performed an out-of-phase arm-swinging task while stepping in place or while standing. The subjects were instructed to stop one of the arms in response to an auditory signal while trying to keep the rest of the movement pattern unchanged. A significant increase was observed in the amplitude of the arm that continued swinging under both the stepping and standing conditions. This increase was similar between the right and left arms. A dynamic model was developed including two coupled non-linear van der Pol oscillators. We assumed that stopping an arm did not eliminate the coupling but introduced a new constraint. Within the model, superposition of two factors, a command to stop the ongoing movement of one arm and the coupling between the two oscillators, has been able to account for the observed effects. The model makes predictions for future experiments. PMID:21628725

On the Origin of Pulsations of Sub-THz Emission from Solar Flares

NASA Astrophysics Data System (ADS)

Zaitsev, V. V.; Stepanov, A. V.; Kaufmann, P.

2014-08-01

We propose a model to explain fast pulsations in sub-THz emission from solar flares. The model is based on the approach of a flaring loop as an equivalent electric circuit and explains the pulse-repetition rate, the high-quality factor, Q≥103, low modulation depth, pulse synchronism at different frequencies, and the dependence of the pulse-repetition rate on the emission flux, observed by Kaufmann et al. ( Astrophys. J. 697, 420, 2009). We solved the nonlinear equation for electric current oscillations using a Van der Pol method and found the steady-state value for the amplitude of the current oscillations. Using the pulse rate variation during the flare on 4 November 2003, we found a decrease of the electric current from 1.7×1012 A in the flare maximum to 4×1010 A just after the burst. Our model is consistent with the plasma mechanism of sub-THz emission suggested recently by Zaitsev, Stepanov, and Melnikov ( Astron. Lett. 39, 650, 2013).

Simulations of pattern dynamics for reaction-diffusion systems via SIMULINK

PubMed Central

2014-01-01

Background Investigation of the nonlinear pattern dynamics of a reaction-diffusion system almost always requires numerical solution of the system’s set of defining differential equations. Traditionally, this would be done by selecting an appropriate differential equation solver from a library of such solvers, then writing computer codes (in a programming language such as C or Matlab) to access the selected solver and display the integrated results as a function of space and time. This “code-based” approach is flexible and powerful, but requires a certain level of programming sophistication. A modern alternative is to use a graphical programming interface such as Simulink to construct a data-flow diagram by assembling and linking appropriate code blocks drawn from a library. The result is a visual representation of the inter-relationships between the state variables whose output can be made completely equivalent to the code-based solution. Results As a tutorial introduction, we first demonstrate application of the Simulink data-flow technique to the classical van der Pol nonlinear oscillator, and compare Matlab and Simulink coding approaches to solving the van der Pol ordinary differential equations. We then show how to introduce space (in one and two dimensions) by solving numerically the partial differential equations for two different reaction-diffusion systems: the well-known Brusselator chemical reactor, and a continuum model for a two-dimensional sheet of human cortex whose neurons are linked by both chemical and electrical (diffusive) synapses. We compare the relative performances of the Matlab and Simulink implementations. Conclusions The pattern simulations by Simulink are in good agreement with theoretical predictions. Compared with traditional coding approaches, the Simulink block-diagram paradigm reduces the time and programming burden required to implement a solution for reaction-diffusion systems of equations. Construction of the block-diagram does not require high-level programming skills, and the graphical interface lends itself to easy modification and use by non-experts. PMID:24725437

Simulations of pattern dynamics for reaction-diffusion systems via SIMULINK.

PubMed

Wang, Kaier; Steyn-Ross, Moira L; Steyn-Ross, D Alistair; Wilson, Marcus T; Sleigh, Jamie W; Shiraishi, Yoichi

2014-04-11

Investigation of the nonlinear pattern dynamics of a reaction-diffusion system almost always requires numerical solution of the system's set of defining differential equations. Traditionally, this would be done by selecting an appropriate differential equation solver from a library of such solvers, then writing computer codes (in a programming language such as C or Matlab) to access the selected solver and display the integrated results as a function of space and time. This "code-based" approach is flexible and powerful, but requires a certain level of programming sophistication. A modern alternative is to use a graphical programming interface such as Simulink to construct a data-flow diagram by assembling and linking appropriate code blocks drawn from a library. The result is a visual representation of the inter-relationships between the state variables whose output can be made completely equivalent to the code-based solution. As a tutorial introduction, we first demonstrate application of the Simulink data-flow technique to the classical van der Pol nonlinear oscillator, and compare Matlab and Simulink coding approaches to solving the van der Pol ordinary differential equations. We then show how to introduce space (in one and two dimensions) by solving numerically the partial differential equations for two different reaction-diffusion systems: the well-known Brusselator chemical reactor, and a continuum model for a two-dimensional sheet of human cortex whose neurons are linked by both chemical and electrical (diffusive) synapses. We compare the relative performances of the Matlab and Simulink implementations. The pattern simulations by Simulink are in good agreement with theoretical predictions. Compared with traditional coding approaches, the Simulink block-diagram paradigm reduces the time and programming burden required to implement a solution for reaction-diffusion systems of equations. Construction of the block-diagram does not require high-level programming skills, and the graphical interface lends itself to easy modification and use by non-experts.

Closed-loop suppression of chaos in nonlinear driven oscillators

NASA Astrophysics Data System (ADS)

Aguirre, L. A.; Billings, S. A.

1995-05-01

This paper discusses the suppression of chaos in nonlinear driven oscillators via the addition of a periodic perturbation. Given a system originally undergoing chaotic motions, it is desired that such a system be driven to some periodic orbit. This can be achieved by the addition of a weak periodic signal to the oscillator input. This is usually accomplished in open loop, but this procedure presents some difficulties which are discussed in the paper. To ensure that this is attained despite uncertainties and possible disturbances on the system, a procedure is suggested to perform control in closed loop. In addition, it is illustrated how a model, estimated from input/output data, can be used in the design. Numerical examples which use the Duffing-Ueda and modified van der Pol oscillators are included to illustrate some of the properties of the new approach.

Fuzzy controller training using particle swarm optimization for nonlinear system control.

PubMed

Karakuzu, Cihan

2008-04-01

This paper proposes and describes an effective utilization of particle swarm optimization (PSO) to train a Takagi-Sugeno (TS)-type fuzzy controller. Performance evaluation of the proposed fuzzy training method using the obtained simulation results is provided with two samples of highly nonlinear systems: a continuous stirred tank reactor (CSTR) and a Van der Pol (VDP) oscillator. The superiority of the proposed learning technique is that there is no need for a partial derivative with respect to the parameter for learning. This fuzzy learning technique is suitable for real-time implementation, especially if the system model is unknown and a supervised training cannot be run. In this study, all parameters of the controller are optimized with PSO in order to prove that a fuzzy controller trained by PSO exhibits a good control performance.

On the Computation of Finite Invariant Sets of Mappings.

DTIC Science & Technology

1988-02-01

for the calculation of such invariant cycles. We refer here only to Doedel [1], looss et al [3], Kevrekidis et al [4], Van Veldhuizen ,[6], where further... van Veldhuizen , On Polygonal Approximations of an Invariant Curve, Dept.of Mathem. and Comp. Science, Vrije Universiteit Amsterdam, Techni- cal Report 1987, Math. Comp. to appear DATE Fl .LMED ...of van der Pol’s equation " x2) x - A(l - x ) X’ + x - 0 (16) As shown, for example in [2], the solution satisfies x - 2 cos(wt)+ A (0.75 sin(wt

Phase shifting two coupled circadian pacemakers - Implications for jet lag

NASA Technical Reports Server (NTRS)

Gander, P. H.; Kronauer, R. E.; Graeber, R. C.

1985-01-01

Two Van der Pol oscillators with reciprocal linear velocity coupling are utilized to model the response of the human circadian timing system to abrupt displacements of the environmental time cues (zeitgebers). The core temperature rhythm and sleep-wake cycle simulated by the model are examined. The relationship between the masking of circadian rhythms by environmental variables and behavioral and physiological events and the rates of resynchronization is studied. The effects of zeitgeber phase shifts and zeitgeber strength on the resynchronization rates are analyzed. The influence of intrinsic pacemakers periods and coupling strength on resynchronization are investigated. The simulated data reveal that: resynchronization after a time zone shift depends on the magnitude of the shift; the time of day of the shift has little influence on resynchronization; the strength of zeitgebers affects the rate and direction of the resynchronization; the intrinsic pacemaker periods have a significant effect on resynchronization; and increasing the coupling between the oscillators results in an increase in the rate of resynchronization. The model data are compared to transmeridian flight studies data and similar resynchronization patterns are observed.

Crosslinking-MS analysis reveals RNA polymerase I domain architecture and basis of rRNA cleavage

PubMed Central

Jennebach, Stefan; Herzog, Franz; Aebersold, Ruedi; Cramer, Patrick

2012-01-01

RNA polymerase (Pol) I contains a 10-subunit catalytic core that is related to the core of Pol II and includes subunit A12.2. In addition, Pol I contains the heterodimeric subcomplexes A14/43 and A49/34.5, which are related to the Pol II subcomplex Rpb4/7 and the Pol II initiation factor TFIIF, respectively. Here we used lysine-lysine crosslinking, mass spectrometry (MS) and modeling based on five crystal structures, to extend the previous homology model of the Pol I core, to confirm the location of A14/43 and to position A12.2 and A49/34.5 on the core. In the resulting model of Pol I, the C-terminal ribbon (C-ribbon) domain of A12.2 reaches the active site via the polymerase pore, like the C-ribbon of the Pol II cleavage factor TFIIS, explaining why the intrinsic RNA cleavage activity of Pol I is strong, in contrast to the weak cleavage activity of Pol II. The A49/34.5 dimerization module resides on the polymerase lobe, like TFIIF, whereas the A49 tWH domain resides above the cleft, resembling parts of TFIIE. This indicates that Pol I and also Pol III are distantly related to a Pol II–TFIIS–TFIIF–TFIIE complex. PMID:22396529

DNA polymerases eta and kappa exchange with the polymerase delta holoenzyme to complete common fragile site synthesis.

PubMed

Barnes, Ryan P; Hile, Suzanne E; Lee, Marietta Y; Eckert, Kristin A

2017-09-01

Common fragile sites (CFSs) are inherently unstable genomic loci that are recurrently altered in human tumor cells. Despite their instability, CFS are ubiquitous throughout the human genome and associated with large tumor suppressor genes or oncogenes. CFSs are enriched with repetitive DNA sequences, one feature postulated to explain why these loci are inherently difficult to replicate, and sensitive to replication stress. We have shown that specialized DNA polymerases (Pols) η and κ replicate CFS-derived sequences more efficiently than the replicative Pol δ. However, we lacked an understanding of how these enzymes cooperate to ensure efficient CFS replication. Here, we designed a model of lagging strand replication with RFC loaded PCNA that allows for maximal activity of the four-subunit human Pol δ holoenzyme, Pol η, and Pol κ in polymerase mixing assays. We discovered that Pol η and κ are both able to exchange with Pol δ stalled at repetitive CFS sequences, enhancing Normalized Replication Efficiency. We used this model to test the impact of PCNA mono-ubiquitination on polymerase exchange, and found no change in polymerase cooperativity in CFS replication compared with unmodified PCNA. Finally, we modeled replication stress in vitro using aphidicolin and found that Pol δ holoenzyme synthesis was significantly inhibited in a dose-dependent manner, preventing any replication past the CFS. Importantly, Pol η and κ were still proficient in rescuing this stalled Pol δ synthesis, which may explain, in part, the CFS instability phenotype of aphidicolin-treated Pol η and Pol κ-deficient cells. In total, our data support a model wherein Pol δ stalling at CFSs allows for free exchange with a specialized polymerase that is not driven by PCNA. Copyright © 2017 Elsevier B.V. All rights reserved.

Information Interaction Study for DER and DMS Interoperability

NASA Astrophysics Data System (ADS)

Liu, Haitao; Lu, Yiming; Lv, Guangxian; Liu, Peng; Chen, Yu; Zhang, Xinhui

The Common Information Model (CIM) is an abstract data model that can be used to represent the major objects in Distribution Management System (DMS) applications. Because the Common Information Model (CIM) doesn't modeling the Distributed Energy Resources (DERs), it can't meet the requirements of DER operation and management for Distribution Management System (DMS) advanced applications. Modeling of DER were studied based on a system point of view, the article initially proposed a CIM extended information model. By analysis the basic structure of the message interaction between DMS and DER, a bidirectional messaging mapping method based on data exchange was proposed.

In vitro characterization of pol I*, an SOS inducible, error-prone from of Escherichia coli DNA polymerase I

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

Hodes, C.S.

E. coli strains carrying mutations in the SOS regulon were screened for the presence of pol I*. Use of pol I* in assays of polymerase fidelity and selectivity has been limited by the low concentration and purity of the enzyme. Therefore, attempts were made to further concentrate and purify pol I*. The template selectivity of pol I* was compared to that of pol I using three models of damaged DNA. UV-irradiated M13 DNA was used in a two-stage termination reaction to determine if pol I* could bypass putative pyrimidine dimers to a greater extent than pol I. In the gelmore » system no reproducibly significant bypass could be detected by either pol I* or pol I. However, the degree of replication by pol I* utilizing UV-irradiated M13 DNA template, was up to 5-fold greater than for pol I. OsO{sub 4}-oxidized M13 DNA was used as a model substrate for oxidative DNA damage. Opposite this substrate incorporation by pol I* is less inhibited than incorporation by pol I. However, in a test of nucleotide selectivity neither pol I*, pol I, nor terminal deoxyribonucleotidyl transferase will incorporate ({alpha}-{sup 32}P)thymine glycol deoxyribonucleotide. The activity of pol I* was compared to that of pol I on the synthetic templates, poly (dA) and poly((dA)+2-AP). Pol I* misincorporated both dCMP and dGMP to a greater extent than pol I when utilizing templates containing 2-aminopurine deoxyribonucleotide.« less

Emergence and analysis of Kuramoto-Sakaguchi-like models as an effective description for the dynamics of coupled Wien-bridge oscillators.

PubMed

English, L Q; Mertens, David; Abdoulkary, Saidou; Fritz, C B; Skowronski, K; Kevrekidis, P G

2016-12-01

We derive the Kuramoto-Sakaguchi model from the basic circuit equations governing two coupled Wien-bridge oscillators. A Wien-bridge oscillator is a particular realization of a tunable autonomous oscillator that makes use of frequency filtering (via an RC bandpass filter) and positive feedback (via an operational amplifier). In the past few years, such oscillators have started to be utilized in synchronization studies. We first show that the Wien-bridge circuit equations can be cast in the form of a coupled pair of van der Pol equations. Subsequently, by applying the method of multiple time scales, we derive the differential equations that govern the slow evolution of the oscillator phases and amplitudes. These equations are directly reminiscent of the Kuramoto-Sakaguchi-type models for the study of synchronization. We analyze the resulting system in terms of the existence and stability of various coupled oscillator solutions and explain on that basis how their synchronization emerges. The phase-amplitude equations are also compared numerically to the original circuit equations and good agreement is found. Finally, we report on experimental measurements of two coupled Wien-bridge oscillators and relate the results to the theoretical predictions.

Selective Perception for Robot Driving

DTIC Science & Technology

1992-05-01

models are theories of human cognitive activity during driving. Van der Molen and Botticher recently reviewed several of these models [ van der Molen 871...how to represent driving knowledge, how to perceive traffic situations, or how to process information to obtain actions. Van der Molen and Botticher...attempted to compare the operations of various models objectively on the same task [Rothengatter 88, van der Molen 87], but the models could be

Synchronization in counter-rotating oscillators.

PubMed

Bhowmick, Sourav K; Ghosh, Dibakar; Dana, Syamal K

2011-09-01

An oscillatory system can have opposite senses of rotation, clockwise or anticlockwise. We present a general mathematical description of how to obtain counter-rotating oscillators from the definition of a dynamical system. A type of mixed synchronization emerges in counter-rotating oscillators under diffusive scalar coupling when complete synchronization and antisynchronization coexist in different state variables. We present numerical examples of limit cycle van der Pol oscillator and chaotic Rössler and Lorenz systems. Stability conditions of mixed synchronization are analytically obtained for both Rössler and Lorenz systems. Experimental evidences of counter-rotating limit cycle and chaotic oscillators and mixed synchronization are given in electronic circuits.

Sitnikov problem in the cyclic kite configuration

NASA Astrophysics Data System (ADS)

Shahbaz Ullah, M.; Bhatnagar, K. B.; Hassan, M. R.

2014-12-01

This manuscript deals with the development of the series solutions of the Sitnikov kite configuration by the methods given of Lindstedt-Poincarė, using Green's function and MacMillan. Next we have developed averaged equation of motion by applying the Van der Pol transformation and averaging technique of Guckenheimer and Holmes (Nonlinear oscillations, dynamical system bifurcations of vector fields. Springer, Berlin, 1983). In addition to the resonance criterion at the 3/2 commensurability we have chosen ω=2 n/3, n=2, ω is the angular velocity of the coordinate system. Lastly the periodicity of the solutions has been examined by the Poincarė section.

Chimera states in complex networks: interplay of fractal topology and delay

NASA Astrophysics Data System (ADS)

Sawicki, Jakub; Omelchenko, Iryna; Zakharova, Anna; Schöll, Eckehard

2017-06-01

Chimera states are an example of intriguing partial synchronization patterns emerging in networks of identical oscillators. They consist of spatially coexisting domains of coherent (synchronized) and incoherent (desynchronized) dynamics. We analyze chimera states in networks of Van der Pol oscillators with hierarchical connectivities, and elaborate the role of time delay introduced in the coupling term. In the parameter plane of coupling strength and delay time we find tongue-like regions of existence of chimera states alternating with regions of existence of coherent travelling waves. We demonstrate that by varying the time delay one can deliberately stabilize desired spatio-temporal patterns in the system.

Mechanism of asymmetric polymerase assembly at the eukaryotic replication fork

PubMed Central

Georgescu, Roxana E; Langston, Lance; Yao, Nina Y; Yurieva, Olga; Zhang, Dan; Finkelstein, Jeff; Agarwal, Tani; O’Donnell, Mike E

2015-01-01

Eukaryotes use distinct polymerases for leading- and lagging-strand replication, but how they target their respective strands is uncertain. We reconstituted Saccharomyces cerevisiae replication forks and found that CMG helicase selects polymerase (Pol) ε to the exclusion of Pol δ on the leading strand. Even if Pol δ assembles on the leading strand, Pol ε rapidly replaces it. Pol δ–PCNA is distributive with CMG, in contrast to its high stability on primed ssDNA. Hence CMG will not stabilize Pol δ, instead leaving the leading strand accessible for Pol ε and stabilizing Pol ε. Comparison of Pol ε and Pol δ on a lagging-strand model DNA reveals the opposite. Pol δ dominates over excess Pol ε on PCNA-primed ssDNA. Thus, PCNA strongly favors Pol δ over Pol ε on the lagging strand, but CMG over-rides and flips this balance in favor of Pol ε on the leading strand. PMID:24997598

Semi-empirical modelling for forest above ground biomass estimation using hybrid and fully PolSAR data

NASA Astrophysics Data System (ADS)

Tomar, Kiledar S.; Kumar, Shashi; Tolpekin, Valentyn A.; Joshi, Sushil K.

2016-05-01

Forests act as sink of carbon and as a result maintains carbon cycle in atmosphere. Deforestation leads to imbalance in global carbon cycle and changes in climate. Hence estimation of forest biophysical parameter like biomass becomes a necessity. PolSAR has the ability to discriminate the share of scattering element like surface, double bounce and volume scattering in a single SAR resolution cell. Studies have shown that volume scattering is a significant parameter for forest biophysical characterization which mainly occurred from vegetation due to randomly oriented structures. This random orientation of forest structure causes shift in orientation angle of polarization ellipse which ultimately disturbs the radar signature and shows overestimation of volume scattering and underestimation of double bounce scattering after decomposition of fully PolSAR data. Hybrid polarimetry has the advantage of zero POA shift due to rotational symmetry followed by the circular transmission of electromagnetic waves. The prime objective of this study was to extract the potential of Hybrid PolSAR and fully PolSAR data for AGB estimation using Extended Water Cloud model. Validation was performed using field biomass. The study site chosen was Barkot Forest, Uttarakhand, India. To obtain the decomposition components, m-alpha and Yamaguchi decomposition modelling for Hybrid and fully PolSAR data were implied respectively. The RGB composite image for both the decomposition techniques has generated. The contribution of all scattering from each plot for m-alpha and Yamaguchi decomposition modelling were extracted. The R2 value for modelled AGB and field biomass from Hybrid PolSAR and fully PolSAR data were found 0.5127 and 0.4625 respectively. The RMSE for Hybrid and fully PolSAR between modelled AGB and field biomass were 63.156 (t ha-1) and 73.424 (t ha-1) respectively. On the basis of RMSE and R2 value, this study suggests Hybrid PolSAR decomposition modelling to retrieve scattering element for AGB estimation from forest.

Polarimetric SAR image classification based on discriminative dictionary learning model

NASA Astrophysics Data System (ADS)

Sang, Cheng Wei; Sun, Hong

2018-03-01

Polarimetric SAR (PolSAR) image classification is one of the important applications of PolSAR remote sensing. It is a difficult high-dimension nonlinear mapping problem, the sparse representations based on learning overcomplete dictionary have shown great potential to solve such problem. The overcomplete dictionary plays an important role in PolSAR image classification, however for PolSAR image complex scenes, features shared by different classes will weaken the discrimination of learned dictionary, so as to degrade classification performance. In this paper, we propose a novel overcomplete dictionary learning model to enhance the discrimination of dictionary. The learned overcomplete dictionary by the proposed model is more discriminative and very suitable for PolSAR classification.

Distributed Energy Resources Customer Adoption Model Plus (DER-CAM+), Version 1.0.0

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

Stadler, Michael; Cardorso, Goncalo; Mashayekh, Salman

DER-CAM+ v1.0.0 is internally referred to as DER-CAM v5.0.0. Due to fundamental changes from previous versions, a new name (DER-CAM+) will be used for DER-CAM version 5.0.0 and above. DER-CAM+ is a Decision Support Tool for Decentralized Energy Systems that has been tailored for microgrid applications, and now explicitly considers electrical and thermal networks within a microgrid, ancillary services, and operating reserve. DER-CAM was initially created as an exclusively economic energy model, able to find the cost minimizing combination and operation profile of a set of DER technologies that meet energy loads of a building or microgrid for a typicalmore » test year. The previous versions of DER-CAM were formulated without modeling the electrical/thermal networks within the microgrid, and hence, used aggregate single-node approaches. Furthermore, they were not able to consider operating reserve constraints, and microgrid revenue streams from participating in ancillary services markets. This new version DER-CAM+ considers these issues by including electrical power flow and thermal flow equations and constraints in the microgrid, revenues from various ancillary services markets, and operating reserve constraints.« less

DNA polymerase ι functions in the generation of tandem mutations during somatic hypermutation of antibody genes.

PubMed

Maul, Robert W; MacCarthy, Thomas; Frank, Ekaterina G; Donigan, Katherine A; McLenigan, Mary P; Yang, William; Saribasak, Huseyin; Huston, Donald E; Lange, Sabine S; Woodgate, Roger; Gearhart, Patricia J

2016-08-22

DNA polymerase ι (Pol ι) is an attractive candidate for somatic hypermutation in antibody genes because of its low fidelity. To identify a role for Pol ι, we analyzed mutations in two strains of mice with deficiencies in the enzyme: 129 mice with negligible expression of truncated Pol ι, and knock-in mice that express full-length Pol ι that is catalytically inactive. Both strains had normal frequencies and spectra of mutations in the variable region, indicating that loss of Pol ι did not change overall mutagenesis. We next examined if Pol ι affected tandem mutations generated by another error-prone polymerase, Pol ζ. The frequency of contiguous mutations was analyzed using a novel computational model to determine if they occur during a single DNA transaction or during two independent events. Analyses of 2,000 mutations from both strains indicated that Pol ι-compromised mice lost the tandem signature, whereas C57BL/6 mice accumulated significant amounts of double mutations. The results support a model where Pol ι occasionally accesses the replication fork to generate a first mutation, and Pol ζ extends the mismatch with a second mutation. @2016.

DNA polymerase ι functions in the generation of tandem mutations during somatic hypermutation of antibody genes

PubMed Central

Donigan, Katherine A.; Huston, Donald E.; Lange, Sabine S.

2016-01-01

DNA polymerase ι (Pol ι) is an attractive candidate for somatic hypermutation in antibody genes because of its low fidelity. To identify a role for Pol ι, we analyzed mutations in two strains of mice with deficiencies in the enzyme: 129 mice with negligible expression of truncated Pol ι, and knock-in mice that express full-length Pol ι that is catalytically inactive. Both strains had normal frequencies and spectra of mutations in the variable region, indicating that loss of Pol ι did not change overall mutagenesis. We next examined if Pol ι affected tandem mutations generated by another error-prone polymerase, Pol ζ. The frequency of contiguous mutations was analyzed using a novel computational model to determine if they occur during a single DNA transaction or during two independent events. Analyses of 2,000 mutations from both strains indicated that Pol ι–compromised mice lost the tandem signature, whereas C57BL/6 mice accumulated significant amounts of double mutations. The results support a model where Pol ι occasionally accesses the replication fork to generate a first mutation, and Pol ζ extends the mismatch with a second mutation. PMID:27455952

Ein statistisches Modell zum Einfluß der thermischen Bewegung auf NMR-Festkörperspektren

NASA Astrophysics Data System (ADS)

Ploss, W.; Freude, D.; Pfeifer, H.; Schmiedel, H.

Es wird ein statistisches Modell zum Einfluß der thermischen Bewegung auf die NMR-Linienform vorgestellt, das die Verschmälerung von Festkörper-Spektren bei wachsender Temperatur beschreibt. Das Modell geht von der Annahme aus, daß nach einer Ortsveränderung eines Kerns infolge thermischer Bewegung jede beliebige Kernresonanzfrequenz mit der durch das Festkörperspektrum vorgegebenen Wahrscheinlichkeit angenommen werden kann. Am Beispiel der Festkörper-Gaußlinie wird der Unterschied zu dem bekannten Modell von ANDERSON und WEISS verdeutlicht.Translated AbstractA Statistical Model for the Influence of Thermal Motion on N. M. R. Spectra in SolidsA theory is proposed which allows to describe the narrowing of n. m. r.-line width in the presence of thermal motions of the spins. The model is based on the assumption, that the local resonance frequency of a given spin immediately after the jump is distributed according to the n. m. r.-line shape of the rigid lattice. The difference to the well-known ANDERSON-WEISS-model of spectral narrowing is demonstrated for a gaussian line shape.

National Dam Inspection Program. Lake Lattimore Dam (NDI-ID Number PA-00406, DER-ID Number 52-78) Delaware River Basin, Pike County, Pennsylvania. Phase I Inspection Report.

DTIC Science & Technology

1980-06-01

V 5 - 1i/ .; t (cl S . /40 T POo. t t tv / I? I H 4O/- /o 31. C1 A Lot,- PoL e (6I 3 / - - - v ... S . OFCHKD. BY ------ DATE-------. . .. . . . . . R JE T : f6. SUBJECT --------------------------. PROECT-!. II Ii I V 1:2 ,,.,, - ) ) .( y...DATE/,/’ -’ REEGER ASSOCIATES SHEET NO. 7, CNKD. BY DATE PROJECT SUBJECT t AXtI Ic C / PA; 4 ( It o’,’ ’- ,’ S ’ L V / 4 LA d1A ’l, V HYC4P) 4,A 4, I

Segmentierung von Aortenaneurysmen in CTA-Bildern mit dem statistischen Verfahren der Active Appearance Models

NASA Astrophysics Data System (ADS)

Greiner, Katharina; Egger, Jan; Großkopf, Stefan; Kaftan, Jens N.; Dörner, Ralf; Freisleben, Bernd

In diesem Beitrag werden Active Appearance Models (AAMs) zur Segmentierung der äußeren Kontur von Aortenaneurysmen eingesetzt. Diese Aufgabe ist wegen des geringen Kontrastes zum umliegenden Gewebe und des Aufbaus der teils thrombotisierten oder kalzifizierten Gefäßwände im Bereich eines Aneurysmas so komplex, dass sie aufgrund der Vielgestalt der Kontur in CT-Angiographie-Bildern die Verwendung eines statistischen Modells für Form und eingeschlossene Textur rechtfertigt. Für die Evaluation des Verfahrens wurden verschiedene statistische Modelle aus Schichten von neun CTA-Datensätzen trainiert und die Segmentierung anhand von Leave-One-Out-Tests überprüft.

A Novel Wake Oscillator Model for Vortex-Induced Vibrations Prediction of A Cylinder Considering the Influence of Reynolds Number

NASA Astrophysics Data System (ADS)

Gao, Xi-feng; Xie, Wu-de; Xu, Wan-hai; Bai, Yu-chuan; Zhu, Hai-tao

2018-04-01

It is well known that the Reynolds number has a significant effect on the vortex-induced vibrations (VIV) of cylinders. In this paper, a novel in-line (IL) and cross-flow (CF) coupling VIV prediction model for circular cylinders has been proposed, in which the influence of the Reynolds number was comprehensively considered. The Strouhal number linked with the vortex shedding frequency was calculated through a function of the Reynolds number. The coefficient of the mean drag force was fitted as a new piecewise function of the Reynolds number, and its amplification resulted from the CF VIV was also taken into account. The oscillating drag and lift forces were modelled with classical van der Pol wake oscillators and their empirical parameters were determined based on the lock-in boundaries and the peak-amplitude formulas. A new peak-amplitude formula for the IL VIV was developed under the resonance condition with respect to the mass-damping ratio and the Reynolds number. When compared with the results from the experiments and some other prediction models, the present model could give good estimations on the vibration amplitudes and frequencies of the VIV both for elastically-mounted rigid and long flexible cylinders. The present model considering the influence of the Reynolds number could generally provide better results than that neglecting the effect of the Reynolds number.

Distributed Energy Systems Integration and Demand Optimization for Autonomous Operations and Electric Grid Transactions

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

Ghatikar, Girish; Mashayekh, Salman; Stadler, Michael

Distributed power systems in the U.S. and globally are evolving to provide reliable and clean energy to consumers. In California, existing regulations require significant increases in renewable generation, as well as identification of customer-side distributed energy resources (DER) controls, communication technologies, and standards for interconnection with the electric grid systems. As DER deployment expands, customer-side DER control and optimization will be critical for system flexibility and demand response (DR) participation, which improves the economic viability of DER systems. Current DER systems integration and communication challenges include leveraging the existing DER and DR technology and systems infrastructure, and enabling optimized cost,more » energy and carbon choices for customers to deploy interoperable grid transactions and renewable energy systems at scale. Our paper presents a cost-effective solution to these challenges by exploring communication technologies and information models for DER system integration and interoperability. This system uses open standards and optimization models for resource planning based on dynamic-pricing notifications and autonomous operations within various domains of the smart grid energy system. It identifies architectures and customer engagement strategies in dynamic DR pricing transactions to generate feedback information models for load flexibility, load profiles, and participation schedules. The models are tested at a real site in California—Fort Hunter Liggett (FHL). Furthermore, our results for FHL show that the model fits within the existing and new DR business models and networked systems for transactive energy concepts. Integrated energy systems, communication networks, and modeling tools that coordinate supply-side networks and DER will enable electric grid system operators to use DER for grid transactions in an integrated system.« less

Cosmological models constructed by van der Waals fluid approximation and volumetric expansion

NASA Astrophysics Data System (ADS)

Samanta, G. C.; Myrzakulov, R.

The universe modeled with van der Waals fluid approximation, where the van der Waals fluid equation of state contains a single parameter ωv. Analytical solutions to the Einstein’s field equations are obtained by assuming the mean scale factor of the metric follows volumetric exponential and power-law expansions. The model describes a rapid expansion where the acceleration grows in an exponential way and the van der Waals fluid behaves like an inflation for an initial epoch of the universe. Also, the model describes that when time goes away the acceleration is positive, but it decreases to zero and the van der Waals fluid approximation behaves like a present accelerated phase of the universe. Finally, it is observed that the model contains a type-III future singularity for volumetric power-law expansion.

Digitalisierung als Inkubator für die Energieversorgung von morgen

NASA Astrophysics Data System (ADS)

Arnold, Christian; Postina, Matthias

Neue Treiber der Digitalisierung bestimmen die Geschicke der etablierten Unternehmen im Energiebereich, dabei haben diese in vielen Fällen noch nicht einmal adäquat auf die altbekannten Treiber der Energiewende reagiert. Eine ganze Branche ist im Umbruch, alte Erlösmodelle brechen ein und Einigkeit scheint bei den Verantwortlichen nur in der Frage zu herrschen, wie in Zukunft noch Geld verdient werden kann. Dieser Beitrag erklärt die prägenden Treiber der Veränderung, analysiert die Ausgangslage und nennt Herausforderungen der Branche. Darüber hinaus legt er den Fokus auf die Betrachtung der neuen digitalen Wertschöpfung. Dazu wird ein Modell eingeführt, welches von der klassischen Wertschöpfungskette über datenbasierte Geschäftsmodelle im Energiesystem bis hin zum Internet of Smart Services reicht. Mit dem Modell geben die Autoren gleichsam Einblick in das geplante Energiewendeprojekt enera.

Kontinuierliche Wanddickenbestimmung und Visualisierung des linken Herzventrikels

NASA Astrophysics Data System (ADS)

Dornheim, Lars; Hahn, Peter; Oeltze, Steffen; Preim, Bernhard; Tönnies, Klaus D.

Zur Bestimmung von Defekten in der Herztätigkeit kann die Veränderung der Wanddicke des linken Ventrikels in zeitlichen MRTAufnahmesequenzen gemessen werden. Derzeit werden für diese Bestimmung im allgemeinen nur die aufwändig manuell erstellte Segmentierungen der Endsystole und Enddiastole benutzt. Wir stellen ein bis auf die Startpunktinitialisierung automatisches Verfahren zur Bestimmung der Wanddicke des linken Ventrikels und ihrer Veränderung vor, das auf einer vollständigen Segmentierung der Herzwand in allen Zeitschritten durch ein dynamisches dreidimensionales Formmodell (Stabiles Feder-Masse-Modell) basiert. Dieses Modell nutzt bei der Segmentierung neben der Grauwertinformation eines Zeitschrittes auch die Segmentierungen der anderen Zeitschritte und ist so aufgebaut, dass die Wanddicken direkt gemessen und visualisiert werden können. Auf diese Weise werden die lokalen Wanddickenextrema über den gesamten Aufnahmezeitraum detektiert, auch wenn sie nicht in die Endsystole bzw. -diastole fallen. Das Verfahren wurde auf sechs 4D-Kardio-MRT-Datensätzen evaluiert und stellte sich als sehr robust bzgl. der einzig nötigen Interaktion heraus.

A Genetic Selection for dinB Mutants Reveals an Interaction between DNA Polymerase IV and the Replicative Polymerase That Is Required for Translesion Synthesis.

PubMed

Scotland, Michelle K; Heltzel, Justin M H; Kath, James E; Choi, Jung-Suk; Berdis, Anthony J; Loparo, Joseph J; Sutton, Mark D

2015-09-01

Translesion DNA synthesis (TLS) by specialized DNA polymerases (Pols) is a conserved mechanism for tolerating replication blocking DNA lesions. The actions of TLS Pols are managed in part by ring-shaped sliding clamp proteins. In addition to catalyzing TLS, altered expression of TLS Pols impedes cellular growth. The goal of this study was to define the relationship between the physiological function of Escherichia coli Pol IV in TLS and its ability to impede growth when overproduced. To this end, 13 novel Pol IV mutants were identified that failed to impede growth. Subsequent analysis of these mutants suggest that overproduced levels of Pol IV inhibit E. coli growth by gaining inappropriate access to the replication fork via a Pol III-Pol IV switch that is mechanistically similar to that used under physiological conditions to coordinate Pol IV-catalyzed TLS with Pol III-catalyzed replication. Detailed analysis of one mutant, Pol IV-T120P, and two previously described Pol IV mutants impaired for interaction with either the rim (Pol IVR) or the cleft (Pol IVC) of the β sliding clamp revealed novel insights into the mechanism of the Pol III-Pol IV switch. Specifically, Pol IV-T120P retained complete catalytic activity in vitro but, like Pol IVR and Pol IVC, failed to support Pol IV TLS function in vivo. Notably, the T120P mutation abrogated a biochemical interaction of Pol IV with Pol III that was required for Pol III-Pol IV switching. Taken together, these results support a model in which Pol III-Pol IV switching involves interaction of Pol IV with Pol III, as well as the β clamp rim and cleft. Moreover, they provide strong support for the view that Pol III-Pol IV switching represents a vitally important mechanism for regulating TLS in vivo by managing access of Pol IV to the DNA.

Modelling Framework and the Quantitative Analysis of Distributed Energy Resources in Future Distribution Networks

NASA Astrophysics Data System (ADS)

Han, Xue; Sandels, Claes; Zhu, Kun; Nordström, Lars

2013-08-01

There has been a large body of statements claiming that the large-scale deployment of Distributed Energy Resources (DERs) could eventually reshape the future distribution grid operation in numerous ways. Thus, it is necessary to introduce a framework to measure to what extent the power system operation will be changed by various parameters of DERs. This article proposed a modelling framework for an overview analysis on the correlation between DERs. Furthermore, to validate the framework, the authors described the reference models of different categories of DERs with their unique characteristics, comprising distributed generation, active demand and electric vehicles. Subsequently, quantitative analysis was made on the basis of the current and envisioned DER deployment scenarios proposed for Sweden. Simulations are performed in two typical distribution network models for four seasons. The simulation results show that in general the DER deployment brings in the possibilities to reduce the power losses and voltage drops by compensating power from the local generation and optimizing the local load profiles.

Nonlinear state-space modelling of the kinematics of an oscillating circular cylinder in a fluid flow

NASA Astrophysics Data System (ADS)

Decuyper, J.; De Troyer, T.; Runacres, M. C.; Tiels, K.; Schoukens, J.

2018-01-01

The flow-induced vibration of bluff bodies is an important problem of many marine, civil, or mechanical engineers. In the design phase of such structures, it is vital to obtain good predictions of the fluid forces acting on the structure. Current methods rely on computational fluid dynamic simulations (CFD), with a too high computational cost to be effectively used in the design phase or for control applications. Alternative methods use heuristic mathematical models of the fluid forces, but these lack the accuracy (they often assume the system to be linear) or flexibility to be useful over a wide operating range. In this work we show that it is possible to build an accurate, flexible and low-computational-cost mathematical model using nonlinear system identification techniques. This model is data driven: it is trained over a user-defined region of interest using data obtained from experiments or simulations, or both. Here we use a Van der Pol oscillator as well as CFD simulations of an oscillating circular cylinder to generate the training data. Then a discrete-time polynomial nonlinear state-space model is fit to the data. This model relates the oscillation of the cylinder to the force that the fluid exerts on the cylinder. The model is finally validated over a wide range of oscillation frequencies and amplitudes, both inside and outside the so-called lock-in region. We show that forces simulated by the model are in good agreement with the data obtained from CFD.

Application of the Multi-Doorway Continuum Shell Model to the Magnetic Dipole Strength Distribution in 58Ni

NASA Astrophysics Data System (ADS)

Spangenberger, H.; Beck, F.; Richter, A.

The usual continuum shell model is extended so as to include a statistical treatment of multi-doorway processes. The total configuration space of the nuclear reaction problem is subdivided into the primary doorway states which are coupled by the initial excitation to the nuclear ground state and the secondary doorway states which represent the complicated nature of multi-step reactions. The latter are evaluated within the exciton model which gives the coupling widths between the various finestructure subspaces. This coupling is determined by a statistical factor related to the exciton model and a dynamical factor given by the interaction matrix elements of the interacting excitons. The whole structure defines the multi-doorway continuum shell model. In this work it is applied to the highly fragmented magnetic dipole strength in 58Ni observed in high resolution electron scattering.Translated AbstractAnwendung des Multi-Doorway-Kontinuum-Schalenmodells auf die Verteilung der magnetischen Dipolstärke von 58NiDas Kontinuum-Schalenmodell wurde so erweitert, daß auch statistische Multi-Doorway-Prozesse berücksichtigt werden können. Hierzu wird der Konfigurationsraum unterteilt in den Raum der primären Doorway-Zustände, die direkt aus dem Grundzustand angeregt werden, und den der sekundären Doorway-Zustände, die die komplizierte Struktur der Multi-Step-Reaktionen repräsentieren. Während die primären Doorway-Zustände inclusive ihrer Anregungen mittels üblicher Schalenmodellmethoden beschrieben werden können, werden die sekundären Doorway-Zustände sowie ihre verschiedenen Kopplungen im Rahmen des Exciton-Modells behandelt. Diese Kopplungen sind durch einen aus dem Exciton-Modell resultierenden Faktor sowie durch einen dynamischen Faktor bestimmt, der sich aus dem Matrixelement der wechselwirkenden Excitonen berechnet. Die Struktur der Kopplungen definiert das Multi-Doorway-Kontinuum-Schalenmodell, das hier auf die Beschreibung der stark fragmentierten magnetischen Dipolstärke in 58Ni angewendet wird.

Replicative DNA polymerase mutations in cancer☆

PubMed Central

Heitzer, Ellen; Tomlinson, Ian

2014-01-01

Three DNA polymerases — Pol α, Pol δ and Pol ɛ — are essential for DNA replication. After initiation of DNA synthesis by Pol α, Pol δ or Pol ɛ take over on the lagging and leading strand respectively. Pol δ and Pol ɛ perform the bulk of replication with very high fidelity, which is ensured by Watson–Crick base pairing and 3′exonuclease (proofreading) activity. Yeast models have shown that mutations in the exonuclease domain of Pol δ and Pol ɛ homologues can cause a mutator phenotype. Recently, we identified germline exonuclease domain mutations (EDMs) in human POLD1 and POLE that predispose to ‘polymerase proofreading associated polyposis’ (PPAP), a disease characterised by multiple colorectal adenomas and carcinoma, with high penetrance and dominant inheritance. Moreover, somatic EDMs in POLE have also been found in sporadic colorectal and endometrial cancers. Tumors with EDMs are microsatellite stable and show an ‘ultramutator’ phenotype, with a dramatic increase in base substitutions. PMID:24583393

DNA stabilization at the Bacillus subtilis PolX core—a binding model to coordinate polymerase, AP-endonuclease and 3′-5′ exonuclease activities

PubMed Central

Baños, Benito; Villar, Laurentino; Salas, Margarita; de Vega, Miguel

2012-01-01

Family X DNA polymerases (PolXs) are involved in DNA repair. Their binding to gapped DNAs relies on two conserved helix-hairpin-helix motifs, one located at the 8-kDa domain and the other at the fingers subdomain. Bacterial/archaeal PolXs have a specifically conserved third helix-hairpin-helix motif (GFGxK) at the fingers subdomain whose putative role in DNA binding had not been established. Here, mutagenesis at the corresponding residues of Bacillus subtilis PolX (PolXBs), Gly130, Gly132 and Lys134 produced enzymes with altered DNA binding properties affecting the three enzymatic activities of the protein: polymerization, located at the PolX core, 3′-5′ exonucleolysis and apurinic/apyrimidinic (AP)-endonucleolysis, placed at the so-called polymerase and histidinol phosphatase domain. Furthermore, we have changed Lys192 of PolXBs, a residue moderately conserved in the palm subdomain of bacterial PolXs and immediately preceding two catalytic aspartates of the polymerization reaction. The results point to a function of residue Lys192 in guaranteeing the right orientation of the DNA substrates at the polymerization and histidinol phosphatase active sites. The results presented here and the recently solved structures of other bacterial PolX ternary complexes lead us to propose a structural model to account for the appropriate coordination of the different catalytic activities of bacterial PolXs. PMID:22844091

Three-dimensional vortex-induced vibrations of supported pipes conveying fluid based on wake oscillator models

NASA Astrophysics Data System (ADS)

Wang, L.; Jiang, T. L.; Dai, H. L.; Ni, Q.

2018-05-01

The present study develops a new three-dimensional nonlinear model for investigating vortex-induced vibrations (VIV) of flexible pipes conveying internal fluid flow. The unsteady hydrodynamic forces associated with the wake dynamics are modeled by two distributed van der Pol wake oscillators. In particular, the nonlinear partial differential equations of motion of the pipe and the wake are derived, taking into account the coupling between the structure and the fluid. The nonlinear equations of motion for the coupled system are then discretized by means of the Galerkin technique, resulting in a high-dimensional reduced-order model of the system. It is shown that the natural frequencies for in-plane and out-of-plane motions of the pipe may be different at high internal flow velocities beyond the threshold of buckling instability. The orientation angle of the postbuckling configuration is time-varying due to the disturbance of hydrodynamic forces, thus yielding sometimes unexpected results. For a buckled pipe with relatively low cross-flow velocity, interestingly, examining the nonlinear dynamics of the pipe indicates that the combined effects of the cross-flow-induced resonance of the in-plane first mode and the internal-flow-induced buckling on the IL and CF oscillation amplitudes may be significant. For higher cross-flow velocities, however, the effect of internal fluid flow on the nonlinear VIV responses of the pipe is not pronounced.

Optimal design of tweezer control for chimera states

NASA Astrophysics Data System (ADS)

Omelchenko, Iryna; Omel'chenko, Oleh E.; Zakharova, Anna; Schöll, Eckehard

2018-01-01

Chimera states are complex spatio-temporal patterns which consist of coexisting domains of spatially coherent and incoherent dynamics in systems of coupled oscillators. In small networks, chimera states usually exhibit short lifetimes and erratic drifting of the spatial position of the incoherent domain. A tweezer feedback control scheme can stabilize and fix the position of chimera states. We analyze the action of the tweezer control in small nonlocally coupled networks of Van der Pol and FitzHugh-Nagumo oscillators, and determine the ranges of optimal control parameters. We demonstrate that the tweezer control scheme allows for stabilization of chimera states with different shapes, and can be used as an instrument for controlling the coherent domains size, as well as the maximum average frequency difference of the oscillators.

Perception for Outdoor Navigation

DTIC Science & Technology

1991-12-01

are theories of human cognitive activity during driving. Van der Molen and Botticher recently reviewed several of these models [40]. The models...represent driving knowledge, how to perceive traffic situations, or how to process information to obtain actions. Van der Molen and Botticher attempted to...Conference on Robotics and Automation. IEEE, 1987. [40] van der Molen , H.H., and Botticher, A.M.T. Risk Models for Traffic Participants: A Concerted

Transient expression and activity of human DNA polymerase iota in loach embryos.

PubMed

Makarova, Irina V; Kazakov, Andrey A; Makarova, Alena V; Khaidarova, Nella V; Kozikova, Larisa V; Nenasheva, Valentina V; Gening, Leonid V; Tarantul, Vyacheslav Z; Andreeva, Ludmila E

2012-02-01

Human DNA polymerase iota (Pol ι) is a Y-family DNA polymerase with unusual biochemical properties and not fully understood functions. Pol ι preferentially incorporates dGTP opposite template thymine. This property can be used to monitor Pol ι activity in the presence of other DNA polymerases, e.g. in cell extracts of tissues and tumors. We have now confirmed the specificity and sensitivity of the method of Pol ι activity detection in cell extracts using an animal model of loach Misgurnus fossilis embryos transiently expressing human Pol ι. The overexpression of Pol ι was shown to be accompanied by an increase in abnormalities in development and the frequency of pycnotic nuclei in fish embryos. Further analysis of fish embryos with constitutive or regulated Pol ι expression may provide insights into Pol ι functions in vertebrate animals.

Engineering Inertial and Primary-Frequency Response for Distributed Energy Resources: Preprint

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

Dall-Anese, Emiliano; Zhao, Changhong; Guggilam, Swaroop

We propose a framework to engineer synthetic-inertia and droop-control parameters for distributed energy resources (DERs) so that the system frequency in a network composed of DERs and synchronous generators conforms to prescribed transient and steady-state performance specifications. Our approach is grounded in a second-order lumped-parameter model that captures the dynamics of synchronous generators and frequency-responsive DERs endowed with inertial and droop control. A key feature of this reduced-order model is that its parameters can be related to those of the originating higher-order dynamical model. This allows one to systematically design the DER inertial and droop-control coefficients leveraging classical frequency-domain responsemore » characteristics of second-order systems. Time-domain simulations validate the accuracy of the model-reduction method and demonstrate how DER controllers can be designed to meet steady-state-regulation and transient-performance specifications.« less

Engineering Inertial and Primary-Frequency Response for Distributed Energy Resources

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

Dall-Anese, Emiliano; Zhao, Changhong; Guggilam, Swaroop

We propose a framework to engineer synthetic-inertia and droop-control parameters for distributed energy resources (DERs) so that the system frequency in a network composed of DERs and synchronous generators conforms to prescribed transient and steady-state performance specifications. Our approach is grounded in a second-order lumped-parameter model that captures the dynamics of synchronous generators and frequency-responsive DERs endowed with inertial and droop control. A key feature of this reduced-order model is that its parameters can be related to those of the originating higherorder dynamical model. This allows one to systematically design the DER inertial and droop-control coefficients leveraging classical frequency-domain responsemore » characteristics of second-order systems. Time-domain simulations validate the accuracy of the model-reduction method and demonstrate how DER controllers can be designed to meet steady-state-regulation and transient-performance specifications.« less

A generalized linear factor model approach to the hierarchical framework for responses and response times.

PubMed

Molenaar, Dylan; Tuerlinckx, Francis; van der Maas, Han L J

2015-05-01

We show how the hierarchical model for responses and response times as developed by van der Linden (2007), Fox, Klein Entink, and van der Linden (2007), Klein Entink, Fox, and van der Linden (2009), and Glas and van der Linden (2010) can be simplified to a generalized linear factor model with only the mild restriction that there is no hierarchical model at the item side. This result is valuable as it enables all well-developed modelling tools and extensions that come with these methods. We show that the restriction we impose on the hierarchical model does not influence parameter recovery under realistic circumstances. In addition, we present two illustrative real data analyses to demonstrate the practical benefits of our approach. © 2014 The British Psychological Society.

Understanding the role of DNA polymerase λ gene in different growth and developmental stages of Oryza sativa L. indica rice cultivars.

PubMed

Sihi, Sayantani; Maiti, Soumitra; Bakshi, Sankar; Nayak, Arup; Chaudhuri, Shubho; Sengupta, Dibyendu Narayan

2017-11-01

DNA polymerase λ (Pol λ) is the only member of DNA polymerase family X present in plants. The enzyme is ddNTP sensitive as it contains the conserved C-terminal Pol β domain. The 1.1 kb partial coding sequence isolated spanned the whole 3' regions of the gene containing functionally important domains of the Pol λ gene. Comparative in silico studies from both indica and japonica cultivars involving homology modelling showed that the model for the partial Pol λ gene was stable and acceptable. The alignment of both the protein models showed a RMS value of 0.783. Apart from this, expression of Pol λ and its relative activity is studied during different development stages of three different indica rice cultivars (IR29, Nonabokra and N22). Enhanced accumulation and higher activity of Pol λ during the early seedling stage was detected. Higher expression and activity were observed in the anthers, which was probably necessary for DNA repair during microspore formation. However, during the maturation stage of seed development and plant growth, expression and the activity of Pol λ decreased due to slow metabolic activity and a reduced rate of cell division respectively. Furthermore, the expression and activity of Pol λ were found to be higher in IR29 in comparison to Nonabokra and N22. IR29 is a rice cultivar susceptible to environmental stresses and hence it encounters higher DNA damages. The enhanced presence and activity of the Pol λ enzyme in IR29 with respect to the other two cultivars, which are more tolerant to the environmental stresses during various developmental stages, is therefore explainable. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Advanced Communication and Control Solutions of Distributed Energy Resources (DER)

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

Asgeirsson, Haukur; Seguin, Richard; Sherding, Cameron

2007-01-10

This report covers work performed in Phase II of a two phase project whose objective was to demonstrate the aggregation of multiple Distributed Energy Resources (DERs) and to offer them into the energy market. The Phase I work (DE-FC36-03CH11161) created an integrated, but distributed, system and procedures to monitor and control multiple DERs from numerous manufacturers connected to the electric distribution system. Procedures were created which protect the distribution network and personnel that may be working on the network. Using the web as the communication medium for control and monitoring of the DERs, the integration of information and security wasmore » accomplished through the use of industry standard protocols such as secure SSL,VPN and ICCP. The primary objective of Phase II was to develop the procedures for marketing the power of the Phase I aggregated DERs in the energy market, increase the number of DER units, and implement the marketing procedures (interface with ISOs) for the DER generated power. The team partnered with the Midwest Independent System Operator (MISO), the local ISO, to address the energy market and demonstrate the economic dispatch of DERs in response to market signals. The selection of standards-based communication technologies offers the ability of the system to be deployed and integrated with other utilities’ resources. With the use of a data historian technology to facilitate the aggregation, the developed algorithms and procedures can be verified, audited, and modified. The team has demonstrated monitoring and control of multiple DERs as outlined in phase I report including procedures to perform these operations in a secure and safe manner. In Phase II, additional DER units were added. We also expanded on our phase I work to enhance communication security and to develop the market model of having DERs, both customer and utility owned, participate in the energy market. We are proposing a two-part DER energy market model--a utility need business model and an independent energy aggregator-business model. The approach of developing two group models of DER energy participation in the market is unique. The Detroit Edison (DECo, Utility)-led team includes: DTE Energy Technologies (Dtech, DER provider), Electrical Distribution Design (EDD, Virginia Tech company supporting EPRI’s Distribution Engineering Workstation, DEW), Systems Integration Specialists Company (SISCO, economic scheduling and real-time protocol integrator), and OSIsoft (PI software system for managing real-time information). This team is focused on developing the application engineering, including software systems necessary for DER’s integration, control and sale into the market place. Phase II Highlights Installed and tested an ICCP link with SSL (security) between DECo, the utility, and DTE Energy Technologies (DTECH), the aggregator, making DER data available to the utility for both monitoring and control. Installed and tested PI process book with circuit & DER operational models for DECo SOC/ROC operator’s use for monitoring of both utility circuit and customer DER parameters. The PI Process Book models also included DER control for the DECo SOC/ROC operators, which was tested and demonstrated control. The DER Tagging and Operating Procedures were developed, which allowed that control to be done in a safe manner, were modified for required MOC/MISO notification procedures. The Distribution Engineering Workstation (DEW) was modified to include temperature normalized load research statistics, using a 30 hour day-ahead weather feed. This allowed day-ahead forecasting of the customer load profile and the entire circuit to determine overload and low voltage problems. This forecast at the point of common coupling was passed to DTech DR SOC for use in their economic dispatch algorithm. Standard Work Instructions were developed for DER notification, sale, and operation into the MISO market. A software mechanism consisting of a suite of new and revised functionality was developed that integrated with the local ISO such that offers can be made electronically without human intervention. A suite of software was developed by DR SOC enabling DER usage in real time and day-ahead: Generation information file exchange with PI and the utility power flow A utility day-ahead information file Energy Offer Web Service Market Result Web Service Real-Time Meter Data Web Service Real-Time Notification Web Service Registered over 20 DER with MISO in Demand Response Market and demonstrated electronic sale to MISO.« less

The use of modified and non-natural nucleotides provide unique insights into pro-mutagenic replication catalyzed by polymerase eta

PubMed Central

Choi, Jung-Suk; Dasari, Anvesh; Hu, Peter; Benkovic, Stephen J.; Berdis, Anthony J.

2016-01-01

This report evaluates the pro-mutagenic behavior of 8-oxo-guanine (8-oxo-G) by quantifying the ability of high-fidelity and specialized DNA polymerases to incorporate natural and modified nucleotides opposite this lesion. Although high-fidelity DNA polymerases such as pol δ and the bacteriophage T4 DNA polymerase replicating 8-oxo-G in an error-prone manner, they display remarkably low efficiencies for TLS compared to normal DNA synthesis. In contrast, pol η shows a combination of high efficiency and low fidelity when replicating 8-oxo-G. These combined properties are consistent with a pro-mutagenic role for pol η when replicating this DNA lesion. Studies using modified nucleotide analogs show that pol η relies heavily on hydrogen-bonding interactions during translesion DNA synthesis. However, nucleobase modifications such as alkylation to the N2 position of guanine significantly increase error-prone synthesis catalyzed by pol η when replicating 8-oxo-G. Molecular modeling studies demonstrate the existence of a hydrophobic pocket in pol η that participates in the increased utilization of certain hydrophobic nucleotides. A model is proposed for enhanced pro-mutagenic replication catalyzed by pol η that couples efficient incorporation of damaged nucleotides opposite oxidized DNA lesions created by reactive oxygen species. The biological implications of this model toward increasing mutagenic events in lung cancer are discussed. PMID:26717984

Live-cell analysis of endogenous GFP-RPB1 uncovers rapid turnover of initiating and promoter-paused RNA Polymerase II.

PubMed

Steurer, Barbara; Janssens, Roel C; Geverts, Bart; Geijer, Marit E; Wienholz, Franziska; Theil, Arjan F; Chang, Jiang; Dealy, Shannon; Pothof, Joris; van Cappellen, Wiggert A; Houtsmuller, Adriaan B; Marteijn, Jurgen A

2018-05-08

Initiation and promoter-proximal pausing are key regulatory steps of RNA Polymerase II (Pol II) transcription. To study the in vivo dynamics of endogenous Pol II during these steps, we generated fully functional GFP-RPB1 knockin cells. GFP-RPB1 photobleaching combined with computational modeling revealed four kinetically distinct Pol II fractions and showed that on average 7% of Pol II are freely diffusing, while 10% are chromatin-bound for 2.4 seconds during initiation, and 23% are promoter-paused for only 42 seconds. This unexpectedly high turnover of Pol II at promoters is most likely caused by premature termination of initiating and promoter-paused Pol II and is in sharp contrast to the 23 minutes that elongating Pol II resides on chromatin. Our live-cell-imaging approach provides insights into Pol II dynamics and suggests that the continuous release and reinitiation of promoter-bound Pol II is an important component of transcriptional regulation. Copyright © 2018 the Author(s). Published by PNAS.

Distributed Energy Resources Customer Adoption Model - Graphical User Interface, Version 2.1.8

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

Ewald, Friedrich; Stadler, Michael; Cardoso, Goncalo F

The DER-CAM Graphical User Interface has been redesigned to consist of a dynamic tree structure on the left side of the application window to allow users to quickly navigate between different data categories and views. Views can either be tables with model parameters and input data, the optimization results, or a graphical interface to draw circuit topology and visualize investment results. The model parameters and input data consist of tables where values are assigned to specific keys. The aggregation of all model parameters and input data amounts to the data required to build a DER-CAM model, and is passed tomore » the GAMS solver when users initiate the DER-CAM optimization process. Passing data to the GAMS solver relies on the use of a Java server that handles DER-CAM requests, queuing, and results delivery. This component of the DER-CAM GUI can be deployed either locally or remotely, and constitutes an intermediate step between the user data input and manipulation, and the execution of a DER-CAM optimization in the GAMS engine. The results view shows the results of the DER-CAM optimization and distinguishes between a single and a multi-objective process. The single optimization runs the DER-CAM optimization once and presents the results as a combination of summary charts and hourly dispatch profiles. The multi-objective optimization process consists of a sequence of runs initiated by the GUI, including: 1) CO2 minimization, 2) cost minimization, 3) a user defined number of points in-between objectives 1) and 2). The multi-objective results view includes both access to the detailed results of each point generated by the process as well as the generation of a Pareto Frontier graph to illustrate the trade-off between objectives. DER-CAM GUI 2.1.8 also introduces the ability to graphically generate circuit topologies, enabling support to DER-CAM 5.0.0. This feature consists of: 1) The drawing area, where users can manually create nodes and define their properties (e.g. point of common coupling, slack bus, load) and connect them through edges representing either power lines, transformers, or heat pipes, all with user defined characteristics (e.g., length, ampacity, inductance, or heat loss); 2) The tables, which display the user-defined topology in the final numerical form that will be passed to the DER-CAM optimization. Finally, the DER-CAM GUI is also deployed with a database schema that allows users to provide different energy load profiles, solar irradiance profiles, and tariff data, that can be stored locally and later used in any DER-CAM model. However, no real data will be delivered with this version.« less

CMG helicase and DNA polymerase ε form a functional 15-subunit holoenzyme for eukaryotic leading-strand DNA replication.

PubMed

Langston, Lance D; Zhang, Dan; Yurieva, Olga; Georgescu, Roxana E; Finkelstein, Jeff; Yao, Nina Y; Indiani, Chiara; O'Donnell, Mike E

2014-10-28

DNA replication in eukaryotes is asymmetric, with separate DNA polymerases (Pol) dedicated to bulk synthesis of the leading and lagging strands. Pol α/primase initiates primers on both strands that are extended by Pol ε on the leading strand and by Pol δ on the lagging strand. The CMG (Cdc45-MCM-GINS) helicase surrounds the leading strand and is proposed to recruit Pol ε for leading-strand synthesis, but to date a direct interaction between CMG and Pol ε has not been demonstrated. While purifying CMG helicase overexpressed in yeast, we detected a functional complex between CMG and native Pol ε. Using pure CMG and Pol ε, we reconstituted a stable 15-subunit CMG-Pol ε complex and showed that it is a functional polymerase-helicase on a model replication fork in vitro. On its own, the Pol2 catalytic subunit of Pol ε is inefficient in CMG-dependent replication, but addition of the Dpb2 protein subunit of Pol ε, known to bind the Psf1 protein subunit of CMG, allows stable synthesis with CMG. Dpb2 does not affect Pol δ function with CMG, and thus we propose that the connection between Dpb2 and CMG helps to stabilize Pol ε on the leading strand as part of a 15-subunit leading-strand holoenzyme we refer to as CMGE. Direct binding between Pol ε and CMG provides an explanation for specific targeting of Pol ε to the leading strand and provides clear mechanistic evidence for how strand asymmetry is maintained in eukaryotes.

CMG helicase and DNA polymerase ε form a functional 15-subunit holoenzyme for eukaryotic leading-strand DNA replication

PubMed Central

Langston, Lance D.; Zhang, Dan; Yurieva, Olga; Georgescu, Roxana E.; Finkelstein, Jeff; Yao, Nina Y.; Indiani, Chiara; O’Donnell, Mike E.

2014-01-01

DNA replication in eukaryotes is asymmetric, with separate DNA polymerases (Pol) dedicated to bulk synthesis of the leading and lagging strands. Pol α/primase initiates primers on both strands that are extended by Pol ε on the leading strand and by Pol δ on the lagging strand. The CMG (Cdc45-MCM-GINS) helicase surrounds the leading strand and is proposed to recruit Pol ε for leading-strand synthesis, but to date a direct interaction between CMG and Pol ε has not been demonstrated. While purifying CMG helicase overexpressed in yeast, we detected a functional complex between CMG and native Pol ε. Using pure CMG and Pol ε, we reconstituted a stable 15-subunit CMG–Pol ε complex and showed that it is a functional polymerase–helicase on a model replication fork in vitro. On its own, the Pol2 catalytic subunit of Pol ε is inefficient in CMG-dependent replication, but addition of the Dpb2 protein subunit of Pol ε, known to bind the Psf1 protein subunit of CMG, allows stable synthesis with CMG. Dpb2 does not affect Pol δ function with CMG, and thus we propose that the connection between Dpb2 and CMG helps to stabilize Pol ε on the leading strand as part of a 15-subunit leading-strand holoenzyme we refer to as CMGE. Direct binding between Pol ε and CMG provides an explanation for specific targeting of Pol ε to the leading strand and provides clear mechanistic evidence for how strand asymmetry is maintained in eukaryotes. PMID:25313033

Using non-linear analogue of Nyquist diagrams for analysis of the equation describing the hemodynamics in blood vessels near pathologies

NASA Astrophysics Data System (ADS)

Cherevko, A. A.; Bord, E. E.; Khe, A. K.; Panarin, V. A.; Orlov, K. J.; Chupakhin, A. P.

2016-06-01

This article considers method of describing the behaviour of hemodynamic parameters near vascular pathologies. We study the influence of arterial aneurysms and arteriovenous malformations on the vascular system. The proposed method involves using generalized model of Van der Pol-Duffing to find out the characteristic behaviour of blood flow parameters. These parameters are blood velocity and pressure in the vessel. The velocity and pressure are obtained during the neurosurgery measurements. It is noted that substituting velocity on the right side of the equation gives good pressure approximation. Thus, the model reproduces clinical data well enough. In regard to the right side of the equation, it means external impact on the system. The harmonic functions with various frequencies and amplitudes are substituted on the right side of the equation to investigate its properties. Besides, variation of the right side parameters provides additional information about pressure. Non-linear analogue of Nyquist diagrams is used to find out how the properties of solution depend on the parameter values. We have analysed 60 cases with aneurysms and 14 cases with arteriovenous malformations. It is shown that the diagrams are divided into classes. Also, the classes are replaced by another one in the definite order with increasing of the right side amplitude.

Maximum Likelihood Shift Estimation Using High Resolution Polarimetric SAR Clutter Model

NASA Astrophysics Data System (ADS)

Harant, Olivier; Bombrun, Lionel; Vasile, Gabriel; Ferro-Famil, Laurent; Gay, Michel

2011-03-01

This paper deals with a Maximum Likelihood (ML) shift estimation method in the context of High Resolution (HR) Polarimetric SAR (PolSAR) clutter. Texture modeling is exposed and the generalized ML texture tracking method is extended to the merging of various sensors. Some results on displacement estimation on the Argentiere glacier in the Mont Blanc massif using dual-pol TerraSAR-X (TSX) and quad-pol RADARSAT-2 (RS2) sensors are finally discussed.

Large-scale hydrological modelling in the semi-arid north-east of Brazil

NASA Astrophysics Data System (ADS)

Güntner, Andreas

2002-07-01

Semi-arid areas are, due to their climatic setting, characterized by small water resources. An increasing water demand as a consequence of population growth and economic development as well as a decreasing water availability in the course of possible climate change may aggravate water scarcity in future, which often exists already for present-day conditions in these areas. Understanding the mechanisms and feedbacks of complex natural and human systems, together with the quantitative assessment of future changes in volume, timing and quality of water resources are a prerequisite for the development of sustainable measures of water management to enhance the adaptive capacity of these regions. For this task, dynamic integrated models, containing a hydrological model as one component, are indispensable tools. The main objective of this study is to develop a hydrological model for the quantification of water availability in view of environmental change over a large geographic domain of semi-arid environments. The study area is the Federal State of Ceará (150 000 km2) in the semi-arid north-east of Brazil. Mean annual precipitation in this area is 850 mm, falling in a rainy season with duration of about five months. Being mainly characterized by crystalline bedrock and shallow soils, surface water provides the largest part of the water supply. The area has recurrently been affected by droughts which caused serious economic losses and social impacts like migration from the rural regions. The hydrological model Wasa (Model of Water Availability in Semi-Arid Environments) developed in this study is a deterministic, spatially distributed model being composed of conceptual, process-based approaches. Water availability (river discharge, storage volumes in reservoirs, soil moisture) is determined with daily resolution. Sub-basins, grid cells or administrative units (municipalities) can be chosen as spatial target units. The administrative units enable the coupling of Wasa in the framework of an integrated model which contains modules that do not work on the basis of natural spatial units. The target units mentioned above are disaggregated in Wasa into smaller modelling units within a new multi-scale, hierarchical approach. The landscape units defined in this scheme capture in particular the effect of structured variability of terrain, soil and vegetation characteristics along toposequences on soil moisture and runoff generation. Lateral hydrological processes at the hillslope scale, as reinfiltration of surface runoff, being of particular importance in semi-arid environments, can thus be represented also within the large-scale model in a simplified form. Depending on the resolution of available data, small-scale variability is not represented explicitly with geographic reference in Wasa, but by the distribution of sub-scale units and by statistical transition frequencies for lateral fluxes between these units. Further model components of Wasa which respect specific features of semi-arid hydrology are: (1) A two-layer model for evapotranspiration comprises energy transfer at the soil surface (including soil evaporation), which is of importance in view of the mainly sparse vegetation cover. Additionally, vegetation parameters are differentiated in space and time in dependence on the occurrence of the rainy season. (2) The infiltration module represents in particular infiltration-excess surface runoff as the dominant runoff component. (3) For the aggregate description of the water balance of reservoirs that cannot be represented explicitly in the model, a storage approach respecting different reservoirs size classes and their interaction via the river network is applied. (4) A model for the quantification of water withdrawal by water use in different sectors is coupled to Wasa. (5) A cascade model for the temporal disaggregation of precipitation time series, adapted to the specific characteristics of tropical convective rainfall, is applied for the generating rainfall time series of higher temporal resolution. All model parameters of Wasa can be derived from physiographic information of the study area. Thus, model calibration is primarily not required. Model applications of Wasa for historical time series generally results in a good model performance when comparing the simulation results of river discharge and reservoir storage volumes with observed data for river basins of various sizes. The mean water balance as well as the high interannual and intra-annual variability is reasonably represented by the model. Limitations of the modelling concept are most markedly seen for sub-basins with a runoff component from deep groundwater bodies of which the dynamics cannot be satisfactorily represented without calibration. Further results of model applications are: (1) Lateral processes of redistribution of runoff and soil moisture at the hillslope scale, in particular reinfiltration of surface runoff, lead to markedly smaller discharge volumes at the basin scale than the simple sum of runoff of the individual sub-areas. Thus, these processes are to be captured also in large-scale models. The different relevance of these processes for different conditions is demonstrated by a larger percentage decrease of discharge volumes in dry as compared to wet years. (2) Precipitation characteristics have a major impact on the hydrological response of semi-arid environments. In particular, underestimated rainfall intensities in the rainfall input due to the rough temporal resolution of the model and due to interpolation effects and, consequently, underestimated runoff volumes have to be compensated in the model. A scaling factor in the infiltration module or the use of disaggregated hourly rainfall data show good results in this respect. The simulation results of Wasa are characterized by large uncertainties. These are, on the one hand, due to uncertainties of the model structure to adequately represent the relevant hydrological processes. On the other hand, they are due to uncertainties of input data and parameters particularly in view of the low data availability. Of major importance is: (1) The uncertainty of rainfall data with regard to their spatial and temporal pattern has, due to the strong non-linear hydrological response, a large impact on the simulation results. (2) The uncertainty of soil parameters is in general of larger importance on model uncertainty than uncertainty of vegetation or topographic parameters. (3) The effect of uncertainty of individual model components or parameters is usually different for years with rainfall volumes being above or below the average, because individual hydrological processes are of different relevance in both cases. Thus, the uncertainty of individual model components or parameters is of different importance for the uncertainty of scenario simulations with increasing or decreasing precipitation trends. (4) The most important factor of uncertainty for scenarios of water availability in the study area is the uncertainty in the results of global climate models on which the regional climate scenarios are based. Both a marked increase or a decrease in precipitation can be assumed for the given data. Results of model simulations for climate scenarios until the year 2050 show that a possible future change in precipitation volumes causes a larger percentage change in runoff volumes by a factor of two to three. In the case of a decreasing precipitation trend, the efficiency of new reservoirs for securing water availability tends to decrease in the study area because of the interaction of the large number of reservoirs in retaining the overall decreasing runoff volumes. Semiaride Gebiete sind auf Grund der klimatischen Bedingungen durch geringe Wasserressourcen gekennzeichnet. Ein zukünftig steigender Wasserbedarf in Folge von Bevölkerungswachstum und ökonomischer Entwicklung sowie eine geringere Wasserverfügbarkeit durch mögliche Klimaänderungen können dort zu einer Verschärfung der vielfach schon heute auftretenden Wasserknappheit führen. Das Verständnis der Mechanismen und Wechselwirkungen des komplexen Systems von Mensch und Umwelt sowie die quantitative Bestimmung zukünftiger Veränderungen in der Menge, der zeitlichen Verteilung und der Qualität von Wasserressourcen sind eine grundlegende Voraussetzung für die Entwicklung von nachhaltigen Maßnahmen des Wassermanagements mit dem Ziel einer höheren Anpassungsfähigkeit dieser Regionen gegenüber künftigen Änderungen. Hierzu sind dynamische integrierte Modelle unerlässlich, die als eine Komponente ein hydrologisches Modell beinhalten. Vorrangiges Ziel dieser Arbeit ist daher die Erstellung eines hydrologischen Modells zur großräumigen Bestimmung der Wasserverfügbarkeit unter sich ändernden Umweltbedingungen in semiariden Gebieten. Als Untersuchungsraum dient der im semiariden tropischen Nordosten Brasiliens gelegene Bundestaat Ceará (150 000 km2). Die mittleren Jahresniederschläge in diesem Gebiet liegen bei 850 mm innerhalb einer etwa fünfmonatigen Regenzeit. Mit vorwiegend kristallinem Grundgebirge und geringmächtigen Böden stellt Oberflächenwasser den größten Teil der Wasserversorgung bereit. Die Region war wiederholt von Dürren betroffen, die zu schweren ökonomischen Schäden und sozialen Folgen wie Migration aus den ländlichen Gebieten geführt haben. Das hier entwickelte hydrologische Modell Wasa (Model of Water Availability in Semi-Arid Environments) ist ein deterministisches, flächendifferenziertes Modell, das aus konzeptionellen, prozess-basierten Ansätzen aufgebaut ist. Die Wasserverfügbarkeit (Abfluss im Gewässernetz, Speicherung in Stauseen, Bodenfeuchte) wird mit täglicher Auflösung bestimmt. Als räumliche Zieleinheiten können Teileinzugsgebiete, Rasterzellen oder administrative Einheiten (Gemeinden) gewählt werden. Letztere ermöglichen die Kopplung des Modells im Rahmen der integrierten Modellierung mit Modulen, die nicht auf der Basis natürlicher Raumeinheiten arbeiten. Im Rahmen eines neuen skalenübergreifenden, hierarchischen Ansatzes werden in Wasa die genannten Zieleinheiten in kleinere räumliche Modellierungseinheiten unterteilt. Die ausgewiesenen Landschaftseinheiten erfassen insbesondere die strukturierte Variabilität von Gelände-, Boden- und Vegetationseigenschaften entlang von Toposequenzen in ihrem Einfluss auf Bodenfeuchte und Abflussbildung. Laterale hydrologische Prozesse auf kleiner Skala, wie die für semiaride Bedingungen bedeutsame Wiederversickerung von Oberflächenabfluss, können somit auch in der erforderlichen großskaligen Modellanwendung vereinfacht wiedergegeben werden. In Abhängigkeit von der Auflösung der verfügbaren Daten wird in Wasa die kleinskalige Variabilität nicht räumlich explizit sondern über die Verteilung von Flächenanteilen subskaliger Einheiten und über statistische Übergangshäufigkeiten für laterale Flüsse zwischen den Einheiten berücksichtigt. Weitere Modellkomponenten von Wasa, die spezifische Bedingungen semiarider Gebiete berücksichtigen, sind: (1) Ein Zwei-Schichten-Modell zur Bestimmung der Evapotranspiration berücksichtigt auch den Energieumsatz an der Bodenoberfläche (inklusive Bodenverdunstung), der in Anbetracht der meist lichten Vegetationsbedeckung von Bedeutung ist. Die Vegetationsparameter werden zudem flächen- und zeitdifferenziert in Abhängigkeit vom Auftreten der Regenzeit modifiziert. (2) Das Infiltrationsmodul bildet insbesondere Oberflächenabfluss durch Infiltrationsüberschuss als dominierender Abflusskomponente ab. (3) Zur aggregierten Beschreibung der Wasserbilanz von im Modell nicht einzeln erfassbaren Stauseen wird ein Speichermodell unter Berücksichtigung verschiedener Größenklassen und ihrer Interaktion über das Gewässernetz eingesetzt. (4) Ein Modell zur Bestimmung der Entnahme durch Wassernutzung in verschiedenen Sektoren ist an Wasa gekoppelt. (5) Ein Kaskadenmodell zur zeitlichen Disaggregierung von Niederschlagszeitreihen, das in dieser Arbeit speziell für tropische konvektive Niederschlagseigenschaften angepasst wird, wird zur Erzeugung höher aufgelöster Niederschlagsdaten verwendet. Alle Modellparameter von Wasa können von physiographischen Gebietsinformationen abgeleitet werden, sodass eine Modellkalibrierung primär nicht erforderlich ist. Die Modellanwendung von Wasa für historische Zeitreihen ergibt im Allgemeinen eine gute Übereinstimmung der Simulationsergebnisse für Abfluss und Stauseespeichervolumen mit Beobachtungsdaten in unterschiedlich großen Einzugsgebieten. Die mittlere Wasserbilanz sowie die hohe monatliche und jährliche Variabilität wird vom Modell angemessen wiedergegeben. Die Grenzen der Anwendbarkeit des Modell-konzepts zeigen sich am deutlichsten in Teilgebieten mit Abflusskomponenten aus tieferen Grundwasserleitern, deren Dynamik ohne Kalibrierung nicht zufriedenstellend abgebildet werden kann. Die Modellanwendungen zeigen weiterhin: (1) Laterale Prozesse der Umverteilung von Bodenfeuchte und Abfluss auf der Hangskala, vor allem die Wiederversickerung von Oberflächenabfluss, führen auf der Skala von Einzugsgebieten zu deutlich kleineren Abflussvolumen als die einfache Summe der Abflüsse der Teilflächen. Diese Prozesse sollten daher auch in großskaligen Modellen abgebildet werden. Die unterschiedliche Ausprägung dieser Prozesse für unterschiedliche Bedingungen zeigt sich an Hand einer prozentual größeren Verringerung der Abflussvolumen in trockenen im Vergleich zu feuchten Jahren. (2) Die Niederschlagseigenschaften haben einen sehr großen Einfluss auf die hydrologische Reaktion in semiariden Gebieten. Insbesondere die durch die grobe zeitliche Auflösung des Modells und durch Interpolationseffekte unterschätzten Niederschlagsintensitäten in den Eingangsdaten und die daraus folgende Unterschätzung von Abflussvolumen müssen im Modell kompensiert werden. Ein Skalierungsfaktor in der Infiltrationsroutine oder die Verwendung disaggregierter stündlicher Niederschlagsdaten zeigen hier gute Ergebnisse. Die Simulationsergebnisse mit Wasa sind insgesamt durch große Unsicherheiten gekennzeichnet. Diese sind einerseits in Unsicherheiten der Modellstruktur zur adäquaten Beschreibung der relevanten hydrologischen Prozesse begründet, andererseits in Daten- und Parametersunsicherheiten in Anbetracht der geringen Datenverfügbarkeit. Von besonderer Bedeutung ist: (1) Die Unsicherheit der Niederschlagsdaten in ihrem räumlichen Muster und ihrer zeitlichen Struktur hat wegen der stark nicht-linearen hydrologischen Reaktion einen großen Einfluss auf die Simulationsergebnisse. (2) Die Unsicherheit von Bodenparametern hat im Vergleich zu Vegetationsparametern und topographischen Parametern im Allgemeinen einen größeren Einfluss auf die Modellunsicherheit. (3) Der Effekt der Unsicherheit einzelner Modellkomponenten und -parameter ist für Jahre mit unter- oder überdurchschnittlichen Niederschlagsvolumen zumeist unterschiedlich, da einzelne hydrologische Prozesse dann jeweils unterschiedlich relevant sind. Die Unsicherheit einzelner Modellkomponenten- und parameter hat somit eine unterschiedliche Bedeutung für die Unsicherheit von Szenarienrechnungen mit steigenden oder fallenden Niederschlagstrends. (4) Der bedeutendste Unsicherheitsfaktor für Szenarien der Wasserverfügbarkeit für die Untersuchungsregion ist die Unsicherheit der den regionalen Klimaszenarien zu Grunde liegenden Ergebnisse globaler Klimamodelle. Eine deutliche Zunahme oder Abnahme der Niederschläge bis 2050 kann gemäß den hier vorliegenden Daten für das Untersuchungsgebiet gleichermaßen angenommen werden. Modellsimulationen für Klimaszenarien bis zum Jahr 2050 ergeben, dass eine mögliche zukünftige Veränderung der Niederschlagsmengen zu einer prozentual zwei- bis dreifach größeren Veränderung der Abflussvolumen führt. Im Falle eines Trends von abnehmenden Niederschlagsmengen besteht in der Untersuchungsregion die Tendenz, dass auf Grund der gegenseitigen Beeinflussung der großen Zahl von Stauseen beim Rückhalt der tendenziell abnehmenden Abflussvolumen die Effizienz von neugebauten Stauseen zur Sicherung der Wasserverfügbarkeit zunehmend geringer wird. --- Anmerkung: Der Autor ist Träger des von der Universitätsgesellschaft Potsdam e.V. vergebenen Wissenschaftspreises zur Förderung des wissenschaftlichen Nachwuchses für die beste Dissertation des Jahres 2002/2003 an der Universität Potsdam.

Mechanism of selective recruitment of RNA polymerases II and III to snRNA gene promoters.

PubMed

Dergai, Oleksandr; Cousin, Pascal; Gouge, Jerome; Satia, Karishma; Praz, Viviane; Kuhlman, Tracy; Lhôte, Philippe; Vannini, Alessandro; Hernandez, Nouria

2018-05-01

RNA polymerase II (Pol II) small nuclear RNA (snRNA) promoters and type 3 Pol III promoters have highly similar structures; both contain an interchangeable enhancer and "proximal sequence element" (PSE), which recruits the SNAP complex (SNAPc). The main distinguishing feature is the presence, in the type 3 promoters only, of a TATA box, which determines Pol III specificity. To understand the mechanism by which the absence or presence of a TATA box results in specific Pol recruitment, we examined how SNAPc and general transcription factors required for Pol II or Pol III transcription of SNAPc-dependent genes (i.e., TATA-box-binding protein [TBP], TFIIB, and TFIIA for Pol II transcription and TBP and BRF2 for Pol III transcription) assemble to ensure specific Pol recruitment. TFIIB and BRF2 could each, in a mutually exclusive fashion, be recruited to SNAPc. In contrast, TBP-TFIIB and TBP-BRF2 complexes were not recruited unless a TATA box was present, which allowed selective and efficient recruitment of the TBP-BRF2 complex. Thus, TBP both prevented BRF2 recruitment to Pol II promoters and enhanced BRF2 recruitment to Pol III promoters. On Pol II promoters, TBP recruitment was separate from TFIIB recruitment and enhanced by TFIIA. Our results provide a model for specific Pol recruitment at SNAPc-dependent promoters. © 2018 Dergai et al.; Published by Cold Spring Harbor Laboratory Press.

Polarimetric SAR Interferometry based modeling for tree height and aboveground biomass retrieval in a tropical deciduous forest

NASA Astrophysics Data System (ADS)

Kumar, Shashi; Khati, Unmesh G.; Chandola, Shreya; Agrawal, Shefali; Kushwaha, Satya P. S.

2017-08-01

The regulation of the carbon cycle is a critical ecosystem service provided by forests globally. It is, therefore, necessary to have robust techniques for speedy assessment of forest biophysical parameters at the landscape level. It is arduous and time taking to monitor the status of vast forest landscapes using traditional field methods. Remote sensing and GIS techniques are efficient tools that can monitor the health of forests regularly. Biomass estimation is a key parameter in the assessment of forest health. Polarimetric SAR (PolSAR) remote sensing has already shown its potential for forest biophysical parameter retrieval. The current research work focuses on the retrieval of forest biophysical parameters of tropical deciduous forest, using fully polarimetric spaceborne C-band data with Polarimetric SAR Interferometry (PolInSAR) techniques. PolSAR based Interferometric Water Cloud Model (IWCM) has been used to estimate aboveground biomass (AGB). Input parameters to the IWCM have been extracted from the decomposition modeling of SAR data as well as PolInSAR coherence estimation. The technique of forest tree height retrieval utilized PolInSAR coherence based modeling approach. Two techniques - Coherence Amplitude Inversion (CAI) and Three Stage Inversion (TSI) - for forest height estimation are discussed, compared and validated. These techniques allow estimation of forest stand height and true ground topography. The accuracy of the forest height estimated is assessed using ground-based measurements. PolInSAR based forest height models showed enervation in the identification of forest vegetation and as a result height values were obtained in river channels and plain areas. Overestimation in forest height was also noticed at several patches of the forest. To overcome this problem, coherence and backscatter based threshold technique is introduced for forest area identification and accurate height estimation in non-forested regions. IWCM based modeling for forest AGB retrieval showed R2 value of 0.5, RMSE of 62.73 (t ha-1) and a percent accuracy of 51%. TSI based PolInSAR inversion modeling showed the most accurate result for forest height estimation. The correlation between the field measured forest height and the estimated tree height using TSI technique is 62% with an average accuracy of 91.56% and RMSE of 2.28 m. The study suggested that PolInSAR coherence based modeling approach has significant potential for retrieval of forest biophysical parameters.

Structural Determination of a Transcribing RNA Polymerase II Complex

DTIC Science & Technology

2000-05-01

A be extended and evaluated by the solution of pol II cocrystal structures, with the use of the pol II model for molecular replacement. Co- crystals...with TFIIB and TFIIE (78) should reveal the trajectory of DNA in the initial pol - II-promoter complex. Cocrystals containing pol II in the act of...transcription (79) will show the locations of nucleic acids in an elongation complex. Cocrystals with TFIIS (80) may indicate the proposed exit pathway

The use of modified and non-natural nucleotides provide unique insights into pro-mutagenic replication catalyzed by polymerase eta.

PubMed

Choi, Jung-Suk; Dasari, Anvesh; Hu, Peter; Benkovic, Stephen J; Berdis, Anthony J

2016-02-18

This report evaluates the pro-mutagenic behavior of 8-oxo-guanine (8-oxo-G) by quantifying the ability of high-fidelity and specialized DNA polymerases to incorporate natural and modified nucleotides opposite this lesion. Although high-fidelity DNA polymerases such as pol δ and the bacteriophage T4 DNA polymerase replicating 8-oxo-G in an error-prone manner, they display remarkably low efficiencies for TLS compared to normal DNA synthesis. In contrast, pol η shows a combination of high efficiency and low fidelity when replicating 8-oxo-G. These combined properties are consistent with a pro-mutagenic role for pol η when replicating this DNA lesion. Studies using modified nucleotide analogs show that pol η relies heavily on hydrogen-bonding interactions during translesion DNA synthesis. However, nucleobase modifications such as alkylation to the N2 position of guanine significantly increase error-prone synthesis catalyzed by pol η when replicating 8-oxo-G. Molecular modeling studies demonstrate the existence of a hydrophobic pocket in pol η that participates in the increased utilization of certain hydrophobic nucleotides. A model is proposed for enhanced pro-mutagenic replication catalyzed by pol η that couples efficient incorporation of damaged nucleotides opposite oxidized DNA lesions created by reactive oxygen species. The biological implications of this model toward increasing mutagenic events in lung cancer are discussed. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

IL-23 secreted by bronchial epithelial cells contributes to allergic sensitization in asthma model: role of IL-23 secreted by bronchial epithelial cells.

PubMed

Lee, Hyun Seung; Park, Da-Eun; Lee, Ji-Won; Chang, Yuna; Kim, Hye Young; Song, Woo-Jung; Kang, Hye-Ryun; Park, Heung-Woo; Chang, Yoon-Seok; Cho, Sang-Heon

2017-01-01

IL-23 has been postulated to be a critical mediator contributing to various inflammatory diseases. Dermatophagoides pteronyssinus (Der p) is one of the most common inhalant allergens. However, the role of IL-23 in Der p-induced mouse asthma model is not well understood, particularly with regard to the development of allergic sensitization in the airways. The objective of this study was to evaluate roles of IL-23 in Der p sensitization and asthma development. BALB/c mice were repeatedly administered Der p intranasally to develop Der p allergic sensitization and asthma. After Der p local administration, changes in IL-23 expression were examined in lung tissues and primary epithelial cells. Anti-IL-23p19 antibody was given during the Der p sensitization period, and its effects were examined. Effects of anti-IL-23p19 antibody at bronchial epithelial levels were also examined in vitro. The expression of IL-23 at bronchial epithelial layers was increased after Der p local administration in mouse. In Der p-induced mouse models, anti-IL-23p19 antibody treatment during allergen sensitization significantly diminished Der p allergic sensitization and several features of allergic asthma including the production of Th2 cytokines and the population of type 2 innate lymphoid cells in lungs. The activation of dendritic cells in lung-draining lymph nodes was also reduced by anti-IL-23 treatment. In murine lung alveolar type II-like epithelial cell line (MLE-12) cells, IL-23 blockade prevented cytokine responses to Der p stimulation, such as IL-1α, granulocyte-macrophage colony-stimulating factor (GM-CSF), IL-33, and also bone marrow-derived dendritic cell activation. In conclusion, IL-23 is another important bronchial epithelial cell-driven cytokine which may contribute to the development of house dust mite allergic sensitization and asthma. Copyright © 2017 the American Physiological Society.

Distinct Mechanisms of Transcription Initiation by RNA Polymerases I and II.

PubMed

Engel, Christoph; Neyer, Simon; Cramer, Patrick

2018-05-20

RNA polymerases I and II (Pol I and Pol II) are the eukaryotic enzymes that catalyze DNA-dependent synthesis of ribosomal RNA and messenger RNA, respectively. Recent work shows that the transcribing forms of both enzymes are similar and the fundamental mechanisms of RNA chain elongation are conserved. However, the mechanisms of transcription initiation and its regulation differ between Pol I and Pol II. Recent structural studies of Pol I complexes with transcription initiation factors provided insights into how the polymerase recognizes its specific promoter DNA, how it may open DNA, and how initiation may be regulated. Comparison with the well-studied Pol II initiation system reveals a distinct architecture of the initiation complex and visualizes promoter- and gene-class-specific aspects of transcription initiation. On the basis of new structural studies, we derive a model of the Pol I transcription cycle and provide a molecular movie of Pol I transcription that can be used for teaching.

Mutual information as an order parameter for quantum synchronization

NASA Astrophysics Data System (ADS)

Ameri, V.; Eghbali-Arani, M.; Mari, A.; Farace, A.; Kheirandish, F.; Giovannetti, V.; Fazio, R.

2015-01-01

Spontaneous synchronization is a fundamental phenomenon, important in many theoretical studies and applications. Recently, this effect has been analyzed and observed in a number of physical systems close to the quantum-mechanical regime. In this work we propose mutual information as a useful order parameter which can capture the emergence of synchronization in very different contexts, ranging from semiclassical to intrinsically quantum-mechanical systems. Specifically, we first study the synchronization of two coupled Van der Pol oscillators in both classical and quantum regimes and later we consider the synchronization of two qubits inside two coupled optical cavities. In all these contexts, we find that mutual information can be used as an appropriate figure of merit for determining the synchronization phases independently of the specific details of the system.

Two distinct mechanisms ensure transcriptional polarity in double-stranded RNA bacteriophages.

PubMed

Yang, Hongyan; Makeyev, Eugene V; Butcher, Sarah J; Gaidelyte, Ausra; Bamford, Dennis H

2003-01-01

In most double-stranded RNA (dsRNA) viruses, RNA transcription occurs inside a polymerase (Pol) complex particle, which contains an RNA-dependent RNA Pol subunit as a minor component. Only plus- but not minus-sense copies of genomic segments are produced during this reaction. In the case of phi6, a dsRNA bacteriophage from the Cystoviridae family, isolated Pol synthesizes predominantly plus strands using virus-specific dsRNAs in vitro, thus suggesting that Pol template preferences determine the transcriptional polarity. Here, we dissect transcription reactions catalyzed by Pol complexes and Pol subunits of two other cystoviruses, phi8 and phi13. While both Pol complexes synthesize exclusively plus strands over a wide range of conditions, isolated Pol subunits can be stimulated by Mn(2+) to produce minus-sense copies on phi13 dsRNA templates. Importantly, all three Pol subunits become more prone to the native-like plus-strand synthesis when the dsRNA templates (including phi13 dsRNA) are activated by denaturation before the reaction. Based on these and earlier observations, we propose a model of transcriptional polarity in Cystoviridae controlled on two independent levels: Pol affinity to plus-strand initiation sites and accessibility of these sites to the Pol in a single-stranded form.

Two Distinct Mechanisms Ensure Transcriptional Polarity in Double-Stranded RNA Bacteriophages

PubMed Central

Yang, Hongyan; Makeyev, Eugene V.; Butcher, Sarah J.; Gaidelyte·, Aušra; Bamford, Dennis H.

2003-01-01

In most double-stranded RNA (dsRNA) viruses, RNA transcription occurs inside a polymerase (Pol) complex particle, which contains an RNA-dependent RNA Pol subunit as a minor component. Only plus- but not minus-sense copies of genomic segments are produced during this reaction. In the case of φ6, a dsRNA bacteriophage from the Cystoviridae family, isolated Pol synthesizes predominantly plus strands using virus-specific dsRNAs in vitro, thus suggesting that Pol template preferences determine the transcriptional polarity. Here, we dissect transcription reactions catalyzed by Pol complexes and Pol subunits of two other cystoviruses, φ8 and φ13. While both Pol complexes synthesize exclusively plus strands over a wide range of conditions, isolated Pol subunits can be stimulated by Mn2+ to produce minus-sense copies on φ13 dsRNA templates. Importantly, all three Pol subunits become more prone to the native-like plus-strand synthesis when the dsRNA templates (including φ13 dsRNA) are activated by denaturation before the reaction. Based on these and earlier observations, we propose a model of transcriptional polarity in Cystoviridae controlled on two independent levels: Pol affinity to plus-strand initiation sites and accessibility of these sites to the Pol in a single-stranded form. PMID:12502836

Assimilation of Dual-Polarimetric Radar Observations with WRF GSI

NASA Technical Reports Server (NTRS)

Li, Xuanli; Mecikalski, John; Fehnel, Traci; Zavodsky, Bradley; Srikishen, Jayanthi

2014-01-01

Dual-polarimetric (dual-pol) radar typically transmits both horizontally and vertically polarized radio wave pulses. From the two different reflected power returns, more accurate estimate of liquid and solid cloud and precipitation can be provided. The upgrade of the traditional NWS WSR-88D radar to include dual-pol capabilities will soon be completed for the entire NEXRAD network. Therefore, the use of dual-pol radar network will have a broad impact in both research and operational communities. The assimilation of dual-pol radar data is especially challenging as few guidelines have been provided by previous research. It is our goal to examine how to best use dual-pol radar data to improve forecast of severe storm and forecast initialization. In recent years, the Development Testbed Center (DTC) has released the community Gridpoint Statistical Interpolation (GSI) DA system for the Weather Research and Forecasting (WRF) model. The community GSI system runs in independently environment, yet works functionally equivalent to operational centers. With collaboration with the NASA Short-term Prediction Research and Transition (SPoRT) Center, this study explores regional assimilation of the dual-pol radar variables from the WSR-88D radars for real case storms. Our presentation will highlight our recent effort on incorporating the horizontal reflectivity (ZH), differential reflectivity (ZDR), specific differential phase (KDP), and radial velocity (VR) data for initializing convective storms, with a significant focus being on an improved representation of hydrometeor fields. In addition, discussion will be provided on the development of enhanced assimilation procedures in the GSI system with respect to dual-pol variables. Beyond the dual-pol variable assimilation procedure developing within a GSI framework, highresolution (=1 km) WRF model simulations and storm scale data assimilation experiments will be examined, emphasizing both model initialization and short-term forecast of precipitation fields and processes. Further details of the methodology of data assimilation, the impact of different dual-pol variables, the influence on precipitation forecast will be presented at the conference.

Energy Policy Case Study - California: Renewables and Distributed Energy Resources

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

Homer, Juliet S.; Bender, Sadie R.; Weimar, Mark R.

2016-09-19

The purpose of this document is to present a case study of energy policies in California related to power system transformation and renewable and distributed energy resources (DERs). Distributed energy resources represent a broad range of technologies that can significantly impact how much, and when, electricity is demanded from the grid. Key policies and proceedings related to power system transformation and DERs are grouped into the following categories: 1.Policies that support achieving environmental and climate goals 2.Policies that promote deployment of DERs 3.Policies that support reliability and integration of DERs 4.Policies that promote market animation and support customer choice. Majormore » challenges going forward are forecasting and modeling DERs, regulatory and utility business model issues, reliability, valuation and pricing, and data management and sharing.« less

Polarization transfer in the {sup 4}He(e(pol), e'p(pol)) {sup 3}He reaction at Q{sup 2} = 0.8 and 1.3 GeV/c){sup 2}.

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

Paolone, M.; Malace, S. P.; Strauch, S.

2010-08-12

Proton recoil polarization was measured in the quasielastic 4He(e(pol),e{prime}p(pol)){sup 3}H reaction at Q{sup 2}=0.8 and 1.3(GeV/c){sup 2} with unprecedented precision. The polarization-transfer coefficients are found to differ from those of the {sup 1}H(e(pol),e{prime}p(pol)) reaction, contradicting a relativistic distorted-wave approximation and favoring either the inclusion of medium-modified proton form factors predicted by the quark-meson coupling model or a spin-dependent charge-exchange final-state interaction. For the first time, the polarization-transfer ratio is studied as a function of the virtuality of the proton.

Regulation of RNA polymerase III transcription during transformation of human IMR90 fibroblasts with defined genetic elements.

PubMed

Durrieu-Gaillard, Stéphanie; Dumay-Odelot, Hélène; Boldina, Galina; Tourasse, Nicolas J; Allard, Delphine; André, Fabrice; Macari, Françoise; Choquet, Armelle; Lagarde, Pauline; Drutel, Guillaume; Leste-Lasserre, Thierry; Petitet, Marion; Lesluyes, Tom; Lartigue-Faustin, Lydia; Dupuy, Jean-William; Chibon, Frédéric; Roeder, Robert G; Joubert, Dominique; Vagner, Stéphan; Teichmann, Martin

2018-01-01

RNA polymerase (Pol) III transcribes small untranslated RNAs that are essential for cellular homeostasis and growth. Its activity is regulated by inactivation of tumor suppressor proteins and overexpression of the oncogene c-MYC, but the concerted action of these tumor-promoting factors on Pol III transcription has not yet been assessed. In order to comprehensively analyse the regulation of Pol III transcription during tumorigenesis we employ a model system that relies on the expression of five genetic elements to achieve cellular transformation. Expression of these elements in six distinct transformation intermediate cell lines leads to the inactivation of TP53, RB1, and protein phosphatase 2A, as well as the activation of RAS and the protection of telomeres by TERT, thereby conducting to full tumoral transformation of IMR90 fibroblasts. Transformation is accompanied by moderately enhanced levels of a subset of Pol III-transcribed RNAs (7SK; MRP; H1). In addition, mRNA and/or protein levels of several Pol III subunits and transcription factors are upregulated, including increased protein levels of TFIIIB and TFIIIC subunits, of SNAPC1 and of Pol III subunits. Strikingly, the expression of POLR3G and of SNAPC1 is strongly enhanced during transformation in this cellular transformation model. Collectively, our data indicate that increased expression of several components of the Pol III transcription system accompanied by a 2-fold increase in steady state levels of a subset of Pol III RNAs is sufficient for sustaining tumor formation.

The translesion DNA polymerases Pol ζ and Rev1 are activated independently of PCNA ubiquitination upon UV radiation in mutants of DNA polymerase δ

PubMed Central

Ma, Emilie; Veaute, Xavier; Coïc, Eric

2017-01-01

Replicative DNA polymerases cannot insert efficiently nucleotides at sites of base lesions. This function is taken over by specialized translesion DNA synthesis (TLS) polymerases to allow DNA replication completion in the presence of DNA damage. In eukaryotes, Rad6- and Rad18-mediated PCNA ubiquitination at lysine 164 promotes recruitment of TLS polymerases, allowing cells to efficiently cope with DNA damage. However, several studies showed that TLS polymerases can be recruited also in the absence of PCNA ubiquitination. We hypothesized that the stability of the interactions between DNA polymerase δ (Pol δ) subunits and/or between Pol δ and PCNA at the primer/template junction is a crucial factor to determine the requirement of PCNA ubiquitination. To test this hypothesis, we used a structural mutant of Pol δ in which the interaction between Pol3 and Pol31 is inhibited. We found that in yeast, rad18Δ-associated UV hypersensitivity is suppressed by pol3-ct, a mutant allele of the POL3 gene that encodes the catalytic subunit of replicative Pol δ. pol3-ct suppressor effect was specifically dependent on the Rev1 and Pol ζ TLS polymerases. This result strongly suggests that TLS polymerases could rely much less on PCNA ubiquitination when Pol δ interaction with PCNA is partially compromised by mutations. In agreement with this model, we found that the pol3-FI allele suppressed rad18Δ-associated UV sensitivity as observed for pol3-ct. This POL3 allele carries mutations within a putative PCNA Interacting Peptide (PIP) motif. We then provided molecular and genetic evidence that this motif could contribute to Pol δ-PCNA interaction indirectly, although it is not a bona fide PIP. Overall, our results suggest that the primary role of PCNA ubiquitination is to allow TLS polymerases to outcompete Pol δ for PCNA access upon DNA damage. PMID:29281621

Nonlinear dynamics of the CAM circadian rhythm in response to environmental forcing.

PubMed

Hartzell, Samantha; Bartlett, Mark S; Virgin, Lawrence; Porporato, Amilcare

2015-03-07

Crassulacean acid metabolism (CAM) photosynthesis functions as an endogenous circadian rhythm coupled to external environmental forcings of energy and water availability. This paper explores the nonlinear dynamics of a new CAM photosynthesis model (Bartlett et al., 2014) and investigates the responses of CAM plant carbon assimilation to different combinations of environmental conditions. The CAM model (Bartlett et al., 2014) consists of a Calvin cycle typical of C3 plants coupled to an oscillator of the type employed in the Van der Pol and FitzHugh-Nagumo systems. This coupled system is a function of environmental variables including leaf temperature, leaf moisture potential, and irradiance. Here, we explore the qualitative response of the system and the expected carbon assimilation under constant and periodically forced environmental conditions. The model results show how the diurnal evolution of these variables entrains the CAM cycle with prevailing environmental conditions. While constant environmental conditions generate either steady-state or periodically oscillating responses in malic acid uptake and release, forcing the CAM system with periodic daily fluctuations in light exposure and leaf temperature results in quasi-periodicity and possible chaos for certain ranges of these variables. This analysis is a first step in quantifying changes in CAM plant productivity with variables such as the mean temperature, daily temperature range, irradiance, and leaf moisture potential. Results may also be used to inform model parametrization based on the observed fluctuating regime. Copyright © 2014 Elsevier Ltd. All rights reserved.

Arabidopsis RNA Polymerases IV and V Are Required To Establish H3K9 Methylation, but Not Cytosine Methylation, on Geminivirus Chromatin

PubMed Central

Jackel, Jamie N.; Storer, Jessica M.; Coursey, Tami

2016-01-01

ABSTRACT In plants, RNA-directed DNA methylation (RdDM) employs small RNAs to target enzymes that methylate cytosine residues. Cytosine methylation and dimethylation of histone 3 lysine 9 (H3K9me2) are often linked. Together they condition an epigenetic defense that results in chromatin compaction and transcriptional silencing of transposons and viral chromatin. Canonical RdDM (Pol IV-RdDM), involving RNA polymerases IV and V (Pol IV and Pol V), was believed to be necessary to establish cytosine methylation, which in turn could recruit H3K9 methyltransferases. However, recent studies have revealed that a pathway involving Pol II and RNA-dependent RNA polymerase 6 (RDR6) (RDR6-RdDM) is likely responsible for establishing cytosine methylation at naive loci, while Pol IV-RdDM acts to reinforce and maintain it. We used the geminivirus Beet curly top virus (BCTV) as a model to examine the roles of Pol IV and Pol V in establishing repressive viral chromatin methylation. As geminivirus chromatin is formed de novo in infected cells, these viruses are unique models for processes involved in the establishment of epigenetic marks. We confirm that Pol IV and Pol V are not needed to establish viral DNA methylation but are essential for its amplification. Remarkably, however, both Pol IV and Pol V are required for deposition of H3K9me2 on viral chromatin. Our findings suggest that cytosine methylation alone is not sufficient to trigger de novo deposition of H3K9me2 and further that Pol IV-RdDM is responsible for recruiting H3K9 methyltransferases to viral chromatin. IMPORTANCE In plants, RNA-directed DNA methylation (RdDM) uses small RNAs to target cytosine methylation, which is often linked to H3K9me2. These epigenetic marks silence transposable elements and DNA virus genomes, but how they are established is not well understood. Canonical RdDM, involving Pol IV and Pol V, was thought to establish cytosine methylation that in turn could recruit H3K9 methyltransferases, but recent studies compel a reevaluation of this view. We used BCTV to investigate the roles of Pol IV and Pol V in chromatin methylation. We found that both are needed to amplify, but not to establish, DNA methylation. However, both are required for deposition of H3K9me2. Our findings suggest that cytosine methylation is not sufficient to recruit H3K9 methyltransferases to naive viral chromatin and further that Pol IV-RdDM is responsible. PMID:27279611

Arabidopsis RNA Polymerases IV and V Are Required To Establish H3K9 Methylation, but Not Cytosine Methylation, on Geminivirus Chromatin.

PubMed

Jackel, Jamie N; Storer, Jessica M; Coursey, Tami; Bisaro, David M

2016-08-15

In plants, RNA-directed DNA methylation (RdDM) employs small RNAs to target enzymes that methylate cytosine residues. Cytosine methylation and dimethylation of histone 3 lysine 9 (H3K9me2) are often linked. Together they condition an epigenetic defense that results in chromatin compaction and transcriptional silencing of transposons and viral chromatin. Canonical RdDM (Pol IV-RdDM), involving RNA polymerases IV and V (Pol IV and Pol V), was believed to be necessary to establish cytosine methylation, which in turn could recruit H3K9 methyltransferases. However, recent studies have revealed that a pathway involving Pol II and RNA-dependent RNA polymerase 6 (RDR6) (RDR6-RdDM) is likely responsible for establishing cytosine methylation at naive loci, while Pol IV-RdDM acts to reinforce and maintain it. We used the geminivirus Beet curly top virus (BCTV) as a model to examine the roles of Pol IV and Pol V in establishing repressive viral chromatin methylation. As geminivirus chromatin is formed de novo in infected cells, these viruses are unique models for processes involved in the establishment of epigenetic marks. We confirm that Pol IV and Pol V are not needed to establish viral DNA methylation but are essential for its amplification. Remarkably, however, both Pol IV and Pol V are required for deposition of H3K9me2 on viral chromatin. Our findings suggest that cytosine methylation alone is not sufficient to trigger de novo deposition of H3K9me2 and further that Pol IV-RdDM is responsible for recruiting H3K9 methyltransferases to viral chromatin. In plants, RNA-directed DNA methylation (RdDM) uses small RNAs to target cytosine methylation, which is often linked to H3K9me2. These epigenetic marks silence transposable elements and DNA virus genomes, but how they are established is not well understood. Canonical RdDM, involving Pol IV and Pol V, was thought to establish cytosine methylation that in turn could recruit H3K9 methyltransferases, but recent studies compel a reevaluation of this view. We used BCTV to investigate the roles of Pol IV and Pol V in chromatin methylation. We found that both are needed to amplify, but not to establish, DNA methylation. However, both are required for deposition of H3K9me2. Our findings suggest that cytosine methylation is not sufficient to recruit H3K9 methyltransferases to naive viral chromatin and further that Pol IV-RdDM is responsible. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Vortex-induced vibrations mitigation through a nonlinear energy sink

NASA Astrophysics Data System (ADS)

Dai, H. L.; Abdelkefi, A.; Wang, L.

2017-01-01

The passive suppression mechanism of the vortex-induced vibrations (VIV) of the cylinder by means of an essentially nonlinear element, the nonlinear energy sink (NES) is investigated. The flow-induced loads on the cylinder are modeled using a prevalent van der Pol oscillator which is experimentally validated, coupling to the structural vibrations in the presence of the NES structure. Based on the coupled nonlinear governing equations of motion, the performed analysis indicates that the mass and damping of NES have significant effects on the coupled frequency and damping of the aero-elastic system, leading to the shift of synchronization region and mitigation of vibration responses. It is demonstrated that the coupled system of flow-cylinder-NES behaves resonant interactions, showing periodic, aperiodic, and multiple stable responses which depend on the values of the NES parameters. In addition, it is found that the occurrence of multiple stable responses can enhance the nonlinear energy pumping effect, resulting in the increment of transferring energy from the flow via the cylinder to the NES, which is related to the essential nonlinearity of the sink stiffness. This results in a significant reduction in the VIV amplitudes of the primary circular cylinder for appropriate NES parameter values.

Ferromagnetic mass fixed on a spring and subjected to an electromagnet powered by self-sustained oscillators

NASA Astrophysics Data System (ADS)

Abobda, L. T.; Woafo, P.

2014-12-01

The study of a ferromagnetic mass, fixed on a spring and subjected to an electromagnet powered by a Van der Pol (VDP) oscillator and by a Hindmarsh-Rose (HR) oscillator is performed, to serve as an electromechanical devices, but also to mimic the action of a natural pacemaker and nerves on a cardiac assist device or artificial heart. The excitation with the VDP oscillator shows in the mechanical part the transition from harmonic, periodic, biperiodic up to bursting oscillations, high displacement without pull-in instability in the free dynamics regime. Under DC plus square wave excitation, there is a coexistence of the bursting oscillations of the free dynamics and the one of the modulated dynamics. Considering the action of a HR oscillator, it is found transition from spikes, bursting oscillations, relaxation spikes, multiperiodic and sinusoidal oscillations under DC or DC plus square wave excitation. These electrical behaviors are transferred to the mechanical part which can then adopt spiking or bursting dynamics as the HR oscillator. For this electromechanical model, the VDP oscillator is more efficient than the HR oscillator to induce pulsatile pumping function with higher amplitude and to react to external influences without pull-in.

Alternative splicing at exon 2 results in the loss of the catalytic activity of mouse DNA polymerase iota in vitro.

PubMed

Kazachenko, Konstantin Y; Miropolskaya, Nataliya A; Gening, Leonid V; Tarantul, Vyacheslav Z; Makarova, Alena V

2017-02-01

Y-family DNA polymerase iota (Pol ι) possesses both DNA polymerase and dRP lyase activities and was suggested to be involved in DNA translesion synthesis and base excision repair in mammals. The 129 strain of mice and its derivatives have a natural nonsense codon mutation in the second exon of the Pol ι gene resulting in truncation of the Pol ι protein. These mice were widely used as a Pol ι-null model for in vivo studies of the Pol ι function. However whether 129-derived strains of mice are fully deficient in the Pol ι functions was a subject of discussion since Pol ι mRNA undergoes alternative splicing at exon 2. Here we report purification of mouse Pol ι lacking the region encoded by exon 2, which includes several conserved residues involved in catalysis. We show that the deletion abrogates both the DNA polymerase and dRP lyase activities of Pol ι in the presence of either Mg 2+ or Mn 2+ ions. Thus, 129-derived strains of mice express catalytically inactive alternatively spliced Pol ι variant, whose cellular functions, if any exist, remain to be established. Copyright © 2017 Elsevier B.V. All rights reserved.

Solution Structures of 2 : 1 And 1 : 1 DNA Polymerase - DNA Complexes Probed By Ultracentrifugation And Small-Angle X-Ray Scattering

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

Tang, K.H.; /Ohio State U.; Niebuhr, M.

2009-04-30

We report small-angle X-ray scattering (SAXS) and sedimentation velocity (SV) studies on the enzyme-DNA complexes of rat DNA polymerase {beta} (Pol {beta}) and African swine fever virus DNA polymerase X (ASFV Pol X) with one-nucleotide gapped DNA. The results indicated formation of a 2 : 1 Pol {beta}-DNA complex, whereas only 1 : 1 Pol X-DNA complex was observed. Three-dimensional structural models for the 2 : 1 Pol {beta}-DNA and 1 : 1 Pol X-DNA complexes were generated from the SAXS experimental data to correlate with the functions of the DNA polymerases. The former indicates interactions of the 8 kDamore » 5{prime}-dRP lyase domain of the second Pol {beta} molecule with the active site of the 1 : 1 Pol {beta}-DNA complex, while the latter demonstrates how ASFV Pol X binds DNA in the absence of DNA-binding motif(s). As ASFV Pol X has no 5{prime}-dRP lyase domain, it is reasonable not to form a 2 : 1 complex. Based on the enhanced activities of the 2 : 1 complex and the observation that the 8 kDa domain is not in an optimal configuration for the 5{prime}-dRP lyase reaction in the crystal structures of the closed ternary enzyme-DNA-dNTP complexes, we propose that the asymmetric 2 : 1 Pol {beta}-DNA complex enhances the function of Pol {beta}.« less

DNA polymerase iota (Pol ι) promotes invasion and metastasis of esophageal squamous cell carcinoma.

PubMed

Zou, Shitao; Shang, Zeng-Fu; Liu, Biao; Zhang, Shuyu; Wu, Jinchang; Huang, Min; Ding, Wei-Qun; Zhou, Jundong

2016-05-31

DNA polymerase iota (Pol ι) is an error-prone DNA polymerase involved in translesion DNA synthesis (TLS) that contributes to the accumulation of DNA mutations. We recently showed that Pol ι is overexpressed in human esophageal squamous cell cancer (ESCC) tissues which promotes ESCC' progression. The present study was aimed at investigating the molecular mechanisms by which Pol ι enhances the invasiveness and metastasis of ESCC cells. We found that the expression of Pol ι is significantly higher in ESCCs with lymph node metastasis compared to those without lymph node metastasis. Kaplan-Meier analysis revealed an inverse correlation between Pol ι expression and patient prognosis. The expression levels of matrix metalloproteinase-2 (MMP-2) and matrix metalloproteinase-9 (MMP-9), two essential regulators of cells' invasiveness, were positively associated with Pol ι expression in ESCC tissues. Ectopic expression of Pol ι enhanced the motility and invasiveness of ESCC cells as evaluated by wound-healing and transwell assays, respectively. A xenograft nude mouse model showed that Pol ι promotes the colonization of ESCC cells in the liver, lung and kidney. Signaling pathway analysis identified the JNK-AP-1 cascade as a mediator of the Pol ι-induced increase in the expression of MMP-2/9 and enhancement of ESCC progression. These data demonstrate the underlying mechanism by which Pol ι promotes ESCC progression, suggesting that Pol ι is a potential novel prognostic biomarker and therapeutic target for ESCC.

DNA polymerase iota (Pol ι) promotes invasion and metastasis of esophageal squamous cell carcinoma

PubMed Central

Liu, Biao; Zhang, Shuyu; Wu, Jinchang; Huang, Min; Ding, Wei-Qun; Zhou, Jundong

2016-01-01

DNA polymerase iota (Pol ι) is an error-prone DNA polymerase involved in translesion DNA synthesis (TLS) that contributes to the accumulation of DNA mutations. We recently showed that Pol ι is overexpressed in human esophageal squamous cell cancer (ESCC) tissues which promotes ESCC' progression. The present study was aimed at investigating the molecular mechanisms by which Pol ι enhances the invasiveness and metastasis of ESCC cells. We found that the expression of Pol ι is significantly higher in ESCCs with lymph node metastasis compared to those without lymph node metastasis. Kaplan-Meier analysis revealed an inverse correlation between Pol ι expression and patient prognosis. The expression levels of matrix metalloproteinase-2 (MMP-2) and matrix metalloproteinase-9 (MMP-9), two essential regulators of cells' invasiveness, were positively associated with Pol ι expression in ESCC tissues. Ectopic expression of Pol ι enhanced the motility and invasiveness of ESCC cells as evaluated by wound-healing and transwell assays, respectively. A xenograft nude mouse model showed that Pol ι promotes the colonization of ESCC cells in the liver, lung and kidney. Signaling pathway analysis identified the JNK-AP-1 cascade as a mediator of the Pol ι-induced increase in the expression of MMP-2/9 and enhancement of ESCC progression. These data demonstrate the underlying mechanism by which Pol ι promotes ESCC progression, suggesting that Pol ι is a potential novel prognostic biomarker and therapeutic target for ESCC. PMID:27057634

An Analysis of the DER Adoption Climate in Japan UsingOptimization Results for Prototype Buildings with U.S. Comparisons

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

Zhou, Nan; Marnay, Chris; Firestone, Ryan

2006-06-16

This research demonstrates economically optimal distributedenergy resource (DER) system choice using the DER choice and operationsoptimization program, the Distributed Energy Resources Customer AdoptionModel (DER-CAM). DER-CAM finds the optimal combination of installedequipment given prevailing utility tariffs and fuel prices, siteelectrical and thermal loads (including absorption cooling), and a menuof available equipment. It provides a global optimization, albeitidealized, that shows how site useful energy loads can be served atminimum cost. Five prototype Japanese commercial buildings are examinedand DER-CAM is applied to select the economically optimal DER system foreach. Based on the optimization results, energy and emission reductionsare evaluated. Significant decreases in fuelmore » consumption, carbonemissions, and energy costs were seen in the DER-CAM results. Savingswere most noticeable in the prototype sports facility, followed by thehospital, hotel, and office building. Results show that DER with combinedheat and power equipment is a promising efficiency and carbon mitigationstrategy, but that precise system design is necessary. Furthermore, aJapan-U.S. comparison study of policy, technology, and utility tariffsrelevant to DER installation is presented.« less

Inaccurate DNA synthesis in cell extracts of yeast producing active human DNA polymerase iota.

PubMed

Makarova, Alena V; Grabow, Corinn; Gening, Leonid V; Tarantul, Vyacheslav Z; Tahirov, Tahir H; Bessho, Tadayoshi; Pavlov, Youri I

2011-01-31

Mammalian Pol ι has an unusual combination of properties: it is stimulated by Mn(2+) ions, can bypass some DNA lesions and misincorporates "G" opposite template "T" more frequently than incorporates the correct "A." We recently proposed a method of detection of Pol ι activity in animal cell extracts, based on primer extension opposite the template T with a high concentration of only two nucleotides, dGTP and dATP (incorporation of "G" versus "A" method of Gening, abbreviated as "misGvA"). We provide unambiguous proof of the "misGvA" approach concept and extend the applicability of the method for the studies of variants of Pol ι in the yeast model system with different cation cofactors. We produced human Pol ι in baker's yeast, which do not have a POLI ortholog. The "misGvA" activity is absent in cell extracts containing an empty vector, or producing catalytically dead Pol ι, or Pol ι lacking exon 2, but is robust in the strain producing wild-type Pol ι or its catalytic core, or protein with the active center L62I mutant. The signature pattern of primer extension products resulting from inaccurate DNA synthesis by extracts of cells producing either Pol ι or human Pol η is different. The DNA sequence of the template is critical for the detection of the infidelity of DNA synthesis attributed to DNA Pol ι. The primer/template and composition of the exogenous DNA precursor pool can be adapted to monitor replication fidelity in cell extracts expressing various error-prone Pols or mutator variants of accurate Pols. Finally, we demonstrate that the mutation rates in yeast strains producing human DNA Pols ι and η are not elevated over the control strain, despite highly inaccurate DNA synthesis by their extracts.

Estimation of Melt Pond Fractions on First Year Sea Ice Using Compact Polarization SAR

NASA Astrophysics Data System (ADS)

Li, Haiyan; Perrie, William; Li, Qun; Hou, Yijun

2017-10-01

Melt ponds are a common feature on Arctic sea ice. They are linked to the sea ice surface albedo and transmittance of energy to the ocean from the atmosphere and thus constitute an important process to parameterize in Arctic climate models and simulations. This paper presents a first attempt to retrieve the melt pond fraction from hybrid-polarized compact polarization (CP) SAR imagery, which has wider swath and shorter revisit time than the quad-polarization systems, e.g., from RADARSAT-2 (RS-2). The co-polarization (co-pol) ratio has been verified to provide estimates of melt pond fractions. However, it is a challenge to link CP parameters and the co-pol ratio. The theoretical possibility is presented, for making this linkage with the CP parameter C22/C11 (the ratio between the elements of the coherence matrix of CP SAR) for melt pond detection and monitoring with the tilted-Bragg scattering model for the ocean surface. The empirical transformed formulation, denoted as the "compact polarization and quad-pol" ("CPQP") model, is proposed, based on 2062 RS-2 quad-pol SAR images, collocated with in situ measurements. We compared the retrieved melt pond fraction with CP parameters simulated from quad-pol SAR data with results retrieved from the co-pol ratio from quad-pol SAR observations acquired during the Arctic-Ice (Arctic-Ice Covered Ecosystem in a Rapidly Changing Environment) field project. The results are shown to be comparable for observed melt pond measurements in spatial and temporal distributions. Thus, the utility of CP mode SAR for melt pond fraction estimation on first year level ice is presented.

A pictorial study of an invariant torus in phase space of four dimensions.

NASA Technical Reports Server (NTRS)

Baxter, R.; Eiserike, H.; Stokes, A.

1972-01-01

An investigation was conducted with the aid of a computer graphics device at Goddard Space Flight Center to study the behavior of the invariant manifolds of a particular fourth-order equation, as a parameter in the equation is varied over the interval from 0 to 1. The equation consists of two coupled Van der Pol equations. For a small parameter value, the manifold is an asymptotically stable torus, where the flow on the torus is simply a rotation. As the value of the parameter is increased, the only thing that changes is the nature of the flow on the torus, which itself persists throughout the parameter variation. It is shown that ultimately the four periodic cycles which appear play a more significant part in the phase profile of the system than does the torus itself.

Distributed Coordinated Control of Large-Scale Nonlinear Networks

DOE PAGES

Kundu, Soumya; Anghel, Marian

2015-11-08

We provide a distributed coordinated approach to the stability analysis and control design of largescale nonlinear dynamical systems by using a vector Lyapunov functions approach. In this formulation the large-scale system is decomposed into a network of interacting subsystems and the stability of the system is analyzed through a comparison system. However finding such comparison system is not trivial. In this work, we propose a sum-of-squares based completely decentralized approach for computing the comparison systems for networks of nonlinear systems. Moreover, based on the comparison systems, we introduce a distributed optimal control strategy in which the individual subsystems (agents) coordinatemore » with their immediate neighbors to design local control policies that can exponentially stabilize the full system under initial disturbances.We illustrate the control algorithm on a network of interacting Van der Pol systems.« less

Comparison of Virtual Oscillator and Droop Control: Preprint

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

Johnson, Brian B; Rodriguez, Miguel; Dhople, Sairaj

Virtual oscillator control and droop control are two techniques that can be used to ensure synchronization and power sharing of parallel inverters in islanded operation. VOC relies on the implementation of non-linear Van der Pol oscillator equations in the control system of the inverter, acting upon the time-domain instantaneous inverter current and terminal voltage. On the other hand, DC explicitly computes active and reactive power produced by the inverter and relies on limited bandwidth low-pass filters. Even though both methods can be engineered to produce the same steady-state characteristics, their dynamic performances are significantly different. This paper presents analytical andmore » experimental results that aim to compare both methods. It is shown that VOC is inherently faster and enables minimizing the circulating currents. The results are verified using three 120V, 1kW inverters.« less

Long-Term Dynamics of Autonomous Fractional Differential Equations

NASA Astrophysics Data System (ADS)

Liu, Tao; Xu, Wei; Xu, Yong; Han, Qun

This paper aims to investigate long-term dynamic behaviors of autonomous fractional differential equations with effective numerical method. The long-term dynamic behaviors predict where systems are heading after long-term evolution. We make some modification and transplant cell mapping methods to autonomous fractional differential equations. The mapping time duration of cell mapping is enlarged to deal with the long memory effect. Three illustrative examples, i.e. fractional Lotka-Volterra equation, fractional van der Pol oscillator and fractional Duffing equation, are studied with our revised generalized cell mapping method. We obtain long-term dynamics, such as attractors, basins of attraction, and saddles. Compared with some existing stability and numerical results, the validity of our method is verified. Furthermore, we find that the fractional order has its effect on the long-term dynamics of autonomous fractional differential equations.

Design and testing of a magnetic suspension and damping system for a space telescope

NASA Technical Reports Server (NTRS)

Ockman, N. J.

1972-01-01

The basic equations of motion are derived for a two dimensional, three degree of freedom simulation of a space telescope coupled to a spacecraft by means of a magnetic suspension and isolation system. The system consists of paramagnetic or ferromagnetic discs confined to the magnetic field between two Helmholtz coils. Damping is introduced by varying the magnetic field in proportion to a velocity signal derived from the telescope. The equations of motion are nonlinear, similar in behavior to the one-dimensional Van der Pol equation. The computer simulation was verified by testing a 264-kilogram air bearing platform which simulates the telescope in a frictionless environment. The simulation demonstrated effective isolation capabilities for disturbance frequencies above resonance. Damping in the system improved the response near resonance and prevented the build-up of large oscillatory amplitudes.

Renormalization Group for nonlinear oscillators in the absence of linear restoring force

NASA Astrophysics Data System (ADS)

Sarkar, A.; Bhattacharjee, J. K.

2010-09-01

Perturbative Renormalization Group (RG) has been very useful in probing periodic orbits in two-dimensional dynamical systems (Sarkar A., Bhattacharjee J. K., Chakraborty S. and Banerjee D., arXiv:1005.2858v1 (2010)). The method relies on finding a linear center, around which perturbation analysis is done. However it is not obvious as to how systems devoid of any linear terms may be approached using this method. We propose here how RG can be done even in the absence of linear terms. We successfully apply the method to extract correct results for a variant of the second-order Riccati equation. In this variant the periodic orbit disappears as a parameter is varied. Our RG captures this disappearance correctly. We have also applied the technique successfully on the force-free Van der Pol-Duffing oscillator.

Fission yeast RNA triphosphatase reads an Spt5 CTD code

DOE PAGES

Doamekpor, Selom K.; Schwer, Beate; Sanchez, Ana M.; ...

2014-11-20

mRNA capping enzymes are directed to nascent RNA polymerase II (Pol2) transcripts via interactions with the carboxy-terminal domains (CTDs) of Pol2 and transcription elongation factor Spt5. Fission yeast RNA triphosphatase binds to the Spt5 CTD, comprising a tandem repeat of nonapeptide motif TPAWNSGSK. Here we report the crystal structure of a Pct1·Spt5-CTD complex, which revealed two CTD docking sites on the Pct1 homodimer that engage TPAWN segments of the motif. Each Spt5 CTD interface, composed of elements from both subunits of the homodimer, is dominated by van der Waals contacts from Pct1 to the tryptophan of the CTD. The boundmore » CTD adopts a distinctive conformation in which the peptide backbone makes a tight U-turn so that the proline stacks over the tryptophan. We show that Pct1 binding to Spt5 CTD is antagonized by threonine phosphorylation. Our results fortify an emerging concept of an “Spt5 CTD code” in which (i) the Spt5 CTD is structurally plastic and can adopt different conformations that are templated by particular cellular Spt5 CTD receptor proteins; and (ii) threonine phosphorylation of the Spt5 CTD repeat inscribes a binary on–off switch that is read by diverse CTD receptors, each in its own distinctive manner.« less

Fission yeast RNA triphosphatase reads an Spt5 CTD code

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

Doamekpor, Selom K.; Schwer, Beate; Sanchez, Ana M.

mRNA capping enzymes are directed to nascent RNA polymerase II (Pol2) transcripts via interactions with the carboxy-terminal domains (CTDs) of Pol2 and transcription elongation factor Spt5. Fission yeast RNA triphosphatase binds to the Spt5 CTD, comprising a tandem repeat of nonapeptide motif TPAWNSGSK. Here we report the crystal structure of a Pct1·Spt5-CTD complex, which revealed two CTD docking sites on the Pct1 homodimer that engage TPAWN segments of the motif. Each Spt5 CTD interface, composed of elements from both subunits of the homodimer, is dominated by van der Waals contacts from Pct1 to the tryptophan of the CTD. The boundmore » CTD adopts a distinctive conformation in which the peptide backbone makes a tight U-turn so that the proline stacks over the tryptophan. We show that Pct1 binding to Spt5 CTD is antagonized by threonine phosphorylation. Our results fortify an emerging concept of an “Spt5 CTD code” in which (i) the Spt5 CTD is structurally plastic and can adopt different conformations that are templated by particular cellular Spt5 CTD receptor proteins; and (ii) threonine phosphorylation of the Spt5 CTD repeat inscribes a binary on–off switch that is read by diverse CTD receptors, each in its own distinctive manner.« less

A Case Study of Using a Multilayered Thermodynamical Snow Model for Radiance Assimilation

NASA Technical Reports Server (NTRS)

Toure, Ally M.; Goita, Kalifa; Royer, Alain; Kim, Edward J.; Durand, Michael; Margulis, Steven A.; Lu, Huizhong

2011-01-01

A microwave radiance assimilation (RA) scheme for the retrieval of snow physical state variables requires a snowpack physical model (SM) coupled to a radiative transfer model. In order to assimilate microwave brightness temperatures (Tbs) at horizontal polarization (h-pol), an SM capable of resolving melt-refreeze crusts is required. To date, it has not been shown whether an RA scheme is tractable with the large number of state variables present in such an SM or whether melt-refreeze crust densities can be estimated. In this paper, an RA scheme is presented using the CROCUS SM which is capable of resolving melt-refreeze crusts. We assimilated both vertical (v) and horizontal (h) Tbs at 18.7 and 36.5 GHz. We found that assimilating Tb at both h-pol and vertical polarization (v-pol) into CROCUS dramatically improved snow depth estimates, with a bias of 1.4 cm compared to-7.3 cm reported by previous studies. Assimilation of both h-pol and v-pol led to more accurate results than assimilation of v-pol alone. The snow water equivalent (SWE) bias of the RA scheme was 0.4 cm, while the bias of the SWE estimated by an empirical retrieval algorithm was -2.9 cm. Characterization of melt-refreeze crusts via an RA scheme is demonstrated here for the first time; the RA scheme correctly identified the location of melt-refreeze crusts observed in situ.

An epitope-specific DerG-PG70 LEAPS vaccine modulates T cell responses and suppresses arthritis progression in two related murine models of rheumatoid arthritis

PubMed Central

Mikecz, Katalin; Glant, Tibor T.; Markovics, Adrienn; Rosenthal, Kenneth S.; Kurko, Julia; Carambula, Roy E.; Cress, Steve; Steiner, Harold L.; Zimmerman, Daniel H.

2017-01-01

Rheumatoid arthritis (RA) is an autoimmune joint disease maintained by aberrant immune responses involving CD4+ T helper (Th)1 and Th17 cells. In this study, we tested the therapeutic efficacy of Ligand Epitope Antigen Presentation System (LEAPS™) vaccines in two Th1 cell-driven mouse models of RA, cartilage proteoglycan (PG)-induced arthritis (PGIA) and PG G1-domain-induced arthritis (GIA). The immunodominant PG peptide PG70 was attached to a DerG or J immune cell binding peptide, and the DerG-PG70 and J-PG70 LEAPS vaccines were administered to the mice after the onset of PGIA or GIA symptoms. As indicated by significant decreases in visual and histopathological scores of arthritis, the DerG-PG70 vaccine inhibited disease progression in both PGIA and GIA, while the J-PG70 vaccine was ineffective. Splenic CD4+ cells from DerG-PG70-treated mice were diminished in Th1 and Th17 populations but enriched in Th2 and regulatory T (Treg) cells. In vitro spleen cell-secreted and serum cytokines from DerG-PG70-treated mice demonstrated a shift from a pro-inflammatory to an anti-inflammatory/regulatory profile. DerG-PG70 peptide tetramers preferentially bound to CD4+ T-cells of GIA spleen cells. We conclude that the DerG-PG70 vaccine (now designated CEL-4000) exerts its therapeutic effect by interacting with CD4+ cells, which results in an antigen-specific down-modulation of pathogenic T-cell responses in both the PGIA and GIA models of RA. Future studies will need to determine the potential of LEAPS vaccination to provide disease suppression in patients with RA. PMID:28583308

In silico structural analysis of group 3, 6 and 9 allergens from Dermatophagoides farinae.

PubMed

Teng, Feixiang; Yu, Lili; Bian, Yonghua; Sun, Jinxia; Wu, Juansong; Ling, Cunbao; Yang, Li; Wang, Yungang; Cui, Yubao

2015-05-01

Dermatophagoides farinae (Hughes; Acari: Pyroglyphidae) are the predominant source of dust mite allergens, which provoke allergic diseases, such as rhinitis, asthma and eczema. Of the 30 allergen groups produced by D. farinae, the Der f 3, Der f 6 and Der f 9 allergens are all trypsin‑associated proteins, however little else is currently known about them. The present study used in silico tools to compare the amino acid sequences, and predict the secondary and tertiary structures of Der f 3, Der f 6 and Der f 9 allergens. Protein sequence alignment detected ~46% identity between Der f 3, Der f 6 and Der f 9. Furthermore, each protein was shown to contain three active sites and two highly conserved trypsin functional domains. Predictions of the secondary and tertiary structure identified α‑helices, β‑sheets and random coils. The active sites of the three proteins appeared to fold onto each other in a three‑dimensional model, constituting the active site of the enzyme. Epitope analysis demonstrated that Der f 3, Der f 6 and Der f 9 have 4‑5 potential epitopes located in random coils, and the epitope sequences of Der f 3, Der f 6 and Der f 9 were shown to overlap in two domains (at amino acids 83‑87 and 179‑180); however the residues in these two domains were not identical. The present study aimed to conduct a biochemical and genetic analysis of these three allergens, and to potentially contribute to the development of vaccines for allergen‑specific immunotherapy.

Implementation effect of productive 4-stage field orientation on the student technopreneur skill in vocational schools

NASA Astrophysics Data System (ADS)

Ismail, Edy; Samsudi, Widjanarko, Dwi; Joyce, Peter; Stearns, Roman

2018-03-01

This model integrates project base learning by creating a product based on environmental needs. The Produktif Orientasi Lapangan 4 Tahap (POL4T) combines technical skills and entrepreneurial elements together in the learning process. This study is to implement the result of technopreneurship learning model development which is environment-oriented by combining technology and entrepreneurship components on Machining Skill Program. This study applies research and development design by optimizing experimental subject. Data were obtained from questionnaires, learning material validation, interpersonal, intrapersonal observation forms, skills, product, teachers and students' responses, and cognitive tasks. Expert validation and t-test calculation are applied to see how effective POL4T learning model. The result of the study is in the form of 4 steps learning model to enhance interpersonal and intrapersonal attitudes, develop practical products which orient to society and appropriate technology so that the products can have high selling value. The model is effective based on the students' post test result, which is better than the pre-test. The product obtained from POL4T model is proven to be better than the productive learning. POL4T model is recommended to be implemented for XI grade students. This is can develop entrepreneurial attitudes that are environment oriented, community needs and technical competencies students.

Scattering property based contextual PolSAR speckle filter

NASA Astrophysics Data System (ADS)

Mullissa, Adugna G.; Tolpekin, Valentyn; Stein, Alfred

2017-12-01

Reliability of the scattering model based polarimetric SAR (PolSAR) speckle filter depends upon the accurate decomposition and classification of the scattering mechanisms. This paper presents an improved scattering property based contextual speckle filter based upon an iterative classification of the scattering mechanisms. It applies a Cloude-Pottier eigenvalue-eigenvector decomposition and a fuzzy H/α classification to determine the scattering mechanisms on a pre-estimate of the coherency matrix. The H/α classification identifies pixels with homogeneous scattering properties. A coarse pixel selection rule groups pixels that are either single bounce, double bounce or volume scatterers. A fine pixel selection rule is applied to pixels within each canonical scattering mechanism. We filter the PolSAR data and depending on the type of image scene (urban or rural) use either the coarse or fine pixel selection rule. Iterative refinement of the Wishart H/α classification reduces the speckle in the PolSAR data. Effectiveness of this new filter is demonstrated by using both simulated and real PolSAR data. It is compared with the refined Lee filter, the scattering model based filter and the non-local means filter. The study concludes that the proposed filter compares favorably with other polarimetric speckle filters in preserving polarimetric information, point scatterers and subtle features in PolSAR data.

Forest height estimation from mountain forest areas using general model-based decomposition for polarimetric interferometric synthetic aperture radar images

NASA Astrophysics Data System (ADS)

Minh, Nghia Pham; Zou, Bin; Cai, Hongjun; Wang, Chengyi

2014-01-01

The estimation of forest parameters over mountain forest areas using polarimetric interferometric synthetic aperture radar (PolInSAR) images is one of the greatest interests in remote sensing applications. For mountain forest areas, scattering mechanisms are strongly affected by the ground topography variations. Most of the previous studies in modeling microwave backscattering signatures of forest area have been carried out over relatively flat areas. Therefore, a new algorithm for the forest height estimation from mountain forest areas using the general model-based decomposition (GMBD) for PolInSAR image is proposed. This algorithm enables the retrieval of not only the forest parameters, but also the magnitude associated with each mechanism. In addition, general double- and single-bounce scattering models are proposed to fit for the cross-polarization and off-diagonal term by separating their independent orientation angle, which remains unachieved in the previous model-based decompositions. The efficiency of the proposed approach is demonstrated with simulated data from PolSARProSim software and ALOS-PALSAR spaceborne PolInSAR datasets over the Kalimantan areas, Indonesia. Experimental results indicate that forest height could be effectively estimated by GMBD.

Non-conventional synchronization of weakly coupled active oscillators

NASA Astrophysics Data System (ADS)

Manevitch, L. I.; Kovaleva, M. A.; Pilipchuk, V. N.

2013-03-01

We present a new type of self-sustained vibrations in the fundamental physical model covering a broad area of applications from wave generation in radiophysics and nonlinear optics to the heart muscle contraction and eyesight disorder in biophysics. Such a diversity of applications is due to the universal physical phenomenon of synchronization. Previous studies of this phenomenon, originating from Huygens famous observation, are based mainly on the model of two weakly coupled Van der Pol oscillators and usually deal with their synchronization in the regimes close to nonlinear normal modes (NNMs). In this work, we show for the first time that, in the important case of threshold excitation, an alternative synchronization mechanism can develop when the conventional synchronization becomes impossible. We identify this mechanism as an appearance of dynamic attractor with the complete periodic energy exchange between the oscillators, which is the dissipative analogue of highly intensive beats in a conservative system. This type of motion is therefore opposite to the NNM-type synchronization with no energy exchange by definition. The analytical description of these vibrations employs the concept of Limiting Phase Trajectories (LPTs) introduced by one of the authors earlier for conservative systems. Finally, within the LPT approach, we describe the transition from the complete energy exchange between the oscillators to the energy localization mostly on one of the two oscillators. The localized mode is an attractor in the range of model parameters wherein the LPT as well as the in-phase and out-of-phase NNMs become unstable.

Passive Electroreception in Fish: AN Analog Model of the Spike Generation Zone.

NASA Astrophysics Data System (ADS)

Harvey, James Robert

Sensory transduction begins in receptor cells specialized to the sensory modality involved and proceeds to the more generalized stage of the first afferent fiber, converting the initial sensory information into neural spikes for transmittal to the central nervous system. We have developed a unique analog electronic model of the generalized step (also known as the spike generation zone (SGZ)) using a tunnel diode, an operational amplifier, resistors, and capacitors. With no externally applied simulated postsynaptic input current, our model represents a 10^{-3}cm^2 patch (100 times the typical in vivo area) of tonically active, nonadaptive, postsynaptic neural membrane that behaves as a pacemaker cell. Similar to the FitzHugh-Nagumo equations, our model is shown to be a simplification of the Hodgkin-Huxley parallel conductance model and can be analyzed by the methods of van der Pol. Measurements using the model yield results which compare favorably to physiological stimulus-response data gathered by Murray for elasmobranch electroreceptors. We then use the model to show that the main contribution to variance in the rate of neural spike output is provided by coincident inputs to the SGZ oscillator (i.e., by synaptic input noise) and not by inherent instability of the SGZ oscillator. Configured for maximum sensitivity, our model is capable of detecting stimulus changes as low as 50 fA in less than a second and this corresponds to a fractional frequency change of Delta f/f ~ 2 times 10^{-3}. Much data exists implying that in vivo detection of Delta f/f is limited to the range of one to ten percent (Weber-Fechner criterion). We propose the variance induced by the synaptic input noise provides a plausible physiological basis for the Weber-Fechner criterion.

Herpes Simplex Virus Processivity Factor UL42 Imparts Increased DNA-Binding Specificity to the Viral DNA Polymerase and Decreased Dissociation from Primer-Template without Reducing the Elongation Rate

PubMed Central

Weisshart, Klaus; Chow, Connie S.; Coen, Donald M.

1999-01-01

Herpes simplex virus DNA polymerase consists of a catalytic subunit, Pol, and a processivity subunit, UL42, that, unlike other established processivity factors, binds DNA directly. We used gel retardation and filter-binding assays to investigate how UL42 affects the polymerase-DNA interaction. The Pol/UL42 heterodimer bound more tightly to DNA in a primer-template configuration than to single-stranded DNA (ssDNA), while Pol alone bound more tightly to ssDNA than to DNA in a primer-template configuration. The affinity of Pol/UL42 for ssDNA was reduced severalfold relative to that of Pol, while the affinity of Pol/UL42 for primer-template DNA was increased ∼15-fold relative to that of Pol. The affinity of Pol/UL42 for circular double-stranded DNA (dsDNA) was reduced drastically relative to that of UL42, but the affinity of Pol/UL42 for short primer-templates was increased modestly relative to that of UL42. Pol/UL42 associated with primer-template DNA ∼2-fold faster than did Pol and dissociated ∼10-fold more slowly, resulting in a half-life of 2 h and a subnanomolar Kd. Despite such stable binding, rapid-quench analysis revealed that the rates of elongation of Pol/UL42 and Pol were essentially the same, ∼30 nucleotides/s. Taken together, these studies indicate that (i) Pol/UL42 is more likely than its subunits to associate with DNA in a primer-template configuration rather than nonspecifically to either ssDNA or dsDNA, and (ii) UL42 reduces the rate of dissociation from primer-template DNA but not the rate of elongation. Two models of polymerase-DNA interactions during replication that may explain these findings are presented. PMID:9847307

N-terminal domains of human DNA polymerase lambda promote primer realignment during translesion DNA synthesis

PubMed Central

Taggart, David J.; Dayeh, Daniel M.; Fredrickson, Saul W.; Suo, Zucai

2014-01-01

The X-family DNA polymerases λ (Polλ) and β (Polβ) possess similar 5′-2-deoxyribose-5-phosphatelyase (dRPase) and polymerase domains. Besides these domains, Polλ also possesses a BRCA1 C-terminal (BRCT) domain and a proline-rich domain at its N terminus. However, it is unclear how these non-enzymatic domains contribute to the unique biological functions of Polλ. Here, we used primer extension assays and a newly developed high-throughput short oligonucleotide sequencing assay (HT-SOSA) to compare the efficiency of lesion bypass and fidelity of human Polβ, Polλ and two N-terminal deletion constructs of Polλ during the bypass of either an abasic site or a 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxodG) lesion. We demonstrate that the BRCT domain of Polλ enhances the efficiency of abasic site bypass by approximately 1.6-fold. In contrast, deletion of the N-terminal domains of Polλ did not affect the efficiency of 8-oxodG bypass relative to nucleotide incorporations opposite undamaged dG. HT-SOSA analysis demonstrated that Polλ and Polβ preferentially generated −1 or −2 frameshift mutations when bypassing an abasic site and the single or double base deletion frequency was highly sequence dependent. Interestingly, the BRCT and proline-rich domains of Polλ cooperatively promoted the generation of −2 frameshift mutations when the abasic site was situated within a sequence context that was susceptible to homology-driven primer realignment. Furthermore, both N-terminal domains of Polλ increased the generation of −1 frameshift mutations during 8-oxodG bypass and influenced the frequency of substitution mutations produced by Polλ opposite the 8-oxodG lesion. Overall, our data support a model wherein the BRCT and proline-rich domains of Polλ act cooperatively to promote primer/template realignment between DNA strands of limited sequence homology. This function of the N-terminal domains may facilitate the role of Polλ as a gap-filling polymerase within the non-homologous end joining pathway. PMID:25108835

Specific amino acid residues in the beta sliding clamp establish a DNA polymerase usage hierarchy in Escherichia coli.

PubMed

Sutton, Mark D; Duzen, Jill M

2006-03-07

Escherichia coli dnaN159 strains encode a mutant form of the beta sliding clamp (beta159), causing them to display altered DNA polymerase (pol) usage. In order to better understand mechanisms of pol selection/switching in E. coli, we have further characterized pol usage in the dnaN159 strain. The dnaN159 allele contains two amino acid substitutions: G66E (glycine-66 to glutamic acid) and G174A (glycine-174 to alanine). Our results indicated that the G174A substitution impaired interaction of the beta clamp with the alpha catalytic subunit of pol III. In light of this finding, we designed two additional dnaN alleles. One of these dnaN alleles contained a G174A substitution (beta-G174A), while the other contained D173A, G174A and H175A substitutions (beta-173-175). Examination of strains bearing these different dnaN alleles indicated that each conferred a distinct UV sensitive phenotype that was dependent upon a unique combination of Delta polB (pol II), Delta dinB (pol IV) and/or Delta umuDC (pol V) alleles. Taken together, these findings indicate that mutations in the beta clamp differentially affect the functions of these three pols, and suggest that pol II, pol IV and pol V are capable of influencing each others' abilities to gain access to the replication fork. These findings are discussed in terms of a model whereby amino acid residues in the vicinity of those mutated in beta159 (G66 and G174) help to define a DNA polymerase usage hierarchy in E. coli following UV irradiation.

Regulation and Modulation of Human DNA Polymerase δ Activity and Function

PubMed Central

Wang, Xiaoxiao; Zhang, Sufang; Zhang, Zhongtao; Lee, Ernest Y. C.

2017-01-01

This review focuses on the regulation and modulation of human DNA polymerase δ (Pol δ). The emphasis is on the mechanisms that regulate the activity and properties of Pol δ in DNA repair and replication. The areas covered are the degradation of the p12 subunit of Pol δ, which converts it from a heterotetramer (Pol δ4) to a heterotrimer (Pol δ3), in response to DNA damage and also during the cell cycle. The biochemical mechanisms that lead to degradation of p12 are reviewed, as well as the properties of Pol δ4 and Pol δ3 that provide insights into their functions in DNA replication and repair. The second focus of the review involves the functions of two Pol δ binding proteins, polymerase delta interaction protein 46 (PDIP46) and polymerase delta interaction protein 38 (PDIP38), both of which are multi-functional proteins. PDIP46 is a novel activator of Pol δ4, and the impact of this function is discussed in relation to its potential roles in DNA replication. Several new models for the roles of Pol δ3 and Pol δ4 in leading and lagging strand DNA synthesis that integrate a role for PDIP46 are presented. PDIP38 has multiple cellular localizations including the mitochondria, the spliceosomes and the nucleus. It has been implicated in a number of cellular functions, including the regulation of specialized DNA polymerases, mitosis, the DNA damage response, mouse double minute 2 homolog (Mdm2) alternative splicing and the regulation of the NADPH oxidase 4 (Nox4). PMID:28737709

Heterogeneous nucleation of polymorphs on polymer surfaces: polymer-molecule interactions using a Coulomb and van der Waals model.

PubMed

Wahlberg, Nanna; Madsen, Anders Ø; Mikkelsen, Kurt V

2018-06-09

The nucleation processes of acetaminophen on poly(methyl methacrylate) and poly(vinyl acetate) have been investigated and the mechanisms of the processes are studied. This is achieved by a combination of theoretical models and computational investigations within the framework of a modified QM/MM method; a Coulomb-van der Waals model. We have combined quantum mechanical computations and electrostatic models at the atomistic level for investigating the stability of different orientations of acetaminophen on the polymer surfaces. Based on the Coulomb-van der Waals model, we have determined the most stable orientation to be a flat orientation, and the strongest interaction is seen between poly(vinyl acetate) and the molecule in a flat orientation in vacuum.

[Effect of DNA polymerase beta on apoptosis and mitochondrial membrane potential induced by hydroquinone, a metabolite of benzene].

PubMed

Chen, Chen; Yang, Mo; Zhang, Zun-zhen; Wu, Mei; Deng, Wen-wen

2011-12-01

To explore the effect and mechanism of DNA polymerase β expression level on cell apoptosis and mitochondrial membrane potential induced by hydroquinone. Polβ wild-type cells (polβ+/+), polβ overexpressed cells (polβ oe) and polβ null cells (polβ-/-) were applied as a model cell system, The effect of cell apoptosis and mitochondrial membrane potential induced by different doses of hydroquinone were analyzed by flow cytometry. The ROS and ·OH assay kit were used to examine the cellular ROS and ·OH level. The activity of cellular SOD and GSH-Px were tested by Chemiluminescence method after exposed to different concentrations of hydroquinone. With the dose of hydroquinone increased, the rate of apoptosis and falling of mitochondrial membrane potential (ΔΨm) in cells were increased compared with the control. When compared with polβ+/+ cells, the rate of apoptosis in polβ-/- cells exposed to 20.00, 40.00, 80.00 µmol/L hydroquinone increased and the rate of apoptosis in polβ oe cells exposed to 10.00, 20.00, 40.00, 80.00 µmol/L hydroquinone decreased (P < 0.05). Compared with polβ+/+ cells (20.60% ± 0.57%, 37.95% ± 0.64%, 44.50% ± 1.27%, 57.55% ± 1.06%), the rate of cell which undergone mitochondrial depolarization in polβ-/- cells treated with 10.00, 20.00, 40.00, 80.00 µmol/L hydroquinone (33.60% ± 1.55%, 46.05% ± 1.77%, 52.75% ± 2.05%, 75.20% ± 0.56%) increased. The rate of cell which undergone mitochondrial depolarization in polβ oe cells exposed to 10.00, 20.00, 40.00, 80.00 µmol/L hydroquinone (16.05% ± 1.20%, 29.80% ± 1.21%, 35.15% ± 1.06%, 53.80% ± 0.85%) decreased (P < 0.05). When compared with polβ+/+ cells, fluorescent intensity of polβ-/- cells treated with different dosages of hydroquinone increased, while which of polβ oe cells decreased (P < 0.05). Compared with polβ+/+ cells, ·OH level of polβ-/- cells treated with 20.00, 40.00 µmol/L hydroquinone significantly enhanced, while which of polβ oe cells decreased sharply (P < 0.05). Under the same concentrations of hydroquinone, the activity of SOD and GSH-Px were decreased most rapidly in polβ-/- cells. The activity of SOD and GSH-Px in polβ oe cells decreased slower than in the polβ-/- cells. Hydroquinone could induced apoptosis by the generation of ROS and decrease of ΔΨm; polβ could protect cells from apoptosis induced by hydroquinone through decrease of ROS level and depolarization of mitochondria.

Analysis on Vertical Scattering Signatures in Forestry with PolInSAR

NASA Astrophysics Data System (ADS)

Guo, Shenglong; Li, Yang; Zhang, Jingjing; Hong, Wen

2014-11-01

We apply accurate topographic phase to the Freeman-Durden decomposition for polarimetric SAR interferometry (PolInSAR) data. The cross correlation matrix obtained from PolInSAR observations can be decomposed into three scattering mechanisms matrices accounting for the odd-bounce, double-bounce and volume scattering. We estimate the phase based on the Random volume over Ground (RVoG) model, and as the initial input parameter of the numerical method which is used to solve the parameters of decomposition. In addition, the modified volume scattering model introduced by Y. Yamaguchi is applied to the PolInSAR target decomposition in forest areas rather than the pure random volume scattering as proposed by Freeman-Durden to make best fit to the actual measured data. This method can accurately retrieve the magnitude associated with each mechanism and their vertical location along the vertical dimension. We test the algorithms with L- and P- band simulated data.

Super elongation complex contains a TFIIF-related subcomplex

PubMed Central

Knutson, Bruce A.; Smith, Marissa L.; Walker-Kopp, Nancy; Xu, Xia

2016-01-01

ABSTRACT Super elongation complex (SEC) belongs to a family of RNA polymerase II (Pol II) elongation factors that has similar properties as TFIIF, a general transcription factor that increases the transcription elongation rate by reducing pausing. Although SEC has TFIIF-like functional properties, it apparently lacks sequence and structural homology. Using HHpred, we find that SEC contains an evolutionarily related TFIIF-like subcomplex. We show that the SEC subunit ELL interacts with the Pol II Rbp2 subunit, as expected for a TFIIF-like factor. These findings suggest a new model for how SEC functions as a Pol II elongation factor and how it suppresses Pol II pausing. PMID:27223670

Despeckling Polsar Images Based on Relative Total Variation Model

NASA Astrophysics Data System (ADS)

Jiang, C.; He, X. F.; Yang, L. J.; Jiang, J.; Wang, D. Y.; Yuan, Y.

2018-04-01

Relatively total variation (RTV) algorithm, which can effectively decompose structure information and texture in image, is employed in extracting main structures of the image. However, applying the RTV directly to polarimetric SAR (PolSAR) image filtering will not preserve polarimetric information. A new RTV approach based on the complex Wishart distribution is proposed considering the polarimetric properties of PolSAR. The proposed polarization RTV (PolRTV) algorithm can be used for PolSAR image filtering. The L-band Airborne SAR (AIRSAR) San Francisco data is used to demonstrate the effectiveness of the proposed algorithm in speckle suppression, structural information preservation, and polarimetric property preservation.

Sensitization by subcutaneous route is superior to intraperitoneal route in induction of asthma by house dust mite in a murine mode

PubMed Central

Aun, Marcelo Vivolo; Saraiva-Romanholo, Beatriz Mangueira; de Almeida, Francine Maria; Brüggemann, Thayse Regina; Kalil, Jorge; Martins, Milton de Arruda; Arantes-Costa, Fernanda Magalhães; Giavina-Bianchi, Pedro

2015-01-01

ABSTRACT Objective To develop a new experimental model of chronic allergic pulmonary disease induced by house dust mite, with marked production of specific immunoglobulin E (IgE), eosinophilic inflammatory infiltrate in the airways and remodeling, comparing two different routes of sensitization. Methods The protocol lasted 30 days. BALB/c mice were divided into six groups and were sensitized subcutaneously or intraperitoneally with saline (negative control), Dermatophagoides pteronyssinus (Der p) 50 or 500mcg in three injections. Subsequently they underwent intranasal challenge with Der p or saline for 7 days and were sacrificed 24 hours after the last challenge. We evaluated the titration of specific IgE anti-Der p, eosinophilic density in peribronchovascular space and airway remodeling. Results Both animals sensitized intraperitoneally and subcutaneously produced specific IgE anti-Der p. Peribronchovascular eosinophilia increased only in mice receiving lower doses of Der p. However, only the group sensitized with Der p 50mcg through subcutaneously route showed significant airway remodeling. Conclusion In this murine model of asthma, both pathways of sensitization led to the production of specific IgE and eosinophilia in the airways. However, only the subcutaneously route was able to induce remodeling. Furthermore, lower doses of Der p used in sensitization were better than higher ones, suggesting immune tolerance. Further studies are required to evaluate the efficacy of this model in the development of bronchial hyperresponsiveness, but it can already be replicated in experiments to create new therapeutic drugs or immunotherapeutic strategies. PMID:26761554

Deficient brain RNA polymerase and altered nucleolar structure persists until day 8 after perinatal asphyxia of the rat.

PubMed

Kastner, Philomena; Mosgoeller, Wilhelm; Fang-Kircher, Susanne; Kitzmueller, Erwin; Kirchner, Liselotte; Hoeger, Harald; Seither, Peter; Lubec, Gert; Lubec, Barbara

2003-01-01

RNA polymerases (POL) are integral constituents of the protein synthesis machinery, with POL I and POL III coding for ribosomal RNA and POL II coding for protein. POL I is located in the nucleolus and transcribes class I genes, those that code for large ribosomal RNA. It has been reported that the POL system is seriously affected in perinatal asphyxia (PA) immediately after birth. Because POL I is necessary for protein synthesis and brain protein synthesis was shown to be deranged after hypoxic-ischemic conditions, we aimed to study whether POL derangement persists in a simple, well-documented animal model of graded global PA at the activity, mRNA, protein, and morphologic level until 8 d after the asphyctic insult. Nuclear POL I activity was determined according to a radiochemical method; mRNA steady state and protein levels of RPA4O-an essential subunit of POL I and III-were evaluated by blotting methods; and the POL I subunit polymerase activating factor-53 was evaluated using immunohistochemistry. Silver staining and transmission electron microscopy were used to examine the nucleolus. At the eighth day after PA, nuclear POL I decreased with the length of the asphyctic period, whereas mRNA and protein levels for RPA4O were unchanged. The subunit polymerase activating factor-53, however, was unambiguously reduced in several brain regions. Dramatic changes of nucleolar morphology were observed, the main finding being nucleolar disintegration at the electron microscopy level. We suggest that severe acidosis and/or deficient protein kinase C in the brain during the asphyctic period may be responsible for disintegration of the nucleolus as well as for decreased POL activity persisting until the eighth day after PA. The biologic effect may be that PA causes impaired RNA and protein synthesis, which has been already observed in hypoxic-ischemic states.

Inaccurate DNA Synthesis in Cell Extracts of Yeast Producing Active Human DNA Polymerase Iota

PubMed Central

Makarova, Alena V.; Grabow, Corinn; Gening, Leonid V.; Tarantul, Vyacheslav Z.; Tahirov, Tahir H.; Bessho, Tadayoshi; Pavlov, Youri I.

2011-01-01

Mammalian Pol ι has an unusual combination of properties: it is stimulated by Mn2+ ions, can bypass some DNA lesions and misincorporates “G” opposite template “T” more frequently than incorporates the correct “A.” We recently proposed a method of detection of Pol ι activity in animal cell extracts, based on primer extension opposite the template T with a high concentration of only two nucleotides, dGTP and dATP (incorporation of “G” versus “A” method of Gening, abbreviated as “misGvA”). We provide unambiguous proof of the “misGvA” approach concept and extend the applicability of the method for the studies of variants of Pol ι in the yeast model system with different cation cofactors. We produced human Pol ι in baker's yeast, which do not have a POLI ortholog. The “misGvA” activity is absent in cell extracts containing an empty vector, or producing catalytically dead Pol ι, or Pol ι lacking exon 2, but is robust in the strain producing wild-type Pol ι or its catalytic core, or protein with the active center L62I mutant. The signature pattern of primer extension products resulting from inaccurate DNA synthesis by extracts of cells producing either Pol ι or human Pol η is different. The DNA sequence of the template is critical for the detection of the infidelity of DNA synthesis attributed to DNA Pol ι. The primer/template and composition of the exogenous DNA precursor pool can be adapted to monitor replication fidelity in cell extracts expressing various error-prone Pols or mutator variants of accurate Pols. Finally, we demonstrate that the mutation rates in yeast strains producing human DNA Pols ι and η are not elevated over the control strain, despite highly inaccurate DNA synthesis by their extracts. PMID:21304950

Mechanism for priming DNA synthesis by yeast DNA Polymerase α

PubMed Central

Perera, Rajika L; Torella, Rubben; Klinge, Sebastian; Kilkenny, Mairi L; Maman, Joseph D; Pellegrini, Luca

2013-01-01

The DNA Polymerase α (Pol α)/primase complex initiates DNA synthesis in eukaryotic replication. In the complex, Pol α and primase cooperate in the production of RNA-DNA oligonucleotides that prime synthesis of new DNA. Here we report crystal structures of the catalytic core of yeast Pol α in unliganded form, bound to an RNA primer/DNA template and extending an RNA primer with deoxynucleotides. We combine the structural analysis with biochemical and computational data to demonstrate that Pol α specifically recognizes the A-form RNA/DNA helix and that the ensuing synthesis of B-form DNA terminates primer synthesis. The spontaneous release of the completed RNA-DNA primer by the Pol α/primase complex simplifies current models of primer transfer to leading- and lagging strand polymerases. The proposed mechanism of nucleotide polymerization by Pol α might contribute to genomic stability by limiting the amount of inaccurate DNA to be corrected at the start of each Okazaki fragment. DOI: http://dx.doi.org/10.7554/eLife.00482.001 PMID:23599895

Expression, purification and characterization of Der f 27, a new allergen from dermatophagoides farinae

PubMed Central

Lin, Jianli; Li, Meng; Liu, Yulin; Jiang, Congli; Wu, Yulan; Wang, Yuanyuan; Gao, Anjian; Liu, Zhigang; Yang, Pingchang; Liu, Xiaoyu

2015-01-01

The house dust mite (HDM), Dermatophagoidesfarinae (D. farina), is one of the most important indoor allergen sources and a major elicitor of allergic asthma; itscharacterization is important in the diagnosis and immunotherapy of mite allergen-relevant diseases. This study aims to characterize a novel allergen, the D. farinae-derived serpin (Der f 27). In this study, the total RNA of D. farinae was extracted, and the Der f 27 gene was cloned and expressed. The allergenicity of recombinant Der f 27 protein was determined by enzyme-linked immunosorbent assay, and Western-blotting with the sera of asthma patients, and skin prick test (SPT) in allergic human subjects. A r-Der f 27 allergic asthma mouse model was established. The cloned Der f 27 gene has been presented at the Gene Bank with an accession number of KM009995. The IgE levels of r-Der f 27 in the serum from r-Der f 27 SPT positive allergic patients were 3 folds more than healthy subjects. The Der f 27 SPT positive ratewas 42.1% in 19 DM-SPT positive patients. Airway hyperresponsiveness, serum specific IgE, and levels of interleukin-4 in the spleen cell culture supernatant were significantly increased in allergic asthma mice sensitized to r-Der f 27. In conclusion, Der f 27 is a new subtype of house mite allergen. PMID:26328010

Air quality impacts of distributed energy resources implemented in the northeastern United States.

PubMed

Carreras-Sospedra, Marc; Dabdub, Donald; Brouwer, Jacob; Knipping, Eladio; Kumar, Naresh; Darrow, Ken; Hampson, Anne; Hedman, Bruce

2008-07-01

Emissions from the potential installation of distributed energy resources (DER) in the place of current utility-scale power generators have been introduced into an emissions inventory of the northeastern United States. A methodology for predicting future market penetration of DER that considers economics and emission factors was used to estimate the most likely implementation of DER. The methodology results in spatially and temporally resolved emission profiles of criteria pollutants that are subsequently introduced into a detailed atmospheric chemistry and transport model of the region. The DER technology determined by the methodology includes 62% reciprocating engines, 34% gas turbines, and 4% fuel cells and other emerging technologies. The introduction of DER leads to retirement of 2625 MW of existing power plants for which emissions are removed from the inventory. The air quality model predicts maximum differences in air pollutant concentrations that are located downwind from the central power plants that were removed from the domain. Maximum decreases in hourly peak ozone concentrations due to DER use are 10 ppb and are located over the state of New Jersey. Maximum decreases in 24-hr average fine particulate matter (PM2.5) concentrations reach 3 microg/m3 and are located off the coast of New Jersey and New York. The main contribution to decreased PM2.5 is the reduction of sulfate levels due to significant reductions in direct emissions of sulfur oxides (SO(x)) from the DER compared with the central power plants removed. The scenario presented here represents an accelerated DER penetration case with aggressive emission reductions due to removal of highly emitting power plants. Such scenario provides an upper bound for air quality benefits of DER implementation scenarios.

On the accuracy of the MB-pol many-body potential for water: Interaction energies, vibrational frequencies, and classical thermodynamic and dynamical properties from clusters to liquid water and ice [How good is the MB-pol many-body potential for water?

DOE PAGES

Reddy, Sandeep K.; Straight, Shelby C.; Bajaj, Pushp; ...

2016-11-17

The MB-pol many-body potential has recently emerged as an accurate molecular model for water simulations from the gas to the condensed phase. Here, the accuracy of MB-pol is systematically assessed across the three phases of water through extensive comparisons with experimental data and high-level ab initio calculations. Individual many-body contributions to the interaction energies as well as vibrational spectra of water clusters calculated with MB-pol are in excellent agreement with reference data obtained at the coupled cluster level. We investigate several structural, thermodynamic, and dynamical properties of the liquid phase at atmospheric pressure through classical molecular dynamics simulations as amore » function of temperature. Furthermore, the structural properties of the liquid phase are in nearly quantitative agreement with X-ray diffraction data available over the temperature range from 268 to 368 K. The analysis of other thermodynamic and dynamical quantities emphasizes the importance of explicitly including nuclear quantum effects in the simulations, especially at low temperature, for a physically correct description of the properties of liquid water. Furthermore, both densities and lattice energies of several ice phases are also correctly reproduced by MB-pol. Following a recent study of DFT models for water, a score is assigned to each computed property, which demonstrates the high and, in many respects, unprecedented accuracy of MB-pol in representing all three phases of water.« less

On the accuracy of the MB-pol many-body potential for water: Interaction energies, vibrational frequencies, and classical thermodynamic and dynamical properties from clusters to liquid water and ice [How good is the MB-pol many-body potential for water?

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

Reddy, Sandeep K.; Straight, Shelby C.; Bajaj, Pushp

The MB-pol many-body potential has recently emerged as an accurate molecular model for water simulations from the gas to the condensed phase. Here, the accuracy of MB-pol is systematically assessed across the three phases of water through extensive comparisons with experimental data and high-level ab initio calculations. Individual many-body contributions to the interaction energies as well as vibrational spectra of water clusters calculated with MB-pol are in excellent agreement with reference data obtained at the coupled cluster level. We investigate several structural, thermodynamic, and dynamical properties of the liquid phase at atmospheric pressure through classical molecular dynamics simulations as amore » function of temperature. Furthermore, the structural properties of the liquid phase are in nearly quantitative agreement with X-ray diffraction data available over the temperature range from 268 to 368 K. The analysis of other thermodynamic and dynamical quantities emphasizes the importance of explicitly including nuclear quantum effects in the simulations, especially at low temperature, for a physically correct description of the properties of liquid water. Furthermore, both densities and lattice energies of several ice phases are also correctly reproduced by MB-pol. Following a recent study of DFT models for water, a score is assigned to each computed property, which demonstrates the high and, in many respects, unprecedented accuracy of MB-pol in representing all three phases of water.« less

An Optimization and Assessment on DG adoption in JapanesePrototype Buildings

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

Zhou, Nan; Marnay, Chris; Firestone, Ryan

2005-11-30

This research investigates a method of choosing economicallyoptimal DER, expanding on prior studies at the Berkeley Lab using the DERdesign optimization program, the Distributed Energy Resources CustomerAdoption Model (DER-CAM). DER-CAM finds the optimal combination ofinstalled equipment from available DER technologies, given prevailingutility tariffs, site electrical and thermal loads, and a menu ofavailable equipment. It provides a global optimization, albeit idealized,that shows how the site energy load scan be served at minimum cost byselection and operation of on-site generation, heat recovery, andcooling. Five prototype Japanese commercial buildings are examined andDER-CAM applied to select thee conomically optimal DER system for each.The fivemore » building types are office, hospital, hotel, retail, and sportsfacility. Based on the optimization results, energy and emissionreductions are evaluated. Furthermore, a Japan-U.S. comparison study ofpolicy, technology, and utility tariffs relevant to DER installation ispresented. Significant decreases in fuel consumption, carbon emissions,and energy costs were seen in the DER-CAM results. Savings were mostnoticeable in the sports facility, followed by the hospital, hotel, andoffice building.« less

Entwicklung von Landnutzungsszenarien für landschaftsökologische Fragestellungen

NASA Astrophysics Data System (ADS)

Fritsch, Uta

2002-04-01

Die Landschaften Mitteleuropas sind das Resultat einer langwierigen Geschichte menschlicher Landnutzung mit ihren unterschiedlichen, z.T. konkurrierenden Nutzungsansprüchen. Durch eine überwiegend intensive Beanspruchung haben die direkten und indirekten Auswirkungen der Landnutzung in vielen Fällen zu Umweltproblemen geführt. Die Disziplin der Landschaftsökologie hat es sich zur Aufgabe gemacht, Konzepte für eine nachhaltige Nutzung der Landschaft zu entwickeln. Eine wichtige Fragestellung stellt dabei die Abschätzung der möglichen Folgen von Landnutzungsänderungen dar. Für die Analyse der relevanten Prozesse in der Landschaft werden häufig mathematische Modelle eingesetzt, welche es erlauben die Landschaft unter aktuellen Verhältnissen oder hinsichtlich veränderter Rahmenbedingungen zu untersuchen. Die hypothetische Änderung der Landnutzung, die als Landnutzungsszenario bezeichnet wird, verkörpert eine wesentliche Modifikation der Rahmenbedingungen, weil Landnutzung mageblich Einfluss auf die natürlichen Prozesse der Landschaft nimmt. Während die Antriebskräfte einer solchen Änderung überwiegend von sozio-ökonomischen und politischen Entscheidungen gesteuert werden, orientiert sich die exakte Verortung der Landnutzungsänderungen an den naturräumlichen Bedingungen und folgt z.T. erkennbaren Regeln. Anhand dieser Vorgaben ist es möglich, räumlich explizite Landnutzungsszenarien zu entwickeln, die als Eingangsdaten für die Modellierung verschiedener landschaftsökologischer Fragestellungen wie z.B. für die Untersuchung des Einflusses der Landnutzung auf den Wasserhaushalt, die Erosionsgefahr oder die Habitatqualität dienen können. Im Rahmen dieser Dissertation wurde das rasterbasierte deterministische Allokationsmodell luck (Land Use Change Scenario Kit) für die explizite Verortung der Landnutzungsänderungen entwickelt. Es basiert auf den in der Landschaftsökologie üblichen räumlichen Daten wie Landnutzung, Boden sowie Topographie und richtet sich bei der Szenarienableitung nach den Leitbildern der Landschaftsplanung. Das Modell fut auf der Hypothese, dass das Landnutzungsmuster als Funktion seiner landschaftsökologischen Faktoren beschrieben werden kann. Das Veränderungspotenzial einer Landnutzungseinheit resultiert im Modell aus einer Kombination der Bewertung der relativen Eignung des Standortes für die jeweilige Landnutzung und der Berücksichtigung von Standorteigenschaften der umliegenden Nachbarn. Die Durchführung der Landnutzungsänderung im Modell ist iterativ angelegt, um den graduellen Prozess des Landschaftswandels nachvollziehen zu können. Als Fallbeispiel für die Anwendung solcher räumlich expliziten Landnutzungsszenarien dient die Fragestellung, inwieweit Landnutzungsänderungen die Hochwasserentstehung beeinflussen. Um den Einfluss auf die Hochwasserentstehung für jede der Landnutzungskategorien – bebaute, landwirtschaftlich genutzte und naturnahe Flächen – abschätzen zu können, wird im Landnutzungsmodell luck exemplarisch für jede Kategorie ein Teilmodell für die Veränderung von Landnutzung angeboten: 1) Ausdehnung der Siedlungsfläche: Dieses Teilmodell fut auf der Annahme, dass sich Siedlungen nur in direkter Nachbarschaft bereits bestehender Bebauung und bevorzugt entlang von Entwicklungsachsen ausbreiten. Steile Hangneigungen stellen für potenzielle Standorte ein Hemmnis bei der Ausbreitung dar. 2) Stilllegung von Grenzertragsackerflächen: Gemä der Hypothese, dass sich die Stilllegung von Ackerflächen an der potenziellen Ertragsleistung der Standorte orientiert, werden in diesem Teilmodell alle Ackerstandorte dahingehend bewertet und die Flächen mit der geringsten Leistungsfähigkeit stillgelegt. Bei homogenen Gebietseigenschaften werden die Stilllegungsflächen zufällig auf die Ackerfläche verteilt. 3) Etablierung von Schutzgebieten in Ufer- und Auenbereichen: Ausgehend von der These, dass sich entlang von Flüssen sensible Flächen befinden, deren Schutz positive Folgen für das Leistungsvermögen der Landschaft haben kann, werden in diesem Teilmodell schützenswerte Ufer- und Auenbereiche auf derzeit landwirtschaftlich genutzten Flächen ausgewiesen. Die Gröe der Schutzgebietsfläche orientiert sich an der Morphologie der umgebenden Landschaft. Die drei Teilmodelle wurden hinsichtlich der implizierten Hypothesen mit vielen unterschiedlichen Ansätzen validiert. Das Resultat dieser intensiven Analyse zeigt für jedes Teilmodell eine zufriedenstellende Tauglichkeit. Die Modellierung der Landnutzungsänderungen wurden in drei mesoskaligen Flusseinzugsgebieten mit einer Fläche zwischen 100 und 500 km² durchgeführt, die sich markant in ihrer Landnutzung unterscheiden. Besonderer Wert wurde bei der Gebietsauswahl darauf gelegt, dass eines der Gebiete intensiv landwirtschaftlich genutzt wird, eines dicht besiedelt und eines vorwiegend bewaldet ist. Im Hinblick auf ihre Relevanz für die vorliegende Fragestellung wurden aus bestehenden Landnutzungstrends die Szenarien für (1) die prognostizierte Siedlungsfläche für das Jahr 2010, (2) die möglichen Konsequenzen des EU-weiten Beschlusses der Agenda 2000 und (3) die Novelle des Bundesnaturschutzgesetzes aus dem Jahr 2001 abgeleitet. Jedes Szenario wurde mit Hilfe des Modells auf die drei Untersuchungsgebiete angewendet. Dabei wurden für die Siedlungsausdehnung in allen drei Gebieten realistische Landnutzungsmuster generiert. Einschränkungen ergeben sich bei der Suche nach Grenzertragsstilllegungsflächen. Hier hat unter homogenen Gebietseigenschaften die zufällige Verteilung von Flächen für die Stilllegung zu einem unrealistischen Ergebnis geführt. Die Güte der Schutzgebietsausweisung ist mageblich an die aktuelle Landnutzung der Aue und die Morphologie des Geländes gebunden. Die besten Ergebnisse werden erzielt, wenn die Flächen in den Ufer- und Auenbereichen mehrheitlich unter derzeitiger Ackernutzung stehen und der Flusslauf sich in das Relief eingetieft hat. Exemplarisch werden für jeden Landnutzungstrend die hydrologischen Auswirkungen anhand eines historischen Hochwassers beschrieben, aus denen jedoch keine pauschale Aussage zum Einfluss der Landnutzung abgeleitet werden kann. Die Studie demonstriert die Bedeutung des Landnutzungsmusters für die natürlichen Prozesse in der Landschaft und unterstreicht die Notwendigkeit einer räumlich expliziten Modellierung für landschaftsökologische Fragestellungen in der Mesoskala. Today′s landscapes in Central Europe are the result of a long history of land-use, which is characterised by many different demands. The immediate and long-term consequences of predominantly intensive land-use have led to environmental problems in many cases. Therefore it is necessary to develop strategies for the maintenance of landscape efficiency which take into account the different claims of utilisation. In this context the estimation of possible impacts of land-use changes represents an important statement of problem. For the analysis of the relevant processes within the landscape, it is common to apply mathematical models. Such models enable the investigation of the landscape under current conditions or with regard to modified boundary conditions. A hypothetic alteration of land-use, which is termed as land-use scenario, represents a substantial modification of the boundary conditions, because land-use exerts a strong influence on the natural processes of the landscape. While the driving forces are predominantly governed by socio-economical and political decisions, the exact location of land-use changes within the landscape mainly depends on the natural conditions and follows partly transparent rules. With these presumptions it is possible to develop land-use scenarios, which can serve as input data for the modelling of different questions of landscape ecology such as the influence of land-use on the water balance, the danger of erosion or the quality of habitat characteristics. In the context of this thesis the grid-based deterministic allocation model luck (Land Use Change Scenario Kit) for the allocation of land-use changes was developed. It is based upon the types of spatial data, which are commonly used in landscape ecology, such as information on land-use, soils as well as topography. The derivation of scenarios follows the approaches of landscape planning. The model is based upon the hypothesis, that land-use structure can be described as a function of its landscape ecological factors. The potential of a site to become subject to land-use changes, results from a combination of its local qualities and the site characteristics of its neighbourhood. Land-use change is realised iteratively in order to simulate the gradual process of changes in the landscape. The influence of land-use changes on flood generation serves as a case study to demonstrate the need for spatial explicit land-use scenarios. For each land-use category – built up areas, agriculturally used areas and natural/semi-natural land – the model luck offers a submodel for investigating the effect of land-use changes on flood generation: 1) Expansion of settlement area: This submodel is based upon the assumption that settlements spread only in the neighbourhood of already existing built-up areas and preferentially along infrastructural axes of development. Steep slopes inhibit the spreading on potential locations. 2) Set-aside of marginal yield sites under agricultural use: Setting-aside of arable land is based on the hypothesis that the selection of arable land to be set-aside depends on the potential yield efficiency of the locations. Within this submodel all fields under agricultural use are valued to that effect and the ones with the least productive efficiency are selected as set-aside locations. In case of homogeneous area qualities the set-aside locations are selected randomly. 3) Establishment of protected areas in waterside and ripearian areas: This submodel takes into consideration that the protection of sensitive areas along the river courses may have positive consequences for the efficiency of the landscape. Therefore this submodel establishes protection zones on waterside and ripearian sites under currently agricultural use, that might be of value for nature conservation. The size of the protection area depends on the morphology of the surrounding landscape. The three submodels were validated with respect to the implied hypotheses by the help of many different approaches. The result of this intensive analysis shows a satisfying suitability for each of the submodels. The simulation of land-use changes was carried out for three mesoscale river catchments with an area between 100 and 500 km². Special attention was paid to the fact that these areas should be markingly different in their land-use: One study area is predominantly under intensive agricultural use, one is densely populated and the third one is covered by forest in large parts of the area. With regard to their relevance to the onhand question from existing land-use trends scenarios were derived for the prognosed settlement area for the year 2010, for the possible consequences of the EU-wide agreement of Agenda 2000 and for the amending federal conservation law dating to the year 2001, which enhances the enlargement of protected areas. Each scenario was applied to the three study areas utilizing the model luck. For the expansion of the settlement areas in all three study areas realistic land-use patterns were generated. Limitations arose only in the context of the search for marginal yield fields. Here, the random distribution of areas to be set-aside under homogeneous conditions led to unrealistic results. The quality of the establishment of protected areas in waterside and ripearian areas is substantially bound to current land-use and the morphology of the area. The best results for this submodel are achieved if waterside and ripearian areas are mainly arable land and if the river has lowered its course into the morphology. The hydrological consequences are described exemplarily for each land-use trend with a historical flood event. The interpretation of the hydrographs does not allow global statements about the influence of land-use. The study demonstrates the significance of land-use pattern for the natural processes in the landscape and underlines the necessity of spatially explicit modelling for landscape ecological questions at the mesoscale.

Grid-Based Surface Generalized Born Model for Calculation of Electrostatic Binding Free Energies.

PubMed

Forouzesh, Negin; Izadi, Saeed; Onufriev, Alexey V

2017-10-23

Fast and accurate calculation of solvation free energies is central to many applications, such as rational drug design. In this study, we present a grid-based molecular surface implementation of "R6" flavor of the generalized Born (GB) implicit solvent model, named GBNSR6. The speed, accuracy relative to numerical Poisson-Boltzmann treatment, and sensitivity to grid surface parameters are tested on a set of 15 small protein-ligand complexes and a set of biomolecules in the range of 268 to 25099 atoms. Our results demonstrate that the proposed model provides a relatively successful compromise between the speed and accuracy of computing polar components of the solvation free energies (ΔG pol ) and binding free energies (ΔΔG pol ). The model tolerates a relatively coarse grid size h = 0.5 Å, where the grid artifact error in computing ΔΔG pol remains in the range of k B T ∼ 0.6 kcal/mol. The estimated ΔΔG pol s are well correlated (r 2 = 0.97) with the numerical Poisson-Boltzmann reference, while showing virtually no systematic bias and RMSE = 1.43 kcal/mol. The grid-based GBNSR6 model is available in Amber (AmberTools) package of molecular simulation programs.

Transition from homogeneous to inhomogeneous limit cycles: Effect of local filtering in coupled oscillators

NASA Astrophysics Data System (ADS)

Banerjee, Tanmoy; Biswas, Debabrata; Ghosh, Debarati; Bandyopadhyay, Biswabibek; Kurths, Jürgen

2018-04-01

We report an interesting symmetry-breaking transition in coupled identical oscillators, namely, the continuous transition from homogeneous to inhomogeneous limit cycle oscillations. The observed transition is the oscillatory analog of the Turing-type symmetry-breaking transition from amplitude death (i.e., stable homogeneous steady state) to oscillation death (i.e., stable inhomogeneous steady state). This novel transition occurs in the parametric zone of occurrence of rhythmogenesis and oscillation death as a consequence of the presence of local filtering in the coupling path. We consider paradigmatic oscillators, such as Stuart-Landau and van der Pol oscillators, under mean-field coupling with low-pass or all-pass filtered self-feedback and through a rigorous bifurcation analysis we explore the genesis of this transition. Further, we experimentally demonstrate the observed transition, which establishes its robustness in the presence of parameter fluctuations and noise.

Emergence of amplitude death scenario in a network of oscillators under repulsive delay interaction

NASA Astrophysics Data System (ADS)

Bera, Bidesh K.; Hens, Chittaranjan; Ghosh, Dibakar

2016-07-01

We report the existence of amplitude death in a network of identical oscillators under repulsive mean coupling. Amplitude death appears in a globally coupled network of identical oscillators with instantaneous repulsive mean coupling only when the number of oscillators is more than two. We further investigate that, amplitude death may emerge even in two coupled oscillators as well as network of oscillators if we introduce delay time in the repulsive mean coupling. We have analytically derived the region of amplitude death island and find out how strength of delay controls the death regime in two coupled or a large network of coupled oscillators. We have verified our results on network of delayed Mackey-Glass systems where parameters are set in hyperchaotic regime. We have also tested our coupling approach in two paradigmatic limit cycle oscillators: Stuart-Landau and Van der Pol oscillators.

Connection between three-body configuration and four-body configuration of the Sitnikov problem when one of the masses approaches zero: circular case

NASA Astrophysics Data System (ADS)

Shahbaz Ullah, M.; Hassan, M. R.

2014-09-01

In this manuscript we have established averaged equation of motion of the Sitnikov restricted three- body and four-body problem when all the primaries are point masses, by applying the Van der Pol transformation and averaging technique of J. Guckenheimer and P. Holmes (in Nonlinear Oscillations, Dynamical System Bifurcations of Vector Fields, Springer, Berlin, 1983). In addition to the resonance criterion at the 3/2 commensurability we have chosen ω=2 n/3, n=4, ω is the angular velocity of the coordinate system. Further we established the Series solution of the three-body and four-body problem in the sense of Sitnikov. Lastly the periodicities of the solutions have been examined by the Poincare section and four-body and three-body problem have been compared by different comparative graphs and surfaces.

Delay-induced stochastic bifurcations in a bistable system under white noise

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

Sun, Zhongkui, E-mail: sunzk@nwpu.edu.cn; Fu, Jin; Xu, Wei

2015-08-15

In this paper, the effects of noise and time delay on stochastic bifurcations are investigated theoretically and numerically in a time-delayed Duffing-Van der Pol oscillator subjected to white noise. Due to the time delay, the random response is not Markovian. Thereby, approximate methods have been adopted to obtain the Fokker-Planck-Kolmogorov equation and the stationary probability density function for amplitude of the response. Based on the knowledge that stochastic bifurcation is characterized by the qualitative properties of the steady-state probability distribution, it is found that time delay and feedback intensity as well as noise intensity will induce the appearance of stochasticmore » P-bifurcation. Besides, results demonstrated that the effects of the strength of the delayed displacement feedback on stochastic bifurcation are accompanied by the sensitive dependence on time delay. Furthermore, the results from numerical simulations best confirm the effectiveness of the theoretical analyses.« less

Learning-Based Adaptive Optimal Tracking Control of Strict-Feedback Nonlinear Systems.

PubMed

Gao, Weinan; Jiang, Zhong-Ping; Weinan Gao; Zhong-Ping Jiang; Gao, Weinan; Jiang, Zhong-Ping

2018-06-01

This paper proposes a novel data-driven control approach to address the problem of adaptive optimal tracking for a class of nonlinear systems taking the strict-feedback form. Adaptive dynamic programming (ADP) and nonlinear output regulation theories are integrated for the first time to compute an adaptive near-optimal tracker without any a priori knowledge of the system dynamics. Fundamentally different from adaptive optimal stabilization problems, the solution to a Hamilton-Jacobi-Bellman (HJB) equation, not necessarily a positive definite function, cannot be approximated through the existing iterative methods. This paper proposes a novel policy iteration technique for solving positive semidefinite HJB equations with rigorous convergence analysis. A two-phase data-driven learning method is developed and implemented online by ADP. The efficacy of the proposed adaptive optimal tracking control methodology is demonstrated via a Van der Pol oscillator with time-varying exogenous signals.

Entwicklung von umwelt- und naturschutzgerechten Verfahren der landwirtschaftlichen Landnutzung für das Biosphärenreservat Schorfheide-Chorin

NASA Astrophysics Data System (ADS)

Meyer-Aurich, Andreas

1999-11-01

Mit der vorliegenden Arbeit werden exemplarisch Chancen und Grenzen der Integration von Umwelt- und Naturschutz in Verfahren der ackerbaulichen Landnutzung aufgezeigt. Die Umsetzung von Zielen des Umwelt- und Naturschutzes in Verfahren der Landnutzung ist mit verschiedenen Schwierigkeiten verbunden. Diese liegen zum einen in der Konkretisierung der Ziele, um diese umsetzen zu können, zum anderen in vielfach unzulänglichem Wissen über den Zusammenhang zwischen unterschiedlichen Formen der Landnutzung und insbesondere den biotischen Naturschutzzielen. Zunächst wird die Problematik der Zielfestlegung und Konkretisierung erörtert. Das Umweltqualitätszielkonzept von Fürst et al. (1992) stellt einen Versuch dar, Ziele des Umwelt- und Naturschutzes zu konkretisieren. Dieses Konzept haben Heidt et al. (1997) auf einen Landschaftsausschnitt von ca. 6000 ha im Biosphärenreservat Schorfheide-Chorin im Nordosten Brandenburgs angewendet. Eine Auswahl der von Heidt et al. (1997) formulierten Umweltqualitätsziele bildet die Basis dieser Arbeit. Für die ausgewählten Umweltqualitätsziele wurden wesentliche Einflussfaktoren der Landnutzung identifiziert und ein Bewertungssystem entwickelt, mit dem die Auswirkungen von landwirtschaftlichen Anbauverfahren auf diese Umweltqualitätsziele abgebildet werden können. Die praktizierte Landnutzung von 20 Betrieben im Biosphärenreservat Schorfheide-Chorin wurde von 1994 bis 1997 hinsichtlich ihrer Auswirkungen auf die Umweltqualitätsziele analysiert. Die Analyse ergab ein sehr differenziertes Bild, das zum Teil Unterschiede in der Auswirkung auf die Umweltqualitätsziele für den Anbau einzelner Kulturen oder für bestimmte Betriebstypen zeigte. Es zeigte sich aber auch, dass es bei der Gestaltung des Anbaus einzelner Kulturarten große Unterschiede gab, die für Umweltqualitätsziele Bedeutung haben. Neben der Analyse der Landnutzung im Biosphärenreservat Schorfheide-Chorin wurde ein System entwickelt, mit dem die modellhafte Abbildung von Verfahren der Landnutzung möglich ist. Die Modellverfahren wurden in eine umfangreiche Datenbank eingebunden. Sie wurden mit Hilfe eines Fuzzy- Regelsystems hinsichtlich ihrer Auswirkungen auf die Umweltqualitätsziele bewertet. Die systematisch bewerteten Verfahren wurden in ein Betriebsmodell integriert, womit eine weitergehende Analyse der Zielbeziehungen und die Berechnung von Szenarien mit unterschiedlichen Rahmenbedingungen ermöglicht wurde. Die Analyse der Beziehung verschiedener Ziele zueinander (Zieldivergenz, Zielkonvergenz) zeigte, dass sich mit der Verfolgung vieler Umweltqualitätsziele auch positive Effekte für andere Umweltqualitätsziele ergaben. Teilweise konnte allerdings auch eine Zieldivergenz festgestellt werden, die auf mögliche Zielkonflikte hinweist. Bei der Analyse der Szenarienergebnisse zeigte sich, dass die vorgeschlagenen Veränderungen von Rahmenbedingungen vielfach eine Verschlechterung für verschiedene Umweltqualitätsziele mit sich bringen. Eine Ursache dafür liegt darin, dass bei der Definition der Szenarien die Bedeutung der Stilllegungen unterschätzt wurde. The objective of this research was to show the opportunities and limitations associated with integrating of environmental goals into agricultural land use management. For this purpose, the impact of agricultural land uses on six environmental quality goals was analysed for an approximately 16.000 ha study region within the biosphere reserve Schorfheide-Chorin in north-eastern Brandenburg (Germany). The environmental quality goals considered were protection of ground water, preservation of groundwater recharge, protection of the soil against wind and water erosion and preservation of animal species typical of the agricultural landscape, in particular partridge, amphibians and cranes. For each environmental quality goal, an evaluation framework is presented which enables an assessment of the impact of agricultural land uses on the environmental quality goals. The evaluation framework was applied to assess the impact of land uses of twenty farms in the study area from 1994 to 1997. It was demonstrated that the impact of agricultural land uses on the environmental quality of the region is very complex, and - although some crops did significantly impact certain aspects, one factor did not overwhelmingly contribute to the overall environmental quality. The evaluation framework was integrated further into a system of modelled cropping practices for optimisation calculations. For this purpose, a model framework was established based on a MS Access database. In the database, cropping practices for 17 crops are stored. Inputs and yields are adapted to the site-specific yield potential. In addition to the cropping practices, the model framework is comprised of an evaluation module and optimisation module. Hence, the impact of the cropping practices can be assessed for each site. This model framework provides the basis for optimisation calculations to forecast various land uses under different conditions. A step-wise integration of the environmental quality goals into the optimisation algorithm of a model farm allows for showing trade-offs between economic and ecological goals. The results of the trade-offs show that an improvement of ecological goal achievement is possible with little impact on the gross margin, as long as the improvement is less than 30% of the starting situation. If improvements greater than 30% are desired, very high losses of gross margin must be taken into consideration. Another result of the calculations shows that high achievements of environmental quality goals often correlate with the percentage of set-aside land within the total area.

Polarimetric SAR Interferometry Evaluation in Mangroves

NASA Technical Reports Server (NTRS)

Lee, Seung-Kuk; Fatoyinbo,Temilola; Osmanoglu, Batuhan; Sun, Guoqing

2014-01-01

TanDEM-X (TDX) enables to generate an interferometric coherence without temporal decorrelation effect that is the most critical factor for a successful Pol-InSAR inversion, as have recently been used for forest parameter retrieval. This paper presents mangrove forest height estimation only using single-pass/single-baseline/dual-polarization TDX data by means of new dual-Pol-InSAR inversion technique. To overcome a lack of one polarization in a conventional Pol- InSAR inversion (i.e. an underdetermined problem), the ground phase in the Pol-InSAR model is directly estimated from TDX interferograms assuming flat underlying topography in mangrove forest. The inversion result is validated against lidar measurement data (NASA's G-LiHT data).

An epitope-specific DerG-PG70 LEAPS vaccine modulates T cell responses and suppresses arthritis progression in two related murine models of rheumatoid arthritis.

PubMed

Mikecz, Katalin; Glant, Tibor T; Markovics, Adrienn; Rosenthal, Kenneth S; Kurko, Julia; Carambula, Roy E; Cress, Steve; Steiner, Harold L; Zimmerman, Daniel H

2017-07-13

Rheumatoid arthritis (RA) is an autoimmune joint disease maintained by aberrant immune responses involving CD4+ T helper (Th)1 and Th17 cells. In this study, we tested the therapeutic efficacy of Ligand Epitope Antigen Presentation System (LEAPS™) vaccines in two Th1 cell-driven mouse models of RA, cartilage proteoglycan (PG)-induced arthritis (PGIA) and PG G1-domain-induced arthritis (GIA). The immunodominant PG peptide PG70 was attached to a DerG or J immune cell binding peptide, and the DerG-PG70 and J-PG70 LEAPS vaccines were administered to the mice after the onset of PGIA or GIA symptoms. As indicated by significant decreases in visual and histopathological scores of arthritis, the DerG-PG70 vaccine inhibited disease progression in both PGIA and GIA, while the J-PG70 vaccine was ineffective. Splenic CD4+ cells from DerG-PG70-treated mice were diminished in Th1 and Th17 populations but enriched in Th2 and regulatory T (Treg) cells. In vitro spleen cell-secreted and serum cytokines from DerG-PG70-treated mice demonstrated a shift from a pro-inflammatory to an anti-inflammatory/regulatory profile. DerG-PG70 peptide tetramers preferentially bound to CD4+ T-cells of GIA spleen cells. We conclude that the DerG-PG70 vaccine (now designated CEL-4000) exerts its therapeutic effect by interacting with CD4+ cells, which results in an antigen-specific down-modulation of pathogenic T-cell responses in both the PGIA and GIA models of RA. Future studies will need to determine the potential of LEAPS vaccination to provide disease suppression in patients with RA. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Interwar Period Officer Education: A Model for the Future

DTIC Science & Technology

2015-05-23

within the Reichswehr.65 The training section directed curriculum development in accordance with Führung und Gefecht der verbundenen Waffen ...Leadership and Battle of the Combined Arms doctrine).66 The Führung und Gefecht der verbundenen Waffen established the doctrinal foundation for officer...display of initiative.68 These doctrinal concepts not only influenced the publication of Führung und Gefecht der verbundenen Waffen , they also

Recent Improvements to the Finite-Fault Rupture Detector Algorithm: FinDer II

NASA Astrophysics Data System (ADS)

Smith, D.; Boese, M.; Heaton, T. H.

2015-12-01

Constraining the finite-fault rupture extent and azimuth is crucial for accurately estimating ground-motion in large earthquakes. Detecting and modeling finite-fault ruptures in real-time is thus essential to both earthquake early warning (EEW) and rapid emergency response. Following extensive real-time and offline testing, the finite-fault rupture detector algorithm, FinDer (Böse et al., 2012 & 2015), was successfully integrated into the California-wide ShakeAlert EEW demonstration system. Since April 2015, FinDer has been scanning real-time waveform data from approximately 420 strong-motion stations in California for peak ground acceleration (PGA) patterns indicative of earthquakes. FinDer analyzes strong-motion data by comparing spatial images of observed PGA with theoretical templates modeled from empirical ground-motion prediction equations (GMPEs). If the correlation between the observed and theoretical PGA is sufficiently high, a report is sent to ShakeAlert including the estimated centroid position, length, and strike, and their uncertainties, of an ongoing fault rupture. Rupture estimates are continuously updated as new data arrives. As part of a joint effort between USGS Menlo Park, ETH Zurich, and Caltech, we have rewritten FinDer in C++ to obtain a faster and more flexible implementation. One new feature of FinDer II is that multiple contour lines of high-frequency PGA are computed and correlated with templates, allowing the detection of both large earthquakes and much smaller (~ M3.5) events shortly after their nucleation. Unlike previous EEW algorithms, FinDer II thus provides a modeling approach for both small-magnitude point-source and larger-magnitude finite-fault ruptures with consistent error estimates for the entire event magnitude range.

Untersuchungen zur Entwicklung von Satellitengalaxien

NASA Astrophysics Data System (ADS)

Seidel, Björn

2002-01-01

Gleichgewichtsmodelle ein- und zweikomponentiger Satellitengalaxien werden erzeugt und die Gezeiteneinwirkungen der als starres äußeres Potential angenommenen Milchstraße auf sie betrachtet. Eine erste Reihe von Simulationen mit anfänglich kugelsymmetrischen einkomponentigen Satelliten zeigt, daß sich nach elliptischer Deformation ein Balken und Schweife ungleicher Länge ausbilden, deren Aussehen sich periodisch ändert. Mithilfe von Vergleichssimulationen wurden folgende Phänomene am Satelliten entdeckt: (1) Hochdichtebereiche in den Schweifen, (2) Niedrigdichtebereiche um den Kern bzw. Balken und (3) ein oft verdeckter Balken. Analysiert wird das Erscheinungsbild in Zeitabhängigkeit. Die Teilchen gehen dem Kern über den Balken verloren und bewegen sich entlang gewisser stets gleich aussehender charakteristischer Strukturen in die Schweife. Nach einer Herleitung allgemeiner Größen des mehrkomponentigen Kingprofils werden drei stabile Standardmodelle zweikomponentiger Satellitengalaxien mit Massenverhältnis 1:10 (baryonische zu dunkle Materie) und unterschiedlicher Verteilung der dunklen und sichtbaren Materie gefunden. Ohne die Allgemeinheit der Ergebnisse zu beeinträchtigen, wurde dabei die Große Magellanische Wolke als Grundlage der Modelle genommen. Nach geeigneter Wahl der Bahn, zu der der Gezeitenradius des verwendeten dreikomponentigen Milchstraßenpotentials sowohl analytisch als auch numerisch berechnet wird, werden Simulationen der Modelle analysiert. Hauptaugenmerk ist das unterschiedliche Verhalten der Komponenten. Hauptergebnisse: (1) Es ist möglich, große Anteile dunkler, jedoch nur geringe sichtbarer Materie abzulösen. Dunkle und sichtbare Materie können unterschiedliche morphologische Strukturen bilden. (2) Je nach Konzentration der Komponenten ist die Eigengravitation der Teilchen mehr oder weniger für das Aussehen bestimmend. (3) Die Kernauflösung des Satelliten findet im Perigalaktikum (PG), sein Zerfall aber erst im Apogalaktikum statt. (4) Die Geschwindigkeitsdispersionen der Komponenten im Kern sind im PG entlang der Sichtlinie kurzzeitig stark erhöht, sie fallen ebenso wie die Dichten und deren Verhältnis mit jedem PG stufenförmig ab; einiges davon sind nur Projektionseffekte. (5) Der radiale Verlauf der Geschwindigkeitsdispersion ist vom Bahnort abhängig er wurde genau untersucht. (6) Der Satellit zerfällt über einen Kreislauf aus Massenverlust, flacher werdendem Potential und kleiner werdendem Gezeitenradius. Equilibrium models of one- and two-component satellite galaxies are created. The tidal influence of the Milky Way, which is modeled as a rigid external potential, is examined. A first set of simulations adopting originally spherically-symmetric, one-component satellites show that after elliptical deformation, a bar and tails of unequal length arise which change their morphology cyclically. By considering comparative simulations, the following phenomena are discovered: (1) High-density regions in the tails, (2) low-density zones around the core or bar, (3) an often concealed bar. The overall morphology as function of time is analysed. The particles are lost from the core via the bar and move along certain morphologically characteristic structures into the tails. After deducing general quantities of the multi-component King model, three stable standard models of two-component satellite galaxies with different distributions of dark and visible matter are found. These models have a mass ratio of 1:10 for baryonic to dark matter. Without restriction to the universality of the results, the Large Magellanic Cloud was taken as basic prototype for these models. To choose the proper orbits, the tidal radius of the three-component model of the potential of the Galaxy is calculated both analytically and numerically. Then the simulations are analysed with the different behaviour of the components being the main focus of interest. Main results: (1) It is possible to detach a large fraction of dark matter but only a small amount of visible matter. Dark and visible matter may form different morphological structures. (2) Depending on the concentrations of the components, self-gravity may be the decisive factor for determining the morphology. (3) The dissolution of the core of the satellite occurs at perigalacticon (PG), but it does not decay before apogalacticon. (4) At PG the core densities of the components, their ratio and the velocity dispersions fall off in steps, the velocity dispersions along the line of sight show a high narrow peak. Some of these effects are just projection effects. (5) The radial dependence of the velocity dispersion is dependent on the orbital position; it is analysed in detail. (6) The satellite decays through a cycle of mass loss, an increasingly shallow potential and decreasing tidal radius.

Analysis of rocket engine injection combustion processes

NASA Technical Reports Server (NTRS)

Salmon, J. W.; Saltzman, D. H.

1977-01-01

Mixing methodology improvement for the JANNAF DER and CICM injection/combustion analysis computer programs was accomplished. ZOM plane prediction model development was improved for installation into the new standardized DER computer program. An intra-element mixing model developing approach was recommended for gas/liquid coaxial injection elements for possible future incorporation into the CICM computer program.

Optimizing DER Participation in Inertial and Primary-Frequency Response

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

Dall-Anese, Emiliano; Zhao, Changhong; Guggilam, Swaroop

This paper develops an approach to enable the optimal participation of distributed energy resources (DERs) in inertial and primary-frequency response alongside conventional synchronous generators. Leveraging a reduced-order model description of frequency dynamics, DERs' synthetic inertias and droop coefficients are designed to meet time-domain performance objectives of frequency overshoot and steady-state regulation. Furthermore, an optimization-based method centered around classical economic dispatch is developed to ensure that DERs share the power injections for inertial- and primary-frequency response in proportion to their power ratings. Simulations for a modified New England test-case system composed of ten synchronous generators and six instances of the IEEEmore » 37-node test feeder with frequency-responsive DERs validate the design strategy.« less

Indoor factors associated with concentrations of house dust mite allergen, Der p 1, in a random sample of houses in Norwich, UK.

PubMed

Luczynska, C; Sterne, J; Bond, J; Azima, H; Burney, P

1998-10-01

Studies of house dust mite allergen concentrations suggest large variations both within and between homes. It is likely that different household characteristics influence allergen levels in different locations within the house. To investigate household characteristics associated with higher concentrations of house dust mite allergen in a random sample of houses. Information on indoor environment was obtained from 158 adults aged 20-44. Dust samples were collected from their living room floor, bedroom floor and mattress. Concentrations of Der p 1, the major allergen from the house dust mite Dermatophagoides pteronyssinus, were measured by monoclonal antibody immunoassay. Associations between mite allergen concentrations and household characteristics were examined using censored-normal regression models. Factors that were related to Der p 1 (P

Chesapeake Bay Sediment Flux Model

DTIC Science & Technology

1993-06-01

1988; Van der Molen , -88- 1991; Yoshida, 1981.) The model developed below is based on both of these approaches. It incorporates the diagenetic...288: pp. 289-333. Van der Molen , D.T. (1991): A simple, dynamic model for the simulation of the release of phosphorus from sediments in shallow...1974; Berner, 1980; van Cappellen and Berner, 1988). These relate the diagenetic production of phosphate to the resulting pore water concentration

Involvement of DNA polymerase beta in repairing oxidative damages induced by antitumor drug adriamycin

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

Liu Shukun; Wu Mei; Zhang Zunzhen, E-mail: zhangzunzhen@163.co

2010-08-01

Adriamycin (ADM) is a widely used antineoplastic drug. However, the increasing cellular resistance has become a serious limitation to ADM clinical application. The most important mechanism related to ADM-induced cell death is oxidative DNA damage mediated by reactive oxygen species (ROS). Base excision repair (BER) is a major pathway in the repair of DNA single strand break (SSB) and oxidized base. In this study, we firstly applied the murine embryo fibroblasts wild-type (pol {beta} +/+) and homozygous pol {beta} null cell (pol {beta} -/-) as a model to investigate ADM DNA-damaging effects and the molecular basis underlying these effects. Here,more » cellular sensitivity to ADM was examined using colorimetric assay and colony forming assay. ADM-induced cellular ROS level and the alteration of superoxide dismutase (SOD) activity were measured by commercial kits. Further, DNA strand break, chromosomal damage and gene mutation were assessed by comet assay, micronucleus test and hprt gene mutation assay, respectively. The results showed that pol {beta} -/- cells were more sensitive to ADM compared with pol {beta} +/+ cells and more severe SSB and chromosomal damage as well as higher hprt gene mutation frequency were observed in pol {beta} -/- cells. ROS level in pol {beta} -/- cells increased along with decreased activity of SOD. These results demonstrated that pol {beta} deficiency could enable ROS accumulation with SOD activity decrease, further elevate oxidative DNA damage, and subsequently result in SSB, chromosome cleavage as well as gene mutation, which may be partly responsible for the cytotoxicity of ADM and the hypersensitivity of pol {beta} -/- cells to ADM. These findings suggested that pol {beta} is vital for repairing oxidative damage induced by ADM.« less

[Exploration of relationship between the expression level of DNA polymerase beta and 60Co gamma-ray radiosensitivity].

PubMed

Cui, Jie; Xu, Xin; Yang, Mo; Chen, Chen; Zhao, Wei; Wu, Mei; Zhang, Zun-zhen

2011-11-01

To explore the relationship between the expression level of DNA polymerase beta (pol beta) and 60Co gamma-ray radiosensitivity and provide a basis on improving the efficiency of radiotherapy theoretically. pol beta wild-type cells (pol beta +/+), pol beta null cells (pol beta -/-) and pol beta overexpressed cells (polp beta oe) were applied as a model system. The radiosensitivity of 60Co gamma-ray on the cell was detected by MTT assay and clone formation assay. The DCFH-DA fluorescent probe was used to examine the cellular ROS after 60Co gamma-rays radiation. MTT assay showed that after radiation by 60Co gamma-rays followed with 72 h incubation, the cell viabilities in the three kinds of cells decreased significantly with a dose-response relationship (r-/+ = -0.976, r-/- = -0.977, r(oe) = -0.982, P<0.05). In addition, the viability of pol beta -/- cell was lower than those of other two kinds of cells at the same dose (P<0.05). Likewise, the colony number and colony formation rate in all tested cells also decreased after exposure to 60Co gamma-rays. The ROS level in the three kinds of cells was enhanced after treatment with 60Co gamma-ray, and the ROS level in pol beta -/- cells was much higher than that in the other two kinds of cells (P<0.05). Cell death caused by 60Co gamma-ray may associated with the DNA oxidative damage mediated by ROS; Overexpression of pol beta could protect against oxidative DNA damage, thus the cell apoptosis/death, thereby leading to reducing the radiosensitivity of 60Co gamma-rays, while null of DNA pol beta could increase radiosensitivity of 60Co gamma-rays by compromising the DNA repair.

Modellierung des Einflusses der Landnutzung auf die Hochwasserentstehung in der Mesoskala

NASA Astrophysics Data System (ADS)

Niehoff, Daniel

2001-10-01

Seit 1990 waren mehrere der großen Flussgebiete Mitteleuropas wiederholt von extremen Hochwassern betroffen. Da sowohl die Landoberfläche als auch die Flusssysteme weiter Teile Mitteleuropas in der Vergangenheit weitreichenden Eingriffen ausgesetzt gewesen sind, wird bei der Suche nach den Ursachen für diese Häufung von Extremereignissen auch die Frage nach der Verantwortung des Menschen hierfür diskutiert. Gewässerausbau, Flächenversiegelung, intensive landwirtschaftliche Bodenbearbeitung, Flurbereinigung und Waldschäden sind nur einige Beispiele und Folgen der anthropogenen Eingriffe in die Landschaft. Aufgrund der Vielfalt der beteiligten Prozesse und deren Wechselwirkungen gibt es allerdings bislang nur Schätzungen darüber, wie sehr sich die Hochwassersituation hierdurch verändert hat. Vorrangiges Ziel dieser Arbeit ist es, mit Hilfe eines hydrologischen Modells systematisch darzustellen, in welcher Weise, in welcher Größenordnung und unter welchen Umständen die Art der Landnutzung auf die Hochwasserentstehung Einfluss nimmt. Dies wird anhand exemplarischer Modellanwendungen in der hydrologischen Mesoskala untersucht. Zu diesem Zweck wurde das deterministische und flächendifferenzierte hydrologische Modell wasim-eth ausgewählt, das sich durch eine ausgewogene Mischung aus physikalisch begründeten und konzeptionellen Ansätzen auszeichnet. Das Modell wurde im Rahmen dieser Arbeit um verschiedene Aspekte erweitert, die für die Charakterisierung des Einflusses der Landnutzung auf die Hochwasserentstehung wichtig sind: (1) Bevorzugtes Fließen in Makroporen wird durch eine Zweiteilung des Bodens in Makroporen und Bodenmatrix dargestellt, die schnelle Infiltration und Perkolation jenseits der hydraulischen Leitfähigkeit der Bodenmatrix ermöglicht. (2) Verschlämmung äußert sich im Modell abhängig von Niederschlagsintensität und Vegetationsbedeckungsgrad als Verschlechterung der Infiltrationsbedingungen an der Bodenoberfläche. (3) Das heterogene Erscheinungsbild bebauter Flächen mit einer Mischung aus versiegelten Bereichen und Freiflächen wird berücksichtigt, indem jede Teilfläche je nach Versiegelungsgrad in einen unversiegelten Bereich und einen versiegelten Bereich mit Anschluss an die Kanalisation aufgeteilt wird. (4) Dezentraler Rückhalt von Niederschlagswasser kann sowohl für natürliche Mulden als auch für gezielt angelegte Versickerungsmulden mit definierten Infiltrationsbedingungen simuliert werden. Das erweiterte Modell wird exemplarisch auf drei mesoskalige Teileinzugsgebiete des Rheins angewandt. Diese drei Gebiete mit einer Fläche von zwischen 100 und 500 km² wurden im Hinblick darauf ausgewählt, dass jeweils eine der drei Hauptlandnutzungskategorien Bebauung, landwirtschaftliche Nutzung oder Wald dominiert. Für die drei Untersuchungsgebiete sind räumlich explizite Landnutzungs- und Landbedeckungsszenarien entworfen worden, deren Einfluss auf die Hochwasserentstehung mit Hilfe des erweiterten hydrologischen Modells simuliert wird. Im Einzelnen werden die Auswirkungen von Verstädterung, Maßnahmen zur Niederschlagsversickerung in Siedlungsgebieten, Stilllegung agrarisch genutzter Flächen, veränderter landwirtschaftlicher Bodenbearbeitung, Aufforstung sowie von Sturmschäden in Wäldern untersucht. Diese Eingriffe beeinflussen die Interzeption von Niederschlag, dessen Infiltration, die oberflächennahen unterirdischen Fließprozesse sowie, zum Beispiel im Fall der Kanalisation, auch die Abflusskonzentration. Die hydrologischen Simulationen demonstrieren, dass die Versiegelung einer Fläche den massivsten Eingriff in die natürlichen Verhältnisse darstellt und deshalb die stärksten (negativen) Veränderungen der Hochwassersituation hervorbringt. Außerdem wird deutlich, dass eine bloße Änderung des Interzeptionsvermögens zu keinen wesentlichen Veränderungen führt, da die Speicherkapazität der Pflanzenoberflächen im Verhältnis zum Volumen hochwasserauslösender Niederschläge eher klein ist. Stärkere Veränderungen ergeben sich hingegen aus einer Änderung der Infiltrationsbedingungen. Die Grenzen der entwickelten Methodik zeigen sich am deutlichsten bei der Simulation veränderter landwirtschaftlicher Bewirtschaftungsmethoden, deren mathematische Beschreibung und zahlenmäßige Charakterisierung aufgrund der Komplexität der beteiligten Prozesse mit großen Unsicherheiten behaftet ist. Die Modellierungsergebnisse belegen darüber hinaus, dass pauschale Aussagen zum Einfluss der Landnutzung auf die Hochwasserentstehung aufgrund der entscheidenden Bedeutung der klimatischen und physiographischen Randbedingungen unzulässig sind. Zu den klimatischen Randbedingungen zählen sowohl Niederschlagsintensität und -dauer als auch die Feuchtebedingungen vor einem hochwasserauslösenden Niederschlag. Die physiographischen Randbedingungen sind von der geomorphologischen und geologischen Ausstattung des Gebiets vorgegeben. Weiterhin muss der räumliche und zeitliche Maßstab, über den Aussagen getroffen werden, klar definiert sein, da sich mit steigender Einzugsgebietsgröße die relative Bedeutung sowohl der verschiedenen Niederschlagstypen als auch der physiographischen Eigenschaften verschiebt. Dies wird in der vorliegenden Arbeit im Gegensatz zu vielen anderen Untersuchungen konsequent berücksichtigt. In Abhängigkeit von Randbedingungen und räumlichen Maßstab sind aufgrund der gewonnen Erkenntnisse folgende Aussagen zum Einfluss von Landnutzungsänderungen auf die Hochwasserentstehung möglich: (1) Für intensive konvektive Niederschlagsereignisse mit tendenziell geringer Vorfeuchte ist der Einfluss der Landnutzung größer als für langanhaltende advektive Niederschläge geringer Intensität, da im ersten Fall veränderte Infiltrationsbedingungen stärker zum Tragen kommen als bei kleinen Niederschlagsintensitäten. (2) In kleinen Einzugsgebieten, wo kleinräumige Konvektivzellen zu Hochwassern führen können, ist der Einfluss der Landnutzung dementsprechend größer als in großen Flussgebieten wie dem Rheingebiet, wo vor allem langanhaltende advektive Ereignisse (unter Umständen verbunden mit Schneeschmelze) relevant sind. (3) In Gebieten mit guten Speichereigenschaften wie mächtigen, gut durchlässigen Böden und gut durchlässigem Gesteinsuntergrund ist der Einfluss der Landnutzung größer als in Gebieten mit geringmächtigen Böden und geringdurchlässigem Festgestein. Dies ist darin begründet, dass in Gebieten mit guten Speichereigenschaften bei einer Verschlechterung der Infiltrationsbedingungen mehr Speicherraum für Niederschlag verloren geht als in anderen Gebieten. Since 1990, several of the large European river basins were affected repeatedly by extreme floods. As both the landscape and the river systems in large parts of Central Europe have undergone major changes in the past, during the search for the causes of this accumulation of extreme events also the impact of human activities on flooding has been discussed. River training, surface sealing, intensive agricultural land-use, consolidation of farmland, and damages to forests are only some examples and consequences of the anthropogenic interferences with the landscape. But due to the diversity of the processes and factors involved, by now it can only be estimated how far the flood situation has changed by these interferences. Therefore, the main target of this thesis is to describe systematically in which way, to what extent and under which circumstances the land-use exerts an influence on storm-runoff generation and subsequently the discharge of rivers. This is investigated by means of exemplary model applications at the hydrological meso-scale. For this task, the deterministic and distributed hydrological model wasim-eth was chosen due to its well-balanced mixture of physically-based and conceptual approaches. In the framework of this thesis, the model has been extended in order to cope with several phenomena which are important when aiming at a characterization of the influence of land-use on flood generation: (1) Preferential flow in macropores is treated by a division of the soil into macropores and a soil matrix. This so-called double-porosity approach allows for fast infiltration and percolation beyond the hydraulic conductivity of the soil matrix. (2) Siltation expresses itself within the model as a deterioration of infiltration conditions at the soil surface, depending on precipitation intensity and the degree of vegetation covering. (3) The heterogeneous appearance of built-up areas, consisting of both sealed areas and pervious areas, is taken into account by dividing each partial area into an unsealed part and a sealed part which is connected to the sewer system. (4) Decentralized storage can be simulated for natural depressions as well as for specific infiltration measures with defined infiltration conditions. The extended model is exemplarily applied to three meso-scale tributaries of the Rhine river. These three catchments with an area of between 100 and 500 km² were chosen with regard to their prevailing land-use, one of them being heavily urbanized, one dominated by agricultural use, and one being mainly forested. For these three catchments, spatially explicit land-use and land-cover scenarios were developed. The impact of these scenarios on storm-runoff generation is being simulated using the extended hydrological model. In this context, namely urbanization, infiltration measures in settlement areas, conversion of farmland to set-aside areas, altered agricultural management practices, affor estation and storm damages in forests are taken into account. These changes influence the interception of rainfall, its infiltration into the soil, the subsurface flow processes next to the soil surface as well as, for example in the case of sewer systems, also runoff concentration. The hydrological simulations demonstrate that sealing of the soil surface is the most intensive intervention in the natural conditions among the ones which are mentioned above. Therefore it results in the strongest (negative) changes of the flooding situation in a catchment. In addition to that, the simulations show that a simple alteration in the interception capacity does not yield significant changes in catchment response, because the storage capacity of vegetation surfaces is rather low compared to the volume of storm events which normally lead to significant floods. More pronounced changes arise from modifications in the infiltration conditions. The limits of the methodology which was chosen for this thesis become obvious when simulating altered agricultural management practices. Due the complexity of the processes involved, mathematical description and parameterization is difficult and therefore afflicted with high uncertainty. In addition to that, the modelling results prove that global statements on the influence of land-use on flood generation are illegitimate because of the paramount importance of the climatic and physiographic boundary conditions. Climatic boundary conditions are precipitation intensity and duration as well as the moisture conditions before a storm event. The physiographic boundary counditions are given by the geomorphological and geological catchment properties. Furthermore, with increasing scale there is a shift in the relative importance of the different types of rainfall as well as the different geophysical catchment properties. Therefore, the spatial and temporal scale for which the results are valid have to be clearly defined. This is taken into account consequently within this thesis - in contrast to many other studies on this topic. Depending on boundary conditions and spatial scale, the findings allow the following statements regarding the influence of land-use changes on storm-runoff generation: (1) For intensive convective storm events with generally low antecedent soil moisture, the influence of land-use is greater than for long-lasting advective storm events with low rainfall intensities, because in the first case changes in the infiltration conditions are more important than during times of low precipitation intensities. (2) In small catchments, where small-scale convective cells can lead to a flood, the influence of land-use is accordingly greater than in large river basins like the Rhine basin, where long-lasting advective rainfalls (possibly in combination with snowmelt) are relevant. (3) In areas with good storage conditions like thick, permeable soils and pervious rock underneath, the influence of land-use is greater than in areas with thin soils and only slightly permeable bedrock. This is due to the fact that in case of deteriorating infiltration conditions, more storage space for precipitation is lost in areas with good storage conditions than in other areas. siehe auch: http://opus.kobv.de/ubp/volltexte/2005/398/

Optimizing Distributed Energy Resources and building retrofits with the strategic DER-CAModel

DOE PAGES

Stadler, M.; Groissböck, M.; Cardoso, G.; ...

2014-08-05

The pressuring need to reduce the import of fossil fuels as well as the need to dramatically reduce CO 2 emissions in Europe motivated the European Commission (EC) to implement several regulations directed to building owners. Most of these regulations focus on increasing the number of energy efficient buildings, both new and retrofitted, since retrofits play an important role in energy efficiency. Overall, this initiative results from the realization that buildings will have a significant impact in fulfilling the 20/20/20-goals of reducing the greenhouse gas emissions by 20%, increasing energy efficiency by 20%, and increasing the share of renewables tomore » 20%, all by 2020. The Distributed Energy Resources Customer Adoption Model (DER-CAM) is an optimization tool used to support DER investment decisions, typically by minimizing total annual costs or CO 2 emissions while providing energy services to a given building or microgrid site. This document shows enhancements made to DER-CAM to consider building retrofit measures along with DER investment options. Specifically, building shell improvement options have been added to DER-CAM as alternative or complementary options to investments in other DER such as PV, solar thermal, combined heat and power, or energy storage. The extension of the mathematical formulation required by the new features introduced in DER-CAM is presented and the resulting model is demonstrated at an Austrian Campus building by comparing DER-CAM results with and without building shell improvement options. Strategic investment results are presented and compared to the observed investment decision at the test site. Results obtained considering building shell improvement options suggest an optimal weighted average U value of about 0.53 W/(m 2K) for the test site. This result is approximately 25% higher than what is currently observed in the building, suggesting that the retrofits made in 2002 were not optimal. Furthermore, the results obtained with DER-CAM illustrate the complexity of interactions between DER and passive measure options, showcasing the need for a holistic optimization approach to effectively optimize energy costs and CO 2 emissions. Lastly, the simultaneous optimization of building shell improvements and DER investments enables building owners to take one step further towards nearly zero energy buildings (nZEB) or nearly zero carbon emission buildings (nZCEB), and therefore support the 20/20/20 goals.« less

Optimizing Distributed Energy Resources and building retrofits with the strategic DER-CAModel

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

Stadler, M.; Groissböck, M.; Cardoso, G.

The pressuring need to reduce the import of fossil fuels as well as the need to dramatically reduce CO 2 emissions in Europe motivated the European Commission (EC) to implement several regulations directed to building owners. Most of these regulations focus on increasing the number of energy efficient buildings, both new and retrofitted, since retrofits play an important role in energy efficiency. Overall, this initiative results from the realization that buildings will have a significant impact in fulfilling the 20/20/20-goals of reducing the greenhouse gas emissions by 20%, increasing energy efficiency by 20%, and increasing the share of renewables tomore » 20%, all by 2020. The Distributed Energy Resources Customer Adoption Model (DER-CAM) is an optimization tool used to support DER investment decisions, typically by minimizing total annual costs or CO 2 emissions while providing energy services to a given building or microgrid site. This document shows enhancements made to DER-CAM to consider building retrofit measures along with DER investment options. Specifically, building shell improvement options have been added to DER-CAM as alternative or complementary options to investments in other DER such as PV, solar thermal, combined heat and power, or energy storage. The extension of the mathematical formulation required by the new features introduced in DER-CAM is presented and the resulting model is demonstrated at an Austrian Campus building by comparing DER-CAM results with and without building shell improvement options. Strategic investment results are presented and compared to the observed investment decision at the test site. Results obtained considering building shell improvement options suggest an optimal weighted average U value of about 0.53 W/(m 2K) for the test site. This result is approximately 25% higher than what is currently observed in the building, suggesting that the retrofits made in 2002 were not optimal. Furthermore, the results obtained with DER-CAM illustrate the complexity of interactions between DER and passive measure options, showcasing the need for a holistic optimization approach to effectively optimize energy costs and CO 2 emissions. Lastly, the simultaneous optimization of building shell improvements and DER investments enables building owners to take one step further towards nearly zero energy buildings (nZEB) or nearly zero carbon emission buildings (nZCEB), and therefore support the 20/20/20 goals.« less

On the accuracy of the MB-pol many-body potential for water: Interaction energies, vibrational frequencies, and classical thermodynamic and dynamical properties from clusters to liquid water and ice

NASA Astrophysics Data System (ADS)

Reddy, Sandeep K.; Straight, Shelby C.; Bajaj, Pushp; Huy Pham, C.; Riera, Marc; Moberg, Daniel R.; Morales, Miguel A.; Knight, Chris; Götz, Andreas W.; Paesani, Francesco

2016-11-01

The MB-pol many-body potential has recently emerged as an accurate molecular model for water simulations from the gas to the condensed phase. In this study, the accuracy of MB-pol is systematically assessed across the three phases of water through extensive comparisons with experimental data and high-level ab initio calculations. Individual many-body contributions to the interaction energies as well as vibrational spectra of water clusters calculated with MB-pol are in excellent agreement with reference data obtained at the coupled cluster level. Several structural, thermodynamic, and dynamical properties of the liquid phase at atmospheric pressure are investigated through classical molecular dynamics simulations as a function of temperature. The structural properties of the liquid phase are in nearly quantitative agreement with X-ray diffraction data available over the temperature range from 268 to 368 K. The analysis of other thermodynamic and dynamical quantities emphasizes the importance of explicitly including nuclear quantum effects in the simulations, especially at low temperature, for a physically correct description of the properties of liquid water. Furthermore, both densities and lattice energies of several ice phases are also correctly reproduced by MB-pol. Following a recent study of DFT models for water, a score is assigned to each computed property, which demonstrates the high and, in many respects, unprecedented accuracy of MB-pol in representing all three phases of water.

DEM modeling of failure mechanisms induced by excavations on the Moon

NASA Astrophysics Data System (ADS)

jiang, mingjing; shen, zhifu; Utili, Stefano

2013-04-01

2D Discrete Element Method (DEM) analyses were performed for excavations supported by retaining walls in lunar environment. The lunar terrain is made of a layer of sand (regolith) which differs from terrestrial sands for two main features: the presence of adhesive attractive forces due to van der Waals interactions and grains being very irregular in shape leading to high interlocking. A simplified contact model based on linear elasticity and perfect plasticity was employed. The contact model includes a moment - relative rotation law to account for high interlocking among grains and a normal adhesion law to account for the van der Waals interactions. Analyses of the excavations were run under both lunar and terrestrial environments. Under lunar environment, gravity is approximately one sixth than the value on Earth and adhesion forces between grains of lunar regolith due to van der Waals interactions are not negligible. From the DEM simulations it emerged that van der Waals interactions may significantly increase the bending moment and deflection of the retaining wall, and the ground displacements. Hence this study indicates that an unsafe estimate of the wall response to an excavation on the Moon would be obtained from physical experiments performed in a terrestrial environment, i.e., considering the effect of gravity but neglecting the van der Waals interactions.

Optical EVPA rotations in blazars: testing a stochastic variability model with RoboPol data

NASA Astrophysics Data System (ADS)

Kiehlmann, S.; Blinov, D.; Pearson, T. J.; Liodakis, I.

2017-12-01

We identify rotations of the polarization angle in a sample of blazars observed for three seasons with the RoboPol instrument. A simplistic stochastic variability model is tested against this sample of rotation events. The model is capable of producing samples of rotations with parameters similar to the observed ones, but fails to reproduce the polarization fraction at the same time. Even though we can neither accept nor conclusively reject the model, we point out various aspects of the observations that are fully consistent with a random walk process.

van der Waals three-body force shell model (VTSM) for the lattice dynamical studies of thallous bromide

NASA Astrophysics Data System (ADS)

Tiwari, Sarvesh K.; Pandey, L. K.; Shukla, Lal Ji; Upadhyaya, K. S.

2009-12-01

The van der Waals three-body force shell model (VTSM) has been developed by modifying the three-body force shell model (TSM) for the lattice dynamics of ionic crystals with cesium chloride (CsCl) structure. This new model incorporates van der Waals interactions along with long-range Coulomb interactions, three-body interactions and short-range second neighbour interactions in the framework of a rigid shell model (RSM). In the present paper, VTSM has been used to study the lattice dynamics of thallous bromide (TlBr), from which adequacy of VTSM has been established. A comparative study of the dynamical behaviour of TlBr has also been done between the present model and TSM, the model over which modification has been made to obtain the present model VTSM. Good agreement has been observed between the theoretical and experimental results, which give confidence that it is an appropriate model for the complete description of ionic crystals with CsCl structure.

The impact of short-term stochastic variability in solar irradiance on optimal microgrid design

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

Schittekatte, Tim; Stadler, Michael; Cardoso, Gonçalo

2016-07-01

This paper proposes a new methodology to capture the impact of fast moving clouds on utility power demand charges observed in microgrids with photovoltaic (PV) arrays, generators, and electrochemical energy storage. It consists of a statistical approach to introduce sub-hourly events in the hourly economic accounting process. The methodology is implemented in the Distributed Energy Resources Customer Adoption Model (DER-CAM), a state of the art mixed integer linear model used to optimally size DER in decentralized energy systems. Results suggest that previous iterations of DER-CAM could undersize battery capacities. The improved model depicts more accurately the economic value of PVmore » as well as the synergistic benefits of pairing PV with storage.« less

Clustering of Alpers disease mutations and catalytic defects in biochemical variants reveal new features of molecular mechanism of the human mitochondrial replicase, Pol γ

PubMed Central

Euro, Liliya; Farnum, Gregory A.; Palin, Eino; Suomalainen, Anu; Kaguni, Laurie S.

2011-01-01

Mutations in Pol γ represent a major cause of human mitochondrial diseases, especially those affecting the nervous system in adults and in children. Recessive mutations in Pol γ represent nearly half of those reported to date, and they are nearly uniformly distributed along the length of the POLG1 gene (Human DNA Polymerase gamma Mutation Database); the majority of them are linked to the most severe form of POLG syndrome, Alpers–Huttenlocher syndrome. In this report, we assess the structure–function relationships for recessive disease mutations by reviewing existing biochemical data on site-directed mutagenesis of the human, Drosophila and yeast Pol γs, and their homologs from the family A DNA polymerase group. We do so in the context of a molecular model of Pol γ in complex with primer–template DNA, which we have developed based upon the recently solved crystal structure of the apoenzyme form. We present evidence that recessive mutations cluster within five distinct functional modules in the catalytic core of Pol γ. Our results suggest that cluster prediction can be used as a diagnosis-supporting tool to evaluate the pathogenic role of new Pol γ variants. PMID:21824913

Effects of self-coupling and asymmetric output on metastable dynamical transient firing patterns in arrays of neurons with bidirectional inhibitory coupling.

PubMed

Horikawa, Yo

2016-04-01

Metastable dynamical transient patterns in arrays of bidirectionally coupled neurons with self-coupling and asymmetric output were studied. First, an array of asymmetric sigmoidal neurons with symmetric inhibitory bidirectional coupling and self-coupling was considered and the bifurcations of its steady solutions were shown. Metastable dynamical transient spatially nonuniform states existed in the presence of a pair of spatially symmetric stable solutions as well as unstable spatially nonuniform solutions in a restricted range of the output gain of a neuron. The duration of the transients increased exponentially with the number of neurons up to the maximum number at which the spatially nonuniform steady solutions were stabilized. The range of the output gain for which they existed reduced as asymmetry in a sigmoidal output function of a neuron increased, while the existence range expanded as the strength of inhibitory self-coupling increased. Next, arrays of spiking neuron models with slow synaptic inhibitory bidirectional coupling and self-coupling were considered with computer simulation. In an array of Class 1 Hindmarsh-Rose type models, in which each neuron showed a graded firing rate, metastable dynamical transient firing patterns were observed in the presence of inhibitory self-coupling. This agreed with the condition for the existence of metastable dynamical transients in an array of sigmoidal neurons. In an array of Class 2 Bonhoeffer-van der Pol models, in which each neuron had a clear threshold between firing and resting, long-lasting transient firing patterns with bursting and irregular motion were observed. Copyright © 2016 Elsevier Ltd. All rights reserved.

Effects of intermediates between vitamins K(2) and K(3) on mammalian DNA polymerase inhibition and anti-inflammatory activity.

PubMed

Mizushina, Yoshiyuki; Maeda, Jun; Irino, Yasuhiro; Nishida, Masayuki; Nishiumi, Shin; Kondo, Yasuyuki; Nishio, Kazuyuki; Kuramochi, Kouji; Tsubaki, Kazunori; Kuriyama, Isoko; Azuma, Takeshi; Yoshida, Hiromi; Yoshida, Masaru

2011-02-10

Previously, we reported that vitamin K(3) (VK(3)), but not VK(1) or VK(2) (=MK-4), inhibits the activity of human DNA polymerase γ (pol γ). In this study, we chemically synthesized three intermediate compounds between VK(2) and VK(3), namely MK-3, MK-2 and MK-1, and investigated the inhibitory effects of all five compounds on the activity of mammalian pols. Among these compounds, MK-2 was the strongest inhibitor of mammalian pols α, κ and λ, which belong to the B, Y and X families of pols, respectively; whereas VK(3) was the strongest inhibitor of human pol γ, an A-family pol. MK-2 potently inhibited the activity of all animal species of pol tested, and its inhibitory effect on pol λ activity was the strongest with an IC(50) value of 24.6 μM. However, MK-2 did not affect the activity of plant or prokaryotic pols, or that of other DNA metabolic enzymes such as primase of pol α, RNA polymerase, polynucleotide kinase or deoxyribonuclease I. Because we previously found a positive relationship between pol λ inhibition and anti-inflammatory action, we examined whether these compounds could inhibit inflammatory responses. Among the five compounds tested, MK-2 caused the greatest reduction in 12-O-tetradecanoylphorbol-13-acetate (TPA)-induced acute inflammation in mouse ear. In addition, in a cell culture system using mouse macrophages, MK-2 displayed the strongest suppression of the production of tumor necrosis factor (TNF)-α induced by lipopolysaccharide (LPS). Moreover, MK-2 was found to inhibit the action of nuclear factor (NF)-κB. In an in vivo mouse model of LPS-evoked acute inflammation, intraperitoneal injection of MK-2 in mice led to suppression of TNF-α production in serum. In conclusion, this study has identified VK(2) and VK(3) intermediates, such as MK-2, that are promising anti-inflammatory candidates.

Polar synchrony and the climatic history of Antarctica deduced from Greenland's

NASA Astrophysics Data System (ADS)

Oh, J.; Rial, J. A.; Reischmann, E.

2012-12-01

Polar synchronization brings new insights into the dynamic processes that link Greenland's Dansgaard-Oeschger (DO) abrupt temperature fluctuations to Antarctic temperature variability. The term synchronization as used here describes how two or more coupled nonlinear oscillators adjust their (initially different) natural rhythms to a common frequency and constant relative phase. It is shown that, consistent with the presence of polar synchronization, the time series of the most representative abrupt climate events of the last glaciation recorded in Greenland and Antarctica can be transformed into one another by a pi/2 phase shift at millennial scale, with Antarctica temperature variations leading Greenland's. For this study we employ Van der Pol Synchronizing Oscillators model to simulate Antarctic temperature proxy based on the synchronized relationship between two poles for the last 800ky after removing ~100ky glaciation cycles. The separated long period (~100ky) signal is reproduced by frequency modulation. As separation techniques, Singular Spectrum Analysis and Empirical Mode Decomposition are adopted and decomposed long period signals are compared with them from linear filter. It is shown that remarkable close simulations of Antarctic temperature proxy are obtained with a model consisting of a few nonlinear differential equations especially when coupling terms have strong effects. This, plus the close reproduction of glaciation cycles by frequency modulation suggests the intriguing possibility that there are simple rules governing the complex behavior of global paleoclimate such as heat and mass transfer through the intervening ocean and atmosphere.

A universal concept based on cellular neural networks for ultrafast and flexible solving of differential equations.

PubMed

Chedjou, Jean Chamberlain; Kyamakya, Kyandoghere

2015-04-01

This paper develops and validates a comprehensive and universally applicable computational concept for solving nonlinear differential equations (NDEs) through a neurocomputing concept based on cellular neural networks (CNNs). High-precision, stability, convergence, and lowest-possible memory requirements are ensured by the CNN processor architecture. A significant challenge solved in this paper is that all these cited computing features are ensured in all system-states (regular or chaotic ones) and in all bifurcation conditions that may be experienced by NDEs.One particular quintessence of this paper is to develop and demonstrate a solver concept that shows and ensures that CNN processors (realized either in hardware or in software) are universal solvers of NDE models. The solving logic or algorithm of given NDEs (possible examples are: Duffing, Mathieu, Van der Pol, Jerk, Chua, Rössler, Lorenz, Burgers, and the transport equations) through a CNN processor system is provided by a set of templates that are computed by our comprehensive templates calculation technique that we call nonlinear adaptive optimization. This paper is therefore a significant contribution and represents a cutting-edge real-time computational engineering approach, especially while considering the various scientific and engineering applications of this ultrafast, energy-and-memory-efficient, and high-precise NDE solver concept. For illustration purposes, three NDE models are demonstratively solved, and related CNN templates are derived and used: the periodically excited Duffing equation, the Mathieu equation, and the transport equation.

Assessment of Distributed Generation Potential in JapaneseBuildings

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

Zhou, Nan; Marnay, Chris; Firestone, Ryan

2005-05-25

To meet growing energy demands, energy efficiency, renewable energy, and on-site generation coupled with effective utilization of exhaust heat will all be required. Additional benefit can be achieved by integrating these distributed technologies into distributed energy resource (DER) systems (or microgrids). This research investigates a method of choosing economically optimal DER, expanding on prior studies at the Berkeley Lab using the DER design optimization program, the Distributed Energy Resources Customer Adoption Model (DER-CAM). DER-CAM finds the optimal combination of installed equipment from available DER technologies, given prevailing utility tariffs, site electrical and thermal loads, and a menu of available equipment.more » It provides a global optimization, albeit idealized, that shows how the site energy loads can be served at minimum cost by selection and operation of on-site generation, heat recovery, and cooling. Five prototype Japanese commercial buildings are examined and DER-CAM applied to select the economically optimal DER system for each. The five building types are office, hospital, hotel, retail, and sports facility. Based on the optimization results, energy and emission reductions are evaluated. Furthermore, a Japan-U.S. comparison study of policy, technology, and utility tariffs relevant to DER installation is presented. Significant decreases in fuel consumption, carbon emissions, and energy costs were seen in the DER-CAM results. Savings were most noticeable in the sports facility (a very favourable CHP site), followed by the hospital, hotel, and office building.« less

Van der Waals model for phase transitions in thermoresponsive surface films.

PubMed

McCoy, John D; Curro, John G

2009-05-21

Phase transitions in polymeric surface films are studied with a simple model based on the van der Waals equation of state. Each chain is modeled by a single bead attached to the surface by an entropic-Hooke's law spring. The surface coverage is controlled by adjusting the chemical potential, and the equilibrium density profile is calculated with density functional theory. The interesting feature of this model is the multivalued nature of the density profile seen at low temperature. This van der Waals loop behavior is resolved with a Maxwell construction between a high-density phase near the wall and a low-density phase in a "vertical" phase transition. Signatures of the phase transition in experimentally measurable quantities are then found. Numerical calculations are presented for isotherms of surface pressure, for the Poisson ratio, and for the swelling ratio.

Refinement of a limit cycle oscillator model of the effects of light on the human circadian pacemaker

NASA Technical Reports Server (NTRS)

Jewett, M. E.; Kronauer, R. E.; Brown, E. N. (Principal Investigator)

1998-01-01

In 1990, Kronauer proposed a mathematical model of the effects of light on the human circadian pacemaker. Although this model predicted many general features of the response of the human circadian pacemaker to light exposure, additional data now available enable us to refine the original model. We first refined the original model by incorporating the results of a dose response curve to light into the model's predicted relationship between light intensity and the strength of the drive onto the pacemaker. Data from three bright light phase resetting experiments were then used to refine the amplitude recovery characteristics of the model. Finally, the model was tested and further refined using data from an extensive phase resetting experiment in which a 3-cycle bright light stimulus was presented against a background of dim light. In order to describe the results of the four resetting experiments, the following major refinements to the original model were necessary: (i) the relationship between light intensity (I) and drive onto the pacemaker was reduced from I1/3 to I0.23 for light levels between 150 and 10,000 lux; (ii) the van der Pol oscillator from the original model was replaced with a higher-order limit cycle oscillator so that amplitude recovery is slower near the singularity and faster near the limit cycle; (iii) a direct effect of light on circadian period (tau x) was incorporated into the model such that as I increases, tau x decreases, which is in accordance with "Aschoff's rule". This refined model generates the following testable predictions: it should be difficult to enhance normal circadian amplitude via bright light; near the critical point of a type 0 phase response curve (PRC) the slope should be steeper than it is in a type 1 PRC; and circadian period measured during forced desynchrony should be directly affected by ambient light intensity.

The steric gate of DNA polymerase ι regulates ribonucleotide incorporation and deoxyribonucleotide fidelity.

PubMed

Donigan, Katherine A; McLenigan, Mary P; Yang, Wei; Goodman, Myron F; Woodgate, Roger

2014-03-28

Accurate DNA synthesis in vivo depends on the ability of DNA polymerases to select dNTPs from a nucleotide pool dominated by NTPs. High fidelity replicative polymerases have evolved to efficiently exclude NTPs while copying long stretches of undamaged DNA. However, to bypass DNA damage, cells utilize specialized low fidelity polymerases to perform translesion DNA synthesis (TLS). Of interest is human DNA polymerase ι (pol ι), which has been implicated in TLS of oxidative and UV-induced lesions. Here, we evaluate the ability of pol ι to incorporate NTPs during DNA synthesis. pol ι incorporates and extends NTPs opposite damaged and undamaged template bases in a template-specific manner. The Y39A "steric gate" pol ι mutant is considerably more active in the presence of Mn(2+) compared with Mg(2+) and exhibits a marked increase in NTP incorporation and extension, and surprisingly, it also exhibits increased dNTP base selectivity. Our results indicate that a single residue in pol ι is able to discriminate between NTPs and dNTPs during DNA synthesis. Because wild-type pol ι incorporates NTPs in a template-specific manner, certain DNA sequences may be "at risk" for elevated mutagenesis during pol ι-dependent TLS. Molecular modeling indicates that the constricted active site of wild-type pol ι becomes more spacious in the Y39A variant. Therefore, the Y39A substitution not only permits incorporation of ribonucleotides but also causes the enzyme to favor faithful Watson-Crick base pairing over mutagenic configurations.

Applying DER-CAM for IIT Microgrid Explansion Planning

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

Shahidehpour, Mohammad; Li, Zuyi; Wang, Jianhui

The Distributed Energy Resources Customer Adoption Model (DER-CAM) is an economic and environmental model of customer DER adoption. This model has been in development at the Lawrence Berkeley National Laboratory since 2000. The objective of the model is to find optimal DER investments while minimizing total energy costs or carbon dioxide (CO2) emissions, or achieving a weighted objective that simultaneously considers both criteria. The Illinois Institute of Technology (IIT) Microgrid project started in August 2008, and the majority of the project was completed in May 2013. IIT Microgrid, funded mostly by a grant from the U.S. Department of Energy asmore » well as State and philanthropic contributions, empowers the campus consumers with the objective of establishing a smart microgrid that is highly reliable, economically viable, environmentally friendly, fuel-efficient, and resilient in extreme circumstances with a self-healing capability. In this project, we apply DER-CAM to study the expansion planning of the IIT Microgrid. First, the load data, environmental data, utility data, and technology data for the IIT Microgrid are gathered and organized to follow the DER-CAM input requirements. Then, DERCAM is applied to study the expansion planning of the IIT Microgrid for different cases, where different objectives in DER-CAM and different utility conditions are tested. Case 1 considers the objective of minimizing energy costs with fixed utility rates and 100% electric utility availability. Case 2 considers the objective of minimizing energy costs with real-time utility rates and 4 emergency weeks when the IIT Microgrid does not have access to the electric utility grid and has to operate in island mode. In Case 3, the utility rates are restored to fixed values and 100% electric utility availability is assumed, but a weighted multi-objective (Obj: a × costs + b × CO2 emissions, where a and b are weights for cost minimization and CO2 emissions minimization) is utilized to consider both energy costs and CO2 emissions. On the basis of the test results, the IIT Microgrid has the potential to benefit from investments in more DER technologies. The current annual energy costs and CO2 emissions for the IIT Microgrid are 6,495.1 k$ and 39,838.5 metric tons, respectively. This represents the baseline for this project.« less

Modeling of thermal storage systems in MILP distributed energy resource models

DOE PAGES

Steen, David; Stadler, Michael; Cardoso, Gonçalo; ...

2014-08-04

Thermal energy storage (TES) and distributed generation technologies, such as combined heat and power (CHP) or photovoltaics (PV), can be used to reduce energy costs and decrease CO 2 emissions from buildings by shifting energy consumption to times with less emissions and/or lower energy prices. To determine the feasibility of investing in TES in combination with other distributed energy resources (DER), mixed integer linear programming (MILP) can be used. Such a MILP model is the well-established Distributed Energy Resources Customer Adoption Model (DER-CAM); however, it currently uses only a simplified TES model to guarantee linearity and short run-times. Loss calculationsmore » are based only on the energy contained in the storage. This paper presents a new DER-CAM TES model that allows improved tracking of losses based on ambient and storage temperatures, and compares results with the previous version. A multi-layer TES model is introduced that retains linearity and avoids creating an endogenous optimization problem. The improved model increases the accuracy of the estimated storage losses and enables use of heat pumps for low temperature storage charging. Ultimately,results indicate that the previous model overestimates the attractiveness of TES investments for cases without possibility to invest in heat pumps and underestimates it for some locations when heat pumps are allowed. Despite a variation in optimal technology selection between the two models, the objective function value stays quite stable, illustrating the complexity of optimal DER sizing problems in buildings and microgrids.« less

Sliding Clamp–DNA Interactions Are Required for Viability and Contribute to DNA Polymerase Management in Escherichia coli

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

Heltzel, J.; Scouten Ponticelli, S; Sanders, L

2009-01-01

Sliding clamp proteins topologically encircle DNA and play vital roles in coordinating the actions of various DNA replication, repair, and damage tolerance proteins. At least three distinct surfaces of the Escherichia coli {beta} clamp interact physically with the DNA that it topologically encircles. We utilized mutant {beta} clamp proteins bearing G66E and G174A substitutions ({beta}159), affecting the single-stranded DNA-binding region, or poly-Ala substitutions in place of residues 148-HQDVR-152 ({beta}148-152), affecting the double-stranded DNA binding region, to determine the biological relevance of clamp-DNA interactions. As part of this work, we solved the X-ray crystal structure of {beta}148-152, which verified that themore » poly-Ala substitutions failed to significantly alter the tertiary structure of the clamp. Based on functional assays, both {beta}159 and {beta}148-152 were impaired for loading and retention on a linear primed DNA in vitro. In the case of {beta}148-152, this defect was not due to altered interactions with the DnaX clamp loader, but rather was the result of impaired {beta}148-152-DNA interactions. Once loaded, {beta}148-152 was proficient for DNA polymerase III (Pol III) replication in vitro. In contrast, {beta}148-152 was severely impaired for Pol II and Pol IV replication and was similarly impaired for direct physical interactions with these Pols. Despite its ability to support Pol III replication in vitro, {beta}148-152 was unable to support viability of E. coli. Nevertheless, physiological levels of {beta}148-152 expressed from a plasmid efficiently complemented the temperature-sensitive growth phenotype of a strain expressing {beta}159 (dnaN159), provided that Pol II and Pol IV were inactivated. Although this strain was impaired for Pol V-dependent mutagenesis, inactivation of Pol II and Pol IV restored the Pol V mutator phenotype. Taken together, these results support a model in which a sophisticated combination of competitive clamp-DNA, clamp-partner, and partner-DNA interactions serve to manage the actions of the different E. coli Pols in vivo.« less

Structural Equation Model Approach to the Use of Response Times for Improving Estimation in Item Response Models

ERIC Educational Resources Information Center

Sen, Rohini

2012-01-01

In the last five decades, research on the uses of response time has extended into the field of psychometrics (Schnikpe & Scrams, 1999; van der Linden, 2006; van der Linden, 2007), where interest has centered around the usefulness of response time information in item calibration and person measurement within an item response theory. framework.…

In der fachsprachlichen Didaktik ist der "fachneutrale" Vorkurs ein Umweg (In Teaching Technical Language, a "Neutral Area" Course is an Evasion)

ERIC Educational Resources Information Center

Becker, Norbert

1974-01-01

In learning to read technical language, texts in specialized technical fields are preferable to "neutral area" or popular science texts. Assorted textbooks are suggested, along with suitable types of exercises and their use. Model preparatory exercises and model drills are included. (Text is in German.) (IFS/WGA)

Data-driven planning of distributed energy resources amidst socio-technical complexities

NASA Astrophysics Data System (ADS)

Jain, Rishee K.; Qin, Junjie; Rajagopal, Ram

2017-08-01

New distributed energy resources (DER) are rapidly replacing centralized power generation due to their environmental, economic and resiliency benefits. Previous analyses of DER systems have been limited in their ability to account for socio-technical complexities, such as intermittent supply, heterogeneous demand and balance-of-system cost dynamics. Here we develop ReMatch, an interdisciplinary modelling framework, spanning engineering, consumer behaviour and data science, and apply it to 10,000 consumers in California, USA. Our results show that deploying DER would yield nearly a 50% reduction in the levelized cost of electricity (LCOE) over the status quo even after accounting for socio-technical complexities. We abstract a detailed matching of consumers to DER infrastructure from our results and discuss how this matching can facilitate the development of smart and targeted renewable energy policies, programmes and incentives. Our findings point to the large-scale economic and technical feasibility of DER and underscore the pertinent role DER can play in achieving sustainable energy goals.

Optimal planning and design of a renewable energy based supply system for microgrids

DOE PAGES

Hafez, Omar; Bhattacharya, Kankar

2012-03-03

This paper presents a technique for optimal planning and design of hybrid renewable energy systems for microgrid applications. The Distributed Energy Resources Customer Adoption Model (DER-CAM) is used to determine the optimal size and type of distributed energy resources (DERs) and their operating schedules for a sample utility distribution system. Using the DER-CAM results, an evaluation is performed to evaluate the electrical performance of the distribution circuit if the DERs selected by the DER-CAM optimization analyses are incorporated. Results of analyses regarding the economic benefits of utilizing the optimal locations identified for the selected DER within the system are alsomore » presented. The actual Brookhaven National Laboratory (BNL) campus electrical network is used as an example to show the effectiveness of this approach. The results show that these technical and economic analyses of hybrid renewable energy systems are essential for the efficient utilization of renewable energy resources for microgird applications.« less

Van der waals forces on thin liquid films in capillary tubes

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

Herdt, G.C.; Swanson, L.W.

1993-10-01

A theory of the van der Waals attraction between a thin liquid films and a capillary tube is presented assuming the presence of a vapor-liquid interface. The model is based on the surface mode analysis method of van Kampen et al. Values for the van der Waals interaction energy per unit area were calculated for liquid films of pentane on a gold substrate assuming a thin liquid film. Results indicate that the effect of capillary curvature on the van der Waals interaction increases as the ratio of the liquid film thickness to the capillary radius is increased. This trend ismore » consistent with predictions based on the Hamaker theory. Deviations from results based on the Hamaker theory are easily explained in terms of retardation of the van der Waals interaction. Because the effect of capillary curvature increases in the regime where retardation effects become important, curvature effects constitute a small correction to the van der Waals forces in a capillary tube.« less

Inflationary universe in terms of a van der Waals viscous fluid

NASA Astrophysics Data System (ADS)

Brevik, I.; Elizalde, E.; Odintsov, S. D.; Timoshkin, A. V.

The inflationary expansion of our early-time universe is considered in terms of the van der Waals equation, as equation of state for the cosmic fluid, where a bulk viscosity contribution is assumed to be present. The corresponding gravitational equations for the energy density in a homogeneous and isotropic Friedmann-Lemaître-Robertson-Walker universe are solved, and an analytic expression for the scale factor is obtained. Attention is paid, specifically, to the role of the viscosity term in the accelerated expansion; the values of the slow-roll parameters, the spectral index, and the tensor-to-scalar ratio for the van der Waals model are calculated and compared with the most recent astronomical data from the Planck satellite. By imposing reasonable restrictions on the parameters of the van der Waals equation, in the presence of viscosity, it is shown to be possible for this model to comply quite precisely with the observational data. One can therefore conclude that the inclusion of viscosity in the theory of the inflationary epoch may definitely improve the cosmological models.

Mechanism of Microhomology-Mediated End-Joining Promoted by Human DNA Polymerase Theta

PubMed Central

Kent, Tatiana; Chandramouly, Gurushankar; McDevitt, Shane Michael; Ozdemir, Ahmet Y.; Pomerantz, Richard T.

2014-01-01

Microhomology-mediated end-joining (MMEJ) is an error-prone alternative double-strand break repair pathway that utilizes sequence microhomology to recombine broken DNA. Although MMEJ is implicated in cancer development, the mechanism of this pathway is unknown. We demonstrate that purified human DNA polymerase θ (Polθ) performs MMEJ of DNA containing 3’ single-strand DNA overhangs with two or more base-pairs of homology, including DNA modeled after telomeres, and show that MMEJ is dependent on Polθ in human cells. Our data support a mechanism whereby Polθ facilitates end-joining and microhomology annealing then utilizes the opposing overhang as a template in trans which stabilizes the DNA synapse. Polθ exhibits a preference for DNA containing a 5’-terminal phosphate, similar to polymerases involved in non-homologous end-joining. Lastly, we identify a conserved loop domain that is essential for MMEJ and higher-order structures of Polθ which likely promote DNA synapse formation. PMID:25643323

IQM-Reifegradmodell für die Bewertung und Verbesserung des Information Lifecycle Management Prozesses

NASA Astrophysics Data System (ADS)

Baškarada, Saša; Gebauer, Marcus; Koronios, Andy; Gao, Jing

Heutige Organisationen produzieren und speichern mehr Informationen als je zuvor. Der resultierende Informationsüberfluss, zusammen mit einem Mangel an Qualitätssicherung für das Information Lifecycle Management, führt zu einem unsicheren Status der Informationsqualität in vielen Organisationen. Weiterhin hat sich herausgestellt, dass das Bewerten, Verbessern und Steuern der Informationsqualität ein offenkundig schwieriges Unterfangen ist. Dieses Kapitel stellt ein Modell zur Bewertung und Verbesserung der Information Quality Management Capability Maturity (IQM-Reifegrad) vor. Es wird ein Satz von Kriterien vorgestellt, der aus Literaturrecherche und Fallstudien abgeleitet wurde. Die Reifegradindikatoren werden validiert und in einem mehrstufigen Reifegradmodell durch eine Delphi-Studie gruppiert. Das abgeleitete IQM-Reifegradmodell hilft Organisationen ihre bestehenden Praktiken im IQM zu bewerten und potentielle Lücken und Verbesserungsstrategien zu ermitteln.

On the accuracy of the MB-pol many-body potential for water: Interaction energies, vibrational frequencies, and classical thermodynamic and dynamical properties from clusters to liquid water and ice

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

Reddy, Sandeep K.; Straight, Shelby C.; Bajaj, Pushp

The MB-pol many-body potential has recently emerged as an accurate molecular model for water simulations from the gas to the condensed phase. In this study, the accuracy of MB-pol is systematically assessed across the three phases of water through extensive comparisons with experimental data and high-level ab initio calculations. Individual many-body contributions to the interaction energies as well as vibrational spectra of water clusters calculated with MB-pol are in excellent agreement with reference data obtained at the coupled cluster level. Several structural, thermodynamic, and dynamical properties of the liquid phase at atmospheric pressure are investigated through classical molecular dynamics simulationsmore » as a function of temperature. The structural properties of the liquid phase are in nearly quantitative agreement with X-ray diffraction data available over the temperature range from 268 to 368 K. The analysis of other thermodynamic and dynamical quantities emphasizes the importance of explicitly including nuclear quantum effects in the simulations, especially at low temperature, for a physically correct description of the properties of liquid water. Furthermore, both densities and lattice energies of several ice phases are also correctly reproduced by MB-pol. Following a recent study of DFT models for water, a score is assigned to each computed property, which demonstrates the high and, in many respects, unprecedented accuracy of MB-pol in representing all three phases of water. Published by AIP Publishing.« less

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

Mendes, Goncalo; Feng, Wei; Stadler, Michael

The following paper conducts a regional analysis of the U.S. and Chinese buildings? potential for adopting Distributed Energy Resources (DER). The expected economics of DER in 2020-2025 is modeled for a commercial and a multi-family residential building in different climate zones. The optimal building energy economic performance is calculated using the Distributed Energy Resources Customer Adoption Model (DER CAM) which minimizes building energy costs for a typical reference year of operation. Several DER such as combined heat and power (CHP) units, photovoltaics, and battery storage are considered. The results indicate DER have economic and environmental competitiveness potential, especially for commercialmore » buildings in hot and cold climates of both countries. In the U.S., the average expected energy cost savings in commercial buildings from DER CAM?s suggested investments is 17percent, while in Chinese buildings is 12percent. The electricity tariffs structure and prices along with the cost of natural gas, represent important factors in determining adoption of DER, more so than climate. High energy pricing spark spreads lead to increased economic attractiveness of DER. The average emissions reduction in commercial buildings is 19percent in the U.S. as a result of significant investments in PV, whereas in China, it is 20percent and driven by investments in CHP. Keywords: Building Modeling and Simulation, Distributed Energy Resources (DER), Energy Efficiency, Combined Heat and Power (CHP), CO2 emissions 1. Introduction The transition from a centralized and fossil-based energy paradigm towards the decentralization of energy supply and distribution has been a major subject of research over the past two decades. Various concerns have brought the traditional model into question; namely its environmental footprint, its structural inflexibility and inefficiency, and more recently, its inability to maintain acceptable reliability of supply. Under such a troubled setting, distributed energy resources (DER) comprising of small, modular, electrical renewable or fossil-based electricity generation units placed at or near the point of energy consumption, has gained much attention as a viable alternative or addition to the current energy system. In 2010, China consumed about 30percent of its primary energy in the buildings sector, leading the country to pay great attention to DER development and its applications in buildings. During the 11th Five Year Plan (FYP), China has implemented 371 renewable energy building demonstration projects, and 210 photovoltaics (PV) building integration projects. At the end of the 12th FYP, China is targeting renewable energy to provide 10percent of total building energy, and to save 30 metric tons of CO2 equivalents (mtce) of energy with building integrated renewables. China is also planning to implement one thousand natural gas-based distributed cogeneration demonstration projects with energy utilization rates over 70percent in the 12th FYP. All these policy targets require significant DER systems development for building applications. China?s fast urbanization makes building energy efficiency a crucial economic issue; however, only limited studies have been done that examine how to design and select suitable building energy technologies in its different regions. In the U.S., buildings consumed 40percent of the total primary energy in 2010 [1] and it is estimated that about 14 billion m2 of floor space of the existing building stock will be remodeled over the next 30 years. Most building?s renovation work has been on building envelope, lighting and HVAC systems. Although interest has emerged, less attention is being paid to DER for buildings. This context has created opportunities for research, development and progressive deployment of DER, due to its potential to combine the production of power and heat (CHP) near the point of consumption and delivering multiple benefits to customers, such as cost« less

Adaptation of the Tinnitus Handicap Inventory into Polish and its testing on a clinical population of tinnitus sufferers.

PubMed

Skarzynski, Piotr H; Raj-Koziak, Danuta; J Rajchel, Joanna; Pilka, Adam; Wlodarczyk, Andrzej W; Skarzynski, Henryk

2017-10-01

To describe how the Tinnitus Handicap Inventory (THI) was translated into Polish (THI-POL) and to present psychometric data on how well it performed in a clinical population of tinnitus sufferers. The original version of THI was adapted into Polish. The reliability of THI-POL was investigated using test-retest, Cronbach's alpha, endorsement rate and item-total correlation. Construct validity and convergent validity were also assessed based on confirmatory factor analysis, inter-item correlation and Pearson product-moment correlations using subscale A (Tinnitus) of the Tinnitus and Hearing Survey (THS-POL); divergent validity was checked using subscale B (Hearing) of THS-POL. A group of 167 adults filled in THI-POL twice over their three-day hospitalisation period. Test-retest reliability for the total THI-POL scores was strong (r = 0.91). Cronbach's alpha coefficient for the total score was high (r = 0.95), confirming the questionnaire's stability. Confirmatory factor analysis (CFA) and inter-item correlation did not confirm the three-factor model. Convergent validity from the Tinnitus subscale of THS showed a positive strong (r = 0.75) correlation. Divergent validity showed only a moderate correlation. All analyses were statistically significant (p <  0.01). THI-POL is a valid and reliable self-administered tool, which allows the overall tinnitus handicap of Polish-speaking patients to be effectively assessed.

Research on Multi-Temporal PolInSAR Modeling and Applications

NASA Astrophysics Data System (ADS)

Hong, Wen; Pottier, Eric; Chen, Erxue

2014-11-01

In the study of theory and processing methodology, we apply accurate topographic phase to the Freeman-Durden decomposition for PolInSAR data. On the other hand, we present a TomoSAR imaging method based on convex optimization regularization theory. The target decomposition and reconstruction performance will be evaluated by multi-temporal Land P-band fully polarimetric images acquired in BioSAR campaigns. In the study of hybrid Quad-Pol system performance, we analyse the expression of range ambiguity to signal ratio (RASR) in this architecture. Simulations are used to testify its advantage in the improvement of range ambiguities.

Research on Multi-Temporal PolInSAR Modeling and Applications

NASA Astrophysics Data System (ADS)

Hong, Wen; Pottier, Eric; Chen, Erxue

2014-11-01

In the study of theory and processing methodology, we apply accurate topographic phase to the Freeman- Durden decomposition for PolInSAR data. On the other hand, we present a TomoSAR imaging method based on convex optimization regularization theory. The target decomposition and reconstruction performance will be evaluated by multi-temporal L- and P-band fully polarimetric images acquired in BioSAR campaigns. In the study of hybrid Quad-Pol system performance, we analyse the expression of range ambiguity to signal ratio (RASR) in this architecture. Simulations are used to testify its advantage in the improvement of range ambiguities.

The Mediation Formula: A Guide to the Assessment of Causal Pathways in Nonlinear Models

DTIC Science & Technology

2011-10-27

through (25), (26) and (27), rather than going through (23) ( van der Laan and Rubin, 2006). 29 values, though disparities in parameters may not...graphs. Epidemiology 22 378–381. Petersen, M., Sinisi, S. and van der Laan, M. (2006). Estimation of direct causal effects. Epidemiology 17 276–284...and J. Halpern, eds.). College Publications, UK, 415–444. van der Laan, M. J. and Rubin, D. (2006). Targeted maximum likelihood learning. The

Structure-Function Based Molecular Relationships in Ewing's Sarcoma

PubMed Central

2015-01-01

Ewing's Sarcoma Oncogene (ews) on chromosome 22q12 is encoding a ubiquitously expressed RNA-binding protein (EWS) with unknown function that is target of tumor-specific chromosomal translocations in Ewing's sarcoma family of tumors. A model of transcription complex was proposed in which the heterodimer Rpb4/7 binds to EAD, connecting it to Core RNA Pol II. The DNA-binding domain, provided by EFP, is bound to the promoter. Rpb4/7 binds RNA, stabilizing the transcription complex. The complex Rpb4/7 can stabilize the preinitiation complexes by converting the conformation of RNA Pol II. EWS may change its conformation, so that NTD becomes accessible. Two different mechanisms of interaction between EWS and RNA Pol II are proposed: (I) an intermolecular EWS-EWS interaction between two molecules, pushing conformation from “closed” to “open” state, or (II) an intramolecular interaction inside the molecule of EWS, pushing conformation of the molecule from “closed” to “open” state. The modified forms of EWS may interact with Pol II subunits hsRpb5 and hsRpb7. The EWS and EFPs binding partners are described schematically in a model, an attempt to link the transcription with the splicing. The proposed model helps to understand the functional molecular interactions in cancer, to find new partners and ways to treat cancer. PMID:25688366

[An experimental study on the therapeutic effects of eustachian tube surfactant in barotitis media].

PubMed

Feng, Lining; Chen, Wenxian; Cong, Rui; Zheng, Guoxi; Gou, Lin; Guo, Qun

2002-11-01

To observe the effect of surfactant on eustachian tube (ET) on the opening of ET as well as it's therapeutic role in barotitis media (BM). 50 guinea pigs were successfully established as BM models by stimulated ascending in altitude chamber. Parts of the models were treated with by middle ear flushing with nature ETS, artificial ETS, artificial phospholipid and saline, after which the eustachian tube pressure opening level (POL) of each group was tested. Others were injected with 1 ml artificial ETS in on side of the middle ear, and 1 ml of saline in the other served as control. Natural ETS decreased the POL from 11.98 to 6.11 kPa (P < 0.01); Artificial ETS reduced the POL from 11.91 to 6.67 kPa (P < 0.01), there were no significant differences between the two groups. Artificial phospholipid decreased the POL from 11.86 to 8.61 kPa (P < 0.05), which was not as effective as natural ETS. While the POL of saline group remained unchanged. After one week of artificial ETS treatment, the congestion in drum membrane alleviated, the hearing threshold of ETS group improved and the effusion in tympanic cavity lessened. The results suggest that artificial ETS is as effective as nature ETS to facilitates the opening of eustachian tube. Artificial ETS may exert therapeutic effects on BM.

The Steric Gate of DNA Polymerase ι Regulates Ribonucleotide Incorporation and Deoxyribonucleotide Fidelity*

PubMed Central

Donigan, Katherine A.; McLenigan, Mary P.; Yang, Wei; Goodman, Myron F.; Woodgate, Roger

2014-01-01

Accurate DNA synthesis in vivo depends on the ability of DNA polymerases to select dNTPs from a nucleotide pool dominated by NTPs. High fidelity replicative polymerases have evolved to efficiently exclude NTPs while copying long stretches of undamaged DNA. However, to bypass DNA damage, cells utilize specialized low fidelity polymerases to perform translesion DNA synthesis (TLS). Of interest is human DNA polymerase ι (pol ι), which has been implicated in TLS of oxidative and UV-induced lesions. Here, we evaluate the ability of pol ι to incorporate NTPs during DNA synthesis. pol ι incorporates and extends NTPs opposite damaged and undamaged template bases in a template-specific manner. The Y39A “steric gate” pol ι mutant is considerably more active in the presence of Mn2+ compared with Mg2+ and exhibits a marked increase in NTP incorporation and extension, and surprisingly, it also exhibits increased dNTP base selectivity. Our results indicate that a single residue in pol ι is able to discriminate between NTPs and dNTPs during DNA synthesis. Because wild-type pol ι incorporates NTPs in a template-specific manner, certain DNA sequences may be “at risk” for elevated mutagenesis during pol ι-dependent TLS. Molecular modeling indicates that the constricted active site of wild-type pol ι becomes more spacious in the Y39A variant. Therefore, the Y39A substitution not only permits incorporation of ribonucleotides but also causes the enzyme to favor faithful Watson-Crick base pairing over mutagenic configurations. PMID:24532793

Effects of van der Waals Force and Thermal Stresses on Pull-in Instability of Clamped Rectangular Microplates

PubMed Central

Batra, Romesh C.; Porfiri, Maurizio; Spinello, Davide

2008-01-01

We study the influence of von Kármán nonlinearity, van der Waals force, and thermal stresses on pull-in instability and small vibrations of electrostatically actuated microplates. We use the Galerkin method to develop a tractable reduced-order model for electrostatically actuated clamped rectangular microplates in the presence of van der Waals forces and thermal stresses. More specifically, we reduce the governing two-dimensional nonlinear transient boundary-value problem to a single nonlinear ordinary differential equation. For the static problem, the pull-in voltage and the pull-in displacement are determined by solving a pair of nonlinear algebraic equations. The fundamental vibration frequency corresponding to a deflected configuration of the microplate is determined by solving a linear algebraic equation. The proposed reduced-order model allows for accurately estimating the combined effects of van der Waals force and thermal stresses on the pull-in voltage and the pull-in deflection profile with an extremely limited computational effort. PMID:27879752

Effects of van der Waals Force and Thermal Stresses on Pull-in Instability of Clamped Rectangular Microplates.

PubMed

Batra, Romesh C; Porfiri, Maurizio; Spinello, Davide

2008-02-15

We study the influence of von Karman nonlinearity, van der Waals force, and a athermal stresses on pull-in instability and small vibrations of electrostatically actuated mi-croplates. We use the Galerkin method to develop a tractable reduced-order model for elec-trostatically actuated clamped rectangular microplates in the presence of van der Waals forcesand thermal stresses. More specifically, we reduce the governing two-dimensional nonlineartransient boundary-value problem to a single nonlinear ordinary differential equation. For thestatic problem, the pull-in voltage and the pull-in displacement are determined by solving apair of nonlinear algebraic equations. The fundamental vibration frequency corresponding toa deflected configuration of the microplate is determined by solving a linear algebraic equa-tion. The proposed reduced-order model allows for accurately estimating the combined effectsof van der Waals force and thermal stresses on the pull-in voltage and the pull-in deflectionprofile with an extremely limited computational effort.

Inter-layer and intra-layer heat transfer in bilayer/monolayer graphene van der Waals heterostructure: Is there a Kapitza resistance analogous?

NASA Astrophysics Data System (ADS)

Rajabpour, Ali; Fan, Zheyong; Vaez Allaei, S. Mehdi

2018-06-01

Van der Waals heterostructures have exhibited interesting physical properties. In this paper, heat transfer in hybrid coplanar bilayer/monolayer (BL-ML) graphene, as a model layered van der Waals heterostructure, was studied using non-equilibrium molecular dynamics (MD) simulations. The temperature profile and inter- and intra-layer heat fluxes of the BL-ML graphene indicated that, there is no fully developed thermal equilibrium between layers and the drop in the average temperature profile at the step-like BL-ML interface is not attributable to the effect of Kapitza resistance. By increasing the length of the system up to 1 μm in the studied MD simulations, the thermally non-equilibrium region was reduced to a small area near the step-like interface. All MD results were compared to a continuum model and a good match was observed between the two approaches. Our results provide a useful understanding of heat transfer in nano- and micro-scale layered materials and van der Waals heterostructures.

Mediator and RNA polymerase II clusters associate in transcription-dependent condensates.

PubMed

Cho, Won-Ki; Spille, Jan-Hendrik; Hecht, Micca; Lee, Choongman; Li, Charles; Grube, Valentin; Cisse, Ibrahim I

2018-06-21

Models of gene control have emerged from genetic and biochemical studies, with limited consideration of the spatial organization and dynamics of key components in living cells. Here we used live cell super-resolution and light sheet imaging to study the organization and dynamics of the Mediator coactivator and RNA polymerase II (Pol II) directly. Mediator and Pol II each form small transient and large stable clusters in living embryonic stem cells. Mediator and Pol II are colocalized in the stable clusters, which associate with chromatin, have properties of phase-separated condensates, and are sensitive to transcriptional inhibitors. We suggest that large clusters of Mediator, recruited by transcription factors at large or clustered enhancer elements, interact with large Pol II clusters in transcriptional condensates in vivo. Copyright © 2018, American Association for the Advancement of Science.

Understanding the nanoscale local buckling behavior of vertically aligned MWCNT arrays with van der Waals interactions

NASA Astrophysics Data System (ADS)

Li, Yupeng; Kim, Hyung-Ick; Wei, Bingqing; Kang, Junmo; Choi, Jae-Boong; Nam, Jae-Do; Suhr, Jonghwan

2015-08-01

The local buckling behavior of vertically aligned carbon nanotubes (VACNTs) has been investigated and interpreted in the view of a collective nanotube response by taking van der Waals interactions into account. To the best of our knowledge, this is the first report on the case of collective VACNT behavior regarding van der Waals force among nanotubes as a lateral support effect during the buckling process. The local buckling propagation and development of VACNTs were experimentally observed and theoretically analyzed by employing finite element modeling with lateral support from van der Waals interactions among nanotubes. Both experimental and theoretical analyses show that VACNTs buckled in the bottom region with many short waves and almost identical wavelengths, indicating a high mode buckling. Furthermore, the propagation and development mechanism of buckling waves follow the wave damping effect.The local buckling behavior of vertically aligned carbon nanotubes (VACNTs) has been investigated and interpreted in the view of a collective nanotube response by taking van der Waals interactions into account. To the best of our knowledge, this is the first report on the case of collective VACNT behavior regarding van der Waals force among nanotubes as a lateral support effect during the buckling process. The local buckling propagation and development of VACNTs were experimentally observed and theoretically analyzed by employing finite element modeling with lateral support from van der Waals interactions among nanotubes. Both experimental and theoretical analyses show that VACNTs buckled in the bottom region with many short waves and almost identical wavelengths, indicating a high mode buckling. Furthermore, the propagation and development mechanism of buckling waves follow the wave damping effect. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr03581c

Developing the Polish Educational Needs Assessment Tool (Pol-ENAT) in rheumatoid arthritis and systemic sclerosis: a cross-cultural validation study using Rasch analysis.

PubMed

Sierakowska, Matylda; Sierakowski, Stanisław; Sierakowska, Justyna; Horton, Mike; Ndosi, Mwidimi

2015-03-01

To undertake cross-cultural adaptation and validation of the educational needs assessment tool (ENAT) for use with people with rheumatoid arthritis (RA) and systemic sclerosis (SSc) in Poland. The study involved two main phases: (1) cross-cultural adaptation of the ENAT from English into Polish and (2) Cross-cultural validation of Polish Educational Needs Assessment Tool (Pol-ENAT). The first phase followed an established process of cross-cultural adaptation of self-report measures. The second phase involved completion of the Pol-ENAT by patients and subjecting the data to Rasch analysis to assess the construct validity, unidimensionality, internal consistency and cross-cultural invariance. An adequate conceptual equivalence was achieved following the adaptation process. The dataset for validation comprised a total of 278 patients, 237 (85.3 %) of which were female. In each disease group (145, RA and 133, SSc), the 7 domains of the Pol-ENAT were found to fit the Rasch model, X (2)(df) = 16.953(14), p = 0.259 and 8.132(14), p = 0.882 for RA and SSc, respectively. Internal consistency of the Pol-ENAT was high (patient separation index = 0.85 and 0.89 for SSc and RA, respectively), and unidimensionality was confirmed. Cross-cultural differential item functioning (DIF) was detected in some subscales, and DIF-adjusted conversion tables were calibrated to enable cross-cultural comparison of data between Poland and the UK. Using a standard process in cross-cultural adaptation, conceptual equivalence was achieved between the original (UK) ENAT and the adapted Pol-ENAT. Fit to the Rasch model, confirmed that the construct validity, unidimensionality and internal consistency of the ENAT have been preserved.

Distributed Generation Market Demand Model (dGen): Documentation

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

Sigrin, Benjamin; Gleason, Michael; Preus, Robert

The Distributed Generation Market Demand model (dGen) is a geospatially rich, bottom-up, market-penetration model that simulates the potential adoption of distributed energy resources (DERs) for residential, commercial, and industrial entities in the continental United States through 2050. The National Renewable Energy Laboratory (NREL) developed dGen to analyze the key factors that will affect future market demand for distributed solar, wind, storage, and other DER technologies in the United States. The new model builds off, extends, and replaces NREL's SolarDS model (Denholm et al. 2009a), which simulates the market penetration of distributed PV only. Unlike the SolarDS model, dGen can modelmore » various DER technologies under one platform--it currently can simulate the adoption of distributed solar (the dSolar module) and distributed wind (the dWind module) and link with the ReEDS capacity expansion model (Appendix C). The underlying algorithms and datasets in dGen, which improve the representation of customer decision making as well as the spatial resolution of analyses (Figure ES-1), also are improvements over SolarDS.« less

Electrostatically frequency tunable micro-beam-based piezoelectric fluid flow energy harvester

NASA Astrophysics Data System (ADS)

Rezaee, Mousa; Sharafkhani, Naser

2017-07-01

This research investigates the dynamic behavior of a sandwich micro-beam based piezoelectric energy harvester with electrostatically adjustable resonance frequency. The system consists of a cantilever micro-beam immersed in a fluid domain and is subjected to the simultaneous action of cross fluid flow and nonlinear electrostatic force. Two parallel piezoelectric laminates are extended along the length of the micro-beam and connected to an external electric circuit which generates an output power as a result of the micro-beam oscillations. The fluid-coupled structure is modeled using Euler-Bernoulli beam theory and the equivalent force terms for the fluid flow. Fluid induced forces comprise the added inertia force which is evaluated using equivalent added mass and the drag and lift forces which are evaluated using relative velocity and Van der Pol equation. In addition to flow velocity and fluid density, the influence of several design parameters such as external electrical resistance, piezo layer position, and dc voltage on the generated power are investigated by using Galerkin and step by step linearization method. It is shown that for given flowing fluid parameters, i.e., density and velocity, one can adjust the applied dc voltage to tune resonance frequency so that the lock-in phenomenon with steady large amplitude oscillations happens, also by adjusting the harvester parameters including the mechanical and electrical ones, the maximal output power of the harvester becomes possible.

Extracting Tree Height from Repeat-Pass PolInSAR Data : Experiments with JPL and ESA Airborne Systems

NASA Technical Reports Server (NTRS)

Lavalle, Marco; Ahmed, Razi; Neumann, Maxim; Hensley, Scott

2013-01-01

In this paper we present our latest developments and experiments with the random-motion-over-ground (RMoG) model used to extract canopy height and other important forest parameters from repeat-pass polarimetricinterferometric SAR (Pol-InSAR) data. More specifically, we summarize the key features of the RMoG model in contrast with the random-volume-over-ground (RVoG) model, describe in detail a possible inversion scheme for the RMoG model and illustrate the results of the RMoG inversion using airborne data collected by the Jet Propulsion Laboratory (JPL) and the European Space Agency (ESA).

Chaotic attractors of relaxation oscillators

NASA Astrophysics Data System (ADS)

Guckenheimer, John; Wechselberger, Martin; Young, Lai-Sang

2006-03-01

We develop a general technique for proving the existence of chaotic attractors for three-dimensional vector fields with two time scales. Our results connect two important areas of dynamical systems: the theory of chaotic attractors for discrete two-dimensional Henon-like maps and geometric singular perturbation theory. Two-dimensional Henon-like maps are diffeomorphisms that limit on non-invertible one-dimensional maps. Wang and Young formulated hypotheses that suffice to prove the existence of chaotic attractors in these families. Three-dimensional singularly perturbed vector fields have return maps that are also two-dimensional diffeomorphisms limiting on one-dimensional maps. We describe a generic mechanism that produces folds in these return maps and demonstrate that the Wang-Young hypotheses are satisfied. Our analysis requires a careful study of the convergence of the return maps to their singular limits in the Ck topology for k >= 3. The theoretical results are illustrated with a numerical study of a variant of the forced van der Pol oscillator.

Resonant frequency calculations using a hybrid perturbation-Galerkin technique

NASA Technical Reports Server (NTRS)

Geer, James F.; Andersen, Carl M.

1991-01-01

A two-step hybrid perturbation Galerkin technique is applied to the problem of determining the resonant frequencies of one or several degree of freedom nonlinear systems involving a parameter. In one step, the Lindstedt-Poincare method is used to determine perturbation solutions which are formally valid about one or more special values of the parameter (e.g., for large or small values of the parameter). In step two, a subset of the perturbation coordinate functions determined in step one is used in Galerkin type approximation. The technique is illustrated for several one degree of freedom systems, including the Duffing and van der Pol oscillators, as well as for the compound pendulum. For all of the examples considered, it is shown that the frequencies obtained by the hybrid technique using only a few terms from the perturbation solutions are significantly more accurate than the perturbation results on which they are based, and they compare very well with frequencies obtained by purely numerical methods.

Singular Hopf bifurcation in a differential equation with large state-dependent delay.

PubMed

Kozyreff, G; Erneux, T

2014-02-08

We study the onset of sustained oscillations in a classical state-dependent delay (SDD) differential equation inspired by control theory. Owing to the large delays considered, the Hopf bifurcation is singular and the oscillations rapidly acquire a sawtooth profile past the instability threshold. Using asymptotic techniques, we explicitly capture the gradual change from nearly sinusoidal to sawtooth oscillations. The dependence of the delay on the solution can be either linear or nonlinear, with at least quadratic dependence. In the former case, an asymptotic connection is made with the Rayleigh oscillator. In the latter, van der Pol's equation is derived for the small-amplitude oscillations. SDD differential equations are currently the subject of intense research in order to establish or amend general theorems valid for constant-delay differential equation, but explicit analytical construction of solutions are rare. This paper illustrates the use of singular perturbation techniques and the unusual way in which solvability conditions can arise for SDD problems with large delays.

Does grandchild care influence grandparents' self-rated health? Evidence from a fixed effects approach.

PubMed

Ates, Merih

2017-10-01

The present study aims to identify, whether and how supplementary grandchild care is causally related to grandparents' self-rated health (SRH). Based on longitudinal data drawn from the German Aging Survey (DEAS; 2008-2014), I compare the results of pooled OLS, pooled OLS with lagged dependant variables (POLS-LD), random and fixed effects (RE, FE) panel regression. The results show that there is a positive but small association between supplementary grandchild care and SRH in POLS, POLS-LD, and RE models. However, the fixed effects model shows that the intrapersonal change in grandchild care does not cause a change in grandparents' SRH. The FE findings indicate that supplementary grandchild care in Germany does not have a causal impact on grandparents' SRH, suggesting that models with between-variation components overestimate the influence of grandchild care on grandparents' health because they do not control for unobserved (time-constant) heterogeneity. Copyright © 2017 Elsevier Ltd. All rights reserved.

Kundenfokus: Startpunkt für die digitale Transformation bei Stadtwerken

NASA Astrophysics Data System (ADS)

Fett, Perry; Küller, Philipp

Big Data, Internet der Dinge, Mobile Computing und soziale Medien - die modernen Informationstechnologien durchdringen den Alltag der meisten Menschen und lösen hierdurch eine digitale Transformation aus. Im Unternehmenskontext manifestiert sich die Digitalisierung durch eine neue Qualität der wissensbasierten Entscheidungsunterstützung und der Automatisierung bzw. Autonomisierung der Geschäftsprozesse. Für Stadtwerke gilt es nun, die Chancen der Digitalisierung zu ihren Gunsten zu nutzen. Ein Startpunkt könnte hierbei sein, wie Stadtwerke zukünftig mit ihren Kunden interagieren. Ausgelöst durch die Liberalisierung der Märkte rückt der Kunde heute stärker in den Mittelpunkt - die Energiewirtschaft steht nun vor der Herausforderung, dem Wettbewerb einen Schritt voraus zu sein und dem Kunden ein absolut positives Kundenerlebnis (Customer Experience) sowohl als Maßnahme zur Kundenbindung als auch zum Kundenaufbau zu bieten. Das vorliegende Kapitel zeigt hierfür die Erfolgskriterien für die gelungene Etablierung des Kundenfokus im eigenen Unternehmen auf. Mit dem Customer-Focus-Cycle-Modell von Fujitsu, angelehnt an den Deming-Kreislauf, wird ein allgemeingültiger Ansatz für ein mögliches Vorgehen beim Aufbau des Kundenfokus vorgestellt. Die sechs Phasen werden dabei anhand praktischer Beispiele erläutert und geben zudem Hinweise zu Methoden und Tools. Aus dem vorgestellten "Werkzeugkasten" wird ferner die Customer-Journey-Methode im Detail erläutert. Weiter soll das präsentierte Reifegradmodell Unternehmen dabei unterstützen, den eigenen Status quo festzustellen und die persönlichen Ziele auf dem Weg zur kundenzentrierten Organisation festzulegen.

Isotopic equilibria in aqueous clusters at low temperatures: Insights from the MB-pol many-body potential

NASA Astrophysics Data System (ADS)

Videla, Pablo E.; Rossky, Peter J.; Laria, Daniel

2018-02-01

By combining path-integrals molecular dynamics simulations with the accurate MB-pol potential energy surface, we investigate the role of alternative potential models on isotopic fractionation ratios between H and D atoms at dangling positions in water clusters at low temperatures. Our results show clear stabilizations of the lighter isotope at dangling sites, characterized by free energy differences ΔG that become comparable to or larger than kBT for temperatures below ˜75 K. The comparison between these results to those previously reported using the empirical q-TIP4P/F water model [P. E. Videla et al., J. Phys. Chem. Lett. 5, 2375 (2014)] reveals that the latter Hamiltonian overestimates the H stabilization by ˜25%. Moreover, predictions from the MB-pol model are in much better agreement with measured results reported for similar isotope equilibria at ice surfaces. The dissection of the quantum kinetic energies into orthogonal directions shows that the dominant differences between the two models are to be found in the anharmonic characteristics of the potential energy surfaces along OH bond directions involved in hydrogen bonds.

Efimov states near a Feshbach resonance and the limits of van der Waals universality at finite background scattering length

NASA Astrophysics Data System (ADS)

Langmack, Christian; Schmidt, Richard; Zwerger, Wilhelm

2018-03-01

We calculate the spectrum of three-body Efimov bound states near a Feshbach resonance within a model which accounts both for the finite range of interactions and the presence of background scattering. The latter may be due to direct interactions in an open channel or a second overlapping Feshbach resonance. It is found that background scattering gives rise to substantial changes in the trimer spectrum as a function of the detuning away from a Feshbach resonance, in particular in the regime where the background channel supports Efimov states on its own. Compared to the situation with negligible background scattering, the regime where van der Waals universality applies is shifted to larger values of the resonance strength if the background scattering length is positive. For negative background scattering lengths, in turn, van der Waals universality extends to even small values of the resonance strength parameter, consistent with experimental results on Efimov states in 39K. Within a simple model, we show that short-range three-body forces do not affect van der Waals universality significantly. Repulsive three-body forces may, however, explain the observed variation between around -8 and -10 of the ratio between the scattering length where the first Efimov trimer appears and the van der Waals length.

The Error-Prone DNA Polymerase κ Promotes Temozolomide Resistance in Glioblastoma through Rad17-Dependent Activation of ATR-Chk1 Signaling.

PubMed

Peng, Chenghao; Chen, Zhengxin; Wang, Shuai; Wang, Hong-Wei; Qiu, Wenjin; Zhao, Lin; Xu, Ran; Luo, Hui; Chen, Yuanyuan; Chen, Dan; You, Yongping; Liu, Ning; Wang, Huibo

2016-04-15

The acquisition of drug resistance is a persistent clinical problem limiting the successful treatment of human cancers, including glioblastoma (GBM). However, the molecular mechanisms by which initially chemoresponsive tumors develop therapeutic resistance remain poorly understood. In this study, we report that Pol κ, an error-prone polymerase that participates in translesion DNA synthesis, was significantly upregulated in GBM cell lines and tumor tissues following temozolomide treatment. Overexpression of Pol κ in temozolomide-sensitive GBM cells conferred resistance to temozolomide, whereas its inhibition markedly sensitized resistant cells to temozolomide in vitro and in orthotopic xenograft mouse models. Mechanistically, depletion of Pol κ disrupted homologous recombination (HR)-mediated repair and restart of stalled replication forks, impaired the activation of ATR-Chk1 signaling, and delayed cell-cycle re-entry and progression. Further investigation of the relationship between Pol κ and temozolomide revealed that Pol κ inactivation facilitated temozolomide-induced Rad17 ubiquitination and proteasomal degradation, subsequently silencing ATR-Chk1 signaling and leading to defective HR repair and the reversal of temozolomide resistance. Moreover, overexpression of Rad17 in Pol κ-depleted GBM cells restored HR efficiency, promoted the clearance of temozolomide-induced DNA breaks, and desensitized cells to the cytotoxic effects of temozolomide observed in the absence of Pol κ. Finally, we found that Pol κ overexpression correlated with poor prognosis in GBM patients undergoing temozolomide therapy. Collectively, our findings identify a potential mechanism by which GBM cells develop resistance to temozolomide and suggest that targeting the DNA damage tolerance pathway may be beneficial for overcoming resistance. Cancer Res; 76(8); 2340-53. ©2016 AACR. ©2016 American Association for Cancer Research.

Design, modeling, simulation and evaluation of a distributed energy system

NASA Astrophysics Data System (ADS)

Cultura, Ambrosio B., II

This dissertation presents the design, modeling, simulation and evaluation of distributed energy resources (DER) consisting of photovoltaics (PV), wind turbines, batteries, a PEM fuel cell and supercapacitors. The distributed energy resources installed at UMass Lowell consist of the following: 2.5kW PV, 44kWhr lead acid batteries and 1500W, 500W & 300W wind turbines, which were installed before year 2000. Recently added to that are the following: 10.56 kW PV array, 2.4 kW wind turbine, 29 kWhr Lead acid batteries, a 1.2 kW PEM fuel cell and 4-140F supercapacitors. Each newly added energy resource has been designed, modeled, simulated and evaluated before its integration into the existing PV/Wind grid-connected system. The Mathematical and Simulink model of each system was derived and validated by comparing the simulated and experimental results. The Simulated results of energy generated from a 10.56kW PV system are in good agreement with the experimental results. A detailed electrical model of a 2.4kW wind turbine system equipped with a permanent magnet generator, diode rectifier, boost converter and inverter is presented. The analysis of the results demonstrates the effectiveness of the constructed simulink model, and can be used to predict the performance of the wind turbine. It was observed that a PEM fuel cell has a very fast response to load changes. Moreover, the model has validated the actual operation of the PEM fuel cell, showing that the simulated results in Matlab Simulink are consistent with the experimental results. The equivalent mathematical equation, derived from an electrical model of the supercapacitor, is used to simulate its voltage response. The model is completely capable of simulating its voltage behavior, and can predict the charge time and discharge time of voltages on the supercapacitor. The bi-directional dc-dc converter was designed in order to connect the 48V battery bank storage to the 24V battery bank storage. This connection was needed in order to increase the reliability of the DER system. Furthermore, the new computer-based Data Acquisition (DAQ) system for the DER has been designed and installed. The DAQ system is an important component in PC-based measurement, which is used in acquiring and storing data. The design and installation of signal conditioning improve the accuracy, effectiveness and safety of measurements, because of capabilities such as amplifications, isolation, and filtering. A Labview program was the software used to interface and communicate between the DAQ devices and the personal computer. The overall simulink model of the DER system is presented in the last chapter. The simulink model is discussed, and the discussion explains the operation of a grid connected DER. This model can be used as the basis or future reference for designs and installations of DER projects. This model can also be used in converting the DER grid connected system into a Smart Grid system, and that will be the next potential research work to explore.

Der Aufbau mentaler Modelle durch bildliche Darstellungen: Eine experimentalle Studie uber die Bedeutung der Merkmalsdimensionen Elaboriertheit und Strukturierheit im Sachunterricht der Grundschule (The Development of Mental Processes through Graphic Representation with Diverging Degrees of Elaboration and Structurization: An Experimental Study Carried Out in Elementary Science Instruction in Primary School).

ERIC Educational Resources Information Center

Martschinke, Sabine

1996-01-01

Examines types of graphical representation as to their suitability for knowledge acquisition in primary grades. Uses the concept of mental models to clarify the relationship between external presentation and internal representation of knowledge. Finds that students who learned with highly elaborated and highly structured pictures displayed the…

Treacher Collins syndrome mutations in Saccharomyces cerevisiae destabilize RNA polymerase I and III complex integrity.

PubMed

Walker-Kopp, Nancy; Jackobel, Ashleigh J; Pannafino, Gianno N; Morocho, Paola A; Xu, Xia; Knutson, Bruce A

2017-11-01

Treacher Collins syndrome (TCS) is a craniofacial disorder that is characterized by the malformation of the facial bones. Mutations in three genes (TCOF1, POLR1C and POLR1D) involved in RNA polymerase I (Pol I) transcription account for more than 90% of disease cases. Two of these TCS-associated genes, POLR1C and POLR1D, encode for essential Pol I/III subunits that form a heterodimer necessary for Pol I/III assembly, and many TCS mutations lie along their evolutionarily conserved dimerization interface. Here we elucidate the molecular basis of TCS mutations in Saccharomyces cerevisiae, and present a new model for how TCS mutations may disrupt Pol I and III complex integrity. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Analysis of the mechanism of nucleosome survival during transcription

PubMed Central

Chang, Han-Wen; Kulaeva, Olga I.; Shaytan, Alexey K.; Kibanov, Mikhail; Kuznedelov, Konstantin; Severinov, Konstantin V.; Kirpichnikov, Mikhail P.; Clark, David J.; Studitsky, Vasily M.

2014-01-01

Maintenance of nucleosomal structure in the cell nuclei is essential for cell viability, regulation of gene expression and normal aging. Our previous data identified a key intermediate (a small intranucleosomal DNA loop, Ø-loop) that is likely required for nucleosome survival during transcription by RNA polymerase II (Pol II) through chromatin, and suggested that strong nucleosomal pausing guarantees efficient nucleosome survival. To evaluate these predictions, we analysed transcription through a nucleosome by different, structurally related RNA polymerases and mutant yeast Pol II having different histone-interacting surfaces that presumably stabilize the Ø-loop. The height of the nucleosomal barrier to transcription and efficiency of nucleosome survival correlate with the net negative charges of the histone-interacting surfaces. Molecular modeling and analysis of Pol II-nucleosome intermediates by DNase I footprinting suggest that efficient Ø-loop formation and nucleosome survival are mediated by electrostatic interactions between the largest subunit of Pol II and core histones. PMID:24234452

Xiao-Qing-Long-Tang shows preventive effect of asthma in an allergic asthma mouse model through neurotrophin regulation

PubMed Central

2013-01-01

Background This study investigates the effect of Xiao-Qing-Long-Tang (XQLT) on neurotrophin in an established mouse model of Dermatophagoides pteronyssinus (Der p)-induced acute allergic asthma and in a LA4 cell line model of lung adenoma. The effects of XQLT on the regulation of nerve growth factor (NGF) and brain-derived neurotrophic factor (BDNF), airway hyper-responsiveness (AHR) and immunoglobulin E were measured. Methods LA4 cells were stimulated with 100 μg/ml Der p 24 h and the supernatant was collected for ELISA analysis. Der p-stimulated LA4 cells with either XQLT pre-treatment or XQLT co-treatment were used to evaluate the XQLT effect on neurotrophin. Balb/c mice were sensitized on days 0 and 7 with a base-tail injection of 50 μg Dermatophagoides pteronyssinus (Der p) that was emulsified in 50 μl incomplete Freund’s adjuvant (IFA). On day 14, mice received an intra-tracheal challenge of 50 μl Der p (2 mg/ml). XQLT (1g/Kg) was administered orally to mice either on days 2, 4, 6, 8, 10 and 12 as a preventive strategy or on day 15 as a therapeutic strategy. Results XQLT inhibited expression of those NGF, BDNF and thymus-and activation-regulated cytokine (TARC) in LA4 cells that were subjected to a Der p allergen. Both preventive and therapeutic treatments with XQLT in mice reduced AHR. Preventive treatment with XQLT markedly decreased NGF in broncho-alveolar lavage fluids (BALF) and BDNF in serum, whereas therapeutic treatment reduced only serum BDNF level. The reduced NGF levels corresponded to a decrease in AHR by XQLT treatment. Reduced BALF NGF and TARC and serum BDNF levels may have been responsible for decreased eosinophil infiltration into lung tissue. Immunohistochemistry showed that p75NTR and TrkA levels were reduced in the lungs of mice under both XQLT treatment protocols, and this reduction may have been correlated with the prevention of the asthmatic reaction by XQLT. Conclusion XQLT alleviated allergic inflammation including AHR, IgE elevation and eosinophil infiltration in Der p stimulated mice by regulating neurotrophin and reducing TARC. These results revealed the potential pharmacological targets on which the XQLT decotion exerts preventive and therapeutic effects in an allergic asthma mouse model. PMID:24010817

Structural classification of marshes with Polarimetric SAR highlighting the temporal mapping of marshes exposed to oil

USGS Publications Warehouse

Ramsey, Elijah W.; Rangoonwala, Amina; Jones, Cathleen E.

2015-01-01

Empirical relationships between field-derived Leaf Area Index (LAI) and Leaf Angle Distribution (LAD) and polarimetric synthetic aperture radar (PolSAR) based biophysical indicators were created and applied to map S. alterniflora marsh canopy structure. PolSAR and field data were collected near concurrently in the summers of 2010, 2011, and 2012 in coastal marshes, and PolSAR data alone were acquired in 2009. Regression analyses showed that LAI correspondence with the PolSAR biophysical indicator variables equaled or exceeded those of vegetation water content (VWC) correspondences. In the final six regressor model, the ratio HV/VV explained 49% of the total 77% explained LAI variance, and the HH-VV coherence and phase information accounted for the remainder. HV/HH dominated the two regressor LAD relationship, and spatial heterogeneity and backscatter mechanism followed by coherence information dominated the final three regressor model that explained 74% of the LAD variance. Regression results applied to 2009 through 2012 PolSAR images showed substantial changes in marsh LAI and LAD. Although the direct cause was not substantiated, following a release of freshwater in response to the 2010 Deepwater Horizon oil spill, the fairly uniform interior marsh structure of 2009 was more vertical and dense shortly after the oil spill cessation. After 2010, marsh structure generally progressed back toward the 2009 uniformity; however, the trend was more disjointed in oil impact marshes.             

A novel variant of DNA polymerase ζ, Rev3ΔC, highlights differential regulation of Pol32 as a subunit of polymerase δ versus ζ in Saccharomyces cerevisiae

PubMed Central

Siebler, Hollie M.; Lada, Artem G.; Baranovskiy, Andrey G.; Tahirov, Tahir H.; Pavlov, Youri I.

2014-01-01

Unrepaired DNA lesions often stall replicative DNA polymerases and are bypassed by translesion synthesis (TLS) to prevent replication fork collapse. Mechanisms of TLS are lesion- and species-specific, with a prominent role of specialized DNA polymerases with relaxed active sites. After nucleotide(s) are incorporated across from the altered base(s), the aberrant primer termini are typically extended by DNA polymerase ζ (pol ζ). As a result, pol ζ is responsible for most DNA damage-induced mutations. The mechanisms of sequential DNA polymerase switches in vivo remain unclear. The major replicative DNA polymerase δ (pol δ) shares two accessory subunits, called Pol31/Pol32 in yeast, with pol ζ. Inclusion of Pol31/Pol32 in the pol δ/pol ζ holoenzymes requires a [4Fe–4S] cluster in C-termini of the catalytic subunits. Disruption of this cluster in Pol ζ or deletion of POL32 attenuates induced mutagenesis. Here we describe a novel mutation affecting the catalytic subunit of pol ζ, rev3ΔC, which provides insight into the regulation of pol switches. Strains with Rev3ΔC, lacking the entire C-terminal domain and therefore the platform for Pol31/Pol32 binding, are partially proficient in Pol32-dependent UV-induced mutagenesis. This suggests an additional role of Pol32 in TLS, beyond being a pol ζ subunit, related to pol δ. In search for members of this regulatory pathway, we examined the effects of Maintenance of Genome Stability 1 (Mgs1) protein on mutagenesis in the absence of Rev3–Pol31/Pol32 interaction. Mgs1 may compete with Pol32 for binding to PCNA. Mgs1 overproduction suppresses induced mutagenesis, but had no effect on UV-mutagenesis in the rev3ΔC strain, suggesting that Mgs1 exerts its inhibitory effect by acting specifically on Pol32 bound to pol ζ. The evidence for differential regulation of Pol32 in pol δ and pol ζ emphasizes the complexity of polymerase switches. PMID:24819597

Monte Carlo investigation of the increased radiation deposition due to gold nanoparticles using kilovoltage and megavoltage photons in a 3D randomized cell model.

PubMed

Douglass, Michael; Bezak, Eva; Penfold, Scott

2013-07-01

Investigation of increased radiation dose deposition due to gold nanoparticles (GNPs) using a 3D computational cell model during x-ray radiotherapy. Two GNP simulation scenarios were set up in Geant4; a single 400 nm diameter gold cluster randomly positioned in the cytoplasm and a 300 nm gold layer around the nucleus of the cell. Using an 80 kVp photon beam, the effect of GNP on the dose deposition in five modeled regions of the cell including cytoplasm, membrane, and nucleus was simulated. Two Geant4 physics lists were tested: the default Livermore and custom built Livermore/DNA hybrid physics list. 10(6) particles were simulated at 840 cells in the simulation. Each cell was randomly placed with random orientation and a diameter varying between 9 and 13 μm. A mathematical algorithm was used to ensure that none of the 840 cells overlapped. The energy dependence of the GNP physical dose enhancement effect was calculated by simulating the dose deposition in the cells with two energy spectra of 80 kVp and 6 MV. The contribution from Auger electrons was investigated by comparing the two GNP simulation scenarios while activating and deactivating atomic de-excitation processes in Geant4. The physical dose enhancement ratio (DER) of GNP was calculated using the Monte Carlo model. The model has demonstrated that the DER depends on the amount of gold and the position of the gold cluster within the cell. Individual cell regions experienced statistically significant (p < 0.05) change in absorbed dose (DER between 1 and 10) depending on the type of gold geometry used. The DER resulting from gold clusters attached to the cell nucleus had the more significant effect of the two cases (DER ≈ 55). The DER value calculated at 6 MV was shown to be at least an order of magnitude smaller than the DER values calculated for the 80 kVp spectrum. Based on simulations, when 80 kVp photons are used, Auger electrons have a statistically insignificant (p < 0.05) effect on the overall dose increase in the cell. The low energy of the Auger electrons produced prevents them from propagating more than 250-500 nm from the gold cluster and, therefore, has a negligible effect on the overall dose increase due to GNP. The results presented in the current work show that the primary dose enhancement is due to the production of additional photoelectrons.

Combined Task and Physical Demands Analyses towards a Comprehensive Human Work Model

DTIC Science & Technology

2014-09-01

new equipment or modifying tasks and providing training (van der Molen, Sluiter, Hulshof , Vink, & Frings-Dresen, 2005). List the Job Duties (the...00 1/SV, Defence Research and Development Canada. van der Molen, H. F., Sluiter, J. K., Hulshof , C. T. J. , Vink, P., & Frings-Dresen, M. H. W

Measurements of Propeller-Induced Unsteady Surface Force and Pressures

DTIC Science & Technology

1986-12-01

investigations using foreshortened hull models in the determination of cavitating propeller-induced pressure pulses include van Manen , 46 Huse,47 van Oossanen...Nov 1974). 46. van Manen , J.D., "The Effect of Cavitation on the Interaction Between Propeller and Ship’s Hull, "International Shipbuilding Progress...and van der Kooij,48 and van der Kooij and Jonk. 49 Examples of more recent publications that have either made use of results from dummy model tests or

The effects of van der Waals attractions on cloud droplet growth by coalescence

NASA Technical Reports Server (NTRS)

Rogers, Jan R.; Davis, Robert H.

1990-01-01

The inclusion of van der Waals attractions in the interaction between cloud droplets has been recently shown to significantly increase the collision efficiencies of the smaller droplets. In the current work, these larger values for the collision efficiencies are used in a population dynamics model of the droplet size distribution evolution with time, in hopes of at least partially resolving the long-standing paradox in cloud microphysics that predicted rates of the onset of precipitation are generally much lower than those which are observed. Evolutions of several initial cloud droplet spectra have been tracked in time. Size evolutions are compared as predicted from the use of collision efficiencies computed using two different models to allow for droplet-droplet contact: one which considers slip flow effects only, and one which considers the combined effects of van der Waals forces and slip flow. The rate at which the droplet mass density function shifts to larger droplet sizes is increased by typically 20-25 percent, when collision efficiencies which include van der Waals forces are used.

The minor house dust mite allergen Der p 13 is a fatty acid-binding protein and an activator of a TLR2-mediated innate immune response.

PubMed

Satitsuksanoa, P; Kennedy, M; Gilis, D; Le Mignon, M; Suratannon, N; Soh, W T; Wongpiyabovorn, J; Chatchatee, P; Vangveravong, M; Rerkpattanapipat, T; Sangasapaviliya, A; Piboonpocanun, S; Nony, E; Ruxrungtham, K; Jacquet, A

2016-10-01

The house dust mite (HDM) allergen Der p 13 could be a lipid-binding protein able to activate key innate signaling pathways in the initiation of the allergic response. We investigated the IgE reactivity of recombinant Der p 13 (rDer p 13), its lipid-binding activities, and its capacity to stimulate airway epithelium cells. Purified rDer p 13 was characterized by mass spectrometry, circular dichroism, fluorescence-based lipid-binding assays, and in silico structural prediction. IgE-binding activity and allergenic potential of Der p 13 were examined by ELISA, basophil degranulation assays, and in vitro airway epithelial cell activation assays. Protein modeling and biophysical analysis indicated that Der p 13 adopts a β-barrel structure with a predominately apolar pocket representing a potential binding site for hydrophobic ligands. Fluorescent lipid-binding assays confirmed that the protein is highly selective for ligands and that it binds a fatty acid with a dissociation constant typical of lipid transporter proteins. The low IgE-binding frequency (7%, n = 224) in Thai HDM-allergic patients as well as the limited propensity to activate basophil degranulation classifies Der p 13 as a minor HDM allergen. Nevertheless, the protein with its presumptively associated lipid(s) triggered the production of IL-8 and GM-CSF in respiratory epithelial cells through a TLR2-, MyD88-, NF-kB-, and MAPK-dependent signaling pathway. Although a minor allergen, Der p 13 may, through its lipid-binding capacity, play a role in the initiation of the HDM-allergic response through TLR2 activation. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

The Selenocysteine tRNA STAF-Binding Region is Essential for Adequate Selenocysteine tRNA Status, Selenoprotein Expression and Early Age Survival of Mice

USDA-ARS?s Scientific Manuscript database

STAF is a transcription activating factor for a number of RNA Pol III-and RNA Pol II-dependent genes including the selenocysteine (Sec) tRNA gene. Here, the role of STAF in regulating expression of Sec tRNA and selenoproteins was examined in an invivo model. Heterozygous inactivation of the Staf gen...

Subunit Compositions of the RNA-Silencing Enzymes Pol IV and Pol V Reveal Their Origins as Specialized Forms of RNA Polymerase II

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

Ream, Thomas S.; Haag, J. R.; Wierzbicki, A. T.

2009-01-30

In addition to RNA polymerases I, II, and III, the essential RNA polymerases present in all eukaryotes, plants have two additional nuclear RNA polymerases, abbreviated as Pol IV and Pol V, that play nonredundant roles in siRNA-directed DNA methylation and gene silencing. We show that Arabidopsis Pol IV and Pol V are composed of subunits that are paralogous or identical to the 12 subunits of Pol II. Four subunits of Pol IV are distinct from their Pol II paralogs, six subunits of Pol V are distinct from their Pol II paralogs, and four subunits differ between Pol IV and Polmore » V. Importantly, the subunit differences occur in key positions relative to the template entry and RNA exit paths. Our findings support the hypothesis that Pol IV and Pol V are Pol II-like enzymes that evolved specialized roles in the production of noncoding transcripts for RNA silencing and genome defense.« less

Repriming by PrimPol is critical for DNA replication restart downstream of lesions and chain-terminating nucleosides.

PubMed

Kobayashi, Kaori; Guilliam, Thomas A; Tsuda, Masataka; Yamamoto, Junpei; Bailey, Laura J; Iwai, Shigenori; Takeda, Shunichi; Doherty, Aidan J; Hirota, Kouji

2016-08-02

PrimPol is a DNA damage tolerance enzyme possessing both translesion synthesis (TLS) and primase activities. To uncover its potential role in TLS-mediated IgVλ hypermutation and define its interplay with other TLS polymerases, PrimPol(-/-) and PrimPol(-/-)/Polη(-/-)/Polζ (-/-) gene knockouts were generated in avian cells. Loss of PrimPol had no significant impact on the rate of hypermutation or the mutation spectrum of IgVλ. However, PrimPol(-/-) cells were sensitive to methylmethane sulfonate, suggesting that it may bypass abasic sites at the IgVλ segment by repriming DNA synthesis downstream of these sites. PrimPol(-/-) cells were also sensitive to cisplatin and hydroxyurea, indicating that it assists in maintaining / restarting replication at a variety of lesions. To accurately measure the relative contribution of the TLS and primase activities, we examined DNA damage sensitivity in PrimPol(-/-) cells complemented with polymerase or primase-deficient PrimPol. Polymerase-defective, but not primase-deficient, PrimPol suppresses the hypersensitivity of PrimPol(-/-) cells. This indicates that its primase, rather than TLS activity, is pivotal for DNA damage tolerance. Loss of TLS polymerases, Polη and Polζ has an additive effect on the sensitivity of PrimPol(-/-) cells. Moreover, we found that PrimPol and Polη-Polζ redundantly prevented cell death and facilitated unperturbed cell cycle progression. PrimPol(-/-) cells also exhibited increased sensitivity to a wide variety of chain-terminating nucleoside analogs (CTNAs). PrimPol could perform close-coupled repriming downstream of CTNAs and oxidative damage in vitro. Together, these results indicate that PrimPol's repriming activity plays a central role in reinitiating replication downstream from CTNAs and other specific DNA lesions.

RNA polymerases IV and V influence the 3' boundaries of Polymerase II transcription units in Arabidopsis.

PubMed

McKinlay, Anastasia; Podicheti, Ram; Wendte, Jered M; Cocklin, Ross; Rusch, Douglas B

2018-02-01

Nuclear multisubunit RNA polymerases IV and V (Pol IV and Pol V) evolved in plants as specialized forms of Pol II. Their functions are best understood in the context of RNA-directed DNA methylation (RdDM), a process in which Pol IV-dependent 24 nt siRNAs direct the de novo cytosine methylation of regions transcribed by Pol V. Pol V has additional functions, independent of Pol IV and 24 nt siRNA biogenesis, in maintaining the repression of transposons and genomic repeats whose silencing depends on maintenance cytosine methylation. Here we report that Pol IV and Pol V play unexpected roles in defining the 3' boundaries of Pol II transcription units. Nuclear run-on assays reveal that in the absence of Pol IV or Pol V, Pol II occupancy downstream of poly A sites increases for approximately 12% of protein-coding genes. This effect is most pronounced for convergently transcribed gene pairs. Although Pols IV and V are detected near transcript ends of the affected Pol II - transcribed genes, their role in limiting Pol II read-through is independent of siRNA biogenesis or cytosine methylation for the majority of these genes. Interestingly, we observed that splicing was less efficient in pol IV or pol V mutant plants, compared to wild-type plants, suggesting that Pol IV or Pol V might affect pre-mRNA processing. We speculate that Pols IV and V (and/or their associated factors) play roles in Pol II transcription termination and pre-mRNA splicing by influencing polymerase elongation rates and/or release at collision sites for convergent genes.

Influence of van der Waals forces on increasing the strength and toughness in dynamic fracture of nanofibre networks: a peridynamic approach

NASA Astrophysics Data System (ADS)

Bobaru, F.

2007-07-01

The peridynamic method is used here to analyse the effect of van der Waals forces on the mechanical behaviour and strength and toughness properties of three-dimensional nanofibre networks under imposed stretch deformation. The peridynamic formulation allows for a natural inclusion of long-range forces (such as van der Waals forces) by considering all interactions as 'long-range'. We use van der Waals interactions only between different fibres and do not need to model individual atoms. Fracture is introduced at the microstructural (peridynamic bond) level for the microelastic type bonds, while van der Waals bonds can reform at any time. We conduct statistical studies to determine a certain volume element for which the network of randomly oriented fibres becomes quasi-isotropic and insensitive to statistical variations. This qualitative study shows that the presence of van der Waals interactions and of heterogeneities (sacrificial bonds) in the strength of the bonds at the crosslinks between fibres can help in increasing the strength and toughness of the nanofibre network. Two main mechanisms appear to control the deformation of nanofibre networks: fibre reorientation (caused by deformation and breakage) and fibre accretion (due to van der Waals interaction). Similarities to the observed toughness of polymer adhesive in the abalone shell composition are explained. The author would like to dedicate this work to the 60th anniversary of Professor Subrata Mukherjee.

Energy Technology Allocation for Distributed Energy Resources: A Technology-Policy Framework

NASA Astrophysics Data System (ADS)

Mallikarjun, Sreekanth

Distributed energy resources (DER) are emerging rapidly. New engineering technologies, materials, and designs improve the performance and extend the range of locations for DER. In contrast, constructing new or modernizing existing high voltage transmission lines for centralized generation are expensive and challenging. In addition, customer demand for reliability has increased and concerns about climate change have created a pull for swift renewable energy penetration. In this context, DER policy makers, developers, and users are interested in determining which energy technologies to use to accommodate different end-use energy demands. We present a two-stage multi-objective strategic technology-policy framework for determining the optimal energy technology allocation for DER. The framework simultaneously considers economic, technical, and environmental objectives. The first stage utilizes a Data Envelopment Analysis model for each end-use to evaluate the performance of each energy technology based on the three objectives. The second stage incorporates factor efficiencies determined in the first stage, capacity limitations, dispatchability, and renewable penetration for each technology, and demand for each end-use into a bottleneck multi-criteria decision model which provides the Pareto-optimal energy resource allocation. We conduct several case studies to understand the roles of various distributed energy technologies in different scenarios. We construct some policy implications based on the model results of set of case studies.

RecQL5 promotes genome stabilization through two parallel mechanisms--interacting with RNA polymerase II and acting as a helicase.

PubMed

Islam, M Nurul; Fox, David; Guo, Rong; Enomoto, Takemi; Wang, Weidong

2010-05-01

The RecQL5 helicase is essential for maintaining genome stability and reducing cancer risk. To elucidate its mechanism of action, we purified a RecQL5-associated complex and identified its major component as RNA polymerase II (Pol II). Bioinformatics and structural modeling-guided mutagenesis revealed two conserved regions in RecQL5 as KIX and SRI domains, already known in transcriptional regulators for Pol II. The RecQL5-KIX domain binds both initiation (Pol IIa) and elongation (Pol IIo) forms of the polymerase, whereas the RecQL5-SRI domain interacts only with the elongation form. Fully functional RecQL5 requires both helicase activity and associations with the initiation polymerase, because mutants lacking either activity are partially defective in the suppression of sister chromatid exchange and resistance to camptothecin-induced DNA damage, and mutants lacking both activities are completely defective. We propose that RecQL5 promotes genome stabilization through two parallel mechanisms: by participation in homologous recombination-dependent DNA repair as a RecQ helicase and by regulating the initiation of Pol II to reduce transcription-associated replication impairment and recombination.

Bacteriophage phi 6 RNA-dependent RNA polymerase: molecular details of initiating nucleic acid synthesis without primer.

PubMed

Laurila, Minni R L; Makeyev, Eugene V; Bamford, Dennis H

2002-05-10

Like most RNA polymerases, the polymerase of double-strand RNA bacteriophage phi6 (phi6pol) is capable of primer-independent initiation. Based on the recently solved phi6pol initiation complex structure, a four-amino acid-long loop (amino acids 630-633) has been suggested to stabilize the first two incoming NTPs through stacking interactions with tyrosine, Tyr(630). A similar loop is also present in the hepatitis C virus polymerase, another enzyme capable of de novo initiation. Here, we use a series of phi6pol mutants to address the role of this element. As predicted, mutants at the Tyr(630) position are inefficient in initiation de novo. Unexpectedly, when the loop is disordered by changing Tyr(630)-Lys(631)-Trp(632) to GSG, phi6pol becomes a primer-dependent enzyme, either extending complementary oligonucleotide or, when the template 3' terminus can adopt a hairpin-like conformation, utilizing a "copy-back" initiation mechanism. In contrast to the wild-type phi6pol, the GSG mutant does not require high GTP concentration for its optimal activity. These findings suggest a general model for the initiation of de novo RNA synthesis.

Interaction between the Rev1 C-terminal Domain and the PolD3 Subunit of Polζ Suggests a Mechanism of Polymerase Exchange upon Rev1/Polζ-Dependent Translesion Synthesis

PubMed Central

Pustovalova, Yulia; Magalhães, Mariana T. Q.; D’Souza, Sanjay; Rizzo, Alessandro A.; Korza, George; Walker, Graham C.; Korzhnev, Dmitry M.

2016-01-01

Translesion synthesis (TLS) is a mutagenic branch of cellular DNA damage tolerance that enables bypass replication over DNA lesions carried out by specialized low-fidelity DNA polymerases. The replicative bypass of most types of DNA damage is performed in a two-step process of Rev1/Polζ-dependent TLS. In the first step, a Y-family TLS enzyme, typically Polη, Polι or Polκ, inserts a nucleotide across DNA lesion. In the second step, a four-subunit B-family DNA polymerase Polζ (Rev3/Rev7/PolD2/PolD3 complex) extends the distorted DNA primer-template. The coordinated action of error-prone TLS enzymes is regulated through their interactions with the two scaffold proteins, the sliding clamp PCNA and the TLS polymerase Rev1. Rev1 interactions with all other TLS enzymes are mediated by its C-terminal domain (Rev1-CT), which can simultaneously bind the Rev7 subunit of Polζ and Rev1-interacting regions (RIRs) from Polη, Polι or Polκ. In this work, we identified a previously unknown RIR motif in the C-terminal part of PolD3 subunit of Polζ whose interaction with the Rev1-CT is among the tightest mediated by RIR motifs. Three-dimensional structure of the Rev1-CT/PolD3-RIR complex determined by NMR spectroscopy revealed a structural basis for the relatively high affinity of this interaction. The unexpected discovery of PolD3-RIR motif suggests a mechanism of 'inserter' to 'extender' DNA polymerase switch upon Rev1/Polζ-dependent TLS, in which the PolD3-RIR binding to the Rev1-CT (i) helps displace the 'inserter' Polη, Polι or Polκ from its complex with Rev1, and (ii) facilitates assembly of the four-subunit 'extender' Polζ through simultaneous interaction of Rev1-CT with Rev7 and PolD3 subunits. PMID:26982350

Subunit compositions of Arabidopsis RNA polymerases I and III reveal Pol I- and Pol III-specific forms of the AC40 subunit and alternative forms of the C53 subunit

PubMed Central

Ream, Thomas S.; Haag, Jeremy R.; Pontvianne, Frederic; Nicora, Carrie D.; Norbeck, Angela D.; Paša-Tolić, Ljiljana; Pikaard, Craig S.

2015-01-01

Using affinity purification and mass spectrometry, we identified the subunits of Arabidopsis thaliana multisubunit RNA polymerases I and III (abbreviated as Pol I and Pol III), the first analysis of their physical compositions in plants. In all eukaryotes examined to date, AC40 and AC19 subunits are common to Pol I (a.k.a. Pol A) and Pol III (a.k.a. Pol C) and are encoded by single genes. Surprisingly, A. thaliana and related species express two distinct AC40 paralogs, one of which assembles into Pol I and the other of which assembles into Pol III. Changes at eight amino acid positions correlate with the functional divergence of Pol I- and Pol III-specific AC40 paralogs. Two genes encode homologs of the yeast C53 subunit and either protein can assemble into Pol III. By contrast, only one of two potential C17 variants, and one of two potential C31 variants were detected in Pol III. We introduce a new nomenclature system for plant Pol I and Pol III subunits in which the 12 subunits that are structurally and functionally homologous among Pols I through V are assigned equivalent numbers. PMID:25813043

De Ontwikkeling van een PBPK Model voor VX; Stand van Zaken V013-813 en 207C (The Development of a PBPK Model for VX: Status Report)

DTIC Science & Technology

2006-02-01

ing. H.C. Trap, dr. ir. M.J. van der werd zes maal gesproken over de Schans, ing. L.F. Chau, B.). Lander, invulling en de voortgang van het I.A. Cordia ...dr. ir. M.J. van der Schans, ing. L.F. Chau, J.P. Oostdijk, B.J. Lander, l.A. Cordia 25 TNO Defensie en Veiligheid, vestiging Rijswijk, Marketing en

Polarimetric scattering model for estimation of above ground biomass of multilayer vegetation using ALOS-PALSAR quad-pol data

NASA Astrophysics Data System (ADS)

Sai Bharadwaj, P.; Kumar, Shashi; Kushwaha, S. P. S.; Bijker, Wietske

Forests are important biomes covering a major part of the vegetation on the Earth, and as such account for seventy percent of the carbon present in living beings. The value of a forest's above ground biomass (AGB) is considered as an important parameter for the estimation of global carbon content. In the present study, the quad-pol ALOS-PALSAR data was used for the estimation of AGB for the Dudhwa National Park, India. For this purpose, polarimetric decomposition components and an Extended Water Cloud Model (EWCM) were used. The PolSAR data orientation angle shifts were compensated for before the polarimetric decomposition. The scattering components obtained from the polarimetric decomposition were used in the Water Cloud Model (WCM). The WCM was extended for higher order interactions like double bounce scattering. The parameters of the EWCM were retrieved using the field measurements and the decomposition components. Finally, the relationship between the estimated AGB and measured AGB was assessed. The coefficient of determination (R2) and root mean square error (RMSE) were 0.4341 and 119 t/ha respectively.

Genome-Wide RNA Polymerase II Profiles and RNA Accumulation Reveal Kinetics of Transcription and Associated Epigenetic Changes During Diurnal Cycles

PubMed Central

Gilardi, Federica; Liechti, Robin; Martin, Olivier; Harshman, Keith; Delorenzi, Mauro; Desvergne, Béatrice; Herr, Winship; Deplancke, Bart; Schibler, Ueli; Rougemont, Jacques; Guex, Nicolas; Hernandez, Nouria; Naef, Felix

2012-01-01

Interactions of cell-autonomous circadian oscillators with diurnal cycles govern the temporal compartmentalization of cell physiology in mammals. To understand the transcriptional and epigenetic basis of diurnal rhythms in mouse liver genome-wide, we generated temporal DNA occupancy profiles by RNA polymerase II (Pol II) as well as profiles of the histone modifications H3K4me3 and H3K36me3. We used these data to quantify the relationships of phases and amplitudes between different marks. We found that rhythmic Pol II recruitment at promoters rather than rhythmic transition from paused to productive elongation underlies diurnal gene transcription, a conclusion further supported by modeling. Moreover, Pol II occupancy preceded mRNA accumulation by 3 hours, consistent with mRNA half-lives. Both methylation marks showed that the epigenetic landscape is highly dynamic and globally remodeled during the 24-hour cycle. While promoters of transcribed genes had tri-methylated H3K4 even at their trough activity times, tri-methylation levels reached their peak, on average, 1 hour after Pol II. Meanwhile, rhythms in tri-methylation of H3K36 lagged transcription by 3 hours. Finally, modeling profiles of Pol II occupancy and mRNA accumulation identified three classes of genes: one showing rhythmicity both in transcriptional and mRNA accumulation, a second class with rhythmic transcription but flat mRNA levels, and a third with constant transcription but rhythmic mRNAs. The latter class emphasizes widespread temporally gated posttranscriptional regulation in the mouse liver. PMID:23209382

Human Pol ζ purified with accessory subunits is active in translesion DNA synthesis and complements Pol η in cisplatin bypass

PubMed Central

Lee, Young-Sam; Gregory, Mark T.; Yang, Wei

2014-01-01

DNA polymerase ζ (Pol ζ) is a eukaryotic B-family DNA polymerase that specializes in translesion synthesis and is essential for normal embryogenesis. At a minimum, Pol ζ consists of a catalytic subunit Rev3 and an accessory subunit Rev7. Mammalian Rev3 contains >3,000 residues and is twice as large as the yeast homolog. To date, no vertebrate Pol ζ has been purified for biochemical characterization. Here we report purification of a series of human Rev3 deletion constructs expressed in HEK293 cells and identification of a minimally catalytically active human Pol ζ variant. With a tagged form of an active Pol ζ variant, we isolated two additional accessory subunits of human Pol ζ, PolD2 and PolD3. The purified four-subunit Pol ζ4 (Rev3–Rev7–PolD2–PolD3) is much more efficient and more processive at bypassing a 1,2-intrastrand d(GpG)-cisplatin cross-link than the two-subunit Pol ζ2 (Rev3–Rev7). We show that complete bypass of cisplatin lesions requires Pol η to insert dCTP opposite the 3′ guanine and Pol ζ4 to extend the primers. PMID:24449906

Human Pol ζ purified with accessory subunits is active in translesion DNA synthesis and complements Pol η in cisplatin bypass.

PubMed

Lee, Young-Sam; Gregory, Mark T; Yang, Wei

2014-02-25

DNA polymerase ζ (Pol ζ) is a eukaryotic B-family DNA polymerase that specializes in translesion synthesis and is essential for normal embryogenesis. At a minimum, Pol ζ consists of a catalytic subunit Rev3 and an accessory subunit Rev7. Mammalian Rev3 contains >3,000 residues and is twice as large as the yeast homolog. To date, no vertebrate Pol ζ has been purified for biochemical characterization. Here we report purification of a series of human Rev3 deletion constructs expressed in HEK293 cells and identification of a minimally catalytically active human Pol ζ variant. With a tagged form of an active Pol ζ variant, we isolated two additional accessory subunits of human Pol ζ, PolD2 and PolD3. The purified four-subunit Pol ζ4 (Rev3-Rev7-PolD2-PolD3) is much more efficient and more processive at bypassing a 1,2-intrastrand d(GpG)-cisplatin cross-link than the two-subunit Pol ζ2 (Rev3-Rev7). We show that complete bypass of cisplatin lesions requires Pol η to insert dCTP opposite the 3' guanine and Pol ζ4 to extend the primers.

Catalytic properties of RNA polymerases IV and V: accuracy, nucleotide incorporation and rNTP/dNTP discrimination

PubMed Central

Marasco, Michelle; Li, Weiyi; Lynch, Michael

2017-01-01

Abstract All eukaryotes have three essential nuclear multisubunit RNA polymerases, abbreviated as Pol I, Pol II and Pol III. Plants are remarkable in having two additional multisubunit RNA polymerases, Pol IV and Pol V, which synthesize noncoding RNAs that coordinate RNA-directed DNA methylation for silencing of transposons and a subset of genes. Based on their subunit compositions, Pols IV and V clearly evolved as specialized forms of Pol II, but their catalytic properties remain undefined. Here, we show that Pols IV and V differ from one another, and Pol II, in nucleotide incorporation rate, transcriptional accuracy and the ability to discriminate between ribonucleotides and deoxyribonucleotides. Pol IV transcription is considerably more error-prone than Pols II or V, which may be tolerable in its synthesis of short RNAs that serve as precursors for siRNAs targeting non-identical members of transposon families. By contrast, Pol V exhibits high fidelity transcription, similar to Pol II, suggesting a need for Pol V transcripts to faithfully reflect the DNA sequence of target loci to which siRNA–Argonaute silencing complexes are recruited. PMID:28977461

Coordinating DNA polymerase traffic during high and low fidelity synthesis.

PubMed

Sutton, Mark D

2010-05-01

With the discovery that organisms possess multiple DNA polymerases (Pols) displaying different fidelities, processivities, and activities came the realization that mechanisms must exist to manage the actions of these diverse enzymes to prevent gratuitous mutations. Although many of the Pols encoded by most organisms are largely accurate, and participate in DNA replication and DNA repair, a sizeable fraction display a reduced fidelity, and act to catalyze potentially error-prone translesion DNA synthesis (TLS) past lesions that persist in the DNA. Striking the proper balance between use of these different enzymes during DNA replication, DNA repair, and TLS is essential for ensuring accurate duplication of the cell's genome. This review highlights mechanisms that organisms utilize to manage the actions of their different Pols. A particular emphasis is placed on discussion of current models for how different Pols switch places with each other at the replication fork during high fidelity replication and potentially error-pone TLS. Copyright (c) 2010 Elsevier B.V. All rights reserved.

Amiloride inhibits the initiation of Coxsackievirus and poliovirus RNA replication by inhibiting VPg uridylylation.

PubMed

Ogram, Sushma A; Boone, Christopher D; McKenna, Robert; Flanegan, James B

2014-09-01

The mechanism of amiloride inhibition of Coxsackievirus B3 (CVB3) and poliovirus type 1 (PV1) RNA replication was investigated using membrane-associated RNA replication complexes. Amiloride was shown to inhibit viral RNA replication and VPgpUpU synthesis. However, the drug had no effect on polymerase elongation activity during either (-) strand or (+) strand synthesis. These findings indicated that amiloride inhibited the initiation of RNA synthesis by inhibiting VPg uridylylation. In addition, in silico binding studies showed that amiloride docks in the VPg binding site on the back of the viral RNA polymerase, 3D(pol). Since VPg binding at this site on PV1 3D(pol) was previously shown to be required for VPg uridylylation, our results suggest that amiloride inhibits VPg binding to 3D(pol). In summary, our findings are consistent with a model in which amiloride inhibits VPgpUpU synthesis and viral RNA replication by competing with VPg for binding to 3D(pol). Copyright © 2014 Elsevier Inc. All rights reserved.

Mapping Forest Height in Gabon Using UAVSAR Multi-Baseline Polarimetric SAR Interferometry and Lidar Fusion

NASA Astrophysics Data System (ADS)

Simard, M.; Denbina, M. W.

2017-12-01

Using data collected by NASA's Uninhabited Aerial Vehicle Synthetic Aperture Radar (UAVSAR) and Land, Vegetation, and Ice Sensor (LVIS) lidar, we have estimated forest canopy height for a number of study areas in the country of Gabon using a new machine learning data fusion approach. Using multi-baseline polarimetric synthetic aperture radar interferometry (PolInSAR) data collected by UAVSAR, forest heights can be estimated using the random volume over ground model. In the case of multi-baseline UAVSAR data consisting of many repeat passes with spatially separated flight tracks, we can estimate different forest height values for each different image pair, or baseline. In order to choose the best forest height estimate for each pixel, the baselines must be selected or ranked, taking care to avoid baselines with unsuitable spatial separation, or severe temporal decorrelation effects. The current baseline selection algorithms in the literature use basic quality metrics derived from the PolInSAR data which are not necessarily indicative of the true height accuracy in all cases. We have developed a new data fusion technique which treats PolInSAR baseline selection as a supervised classification problem, where the classifier is trained using a sparse sampling of lidar data within the PolInSAR coverage area. The classifier uses a large variety of PolInSAR-derived features as input, including radar backscatter as well as features based on the PolInSAR coherence region shape and the PolInSAR complex coherences. The resulting data fusion method produces forest height estimates which are more accurate than a purely radar-based approach, while having a larger coverage area than the input lidar training data, combining some of the strengths of each sensor. The technique demonstrates the strong potential for forest canopy height and above-ground biomass mapping using fusion of PolInSAR with data from future spaceborne lidar missions such as the upcoming Global Ecosystems Dynamics Investigation (GEDI) lidar.

Two distinct modes of RecA action are required for DNA polymerase V-catalyzed translesion synthesis.

PubMed

Pham, Phuong; Seitz, Erica M; Saveliev, Sergei; Shen, Xuan; Woodgate, Roger; Cox, Michael M; Goodman, Myron F

2002-08-20

SOS mutagenesis in Escherichia coli requires DNA polymerase V (pol V) and RecA protein to copy damaged DNA templates. Here we show that two distinct biochemical modes for RecA protein are necessary for pol V-catalyzed translesion synthesis. One RecA mode is characterized by a strong stimulation in nucleotide incorporation either directly opposite a lesion or at undamaged template sites, but by the absence of lesion bypass. A separate RecA mode is necessary for translesion synthesis. The RecA1730 mutant protein, which was identified on the basis of its inability to promote pol V (UmuD'(2)C)-dependent UV-mutagenesis, appears proficient for the first mode of RecA action but is deficient in the second mode. Data are presented suggesting that the two RecA modes are "nonfilamentous". That is, contrary to current models for SOS mutagenesis, formation of a RecA nucleoprotein filament may not be required for copying damaged DNA templates. Instead, SOS mutagenesis occurs when pol V interacts with two RecA molecules, first at a 3' primer end, upstream of a template lesion, where RecA mode 1 stimulates pol V activity, and subsequently at a site immediately downstream of the lesion, where RecA mode 2 cocatalyzes lesion bypass. We posit that in vivo assembly of a RecA nucleoprotein filament may be required principally to target pol V to a site of DNA damage and to stabilize the pol V-RecA interaction at the lesion. However, it is only a RecA molecule located at the 3' filament tip, proximal to a damaged template base, that is directly responsible for translesion synthesis.

Two distinct modes of RecA action are required for DNA polymerase V-catalyzed translesion synthesis

PubMed Central

Pham, Phuong; Seitz, Erica M.; Saveliev, Sergei; Shen, Xuan; Woodgate, Roger; Cox, Michael M.; Goodman, Myron F.

2002-01-01

SOS mutagenesis in Escherichia coli requires DNA polymerase V (pol V) and RecA protein to copy damaged DNA templates. Here we show that two distinct biochemical modes for RecA protein are necessary for pol V-catalyzed translesion synthesis. One RecA mode is characterized by a strong stimulation in nucleotide incorporation either directly opposite a lesion or at undamaged template sites, but by the absence of lesion bypass. A separate RecA mode is necessary for translesion synthesis. The RecA1730 mutant protein, which was identified on the basis of its inability to promote pol V (UmuD′2C)-dependent UV-mutagenesis, appears proficient for the first mode of RecA action but is deficient in the second mode. Data are presented suggesting that the two RecA modes are “nonfilamentous”. That is, contrary to current models for SOS mutagenesis, formation of a RecA nucleoprotein filament may not be required for copying damaged DNA templates. Instead, SOS mutagenesis occurs when pol V interacts with two RecA molecules, first at a 3′ primer end, upstream of a template lesion, where RecA mode 1 stimulates pol V activity, and subsequently at a site immediately downstream of the lesion, where RecA mode 2 cocatalyzes lesion bypass. We posit that in vivo assembly of a RecA nucleoprotein filament may be required principally to target pol V to a site of DNA damage and to stabilize the pol V-RecA interaction at the lesion. However, it is only a RecA molecule located at the 3′ filament tip, proximal to a damaged template base, that is directly responsible for translesion synthesis. PMID:12177433

Materials perspective on Casimir and van der Waals interactions

NASA Astrophysics Data System (ADS)

Woods, L. M.; Dalvit, D. A. R.; Tkatchenko, A.; Rodriguez-Lopez, P.; Rodriguez, A. W.; Podgornik, R.

2016-10-01

Interactions induced by electromagnetic fluctuations, such as van der Waals and Casimir forces, are of universal nature present at any length scale between any types of systems. Such interactions are important not only for the fundamental science of materials behavior, but also for the design and improvement of micro- and nanostructured devices. In the past decade, many new materials have become available, which has stimulated the need for understanding their dispersive interactions. The field of van der Waals and Casimir forces has experienced an impetus in terms of developing novel theoretical and computational methods to provide new insights into related phenomena. The understanding of such forces has far reaching consequences as it bridges concepts in materials, atomic and molecular physics, condensed-matter physics, high-energy physics, chemistry, and biology. This review summarizes major breakthroughs and emphasizes the common origin of van der Waals and Casimir interactions. Progress related to novel ab initio modeling approaches and their application in various systems, interactions in materials with Dirac-like spectra, force manipulations through nontrivial boundary conditions, and applications of van der Waals forces in organic and biological matter are examined. The outlook of the review is to give the scientific community a materials perspective of van der Waals and Casimir phenomena and stimulate the development of experimental techniques and applications.

Subunit Compositions of the RNA-Silencing Enzymes Pol IV and Pol V Reveal Their Origins as Specialized Forms of RNA Polymerase II

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

Ream, Thomas S.; Haag, J. R.; Wierzbicki, A. T.

2009-01-30

In addition to RNA polymerases I, II and III, which are multi-subunit RNA polymerases found in all eukaryotes, plants have catalytic subunits for two additional nuclear RNA polymerases, abbreviated as Pol IV and Pol V (formerly Pol IVa and Pol IVb, respectively). Pol IV and Pol V play non-redundant roles in siRNA-directed DNA methylation and gene silencing pathways.

Subunit compositions of Arabidopsis RNA polymerases I and III reveal Pol I- and Pol III-specific forms of the AC40 subunit and alternative forms of the C53 subunit

DOE PAGES

Ream, Thomas S.; Haag, Jeremy R.; Pontvianne, Frederic; ...

2015-05-02

Using affinity purification and mass spectrometry, we identified the subunits of Arabidopsis thaliana multisubunit RNA Polymerases I and III (abbreviated as Pol I and Pol III), providing the first description of their physical compositions in plants. AC40 and AC19 subunits are typically common to Pol I (a.k.a. Pol A) and Pol III (a.k.a. Pol C) and are encoded by single genes whose mutation, in humans, is a cause of the craniofacial disorder, Treacher-Collins Syndrome. Surprisingly, A. thaliana, and related species, express two distinct AC40 paralogs, one of which assembles into Pol I and the other of which assembles into Polmore » III. Changes at eight amino acid positions correlate with this functional divergence of Pol I and Pol III-specific AC40 paralogs. Two genes encode homologs of the yeast C53 subunit, and either variant can assemble into Pol III. By contrast, only one of two potential C17 variants, and one of two potential C31 variants were detected in Pol III. We introduce a new nomenclature system for plant Pol I and Pol III subunits in which the twelve subunits that are structurally and functionally homologous among Pols I through V are assigned equivalent numbers.« less

Subunit compositions of Arabidopsis RNA polymerases I and III reveal Pol I- and Pol III-specific forms of the AC40 subunit and alternative forms of the C53 subunit

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

Ream, Thomas S.; Haag, Jeremy R.; Pontvianne, Frederic

Using affinity purification and mass spectrometry, we identified the subunits of Arabidopsis thaliana multisubunit RNA Polymerases I and III (abbreviated as Pol I and Pol III), providing the first description of their physical compositions in plants. AC40 and AC19 subunits are typically common to Pol I (a.k.a. Pol A) and Pol III (a.k.a. Pol C) and are encoded by single genes whose mutation, in humans, is a cause of the craniofacial disorder, Treacher-Collins Syndrome. Surprisingly, A. thaliana, and related species, express two distinct AC40 paralogs, one of which assembles into Pol I and the other of which assembles into Polmore » III. Changes at eight amino acid positions correlate with this functional divergence of Pol I and Pol III-specific AC40 paralogs. Two genes encode homologs of the yeast C53 subunit, and either variant can assemble into Pol III. By contrast, only one of two potential C17 variants, and one of two potential C31 variants were detected in Pol III. We introduce a new nomenclature system for plant Pol I and Pol III subunits in which the twelve subunits that are structurally and functionally homologous among Pols I through V are assigned equivalent numbers.« less

Spatial and Functional Relationships Among Pol V-Associated loci, Pol IV-Dependent siRNAs, and Cytosine Methylation in the Arabidopsis Epigenome

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

Wierzbicki, A. T.; Cocklin, Ross; Mayampurath, Anoop

2012-08-15

Multisubunit RNA polymerases IV and V (Pols IV and V) mediate RNA-directed DNA methylation and transcriptional silencing of retrotransposons and heterochromatic repeats in plants. We identified genomic sites of Pol V occupancy in parallel with siRNA deep sequencing and methylcytosine mapping, comparing wild-type plants with mutants defective for Pol IV, Pol V, or both Pols IV and V. Approximately 60% of Pol V-associated regions encompass regions of 24-nucleotide (nt) siRNA complementarity and cytosine methylation, consistent with cytosine methylation being guided by base-pairing of Pol IV-dependent siRNAs with Pol V transcripts. However, 27% of Pol V peaks do not overlap sitesmore » of 24-nt siRNA biogenesis or cytosine methylation, indicating that Pol V alone does not specify sites of cytosine methylation. Surprisingly, the number of methylated CHH motifs, a hallmark of RNA-directed de novo methylation, is similar in wild-type plants and Pol IV or Pol V mutants. In the mutants, methylation is lost at 50%-60% of the CHH sites that are methylated in the wild type but is gained at new CHH positions, primarily in pericentromeric regions. These results indicate that Pol IV and Pol V are not required for cytosine methyltransferase activity but shape the epigenome by guiding CHH methylation to specific genomic sites.« less

Dynamical screening of the van der Waals interaction between graphene layers.

PubMed

Dappe, Y J; Bolcatto, P G; Ortega, J; Flores, F

2012-10-24

The interaction between graphene layers is analyzed combining local orbital DFT and second order perturbation theory. For this purpose we use the linear combination of atomic orbitals-orbital occupancy (LCAO-OO) formalism, that allows us to separate the interaction energy as the sum of a weak chemical interaction between graphene layers plus the van der Waals interaction (Dappe et al 2006 Phys. Rev. B 74 205434). In this work, the weak chemical interaction is calculated by means of corrected-LDA calculations using an atomic-like sp(3)d(5) basis set. The van der Waals interaction is calculated by means of second order perturbation theory using an atom-atom interaction approximation and the atomic-like-orbital occupancies. We also analyze the effect of dynamical screening in the van der Waals interaction using a simple model. We find that this dynamical screening reduces by 40% the van der Waals interaction. Taking this effect into account, we obtain a graphene-graphene interaction energy of 70 ± 5 meV/atom in reasonable agreement with the experimental evidence.

CXCR4 Protein Epitope Mimetic Antagonist POL5551 Disrupts Metastasis and Enhances Chemotherapy Effect in Triple-Negative Breast Cancer.

PubMed

Xiang, Jingyu; Hurchla, Michelle A; Fontana, Francesca; Su, Xinming; Amend, Sarah R; Esser, Alison K; Douglas, Garry J; Mudalagiriyappa, Chidananda; Luker, Kathryn E; Pluard, Timothy; Ademuyiwa, Foluso O; Romagnoli, Barbara; Tuffin, Gérald; Chevalier, Eric; Luker, Gary D; Bauer, Michael; Zimmermann, Johann; Aft, Rebecca L; Dembowsky, Klaus; Weilbaecher, Katherine N

2015-11-01

The SDF-1 receptor CXCR4 has been associated with early metastasis and poorer prognosis in breast cancers, especially the most aggressive triple-negative subtype. In line with previous reports, we found that tumoral CXCR4 expression in patients with locally advanced breast cancer was associated with increased metastases and rapid tumor progression. Moreover, high CXCR4 expression identified a group of bone marrow-disseminated tumor cells (DTC)-negative patients at high risk for metastasis and death. The protein epitope mimetic (PEM) POL5551, a novel CXCR4 antagonist, inhibited binding of SDF-1 to CXCR4, had no direct effects on tumor cell viability, but reduced migration of breast cancer cells in vitro. In two orthotopic models of triple-negative breast cancer, POL5551 had little inhibitory effect on primary tumor growth, but significantly reduced distant metastasis. When combined with eribulin, a chemotherapeutic microtubule inhibitor, POL5551 additively reduced metastasis and prolonged survival in mice after resection of the primary tumor compared with single-agent eribulin. Hypothesizing that POL5551 may mobilize tumor cells from their microenvironment and sensitize them to chemotherapy, we used a "chemotherapy framing" dosing strategy. When administered shortly before and after eribulin treatment, three doses of POL5551 with eribulin reduced bone and liver tumor burden more effectively than chemotherapy alone. These data suggest that sequenced administration of CXCR4 antagonists with cytotoxic chemotherapy synergize to reduce distant metastases. ©2015 American Association for Cancer Research.

The BRITE spectropolarimetric survey

NASA Astrophysics Data System (ADS)

Neiner, C.; Lèbre, A.

2014-12-01

The BRITE constellation of nanosatellites observes very bright stars to perform seismology. We have set up a spectropolarimetric survey of all BRITE targets, i.e. all ˜600 stars brighter than V=4, with Narval at TBL, ESPaDOnS at CFHT and HarpsPol at ESO. We plan to reach a magnetic detection threshold of B_{pol} = 50 G for stars hotter than F5 and B_{pol} = 5 G for cooler stars. This program will allow us to combine magnetic information with the BRITE seismic information and obtain a better interpretation and modelling of the internal structure of the stars. It will also lead to new discoveries of very bright magnetic stars, which are unique targets for follow-up and multi-technique studies.

Analysis of predicted B and T-cell epitopes in Der p 23, allergen from Dermatophagoides pteronyssinus.

PubMed

Fanuel, Songwe; Tabesh, Saeideh; Sadroddiny, Esmaeil; Kardar, Gholam Ali

2017-01-01

House dust mite (HDM) allergy is the leading cause of IgE-mediated hypersensitivity. Therefore identifying potential epitopes in the Dermatophagoide pteronyssinus 23 (Der p 23), a major house dust mite allergen will aid in the development of therapeutic vaccines and diagnostic kits for HDM allergy. Experimental methods of epitope discovery have been widely exploited for the mapping of potential allergens. This study sought to use immunoinformatic methods to analyze the structure of Der p 23 for potential immunoreactive B and T-cell epitopes that could be useful for AIT and allergy diagnosis. We retrieved a Der p 23 allergen sequence from Genbank database and then analyzed it using a combination of web-based sequence analysis tools including the Immune Epitope Database (IEDB), Protparam, BCPREDS, ABCpred, BepiPred, Bcepred among others to predict the physiochemical properties and epitope spectra of the Der p 23 allergen. We then built 3D models of the predicted B-cell epitopes, T cell epitopes and Der p 23 for sequence structure homology analysis. Our results identified peptides 'TRWNEDE', 'TVHPTTTEQPDDK', and 'NDDDPTT' as immunogenic linear B-cell epitopes while 'CPSRFGYFADPKDPH' and 'CPGNTRWNEDEETCT' were found to be the most suitable T-cell epitopes that interacted well with a large number of MHC II alleles. Both epitopes had high population coverage as well as showing a 100% conservancy. These five Der p 23 epitopes are useful for AIT vaccines and HDM allergy diagnosis development.

Catalytic properties of RNA polymerases IV and V: accuracy, nucleotide incorporation and rNTP/dNTP discrimination.

PubMed

Marasco, Michelle; Li, Weiyi; Lynch, Michael; Pikaard, Craig S

2017-11-02

All eukaryotes have three essential nuclear multisubunit RNA polymerases, abbreviated as Pol I, Pol II and Pol III. Plants are remarkable in having two additional multisubunit RNA polymerases, Pol IV and Pol V, which synthesize noncoding RNAs that coordinate RNA-directed DNA methylation for silencing of transposons and a subset of genes. Based on their subunit compositions, Pols IV and V clearly evolved as specialized forms of Pol II, but their catalytic properties remain undefined. Here, we show that Pols IV and V differ from one another, and Pol II, in nucleotide incorporation rate, transcriptional accuracy and the ability to discriminate between ribonucleotides and deoxyribonucleotides. Pol IV transcription is considerably more error-prone than Pols II or V, which may be tolerable in its synthesis of short RNAs that serve as precursors for siRNAs targeting non-identical members of transposon families. By contrast, Pol V exhibits high fidelity transcription, similar to Pol II, suggesting a need for Pol V transcripts to faithfully reflect the DNA sequence of target loci to which siRNA-Argonaute silencing complexes are recruited. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

A major role of DNA polymerase δ in replication of both the leading and lagging DNA strands

PubMed Central

Prakash, Louise; Prakash, Satya

2015-01-01

SUMMARY Genetic studies with S. cerevisiae Polδ (pol3-L612M) and Polε (pol2-M644G) mutant alleles, each of which display a higher rate for the generation of a specific mismatch, have led to the conclusion that Polε is the primary leading strand replicase and that Polδ is restricted to replicating the lagging strand template. Contrary to this widely accepted view, here we show that Polδ plays a major role in the replication of both DNA strands, and that the paucity of pol3-L612M generated errors on the leading strand results from their more proficient removal. Thus, the apparent lack of Polδ contribution to leading strand replication is due to differential mismatch removal rather than differential mismatch generation. Altogether, our genetic studies with Pol3 and Pol2 mutator alleles support the conclusion that Polδ, and not Polε, is the major DNA polymerase for carrying out both leading and lagging DNA synthesis. PMID:26145172

Evaluation der zentralen TUM-Lernplattform

NASA Astrophysics Data System (ADS)

Schulze, Elvira; Baume, Matthias; Graf, Stephan; Gergintchev, Ivan

Die Notwendigkeit der Qualitätssicherung und -kontrolle für innovative universitäre Lehr-/Lernszenarien ist in der Praxis unbestritten. Die Wirksamkeit der Einführung der zentralen Lernplattform CLIX Campus der imc AG an der TUM wurde mittels quantitativer und qualitativer Evaluation überprüft. Als statistische Bewertungsgrundlage wurde der Erreichungsgrad bestimmter Projektziele herangezogen. Aufbauend auf den theoretischen Grundlagen der Evaluation von Bildungsangeboten gibt diese Studie Aufschluss über die Ergebnisse der Datenerhebungen sowie die Einschätzung der Plattform aus Nutzersicht und belegt die wesentliche Bedeutung der durchgängigen IT-Infrastruktur und speziell der einheitlichen Verfügbarkeit der eLearning Angebote.

A transition-based joint model for disease named entity recognition and normalization.

PubMed

Lou, Yinxia; Zhang, Yue; Qian, Tao; Li, Fei; Xiong, Shufeng; Ji, Donghong

2017-08-01

Disease named entities play a central role in many areas of biomedical research, and automatic recognition and normalization of such entities have received increasing attention in biomedical research communities. Existing methods typically used pipeline models with two independent phases: (i) a disease named entity recognition (DER) system is used to find the boundaries of mentions in text and (ii) a disease named entity normalization (DEN) system is used to connect the mentions recognized to concepts in a controlled vocabulary. The main problems of such models are: (i) there is error propagation from DER to DEN and (ii) DEN is useful for DER, but pipeline models cannot utilize this. We propose a transition-based model to jointly perform disease named entity recognition and normalization, casting the output construction process into an incremental state transition process, learning sequences of transition actions globally, which correspond to joint structural outputs. Beam search and online structured learning are used, with learning being designed to guide search. Compared with the only existing method for joint DEN and DER, our method allows non-local features to be used, which significantly improves the accuracies. We evaluate our model on two corpora: the BioCreative V Chemical Disease Relation (CDR) corpus and the NCBI disease corpus. Experiments show that our joint framework achieves significantly higher performances compared to competitive pipeline baselines. Our method compares favourably to other state-of-the-art approaches. Data and code are available at https://github.com/louyinxia/jointRN. dhji@whu.edu.cn. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Characterization of Mycobacterium smegmatis PolD2 and PolD1 as RNA/DNA polymerases homologous to the POL domain of bacterial DNA ligase D

PubMed Central

Zhu, Hui; Bhattarai, Hitesh; Yan, Han-Guang; Shuman, Stewart; Glickman, Michael S.

2013-01-01

Mycobacteria exploit nonhomologous end-joining (NHEJ) to repair DNA double-strand breaks. The core NHEJ machinery comprises the homodimeric DNA end-binding protein Ku and DNA ligase D (LigD), a modular enzyme composed of a C-terminal ATP-dependent ligase domain (LIG), a central 3’-phosphoesterase domain (PE), and an N-terminal polymerase domain (POL). LigD POL is proficient at adding templated and nontemplated deoxynucleotide and ribonucleotides to DNA ends in vitro and is the catalyst in vivo of unfaithful NHEJ events involving nontemplated single-nucleotide additions to blunt DSB ends. Here, we identify two mycobacterial proteins, PolD1 and PolD2, as stand-alone homologs of the LigD POL domain. Biochemical characterization of PolD1 and PolD2 shows that they resemble LigD POL in their monomeric quaternary structures, their ability to add templated and nontemplated nucleotides to primer-templates and blunt ends, and their preference for rNTPs versus dNTPs. Deletion of polD1, polD2, or both, in an M. smegmatis strain carrying an inactivating mutation in LigD POL failed to reveal a role for PolD1 or PolD2 in templated nucleotide additions during NHEJ of 5’-overhang DSBs or in clastogen resistance. Whereas our results document the existence and characteristics of new stand-alone members of the LigD POL family of RNA/DNA polymerases, they imply that other polymerases can perform fill-in synthesis during mycobacterial NHEJ. PMID:23198659

Spectral asymmetry of atoms in the van der Waals potential of an optical nanofiber

NASA Astrophysics Data System (ADS)

Patterson, B. D.; Solano, P.; Julienne, P. S.; Orozco, L. A.; Rolston, S. L.

2018-03-01

We measure the modification of the transmission spectra of cold 87Rb atoms in the proximity of an optical nanofiber (ONF). Van der Waals interactions between the atoms an the ONF surface decrease the resonance frequency of atoms closer to the surface. An asymmetric spectra of the atoms holds information of their spatial distribution around the ONF. We use a far-detuned laser beam coupled to the ONF to thermally excite atoms at the ONF surface. We study the change of transmission spectrum of these atoms as a function of heating laser power. A semiclassical phenomenological model for the thermal excitation of atoms in the atom-surface van der Waals bound states is in good agreement with the measurements. This result suggests that van der Waals potentials could be used to trap and probe atoms at few nanometers from a dielectric surface, a key tool for hybrid photonic-atomic quantum systems.

Defect of Fe-S cluster binding by DNA polymerase δ in yeast suppresses UV-induced mutagenesis, but enhances DNA polymerase ζ - dependent spontaneous mutagenesis.

PubMed

Stepchenkova, E I; Tarakhovskaya, E R; Siebler, H M; Pavlov, Y I

2017-01-01

Eukaryotic genomes are duplicated by a complex machinery, utilizing high fidelity replicative B-family DNA polymerases (pols) α, δ and ε. Specialized error-prone pol ζ, the fourth B-family member, is recruited when DNA synthesis by the accurate trio is impeded by replication stress or DNA damage. The damage tolerance mechanism dependent on pol ζ prevents DNA/genome instability and cell death at the expense of increased mutation rates. The pol switches occurring during this specialized replication are not fully understood. The loss of pol ζ results in the absence of induced mutagenesis and suppression of spontaneous mutagenesis. Disruption of the Fe-S cluster motif that abolish the interaction of the C-terminal domain (CTD) of the catalytic subunit of pol ζ with its accessory subunits, which are shared with pol δ, leads to a similar defect in induced mutagenesis. Intriguingly, the pol3-13 mutation that affects the Fe-S cluster in the CTD of the catalytic subunit of pol δ also leads to defective induced mutagenesis, suggesting the possibility that Fe-S clusters are essential for the pol switches during replication of damaged DNA. We confirmed that yeast strains with the pol3-13 mutation are UV-sensitive and defective in UV-induced mutagenesis. However, they have increased spontaneous mutation rates. We found that this increase is dependent on functional pol ζ. In the pol3-13 mutant strain with defective pol δ, there is a sharp increase in transversions and complex mutations, which require functional pol ζ, and an increase in the occurrence of large deletions, whose size is controlled by pol ζ. Therefore, the pol3-13 mutation abrogates pol ζ-dependent induced mutagenesis, but allows for pol ζ recruitment for the generation of spontaneous mutations and prevention of larger deletions. These results reveal differential control of the two major types of pol ζ-dependent mutagenesis by the Fe-S cluster present in replicative pol δ. Copyright © 2016 Elsevier B.V. All rights reserved.

Variabilität des Reviergesangs des Buchfinken (Fringilla coelebs) zur Raum-Zeit-Beschreibung von Metapopulationen

NASA Astrophysics Data System (ADS)

Nolte, Björn

2003-10-01

Der Buchfinkengesang wurde in Potsdam in zwei Hauptpopulationen über drei Jahre aufgenommen. Jedes Individuum wurde eindeutig am individuellen Strophentypenrepertoire identifiziert. Ein weiterer Punkt der die individuelle Wiedererkennung bestätigt ist die hohe Standorttreue der adulten Männchen. Die beschriebene Methode eignet sich für die Untersuchung von gesamten Populationen, um den Wandel des Gesangs von Populationen in Raum und Zeit zu beschreiben. Die Haupterkenntnisse der Arbeit sind: - Die Gesamtanzahl der Grundstrophentypen innerhalb einer Population bleibt über Jahre konstant. - Die relative Häufigkeit jedes einzelnen Strophentyps variiert von Jahr zu Jahr und von Population zu Population. - Gesangslernen erfolgt exakt mit einem Korrektheitsgrad von mindestens 96%. - Das Song-Sharing ist innerhalb der Population hoch. Die diskutierten Mechanismen für das Song-Sharing sind: Die Lebenserwartung, das Zugverhalten, das Lernverhalten, die Etabliertheit von Strophentypen, Weibchenpräferenzen und die Reaktionen der territorialen Männchen. - Weiterhin wurde ein Modell zur kulturellen Evolution des Buchfinkengesangs programmiert, um die Rolle der Einflussfaktoren, wie Fehlerquote, Abwanderungsrate und Laufzeit zu ermitteln. Der Wandel des Dialektes erfolgt graduell in Raum und Zeit. Daher sind keine scharfen Dialektgrenzen anzutreffen. Trotz dieser Tatsache markieren die etablierten Strophentypen die Population. 50 % der Juvenilen siedeln am Geburtsort, auf diese Weise bleibt der Dialekt erhalten und Inzest wird vermieden. -Analysiert man das Repertoire benachbarten Männchen bei isolierten Alleen, so entspricht die Gesangsangleichung in etwa dem Zufall. -Intraindividuelle Vergleiche der quantitativen Parameter des jeweiligen Strophentyps wurden saisonal und annuell durchgeführt. Saisonal konnten für einen Strophentyp ein Trend ermittelt werden. Bei jährlichen Vergleichen konnten intraindividuell ausschließlich nicht signifikante Ergebnisse ermittelt werden, wohingegen die interindividuelle Variation in zwei Fällen signifikant war. In einem Fall bestand ein Trend und in einem weiteren Fall war die Variationsunterschiede nicht signifikant. - Der Verlauf der Brutsaison lässt sich an der jährlichen Gesangsaktivität nachvollziehen. Chaffinch song was recorded in Potsdam in two major populations of chaffinches over a period of three years. Each male was identified unambiguously because of their individual song type repertoires. These are usually easy to distinguish from sonagrams as the variation is discontinuous. A further point for individual recognition is the fixed territorial behaviour of adult males. The described method is employed to examine whole populations and to observe changes with space and time in the song of a population. The major findings of the study are: - The total amount of basic song types in each population is constant over years. - The quantity of each basic song type is different and varies from year to year and from population to population. - Song copying is extremely accurate on at least 96% of occasions. - Song-type sharing is high within populations. Discussed mechanisms for song neighbourhoods are: expectation of life, semi-migratory behaviour, learning skills, establishment of song types, female choice and male vs male interaction. Furthermore a model of cultural evolution of chaffinch song was programmed to determine the role of factors like error rate, rate of emigration and running time. The changes are gradual in space and time. Hence the dialect borders are smooth. Despite this fact established song types mark the population. As every second juvenile bird settles in the population of his birth inbreeding is avoided and the dialect structure is retained. - Analysing the repertoires of neighbouring males (“next door neighbours”) in isolated avenues to examine mutual influences suggests that these have the same amount of song types in common than would be expected by chance. - Within intraindividual comparisons the quantitative parameters of the same song types remain seasonal and annual constant, whereas interindividual variations within the same song tip are statistically significant. - The breeding biology of the chaffinch can be observed by seasonal singing activity during the breeding cycle.

The Prediction of Jet Noise Ground Effects Using an Acoustic Analogy and a Tailored Green's Function

NASA Technical Reports Server (NTRS)

Miller, Steven A. E.

2013-01-01

An assessment of an acoustic analogy for the mixing noise component of jet noise in the presence of an infinite surface is presented. The reflection of jet noise by the ground changes the distribution of acoustic energy and is characterized by constructive and destructive interference patterns. The equivalent sources are modeled based on the two-point cross- correlation of the turbulent velocity fluctuations and a steady Reynolds-Averaged Navier-Stokes (RANS) solution. Propagation effects, due to reflection by the surface and refaction by the jet shear layer, are taken into account by calculating the vector Green's function of the linearized Euler equations (LEE). The vector Green's function of the LEE is written in relation to Lilley's equation; that is, approximated with matched asymptotic solutions and the Green's function of the convective Helmholtz equation. The Green's function of the convective Helmholtz equation for an infinite flat plane with impedance is the Weyl-van der Pol equation. Predictions are compared with an unheated Mach 0.95 jet produced by a nozzle with an exit diameter of 0.3302 meters. Microphones are placed at various heights and distances from the nozzle exit in the peak jet noise direction above an acoustically hard and an asphalt surface. The predictions are shown to accurately capture jet noise ground effects that are characterized by constructive and destructive interference patterns in the mid- and far-field and capture overall trends in the near-field.

Measuring the thermal boundary resistance of van der Waals contacts using an individual carbon nanotube.

PubMed

Hirotani, Jun; Ikuta, Tatsuya; Nishiyama, Takashi; Takahashi, Koji

2013-01-16

Interfacial thermal transport via van der Waals interaction is quantitatively evaluated using an individual multi-walled carbon nanotube bonded on a platinum hot-film sensor. The thermal boundary resistance per unit contact area was obtained at the interface between the closed end or sidewall of the nanotube and platinum, gold, or a silicon dioxide surface. When taking into consideration the surface roughness, the thermal boundary resistance at the sidewall is found to coincide with that at the closed end. A new finding is that the thermal boundary resistance between a carbon nanotube and a solid surface is independent of the materials within the experimental errors, which is inconsistent with a traditional phonon mismatch model, which shows a clear material dependence of the thermal boundary resistance. Our data indicate the inapplicability of existing phonon models when weak van der Waals forces are dominant at the interfaces.

DNA replication error-induced extinction of diploid yeast.

PubMed

Herr, Alan J; Kennedy, Scott R; Knowels, Gary M; Schultz, Eric M; Preston, Bradley D

2014-03-01

Genetic defects in DNA polymerase accuracy, proofreading, or mismatch repair (MMR) induce mutator phenotypes that accelerate adaptation of microbes and tumor cells. Certain combinations of mutator alleles synergistically increase mutation rates to levels that drive extinction of haploid cells. The maximum tolerated mutation rate of diploid cells is unknown. Here, we define the threshold for replication error-induced extinction (EEX) of diploid Saccharomyces cerevisiae. Double-mutant pol3 alleles that carry mutations for defective DNA polymerase-δ proofreading (pol3-01) and accuracy (pol3-L612M or pol3-L612G) induce strong mutator phenotypes in heterozygous diploids (POL3/pol3-01,L612M or POL3/pol3-01,L612G). Both pol3-01,L612M and pol3-01,L612G alleles are lethal in the homozygous state; cells with pol3-01,L612M divide up to 10 times before arresting at random stages in the cell cycle. Antimutator eex mutations in the pol3 alleles suppress this lethality (pol3-01,L612M,eex or pol3-01,L612G,eex). MMR defects synergize with pol3-01,L612M,eex and pol3-01,L612G,eex alleles, increasing mutation rates and impairing growth. Conversely, inactivation of the Dun1 S-phase checkpoint kinase suppresses strong pol3-01,L612M,eex and pol3-01,L612G,eex mutator phenotypes as well as the lethal pol3-01,L612M phenotype. Our results reveal that the lethal error threshold in diploids is 10 times higher than in haploids and likely determined by homozygous inactivation of essential genes. Pronounced loss of fitness occurs at mutation rates well below the lethal threshold, suggesting that mutator-driven cancers may be susceptible to drugs that exacerbate replication errors.

An Open Source Extensible Smart Energy Framework

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

Rankin, Linda

Aggregated distributed energy resources are the subject of much interest in the energy industry and are expected to play an important role in meeting our future energy needs by changing how we use, distribute and generate electricity. This energy future includes an increased amount of energy from renewable resources, load management techniques to improve resiliency and reliability, and distributed energy storage and generation capabilities that can be managed to meet the needs of the grid as well as individual customers. These energy assets are commonly referred to as Distributed Energy Resources (DER). DERs rely on a means to communicate informationmore » between an energy provider and multitudes of devices. Today DER control systems are typically vendor-specific, using custom hardware and software solutions. As a result, customers are locked into communication transport protocols, applications, tools, and data formats. Today’s systems are often difficult to extend to meet new application requirements, resulting in stranded assets when business requirements or energy management models evolve. By partnering with industry advisors and researchers, an implementation DER research platform was developed called the Smart Energy Framework (SEF). The hypothesis of this research was that an open source Internet of Things (IoT) framework could play a role in creating a commodity-based eco-system for DER assets that would reduce costs and provide interoperable products. SEF is based on the AllJoynTM IoT open source framework. The demonstration system incorporated DER assets, specifically batteries and smart water heaters. To verify the behavior of the distributed system, models of water heaters and batteries were also developed. An IoT interface for communicating between the assets and a control server was defined. This interface supports a series of “events” and telemetry reporting, similar to those defined by current smart grid communication standards. The results of this effort demonstrated the feasibility and application potential of using IoT frameworks for the creation of commodity-based DER systems. All of the identified commodity-based system requirements were met by the AllJoyn framework. By having commodity solutions, small vendors can enter the market and the cost of implementation for all parties is reduced. Utilities and aggregators can choose from multiple interoperable products reducing the risk of stranded assets. Based on this research it is recommended that interfaces based on existing smart grid communication protocol standards be created for these emerging IoT frameworks. These interfaces should be standardized as part of the IoT framework allowing for interoperability testing and certification. Similarly, IoT frameworks are introducing application level security. This type of security is needed for protecting application and platforms and will be important moving forward. Recommendations are that along with DER-based data model interfaces, platform and application security requirements also be prescribed when IoT devices support DER applications.« less

Improvement of Forest Height Retrieval By Integration of Dual-Baseline PolInSAR Data And External DEM Data

NASA Astrophysics Data System (ADS)

Xie, Q.; Wang, C.; Zhu, J.; Fu, H.; Wang, C.

2015-06-01

In recent years, a lot of studies have shown that polarimetric synthetic aperture radar interferometry (PolInSAR) is a powerful technique for forest height mapping and monitoring. However, few researches address the problem of terrain slope effect, which will be one of the major limitations for forest height inversion in mountain forest area. In this paper, we present a novel forest height retrieval algorithm by integration of dual-baseline PolInSAR data and external DEM data. For the first time, we successfully expand the S-RVoG (Sloped-Random Volume over Ground) model for forest parameters inversion into the case of dual-baseline PolInSAR configuration. In this case, the proposed method not only corrects terrain slope variation effect efficiently, but also involves more observations to improve the accuracy of parameters inversion. In order to demonstrate the performance of the inversion algorithm, a set of quad-pol images acquired at the P-band in interferometric repeat-pass mode by the German Aerospace Center (DLR) with the Experimental SAR (E-SAR) system, in the frame of the BioSAR2008 campaign, has been used for the retrieval of forest height over Krycklan boreal forest in northern Sweden. At the same time, a high accuracy external DEM in the experimental area has been collected for computing terrain slope information, which subsequently is used as an inputting parameter in the S-RVoG model. Finally, in-situ ground truth heights in stand-level have been collected to validate the inversion result. The preliminary results show that the proposed inversion algorithm promises to provide much more accurate estimation of forest height than traditional dualbaseline inversion algorithms.

[Experimental study on the Der f 1 mRNA molecules derived from dermatophagoides farinae for specific immunotherapy on murine model of asthma].

PubMed

Jiang, Yu-xin; Yin, Kang; Jin, Wen-jie; Wu, Lu-yi; Li, Chao-pin

2014-08-01

To investigate the effect of Der f 1 mRNA molecules for specific immunotherapy on murine model of asthma. Fifty BALB/c mice were randomly divided into 5 groups: PBS group, Der f 1 sensitization group, Der f 1 specific immunotherapy (SIT) group, beta-actin mRNA SIT group, and Derf 1 mRNA SIT group. On days 0, 7 and 14, mice in PBS group received PBS injection; mice in the other groups were intraperitoneally injected with 10 microg Derf 1. At day 21, the mice in the 4 experimental groups were challenged with a 30-min inhaled dose of Der f 1 (100 microg/ml) for 7 successive days. Two weeks after the final sensitization, the mice in the above five groups were im- munized by intradermal injection with PBS, 1 microg Der f 1, 10 microg Der f 1, 2 microg beta-actin mRNA, and 2 microg Der f 1 mRNA, respectively for 3 times at one-week intervals. Two weeks after the last intradermal injection, all mice were sacrificed and bronchoalveolar lavage fluid (BALF) was collected. ELISA was performed to detect the levels of IFN-gamma and IL-13 in BALF, the number of eosinophils in the BALF was recorded. Splenocytes were prepared, and cultured with Der f 1 al- lergen (10 Jg/ml) for 72 h. Splenocytes of PBS group was cultured without Derf 1 allergen. The levels of IFN-gamma and IL-13 in splenocyte culture supernatant were measured by ELISA, as well as serum antibody levels of total IgE, allergen- specific IgE (sIgE), sIgG1, and sIgG2a. Lung sections were stained in hematoxylin and eosin, and observed under the microsope. Except for PBS group, mice in the other 4 group showed symptoms of acute asthma attack. Com- pared with Derf 1 sensitization group [(897.56 +/- 105.73) pg/ml] and beta-actin mRNA SIT group [(219.47 +/- 64.72) pg/ml], the level of IFN-gamma in BALF from Der f 1 mRNA SIT group [(897.56 +/- 105.73) pg/ml] and Derfl SIT group [(864.48 +/- 70.62)pg/ml] significantly increased (P<0.01). However, the level of IL-13 in BALF from Derf 1 mRNA SIT group [(241.64 +/- 31.41) pg/ml] and Derf 1 SIT group [(321.94 +/- 41.07)pg/ml] was significantly lower than that of Der f 1 sensitization group [(520.62 +/- 43.77) pg/ml] and beta-actin mRNA SIT group [(507.22 +/- 42.26) pg/ml](P<0.01). The number of eosinophils in Der f 1 mRNA SIT group [(1.33 +/- 0.44) x 10(5)/ml] and Der f 1 SIT group [(1.48 +/- 0.39) x 10(5)/ml] was also lower than that of Der f 1 sensitization group [(3.54 +/- 0.52)x10(5)/ml] and beta-actin mRNA SIT group [(2.98-0.53) x 10(5)/ml] (P<0.01). The levels of IFN-GAMMA and IL-13 in splenocyte culture supernatant showed that IFN-gamma level in Der f 1 mRNA SIT group [(420.91+69.92) pg/ml] and Der f 1 SIT group [(334.92 +/- 43.72) pg/ml] was significantly higher than that of Der f 1 sensitization group[(123.75 +/- 5.48) pg/ml] and beta-actin mRNA SIT group[(128.84 +/- 59.00) pg/ml] (P<0.01). However, IL-13 level of Der f 1 mRNA SIT group [(268.51 +/- 40.42) pg/ml] and Der f 1 SIT group [(285.26 +/- 62.21) pg/ml] was significantly lower than that of Derf 1 sensitization group [(613.89 +/- 51.54) pg/ml] and beta-actin mRNA SIT group [(524.05 +/- 39.12) pg/ml] (P<0.01). Compared with Der f 1 sensitization group [total IgE: (94.34 +/- 11.66) ng/ml, sIgE: (65.67 +/- 9.47) ng/ml, sIgG1: (75.18 +/- 9.52) ng/ml, sIgG2a: (2.81 +/- 1.17) ng/ml] and beta-actin mRNA SIT group[total IgE: (86.48 +/- 10.26) ng/ml, sIgE: (62.36 +/- 8.35) ng/ml, sIgG1: (69.51 +/- 8.98) ng/ml, IgG2a: (1.06 +/- 0.11) ng/ml], the serum antibody levels of total IgE [(33.72 +/- 9.78) ng/ml], sIgE [(22.76 +/- 8.09) ng/ml], sIgG1 [(17.87 +/- 7.59) ng/ml] of Der f 1 mRNA SIT group decreased significantly (P<0.01), whereas the level of IgG% [(7.74 +/- 0.88) ng/ml] increased (P<0.01). Compared with Der f 1 sensitization group, the asthmatic symptoms were relieved after immunization with Der f 1 mRNA for specific immunotherapy, including intact structure of respiratory and alveolar epithelial cells, decreased inflammatory cell infiltration, and similar to those in Der f 1 SIT group. However, the breakage and detachment of bronchial epithelial cells occurred in beta-actin mRNA SIT group. Derf 1 mRNA vaccine can correct Th1 and Th2 imbalance.

Methoden der digitalen Planung

NASA Astrophysics Data System (ADS)

Westkämper, Engelbert; Niemann, Jörg; Warschat, Joachim; Scheer, August-Wilhelm; Thomas, Oliver

Die industrielle Produktion ist das Herz der verarbeitenden Industrie in Deutschland. Mit einem Beitrag von rund 500 Mrd. EUR pro Jahr erwirtschaftet das verarbeitende Gewerbe etwa ein Viertel der gesamtwirtschaftlichen Wertschöpfung in Deutschland. Gemessen am Produktionswert der Gesamtwirtschaft betrug der industrielle Anteil sogar über ein Drittel. Der Erhalt und der Ausbau der Wettbewerbsfähigkeit unter den gegebenen Rahmenbedingungen der globalen Märkte ist eine der größten Herausforderungen der deutschen Wirtschaft [5, 8]. In diesem Beitrag soll - ausgehend von einer Strategie der Ausrüster von Fabriken in einer globalen Produktion - diskutiert werden, wie mit der digitalen Fabrik Potentiale in den Planungs- und Wandlungsprozessen erschlossen werden können.

Wind Field Extractions from SAR Sentinel-1 Images Using Electromagnetic Models

NASA Astrophysics Data System (ADS)

La, Tran Vu; Khenchaf, Ali; Comblet, Fabrice; Nahum, Carole

2016-08-01

Among available wind sources, i.e. measured data, numeric weather models, the retrieval of wind vectors from Synthetic Aperture Radar (SAR) data / images is particularly preferred due to a lot of SAR systems (available data in most meteorological conditions, revisit mode, high resolution, etc.). For this purpose, the retrieval of wind vectors is principally based on the empirical (EP) models, e.g. CMOD series in C-band. Little studies have been reported about the use of the electromagnetic (EM) models for wind vector retrieval, since it is quite complicated to invert. However, the EM models can be applied for most cases of polarization, frequency and wind regime. In order to evaluate the advantages and limits of the EM models for wind vector retrieval, we compare in this study estimated results by the EM and EP models for both cases of polarization (vertical-vertical, or VV-pol and horizontal- horizontal, or HH-pol).

[Management of Pregnancy-Associated Venous Thromboembolism - Current Recommendations].

PubMed

Linnemann, Birgit

2017-06-01

Diagnostik in der Schwangerschaft  Studien belegen den hohen Stellenwert der Kompressionssonografie der Beinvenen plus Duplexsonografie der Beckenvenen in der Diagnostik der Becken- und Beinvenenthrombose auch bei Schwangeren. Perfusionsszintigrafie und CT-Angiografie der Pulmonalarterien sind bei vergleichbarer fötaler Strahlenbelastung gleich aussagekräftig. Aufgrund der mütterlichen Strahlenbelastung favorisieren aktuelle Leitlinien bei fehlender struktureller Lungenerkrankung die Perfusionsszintigrafie als primäre Bildgebung. Es gibt keinen Grund, einer Schwangeren mit Lungenembolieverdacht eine notwendige radiologische Diagnosesicherung vorzuenthalten. Antikoagulation in der Schwangerschaft  Heparine bleiben Antikoagulans der 1. Wahl bei der Behandlung der venöses Thromboembolien (VTE) in der Schwangerschaft. Neue orale Antikoagulantien (NOAK) sind aufgrund ihrer geringen Molekülgröße plazentagängig und daher in der Schwangerschaft kontraindiziert. Peripartales Vorgehen  Zur Minimierung des postpartalen Blutungsrisikos vor der Geburt ist in den letzten Wochen vor der Geburt eine Aufteilung der NMH-Injektion auf 2 Tagesdosen sinnvoll. Bei der Entbindung ist eine interdisziplinäre Abstimmung wichtig. Postpartal kann eine NMH-Therapie fortgesetzt oder Warfarin eingesetzt werden (Kein Phenprocoumon, da es in die Muttermilch übergeht).

Getting the Right Answers for the Right Reasons: Toward Predictive Molecular Simulations of Water with Many-Body Potential Energy Functions.

PubMed

Paesani, Francesco

2016-09-20

The central role played by water in fundamental processes relevant to different disciplines, including chemistry, physics, biology, materials science, geology, and climate research, cannot be overemphasized. It is thus not surprising that, since the pioneering work by Stillinger and Rahman, many theoretical and computational studies have attempted to develop a microscopic description of the unique properties of water under different thermodynamic conditions. Consequently, numerous molecular models based on either molecular mechanics or ab initio approaches have been proposed over the years. However, despite continued progress, the correct prediction of the properties of water from small gas-phase clusters to the liquid phase and ice through a single molecular model remains challenging. To large extent, this is due to the difficulties encountered in the accurate modeling of the underlying hydrogen-bond network in which both number and strength of the hydrogen bonds vary continuously as a result of a subtle interplay between energetic, entropic, and nuclear quantum effects. In the past decade, the development of efficient algorithms for correlated electronic structure calculations of small molecular complexes, accompanied by tremendous progress in the analytical representation of multidimensional potential energy surfaces, opened the doors to the design of highly accurate potential energy functions built upon rigorous representations of the many-body expansion (MBE) of the interaction energies. This Account provides a critical overview of the performance of the MB-pol many-body potential energy function through a systematic analysis of energetic, structural, thermodynamic, and dynamical properties as well as of vibrational spectra of water from the gas to the condensed phase. It is shown that MB-pol achieves unprecedented accuracy across all phases of water through a quantitative description of each individual term of the MBE, with a physically correct representation of both short- and long-range many-body contributions. Comparisons with experimental data probing different regions of the water potential energy surface from clusters to bulk demonstrate that MB-pol represents a major step toward the long-sought-after "universal model" capable of accurately describing the molecular properties of water under different conditions and in different environments. Along this path, future challenges include the extension of the many-body scheme adopted by MB-pol to the description of generic solutes as well as the integration of MB-pol in an efficient theoretical and computational framework to model acid-base reactions in aqueous environments. In this context, given the nontraditional form of the MB-pol energy and force expressions, synergistic efforts by theoretical/computational chemists/physicists and computer scientists will be critical for the development of high-performance software for many-body molecular dynamics simulations.

Condom Use Following a Pilot Test of the Popular Opinion Leader Intervention in the Barbados Defence Force

DTIC Science & Technology

2013-01-01

and if it exhibited effects on condom use in the BDF population. The POL intervention was originally designed to reduce sexual risk behavior in...increase condom use in the BDF. We adapted the POL intervention as an improvement to the peer educator model in the context of the BDF’s ongoing prevention...measuring respondent demographics, detailed questions regarding specific sexual behaviors and condom use, alcohol abuse, and psychoso- cial measurements

Combined VEGF and CXCR4 antagonism targets the GBM stem cell population and synergistically improves survival in an intracranial mouse model of glioblastoma.

PubMed

Barone, Amy; Sengupta, Rajarshi; Warrington, Nicole M; Smith, Erin; Wen, Patrick Y; Brekken, Rolf A; Romagnoli, Barbara; Douglas, Garry; Chevalier, Eric; Bauer, Michael P; Dembowsky, Klaus; Piwnica-Worms, David; Rubin, Joshua B

2014-10-30

Glioblastoma recurrence involves the persistence of a subpopulation of cells with enhanced tumor-initiating capacity (TIC) that reside within the perivascular space, or niche (PVN). Anti-angiogenic therapies may prevent the formation of new PVN but have not prevented recurrence in clinical trials, suggesting they cannot abrogate TIC activity. We hypothesized that combining anti-angiogenic therapy with blockade of PVN function would have superior anti-tumor activity. We tested this hypothesis in an established intracranial xenograft model of GBM using a monoclonal antibody specific for murine and human VEGF (mcr84) and a Protein Epitope Mimetic (PEM) CXCR4 antagonist, POL5551. When doses of POL5551 were increased to overcome an mcr84-induced improvement in vascular barrier function, combinatorial therapy significantly inhibited intracranial tumor growth and improved survival. Anti-tumor activity was associated with significant changes in tumor cell proliferation and apoptosis, and a reduction in the numbers of perivascular cells expressing the TIC marker nestin. A direct effect on TICs was demonstrated for POL5551, but not mcr84, in three primary patient-derived GBM isolates. These findings indicate that targeting the structure and function of the PVN has superior anti-tumor effect and provide a strong rationale for clinical evaluation of POL5551 and Avastin in patients with GBM.

Dependence of the microwave radar cross section on ocean surface variables: Comparison of measurements and theory using data from the Frontal Air-Sea Interaction Experiment

NASA Astrophysics Data System (ADS)

Weissman, David E.

1990-03-01

The purpose of this investigation was to study the ability of theoretical radar cross section (RCS) models to predict the absolute magnitude of the ocean radar cross section under a wide variety of sea and atmospheric conditions. The dependence of the RCS on wind stress (as opposed to wind speed) was also studied. An extensive amount of experimental data was acquired during the Frontal Air-Sea Interaction Experiment (FASINEX). This consisted of RCS data from the NASA-Jet Propulsion Laboratory Ku band scatterometer mounted on a C130 aircraft (10 separate flights), as well as a wide variety of atmospheric measurements (including stress) and sea conditions. Measurements across an ocean front demonstrated that the vertical polarization (V-pol) and horizontal polarization (H-pol) radar cross section were more strongly dependent on wind stress than on wind magnitude. Current theoretical models for the RCS, based on stress, were tested with this data. In situations where the Bragg scattering theory does not agree with the measured radar cross section (magnitude and angle dependence), revisions are hypothesized and evaluated. For example, the V-pol theory worked well in most cases studied, while the H-pol theory was usually too low by about a factor of 2 at incidence angles of 50° and 60°.

Epistatic role of base excision repair and mismatch repair pathways in mediating cisplatin cytotoxicity

PubMed Central

Kothandapani, Anbarasi; Sawant, Akshada; Dangeti, Venkata Srinivas Mohan Nimai; Sobol, Robert W.; Patrick, Steve M.

2013-01-01

Base excision repair (BER) and mismatch repair (MMR) pathways play an important role in modulating cis-Diamminedichloroplatinum (II) (cisplatin) cytotoxicity. In this article, we identified a novel mechanistic role of both BER and MMR pathways in mediating cellular responses to cisplatin treatment. Cells defective in BER or MMR display a cisplatin-resistant phenotype. Targeting both BER and MMR pathways resulted in no additional resistance to cisplatin, suggesting that BER and MMR play epistatic roles in mediating cisplatin cytotoxicity. Using a DNA Polymerase β (Polβ) variant deficient in polymerase activity (D256A), we demonstrate that MMR acts downstream of BER and is dependent on the polymerase activity of Polβ in mediating cisplatin cytotoxicity. MSH2 preferentially binds a cisplatin interstrand cross-link (ICL) DNA substrate containing a mismatch compared with a cisplatin ICL substrate without a mismatch, suggesting a novel mutagenic role of Polβ in activating MMR in response to cisplatin. Collectively, these results provide the first mechanistic model for BER and MMR functioning within the same pathway to mediate cisplatin sensitivity via non-productive ICL processing. In this model, MMR participation in non-productive cisplatin ICL processing is downstream of BER processing and dependent on Polβ misincorporation at cisplatin ICL sites, which results in persistent cisplatin ICLs and sensitivity to cisplatin. PMID:23761438

Translesion synthesis DNA polymerases promote error-free replication through the minor-groove DNA adduct 3-deaza-3-methyladenine.

PubMed

Yoon, Jung-Hoon; Roy Choudhury, Jayati; Park, Jeseong; Prakash, Satya; Prakash, Louise

2017-11-10

N3-Methyladenine (3-MeA) is formed in DNA by reaction with S -adenosylmethionine, the reactive methyl donor, and by reaction with alkylating agents. 3-MeA protrudes into the DNA minor groove and strongly blocks synthesis by replicative DNA polymerases (Pols). However, the mechanisms for replicating through this lesion in human cells remain unidentified. Here we analyzed the roles of translesion synthesis (TLS) Pols in the replication of 3-MeA-damaged DNA in human cells. Because 3-MeA has a short half-life in vitro , we used the stable 3-deaza analog, 3-deaza-3-methyladenine (3-dMeA), which blocks the DNA minor groove similarly to 3-MeA. We found that replication through the 3-dMeA adduct is mediated via three different pathways, dependent upon Polι/Polκ, Polθ, and Polζ. As inferred from biochemical studies, in the Polι/Polκ pathway, Polι inserts a nucleotide (nt) opposite 3-dMeA and Polκ extends synthesis from the inserted nt. In the Polθ pathway, Polθ carries out both the insertion and extension steps of TLS opposite 3-dMeA, and in the Polζ pathway, Polζ extends synthesis following nt insertion by an as yet unidentified Pol. Steady-state kinetic analyses indicated that Polι and Polθ insert the correct nt T opposite 3-dMeA with a much reduced catalytic efficiency and that both Pols exhibit a high propensity for inserting a wrong nt opposite this adduct. However, despite their low fidelity of synthesis opposite 3-dMeA, TLS opposite this lesion replicates DNA in a highly error-free manner in human cells. We discuss the implications of these observations for TLS mechanisms in human cells. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

In vitro transcription activities of Pol IV, Pol V and RDR2 reveal coupling of Pol IV and RDR2 for dsRNA synthesis in plant RNA silencing

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

Haag, Jeremy R.; Ream, Thomas S.; Marasco, Michelle

2012-12-14

In Arabidopsis, RNA-dependent DNA methylation and transcriptional silencing involves three nuclear RNA polymerases that are biochemically undefined: the presumptive DNA-dependent RNA polymerases, Pol IV and Pol V and the putative RNA-dependent RNA polymerase, RDR2. Here, we demonstrate their RNA polymerase activities in vitro. Unlike Pol II, Pols IV and V require an RNA primer, are insensitive to alpha-amanitin and differ in their ability to displace non-template DNA during transcription. Biogenesis of 24 nt small interfering RNAs (siRNAs) requires both Pol IV and RDR2, which physically associate in vivo. Pol IV does not require RDR2 for activity, but RDR2 is nonfunctionalmore » in the absence of associated Pol IV, suggesting that their coupling explains the channeling of Pol IV transcripts into double-stranded RNAs that are then diced into 24 nt siRNAs.« less

Differential action and differential expression of DNA polymerase I during Escherichia coli colony development.

PubMed Central

Shapiro, J A

1992-01-01

A mini-Tn10 insertion in the polA cistron (polA2099) was isolated in a search for mutations that affect patterned Mudlac replication in colonies. The polA2099 mutation had a dramatic effect on cell morphogenesis during the first few hours of microcolony development. Abnormal microcolonies containing filamentous cells were produced as a result of SOS induction. Despite gross abnormalities in early microcolonies, mature polA2099 colonies after 2 to 4 days were morphologically indistinguishable from Pol+ colonies, and 44-h polA2099 colonies displayed a cell size distribution very similar to that of Pol+ colonies. These results suggested the involvement of a protective factor produced during colony growth that compensated for the polA deficiency. The action of a diffusible substance that stimulates growth of polA2099 microcolonies was shown by spotting dilute polA2099 cultures next to established colonies. Differential transcription of polA during colony development was visualized by growing colonies containing polA-lacZ fusions on beta-galactosidase indicator agar. When polA-lacZ colonies were inoculated next to established colonies, a diffusible factor was seen to inhibit polA transcription during the earliest stages of colony development. These results show that a basic housekeeping function, DNA polymerase I, is subject to multicellular control by the changing conditions which the bacteria create as they proliferate on agar. Images PMID:1331025

The Economics of van der Waals Force Engineering

NASA Astrophysics Data System (ADS)

Pinto, Fabrizio

2008-01-01

As micro-electro-mechanical system (MEMS) fabrication continues on an ever-decreasing scale, new technological challenges must be successfully negotiated if Moore's Law is to be an even approximately valid model of the future of device miniaturization. Among the most significant obstacles is the existence of strong surface forces related to quantum mechanical van der Waals interatomic interactions, which rapidly diverge as the distance between any two neutral boundaries decreases. The van der Waals force is a contributing factor in several device failures and limitations, including, for instance, stiction and oscillator non-linearities. In the last decade, however, it has been conclusively shown that van der Waals forces are not just a MEMS limitation but can be engineered in both magnitude and sign so as to enable classes of proprietary inventions which either deliver novel capabilities or improve upon existing ones. The evolution of van der Waals force research from an almost exclusively theoretical field in quantum-electro-dynamics to an enabling nanotechnology discipline represents a useful example of the ongoing paradigm shift from government-centered to private-capital funded R&D in cutting-edge physics leading to potentially profitable products. In this paper, we discuss the reasons van der Waals force engineering may lead to the creation of thriving markets both in the short and medium terms by highlighting technical challenges that can be competitively addressed by this novel approach. We also discuss some notable obstacles to the cultural transformation of the academic research community required for the emergence of a functional van der Waals force engineering industry worldwide.

Materials perspective on Casimir and van der Waals interactions

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

Woods, L. M.; Dalvit, D. A. R.; Tkatchenko, A.

Interactions induced by electromagnetic fluctuations, such as van der Waals and Casimir forces, are of universal nature present at any length scale between any types of systems. In such interactions these are important not only for the fundamental science of materials behavior, but also for the design and improvement of micro- and nanostructured devices. In the past decade, many new materials have become available, which has stimulated the need for understanding their dispersive interactions. The field of van der Waals and Casimir forces has experienced an impetus in terms of developing novel theoretical and computational methods to provide new insightsmore » into related phenomena. The understanding of such forces has far reaching consequences as it bridges concepts in materials, atomic and molecular physics, condensed-matter physics, high-energy physics, chemistry, and biology. Our review summarizes major breakthroughs and emphasizes the common origin of van der Waals and Casimir interactions. Progress related to novel ab initio modeling approaches and their application in various systems, interactions in materials with Dirac-like spectra, force manipulations through nontrivial boundary conditions, and applications of van der Waals forces in organic and biological matter are examined. Finally, the outlook of the review is to give the scientific community a materials perspective of van der Waals and Casimir phenomena and stimulate the development of experimental techniques and applications.« less

Materials perspective on Casimir and van der Waals interactions

DOE PAGES

Woods, L. M.; Dalvit, D. A. R.; Tkatchenko, A.; ...

2016-11-02

Interactions induced by electromagnetic fluctuations, such as van der Waals and Casimir forces, are of universal nature present at any length scale between any types of systems. In such interactions these are important not only for the fundamental science of materials behavior, but also for the design and improvement of micro- and nanostructured devices. In the past decade, many new materials have become available, which has stimulated the need for understanding their dispersive interactions. The field of van der Waals and Casimir forces has experienced an impetus in terms of developing novel theoretical and computational methods to provide new insightsmore » into related phenomena. The understanding of such forces has far reaching consequences as it bridges concepts in materials, atomic and molecular physics, condensed-matter physics, high-energy physics, chemistry, and biology. Our review summarizes major breakthroughs and emphasizes the common origin of van der Waals and Casimir interactions. Progress related to novel ab initio modeling approaches and their application in various systems, interactions in materials with Dirac-like spectra, force manipulations through nontrivial boundary conditions, and applications of van der Waals forces in organic and biological matter are examined. Finally, the outlook of the review is to give the scientific community a materials perspective of van der Waals and Casimir phenomena and stimulate the development of experimental techniques and applications.« less

Genetic Control of Replication through N1-methyladenine in Human Cells*

PubMed Central

Conde, Juan; Yoon, Jung-Hoon; Roy Choudhury, Jayati; Prakash, Louise; Prakash, Satya

2015-01-01

N1-methyl adenine (1-MeA) is formed in DNA by reaction with alkylating agents and naturally occurring methyl halides. The 1-MeA lesion impairs Watson-Crick base pairing and blocks normal DNA replication. Here we identify the translesion synthesis (TLS) DNA polymerases (Pols) required for replicating through 1-MeA in human cells and show that TLS through this lesion is mediated via three different pathways in which Pols ι and θ function in one pathway and Pols η and ζ, respectively, function in the other two pathways. Our biochemical studies indicate that in the Polι/Polθ pathway, Polι would carry out nucleotide insertion opposite 1-MeA from which Polθ would extend synthesis. In the Polη pathway, this Pol alone would function at both the nucleotide insertion and extension steps of TLS, and in the third pathway, Polζ would extend from the nucleotide inserted opposite 1-MeA by an as yet unidentified Pol. Whereas by pushing 1-MeA into the syn conformation and by forming Hoogsteen base pair with the T residue, Polι would carry out TLS opposite 1-MeA, the ability of Polη to replicate through 1-MeA suggests that despite its need for Watson-Crick hydrogen bonding, Polη can stabilize the adduct in its active site. Remarkably, even though Pols η and ι are quite error-prone at inserting nucleotides opposite 1-MeA, TLS opposite this lesion in human cells occurs in a highly error-free fashion. This suggests that the in vivo fidelity of TLS Pols is regulated by factors such as post-translational modifications, protein-protein interactions, and possibly others. PMID:26491020

Analysis of Gas-Particle Flows through Multi-Scale Simulations

NASA Astrophysics Data System (ADS)

Gu, Yile

Multi-scale structures are inherent in gas-solid flows, which render the modeling efforts challenging. On one hand, detailed simulations where the fine structures are resolved and particle properties can be directly specified can account for complex flow behaviors, but they are too computationally expensive to apply for larger systems. On the other hand, coarse-grained simulations demand much less computations but they necessitate constitutive models which are often not readily available for given particle properties. The present study focuses on addressing this issue, as it seeks to provide a general framework through which one can obtain the required constitutive models from detailed simulations. To demonstrate the viability of this general framework in which closures can be proposed for different particle properties, we focus on the van der Waals force of interaction between particles. We start with Computational Fluid Dynamics (CFD) - Discrete Element Method (DEM) simulations where the fine structures are resolved and van der Waals force between particles can be directly specified, and obtain closures for stress and drag that are required for coarse-grained simulations. Specifically, we develop a new cohesion model that appropriately accounts for van der Waals force between particles to be used for CFD-DEM simulations. We then validate this cohesion model and the CFD-DEM approach by showing that it can qualitatively capture experimental results where the addition of small particles to gas fluidization reduces bubble sizes. Based on the DEM and CFD-DEM simulation results, we propose stress models that account for the van der Waals force between particles. Finally, we apply machine learning, specifically neural networks, to obtain a drag model that captures the effects from fine structures and inter-particle cohesion. We show that this novel approach using neural networks, which can be readily applied for other closures other than drag here, can take advantage of the large amount of data generated from simulations, and therefore offer superior modeling performance over traditional approaches.

A new parameterization of an empirical model for wind/ocean scatterometry

NASA Technical Reports Server (NTRS)

Woiceshyn, P. M.; Wurtele, M. G.; Boggs, D. H.; Mcgoldrick, L. F.; Peteherych, S.

1984-01-01

The power law form of the SEASAT A Scatterometer System (SASS) empirical backscatter-to-wind model function does not uniformly meet the instrument performance over the range 4 to 24 /ms. Analysis indicates that the horizontal polarization (H-Pol) and vertical polarization (V-Pol) components of the benchmark SASS1 model function yield self-consistent results only for a small mid-range of speeds at larger incidence angles, and for a somewhat larger range of speeds at smaller incidence angles. Comparison of SASS1 to in situ data over the Gulf of Alaska region further underscores the shortcomings of the power law form. Finally, a physically based empirical SASS model is proposed which corrects some of the deficiencies of power law models like SASS1. The new model allows the mutual determination of sea surface wind stress and wind speed in a consistent manner from SASS backscatter measurements.

The nonlinear effect of resistive inhomogeneities on van der Pauw measurements

NASA Astrophysics Data System (ADS)

Koon, Daniel W.

2005-03-01

The resistive weighting function [D. W. Koon and C. J. Knickerbocker, Rev. Sci. Instrum. 63, 207 (1992)] quantifies the effect of small local inhomogeneities on van der Pauw resistivity measurements, but assumes such effects to be linear. This talk will describe deviations from linearity for a square van der Pauw geometry, modeled using a 5 x 5 grid network of discrete resistors and introducing both positive and negative perturbations to local resistors, covering nearly two orders of magnitude in -δρ/ρ or -δσ/σ. While there is a relatively modest quadratic nonlinearity for inhomogeneities of decreasing conductivity, the nonlinear term for inhomogeneities of decreasing resistivity is approximately cubic and can exceed the linear term.

Quality control mechanisms exclude incorrect polymerases from the eukaryotic replication fork

PubMed Central

Schauer, Grant D.; O’Donnell, Michael E.

2017-01-01

The eukaryotic genome is primarily replicated by two DNA polymerases, Pol ε and Pol δ, that function on the leading and lagging strands, respectively. Previous studies have established recruitment mechanisms whereby Cdc45-Mcm2-7-GINS (CMG) helicase binds Pol ε and tethers it to the leading strand, and PCNA (proliferating cell nuclear antigen) binds tightly to Pol δ and recruits it to the lagging strand. The current report identifies quality control mechanisms that exclude the improper polymerase from a particular strand. We find that the replication factor C (RFC) clamp loader specifically inhibits Pol ε on the lagging strand, and CMG protects Pol ε against RFC inhibition on the leading strand. Previous studies show that Pol δ is slow and distributive with CMG on the leading strand. However, Saccharomyces cerevisiae Pol δ–PCNA is a rapid and processive enzyme, suggesting that CMG may bind and alter Pol δ activity or position it on the lagging strand. Measurements of polymerase binding to CMG demonstrate Pol ε binds CMG with a Kd value of 12 nM, but Pol δ binding CMG is undetectable. Pol δ, like bacterial replicases, undergoes collision release upon completing replication, and we propose Pol δ–PCNA collides with the slower CMG, and in the absence of a stabilizing Pol δ–CMG interaction, the collision release process is triggered, ejecting Pol δ on the leading strand. Hence, by eviction of incorrect polymerases at the fork, the clamp machinery directs quality control on the lagging strand and CMG enforces quality control on the leading strand. PMID:28069954

PCNA mono-ubiquitination and activation of translesion DNA polymerases by DNA polymerase {alpha}.

PubMed

Suzuki, Motoshi; Niimi, Atsuko; Limsirichaikul, Siripan; Tomida, Shuta; Miao Huang, Qin; Izuta, Shunji; Usukura, Jiro; Itoh, Yasutomo; Hishida, Takashi; Akashi, Tomohiro; Nakagawa, Yoshiyuki; Kikuchi, Akihiko; Pavlov, Youri; Murate, Takashi; Takahashi, Takashi

2009-07-01

Translesion DNA synthesis (TLS) involves PCNA mono-ubiquitination and TLS DNA polymerases (pols). Recent evidence has shown that the mono-ubiquitination is induced not only by DNA damage but also by other factors that induce stalling of the DNA replication fork. We studied the effect of spontaneous DNA replication errors on PCNA mono-ubiquitination and TLS induction. In the pol1L868F strain, which expressed an error-prone pol alpha, PCNA was spontaneously mono-ubiquitinated. Pol alpha L868F had a rate-limiting step at the extension from mismatched primer termini. Electron microscopic observation showed the accumulation of a single-stranded region at the DNA replication fork in yeast cells. For pol alpha errors, pol zeta participated in a generation of +1 frameshifts. Furthermore, in the pol1L868F strain, UV-induced mutations were lower than in the wild-type and a pol delta mutant strain (pol3-5DV), and deletion of the RAD30 gene (pol eta) suppressed this defect. These data suggest that nucleotide misincorporation by pol alpha induces exposure of single-stranded DNA, PCNA mono-ubiquitination and activates TLS pols.

Hepatitis B Virus Polymerase Localizes to the Mitochondria, and Its Terminal Protein Domain Contains the Mitochondrial Targeting Signal.

PubMed

Unchwaniwala, Nuruddin; Sherer, Nathan M; Loeb, Daniel D

2016-10-01

To understand subcellular sites of hepatitis B virus (HBV) replication, we visualized core (Cp), polymerase (Pol), and pregenomic RNA (pgRNA) in infected cells. Interestingly, we found that the majority of Pol localized to the mitochondria in cells undergoing viral replication. The mitochondrial localization of Pol was independent of both the cell type and other viral components, indicating that Pol contains an intrinsic mitochondrial targeting signal (MTS). Neither Cp nor pgRNA localized to the mitochondria during active replication, suggesting a role other than DNA synthesis for Pol at the mitochondria. The Pol of duck hepatitis B virus (DHBV) also localized to the mitochondria. This result indicates that localization of Pol to mitochondria is likely a feature of all hepadnaviruses. To map the MTS within HBV Pol, we generated a series of Pol-green fluorescent protein (Pol-GFP) fusions and found that a stretch spanning amino acids (aa) 141 to 160 of Pol was sufficient to target GFP to the mitochondria. Surprisingly, deleting aa 141 to 160 in full-length Pol did not fully ablate Pol's mitochondrial localization, suggesting that additional sequences are involved in mitochondrial targeting. Only by deleting the N-terminal 160 amino acids in full-length Pol was mitochondrial localization ablated. Crucial residues for pgRNA packaging are contained within aa 141 to 160, indicating a multifunctional role of this region of Pol in the viral life cycle. Our studies show an unexpected Pol trafficking behavior that is uncoupled from its role in viral DNA synthesis. Chronic infection by HBV is a serious health concern. Existing therapies for chronically infected individuals are not curative, underscoring the need for a better understanding of the viral life cycle to develop better antiviral therapies. To date, the most thoroughly studied function of Pol is to package the pgRNA and reverse transcribe it to double-stranded DNA within capsids. This study provides evidence for mitochondrial localization of Pol and defines the MTS. Recent findings have implicated a non-reverse transcription role for Pol in evading host innate immune responses. Mitochondria play an important role in controlling cellular metabolism, apoptosis, and innate immunity. Pol may alter one or more of these host mitochondrial functions to gain a replicative advantage and persist in chronically infected individuals. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

The potential for distributed generation in Japanese prototype buildings: A DER-CAM analysis of policy, tariff design, building energy use, and technology development (English Version)

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

Zhou, Nan; Marnay, Chris; Firestone, Ryan

The August 2003 blackout of the northeastern U.S. and CANADA caused great economic losses and inconvenience to New York City and other affected areas. The blackout was a warning to the rest of the world that the ability of conventional power systems to meet growing electricity demand is questionable. Failure of large power systems can lead to serious emergencies. Introduction of on-site generation, renewable energy such as solar and wind power and the effective utilization of exhaust heat is needed, to meet the growing energy demands of the residential and commercial sectors. Additional benefit can be achieved by integrating thesemore » distributed technologies into distributed energy resource (DER) systems. This work demonstrates a method for choosing and designing economically optimal DER systems. An additional purpose of this research is to establish a database of energy tariffs, DER technology cost and performance characteristics, and building energy consumption for Japan. This research builds on prior DER studies at the Ernest Orlando Lawrence Berkeley National Laboratory (LBNL) and with their associates in the Consortium for Electric Reliability Technology Solutions (CERTS) and operation, including the development of the microgrid concept, and the DER selection optimization program, the Distributed Energy Resources Customer Adoption Model (DER-CAM). DER-CAM is a tool designed to find the optimal combination of installed equipment and an idealized operating schedule to minimize a site's energy bills, given performance and cost data on available DER technologies, utility tariffs, and site electrical and thermal loads over a test period, usually an historic year. Since hourly electric and thermal energy data are rarely available, they are typically developed by building simulation for each of six end use loads used to model the building: electric-only loads, space heating, space cooling, refrigeration, water heating, and natural-gas-only loads. DER-CAM provides a global optimization, albeit idealized, that shows how the necessary useful energy loads can be provided for at minimum cost by selection and operation of on-site generation, heat recovery, cooling, and efficiency improvements. This study examines five prototype commercial buildings and uses DER-CAM to select the economically optimal DER system for each. The five building types are office, hospital, hotel, retail, and sports facility. Each building type was considered for both 5,000 and 10,000 square meter floor sizes. The energy consumption of these building types is based on building energy simulation and published literature. Based on the optimization results, energy conservation and the emissions reduction were also evaluated. Furthermore, a comparison study between Japan and the U.S. has been conducted covering the policy, technology and the utility tariffs effects on DER systems installations. This study begins with an examination of existing DER research. Building energy loads were then generated through simulation (DOE-2) and scaled to match available load data in the literature. Energy tariffs in Japan and the U.S. were then compared: electricity prices did not differ significantly, while commercial gas prices in Japan are much higher than in the U.S. For smaller DER systems, the installation costs in Japan are more than twice those in the U.S., but this difference becomes smaller with larger systems. In Japan, DER systems are eligible for a 1/3 rebate of installation costs, while subsidies in the U.S. vary significantly by region and application. For 10,000 m{sup 2} buildings, significant decreases in fuel consumption, carbon emissions, and energy costs were seen in the economically optimal results. This was most noticeable in the sports facility, followed the hospital and hotel. This research demonstrates that office buildings can benefit from CHP, in contrast to popular opinion. For hospitals and sports facilities, the use of waste heat is particularly effective for water and space heating. For the other building types, waste heat is most effectively used for both heating and cooling. The same examination was done for the 5,000 m{sup 2} buildings. Although CHP installation capacity is smaller and the payback periods are longer, economic, fuel efficiency, and environmental benefits are still seen. While these benefits remain even when subsidies are removed, the increased installation costs lead to lower levels of installation capacity and thus benefit.« less

dNTP pool levels modulate mutator phenotypes of error-prone DNA polymerase ε variants.

PubMed

Williams, Lindsey N; Marjavaara, Lisette; Knowels, Gary M; Schultz, Eric M; Fox, Edward J; Chabes, Andrei; Herr, Alan J

2015-05-12

Mutator phenotypes create genetic diversity that fuels tumor evolution. DNA polymerase (Pol) ε mediates leading strand DNA replication. Proofreading defects in this enzyme drive a number of human malignancies. Here, using budding yeast, we show that mutator variants of Pol ε depend on damage uninducible (Dun)1, an S-phase checkpoint kinase that maintains dNTP levels during a normal cell cycle and up-regulates dNTP synthesis upon checkpoint activation. Deletion of DUN1 (dun1Δ) suppresses the mutator phenotype of pol2-4 (encoding Pol ε proofreading deficiency) and is synthetically lethal with pol2-M644G (encoding altered Pol ε base selectivity). Although pol2-4 cells cycle normally, pol2-M644G cells progress slowly through S-phase. The pol2-M644G cells tolerate deletions of mediator of the replication checkpoint (MRC) 1 (mrc1Δ) and radiation sensitive (Rad) 9 (rad9Δ), which encode mediators of checkpoint responses to replication stress and DNA damage, respectively. The pol2-M644G mutator phenotype is partially suppressed by mrc1Δ but not rad9Δ; neither deletion suppresses the pol2-4 mutator phenotype. Thus, checkpoint activation augments the Dun1 effect on replication fidelity but is not required for it. Deletions of genes encoding key Dun1 targets that negatively regulate dNTP synthesis, suppress the dun1Δ pol2-M644G synthetic lethality and restore the mutator phenotype of pol2-4 in dun1Δ cells. DUN1 pol2-M644G cells have constitutively high dNTP levels, consistent with checkpoint activation. In contrast, pol2-4 and POL2 cells have similar dNTP levels, which decline in the absence of Dun1 and rise in the absence of the negative regulators of dNTP synthesis. Thus, dNTP pool levels correlate with Pol ε mutator severity, suggesting that treatments targeting dNTP pools could modulate mutator phenotypes for therapy.

Comparison of the kinetic parameters of the truncated catalytic subunit and holoenzyme of human DNA polymerase ε

PubMed Central

Zahurancik, Walter J.; Baranovskiy, Andrey G.; Tahirov, Tahir H.; Suo, Zucai

2015-01-01

Numerous genetic studies have provided compelling evidence to establish DNA polymerase ε (Polε) as the primary DNA polymerase responsible for leading strand synthesis during eukaryotic nuclear genome replication. Polε is a heterotetramer consisting of a large catalytic subunit that contains the conserved polymerase core domain as well as a 3′ → 5′ exonuclease domain common to many replicative polymerases. In addition, Polε possesses three small subunits that lack a known catalytic activity but associate with components involved in a variety of DNA replication and maintenance processes. Previous enzymatic characterization of the Polε heterotetramer from budding yeast suggested that the small subunits slightly enhance DNA synthesis by Polε in vitro. However, similar studies of the human Polε heterote-tramer (hPolε) have been limited by the difficulty of obtaining hPolε in quantities suitable for thorough investigation of its catalytic activity. Utilization of a baculovirus expression system for overexpression and purification of hPolε from insect host cells has allowed for isolation of greater amounts of active hPolε, thus enabling a more detailed kinetic comparison between hPolε and an active N-terminal fragment of the hPolε catalytic subunit (p261N), which is readily overexpressed in Escherichia coli. Here, we report the first pre-steady-state studies of fully-assembled hPolε. We observe that the small subunits increase DNA binding by hPolε relative to p261N, but do not increase processivity during DNA synthesis on a single-stranded M13 template. Interestingly, the 3′ → 5′ exonuclease activity of hPolε is reduced relative to p261N on matched and mismatched DNA substrates, indicating that the presence of the small subunits may regulate the proofreading activity of hPolε and sway hPolε toward DNA synthesis rather than proofreading. PMID:25684708

Bildbasierte Navigation eines mobilen Roboters mittels omnidirektionaler und schwenkbarer Kamera

NASA Astrophysics Data System (ADS)

Nierobisch, Thomas; Hoffmann, Frank; Krettek, Johannes; Bertram, Torsten

Dieser Beitrag präsentiert einen neuartigen Ansatz zur entkoppelten Regelung der Kamera-Blickrichtung und der Bewegung eines mobilen Roboters im Kontext der bildbasierten Navigation. Eine schwenkbare monokulare Kamera hält unabhängig von der Roboterbewegung die relevanten Merkmale für die Navigation im Sichtfeld. Die Entkopplung der Kamerablickrichtung von der eigentlichen Roboterbewegung wird durch die Projektion der Merkmale auf eine virtuelle Bildebene realisiert. In der virtuellen Bildebene hängt die Ausprägung der visuellen Merkmale für die bildbasierte Regelung nur von der Roboterposition ab und ist unabhängig gegenüber der tatsächlichen Blickrichtung der Kamera. Durch die Schwenkbarkeit der monokularen Kamera wird der Arbeitsbereich, über dem sich ein Referenzbild zur bildbasierten Regelung eignet, gegenüber einer statischen Kamera signifikant vergrößert. Dies ermöglicht die Navigation auch in texturarmen Umgebungen, die wenig verwertbare Textur- und Strukturmerkmale aufweisen.

A Role for MINIYO and QUATRE-QUART2 in the Assembly of RNA Polymerases II, IV, and V in Arabidopsis.

PubMed

Li, Yaoxi; Yuan, Yuxiang; Fang, Xiaofeng; Lu, Xiuli; Lian, Bi; Zhao, Gaozhan; Qi, Yijun

2018-02-01

RNA polymerases IV and V (Pol IV and Pol V) are required for the generation of noncoding RNAs in RNA-directed DNA methylation (RdDM). Their subunit compositions resemble that of Pol II. The mechanism and accessory factors involved in their assembly remain largely unknown. In this study, we identified mutant alleles of MINIYO ( IYO ), QUATRE-QUART2 ( QQT2 ), and NUCLEAR RNA POLYMERASE B11/D11/E11 ( NRPB/D/E11 ) that cause defects in RdDM in Arabidopsis thaliana We found that Pol IV-dependent small interfering RNAs and Pol V-dependent transcripts were greatly reduced in the mutants. NRPE1, the largest subunit of Pol V, failed to associate with other Pol V subunits in the iyo and qqt2 mutants, suggesting the involvement of IYO and QQT2 in Pol V assembly. In addition, we found that IYO and QQT2 were mutually dependent for their association with the NRPE3 subassembly prior to the assembly of Pol V holoenzyme. Finally, we show that IYO and QQT2 are similarly required for the assembly of Pol II and Pol IV. Our findings reveal IYO and QQT2 as cofactors for the assembly of Pol II, Pol IV, and Pol V and provide mechanistic insights into how RNA polymerases are assembled in plants. © 2018 American Society of Plant Biologists. All rights reserved.

Component-Resolved Diagnostic Study of Dermatophagoides Pteronyssinus Major Allergen Molecules in a Southern Chinese Cohort.

PubMed

Zeng, G; Luo, W; Zheng, P; Wei, N; Huang, H; Sun, B; Zhao, X

2015-01-01

Little is known about component-resolved diagnosis (CRD) for Dermatophagoides pteronyssinus (Der p) sensitization in the Chinese population. We aimed to evaluate sensitization to Der p components in southern China. Two-hundred immunotherapy-naïve patients with asthma and/or rhinitis positive to specific IgE (sIgE) against Der p extract, along with 20 Der p-negative nonallergic healthy controls, were tested for sIgE against Der p 1, Der p 2, and Der p 10 using ImmunoCAP 100. Seventy-five were further examined with the ImmunoCAP Immuno Solid-phase Allergen Chip (ISAC). Der p 10-positive patients were also tested for sIgE against crude extracts of cockroach, moth, and shrimp. In total, 183 (91.5%) of the 200 patients were sensitized to Der p 1 and/or Der p 2. The proportion of positive results and the median level of s1gE against Der p 1 were higher in children than in adults. Der p 1 and Der p 2 correlated with Der p in sIgE levels. ImmunoCAP ISAC demonstrated 100% specificity and 84% sensitivity in detecting Der p 1, Der p 2, and Der p 10 compared with ImmunoCAP 100. Sensitization to Der p 10 correlated well with sIgE to shrimp, moths, cockroaches, Pen m 1, Bla g 7, and Ani s 3. The detection of Der p 1 and Der p 2 provided a good reflection of atopy to Der p in a Chinese cohort. Sensitization to Der p 10 may result from cross-reactivity with seafood and cockroaches in coastal southern China. ImmunoCAP ISAC may be a useful tool for CRD, with comparable performance to ImmunoCAP 100.

Beyond Radar Backscatter: Estimating Forest Structure and Biomass with Radar Interferometry and Lidar Remote Sensing

NASA Astrophysics Data System (ADS)

Lavalle, M.; Ahmed, R.

2014-12-01

Mapping forest structure and aboveground biomass globally is a major challenge that the remote sensing community has been facing for decades. Radar backscatter is sensitive to biomass only up to a certain amount (about 150 tons/ha at L-band and 300 tons/ha at P-band), whereas lidar remote sensing is strongly limited by poor spatial coverage. In recent years radar interferometry, including its extension to polarimetric radar interferometry (PolInSAR), has emerged as a new technique to overcome the limitations of radar backscatter. The idea of PolInSAR is to use jointly interferometric and polarimetric radar techniques to separate different scattering mechanisms and retrieve the vertical structure of forests. The advantage is to map ecosystem structure continuously over large areas and independently of cloud coverage. Experiments have shown that forest height - an important proxy for biomass - can be estimated using PolInSAR with accuracy between 15% and 20% at plot level. At AGU we will review the state-of-art of repeat-pass PolInSAR for biomass mapping, including its potential and limitations, and discuss how merging lidar data with PolInSAR data can be beneficial not only for product cross-validation but also for achieving better estimation of ecosystem properties over large areas. In particular, lidar data are expected to aid the inversion of PolInSAR models by providing (1) better identification of ground under the canopy, (2) approximate information of canopy structure in limited areas, and (3) maximum tree height useful for mapping PolInSAR temporal decorrelation. We will show our tree height and biomass maps using PolInSAR L-band JPL/UAVSAR data collected in tropical and temperate forests, and P-band ONERA/TROPISAR data acquired in French Guiana. LVIS lidar data will be used, as well as SRTM data, field measurements and inventory data to support our study. The use of two different radar frequencies and repeat-pass JPL UAVSAR data will offer also the opportunity to compare our results with the new airborne P-band ECOSAR and L-band DBSAR instruments developed at the NASA Goddard Space Flight Center.

A dominant mutation in mediator of paramutation2, one of three second-largest subunits of a plant-specific RNA polymerase, disrupts multiple siRNA silencing processes.

PubMed

Sidorenko, Lyudmila; Dorweiler, Jane E; Cigan, A Mark; Arteaga-Vazquez, Mario; Vyas, Meenal; Kermicle, Jerry; Jurcin, Diane; Brzeski, Jan; Cai, Yu; Chandler, Vicki L

2009-11-01

Paramutation involves homologous sequence communication that leads to meiotically heritable transcriptional silencing. We demonstrate that mop2 (mediator of paramutation2), which alters paramutation at multiple loci, encodes a gene similar to Arabidopsis NRPD2/E2, the second-largest subunit of plant-specific RNA polymerases IV and V. In Arabidopsis, Pol-IV and Pol-V play major roles in RNA-mediated silencing and a single second-largest subunit is shared between Pol-IV and Pol-V. Maize encodes three second-largest subunit genes: all three genes potentially encode full length proteins with highly conserved polymerase domains, and each are expressed in multiple overlapping tissues. The isolation of a recessive paramutation mutation in mop2 from a forward genetic screen suggests limited or no functional redundancy of these three genes. Potential alternative Pol-IV/Pol-V-like complexes could provide maize with a greater diversification of RNA-mediated transcriptional silencing machinery relative to Arabidopsis. Mop2-1 disrupts paramutation at multiple loci when heterozygous, whereas previously silenced alleles are only up-regulated when Mop2-1 is homozygous. The dramatic reduction in b1 tandem repeat siRNAs, but no disruption of silencing in Mop2-1 heterozygotes, suggests the major role for tandem repeat siRNAs is not to maintain silencing. Instead, we hypothesize the tandem repeat siRNAs mediate the establishment of the heritable silent state-a process fully disrupted in Mop2-1 heterozygotes. The dominant Mop2-1 mutation, which has a single nucleotide change in a domain highly conserved among all polymerases (E. coli to eukaryotes), disrupts both siRNA biogenesis (Pol-IV-like) and potentially processes downstream (Pol-V-like). These results suggest either the wild-type protein is a subunit in both complexes or the dominant mutant protein disrupts both complexes. Dominant mutations in the same domain in E. coli RNA polymerase suggest a model for Mop2-1 dominance: complexes containing Mop2-1 subunits are non-functional and compete with wild-type complexes.

Quantitative Analysis of the Mutagenic Potential of 1-Aminopyrene-DNA Adduct Bypass Catalyzed by Y-Family DNA Polymerases

PubMed Central

Sherrer, Shanen M.; Taggart, David J.; Pack, Lindsey R.; Malik, Chanchal K.; Basu, Ashis K.; Suo, Zucai

2012-01-01

N- (deoxyguanosin-8-yl)-1-aminopyrene (dGAP) is the predominant nitro polyaromatic hydrocarbon product generated from the air pollutant 1-nitropyrene reacting with DNA. Previous studies have shown that dGAP induces genetic mutations in bacterial and mammalian cells. One potential source of these mutations is the error-prone bypass of dGAP lesions catalyzed by the low-fidelity Y-family DNA polymerases. To provide a comparative analysis of the mutagenic potential of the translesion DNA synthesis (TLS) of dGAP, we employed short oligonucleotide sequencing assays (SOSAs) with the model Y-family DNA polymerase from Sulfolobus solfataricus, DNA Polymerase IV (Dpo4), and the human Y-family DNA polymerases eta (hPolη), kappa (hPolκ), and iota (hPolι). Relative to undamaged DNA, all four enzymes generated far more mutations (base deletions, insertions, and substitutions) with a DNA template containing a site-specifically placed dGAP. Opposite dGAP and at an immediate downstream template position, the most frequent mutations made by the three human enzymes were base deletions and the most frequent base substitutions were dAs for all enzymes. Based on the SOSA data, Dpo4 was the least error-prone Y-family DNA polymerase among the four enzymes during the TLS of dGAP. Among the three human Y-family enzymes, hPolκ made the fewest mutations at all template positions except opposite the lesion site. hPolκ was significantly less error-prone than hPolι and hPolη during the extension of dGAP bypass products. Interestingly, the most frequent mutations created by hPolι at all template positions were base deletions. Although hRev1, the fourth human Y-family enzyme, could not extend dGAP bypass products in our standing start assays, it preferentially incorporated dCTP opposite the bulky lesion. Collectively, these mutagenic profiles suggest that hPolkk and hRev1 are the most suitable human Y-family DNA polymerases to perform TLS of dGAP in humans. PMID:22917544

Ubiquitin mediates the physical and functional interaction between human DNA polymerases η and ι

PubMed Central

McIntyre, Justyna; Vidal, Antonio E.; McLenigan, Mary P.; Bomar, Martha G.; Curti, Elena; McDonald, John P.; Plosky, Brian S.; Ohashi, Eiji; Woodgate, Roger

2013-01-01

Human DNA polymerases η and ι are best characterized for their ability to facilitate translesion DNA synthesis (TLS). Both polymerases (pols) co-localize in ‘replication factories’ in vivo after cells are exposed to ultraviolet light and this co-localization is mediated through a physical interaction between the two TLS pols. We have mapped the polη-ι interacting region to their respective ubiquitin-binding domains (UBZ in polη and UBM1 and UBM2 in polι), and demonstrate that ubiquitination of either TLS polymerase is a prerequisite for their physical and functional interaction. Importantly, while monoubiquitination of polη precludes its ability to interact with proliferating cell nuclear antigen (PCNA), it enhances its interaction with polι. Furthermore, a polι-ubiquitin chimera interacts avidly with both polη and PCNA. Thus, the ubiquitination status of polη, or polι plays a key regulatory function in controlling the protein partners with which each polymerase interacts, and in doing so, determines the efficiency of targeting the respective polymerase to stalled replication forks where they facilitate TLS. PMID:23248005

Role of damage-specific DNA polymerases in M13 phage mutagenesis induced by a major lipid peroxidation product trans-4-hydroxy-2-nonenal.

PubMed

Janowska, Beata; Kurpios-Piec, Dagmara; Prorok, Paulina; Szparecki, Grzegorz; Komisarski, Marek; Kowalczyk, Paweł; Janion, Celina; Tudek, Barbara

2012-01-03

One of the major lipid peroxidation products trans-4-hydroxy-2-nonenal (HNE), forms cyclic propano- or ethenoadducts bearing six- or seven-carbon atom side chains to G>C≫A>T. To specify the role of SOS DNA polymerases in HNE-induced mutations, we tested survival and mutation spectra in the lacZα gene of M13mp18 phage, whose DNA was treated in vitro with HNE, and which was grown in uvrA(-)Escherichia coli strains, carrying one, two or all three SOS DNA polymerases. When Pol IV was the only DNA SOS polymerase in the bacterial host, survival of HNE-treated M13 DNA was similar to, but mutation frequency was lower than in the strain containing all SOS DNA polymerases. When only Pol II or Pol V were present in host bacteria, phage survival decreased dramatically. Simultaneously, mutation frequency was substantially increased, but exclusively in the strain carrying only Pol V, suggesting that induction of mutations by HNE is mainly dependent on Pol V. To determine the role of Pol II and Pol IV in HNE induced mutagenesis, Pol II or Pol IV were expressed together with Pol V. This resulted in decrease of mutation frequency, suggesting that both enzymes can compete with Pol V, and bypass HNE-DNA adducts in an error-free manner. However, HNE-DNA adducts were easily bypassed by Pol IV and only infrequently by Pol II. Mutation spectrum established for strains expressing only Pol V, showed that in uvrA(-) bacteria the frequency of base substitutions and recombination increased in relation to NER proficient strains, particularly mutations at adenine sites. Among base substitutions A:T→C:G, A:T→G:C, G:C→A:T and G:C→T:A prevailed. The results suggest that Pol V can infrequently bypass HNE-DNA adducts inducing mutations at G, C and A sites, while bypass by Pol IV and Pol II is error-free, but for Pol II infrequent. Copyright © 2011 Elsevier B.V. All rights reserved.

Thin Film Evaporation Model with Retarded Van Der Waals Interaction (Postprint)

DTIC Science & Technology

2013-11-01

Waals interaction. The retarded van der Waals interaction is derived from Hamaker theory, the summation of retarded pair potentials for all molecules...interaction is derived from Hamaker theory, the summation of retarded pair potentials for all molecules for a given geometry. When combined, the governing...interaction force is the negative derivative with respect to distance of the interaction energy. The method due to Hamaker essentially sums all pair

Graded Interface Models for more accurate Determination of van der Waals-London Dispersion Interactions across Grain Boundaries

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

van Benthem, Klaus; Tan, Guolong; French, Roger H

2006-01-01

Attractive van der Waals V London dispersion interactions between two half crystals arise from local physical property gradients within the interface layer separating the crystals. Hamaker coefficients and London dispersion energies were quantitatively determined for 5 and near- 13 grain boundaries in SrTiO3 by analysis of spatially resolved valence electron energy-loss spectroscopy (VEELS) data. From the experimental data, local complex dielectric functions were determined, from which optical properties can be locally analysed. Both local electronic structures and optical properties revealed gradients within the grain boundary cores of both investigated interfaces. The obtained results show that even in the presence ofmore » atomically structured grain boundary cores with widths of less than 1 nm, optical properties have to be represented with gradual changes across the grain boundary structures to quantitatively reproduce accurate van der Waals V London dispersion interactions. London dispersion energies of the order of 10% of the apparent interface energies of SrTiO3 were observed, demonstrating their significance in the grain boundary formation process. The application of different models to represent optical property gradients shows that long-range van der Waals V London dispersion interactions scale significantly with local, i.e atomic length scale property variations.« less

Li intercalation in graphite: A van der Waals density-functional study

NASA Astrophysics Data System (ADS)

Hazrati, E.; de Wijs, G. A.; Brocks, G.

2014-10-01

Modeling layered intercalation compounds from first principles poses a problem, as many of their properties are determined by a subtle balance between van der Waals interactions and chemical or Madelung terms, and a good description of van der Waals interactions is often lacking. Using van der Waals density functionals we study the structures, phonons and energetics of the archetype layered intercalation compound Li-graphite. Intercalation of Li in graphite leads to stable systems with calculated intercalation energies of -0.2 to -0.3 eV/Li atom, (referred to bulk graphite and Li metal). The fully loaded stage 1 and stage 2 compounds LiC6 and Li1 /2C6 are stable, corresponding to two-dimensional √{3 }×√{3 } lattices of Li atoms intercalated between two graphene planes. Stage N >2 structures are unstable compared to dilute stage 2 compounds with the same concentration. At elevated temperatures dilute stage 2 compounds easily become disordered, but the structure of Li3 /16C6 is relatively stable, corresponding to a √{7 }×√{7 } in-plane packing of Li atoms. First-principles calculations, along with a Bethe-Peierls model of finite temperature effects, allow for a microscopic description of the observed voltage profiles.

Das Smart Meter Gateway - Der kritische Erfolgsfaktor für die Digitalisierung der Energiewende

NASA Astrophysics Data System (ADS)

Abs, Paul-Vincent

Der kritische Erfolgsfaktor der Digitalisierung in der Energiewirtschaft liegt im bevorstehenden hohen Investitionsvolumen und der Beherrschung der neuen Technik. Ein Weg zur Kostenminimierung liegt im Zusammenschluss der einzelnen Akteure, um gemeinsame Skalenvorteile zu heben. Auch bieten neue Geschäftsmodelle die Möglichkeit, zusätzliche Erlöse zu generieren.

Inhibitory effect of tocotrienol on eukaryotic DNA polymerase {lambda} and angiogenesis

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

Mizushina, Yoshiyuki; Nakagawa, Kiyotaka; Shibata, Akira

2006-01-20

Tocotrienols, vitamin E compounds that have an unsaturated side chain with three double bonds, selectively inhibited the activity of mammalian DNA polymerase {lambda} (pol {lambda}) in vitro. These compounds did not influence the activities of replicative pols such as {alpha}, {delta}, and {epsilon}, or even the activity of pol {beta} which is thought to have a very similar three-dimensional structure to the pol {beta}-like region of pol {lambda}. Since {delta}-tocotrienol had the strongest inhibitory effect among the four ({alpha}- to {delta}-) tocotrienols, the isomer's structure might be an important factor in the inhibition of pol {lambda}. The inhibitory effect ofmore » {delta}-tocotrienol on both intact pol {lambda} (residues 1-575) and a truncated pol {lambda} lacking the N-terminal BRCA1 C-terminus (BRCT) domain (residues 133-575, del-1 pol {lambda}) was dose-dependent, with 50% inhibition observed at a concentration of 18.4 and 90.1 {mu}M, respectively. However, del-2 pol {lambda} (residues 245-575) containing the C-terminal pol {beta}-like region was unaffected. Tocotrienols also inhibited the proliferation of and formation of tubes by bovine aortic endothelial cells, with {delta}-tocotrienol having the greatest effect. These results indicated that tocotrienols targeted both pol {lambda} and angiogenesis as anti-cancer agents. The relationship between the inhibition of pol {lambda} and anti-angiogenesis by {delta}-tocotrienol was discussed.« less

RNA polymerase III mutants in TFIIFα-like C37 that cause terminator readthrough with no decrease in transcription output.

PubMed

Rijal, Keshab; Maraia, Richard J

2013-01-07

How eukaryotic RNA polymerases switch from elongation to termination is unknown. Pol III subunits Rpc53 and Rpc37 (C53/37) form a heterodimer homologous to TFIIFβ/α. C53/37 promotes efficient termination and together with C11 also mediates pol III recycling in vitro. We previously developed Schizosaccharomyces pombe strains that report on two pol III termination activities: RNA oligo(U) 3'-end cleavage, and terminator readthrough. We randomly mutagenized C53 and C37 and isolated many C37 mutants with terminator readthrough but no comparable C53 mutants. The majority of C37 mutants have strong phenotypes with up to 40% readthrough and map to a C-terminal tract previously localized near Rpc2p in the pol III active center while a minority represent a distinct class with weaker phenotype, less readthrough and 3'-oligo(U) lengthening. Nascent pre-tRNAs released from a terminator by C37 mutants have shorter 3'-oligo(U) tracts than in cleavage-deficient C11 double mutants indicating RNA 3'-end cleavage during termination. We asked whether termination deficiency affects transcription output in the mutants in vivo both by monitoring intron-containing nascent transcript levels and (14)C-uridine incorporation. Surprisingly, multiple termination mutants have no decrease in transcript output relative to controls. These data are discussed in context of current models of pol III transcription.

Distinguishing Core and Holoenzyme Mechanisms of Transcription Termination by RNA Polymerase III

PubMed Central

Arimbasseri, Aneeshkumar G.

2013-01-01

Transcription termination by RNA polymerase (Pol) III serves multiple purposes; it delimits interference with downstream genes, forms 3′ oligo(U) binding sites for the posttranscriptional processing factor, La protein, and resets the polymerase complex for reinitiation. Although an interplay of several Pol III subunits is known to collectively control these activities, how they affect molecular function of the active center during termination is incompletely understood. We have approached this using immobilized Pol III-nucleic acid scaffolds to examine the two major components of termination, transcription pausing and RNA release. This allowed us to distinguish two mechanisms of termination by isolated Saccharomyces cerevisiae Pol III. A core mechanism can operate in the absence of C53/37 and C11 subunits but requires synthesis of 8 or more 3′ U nucleotides, apparently reflecting inherent sensitivity to an oligo(rU·dA) hybrid that is the termination signal proper. The holoenzyme mechanism requires fewer U nucleotides but uses C53/37 and C11 to slow elongation and prevent terminator arrest. N-terminal truncation of C53 or point mutations that disable the cleavage activity of C11 impair their antiarrest activities. The data are consistent with a model in which C53, C37, and C11 activities are functionally integrated with the active center of Pol III during termination. PMID:23401852

Polarimetric SAR Models for Oil Fields Monitoring in China Seas

NASA Astrophysics Data System (ADS)

Buono, A.; Nunziata, F.; Li, X.; Wei, Y.; Ding, X.

2014-11-01

In this study, physical-based models for polarimetric Synthetic Aperture Radar (SAR) oil fields monitoring are proposed. They all share a physical rationale relying on the different scattering mechanisms that characterize a free sea surface, an oil slick-covered sea surface, and a metallic target. In fact, sea surface scattering is well modeled by a Bragg-like behaviour, while a strong departure from Bragg scattering is in place when dealing with oil slicks and targets. Furthermore, the proposed polarimetric models aim at addressing simultaneously target and oil slick detection, providing useful extra information with respect to single-pol SAR data in order to approach oil discrimination and classification. Experiments undertaken over East and South China Sea from actual C-band RadarSAT-2 full-pol SAR data witness the soundness of the proposed rationale.

Polarimetric SAR Models for Oil Fields Monitoring in China Seas

NASA Astrophysics Data System (ADS)

Buono, A.; Nunziata, F.; Li, X.; Wei, Y.; Ding, X.

2014-11-01

In this study, physical-based models for polarimetric Synthetic Aperture Radar (SAR) oil fields monitoring are proposed. They all share a physical rationale relying on the different scattering mechanisms that characterize a free sea surface, an oil slick-covered sea surface, and a metallic target. In fact, sea surface scattering is well modeled by a Bragg-like behaviour, while a strong departure from Bragg scattering is in place when dealing with oil slicks and targets. Furthermore, the proposed polarimetric models aim at addressing simultaneously target and oil slick detection, providing useful extra information with respect to single-pol SAR data in order to approach oil discrimination and classification.Experiments undertaken over East and South China Sea from actual C-band RadarSAT-2 full-pol SAR data witness the soundness of the proposed rationale.

Homologous recombination mediates S-phase-dependent radioresistance in cells deficient in DNA polymerase eta.

PubMed

Nicolay, Nils H; Carter, Rebecca; Hatch, Stephanie B; Schultz, Niklas; Prevo, Remko; McKenna, W Gillies; Helleday, Thomas; Sharma, Ricky A

2012-11-01

DNA polymerase eta (pol η) is the only DNA polymerase causally linked to carcinogenesis in humans. Inherited deficiency of pol η in the variant form of xeroderma pigmentosum (XPV) predisposes to UV-light-induced skin cancer. Pol η-deficient cells demonstrate increased sensitivity to cisplatin and oxaliplatin chemotherapy. We have found that XP30R0 fibroblasts derived from a patient with XPV are more resistant to cell kill by ionising radiation (IR) than the same cells complemented with wild-type pol η. This phenomenon has been confirmed in Burkitt's lymphoma cells, which either expressed wild-type pol η or harboured a pol η deletion. Pol η deficiency was associated with accumulation of cells in S-phase, which persisted after IR. Cells deficient in pol η demonstrated increased homologous recombination (HR)-directed repair of double strand breaks created by IR. Depletion of the HR protein, X-ray repair cross-complementing protein 3 (XRCC3), abrogated the radioresistance observed in pol η-deficient cells as compared with pol η-complemented cells. These findings suggest that HR mediates S-phase-dependent radioresistance associated with pol η deficiency. We propose that pol η protein levels in tumours may potentially be used to identify patients who require treatment with chemo-radiotherapy rather than radiotherapy alone for adequate tumour control.

Strand displacement synthesis by yeast DNA polymerase ε

PubMed Central

Ganai, Rais A.; Zhang, Xiao-Ping; Heyer, Wolf-Dietrich; Johansson, Erik

2016-01-01

DNA polymerase ε (Pol ε) is a replicative DNA polymerase with an associated 3′–5′ exonuclease activity. Here, we explored the capacity of Pol ε to perform strand displacement synthesis, a process that influences many DNA transactions in vivo. We found that Pol ε is unable to carry out extended strand displacement synthesis unless its 3′–5′ exonuclease activity is removed. However, the wild-type Pol ε holoenzyme efficiently displaced one nucleotide when encountering double-stranded DNA after filling a gap or nicked DNA. A flap, mimicking a D-loop or a hairpin structure, on the 5′ end of the blocking primer inhibited Pol ε from synthesizing DNA up to the fork junction. This inhibition was observed for Pol ε but not with Pol δ, RB69 gp43 or Pol η. Neither was Pol ε able to extend a D-loop in reconstitution experiments. Finally, we show that the observed strand displacement synthesis by exonuclease-deficient Pol ε is distributive. Our results suggest that Pol ε is unable to extend the invading strand in D-loops during homologous recombination or to add more than two nucleotides during long-patch base excision repair. Our results support the hypothesis that Pol ε participates in short-patch base excision repair and ribonucleotide excision repair. PMID:27325747

Rückwärtsintegration - Zu den Verhältnissen Gymnasium, Hochschule und Arbeitswelt

NASA Astrophysics Data System (ADS)

Schmid, Gerhard; Heppner, Winfried; Focht, Eva

In seiner 2007 erschienen Sammlung von Vorträgen und Essays beschäftigt sich Wolfgang Frühwald, mit der Frage "Wieviel Wissen brauchen wir?“ [1] Die Kernproblematik moderner Wissenschaft und Forschung sieht der Autor, emeritierter Ordinarius für Neuere Deutsche Literaturwissenschaft und von 1992 bis 1997 Präsident der Deutschen Forschungsgemeinschaft, einerseits in der zunehmenden Spezialisierung der Wissenschaftsbereiche, andererseits in der Gefahr der Abkoppelung der Naturwissenschaften von den Geisteswissenschaften. Wiederholt plädiert er dafür, über der rasanten Entwicklung beispielsweise in der Biologie und Physik, die historische, gesellschaftliche und besonders die ethische Dimension der Forschung nicht zu übersehen und fordert eine übergeordnete Theorie der Wissenschaft, die nur im Dialog zwischen den einzelnen Fachgebieten zu entwickeln sei.

Van der Waals interactions and the limits of isolated atom models at interfaces

PubMed Central

Kawai, Shigeki; Foster, Adam S.; Björkman, Torbjörn; Nowakowska, Sylwia; Björk, Jonas; Canova, Filippo Federici; Gade, Lutz H.; Jung, Thomas A.; Meyer, Ernst

2016-01-01

Van der Waals forces are among the weakest, yet most decisive interactions governing condensation and aggregation processes and the phase behaviour of atomic and molecular matter. Understanding the resulting structural motifs and patterns has become increasingly important in studies of the nanoscale regime. Here we measure the paradigmatic van der Waals interactions represented by the noble gas atom pairs Ar–Xe, Kr–Xe and Xe–Xe with a Xe-functionalized tip of an atomic force microscope at low temperature. Individual rare gas atoms were fixed at node sites of a surface-confined two-dimensional metal–organic framework. We found that the magnitude of the measured force increased with the atomic radius, yet detailed simulation by density functional theory revealed that the adsorption induced charge redistribution strengthened the van der Waals forces by a factor of up to two, thus demonstrating the limits of a purely atomic description of the interaction in these representative systems. PMID:27174162

Classification Comparisons Between Compact Polarimetric and Quad-Pol SAR Imagery

NASA Astrophysics Data System (ADS)

Souissi, Boularbah; Doulgeris, Anthony P.; Eltoft, Torbjørn

2015-04-01

Recent interest in dual-pol SAR systems has lead to a novel approach, the so-called compact polarimetric imaging mode (CP) which attempts to reconstruct fully polarimetric information based on a few simple assumptions. In this work, the CP image is simulated from the full quad-pol (QP) image. We present here the initial comparison of polarimetric information content between QP and CP imaging modes. The analysis of multi-look polarimetric covariance matrix data uses an automated statistical clustering method based upon the expectation maximization (EM) algorithm for finite mixture modeling, using the complex Wishart probability density function. Our results showed that there are some different characteristics between the QP and CP modes. The classification is demonstrated using a E-SAR and Radarsat2 polarimetric SAR images acquired over DLR Oberpfaffenhofen in Germany and Algiers in Algeria respectively.

Urban-area extraction from polarimetric SAR image using combination of target decomposition and orientation angle

NASA Astrophysics Data System (ADS)

Zou, Bin; Lu, Da; Wu, Zhilu; Qiao, Zhijun G.

2016-05-01

The results of model-based target decomposition are the main features used to discriminate urban and non-urban area in polarimetric synthetic aperture radar (PolSAR) application. Traditional urban-area extraction methods based on modelbased target decomposition usually misclassified ground-trunk structure as urban-area or misclassified rotated urbanarea as forest. This paper introduces another feature named orientation angle to improve urban-area extraction scheme for the accurate mapping in urban by PolSAR image. The proposed method takes randomness of orientation angle into account for restriction of urban area first and, subsequently, implements rotation angle to improve results that oriented urban areas are recognized as double-bounce objects from volume scattering. ESAR L-band PolSAR data of the Oberpfaffenhofen Test Site Area was used to validate the proposed algorithm.

Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing

PubMed Central

Kwak, Hojoong; Fuda, Nicholas J.; Core, Leighton J.; Lis, John T.

2014-01-01

Transcription regulation occurs frequently through promoter-associated pausing of RNA polymerase II (Pol II). We developed a Precision nuclear Run-On and sequencing assay (PRO-seq) to map the genome-wide distribution of transcriptionally-engaged Pol II at base-pair resolution. Pol II accumulates immediately downstream of promoters, at intron-exon junctions that are efficiently used for splicing, and over 3' poly-adenylation sites. Focused analyses of promoters reveal that pausing is not fixed relative to initiation sites nor is it specified directly by the position of a particular core promoter element or the first nucleosome. Core promoter elements function beyond initiation, and when optimally positioned they act collectively to dictate the position and strength of pausing. We test this ‘Complex Interaction’ model with insertional mutagenesis of the Drosophila Hsp70 core promoter. PMID:23430654

Both High-Fidelity Replicative and Low-Fidelity Y-Family Polymerases Are Involved in DNA Rereplication

PubMed Central

Sekimoto, Takayuki; Oda, Tsukasa; Kurashima, Kiminori; Hanaoka, Fumio

2014-01-01

DNA rereplication is a major form of aberrant replication that causes genomic instabilities, such as gene amplification. However, little is known about which DNA polymerases are involved in the process. Here, we report that low-fidelity Y-family polymerases (Y-Pols), Pol η, Pol ι, Pol κ, and REV1, significantly contribute to DNA synthesis during rereplication, while the replicative polymerases, Pol δ and Pol ε, play an important role in rereplication, as expected. When rereplication was induced by depletion of geminin, these polymerases were recruited to rereplication sites in human cell lines. This finding was supported by RNA interference (RNAi)-mediated knockdown of the polymerases, which suppressed rereplication induced by geminin depletion. Interestingly, epistatic analysis indicated that Y-Pols collaborate in a common pathway, independently of replicative polymerases. We also provide evidence for a catalytic role for Pol η and the involvement of Pol η and Pol κ in cyclin E-induced rereplication. Collectively, our findings indicate that, unlike normal S-phase replication, rereplication induced by geminin depletion and oncogene activation requires significant contributions of both Y-Pols and replicative polymerases. These findings offer important mechanistic insights into cancer genomic instability. PMID:25487575

Evaluation of van der Waals density functionals for layered materials

NASA Astrophysics Data System (ADS)

Tawfik, Sherif Abdulkader; Gould, Tim; Stampfl, Catherine; Ford, Michael J.

2018-03-01

In 2012, Björkman et al. posed the question "Are we van der Waals ready?" [T. Björkman et al., J. Phys.: Condens. Matter 24, 424218 (2012), 10.1088/0953-8984/24/42/424218] about the ability of ab initio modeling to reproduce van der Waals (vdW) dispersion forces in layered materials. The answer at that time was no, however. Here we report on a new generation of vdW dispersion models and show that one, i.e., the fractionally ionic atom theory with many-body dispersions, offers close to quantitative predictions for layered structures. Furthermore, it does so from a qualitatively correct picture of dispersion forces. Other methods, such as D3 and optB88vdW, also work well, albeit with some exceptions. We thus argue that we are nearly vdW ready and that some modern dispersion methods are accurate enough to be used for nanomaterial prediction, albeit with some caution required.

Study of interaction in silica glass via model potential approach

NASA Astrophysics Data System (ADS)

Mann, Sarita; Rani, Pooja

2016-05-01

Silica is one of the most commonly encountered substances in daily life and in electronics industry. Crystalline SiO2 (in several forms: quartz, cristobalite, tridymite) is an important constituent of many minerals and gemstones, both in pure form and mixed with related oxides. Cohesive energy of amorphous SiO2 has been investigated via intermolecular potentials i.e weak Van der Waals interaction and Morse type short-range interaction. We suggest a simple atom-atom based Van der Waals as well as Morse potential to find cohesive energy of glass. It has been found that the study of silica structure using two different model potentials is significantly different. Van der Waals potential is too weak (P.E =0.142eV/molecule) to describe the interaction between silica molecules. Morse potential is a strong potential, earlier given for intramolecular bonding, but if applied for intermolecular bonding, it gives a value of P.E (=-21.92eV/molecule) to appropriately describe the structure of silica.

DNA Polymerases η and ζ Combine to Bypass O(2)-[4-(3-Pyridyl)-4-oxobutyl]thymine, a DNA Adduct Formed from Tobacco Carcinogens.

PubMed

Gowda, A S Prakasha; Spratt, Thomas E

2016-03-21

4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) and N'-nitrosonornicotine (NNN) are important human carcinogens in tobacco products. They are metabolized to produce a variety 4-(3-pyridyl)-4-oxobutyl (POB) DNA adducts including O(2)-[4-(3-pyridyl)-4-oxobut-1-yl]thymidine (O(2)-POB-dT), the most abundant POB adduct in NNK- and NNN-treated rodents. To evaluate the mutagenic properties of O(2)-POB-dT, we measured the rate of insertion of dNTPs opposite and extension past O(2)-POB-dT and O(2)-Me-dT by purified human DNA polymerases η, κ, ι, and yeast polymerase ζ in vitro. Under conditions of polymerase in excess, polymerase η was most effective at the insertion of dNTPs opposite O(2)-alkyl-dTs. The time courses were biphasic suggesting the formation of inactive DNA-polymerase complexes. The kpol parameter was reduced approximately 100-fold in the presence of the adduct for pol η, κ, and ι. Pol η was the most reactive polymerase for the adducts due to a higher burst amplitude. For all three polymerases, the nucleotide preference was dATP > dTTP ≫ dGTP and dCTP. Yeast pol ζ was most effective in bypassing the adducts; the kcat/Km values were reduced only 3-fold in the presence of the adducts. The identity of the nucleotide opposite the O(2)-alkyl-dT did not significantly affect the ability of pol ζ to bypass the adducts. The data support a model in which pol η inserts ATP or dTTP opposite O(2)-POB-dT, and then, pol ζ extends past the adduct.

Lysines in the RNA Polymerase II C-Terminal Domain Contribute to TAF15 Fibril Recruitment.

PubMed

Janke, Abigail M; Seo, Da Hee; Rahmanian, Vahid; Conicella, Alexander E; Mathews, Kaylee L; Burke, Kathleen A; Mittal, Jeetain; Fawzi, Nicolas L

2018-05-01

Many cancer-causing chromosomal translocations result in transactivating protein products encoding FET family (FUS, EWSR1, TAF15) low-complexity (LC) domains fused to a DNA binding domain from one of several transcription factors. Recent work demonstrates that higher-order assemblies of FET LC domains bind the carboxy-terminal domain of the large subunit of RNA polymerase II (RNA pol II CTD), suggesting FET oncoproteins may mediate aberrant transcriptional activation by recruiting RNA polymerase II to promoters of target genes. Here we use nuclear magnetic resonance (NMR) spectroscopy and hydrogel fluorescence microscopy localization and fluorescence recovery after photobleaching to visualize atomic details of a model of this process, interactions of RNA pol II CTD with high-molecular weight TAF15 LC assemblies. We report NMR resonance assignments of the intact degenerate repeat half of human RNA pol II CTD alone and verify its predominant intrinsic disorder by molecular simulation. By measuring NMR spin relaxation and dark-state exchange saturation transfer, we characterize the interaction of RNA pol II CTD with amyloid-like hydrogel fibrils of TAF15 and hnRNP A2 LC domains and observe that heptads far from the acidic C-terminal tail of RNA pol II CTD bind TAF15 fibrils most avidly. Mutation of CTD lysines in heptad position 7 to consensus serines reduced the overall level of TAF15 fibril binding, suggesting that electrostatic interactions contribute to complex formation. Conversely, mutations of position 7 asparagine residues and truncation of the acidic tail had little effect. Thus, weak, multivalent interactions between TAF15 fibrils and heptads throughout RNA pol II CTD collectively mediate complex formation.

DNA Polymerase β as a Novel Target for Chemotherapeutic Intervention of Colorectal Cancer

PubMed Central

Jaiswal, Aruna S.; Banerjee, Sanjeev; Aneja, Ritu; Sarkar, Fazlul H.; Ostrov, David A.; Narayan, Satya

2011-01-01

Chemoprevention presents a major strategy for the medical management of colorectal cancer. Most drugs used for colorectal cancer therapy induce DNA-alkylation damage, which is primarily repaired by the base excision repair (BER) pathway. Thus, blockade of BER pathway is an attractive option to inhibit the spread of colorectal cancer. Using an in silico approach, we performed a structure-based screen by docking small-molecules onto DNA polymerase β (Pol-β) and identified a potent anti-Pol-β compound, NSC-124854. Our goal was to examine whether NSC-124854 could enhance the therapeutic efficacy of DNA-alkylating agent, Temozolomide (TMZ), by blocking BER. First, we determined the specificity of NSC-124854 for Pol-β by examining in vitro activities of APE1, Fen1, DNA ligase I, and Pol-β-directed single nucleotide (SN)- and long-patch (LP)-BER. Second, we investigated the effect of NSC-124854 on the efficacy of TMZ to inhibit the growth of mismatch repair (MMR)-deficient and MMR-proficient colon cancer cell lines using in vitro clonogenic assays. Third, we explored the effect of NSC-124854 on TMZ-induced in vivo tumor growth inhibition of MMR-deficient and MMR-proficient colonic xenografts implanted in female homozygous SCID mice. Our data showed that NSC-124854 has high specificity to Pol-β and blocked Pol-β-directed SN- and LP-BER activities in in vitro reconstituted system. Furthermore, NSC-124854 effectively induced the sensitivity of TMZ to MMR-deficient and MMR-proficient colon cancer cells both in vitro cell culture and in vivo xenograft models. Our findings suggest a potential novel strategy for the development of highly specific structure-based inhibitor for the prevention of colonic tumor progression. PMID:21311763

a Novel Two-Component Decomposition for Co-Polar Channels of GF-3 Quad-Pol Data

NASA Astrophysics Data System (ADS)

Kwok, E.; Li, C. H.; Zhao, Q. H.; Li, Y.

2018-04-01

Polarimetric target decomposition theory is the most dynamic and exploratory research area in the field of PolSAR. But most methods of target decomposition are based on fully polarized data (quad pol) and seldom utilize dual-polar data for target decomposition. Given this, we proposed a novel two-component decomposition method for co-polar channels of GF-3 quad-pol data. This method decomposes the data into two scattering contributions: surface, double bounce in dual co-polar channels. To save this underdetermined problem, a criterion for determining the model is proposed. The criterion can be named as second-order averaged scattering angle, which originates from the H/α decomposition. and we also put forward an alternative parameter of it. To validate the effectiveness of proposed decomposition, Liaodong Bay is selected as research area. The area is located in northeastern China, where it grows various wetland resources and appears sea ice phenomenon in winter. and we use the GF-3 quad-pol data as study data, which which is China's first C-band polarimetric synthetic aperture radar (PolSAR) satellite. The dependencies between the features of proposed algorithm and comparison decompositions (Pauli decomposition, An&Yang decomposition, Yamaguchi S4R decomposition) were investigated in the study. Though several aspects of the experimental discussion, we can draw the conclusion: the proposed algorithm may be suitable for special scenes with low vegetation coverage or low vegetation in the non-growing season; proposed decomposition features only using co-polar data are highly correlated with the corresponding comparison decomposition features under quad-polarization data. Moreover, it would be become input of the subsequent classification or parameter inversion.

Interactions and Localization of Escherichia coli Error-Prone DNA Polymerase IV after DNA Damage.

PubMed

Mallik, Sarita; Popodi, Ellen M; Hanson, Andrew J; Foster, Patricia L

2015-09-01

Escherichia coli's DNA polymerase IV (Pol IV/DinB), a member of the Y family of error-prone polymerases, is induced during the SOS response to DNA damage and is responsible for translesion bypass and adaptive (stress-induced) mutation. In this study, the localization of Pol IV after DNA damage was followed using fluorescent fusions. After exposure of E. coli to DNA-damaging agents, fluorescently tagged Pol IV localized to the nucleoid as foci. Stepwise photobleaching indicated ∼60% of the foci consisted of three Pol IV molecules, while ∼40% consisted of six Pol IV molecules. Fluorescently tagged Rep, a replication accessory DNA helicase, was recruited to the Pol IV foci after DNA damage, suggesting that the in vitro interaction between Rep and Pol IV reported previously also occurs in vivo. Fluorescently tagged RecA also formed foci after DNA damage, and Pol IV localized to them. To investigate if Pol IV localizes to double-strand breaks (DSBs), an I-SceI endonuclease-mediated DSB was introduced close to a fluorescently labeled LacO array on the chromosome. After DSB induction, Pol IV localized to the DSB site in ∼70% of SOS-induced cells. RecA also formed foci at the DSB sites, and Pol IV localized to the RecA foci. These results suggest that Pol IV interacts with RecA in vivo and is recruited to sites of DSBs to aid in the restoration of DNA replication. DNA polymerase IV (Pol IV/DinB) is an error-prone DNA polymerase capable of bypassing DNA lesions and aiding in the restart of stalled replication forks. In this work, we demonstrate in vivo localization of fluorescently tagged Pol IV to the nucleoid after DNA damage and to DNA double-strand breaks. We show colocalization of Pol IV with two proteins: Rep DNA helicase, which participates in replication, and RecA, which catalyzes recombinational repair of stalled replication forks. Time course experiments suggest that Pol IV recruits Rep and that RecA recruits Pol IV. These findings provide in vivo evidence that Pol IV aids in maintaining genomic stability not only by bypassing DNA lesions but also by participating in the restoration of stalled replication forks. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Deorientation of PolSAR coherency matrix for volume scattering retrieval

NASA Astrophysics Data System (ADS)

Kumar, Shashi; Garg, R. D.; Kushwaha, S. P. S.

2016-05-01

Polarimetric SAR data has proven its potential to extract scattering information for different features appearing in single resolution cell. Several decomposition modelling approaches have been developed to retrieve scattering information from PolSAR data. During scattering power decomposition based on physical scattering models it becomes very difficult to distinguish volume scattering as a result from randomly oriented vegetation from scattering nature of oblique structures which are responsible for double-bounce and volume scattering , because both are decomposed in same scattering mechanism. The polarization orientation angle (POA) of an electromagnetic wave is one of the most important character which gets changed due to scattering from geometrical structure of topographic slopes, oriented urban area and randomly oriented features like vegetation cover. The shift in POA affects the polarimetric radar signatures. So, for accurate estimation of scattering nature of feature compensation in polarization orientation shift becomes an essential procedure. The prime objective of this work was to investigate the effect of shift in POA in scattering information retrieval and to explore the effect of deorientation on regression between field-estimated aboveground biomass (AGB) and volume scattering. For this study Dudhwa National Park, U.P., India was selected as study area and fully polarimetric ALOS PALSAR data was used to retrieve scattering information from the forest area of Dudhwa National Park. Field data for DBH and tree height was collect for AGB estimation using stratified random sampling. AGB was estimated for 170 plots for different locations of the forest area. Yamaguchi four component decomposition modelling approach was utilized to retrieve surface, double-bounce, helix and volume scattering information. Shift in polarization orientation angle was estimated and deorientation of coherency matrix for compensation of POA shift was performed. Effect of deorientation on RGB color composite for the forest area can be easily seen. Overestimation of volume scattering and under estimation of double bounce scattering was recorded for PolSAR decomposition without deorientation and increase in double bounce scattering and decrease in volume scattering was noticed after deorientation. This study was mainly focused on volume scattering retrieval and its relation with field estimated AGB. Change in volume scattering after POA compensation of PolSAR data was recorded and a comparison was performed on volume scattering values for all the 170 forest plots for which field data were collected. Decrease in volume scattering after deorientation was noted for all the plots. Regression between PolSAR decomposition based volume scattering and AGB was performed. Before deorientation, coefficient determination (R2) between volume scattering and AGB was 0.225. After deorientation an improvement in coefficient of determination was found and the obtained value was 0.613. This study recommends deorientation of PolSAR data for decomposition modelling to retrieve reliable volume scattering information from forest area.

Discrete Latent Markov Models for Normally Distributed Response Data

ERIC Educational Resources Information Center

Schmittmann, Verena D.; Dolan, Conor V.; van der Maas, Han L. J.; Neale, Michael C.

2005-01-01

Van de Pol and Langeheine (1990) presented a general framework for Markov modeling of repeatedly measured discrete data. We discuss analogical single indicator models for normally distributed responses. In contrast to discrete models, which have been studied extensively, analogical continuous response models have hardly been considered. These…

CHONDRICHTHYES, Knorpelfische

NASA Astrophysics Data System (ADS)

Goldschmid, Alfred

Die über 1.100 Arten der Knorpelfische sind nur etwa 4% aller heute lebenden Fischarten. Ihrknorpeliges Endoskelett kann zwar verkalken, wird abernie zu Knochen umgebaut. Der Schädel besteht nur aus Neurocranium und Viscerocranium, ein Dermatocranium fehlt. Knochen findet sich nur in den Plakoidschuppen der Körperdecke. Eine Schwimmblase wie bei den Knochenfischen wird nie gebildet. Mund- und Nasenöffnungen liegen ventral; der Endolymphgang bleibt zeitlebens mit der Epidermis verbunden. Der mediale Teil der Beckenflosse der Männchen dient als Kopulationsorgan (Mixopterygium, Klasper) (Abb. 208, 209B) bei der inneren Befruchtung.

Regulation of oxidative DNA damage repair by DNA polymerase λ and MutYH by cross-talk of phosphorylation and ubiquitination

PubMed Central

Markkanen, Enni; van Loon, Barbara; Ferrari, Elena; Parsons, Jason L.; Dianov, Grigory L.; Hübscher, Ulrich

2012-01-01

It is of pivotal importance for genome stability that repair DNA polymerases (Pols), such as Pols λ and β, which all exhibit considerably reduced fidelity when replicating undamaged DNA, are tightly regulated, because their misregulation could lead to mutagenesis. Recently, we found that the correct repair of the abundant and highly miscoding oxidative DNA lesion 7,8-dihydro-8-oxo-2′-deoxyguanine (8-oxo-G) is performed by an accurate repair pathway that is coordinated by the MutY glycosylase homologue (MutYH) and Pol λ in vitro and in vivo. Pol λ is phosphorylated by Cdk2/cyclinA in late S and G2 phases of the cell cycle, promoting Pol λ stability by preventing it from being targeted for proteasomal degradation by ubiquitination. However, it has remained a mystery how the levels of Pol λ are controlled, how phosphorylation promotes its stability, and how the engagement of Pol λ in active repair complexes is coordinated. Here, we show that the E3 ligase Mule mediates the degradation of Pol λ and that the control of Pol λ levels by Mule has functional consequences for the ability of mammalian cells to deal with 8-oxo-G lesions. Furthermore, we demonstrate that phosphorylation of Pol λ by Cdk2/cyclinA counteracts its Mule-mediated degradation by promoting recruitment of Pol λ to chromatin into active 8-oxo-G repair complexes through an increase in Pol λ’s affinity to chromatin-bound MutYH. Finally, MutYH appears to promote the stability of Pol λ by binding it to chromatin. In contrast, Pol λ not engaged in active repair on chromatin is subject for proteasomal degradation. PMID:22203964

Structural relationship of curcumin derivatives binding to the BRCT domain of human DNA polymerase lambda.

PubMed

Takeuchi, Toshifumi; Ishidoh, Tomomi; Iijima, Hiroshi; Kuriyama, Isoko; Shimazaki, Noriko; Koiwai, Osamu; Kuramochi, Kouji; Kobayashi, Susumu; Sugawara, Fumio; Sakaguchi, Kengo; Yoshida, Hiromi; Mizushina, Yoshiyuki

2006-03-01

We previously reported that phenolic compounds, petasiphenol and curcumin (diferuloylmethane), were a selective inhibitor of DNA polymerase lambda (pol lambda) in vitro. The purpose of this study was to investigate the molecular structural relationship of curcumin and 13 chemically synthesized derivatives of curcumin. The inhibitory effect on pol lambda (full-length, i.e. intact pol lambda including the BRCA1 C- terminal [BRCT] domain) by some derivatives was stronger than that by curcumin, and monoacetylcurcumin (compound 13) was the strongest pol lambda inhibitor of all the compounds tested, achieving 50% inhibition at a concentration of 3.9 microm. The compound did not influence the activities of replicative pols such as alpha, delta, and epsilon. It had no effect on pol beta activity either, although the three-dimensional structure of pol beta is thought to be highly similar to that of pol lambda. Compound 13 did not inhibit the activity of the C-terminal catalytic domain of pol lambda including the pol beta-like core, in which the BRCT motif was deleted from its N-terminal region. MALDI-TOF MS analysis demonstrated that compound 13 bound selectively to the N-terminal domain of pol lambda, but did not bind to the C-terminal region. Based on these results, the pol lambda-inhibitory mechanism of compound 13 is discussed.

Homologous recombination mediates S-phase-dependent radioresistance in cells deficient in DNA polymerase eta

PubMed Central

Sharma, Ricky A.

2012-01-01

DNA polymerase eta (pol η) is the only DNA polymerase causally linked to carcinogenesis in humans. Inherited deficiency of pol η in the variant form of xeroderma pigmentosum (XPV) predisposes to UV-light-induced skin cancer. Pol η-deficient cells demonstrate increased sensitivity to cisplatin and oxaliplatin chemotherapy. We have found that XP30R0 fibroblasts derived from a patient with XPV are more resistant to cell kill by ionising radiation (IR) than the same cells complemented with wild-type pol η. This phenomenon has been confirmed in Burkitt’s lymphoma cells, which either expressed wild-type pol η or harboured a pol η deletion. Pol η deficiency was associated with accumulation of cells in S-phase, which persisted after IR. Cells deficient in pol η demonstrated increased homologous recombination (HR)-directed repair of double strand breaks created by IR. Depletion of the HR protein, X-ray repair cross-complementing protein 3 (XRCC3), abrogated the radioresistance observed in pol η-deficient cells as compared with pol η-complemented cells. These findings suggest that HR mediates S-phase-dependent radioresistance associated with pol η deficiency. We propose that pol η protein levels in tumours may potentially be used to identify patients who require treatment with chemo-radiotherapy rather than radiotherapy alone for adequate tumour control. PMID:22822095

Strand displacement synthesis by yeast DNA polymerase ε.

PubMed

Ganai, Rais A; Zhang, Xiao-Ping; Heyer, Wolf-Dietrich; Johansson, Erik

2016-09-30

DNA polymerase ε (Pol ε) is a replicative DNA polymerase with an associated 3'-5' exonuclease activity. Here, we explored the capacity of Pol ε to perform strand displacement synthesis, a process that influences many DNA transactions in vivo We found that Pol ε is unable to carry out extended strand displacement synthesis unless its 3'-5' exonuclease activity is removed. However, the wild-type Pol ε holoenzyme efficiently displaced one nucleotide when encountering double-stranded DNA after filling a gap or nicked DNA. A flap, mimicking a D-loop or a hairpin structure, on the 5' end of the blocking primer inhibited Pol ε from synthesizing DNA up to the fork junction. This inhibition was observed for Pol ε but not with Pol δ, RB69 gp43 or Pol η. Neither was Pol ε able to extend a D-loop in reconstitution experiments. Finally, we show that the observed strand displacement synthesis by exonuclease-deficient Pol ε is distributive. Our results suggest that Pol ε is unable to extend the invading strand in D-loops during homologous recombination or to add more than two nucleotides during long-patch base excision repair. Our results support the hypothesis that Pol ε participates in short-patch base excision repair and ribonucleotide excision repair. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Redundancy of mammalian Y family DNA polymerases in cellular responses to genomic DNA lesions induced by ultraviolet light

PubMed Central

Jansen, Jacob G.; Temviriyanukul, Piya; Wit, Niek; Delbos, Frédéric; Reynaud, Claude-Agnès; Jacobs, Heinz; de Wind, Niels

2014-01-01

Short-wave ultraviolet light induces both mildly helix-distorting cyclobutane pyrimidine dimers (CPDs) and severely distorting (6–4) pyrimidine pyrimidone photoproducts ((6–4)PPs). The only DNA polymerase (Pol) that is known to replicate efficiently across CPDs is Polη, a member of the Y family of translesion synthesis (TLS) DNA polymerases. Phenotypes of Polη deficiency are transient, suggesting redundancy with other DNA damage tolerance pathways. Here we performed a comprehensive analysis of the temporal requirements of Y-family Pols ι and κ as backups for Polη in (i) bypassing genomic CPD and (6–4)PP lesions in vivo, (ii) suppressing DNA damage signaling, (iii) maintaining cell cycle progression and (iv) promoting cell survival, by using mouse embryonic fibroblast lines with single and combined disruptions in these Pols. The contribution of Polι is restricted to TLS at a subset of the photolesions. Polκ plays a dominant role in rescuing stalled replication forks in Polη-deficient mouse embryonic fibroblasts, both at CPDs and (6–4)PPs. This dampens DNA damage signaling and cell cycle arrest, and results in increased survival. The role of relatively error-prone Pols ι and κ as backups for Polη contributes to the understanding of the mutator phenotype of xeroderma pigmentosum variant, a syndrome caused by Polη defects. PMID:25170086

Costs and Operating Dynamics of Integrating Distributed Energy Resources in Commercial and Industrial Buildings with Electric Vehicle Charging

NASA Astrophysics Data System (ADS)

Flores, Robert Joseph

Growing concerns over greenhouse gas and pollutant emissions have increased the pressure to shift energy conversion paradigms from current forms to more sustainable methods, such as through the use of distributed energy resources (DER) at industrial and commercial buildings. This dissertation is concerned with the optimal design and dispatch of a DER system installed at an industrial or commercial building. An optimization model that accurately captures typical utility costs and the physical constraints of a combined cooling, heating, and power (CCHP) system is designed to size and operate a DER system at a building. The optimization model is then used with cooperative game theory to evaluate the financial performance of a CCHP investment. The CCHP model is then modified to include energy storage, solar powered generators, alternative fuel sources, carbon emission limits, and building interactions with public and fleet PEVs. Then, a separate plugin electric vehicle (PEV) refueling model is developed to determine the cost to operate a public Level 3 fast charging station. The CCHP design and dispatch results show the size of the building load and consistency of the thermal loads are critical to positive financial performance. While using the CCHP system to produce cooling can provide savings, heat production drives positive financial performance. When designing the DER system to reduce carbon emissions, the use of renewable fuels can allow for a gas turbine system with heat recovery to reduce carbon emissions for a large university by 67%. Further reductions require large photovoltaic installations coupled with energy storage or the ability to export electricity back to the grid if costs are to remain relatively low. When considering Level 3 fast charging equipment, demand charges at low PEV travel levels are sufficiently high to discourage adoption. Integration of the equipment can reduce demand charge costs only if the building maximum demand does not coincide with PEV refueling. Electric vehicle refueling does not typically affect DER design at low PEV travel levels, but can as electric vehicle travel increases. However, as PEV travel increases, the stochastic nature of PEV refueling disappears, and the optimization problem may become deterministic.

SU-F-T-661: Dependence of Gold Nano Particles Cluster Morphology On Dose Enhancement of Photon Radiation Therapy Apply for Radiation Biology Effect

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

Ahn, S; Chung, K; Han, Y

Purpose: Injected gold nano particles (GNPs) to a body for dose enhancement are known to form in the tumorcell cluster morphology. We investigated the dependence of dose enhancement on the morphology characteristic with an approximated morphology model by using Monte Carlo simulations. Methods: For MC simulation, TOPAS version 2.0P-03 was used. GNP cluster morphology was approximated as a body center cubic(BCC) model by placing 8 GNPs at the corner and one at the center of cube with length from 2.59 µm to 0.25 µm located in a 4 µm length water filled cube phantom. 4 µm length square shaped beamsmore » of poly-energetic 50, 260 kVp photons were irradiated to the water filled cube phantom with 100 nm diameter GNPs in it. Dose enhancement ratio(DER) was computed as a function of distance from the surface of the GNP at the cube center for 18 cubes geometries. For scoring particles, 10 nm width of concentric shell shaped detector was constructed up to 100 nm from the center. Total dose in a sphere of 100 nm radius of detector were normalized to 2.59 µm length cube morphology. To verified biological effect of BCC model applied to cell survival curve fitting. Results: DER increase as the distance of the GNPs reduces. DER was largest for 0.25 µm length cube. Dependence of GNP distance DER increment was 1.73, 1.60 for 50 kVp, 260 kVp photons, respectively. Also, Using BCC model applied to cell survival curve was well prediction. Conclusion: DER with GNPs was larger when they are closely packed in the phantom. Therefore, better therapeutic effects can be expected with close-packed GNPs. This research was supported by the NRF funded by the Ministry of Science, ICT & Future Planning (2012M3A9B6055201 and 2012R1A1A2042414), Samsung Medical Center grant[GFO1130081].« less

Data-Driven Residential Load Modeling and Validation in GridLAB-D

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

Gotseff, Peter; Lundstrom, Blake

Accurately characterizing the impacts of high penetrations of distributed energy resources (DER) on the electric distribution system has driven modeling methods from traditional static snap shots, often representing a critical point in time (e.g., summer peak load), to quasi-static time series (QSTS) simulations capturing all the effects of variable DER, associated controls and hence, impacts on the distribution system over a given time period. Unfortunately, the high time resolution DER source and load data required for model inputs is often scarce or non-existent. This paper presents work performed within the GridLAB-D model environment to synthesize, calibrate, and validate 1-second residentialmore » load models based on measured transformer loads and physics-based models suitable for QSTS electric distribution system modeling. The modeling and validation approach taken was to create a typical GridLAB-D model home that, when replicated to represent multiple diverse houses on a single transformer, creates a statistically similar load to a measured load for a given weather input. The model homes are constructed to represent the range of actual homes on an instrumented transformer: square footage, thermal integrity, heating and cooling system definition as well as realistic occupancy schedules. House model calibration and validation was performed using the distribution transformer load data and corresponding weather. The modeled loads were found to be similar to the measured loads for four evaluation metrics: 1) daily average energy, 2) daily average and standard deviation of power, 3) power spectral density, and 4) load shape.« less

Influence of laser linewidth and polarization modulator length on polarization shift keying for free space optical communication.

PubMed

Han, Biao; Zhao, Wei; Xie, Xiaoping; Su, Yulong; Wang, Wei; Hu, Hui

2015-04-06

Modulating signal with polarization modulator (PolM) is the simplest method for polarization shift keying (PolSK) in free space optical communication. However, this method has an intrinsic drawback on degree of polarization (DOP) reduction for the existence of polarization mode dispersion (PMD) in PolM. In this work, we analyze this change of DOP and its influence on PolSK using coherency matrix. We demonstrate that the decrease of DOP after PolM will generate extra loss and bit error ratio (BER) for PolSK communication, while this loss and BER will aggravate with the increase of laser linewidth and PolM length. For a practical PolSK system, laser linewidth should be less than 0.008nm.

Emergence of DNA Polymerase ε Antimutators That Escape Error-Induced Extinction in Yeast

PubMed Central

Williams, Lindsey N.; Herr, Alan J.; Preston, Bradley D.

2013-01-01

DNA polymerases (Pols) ε and δ perform the bulk of yeast leading- and lagging-strand DNA synthesis. Both Pols possess intrinsic proofreading exonucleases that edit errors during polymerization. Rare errors that elude proofreading are extended into duplex DNA and excised by the mismatch repair (MMR) system. Strains that lack Pol proofreading or MMR exhibit a 10- to 100-fold increase in spontaneous mutation rate (mutator phenotype), and inactivation of both Pol δ proofreading (pol3-01) and MMR is lethal due to replication error-induced extinction (EEX). It is unclear whether a similar synthetic lethal relationship exists between defects in Pol ε proofreading (pol2-4) and MMR. Using a plasmid-shuffling strategy in haploid Saccharomyces cerevisiae, we observed synthetic lethality of pol2-4 with alleles that completely abrogate MMR (msh2Δ, mlh1Δ, msh3Δ msh6Δ, or pms1Δ mlh3Δ) but not with partial MMR loss (msh3Δ, msh6Δ, pms1Δ, or mlh3Δ), indicating that high levels of unrepaired Pol ε errors drive extinction. However, variants that escape this error-induced extinction (eex mutants) frequently emerged. Five percent of pol2-4 msh2Δ eex mutants encoded second-site changes in Pol ε that reduced the pol2-4 mutator phenotype between 3- and 23-fold. The remaining eex alleles were extragenic to pol2-4. The locations of antimutator amino-acid changes in Pol ε and their effects on mutation spectra suggest multiple mechanisms of mutator suppression. Our data indicate that unrepaired leading- and lagging-strand polymerase errors drive extinction within a few cell divisions and suggest that there are polymerase-specific pathways of mutator suppression. The prevalence of suppressors extragenic to the Pol ε gene suggests that factors in addition to proofreading and MMR influence leading-strand DNA replication fidelity. PMID:23307893

Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly.

PubMed

Bernecky, Carrie; Grob, Patricia; Ebmeier, Christopher C; Nogales, Eva; Taatjes, Dylan J

2011-03-01

The macromolecular assembly required to initiate transcription of protein-coding genes, known as the Pre-Initiation Complex (PIC), consists of multiple protein complexes and is approximately 3.5 MDa in size. At the heart of this assembly is the Mediator complex, which helps regulate PIC activity and interacts with the RNA polymerase II (pol II) enzyme. The structure of the human Mediator-pol II interface is not well-characterized, whereas attempts to structurally define the Mediator-pol II interaction in yeast have relied on incomplete assemblies of Mediator and/or pol II and have yielded inconsistent interpretations. We have assembled the complete, 1.9 MDa human Mediator-pol II-TFIIF complex from purified components and have characterized its structural organization using cryo-electron microscopy and single-particle reconstruction techniques. The orientation of pol II within this assembly was determined by crystal structure docking and further validated with projection matching experiments, allowing the structural organization of the entire human PIC to be envisioned. Significantly, pol II orientation within the Mediator-pol II-TFIIF assembly can be reconciled with past studies that determined the location of other PIC components relative to pol II itself. Pol II surfaces required for interacting with TFIIB, TFIIE, and promoter DNA (i.e., the pol II cleft) are exposed within the Mediator-pol II-TFIIF structure; RNA exit is unhindered along the RPB4/7 subunits; upstream and downstream DNA is accessible for binding additional factors; and no major structural re-organization is necessary to accommodate the large, multi-subunit TFIIH or TFIID complexes. The data also reveal how pol II binding excludes Mediator-CDK8 subcomplex interactions and provide a structural basis for Mediator-dependent control of PIC assembly and function. Finally, parallel structural analysis of Mediator-pol II complexes lacking TFIIF reveal that TFIIF plays a key role in stabilizing pol II orientation within the assembly.

Molecular Architecture of the Human Mediator–RNA Polymerase II–TFIIF Assembly

PubMed Central

Bernecky, Carrie; Grob, Patricia; Ebmeier, Christopher C.; Nogales, Eva; Taatjes, Dylan J.

2011-01-01

The macromolecular assembly required to initiate transcription of protein-coding genes, known as the Pre-Initiation Complex (PIC), consists of multiple protein complexes and is approximately 3.5 MDa in size. At the heart of this assembly is the Mediator complex, which helps regulate PIC activity and interacts with the RNA polymerase II (pol II) enzyme. The structure of the human Mediator–pol II interface is not well-characterized, whereas attempts to structurally define the Mediator–pol II interaction in yeast have relied on incomplete assemblies of Mediator and/or pol II and have yielded inconsistent interpretations. We have assembled the complete, 1.9 MDa human Mediator–pol II–TFIIF complex from purified components and have characterized its structural organization using cryo-electron microscopy and single-particle reconstruction techniques. The orientation of pol II within this assembly was determined by crystal structure docking and further validated with projection matching experiments, allowing the structural organization of the entire human PIC to be envisioned. Significantly, pol II orientation within the Mediator–pol II–TFIIF assembly can be reconciled with past studies that determined the location of other PIC components relative to pol II itself. Pol II surfaces required for interacting with TFIIB, TFIIE, and promoter DNA (i.e., the pol II cleft) are exposed within the Mediator–pol II–TFIIF structure; RNA exit is unhindered along the RPB4/7 subunits; upstream and downstream DNA is accessible for binding additional factors; and no major structural re-organization is necessary to accommodate the large, multi-subunit TFIIH or TFIID complexes. The data also reveal how pol II binding excludes Mediator–CDK8 subcomplex interactions and provide a structural basis for Mediator-dependent control of PIC assembly and function. Finally, parallel structural analysis of Mediator–pol II complexes lacking TFIIF reveal that TFIIF plays a key role in stabilizing pol II orientation within the assembly. PMID:21468301

Efficiency and Fidelity of Human DNA Polymerases λ and β during Gap-Filling DNA Synthesis

PubMed Central

Brown, Jessica A.; Pack, Lindsey R.; Sanman, Laura E.; Suo, Zucai

2010-01-01

The base excision repair (BER) pathway coordinates the replacement of 1 to 10 nucleotides at sites of single-base lesions. This process generates DNA substrates with various gap sizes which can alter the catalytic efficiency and fidelity of a DNA polymerase during gap-filling DNA synthesis. Here, we quantitatively determined the substrate specificity and base substitution fidelity of human DNA polymerase λ (Pol λ), an enzyme proposed to support the known BER DNA polymerase β (Pol β), as it filled 1- to 10-nucleotide gaps at 1-nucleotide intervals. Pol λ incorporated a correct nucleotide with relatively high efficiency until the gap size exceeded 9 nucleotides. Unlike Pol λ, Pol β did not have an absolute threshold on gap size as the catalytic efficiency for a correct dNTP gradually decreased as the gap size increased from 2 to 10 nucleotides and then recovered for non-gapped DNA. Surprisingly, an increase in gap size resulted in lower polymerase fidelity for Pol λ, and this downregulation of fidelity was controlled by its non-enzymatic N-terminal domains. Overall, Pol λ was up to 160-fold more error-prone than Pol β, thereby suggesting Pol λ would be more mutagenic during long gap-filling DNA synthesis. In addition, dCTP was the preferred misincorporation for Pol λ and its N-terminal domain truncation mutants. This nucleotide preference was shown to be dependent upon the identity of the adjacent 5′-template base. Our results suggested that both Pol λ and Pol β would catalyze nucleotide incorporation with the highest combination of efficiency and accuracy when the DNA substrate contains a single-nucleotide gap. Thus, Pol λ, like Pol β, is better suited to catalyze gap-filling DNA synthesis during short-patch BER in vivo, although, Pol λ may play a role in long-patch BER. PMID:20961817

Crystal Structures of Mite Allergens Der f 1 and Der p 1 Reveal Differences in Surface-Exposed Residues that May Influence Antibody Binding

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

Chruszcz, Maksymilian; Chapman, Martin D.; Vailes, Lisa D.

2009-12-01

The Group 1 mite allergens, Der f 1 and Der p 1, are potent allergens excreted by Dermatophagoides farinae and Dermatophagoides pteronyssinus, respectively. The human IgE antibody responses to the Group 1 allergens show more cross-reactivity than the murine IgG antibody responses which are largely species-specific. Here, we report the crystal structure of the mature form of Der f 1, which was isolated from its natural source, and a new, high-resolution structure of mature recombinant Der p 1. Unlike Der p 1, Der f 1 is monomeric both in the crystalline state and in solution. Moreover, no metal binding ismore » observed in the structure of Der f 1, despite the fact that all amino acids involved in Ca{sup 2+} binding in Der p 1 are completely conserved in Der f 1. Although Der p 1 and Der f 1 share extensive sequence identity, comparison of the crystal structures of both allergens revealed structural features which could explain the differences in murine and human IgE antibody responses to these allergens. There are structural differences between Der f 1 and Der p 1 which are unevenly distributed on the allergens' surfaces. This uneven spatial arrangement of conserved versus altered residues could explain both the specificity and cross-reactivity of antibodies against Der f 1 and Der p 1.« less

Werner Heisenberg zum 100. Geburtstag: Pionier der Quantenmechanik

NASA Astrophysics Data System (ADS)

Jacobi, Manfred

2001-11-01

Werner Heisenberg war eine der prägendsten Gestalten der Physik des 20. Jahrhunderts. Zu seinen wichtigsten Verdiensten gehören die Grundlegung der Quantenmechanik, die Formulierung der Unschärferelationen sowie die Beteiligung an der Ausarbeitung der Kopenhagener Deutung der Quantenmechanik. Darüber hinaus lieferte er Arbeiten von fundamentalem Charakter zur Theorie des Atomkerns, zur kosmischen Strahlung und zur Quantenfeldtheorie. Während des Krieges war er an den Arbeiten des Uranvereins beteiligt, der die Möglichkeit einer Entwicklung von Kernwaffen untersuchte, jedoch über Vorarbeiten zur Reaktorphysik nicht hinauskam. Wegen dieser Tätigkeit wurde er bei Kriegsende für einige Monate in England interniert. Nach seiner Rückkehr widmete er sich vor allem dem Aufbau der Physik in Deutschland, die während der NS-Zeit nahezu ihrer gesamten Substanz beraubt worden war.

Building damage assessment from PolSAR data using texture parameters of statistical model

NASA Astrophysics Data System (ADS)

Li, Linlin; Liu, Xiuguo; Chen, Qihao; Yang, Shuai

2018-04-01

Accurate building damage assessment is essential in providing decision support for disaster relief and reconstruction. Polarimetric synthetic aperture radar (PolSAR) has become one of the most effective means of building damage assessment, due to its all-day/all-weather ability and richer backscatter information of targets. However, intact buildings that are not parallel to the SAR flight pass (termed oriented buildings) and collapsed buildings share similar scattering mechanisms, both of which are dominated by volume scattering. This characteristic always leads to misjudgments between assessments of collapsed buildings and oriented buildings from PolSAR data. Because the collapsed buildings and the intact buildings (whether oriented or parallel buildings) have different textures, a novel building damage assessment method is proposed in this study to address this problem by introducing texture parameters of statistical models. First, the logarithms of the estimated texture parameters of different statistical models are taken as a new texture feature to describe the collapse of the buildings. Second, the collapsed buildings and intact buildings are distinguished using an appropriate threshold. Then, the building blocks are classified into three levels based on the building block collapse rate. Moreover, this paper also discusses the capability for performing damage assessment using texture parameters from different statistical models or using different estimators. The RADARSAT-2 and ALOS-1 PolSAR images are used to present and analyze the performance of the proposed method. The results show that using the texture parameters avoids the problem of confusing collapsed and oriented buildings and improves the assessment accuracy. The results assessed by using the K/G0 distribution texture parameters estimated based on the second moment obtain the highest extraction accuracies. For the RADARSAT-2 and ALOS-1 data, the overall accuracy (OA) for these three types of buildings is 73.39% and 68.45%, respectively.

Functional diversification of maize RNA polymerase IV and V subtypes via alternative catalytic subunits

DOE PAGES

Haag, Jeremy R.; Brower-Toland, Brent; Krieger, Elysia K.; ...

2014-10-02

Unlike nuclear multisubunit RNA polymerases I, II, and III, whose subunit compositions are conserved throughout eukaryotes, plant RNA polymerases IV and V are nonessential, Pol II-related enzymes whose subunit compositions are still evolving. Whereas Arabidopsis Pols IV and V differ from Pol II in four or five of their 12 subunits, respectively, and differ from one another in three subunits, proteomic analyses show that maize Pols IV and V differ from Pol II in six subunits but differ from each other only in their largest subunits. Use of alternative catalytic second subunits, which are nonredundant for development and paramutation, yieldsmore » at least two sub-types of Pol IV and three subtypes of Pol V in maize. Pol IV/Pol V associations with MOP1, RMR1, AGO121, Zm_DRD1/CHR127, SHH2a, and SHH2b extend parallels between paramutation in maize and the RNA-directed DNA methylation pathway in Arabidopsis.« less

Long non-coding RNA produced by RNA polymerase V determines boundaries of heterochromatin

PubMed Central

Böhmdorfer, Gudrun; Sethuraman, Shriya; Rowley, M Jordan; Krzyszton, Michal; Rothi, M Hafiz; Bouzit, Lilia; Wierzbicki, Andrzej T

2016-01-01

RNA-mediated transcriptional gene silencing is a conserved process where small RNAs target transposons and other sequences for repression by establishing chromatin modifications. A central element of this process are long non-coding RNAs (lncRNA), which in Arabidopsis thaliana are produced by a specialized RNA polymerase known as Pol V. Here we show that non-coding transcription by Pol V is controlled by preexisting chromatin modifications located within the transcribed regions. Most Pol V transcripts are associated with AGO4 but are not sliced by AGO4. Pol V-dependent DNA methylation is established on both strands of DNA and is tightly restricted to Pol V-transcribed regions. This indicates that chromatin modifications are established in close proximity to Pol V. Finally, Pol V transcription is preferentially enriched on edges of silenced transposable elements, where Pol V transcribes into TEs. We propose that Pol V may play an important role in the determination of heterochromatin boundaries. DOI: http://dx.doi.org/10.7554/eLife.19092.001 PMID:27779094

Bereits nach Ablauf der Halbwertszeit droht der vollständige Zerfall Die britische Atomic Scientists’ Association, die Ideologie der „objektiven” Wissenschaft und die H-Bombe

NASA Astrophysics Data System (ADS)

Laucht, Christoph

Präsident Harry Trumans Verlautbarung vom 31.1.1950, seine Regierung wolle die Entwicklung der Wasserstoffbombe vorantreiben, fand große Beachtung in den britischen Medien. Die illustrierte Zeitschrift Picture Post widmete der HBombe einen Artikel, der unter anderem kurze Stellungnahmen der britischen Atomwissenschaftler Eric Burhop, Kathleen Lonsdale, Harrie Massey, Rudolf Peierls und Maurice Pryce enthielt, die alle Mitglieder der Atomic Scientists' Association (ASA) waren.

Inhibition of DNA polymerase λ and associated inflammatory activities of extracts from steamed germinated soybeans.

PubMed

Mizushina, Yoshiyuki; Kuriyama, Isoko; Yoshida, Hiromi

2014-04-01

During the screening of selective DNA polymerase (pol) inhibitors from more than 50 plant food materials, we found that the extract from steamed germinated soybeans (Glycine max L.) inhibited human pol λ activity. Among the three processed soybean samples tested (boiled soybeans, steamed soybeans, and steamed germinated soybeans), both the hot water extract and organic solvent extract from the steamed germinated soybeans had the strongest pol λ inhibition. We previously isolated two glucosyl compounds, a cerebroside (glucosyl ceramide, AS-1-4, compound ) and a steroidal glycoside (eleutheroside A, compound ), from dried soybean, and these compounds were prevalent in the extracts of the steamed germinated soybeans as pol inhibitors. The hot water and organic solvent extracts of the steamed germinated soybeans and compounds and selectively inhibited the activity of eukaryotic pol λ in vitro but did not influence the activities of other eukaryotic pols, including those from the A-family (pol γ), B-family (pols α, δ, and ε), and Y-family (pols η, ι, and κ), and also showed no effect on the activity of pol β, which is of the same family (X) as pol λ. The tendency for in vitro pol λ inhibition by these extracts and compounds showed a positive correlation with the in vivo suppression of TPA (12-O-tetradecanoylphorbol-13-acetate)-induced inflammation in mouse ear. These results suggest that steamed germinated soybeans, especially the glucosyl compound components, may be useful for their anti-inflammatory properties.

An ATP-dependent ligase with substrate flexibility involved in assembly of the peptidyl nucleoside antibiotic polyoxin.

PubMed

Gong, Rong; Qi, Jianzhao; Wu, Pan; Cai, You-Sheng; Ma, Hongmin; Liu, Yang; Duan, He; Wang, Meng; Deng, Zixin; Price, Neil P J; Chen, Wenqing

2018-04-27

Polyoxin (POL) is an unusual peptidyl nucleoside antibiotic, in which peptidyl moiety and nucleoside skeleton are linked by an amide bond. However, their biosynthesis remains poorly understood. Here, we report the deciphering of PolG as an ATP-dependent ligase responsible for the assembly of POL. A polG mutant is capable of accumulating multiple intermediates, including the peptidyl moiety (carbamoylpolyoxamic acid, CPOAA) and the nucleosides skeletons (POL-C and the previously overlooked thymine POL-C). We further demonstrated that PolG employs an ATP-dependent mechanism for amide bond formation, and that the generation of the hybrid nucleoside antibiotic, POL-N, is also governed by PolG. Finally, we determined that the deduced ATP-binding sites are functionally essential for PolG, and that they are highly conserved in a number of related ATP-dependent ligases. These insights have allowed us proposed a catalytic mechanism for the assembly of peptidyl nucleoside antibiotic via an acyl-phosphate intermediate, and have opened the way for the combinatorial biosynthesis/pathway engineering of this group of nucleoside antibiotics. Importance POL is well known for its remarkable antifungal bioactivities and unusual structural features. Actually, elucidation of the POL assembly logic not only provides the enzymatic basis for further biosynthetic understanding of related peptidyl nucleoside antibiotics, but also contributes to the rational generation of more hybrid nucleoside antibiotics via synthetic biology strategy. Copyright © 2018 American Society for Microbiology.

Step-wise and lineage-specific diversification of plant RNA polymerase genes and origin of the largest plant-specific subunits.

PubMed

Wang, Yaqiong; Ma, Hong

2015-09-01

Proteins often function as complexes, yet little is known about the evolution of dissimilar subunits of complexes. DNA-directed RNA polymerases (RNAPs) are multisubunit complexes, with distinct eukaryotic types for different classes of transcripts. In addition to Pol I-III, common in eukaryotes, plants have Pol IV and V for epigenetic regulation. Some RNAP subunits are specific to one type, whereas other subunits are shared by multiple types. We have conducted extensive phylogenetic and sequence analyses, and have placed RNAP gene duplication events in land plant history, thereby reconstructing the subunit compositions of the novel RNAPs during land plant evolution. We found that Pol IV/V have experienced step-wise duplication and diversification of various subunits, with increasingly distinctive subunit compositions. Also, lineage-specific duplications have further increased RNAP complexity with distinct copies in different plant families and varying divergence for subunits of different RNAPs. Further, the largest subunits of Pol IV/V probably originated from a gene fusion in the ancestral land plants. We propose a framework of plant RNAP evolution, providing an excellent model for protein complex evolution. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Many-Body Interactions in Ice

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

Pham, C. Huy; Reddy, Sandeep K.; Chen, Karl

Many-body effects in ice are investigated through a systematic analysis of the lattice energies of several proton ordered and disordered phases, which are calculated with different flexible water models, ranging from pairwise additive (q-TIP4P/F) to polarizable (TTM3-F and AMOE-BA BA) and explicit many-body (MB-pol) potential energy functions. Comparisons with available experimental and diffusion Monte Carlo data emphasize the importance of an accurate description of the individual terms of the many-body expansion of the interaction energy between water molecules for the correct prediction of the energy ordering of the ice phases. Further analysis of the MB-pol results, in terms of fundamentalmore » energy contributions, demonstrates that the differences in lattice energies between different ice phases are sensitively dependent on the subtle balance between short-range two-body and three-body interactions, many-body induction, and dispersion energy. Here, by correctly reproducing many-body effects at both short range and long range, it is found that MB-pol accurately predicts the energetics of different ice phases, which provides further support for the accuracy of MB-pol in representing the properties of water from the gas to the condensed phase.« less

Many-Body Interactions in Ice

DOE PAGES

Pham, C. Huy; Reddy, Sandeep K.; Chen, Karl; ...

2017-02-28

Many-body effects in ice are investigated through a systematic analysis of the lattice energies of several proton ordered and disordered phases, which are calculated with different flexible water models, ranging from pairwise additive (q-TIP4P/F) to polarizable (TTM3-F and AMOE-BA BA) and explicit many-body (MB-pol) potential energy functions. Comparisons with available experimental and diffusion Monte Carlo data emphasize the importance of an accurate description of the individual terms of the many-body expansion of the interaction energy between water molecules for the correct prediction of the energy ordering of the ice phases. Further analysis of the MB-pol results, in terms of fundamentalmore » energy contributions, demonstrates that the differences in lattice energies between different ice phases are sensitively dependent on the subtle balance between short-range two-body and three-body interactions, many-body induction, and dispersion energy. Here, by correctly reproducing many-body effects at both short range and long range, it is found that MB-pol accurately predicts the energetics of different ice phases, which provides further support for the accuracy of MB-pol in representing the properties of water from the gas to the condensed phase.« less

Geology of ultra-high-pressure rocks from the Dabie Shan, Eastern China

NASA Astrophysics Data System (ADS)

Schmid, Robert

2001-02-01

A multidisciplinary study has been carried out to contribute to the understanding of the geologic evolution of the largest known occurrence of ultra-high-pressure (UHP) rocks on Earth, the Dabie Shan of eastern China. Geophysical data, collected along a ca. 20 km E-W trending seismic line in the eastern Dabie Shan, indicate that the crust comprises three layers. The upper crust has a homogeneously low reflectivity and exhibits roughly subhorizontal reflectors down to ca. 15 km. It is therefore interpreted to portray a crustal UHP slab thrust over non-UHP crust. An aprubt change in intensity and geometry of observed reflectors marks the boundary of a mid- to lower crustal zone which is present down to ca. 33 km. This crustal zone likely represents cratonal Yangtze crust that was unaffected by the Triassic UHP event and which has acted as the footwall during exhumation of the crustal wedge. Strong and continuous reflectors occurring at ca. 33-40 km depth most likely trace the Moho at the base of the crust. Any trace of a crustal root, that may have formed in response to collision tectonics, is therefore not preserved. A shollow tomographic velocity modell based on inversion of the first arrivals is constructed additionally. This model clearly images the distinct lithologies on both sides of the Tan Lu fault. Sediments to the east exhibit velocities of about 3.4 - 5.0 km* s^-1, whereas the gneisses have 5.2 - 6.0 km*s^-1. Geometry of velocity isolines may trace the structures present in the rocks. Thus the sediments dip shallowly towards the fault, whereas isoclinal folds are imaged to occur in the gneisses. Field data from the UHP unit of the Dabie Shan enables definition of basement-cover sequences that represent sections of the former passive margin of the Yangtze craton. One of the cover sequences, the Changpu unit, still displays a stratigraphic contact with basement gneisses, while the other, the Ganghe unit, includes no relative basement exposure. The latter unit is in tectonic contact with the basement of the former unit via a greenschist-facies blastomylonite. The Changpu unit is chiefly constituted by calc-arenitic metasediments intercalated with meta-basalts, whereas the Ganghe unit contains arenitic-volcanoclastic metasediments that are likewise associated with meta-basalts. The basement comprises a variety of felsic gneisses, ranging from preserved eclogitic- to greenschist-facies paragenesis, and locally contains mafic-ultramafic meta-plutons in addition to minor basaltic rocks. Metabasites of all lithologies are eclogite-facies or are retrogressed equivalents, which, with the exception of those from the Ganghe unit, bear coesite and thus testify to an UHP metamorphic overprint. Mineral chemistry of the analysed samples reveal large compositional variations among the main minerals, i.e. garnet and omphacite, indicating either distinct protoliths or different degrees of interaction with their host-rocks. Contents of ferric iron in low Fetot omphacites are determined by wet chemical titration and found to be rather high, i.e. 30-40 %. However, a even more conservative estimate of 50% is applied in the corresponding calculations, in order to be comparable with previous studies. Textural constraints and compositional zonation pattern are compatible with equilibrium conditions during peak metamorphism followed by a retrogressive overprint. P-T data are calculated with special focus on the application of the garnet-omphacite-phengite barometer, combined with Fe-Mg exchange thermometers. Maximum pressures range from 42-48 kbar (for the Changpu unit) to ~37 kbar (for the Ganghe unit and basement rocks). Temperatures during the eclogite metamorphism reached ca. 750 °C. Although the sample suite reveals variable peak-pressures, temperatures are in reasonable agreement. Pressure differences are interpreted to be due to strongly Ca-dominated garnet (up to 50 mol % grossular in the Changpu unit) and modification of peak-compositions during retrogressive metamorphism. The integrated geological data presented in this thesis allow it to be concluded that, i) basement and cover rocks are present in the Dabie Shan and both experienced UHP conditions ii) the Dabie Shan is the metamorphic equivalent of the former passive margin of the Yangtze craton iii) felsic gneisses undergoing UHP metamorphism are affected by volume changes due to phase transitions (qtz coe), which directly influence the tectono-metamorphic processes iv) initial differences in temperature may account for the general lack of lower crustal rocks in UHP-facies Um das Verständnis der geologischen Entwicklung des größten bekannten Vorkommens von ultra-hochdruck (UHP) Gesteinen auf der Erde, des Dabie Shan im östlichen China, zu erhöhen, wurde eine multidisziplinäre Studie durchgeführt. Geophysikalische Daten wurden entlang einer ca. 20 km langen seismischen Linie im östlichen Dabie Shan gesammelt. Diese reflektionsseismischen Daten zeigen, dass die Kruste aus drei Lagen besteht. Die Oberkruste besitzt eine durchgehend niedrige Reflektivität und meist subhorizontale Reflektoren bis in eine Tiefe von ca. 15 km. Aufgrund dieser Charakteristika wird diese Zone als UHP-bezogener krustaler Keil interpretiert, der auf nicht UHP Kruste überschoben wurde. Ein abrupter Wechsel in der Geometrie aber auch Intensität der Reflektoren markiert die Grenze zu einer mittel- bis unterkrustalen Zone, die sich bis ca. 33 km Tiefe erstreckt. Diese Zone repräsentiert wahrscheinlich kratonale Yangtze Kruste, die von der triassischen UHP-Orogenese nicht erfasst wurde, aber während der Exhumierung das Liegende relativ zum UHP Keil war. Starke und kontinuierliche Reflektoren im Tiefenintervall von 33-40 km bilden höchstwahrscheinlich die Moho an der Basis der Kruste ab. Relikte einer Krustenwurzel, die sich wahrscheinlich während der Kollisionstektonik gebildet hatte, sind nicht sichtbar. Ein flaches tomographisches Geschwindigkeitsmodell, das auf der Inversion der Ersteinsätze gründet, konnte zusätzlich erstellt werden. Dieses Modell bildet deutlich die unterschiedlichen Lithologien auf beiden Seiten der Tan Lu Störung ab. Sedimente östlich der Störung zeigen Geschwindigkeiten von 3.4 - 5.0 km* s^-1, wohingegen die Gneise im Westen 5.2 - 6.0 km*s^-1 aufweisen. Die Geometrie der Geschwindigkeits-Isolinien kann als Ausdruck der Strukturen der Gesteine angenommen werden. Somit zeigen die Sedimente ein nordwestliches Einfallen zur Störung hin, wohingegen isoklinale Falten in den Gneisen abgebildet werden. Geländedaten aus der UHP Einheit des Dabie Shan ermöglichen die Definition von Grundgebirgs- und Deckeinheiten, die Teile des ehemaligen passiven Kontinentalrandes des Yangtze Kratons repräsentieren. Eine der Deckeinheiten, die Changpu Einheit, besitzt nach wie vor einen stratigraphischen Kontakt zu den Grundgebirgs-Gneisen. Der anderen Einheit hingegen, der Ganghe Einheit, fehlt ein entsprechendes Grundgebirge. Diese Einheit steht vielmehr über einen Blasto-Mylonit in tektonischem Kontakt zum Grundgebirge der vorherigen. Die Changpu Einheit baut sich aus kalk-arenitischen Metasedimenten auf, die mit Metabasalten assoziiert sind. Die Ganghe Einheit wird von arenitisch-vulkanoklastischen Metasedimenten, die ebenfalls mit metabasaltischen Gesteinen vergesellschaftet sind, dominiert. Das Grundgebirge baut sich aus diversen felsischen Gneisen auf, die von reliktisch eklogitfaziell bis grünschieferfaziell ausgeprägt sind, und in denen, zusätzlich zu Metabasalten, sporadisch mafisch-ultramafische Meta-Plutone auftreten. Mit Ausnahme der Ganghe Einheit, führen die Metabasite Coesit und belegen somit das UHP Ereignis. Die Mineralchemie der analysierten Proben dokumentiert deutliche Variationen in der Zusammensetzung der Hauptminerale, Granat und Omphazit, was entweder unterschiedliche Protolithe oder unterschiedliche Grade von Stoffaustausch mit den Wirtsgesteinen reflektiert. Gehalte von dreiwertigem Eisen in Omphaziten mit geringen Gesamteisengehalten, wurden mittels Titration bestimmt, wobei sich Werte von 30-40 % ergaben. Dennoch wurde ein noch konservativerer Wert von 50% dreiwertigem Eisen in den entsprechenden Berechnungen angenommen, hauptsächlich, um mit anderen Arbeiten vergleichbar zu sein. Texturen und chemische Zonierungen in den Mineralen sind kompatibel mit Gleichgewichtsbedingungen während dem Höhepunkt der Metamorphose, der retrograd überprägt wird. P-T Daten wurden mit deutlicher Betonung auf das Granat-Omphazit-Phengit Barometer, das mit Fe-Mg Austausch-Thermometern kombiniert wurde, berechnet. Höchstdrucke reichen von 42-48 kbar (für die Changpu Einheit) bis ca. 37 kbar (für das Grundgebirge und die Ganghe Einheit). Während der eklogitfaziellen Metamorphose wurden Temperaturen von ca. 750 °C erreicht. Obwohl die maximalen Drucke deutlich schwanken, sind die Temperaturbestimmungen in guter Übereinstimmung. Die Druckschwankungen können zum einen durch deutlich Ca-dominierte Granate (bis zu 50 mol% Grossular in der Changpu Einheit) und/oder zum anderen durch Modifikationen der Mineralzusammensetzungen während der retrograden Metamorphose erklärt werden. Die präsentierten integrativen geologischen Daten ermöglichen die folgenden Schlussfolgerungen i) Grundgebirgs- und Deckeinheiten treten im Dabie Shan auf und wurden beide UHP metamorph überprägt ii) Der Dabie Shan ist das metamorphe Äquivalent des früheren passiven Kontinentalrandes des Yangtze Kratons iii) felsische Gneise, die eine UHP Metamorphose durchlaufen, sind von Volumenver-änderungen betroffen, die durch großräumige Phasenumwandlungen (Quarz Coesit) hervorgerufen werden, was direkt die tektono-metamorphen Prozesse beeinflusst iv) Initiale Unterschiede in der Temperatur sind möglicherweise dafür verantwortlich, dass generell Unterkrustengesteine in UHP Fazies fehlen

Einstellung und Wissen von Lehramtsstudierenden zur Evolution - ein Vergleich zwischen Deutschland und der Türkei

NASA Astrophysics Data System (ADS)

Graf, Dittmar; Soran, Haluk

Es wird eine Untersuchung vorgestellt, in der Wissen und Überzeugungen von Lehramtsstudierenden aller Fächer zum Thema Evolution an zwei Universitäten in Deutschland und der Türkei erhoben worden sind. Die Befragung wurde in Dortmund und in Ankara durchgeführt. Es stellte sich heraus, dass ausgeprägte Defizite im Verständnis der Evolutionsmechanismen herrschen. Viele Studierende, insbesondere aus der Türkei, sind nicht von der Faktizität der Evolution überzeugt. Dies gilt sowohl für Studierende mit Fach Biologie als auch für Studierende mit anderen Fächern. Näher untersucht worden sind die Faktoren, die die Überzeugungen zur Evolution beeinflussen können, was ja in Anbetracht der hohen Ablehnungsrate der Evolution von besonderem Interesse ist. Das Vertrauen in die Wissenschaft spielt hierbei eine besondere Rolle: Wer der Wissenschaft vertraut, ist auch eher von der Evolution überzeugt, als diejenigen, die skeptisch gegenüber der Wissenschaft sind.

NATO NEC C2 Maturity Model

DTIC Science & Technology

2010-02-01

Academy of the United Kingdom Petra Eggenhofer Germany Universität der Bundeswehr München, Germany Fred van Ettinger Ne herlands C2 Centre of Excellence...C2 Centre of Excellence Jose Martins Portugal Military Academy, Portugal Jimmie McEver USA Evidence Based Research, Inc. Allen Murashige USA HQ USAF...integrating the results from the disparate case studies undertaken to validate the N2C2M2. Ms. Petra Eggenhofer from the Universität der Bundeswehr München

Problems of low-parameter equations of state

NASA Astrophysics Data System (ADS)

Petrik, G. G.

2017-11-01

The paper focuses on the system approach to problems of low-parametric equations of state (EOS). It is a continuation of the investigations in the field of substantiated prognosis of properties on two levels, molecular and thermodynamic. Two sets of low-parameter EOS have been considered based on two very simple molecular-level models. The first one consists of EOS of van der Waals type (a modification of van der Waals EOS proposed for spheres). The main problem of these EOS is a weak connection with the micro-level, which raise many uncertainties. The second group of EOS has been derived by the author independently of the ideas of van der Waals based on the model of interacting point centers (IPC). All the parameters of the EOS have a meaning and are associated with the manifestation of attractive and repulsive forces. The relationship between them is found to be the control parameter of the thermodynamic level. In this case, EOS IPC passes into a one-parameter family. It is shown that many EOS of vdW-type can be included in the framework of the PC model. Simultaneously, all their parameters acquire a physical meaning.

Nucleosome Positioning and NDR Structure at RNA Polymerase III Promoters

NASA Astrophysics Data System (ADS)

Helbo, Alexandra Søgaard; Lay, Fides D.; Jones, Peter A.; Liang, Gangning; Grønbæk, Kirsten

2017-02-01

Chromatin is structurally involved in the transcriptional regulation of all genes. While the nucleosome positioning at RNA polymerase II (pol II) promoters has been extensively studied, less is known about the chromatin structure at pol III promoters in human cells. We use a high-resolution analysis to show substantial differences in chromatin structure of pol II and pol III promoters, and between subtypes of pol III genes. Notably, the nucleosome depleted region at the transcription start site of pol III genes extends past the termination sequences, resulting in nucleosome free gene bodies. The +1 nucleosome is located further downstream than at pol II genes and furthermore displays weak positioning. The variable position of the +1 location is seen not only within individual cell populations and between cell types, but also between different pol III promoter subtypes, suggesting that the +1 nucleosome may be involved in the transcriptional regulation of pol III genes. We find that expression and DNA methylation patterns correlate with distinct accessibility patterns, where DNA methylation associates with the silencing and inaccessibility at promoters. Taken together, this study provides the first high-resolution map of nucleosome positioning and occupancy at human pol III promoters at specific loci and genome wide.

Kinetic Analysis of the Bypass of a Bulky DNA Lesion Catalyzed by Human Y-family DNA Polymerases

PubMed Central

Sherrer, Shanen M.; Sanman, Laura E.; Xia, Cynthia X.; Bolin, Eric R.; Malik, Chanchal K.; Efthimiopoulos, Georgia; Basu, Ashis K.; Suo, Zucai

2012-01-01

1-Nitropyrene (1-NP), a mutagen and potential carcinogen, is the most abundant nitro polyaromatic hydrocarbon in diesel exhaust, which reacts with DNA to form predominantly N-(deoxyguanosin-8-yl)-1-aminopyrene (dGAP). If not repaired, this DNA lesion is presumably bypassed in vivo by any of human Y-family DNA polymerases kappa (hPolκ), iota (hPolτ), eta (hPolη), and Rev1 (hRev1). Our running start assays demonstrated that each of these enzymes was indeed capable of traversing a site-specifically placed dGAP on a synthetic DNA template but hRev1 was stopped after lesion bypass. The time required to bypass 50% of the dGAP sites (t50bypass ) encountered by hPolη, hPolκ and hPolτ was determined to be 2.5 s, 4.1 s, and 106.5 s, respectively. The efficiency order of catalyzing translesion synthesis of dGAP (hPolη > hPolκ > hPolτ >> hRev1) is the same as the order for these human Y-family enzymes to elongate undamaged DNA. Although hPolη bypassed dGAP efficiently, replication by both hPolκ and hPolτ was strongly stalled at the lesion site and at a site immediately downstream from dGAP. By employing pre-steady state kinetic methods, a kinetic basis was established for polymerase pausing at these DNA template sites. Besides efficiency of bypass, the fidelity of those low-fidelity polymerases at these pause sites was also significantly decreased. Thus, if the translesion DNA synthesis of dGAP in vivo is catalyzed by a human Y-family DNA polymerase, e.g. hPolη, the process is certainly mutagenic. PMID:22324639

Parp1 activation in mouse embryonic fibroblasts promotes Pol β-dependent cellular hypersensitivity to alkylation damage

PubMed Central

Jelezcova, Elena; Trivedi, Ram N.; Wang, Xiao-hong; Tang, Jiang-bo; Brown, Ashley R.; Goellner, Eva M.; Schamus, Sandy; Fornsaglio, Jamie L.; Sobol, Robert W.

2010-01-01

Alkylating agents induce cell death in wild-type (WT) mouse embryonic fibroblasts (MEFs) by multiple mechanisms, including apoptosis, autophagy and necrosis. DNA polymerase β (Pol β) knockout (KO) MEFs are hypersensitive to the cytotoxic effect of alkylating agents, as compared to WT MEFs. To test the hypothesis that Parp1 is preferentially activated by methyl methanesulfonate (MMS) exposure of Pol β KO MEFs, we have examined the relationship between Pol β expression, Parp1 activation and cell survival following MMS exposure in a series of WT and Pol β deficient MEF cell lines. Consistent with our hypothesis, we observed elevated Parp1 activation in Pol β KO MEFs as compared to matched WT MEFs. Both the MMS-induced activation of Parp1 and the MMS-induced cytoxicity of Pol β KO MEFs are attenuated by pre-treatment with the Parp1/Parp2 inhibitor PJ34. Further, elevated Parp1 activation is observed following knockdown (KD) of endogenous Pol β, as compared to WT cells. Pol β KD MEFs are hypersensitive to MMS and both the MMS-induced hypersensitivity and Parp1 activation is prevented by pre-treatment with PJ34. In addition, the MMS-induced cellular sensitivity of Pol β KO MEFs is reversed when Parp1 is also deleted (Pol β/Parp1 double KO MEFs) and we observe no MMS sensitivity differential between Pol β/Parp1 double KO MEFs and those that express recombinant mouse Pol β. These studies suggest that Parp1 may function as a sensor of BER to initiate cell death when BER is aborted or fails. Parp1 may therefore function in BER as a tumor suppressor by initiating cell death and preventing the accumulation of cells with chromosomal damage due to a BER defect. PMID:20096707

RNA polymerase III mutants in TFIIFα-like C37 that cause terminator readthrough with no decrease in transcription output

PubMed Central

Rijal, Keshab; Maraia, Richard J.

2013-01-01

How eukaryotic RNA polymerases switch from elongation to termination is unknown. Pol III subunits Rpc53 and Rpc37 (C53/37) form a heterodimer homologous to TFIIFβ/α. C53/37 promotes efficient termination and together with C11 also mediates pol III recycling in vitro. We previously developed Schizosaccharomyces pombe strains that report on two pol III termination activities: RNA oligo(U) 3′-end cleavage, and terminator readthrough. We randomly mutagenized C53 and C37 and isolated many C37 mutants with terminator readthrough but no comparable C53 mutants. The majority of C37 mutants have strong phenotypes with up to 40% readthrough and map to a C-terminal tract previously localized near Rpc2p in the pol III active center while a minority represent a distinct class with weaker phenotype, less readthrough and 3′-oligo(U) lengthening. Nascent pre-tRNAs released from a terminator by C37 mutants have shorter 3′-oligo(U) tracts than in cleavage-deficient C11 double mutants indicating RNA 3′-end cleavage during termination. We asked whether termination deficiency affects transcription output in the mutants in vivo both by monitoring intron-containing nascent transcript levels and 14C-uridine incorporation. Surprisingly, multiple termination mutants have no decrease in transcript output relative to controls. These data are discussed in context of current models of pol III transcription. PMID:23093604

Characterization of human translesion DNA synthesis across a UV-induced DNA lesion

PubMed Central

Hedglin, Mark; Pandey, Binod; Benkovic, Stephen J

2016-01-01

Translesion DNA synthesis (TLS) during S-phase uses specialized TLS DNA polymerases to replicate a DNA lesion, allowing stringent DNA synthesis to resume beyond the offending damage. Human TLS involves the conjugation of ubiquitin to PCNA clamps encircling damaged DNA and the role of this post-translational modification is under scrutiny. A widely-accepted model purports that ubiquitinated PCNA recruits TLS polymerases such as pol η to sites of DNA damage where they may also displace a blocked replicative polymerase. We provide extensive quantitative evidence that the binding of pol η to PCNA and the ensuing TLS are both independent of PCNA ubiquitination. Rather, the unique properties of pols η and δ are attuned to promote an efficient and passive exchange of polymerases during TLS on the lagging strand. DOI: http://dx.doi.org/10.7554/eLife.19788.001 PMID:27770570

a Method of Time-Series Change Detection Using Full Polsar Images from Different Sensors

NASA Astrophysics Data System (ADS)

Liu, W.; Yang, J.; Zhao, J.; Shi, H.; Yang, L.

2018-04-01

Most of the existing change detection methods using full polarimetric synthetic aperture radar (PolSAR) are limited to detecting change between two points in time. In this paper, a novel method was proposed to detect the change based on time-series data from different sensors. Firstly, the overall difference image of a time-series PolSAR was calculated by ominous statistic test. Secondly, difference images between any two images in different times ware acquired by Rj statistic test. Generalized Gaussian mixture model (GGMM) was used to obtain time-series change detection maps in the last step for the proposed method. To verify the effectiveness of the proposed method, we carried out the experiment of change detection by using the time-series PolSAR images acquired by Radarsat-2 and Gaofen-3 over the city of Wuhan, in China. Results show that the proposed method can detect the time-series change from different sensors.

A switch between DNA polymerases δ and λ promotes error-free bypass of 8-oxo-G lesions

PubMed Central

Markkanen, Enni; Castrec, Benoît; Villani, Giuseppe; Hübscher, Ulrich

2012-01-01

7,8-Dihydro-8-oxoguanine (8-oxo-G) is a highly abundant and mutagenic lesion. Replicative DNA polymerases (pols) are slowed down at 8-oxo-G and insert both correct cytosine (C) and incorrect adenine (A) opposite 8-oxo-G, but they preferentially extend A:8-oxo-G mispairs. Nevertheless, 8-oxo-G bypass is fairly accurate in vivo. Thus, the question how correct bypass of 8-oxo-G lesions is accomplished despite the poor extension of C:8-oxo-G base pairs by replicative pols remains unanswered. Here we show that replicative pol δ pauses in front of 8-oxo-G and displays difficulties extending from correct C:8-oxo-G in contrast to extension from incorrect A:8-oxo-G. This leads to stalling of pol δ at 8-oxo-G after incorporation of correct C. This stalling at C:8-oxo-G can be overcome by a switch from pol δ to pols λ, β, or η, all of which are able to assist pol δ in 8-oxo-G bypass by translesion synthesis (TLS). Importantly, however, only pol λ selectively catalyzes the correct TLS past 8-oxo-G, whereas pols β and η show no selectivity and even preferentially enhance incorrect TLS. The selectivity of pol λ to promote the correct bypass depends on its N-terminal domain. Furthermore, pol λ−/− mouse embryonic fibroblast extracts display reduced 8-oxo-G TLS. Finally, the correct bypass of 8-oxo-G in gapped plasmids in mouse embryonic fibroblasts and HeLa cells is promoted in the presence of pol λ. Our findings suggest that even though 8-oxo-G is not a blocking lesion per se, correct replication over 8-oxo-G is promoted by a pol switch between pols δ and λ. PMID:23175785

A model to estimate the size of nanoparticle agglomerates in gas-solid fluidized beds

NASA Astrophysics Data System (ADS)

de Martín, Lilian; van Ommen, J. Ruud

2013-11-01

The estimation of nanoparticle agglomerates' size in fluidized beds remains an open challenge, mainly due to the difficulty of characterizing the inter-agglomerate van der Waals force. The current approach is to describe micron-sized nanoparticle agglomerates as micron-sized particles with 0.1-0.2-μm asperities. This simplification does not capture the influence of the particle size on the van der Waals attraction between agglomerates. In this paper, we propose a new description where the agglomerates are micron-sized particles with nanoparticles on the surface, acting as asperities. As opposed to previous models, here the van der Waals force between agglomerates decreases with an increase in the particle size. We have also included an additional force due to the hydrogen bond formation between the surfaces of hydrophilic and dry nanoparticles. The average size of the fluidized agglomerates has been estimated equating the attractive force obtained from this method to the weight of the individual agglomerates. The results have been compared to 54 experimental values, most of them collected from the literature. Our model approximates without a systematic error the size of most of the nanopowders, both in conventional and centrifugal fluidized beds, outperforming current models. Although simple, the model is able to capture the influence of the nanoparticle size, particle density, and Hamaker coefficient on the inter-agglomerate forces.

Each Monomer of the Dimeric Accessory Protein for Human Mitochondrial DNA Polymerase Has a Distinct Role in Conferring Processivity*

PubMed Central

Lee, Young-Sam; Lee, Sujin; Demeler, Borries; Molineux, Ian J.; Johnson, Kenneth A.; Yin, Y. Whitney

2010-01-01

The accessory protein polymerase (pol) γB of the human mitochondrial DNA polymerase stimulates the synthetic activity of the catalytic subunit. pol γB functions by both accelerating the polymerization rate and enhancing polymerase-DNA interaction, thereby distinguishing itself from the accessory subunits of other DNA polymerases. The molecular basis for the unique functions of human pol γB lies in its dimeric structure, where the pol γB monomer proximal to pol γA in the holoenzyme strengthens the interaction with DNA, and the distal pol γB monomer accelerates the reaction rate. We further show that human pol γB exhibits a catalytic subunit- and substrate DNA-dependent dimerization. By duplicating the monomeric pol γB of lower eukaryotes, the dimeric mammalian proteins confer additional processivity to the holoenzyme polymerase. PMID:19858216

Zusammenarbeit aus Sicht eines outgesourcten Instandhalters

NASA Astrophysics Data System (ADS)

Grüßer, Stefan; Loeven, Heinz-Wilhelm

Dauerhafter Unternehmenserfolg ist nur mit einer fortschrittlichen Instandhaltung zu erzielen. Durch den enormen Kostendruck infolge der Globalisierung und die Innovationssprünge auf der technischen Seite wird auch die Frage nach der modernen Organisationsform für die Instandhaltung gestellt. Eine Möglichkeit der Kostenoptimierung ist das Outsourcing von Instandhaltungsleistungen. Hierbei ist es unerlässlich, dass sich die Mitarbeiter zum Dienstleister entwickeln. In diesem Beitrag wird die Entwicklung der InfraServ Knapsack von einer internen Instandhaltungsabteilung hin zu einem Industriellen Dienstleister beschrieben und Aspekte der Zusammenarbeit mit externen Kunden aus der Sicht des outgesourcten Instandhalters geschildert. Es werden die wichtigen Entwicklungsschritte zur Dienstleistungsorientierung der früheren Eigeninstandhaltung aufgezeigt. Dieser Beitrag ist nicht als "Königsweg“ zu verstehen, er soll vielmehr anhand der Erfahrungen einer outgesourcten Eigeninstandhaltung Anregungen für die Entwicklung der eigenen Instandhaltungsorganisation liefern.

Optimizing Power–Frequency Droop Characteristics of Distributed Energy Resources

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

Guggilam, Swaroop S.; Zhao, Changhong; Dall Anese, Emiliano

This paper outlines a procedure to design power-frequency droop slopes for distributed energy resources (DERs) installed in distribution networks to optimally participate in primary frequency response. In particular, the droop slopes are engineered such that DERs respond in proportion to their power ratings and they are not unfairly penalized in power provisioning based on their location in the distribution network. The main contribution of our approach is that a guaranteed level of frequency regulation can be guaranteed at the feeder head, while ensuring that the outputs of individual DERs conform to some well-defined notion of fairness. The approach we adoptmore » leverages an optimization-based perspective and suitable linearizations of the power-flow equations to embed notions of fairness and information regarding the physics of the power flows within the distribution network into the droop slopes. Time-domain simulations from a differential algebraic equation model of the 39-bus New England test-case system augmented with three instances of the IEEE 37-node distribution-network with frequency-sensitive DERs are provided to validate our approach.« less

Brain-derived neurotrophic factor as a regulator of systemic and brain energy metabolism and cardiovascular health

PubMed Central

Rothman, Sarah M; Griffioen, Kathleen J; Wan, Ruiqian; Mattson, Mark P

2012-01-01

Overweight sedentary individuals are at increased risk for cardiovascular disease, diabetes, and some neurological disorders. Beneficial effects of dietary energy restriction (DER) and exercise on brain structural plasticity and behaviors have been demonstrated in animal models of aging and acute (stroke and trauma) and chronic (Alzheimer's and Parkinson's diseases) neurological disorders. The findings described later, and evolutionary considerations, suggest brain-derived neurotrophic factor (BDNF) plays a critical role in the integration and optimization of behavioral and metabolic responses to environments with limited energy resources and intense competition. In particular, BDNF signaling mediates adaptive responses of the central, autonomic, and peripheral nervous systems from exercise and DER. In the hypothalamus, BDNF inhibits food intake and increases energy expenditure. By promoting synaptic plasticity and neurogenesis in the hippocampus, BDNF mediates exercise- and DER-induced improvements in cognitive function and neuroprotection. DER improves cardiovascular stress adaptation by a mechanism involving enhancement of brainstem cholinergic activity. Collectively, findings reviewed in this paper provide a rationale for targeting BDNF signaling for novel therapeutic interventions in a range of metabolic and neurological disorders. PMID:22548651

Isotope engineering of van der Waals interactions in hexagonal boron nitride

NASA Astrophysics Data System (ADS)

Vuong, T. Q. P.; Liu, S.; van der Lee, A.; Cuscó, R.; Artús, L.; Michel, T.; Valvin, P.; Edgar, J. H.; Cassabois, G.; Gil, B.

2018-02-01

Hexagonal boron nitride is a model lamellar compound where weak, non-local van der Waals interactions ensure the vertical stacking of two-dimensional honeycomb lattices made of strongly bound boron and nitrogen atoms. We study the isotope engineering of lamellar compounds by synthesizing hexagonal boron nitride crystals with nearly pure boron isotopes (10B and 11B) compared to those with the natural distribution of boron (20 at% 10B and 80 at% 11B). On the one hand, as with standard semiconductors, both the phonon energy and electronic bandgap varied with the boron isotope mass, the latter due to the quantum effect of zero-point renormalization. On the other hand, temperature-dependent experiments focusing on the shear and breathing motions of adjacent layers revealed the specificity of isotope engineering in a layered material, with a modification of the van der Waals interactions upon isotope purification. The electron density distribution is more diffuse between adjacent layers in 10BN than in 11BN crystals. Our results open perspectives in understanding and controlling van der Waals bonding in layered materials.

Isotope engineering of van der Waals interactions in hexagonal boron nitride.

PubMed

Vuong, T Q P; Liu, S; Van der Lee, A; Cuscó, R; Artús, L; Michel, T; Valvin, P; Edgar, J H; Cassabois, G; Gil, B

2018-02-01

Hexagonal boron nitride is a model lamellar compound where weak, non-local van der Waals interactions ensure the vertical stacking of two-dimensional honeycomb lattices made of strongly bound boron and nitrogen atoms. We study the isotope engineering of lamellar compounds by synthesizing hexagonal boron nitride crystals with nearly pure boron isotopes ( 10 B and 11 B) compared to those with the natural distribution of boron (20 at% 10 B and 80 at% 11 B). On the one hand, as with standard semiconductors, both the phonon energy and electronic bandgap varied with the boron isotope mass, the latter due to the quantum effect of zero-point renormalization. On the other hand, temperature-dependent experiments focusing on the shear and breathing motions of adjacent layers revealed the specificity of isotope engineering in a layered material, with a modification of the van der Waals interactions upon isotope purification. The electron density distribution is more diffuse between adjacent layers in 10 BN than in 11 BN crystals. Our results open perspectives in understanding and controlling van der Waals bonding in layered materials.

Interplay of activation kinetics and the derivative conductance determines resonance properties of neurons

NASA Astrophysics Data System (ADS)

Pena, Rodrigo F. O.; Ceballos, Cesar C.; Lima, Vinicius; Roque, Antonio C.

2018-04-01

In a neuron with hyperpolarization activated current (Ih), the correct input frequency leads to an enhancement of the output response. This behavior is known as resonance and is well described by the neuronal impedance. In a simple neuron model we derive equations for the neuron's resonance and we link its frequency and existence with the biophysical properties of Ih. For a small voltage change, the component of the ratio of current change to voltage change (d I /d V ) due to the voltage-dependent conductance change (d g /d V ) is known as derivative conductance (GhDer). We show that both GhDer and the current activation kinetics (characterized by the activation time constant τh) are mainly responsible for controlling the frequency and existence of resonance. The increment of both factors (GhDer and τh) greatly contributes to the appearance of resonance. We also demonstrate that resonance is voltage dependent due to the voltage dependence of GhDer. Our results have important implications and can be used to predict and explain resonance properties of neurons with the Ih current.

Heterologous Expression of Der Homologs in an Escherichia coli der Mutant and Their Functional Complementation

PubMed Central

Choi, Eunsil; Kang, Nalae; Jeon, Young; Pai, Hyun-Sook

2016-01-01

ABSTRACT The unique Escherichia coli GTPase Der (double Era-like GTPase), which contains tandemly repeated GTP-binding domains, has been shown to play an essential role in 50S ribosomal subunit biogenesis. The depletion of Der results in the accumulation of precursors of 50S ribosomal subunits that are structurally unstable at low Mg2+ concentrations. Der homologs are ubiquitously found in eubacteria. Conversely, very few are conserved in eukaryotes, and none is conserved in archaea. In the present study, to verify their conserved role in bacterial 50S ribosomal subunit biogenesis, we cloned Der homologs from two gammaproteobacteria, Klebsiella pneumoniae and Salmonella enterica serovar Typhimurium; two pathogenic bacteria, Staphylococcus aureus and Neisseria gonorrhoeae; and the extremophile Deinococcus radiodurans and then evaluated whether they could functionally complement the E. coli der-null phenotype. Only K. pneumoniae and S. Typhimurium Der proteins enabled the E. coli der-null strain to grow under nonpermissive conditions. Sucrose density gradient experiments revealed that the expression of K. pneumoniae and S. Typhimurium Der proteins rescued the structural instability of 50S ribosomal subunits, which was caused by E. coli Der depletion. To determine what allows their complementation, we constructed Der chimeras. We found that only Der chimeras harboring both the linker and long C-terminal regions could reverse the growth defects of the der-null strain. Our findings suggest that ubiquitously conserved essential GTPase Der is involved in 50S ribosomal subunit biosynthesis in various bacteria and that the linker and C-terminal regions may participate in species-specific recognition or interaction with the 50S ribosomal subunit. IMPORTANCE In Escherichia coli, Der (double Era-like GTPase) is an essential GTPase that is important for the production of mature 50S ribosomal subunits. However, to date, its precise role in ribosome biogenesis has not been clarified. In this study, we used five Der homologs from gammaproteobacteria, pathogenic bacteria, and an extremophile to elucidate their conserved function in 50S ribosomal subunit biogenesis. Among them, Klebsiella pneumoniae and Salmonella enterica serovar Typhimurium Der homologs implicated the participation of Der in ribosome assembly in E. coli. Our results show that the linker and C-terminal regions of Der homologs are correlated with its functional complementation in E. coli der mutants, suggesting that they are involved in species-specific recognition or interaction with 50S ribosomal subunits. PMID:27297882

Structure-based design and screening of inhibitors for an essential bacterial GTPase, Der.

PubMed

Hwang, Jihwan; Tseitin, Vladimir; Ramnarayan, Kal; Shenderovich, Mark D; Inouye, Masayori

2012-05-01

Der is an essential and widely conserved GTPase that assists assembly of a large ribosomal subunit in bacteria. Der associates specifically with the 50S subunit in a GTP-dependent manner and the cells depleted of Der accumulate the structurally unstable 50S subunit, which dissociates into an aberrant subunit at a lower Mg(2+) concentration. As Der is an essential and ubiquitous protein in bacteria, it may prove to be an ideal cellular target against which new antibiotics can be developed. In the present study, we describe our attempts to identify novel antibiotics specifically targeting Der GTPase. We performed the structure-based design of Der inhibitors using the X-ray crystal structure of Thermotoga maritima Der (TmDer). Virtual screening of commercially available chemical library retrieved 257 small molecules that potentially inhibit Der GTPase activity. These 257 chemicals were tested for their in vitro effects on TmDer GTPase and in vivo antibacterial activities. We identified three structurally diverse compounds, SBI-34462, -34566 and -34612, that are both biologically active against bacterial cells and putative enzymatic inhibitors of Der GTPase homologs. We also presented the possible interactions of each compound with the Der GTP-binding site to understand the mechanism of inhibition. Therefore, our lead compounds inhibiting Der GTPase provide scaffolds for the development of novel antibiotics against antibiotic-resistant pathogenic bacteria.

The Crystal Structure of PF-8, the DNA Polymerase Accessory Subunit from Kaposi's Sarcoma-Associated Herpesvirus

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

Baltz, Jennifer L.; Filman, David J.; Ciustea, Mihai

2009-12-01

Kaposi's sarcoma-associated herpesvirus is an emerging pathogen whose mechanism of replication is poorly understood. PF-8, the presumed processivity factor of Kaposi's sarcoma-associated herpesvirus DNA polymerase, acts in combination with the catalytic subunit, Pol-8, to synthesize viral DNA. We have solved the crystal structure of residues 1 to 304 of PF-8 at a resolution of 2.8 {angstrom}. This structure reveals that each monomer of PF-8 shares a fold common to processivity factors. Like human cytomegalovirus UL44, PF-8 forms a head-to-head dimer in the form of a C clamp, with its concave face containing a number of basic residues that are predictedmore » to be important for DNA binding. However, there are several differences with related proteins, especially in loops that extend from each monomer into the center of the C clamp and in the loops that connect the two subdomains of each protein, which may be important for determining PF-8's mode of binding to DNA and to Pol-8. Using the crystal structures of PF-8, the herpes simplex virus catalytic subunit, and RB69 bacteriophage DNA polymerase in complex with DNA and initial experiments testing the effects of inhibition of PF-8-stimulated DNA synthesis by peptides derived from Pol-8, we suggest a model for how PF-8 might form a ternary complex with Pol-8 and DNA. The structure and the model suggest interesting similarities and differences in how PF-8 functions relative to structurally similar proteins.« less

Regulation of TFIIIB during F9 cell differentiation.

PubMed

Athineos, Dimitris; Marshall, Lynne; White, Robert J

2010-03-12

Differentiation of F9 embryonal carcinoma (EC) cells into parietal endoderm (PE) provides a tractable model system for studying molecular events during early and inaccessible stages of murine development. PE formation is accompanied by extensive changes in gene expression both in vivo and in culture. One of the most dramatic is the ~10-fold decrease in transcriptional output by RNA polymerase (pol) III. This has been attributed to changes in activity of TFIIIB, a factor that is necessary and sufficient to recruit pol III to promoters. The goal of this study was to identify molecular changes that can account for the low activity of TFIIIB following F9 cell differentiation. Three essential subunits of TFIIIB decrease in abundance as F9 cells differentiate; these are Brf1 and Bdp1, which are pol III-specific, and TBP, which is also used by pols I and II. The decreased levels of Brf1 and Bdp1 proteins can be explained by reduced expression of the corresponding mRNAs. However, this is not the case for TBP, which is regulated post-transcriptionally. In proliferating cells, pol III transcription is stimulated by the proto-oncogene product c-Myc and the mitogen-activated protein kinase Erk, both of which bind to TFIIIB. However, c-Myc levels fall during differentiation and Erk becomes inactive through dephosphorylation. The diminished abundance of TFIIIB is therefore likely to be compounded by changes to these positive regulators that are required for its full activity. In addition, PE cells have elevated levels of the retinoblastoma protein RB, which is known to bind and repress TFIIIB. The low activity of TFIIIB in PE can be attributed to a combination of changes, any one of which could be sufficient to inhibit pol III transcription. Declining levels of essential TFIIIB subunits and of activators that are required for maximal TFIIIB activity are accompanied by an increase in a potent repressor of TFIIIB. These events provide fail-safe guarantees to ensure that pol III output is appropriate to the diminished metabolic requirements of terminally differentiated cells.

Kants Theorie der Sonne: Physikgeschichte

NASA Astrophysics Data System (ADS)

Jacobi, Manfred

2005-01-01

Im Rahmen seiner Kosmogonie entwickelte der junge Immanuel Kant eine Theorie der Sonne. Sie ist ein einzigartiges Zeugnis seiner intuitiven Vorstellungskraft und beweist auch die Leistungsfähigkeit der damaligen, vorwiegend von Newton geprägten Weltsicht. Entstehung, Aufbau und Dynamik der Sonne werden in Kants Theorie ebenso erklärt wie etwa das Phänomen der Sonnenflecken.

Modeling Subsurface Storm and Tile Drain Systems in GSSHA with SUPERLINK

DTIC Science & Technology

2014-09-01

side is computed as . ( )e Kq d m m L   2 0 01 2 (7) de is defined as ( van der Molen and Wesseling (1991)) ERDC/CHL TR-14-11 15...Conservation Service. Van der Molen , W.H., and J. Wesseling. 1991. A solution in closed form and a series solution to replace the tables for thickness of...effective lateral hydraulic conductivity (cm hr-1) C = 1 in the present version. Hooghoudt ( van Schilfgaarde 1974) characterized flow to cylindrical

MATE (Mentale Aspecten van Team Effectiviteit) (MATE (Mental Aspects of Team Effectiveness))

DTIC Science & Technology

2008-05-01

0 Auteur (s) drs. J.P. van Meer drs. MI. 1 ’ IIart0 drs. 1. van der 16. Rubricering rapport Ongerubriceerd Vastgesteld door Ikol drs. L.A. de Vos...team Auteur (s) Teamntraining drs. J.P. van Meer drs. M.H.E. I Hart Programmanummer Projectnummer drs. 1. van der Beijl V406 015.34095 Rubricering...Murphy & Cleveland (1995) geven inzicht in de tearngedragingen die meetbaar zijn en de theorie over Shared Mental Models (Espevik et al, 2006) laat zien

Funkmesstechnik

NASA Astrophysics Data System (ADS)

Plaßmann, Wilfried

Ein Hauptgebiet der Funkmesstechnik ist durch den Begriff RADAR (radio detection and ranging gekennzeichnet. Bei diesem Verfahren werden impulsförmige elektromagnetische Wellen von einer Antenne ausgesendet und an Körpern oder Stoffverteilungen (Wolken) reflektiert. Die Sendeantenne wird auf Empfang umgeschaltet, und anhand des Echos sind Rückschlüsse auf die Lage und die Beschaffenheit der Körper oder der Stoffverteilungen möglich. Angewendet wird die Radartechnik bei der Kontrolle und der Sicherung des Land-, Wasser- und Flugverkehrs, in der Meteorologie zur Wetterprognose, in der Astrologie und im militärischen Bereich.

Spatiotemporal recruitment of human DNA polymerase delta to sites of UV damage

PubMed Central

Chea, Jennifer; Zhang, Sufang; Zhao, Hong; Zhang, Zhongtao; Lee, Ernest Y.C.; Darzynkiewicz, Zbigniew; Lee, Marietta Y.W.T.

2012-01-01

Human DNA polymerase δ (Pol δ) is involved in various DNA damage responses in addition to its central role in DNA replication. The Pol δ4 holoenzyme consists of four subunits, p125, p50, p68 and p12. It has been established that the p12 subunit is rapidly degraded in response to DNA damage by UV leading to the in vivo conversion of Pol δ4 to Pol δ3, a trimeric form lacking the p12 subunit. We provide the first analysis of the time-dependent recruitment of the individual Pol δ subunits to sites of DNA damage produced by UV irradiation through 5 μm polycarbonate filters by immunofluorescence microscopy and laser scanning cytometry (LSC). Quantitative analysis demonstrates that the recruitments of the three large subunits was near complete by 2 h and did not change significantly up to 4 h after UV exposure. However, the recruitment of p12 was incomplete even at 4 h, with about 70% of the Pol δ lacking the p12 subunit. ChIP analysis of Pol δ after global UV irradiation further demonstrates that only p125, p50 and p68 were present. Thus, Pol δ3 is the predominant form of Pol δ at sites of UV damage as a result of p12 degradation. Using LSC, we have further confirmed that Pol δ was recruited to CPD damage sites in all phases of the cell cycle. Collectively, our results show that Pol δ at the DNA damage site is the Pol δ trimer lacking p12 regardless of the cell cycle phase. PMID:22801543

Mechanism of Error-Free DNA Replication Past Lucidin-Derived DNA Damage by Human DNA Polymerase κ.

PubMed

Yockey, Oliver P; Jha, Vikash; Ghodke, Pratibha P; Xu, Tianzuo; Xu, Wenyan; Ling, Hong; Pradeepkumar, P I; Zhao, Linlin

2017-11-20

DNA damage impinges on genetic information flow and has significant implications in human disease and aging. Lucidin-3-O-primeveroside (LuP) is an anthraquinone derivative present in madder root, which has been used as a coloring agent and food additive. LuP can be metabolically converted to genotoxic compound lucidin, which subsequently forms lucidin-specific N 2 -2'-deoxyguanosine (N 2 -dG) and N 6 -2'-deoxyadenosine (N 6 -dA) DNA adducts. Lucidin is mutagenic and carcinogenic in rodents but has low carcinogenic risks in humans. To understand the molecular mechanism of low carcinogenicity of lucidin in humans, we performed DNA replication assays using site-specifically modified oligodeoxynucleotides containing a structural analogue (LdG) of lucidin-N 2 -dG DNA adduct and determined the crystal structures of DNA polymerase (pol) κ in complex with LdG-bearing DNA and an incoming nucleotide. We examined four human pols (pol η, pol ι, pol κ, and Rev1) in their efficiency and accuracy during DNA replication with LdG; these pols are key players in translesion DNA synthesis. Our results demonstrate that pol κ efficiently and accurately replicates past the LdG adduct, whereas DNA replication by pol η, pol ι is compromised to different extents. Rev1 retains its ability to incorporate dCTP opposite the lesion albeit with decreased efficiency. Two ternary crystal structures of pol κ illustrate that the LdG adduct is accommodated by pol κ at the enzyme active site during insertion and postlesion-extension steps. The unique open active site of pol κ allows the adducted DNA to adopt a standard B-form for accurate DNA replication. Collectively, these biochemical and structural data provide mechanistic insights into the low carcinogenic risk of lucidin in humans.

Distributed Generation Market Demand Model | NREL

Science.gov Websites

Demand Model The Distributed Generation Market Demand (dGen) model simulates the potential adoption of distributed energy resources (DERs) for residential, commercial, and industrial entities in the dGen model can help develop deployment forecasts for distributed resources, including sensitivity to

Respiratory allergen from house dust mite is present in human milk and primes for allergic sensitization in a mouse model of asthma.

PubMed

Macchiaverni, P; Rekima, A; Turfkruyer, M; Mascarell, L; Airouche, S; Moingeon, P; Adel-Patient, K; Condino-Neto, A; Annesi-Maesano, I; Prescott, S L; Tulic, M K; Verhasselt, V

2014-03-01

There is an urgent need to identify environmental risk and protective factors in early life for the prevention of allergy. Our study demonstrates the presence of respiratory allergen from house dust mite, Der p 1, in human breast milk. Der p 1 in milk is immunoreactive, present in similar amounts as dietary egg antigen, and can be found in breast milk from diverse regions of the world. In a mouse model of asthma, oral exposure to Der p through breast milk strongly promotes sensitization rather than protect the progeny as we reported with egg antigen. These data highlight that antigen administration to the neonate through the oral route may contribute to child allergic sensitization and have important implications for the design of studies assessing early oral antigen exposure for allergic disease prevention. The up-to-now unknown worldwide presence of respiratory allergen in maternal milk allows new interpretation and design of environmental control epidemiological studies for allergic disease prevention. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Anti-Armor Defense Data Study (A2D2). Phase 2. Volume 4. US Anti-Tank Defense at Krinkelt-Rocherath, Belgium (December, 1944)

DTIC Science & Technology

1991-02-15

Geschicbte der Stammdivision der Waffen -SS, Band V: 194 -1945. Osnabruck: Munln-Verlag, 1982. (Includes translation) (Stuttgart] 105 Weidinger, Otto, ed...1960. C -68 Weidinger, Otto. Division Das Reich. Der Weg der 2.SS Panzer-Division "Das Reich". Die Geschichte der Stammdivision der Waffen -SS, Band

Series-nonuniform rational B-spline signal feedback: From chaos to any embedded periodic orbit or target point.

PubMed

Shao, Chenxi; Xue, Yong; Fang, Fang; Bai, Fangzhou; Yin, Peifeng; Wang, Binghong

2015-07-01

The self-controlling feedback control method requires an external periodic oscillator with special design, which is technically challenging. This paper proposes a chaos control method based on time series non-uniform rational B-splines (SNURBS for short) signal feedback. It first builds the chaos phase diagram or chaotic attractor with the sampled chaotic time series and any target orbit can then be explicitly chosen according to the actual demand. Second, we use the discrete timing sequence selected from the specific target orbit to build the corresponding external SNURBS chaos periodic signal, whose difference from the system current output is used as the feedback control signal. Finally, by properly adjusting the feedback weight, we can quickly lead the system to an expected status. We demonstrate both the effectiveness and efficiency of our method by applying it to two classic chaotic systems, i.e., the Van der Pol oscillator and the Lorenz chaotic system. Further, our experimental results show that compared with delayed feedback control, our method takes less time to obtain the target point or periodic orbit (from the starting point) and that its parameters can be fine-tuned more easily.

Series-nonuniform rational B-spline signal feedback: From chaos to any embedded periodic orbit or target point

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

Shao, Chenxi, E-mail: cxshao@ustc.edu.cn; Xue, Yong; Fang, Fang

2015-07-15

The self-controlling feedback control method requires an external periodic oscillator with special design, which is technically challenging. This paper proposes a chaos control method based on time series non-uniform rational B-splines (SNURBS for short) signal feedback. It first builds the chaos phase diagram or chaotic attractor with the sampled chaotic time series and any target orbit can then be explicitly chosen according to the actual demand. Second, we use the discrete timing sequence selected from the specific target orbit to build the corresponding external SNURBS chaos periodic signal, whose difference from the system current output is used as the feedbackmore » control signal. Finally, by properly adjusting the feedback weight, we can quickly lead the system to an expected status. We demonstrate both the effectiveness and efficiency of our method by applying it to two classic chaotic systems, i.e., the Van der Pol oscillator and the Lorenz chaotic system. Further, our experimental results show that compared with delayed feedback control, our method takes less time to obtain the target point or periodic orbit (from the starting point) and that its parameters can be fine-tuned more easily.« less

Sitnikov problem in the square configuration: elliptic case

NASA Astrophysics Data System (ADS)

Shahbaz Ullah, M.

2016-05-01

This paper is extension to the classical Sitnikov problem, when the four primaries of equal masses lie at the vertices of a square for all time and moving in elliptic orbits around their center of mass of the system, the distances between the primaries vary with time but always in such a way that their mutual distances remain in the same ratio. First we have established averaged equation of motion of the Sitnikov five-body problem in the light of Jalali and Pourtakdoust (Celest. Mech. Dyn. Astron. 68:151-162, 1997), by applying the Van der Pol transformation and averaging technique of Guckenheimer and Holmes (Nonlinear oscillations, dynamical system bifurcations of vector fields, Springer, Berlin, 1983). Next the Hamiltonian equation of motion has been solved with the help of action angle variables I and φ. Finally the periodicity and stability of the Sitnikov five-body problem have been examined with the help of Poincare surfaces of section (PSS). It is shown that chaotic region emerging from the destroyed islands, can easily be seen by increasing the eccentricity of the primaries to e = 0.21. It is valid for bounded small amplitude solutions z_{max} ( z_{max} = 0.65 ) and 0 ≤ e < 0.3.

General Linearized Theory of Quantum Fluctuations around Arbitrary Limit Cycles

NASA Astrophysics Data System (ADS)

Navarrete-Benlloch, Carlos; Weiss, Talitha; Walter, Stefan; de Valcárcel, Germán J.

2017-09-01

The theory of Gaussian quantum fluctuations around classical steady states in nonlinear quantum-optical systems (also known as standard linearization) is a cornerstone for the analysis of such systems. Its simplicity, together with its accuracy far from critical points or situations where the nonlinearity reaches the strong coupling regime, has turned it into a widespread technique, being the first method of choice in most works on the subject. However, such a technique finds strong practical and conceptual complications when one tries to apply it to situations in which the classical long-time solution is time dependent, a most prominent example being spontaneous limit-cycle formation. Here, we introduce a linearization scheme adapted to such situations, using the driven Van der Pol oscillator as a test bed for the method, which allows us to compare it with full numerical simulations. On a conceptual level, the scheme relies on the connection between the emergence of limit cycles and the spontaneous breaking of the symmetry under temporal translations. On the practical side, the method keeps the simplicity and linear scaling with the size of the problem (number of modes) characteristic of standard linearization, making it applicable to large (many-body) systems.

Functional diversification of maize RNA polymerase IV and V subtypes via alternative catalytic subunits

PubMed Central

Haag, Jeremy R.; Brower-Toland, Brent; Krieger, Elysia K.; Sidorenko, Lyudmila; Nicora, Carrie D.; Norbeck, Angela D.; Irsigler, Andre; LaRue, Huachun; Brzeski, Jan; McGinnis, Karen; Ivashuta, Sergey; Pasa-Tolic, Ljiljana; Chandler, Vicki L.; Pikaard, Craig S.

2014-01-01

Summary Unlike nuclear multisubunit RNA polymerases I, II and III, whose subunit compositions are conserved throughout eukaryotes, plant RNA Polymerases IV and V are non-essential, Pol II-related enzymes whose subunit compositions are still evolving. Whereas Arabidopsis Pols IV and V differ from Pol II in four or five of their twelve subunits, respectively, and differ from one another in three subunits, proteomic analyses show that maize Pols IV and V differ from Pol II in six subunits, but differ from each other only in their largest subunits. Use of alternative catalytic second-subunits, which are non-redundant for development and paramutation, yields at least two subtypes of Pol IV, and three subtypes of Pol V in maize. Pol IV/V associations with MOP1, RMR1, AGO121, Zm_DRD1/CHR127, SHH2a and SHH2b extend parallels between paramutation in maize and the RNA-directed DNA methylation pathway in Arabidopsis. PMID:25284785

DNA polymerase η modulates replication fork progression and DNA damage responses in platinum-treated human cells

NASA Astrophysics Data System (ADS)

Sokol, Anna M.; Cruet-Hennequart, Séverine; Pasero, Philippe; Carty, Michael P.

2013-11-01

Human cells lacking DNA polymerase η (polη) are sensitive to platinum-based cancer chemotherapeutic agents. Using DNA combing to directly investigate the role of polη in bypass of platinum-induced DNA lesions in vivo, we demonstrate that nascent DNA strands are up to 39% shorter in human cells lacking polη than in cells expressing polη. This provides the first direct evidence that polη modulates replication fork progression in vivo following cisplatin and carboplatin treatment. Severe replication inhibition in individual platinum-treated polη-deficient cells correlates with enhanced phosphorylation of the RPA2 subunit of replication protein A on serines 4 and 8, as determined using EdU labelling and immunofluorescence, consistent with formation of DNA strand breaks at arrested forks in the absence of polη. Polη-mediated bypass of platinum-induced DNA lesions may therefore represent one mechanism by which cancer cells can tolerate platinum-based chemotherapy.

Dynamic Power Distribution System Management With a Locally Connected Communication Network

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

Dall-Anese, Emiliano; Zhang, Kaiqing; Basar, Tamer

Coordinated optimization and control of distribution-level assets can enable a reliable and optimal integration of massive amount of distributed energy resources (DERs) and facilitate distribution system management (DSM). Accordingly, the objective is to coordinate the power injection at the DERs to maintain certain quantities across the network, e.g., voltage magnitude, line flows, or line losses, to be close to a desired profile. By and large, the performance of the DSM algorithms has been challenged by two factors: i) the possibly non-strongly connected communication network over DERs that hinders the coordination; ii) the dynamics of the real system caused by themore » DERs with heterogeneous capabilities, time-varying operating conditions, and real-time measurement mismatches. In this paper, we investigate the modeling and algorithm design and analysis with the consideration of these two factors. In particular, a game theoretic characterization is first proposed to account for a locally connected communication network over DERs, along with the analysis of the existence and uniqueness of the Nash equilibrium (NE) therein. To achieve the equilibrium in a distributed fashion, a projected-gradient-based asynchronous DSM algorithm is then advocated. The algorithm performance, including the convergence speed and the tracking error, is analytically guaranteed under the dynamic setting. Extensive numerical tests on both synthetic and realistic cases corroborate the analytical results derived.« less

Zu einer inhaltsorientierten Theorie des Lernens und Lehrens der biologischen Evolution

NASA Astrophysics Data System (ADS)

Wallin, Anita

Der Zweck dieser Studie (zwecks Überblick siehe dazu Abb. 9.1) war zu untersuchen, wie die Schüler der Sekundarstufe II ein Verständnis von der Theorie der biologischen Evolution entwickeln. Vom Ausgangspunkt "Vorurteile der Schüler“ ausgehend wurden Unterrichtssequenzen entwickelt und drei verschiedene Lernexperimente in einem zyklischen Prozess durchgeführt. Das Wissen der Schüler wurde vor, während und nach den Unterrichtssequenzen mit Hilfe von schriftlichen Tests, Interviews und Diskussionsrunden in kleinen Gruppen abgefragt. Etwa 80 % der Schüler hatten vor dem Unterricht alternative Vorstellungen von Evolution, und in dem Nachfolgetest erreichten circa 75 % ein wissenschaftliches Niveau. Die Argumentation der Schüler in den verschiedenen Tests wurde sorgfältig unter Rücksichtnahme auf Vorurteile, der konzeptionellen Struktur der Theorie der Evolution und den Zielen des Unterrichts analysiert. Daraus konnten Einsichten in solche Anforderungen an Lehren und Lernen gewonnen werden, die Herausforderungen an Schüler und Lehrer darstellen, wenn sie anfangen, evolutionäre Biologie zu lernen oder zu lehren. Ein wichtiges Ergebnis war, dass das Verständnis existierender Variation in einer Population der Schlüssel zum Verständnis von natürlicher Selektion ist. Die Ergebnisse sind in einer inhaltsorientierten Theorie zusammengefasst, welche aus drei verschiedenen Aspekten besteht: 1) den inhaltsspezifischen Aspekten, die einzigartig für jedes wissenschaftliche Feld sind; 2) den Aspekten, die die Natur der Wissenschaft betreffen; und 3) den allgemeinen Aspekten. Diese Theorie kann in neuen Experimenten getestet und weiter entwickelt werden.

In vivo evidence for translesion synthesis by the replicative DNA polymerase δ

PubMed Central

Hirota, Kouji; Tsuda, Masataka; Mohiuddin; Tsurimoto, Toshiki; Cohen, Isadora S.; Livneh, Zvi; Kobayashi, Kaori; Narita, Takeo; Nishihara, Kana; Murai, Junko; Iwai, Shigenori; Guilbaud, Guillaume; Sale, Julian E.; Takeda, Shunichi

2016-01-01

The intolerance of DNA polymerase δ (Polδ) to incorrect base pairing contributes to its extremely high accuracy during replication, but is believed to inhibit translesion synthesis (TLS). However, chicken DT40 cells lacking the POLD3 subunit of Polδ are deficient in TLS. Previous genetic and biochemical analysis showed that POLD3 may promote lesion bypass by Polδ itself independently of the translesion polymerase Polζ of which POLD3 is also a subunit. To test this hypothesis, we have inactivated Polδ proofreading in pold3 cells. This significantly restored TLS in pold3 mutants, enhancing dA incorporation opposite abasic sites. Purified proofreading-deficient human Polδ holoenzyme performs TLS of abasic sites in vitro much more efficiently than the wild type enzyme, with over 90% of TLS events resulting in dA incorporation. Furthermore, proofreading deficiency enhances the capability of Polδ to continue DNA synthesis over UV lesions both in vivo and in vitro. These data support Polδ contributing to TLS in vivo and suggest that the mutagenesis resulting from loss of Polδ proofreading activity may in part be explained by enhanced lesion bypass. PMID:27185888

RNA Pol IV and V in Gene Silencing: Rebel Polymerases Evolving Away From Pol II’s Rules

PubMed Central

Zhou, Ming; Law, Julie A.

2015-01-01

Noncoding RNAs regulate gene expression at both the transcriptional and post-transcriptional levels, and play critical roles in development, imprinting and the maintenance of genome integrity in eukaryotic organisms [1–3]. Therefore, it is important to understand how the production of such RNAs are controlled. In addition to the three canonical DNA dependent RNA polymerases (Pol) Pol I, II and III, two non-redundant plant-specific RNA polymerases, Pol IV and Pol V, have been identified and shown to generate noncoding RNAs that are required for transcriptional gene silencing via the RNA-directed DNA methylation (RdDM) pathway. Thus, somewhat paradoxically, transcription is required for gene silencing. This paradox extends beyond plants, as silencing pathways in yeast, fungi, flies, worms, and mammals also require transcriptional machinery [4,5]. As plants have evolved specialized RNA polymerases to carry out gene silencing in a manner that is separate from the essential roles of Pol II, their characterization offers unique insight into how RNA polymerases facilitate gene silencing. In this review, we focus on the mechanisms of Pol IV and Pol V function, including their compositions, their transcripts, and their modes of recruitment to chromatin. PMID:26344361

Human PrimPol activity is enhanced by RPA.

PubMed

Martínez-Jiménez, María I; Lahera, Antonio; Blanco, Luis

2017-04-10

Human PrimPol is a primase belonging to the AEP superfamily with the unique ability to synthesize DNA primers de novo, and a non-processive DNA polymerase able to bypass certain DNA lesions. PrimPol facilitates both mitochondrial and nuclear replication fork progression either acting as a conventional TLS polymerase, or repriming downstream of blocking lesions. In vivo assays have shown that PrimPol is rapidly recruited to sites of DNA damage by interaction with the human replication protein A (RPA). In agreement with previous findings, we show here that the higher affinity of RPA for ssDNA inhibits PrimPol activities in short ssDNA templates. In contrast, once the amount of ssDNA increases up to a length in which both proteins can simultaneously bind ssDNA, as expected during replicative stress conditions, PrimPol and RPA functionally interact, and their binding capacities are mutually enhanced. When using M13 ssDNA as template, RPA stimulated both the primase and polymerase activities of PrimPol, either alone or in synergy with Polε. These new findings supports the existence of a functional PrimPol/RPA association that allows repriming at the exposed ssDNA regions formed in the leading strand upon replicase stalling.

Longitudinale und Transversale Impulsverteilungen der Hadronen im Endzustand der Tiefinelastischen Myon-Nukleon-Streuung (in german)

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

Ecker, Uwe

1991-01-01

The Fermilab experiment E665 took its first data during the period 1987 /1988. 490 GeV and 100 GeV muons are scattered off various nuclear targets. In this analysis a study of the longitudinal and transverse momentum distributions of charged final state hadrons produced in muon-deuterium-interactions is performed. Semi inclusive muoproduction data are presented in a kinematic regime up to a previously unreached invariant mass ofmore » $$\\sim$$30 GeV. The data are discussed in the framework of the quark parton model and quantum chromodynamics. A comparison to various leptoproduction and $e^+e^-$ -annihilation experiments is shown. Subsequently the data are confronted with predictions from the Lund model. The data agree well with a QCD based parton model picture.« less

Transplantate und Implantate im Mittelohrbereich - Teil 1 (Stand 2002)

NASA Astrophysics Data System (ADS)

Kempf, Hans-Georg; Lenarz, Thomas; Eckert, Karl-Ludwig

In Deutschland leben ungefähr 12 Millionen Menschen, die an einer ein- oder beidseitigen Schwerhörigkeit leiden. Diese kann angeboren oder im Laufe des Lebens erworben sein. Klinisch und therapeutisch wichtig ist die Unterscheidung, ob die Ursache der Schwerhörigkeit im Bereich des Mittelohres, d. h. der Schallübertragung, oder im Bereich des Innenohres, der Hörnerven und der zentralen Hörbahnabschnitte, d. h. der Schallempfindung, liegt. 2,5 Millionen Schwerhörige haben dabei das Problem der Schallübertragung, d.h. die Störung liegt im Mittelohrbereich, und hier kann man in der Regel mit operativen, mikrochirurgisch durchgeführten Massnahmen helfen [1, 2]. Im Vordergrund steht als Ursache hier die chronische Mittelohrentzündung, die sich als Perforation des Trommelfells, als Defekt oder Unterbrechung der Gehörknöchelchen oder auch als Cholesteatom, einer sogenannte Knocheneiterung äussern kann [3]. Therapeutisch und damit als Prinzip der operativen Hörverbesserung steht primär der Verschluss des Trommelfells oder eine Rekonstruktion der Gehörknöchelchen an.

Forces dictating colloidal interactions between viruses and soil

USGS Publications Warehouse

Chattopadhyay, Sandip; Puls, Robert W.

2000-01-01

The fate and transport of viruses in soil and aquatic environments were studied with respect to the different forces involved in the process of sorption of these viruses on soil particles. In accordance with the classical DLVO theory, we have calculated the repulsive electrostatic forces and the attractive van der Waals forces. Bacteriophages have been used as model sorbates, while different clays have been used as model sorbents. The equations used for the determination of the change in free energy for the process (ΔG) takes into consideration the roughness of the sorbent surfaces. Results indicate that attractive van der Waals forces predominate the process of sorption of the selected bacteriophages on clays.

Electrostatics of electron-hole interactions in van der Waals heterostructures

NASA Astrophysics Data System (ADS)

Cavalcante, L. S. R.; Chaves, A.; Van Duppen, B.; Peeters, F. M.; Reichman, D. R.

2018-03-01

The role of dielectric screening of electron-hole interaction in van der Waals heterostructures is theoretically investigated. A comparison between models available in the literature for describing these interactions is made and the limitations of these approaches are discussed. A simple numerical solution of Poisson's equation for a stack of dielectric slabs based on a transfer matrix method is developed, enabling the calculation of the electron-hole interaction potential at very low computational cost and with reasonable accuracy. Using different potential models, direct and indirect exciton binding energies in these systems are calculated within Wannier-Mott theory, and a comparison of theoretical results with recent experiments on excitons in two-dimensional materials is discussed.

Polμ tumor variants decrease the efficiency and accuracy of NHEJ

PubMed Central

Sastre-Moreno, Guillermo; Pryor, John M.; Díaz-Talavera, Alberto; Ruiz, José F.; Ramsden, Dale A.

2017-01-01

Abstract The non homologous end-joining (NHEJ) pathway of double-strand break (DSB) repair often requires DNA synthesis to fill the gaps generated upon alignment of the broken ends, a complex task performed in human cells by two specialized DNA polymerases, Polλ and Polμ. It is now well established that Polμ is the one adapted to repair DSBs with non-complementary ends, the most challenging scenario, although the structural basis and physiological implications of this adaptation are not fully understood. Here, we demonstrate that two human Polμ point mutations, G174S and R175H, previously identified in two different tumor samples and affecting two adjacent residues, limit the efficiency of accurate NHEJ by Polμ in vitro and in vivo. Moreover, we show that this limitation is the consequence of a decreased template dependency during NHEJ, which renders the error-rate of the mutants higher due to the ability of Polμ to randomly incorporate nucleotides at DSBs. These results highlight the relevance of the 8 kDa domain of Polμ for accurate and efficient NHEJ, but also its contribution to the error-prone behavior of Polμ at 2-nt gaps. This work provides the first demonstration that mutations affecting Polμ identified in tumors can alter the efficiency and fidelity of NHEJ. PMID:28973441

Organizational differences between cytoplasmic male sterile and male fertile Brassica mitochondrial genomes are confined to a single transposed locus.

PubMed Central

L'Homme, Y; Brown, G G

1993-01-01

Comparison of the physical maps of male fertile (cam) and male sterile (pol) mitochondrial genomes of Brassica napus indicates that structural differences between the two mtDNAs are confined to a region immediately upstream of the atp6 gene. Relative to cam mtDNA, pol mtDNA possesses a 4.5 kb segment at this locus that includes a chimeric gene that is cotranscribed with atp6 and lacks an approximately 1kb region located upstream of the cam atp6 gene. The 4.5 kb pol segment is present and similarly organized in the mitochondrial genome of the common nap B.napus cytoplasm; however, the nap and pol DNA regions flanking this segment are different and the nap sequences are not expressed. The 4.5 kb CMS-associated pol segment has thus apparently undergone transposition during the evolution of the nap and pol cytoplasms and has been lost in the cam genome subsequent to the pol-cam divergence. This 4.5 kb segment comprises the single DNA region that is expressed differently in fertile, pol CMS and fertility restored pol cytoplasm plants. The finding that this locus is part of the single mtDNA region organized differently in the fertile and male sterile mitochondrial genomes provides strong support for the view that it specifies the pol CMS trait. Images PMID:8388101

Virtuelle Kraftwerke für Smart Markets

NASA Astrophysics Data System (ADS)

Dürr, Thomas; Heyne, Jean-Christoph

In den zurückliegenden Jahren haben insbesondere zwei Trends die Stromversorgung bestimmt: der starke Anstieg der dezentralen und der Ausbau der regenerativen Stromerzeugung, die vor allem in den Verteilnetzen stattfinden. Angesichts dieser Entwicklung gewinnen virtuelle Kraftwerke (VK) immer mehr an Bedeutung. In der frühen Phase waren VK insbesondere eine Möglichkeit, kleine dezentrale Erzeuger zu einer größeren Einheit zu bündeln und sie so marktfähig zu machen. Heute werden sie - überwacht und gesteuert über ein Dezentrales Energie-Management-System (DEMS) - gemeinsam mit Demand Response betrieben, also dem Reagieren eines Energieabnehmers auf Marktpreise. Das Demand Side Management soll zur Flexibilisierung der Industrie beitragen. Da der Ausbau der Übertragungsnetze nur schleppend vorankommt, kann die Nutzung von lastseitiger Flexibilität einen wichtigen Beitrag zur Versorgungssicherheit leisten. Im zweiten Teil des Beitrags geht es um die Entwicklung der Märkte. Großes Interesse besteht immer noch an der Regelenergie, zumal der Bedarf bis 2050 deutlich steigen wird. Die Spotmärkte Intraday und Day-Ahead wachsen kontinuierlich, deshalb werden sie für VK immer wichtiger. Am Ende gibt der Beitrag einen Ausblick auf die künftige Entwicklung, in der Regelenergie- und Spotmärkte noch eine Rolle spielen, aber andere Geschäftsmodelle wichtiger werden. Darüber hinaus geht es um langfristige Entwicklungen, die z. B. zusätzliche Serviceleistungen durch VK betreffen.

Betriebsführung multimodaler Energiesysteme

NASA Astrophysics Data System (ADS)

Mackensen, Reinhard

Die Transformation des Energiesystems von einer zentral geprägten, unidirektional orientierten und in unterschiedliche Sektoren separierten Struktur hin zu einer umfassenden, multimodalen, dezentralen und flexiblen Erzeuger- und Verbraucherlandschaft findet auf verschiedenen Ebenen statt. Randbedingung bei dieser Umwälzung ist immer die Einhaltung der Teilziele Versorgungssicherheit, Wirtschaftlichkeit und Effizienz. Im Einzelnen schlägt sich diese Transformation in einer Diversifizierung der Akteurslandschaft durch die Mechanismen des Unbundling nieder. Weiterhin finden eine Dezentralisierung der Erzeugerlandschaft und damit eine Substitution von mehrheitlich fossil betriebener Großkraftwerkstechnologie durch eine Vielzahl dezentraler Erzeuger mit zumeist regenerativem Charakter statt. Dieser Wandel hat im Wesentlichen zwei Hauptkonsequenzen. Zum einen ergeben sich durch dezentrale, flächige Verteilung der Erzeuger neue Anforderungen an den Energieaustausch, bspw. aus der Erweiterung der Stromnetze für einen bidirektionalen Energieaustausch, zum anderen werden Abstimmungsmechanismen erforderlich, welche die fluktuierende Einspeisung derart mit dem Verbrauch in Waage hält, dass sowohl elektrische Netzrestriktionen, die Qualität der Versorgung und Aspekte der Energieeffizienz und damit der Wirtschaftlichkeit berücksichtigt werden. Mögliche Antworten auf die mit dieser Betrachtung einhergehenden Fragen liegen in der Konzeption eines multimodalen Energiesystems, also in der Gesamtbetrachtung der Sektoren Strom, Wärme und Verkehr. Dieses Kapitel soll Mechanismen darlegen und Wege aufzeigen, wie eine solche Konzeption gestaltet werden kann und wie solche komplexen Systeme in der Praxis betrieben werden können.

Characterization of the hyperrecombination phenotype of the pol3-t mutation of Saccharomyces cerevisiae.

PubMed

Galli, Alvaro; Cervelli, Tiziana; Schiestl, Robert H

2003-05-01

The DNA polymerase delta (Pol3p/Cdc2p) allele pol3-t of Saccharomyces cerevisiae has previously been shown to increase the frequency of deletions between short repeats (several base pairs), between homologous DNA sequences separated by long inverted repeats, and between distant short repeats, increasing the frequency of genomic deletions. We found that the pol3-t mutation increased intrachromosomal recombination events between direct DNA repeats up to 36-fold and interchromosomal recombination 14-fold. The hyperrecombination phenotype of pol3-t was partially dependent on the Rad52p function but much more so on Rad1p. However, in the double-mutant rad1 Delta rad52 Delta, the pol3-t mutation still increased spontaneous intrachromosomal recombination frequencies, suggesting that a Rad1p Rad52p-independent single-strand annealing pathway is involved. UV and gamma-rays were less potent inducers of recombination in the pol3-t mutant, indicating that Pol3p is partly involved in DNA-damage-induced recombination. In contrast, while UV- and gamma-ray-induced intrachromosomal recombination was almost completely abolished in the rad52 or the rad1 rad52 mutant, there was still good induction in those mutants in the pol3-t background, indicating channeling of lesions into the above-mentioned Rad1p Rad52p-independent pathway. Finally, a heterozygous pol3-t/POL3 mutant also showed an increased frequency of deletions and MMS sensitivity at the restrictive temperature, indicating that even a heterozygous polymerase delta mutation might increase the frequency of genetic instability.

Therapeutic effects of eustachian tube surfactant in barotitis media in guinea pigs.

PubMed

Feng, Li-Ning; Chen, Wen-Xian; Cong, Rui; Gou, Lin

2003-07-01

Previous research has shown that the eustachian tube (ET) in animals and humans is lined with a substance that lowers surface tension and thus facilitates the opening of the eustachian tube and aeration of the middle ear. The aims of the present study were to observe the role of eustachian tube surfactant (ETS) on the opening of the ET and to explore the therapeutic effect of natural and artificial ETS on barotitis media (BOM). BOM was successfully established in 50 guinea pigs by simulated ascent in an altitude chamber. Subsets of the affected ears were treated by flushing with natural ETS, artificial ETS, artificial phospholipid, or saline. The effects were evaluated by measuring eustachian tube pressure opening level (POL). Other animals with BOM were treated with artificial ETS on one side and saline in the other, after which the clinical signs were observed. The POL of the saline group remained unchanged. Natural ETS decreased the POL from 11.98 to 6.11 kPa (p < 0.01); artificial ETS reduced the POL from 11.91 to 6.67 kPa (p < 0.01); there was no significant difference between the two treatments. Artificial phospholipid was less effective, decreasing POL from 11.86 to 8.61 kPa (p < 0.05). Clinical observations showed that after 1 wk of treatment with artificial ETS, the congestion in the tympanic membrane was alleviated, the hearing threshold improved, and the effusion in tympanic cavity diminished. Artificial ETS was as effective as natural ETS in facilitating the opening of eustachian tube and had definite therapeutic effects on BOM in this model.

The community popular opinion leader HIV prevention programme: conceptual basis and intervention procedures.

PubMed

2007-04-01

To describe the community popular opinion leader (C-POL) intervention employed in the NIMH Collaborative HIV/STD Prevention Trial, including its theoretical, conceptual, and empirical basis, intervention procedures and methods, core elements, and how its content was culturally tailored to address the needs of varied populations. The programme is designed to identify, recruit, train, and intensively engage C-POLs of a target population to convey HIV risk reduction messages to people in their communities, with the intention of reducing high-risk behavior at a population level. Based on the diffusion of innovation theory, the intervention identified, trained, and engaged C-POL within a high-risk community population to advocate, recommend, and endorse the importance of safer behavior to other members of the same population. Nine core elements of the intervention are discussed. Data collected during rapid ethnography were used to adapt the content of the intervention for food market owners and workers in China, male patrons of wine shops and at-risk women congregating nearby in India, young people in social gathering venues in Peruvian barrios, dormitory students in Russia, and people congregating in commercial areas of growth points in Zimbabwe. The C-POL intervention model taps into community strengths, altruism, and people's desire to do something to help fight against AIDS. With few exceptions, C-POLs participated enthusiastically in the training sessions and reported having conversations in the community. Rapid ethnography can be used to tailor an intervention to diverse settings while maintaining fidelity to the core elements of the intervention.

Craniota, Wirbel- oder Schädeltiere

NASA Astrophysics Data System (ADS)

Schultze, Hans-Peter

Zu den Craniota zählen alle Chordatiere, die eine dreiteilige Regionalisierung des Körpers in Kopf, Rumpf und Schwanz aufweisen. Der Kopf umfasst (1) das Neurocranium mit Gehirn und komplexen Sinnesorganen zur Wahrnehmung der Umgebung, (2) das Viscerocranium zur Nahrungsaufnahme und zur Ventilation der Kiemen bei den primär wasserlebenden Craniota und (3) das Dermatocranium (S. 38). Letzteres entsteht durch Verknöcherungen im Bindegewebe des Integuments, es dient dem Schutz des Kopfes und trägt im Mundbreich die Zähne. Zusammen bilden die drei Skelettstrukturen die funktionelle Einheit Schädel (Cranium). Außer der (somatischen) Rumpfmuskulatur und dem Axialskelett liegen im Rumpf Kreislauf-, Atmungs-, Verdauungs-, Exkretions- und Fortpflanzungsorgane. Der Schwanz, der Abschnitt hinter der Afteröffnung, die das Ende der Leibeshöhle markiert, dient mit Muskeln und Schwanzflosse der Fortbewegung.

Processing closely spaced lesions during Nucleotide Excision Repair triggers mutagenesis in E. coli

PubMed Central

Isogawa, Asako; Fujii, Shingo

2017-01-01

It is generally assumed that most point mutations are fixed when damage containing template DNA undergoes replication, either right at the fork or behind the fork during gap filling. Here we provide genetic evidence for a pathway, dependent on Nucleotide Excision Repair, that induces mutations when processing closely spaced lesions. This pathway, referred to as Nucleotide Excision Repair-induced Mutagenesis (NERiM), exhibits several characteristics distinct from mutations that occur within the course of replication: i) following UV irradiation, NER-induced mutations are fixed much more rapidly (t ½ ≈ 30 min) than replication dependent mutations (t ½ ≈ 80–100 min) ii) NERiM specifically requires DNA Pol IV in addition to Pol V iii) NERiM exhibits a two-hit dose-response curve that suggests processing of closely spaced lesions. A mathematical model let us define the geometry (infer the structure) of the toxic intermediate as being formed when NER incises a lesion that resides in close proximity of another lesion in the complementary strand. This critical NER intermediate requires Pol IV / Pol II for repair, it is either lethal if left unrepaired or mutation-prone when repaired. Finally, NERiM is found to operate in stationary phase cells providing an intriguing possibility for ongoing evolution in the absence of replication. PMID:28686598

Comparative molecular dynamics studies of heterozygous open reading frames of DNA polymerase eta (η) in pathogenic yeast Candida albicans

NASA Astrophysics Data System (ADS)

Satpati, Suresh; Manohar, Kodavati; Acharya, Narottam; Dixit, Anshuman

2017-01-01

Genomic instability in Candida albicans is believed to play a crucial role in fungal pathogenesis. DNA polymerases contribute significantly to stability of any genome. Although Candida Genome database predicts presence of S. cerevisiae DNA polymerase orthologs; functional and structural characterizations of Candida DNA polymerases are still unexplored. DNA polymerase eta (Polη) is unique as it promotes efficient bypass of cyclobutane pyrimidine dimers. Interestingly, C. albicans is heterozygous in carrying two Polη genes and the nucleotide substitutions were found only in the ORFs. As allelic differences often result in functional differences of the encoded proteins, comparative analyses of structural models and molecular dynamic simulations were performed to characterize these orthologs of DNA Polη. Overall structures of both the ORFs remain conserved except subtle differences in the palm and PAD domains. The complementation analysis showed that both the ORFs equally suppressed UV sensitivity of yeast rad30 deletion strain. Our study has predicted two novel molecular interactions, a highly conserved molecular tetrad of salt bridges and a series of π-π interactions spanning from thumb to PAD. This study suggests these ORFs as the homologues of yeast Polη, and due to its heterogeneity in C. albicans they may play a significant role in pathogenicity.

Miocene climate as recorded on slope carbonates : examples from Malta (Central Mediterranean) and Northeastern Australia (Marion Plateau, ODP LEG 194)

NASA Astrophysics Data System (ADS)

John, Cédric Michaël

2003-08-01

This study investigated the slope carbonates of two Miocene carbonate systems: the Maltese Islands (in the Central Mediterranean) and the Marion Plateau (Northeastern Australia, drilled during ODP Leg 194). The aim of the study was to trace the impact of the Miocene cooling steps (events Mi1-Mi6) in these carbonate systems, especially the Mi3 event, which took place around 13.6 Ma and deeply impacted the marine oxygen isotope record. This event also profoundly impacted oceanographic and climatic patterns, eventually leading to the establishment of the modern ice-house world. In particular, East Antarctica became ice covered at that period. The rational behind the present study was to investigate the impact that this event had on shallow water systems in order to complement the deep-sea record and hence acquire a more global perspective on Miocene climate change. The Maltese Islands were investigated for trends in bulk-rock carbon and oxygen isotopes, as well as bulk-rock mineralogy, clay minerals analysis and organic geochemisty. Results showed that the mid Miocene cooling event deeply impacted sedimentation at that location by changing sedimentation from carbonate to clay-rich sediments. Moreover, it was discovered that each phase of Antarctic glaciation, not just the major mid Miocene event, resulted in higher terrigenous input on Malta. Mass accumulation rates revealed that this was linked to increased runoff during periods when Antarctica was glaciated, and thus that the carbonate sediments were “diluted” by clay-rich sediments. The model subsequently developed to explain this implies feedback from Antarctic glaciations creating cold, dense air masses that push the ITCZ Northward, thus increasing precipitation on the North African subcontinent. Increased precipitation (or stronger African monsoon) accelerated continental weathering and runoff, thus bringing more terrigenous sediment to the paleo-location of the slope sediments of Malta. Spectral analysis of carbonate content and organic matter geochemical analysis furthermore suggest that the clay-rich intervals are similar to sapropelic deposits. On the Marion Plateau, trends in oxygen and carbon isotopes were obtained by measuring Cibicidoides spp foraminifers. Moreover, carbonate content was reconstructed using a chemical method (coulometer). Results show that the mid Miocene cooling step profoundly affected this system: a major drop in accumulation rates of carbonates occurs precisely at 13.8 Ma, around the time of the East Antarctic ice sheet formation. Moreover, sedimentation changes occurred at that time, carbonate fragments coming from neritic environments becoming less abundant, planktonic foraminifer content increasing and quartz and reworked glauconite being deposited. Conversely, a surprising result is that the major N12-N14 sea-level fall occurring around 11.5 Ma did not impact the accumulation of carbonates on the slope. This was unexpected since carbonate platform are very sensitive to sea-level changes. The model developed to explain that mass accumulation rates of carbonates diminished around 13.6 Ma (Mi3 Event) instead of 11.5 Ma (N12-N14 event), suggests that oceanic currents were controlling slope carbonate deposition on the Marion Plateau prior to the mid-Miocene, and that the mid Miocene event considerably increase their strength, hence reducing the amount of carbonate being deposited on slope sites. Moreover, by combining results from deep-sea oxygen isotopes with sea-level estimates based on coastal onlaps made during Leg 194, we constrain the amplitude of the N12-N14 sea-level fall to 90 meters. When integrating isotopic results from this study, this amplitude is lowered to 70 meters. A general conclusion of this work is that the mid Miocene climatic shift did impact carbonate systems, at least at the two locations studied. However, the nature of this response was highly dependant on the regional settings, in particular the presence of land mass (Malta) and the absence of a barrier to shelter from the effects of open ocean (Marion Plateau). Im Rahmen dieser Doktorarbeit wurden die Hangkarbonate von zwei miozänen heterozoischen Karbonatsystemen näher untersucht: die Malta Inselgruppe (zentrales Mittelmeer) und das Marion Plateau (Nordost Australien, ODP Leg 194). Die Auswirkungen der mittelmiozänen Abkühlung (Mi3), die auf 13.6 Ma datiert wird und starken Einfluß auf die Sauerstoffisotopenkurve hatte, in den oben genannten Flachwassersystemen stellten das Ziel dieser Arbeit dar. Dieses Abkühlungsereignis beeinflußte außerdem sehr stark die ozeanographischen und klimatischen Muster, die im weiteren Verlauf zum modernen Eishausklima führten. So steht insbesondere die Vereisung von Ostantarktika mit diesem Ereignis in Verbindung. Diese Arbeit untersucht den Einfluß dieses Ereignisses auf Flachwassersysteme, um vorliegende Untersuchungen in Tiefwassersystemen zu ergänzen und so zum globalen Verständnis des miozänen Klimawechsels beizutragen. Die Profile auf der Maltainselgruppe wurden mit Hilfe von Kohlenstoff- und Sauerstoffisotopen Auswertungen im Gesamtgestein, Gesamtgesteinmineralogie, Tonmineralanalyse und organischer Geochemie untersucht. Durch einen Wechsel von karbonatischeren zu tonigeren Sedimenten beeinflußte das mittelmiozäne Abkühlungsereignis die Sedimentation in diesem Gebiet sehr stark. Weiterhin wurde beobachtet, daß jede Phase der antarktischen Vereisung, nicht nur das mittelmiozäne Hauptereignis, zu einem erhöhten terrigenen Eintrag in den Hangsedimenten der Maltainselgruppe führte. Akkumulationsraten zeigen, daß dieser erhöhte terrigene Eintrag den einzelnen Vereisungsperioden zusammenhängt und die karbonatischen Sedimente durch tonreiche Sedimente “verunreinigt” wurden. Das daraufhin entwickelte Modell erklärt diesen erhöhten terrigenen Eintrag mit einer nordwärtigen Verlagerung der innertropischen Konvergenzzone durch die Bildung von kalten, dichten Luftmassen, die zu verstärkten Niederschlägen in Nordafrika führten. Diese verstärkten Niederschläge (oder verstärkter afrikanischer Monsun) beeinflußten die kontinentale Verwitterung und den Eintrag, mit der Folge, daß verstärkt terrigene Sedimente im Bereich der Hangsedimente der Maltainselgruppe abgelagert wurden. Die tonreichen Intervalle weisen Ähnlichkeiten zu sapropelischen Ablagerungen auf, was mit Hilfe der Spektral analyse des Karbonatgehalts und der geochemischen Analyse des organischen Materials gezeigt wurde. Auf dem Marion Plateau wurden die Sauerstoff- und Kohlenstoffisotopenkurven anhand von Foraminiferen der Gattung Cibicidoides spp. rekonstruiert. Der Karbonatgehalt wurde mit Hilfe einer chemischen Methode (Coulometer) ermittelt. Genauso wie die Sedimente der Maltainselgruppe beeinflußte das mittelmiozäne Abkühlungsereignis (Mi3) auch die Sedimente auf dem Marion Plateau. So kam es bei 13,8 Ma, in etwa zur Zeit der Vereisung von Ostantarktika, zu einem Abfall der Karbonatakkumulationsraten. Weiterhin traten Änderungen in der Zusammensetzung der Sedimente auf, so nehmen neritische Karbonatfragmente ab, der planktische Foraminiferengehalt nimmt zu und es wurden verstärkt Quarz und Glaukonit abgelagert. Ein überraschendes Ergebnis ist die Tatsache, daß der große N12-N14 Meeresspiegelabfall um 11,5 Ma die Akkumulationsraten der Karbonate auf dem Hang nicht beeinflußte. Dieses Ergebnis ist umso erstaunlicher, da Karbonatplattformen normalerweise sehr sensitiv auf Meeresspiegeländerungen reagieren. Der Grund, warum sich die Karbonatakkumulationsraten schon um 13,6 Ma (Mi3) und nicht erst um 11,5 Ma (N12-N14) verringerten, liegt in der Tatsache, daß die ozeanischen Strömungen die Karbonatsedimentation auf dem Hang des Marion Plateau schon im Miozän kontrollierten. Das mittelmiozäne Ereignis (Mi3) erhöhte die Stärke diese Strömungen und als eine Ursache wurde die Karbonatakkumulation auf den Hängen reduziert. Die Amplitude des N12-N14 Meeresspiegelabfalls liegt bei 90 m unter der Berücksichtigung der Sauerstoffisotopendaten aus der Tiefsee und Berechnungen des Meeresspiegels anhand des “coastal onlaps”, die während Leg 194 gemacht wurden. Die Isotopendaten dieser Arbeit weisen hingegen auf einen verringerten Meeresspiegelabfall von 70 m hin. Als allgemeine Schlußfolgerung kann gesagt werden, daß der mittelmiozäne Klimaumschwung die Karbonatsysteme zumindest an den beiden untersuchten Lokalitäten beeinflußt hat. Allerdings waren die Auswirkungen sehr von den unterschiedlichen lokalen Gegebenheiten abhängig. Insbesondere wirkten sich die Anwesenheit einer Landmasse (Malta) und die Abwesenheit einer Barriere vor den Einflüssen des offenen Ozeans (Marion Plateau) stark auf die Ablagerung der Karbonate aus.

„3D-augmented-reality“-Visualisierung für die navigierte Osteosynthese von Beckenfrakturen

PubMed Central

Befrui, N.; Fischer, M.; Fuerst, B.; Lee, S.-C.; Fotouhi, J.; Weidert, S.; Johnson, A.; Euler, E.; Osgood, G.; Navab, N.; Böcker, W.

2018-01-01

Zusammenfassung Hintergrund Trotz großer Fortschritte in der Entwicklung der Hard- und Software von Navigationssystemen finden diese aufgrund ihrer vermeintlichen Komplexität, umständlichen Integration in klinische Arbeitsabläufe und fraglichen Vorteilen gegenüber konventionellen bildgebenden Verfahren bisher wenig Einsatz in den heutigen Operationssälen. Ziel der Arbeit Entwicklung einer „Augmented-reality“(AR)-Darstellung zur chirurgischen Navigation ohne Infrarot(„IR“)-Tracking-Marker und Vergleich zum konventioneller Röntgen in einem simulierten Eingriff. Material und Methoden Navigationssystem bestehend aus „Cone-beam-CT“(CBCT)-fähigem C-Bogen und „Red-green-blue-depth“(RGBD)-Kamera. Testung durch Kirschner(K)-Draht-Platzierung in Modellen unter Berücksichtigung der benötigten Zeit, der Strahlendosis und der Benutzerfreundlichkeit der Systeme. Ergebnisse Eine signifikante Reduktion der benötigten Zeit, der Röntgenbilder und der gesamten Strahlendosis bei der AR-Navigation gegenüber dem konventionellen Röntgen bei gleichbleibender Präzision. Schlussfolgerung Die AR-Navigation mithilfe der RGBD-Kamera bietet flexible und intuitive Darstellungsmöglichkeiten des Operations-situs für navigierte Osteosynthesen ohne Tracking-Marker. Hiermit ist es möglich, Operationen schneller, einfacher und mit geringerer Strahlenbelastung für Patient und OP-Personal durchzuführen. PMID:29500506

Compact Polarimetry Potentials

NASA Technical Reports Server (NTRS)

Truong-Loi, My-Linh; Dubois-Fernandez, Pascale; Pottier, Eric

2011-01-01

The goal of this study is to show the potential of a compact-pol SAR system for vegetation applications. Compact-pol concept has been suggested to minimize the system design while maximize the information and is declined as the ?/4, ?/2 and hybrid modes. In this paper, the applications such as biomass and vegetation height estimates are first presented, then, the equivalence between compact-pol data simulated from full-pol data and compact-pol data processed from raw data as such is shown. Finally, a calibration procedure using external targets is proposed.

Association of pediatric asthma severity with exposure to common household dust allergens

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

Gent, Janneane F., E-mail: janneane.gent@yale.edu; Belanger, Kathleen; Triche, Elizabeth W.

Background: Reducing exposure to household dust inhalant allergens has been proposed as one strategy to reduce asthma. Objective: To examine the dose-response relationships and health impact of five common household dust allergens on disease severity, quantified using both symptom frequency and medication use, in atopic and non-atopic asthmatic children. Methods: Asthmatic children (N=300) aged 4-12 years were followed for 1 year. Household dust samples from two indoor locations were analyzed for allergens including dust mite (Der p 1, Der f 1), cat (Fel d 1), dog (Can f 1), cockroach (Bla g 1). Daily symptoms and medication use were collectedmore » in monthly telephone interviews. Annual disease severity was examined in models including allergens, specific IgE sensitivity and adjusted for age, gender, atopy, ethnicity, and mother's education. Results: Der p 1 house dust mite allergen concentration of 2.0 {mu}g/g or more from the main room and the child's bed was related to increased asthma severity independent of allergic status (respectively, OR 2.93, 95% CI 1.37, 6.30 for 2.0-10.0 {mu}g/g and OR 2.55 95% CI 1.13, 5.73 for {>=}10.0 {mu}g/g). Higher pet allergen levels were associated with greater asthma severity, but only for those sensitized (cat OR 2.41 95% CI 1.19, 4.89; dog OR 2.06 95% CI 1.01, 4.22). Conclusion: Higher levels of Der p 1 and pet allergens were associated with asthma severity, but Der p 1 remained an independent risk factor after accounting for pet allergens and regardless of Der p 1 specific IgE status.« less

Early-life house dust mite allergens, childhood mite sensitization, and respiratory outcomes.

PubMed

Casas, L; Sunyer, J; Tischer, C; Gehring, U; Wickman, M; Garcia-Esteban, R; Lehmann, I; Kull, I; Reich, A; Lau, S; Wijga, A; Antó, J M; Nawrot, T S; Heinrich, J; Keil, T; Torrent, M

2015-07-01

Exposure to indoor allergens during early life may play a role in the development of the immune system and inception of asthma. To describe the house dust mite (HDM) allergen concentrations in bedroom dust during early life and to evaluate its associations with HDM sensitization, wheezing, and asthma, from birth to school age, in 5 geographically spread European birth cohorts. We included 4334 children from INMA-Menorca (Spain), BAMSE (Sweden), LISAplus and MAS (Germany), and PIAMA-NHS (the Netherlands). Dust samples were collected from bedrooms during early life and analyzed for Dermatophagoides pteronyssinus (Der p1) and Dermatophagoides farinae (Der f1). HDM concentrations were divided into four categories. Sensitization was determined by specific IgE. Wheezing and asthma information up to 8/10 years was collected through questionnaires. We performed mixed-effects logistic regression models and expressed associations as odds ratios with 95% confidence intervals. House dust mite concentrations varied across cohorts. Mean allergen concentrations were highest in INMA-Menorca (geometric mean (GM) Der p1 = 3.3 μg/g) and LISAplus (GM Der f1 = 2.1 μg/g) and lowest in BAMSE (GM Der p1 = 0.1 μg/g, Der f1 = 0.3 μg/g). Moderate and high HDM concentrations were significantly (P-values < 0.05) associated with 50-90% higher prevalence of HDM sensitization. No significant associations were observed with respiratory outcomes. Our study based on geographically spread regions, a large sample size, and a wide range of allergen concentration shows that HDM allergen concentrations vary across regions and that exposure during early life plays a role in the development of allergic sensitization but not in the development of respiratory outcomes. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

The levels of the GluN2A NMDA receptor subunit are modified in both the neonatal and adult rat brain by an early experience involving denial of maternal contact.

PubMed

Manatos, V; Stylianopoulou, F; Stamatakis, A

2016-01-26

The composition of the N-methyl-d-aspartate receptor receptor in GluN2A/GluN2B subunits is important in determining its characteristics and its role in plasticity, a property of the brain which is known to be critically affected by early experiences. In the present work we employed an early experience model involving either receipt (RER) or denial (DER) of the expected reward of maternal contact within the context of learning by the pups of a T-maze on postnatal days (PND) 10-13. We investigated the effects of the RER and DER early experiences on GluN1, GluN2A and GluN2B levels in the prefrontal cortex (PFC), hippocampus and amygdala of the rat. We show that on PND13 the DER animals had lower GluN2A levels in the PFC. In adulthood DER males had higher GluN2A levels in the hippocampus, both under basal conditions and after exposure to a novel environment. The early experiences did not affect the response to the novelty. After exposure to a novel environment animals of all three groups (DER, RER, Control) responded with an increase in GluN2A levels in the brain areas examined. We did not detect any effects on GluN1 or GluN2B levels. The alterations in GluN2A levels observed in the DER animals could in part be responsible for their behavioral phenotype, described previously, which includes an increased susceptibility for the expression of depressive-like behavior. Copyright © 2015. Published by Elsevier Ireland Ltd.

The generalized van der Waals theory of pure fluids and mixtures: Annual report for September 1985 to November 1986

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

Sandler, S.I.

1986-01-01

The objective of the work is to use the generalized van der Waals theory, as derived earlier (''The Generalized van der Waals Partition Function I. Basic Theory'' by S.I. Sandler, Fluid Phase Equilibria 19, 233 (1985)) to: (1) understand the molecular level assumptions inherent in current thermodynamic models; (2) use theory and computer simulation studies to test these assumptions; and (3) develop new, improved thermodynamic models based on better molecular level assumptions. From such a fundamental study, thermodynamic models will be developed that will be applicable to mixtures of molecules of widely different size and functionality, as occurs in themore » processing of heavy oils, coal liquids and other synthetic fuels. An important aspect of our work is to reduce our fundamental theoretical developments to engineering practice through extensive testing and evaluation with experimental data on real mixtures. During the first year of this project important progress was made in the areas specified in the original proposal, as well as several subsidiary areas identified as the work progressed. Some of this work has been written up and submitted for publication. Manuscripts acknowledging DOE support, together with a very brief description, are listed herein.« less

The dynamic assembly of distinct RNA polymerase I complexes modulates rDNA transcription.

PubMed

Torreira, Eva; Louro, Jaime Alegrio; Pazos, Irene; González-Polo, Noelia; Gil-Carton, David; Duran, Ana Garcia; Tosi, Sébastien; Gallego, Oriol; Calvo, Olga; Fernández-Tornero, Carlos

2017-03-06

Cell growth requires synthesis of ribosomal RNA by RNA polymerase I (Pol I). Binding of initiation factor Rrn3 activates Pol I, fostering recruitment to ribosomal DNA promoters. This fundamental process must be precisely regulated to satisfy cell needs at any time. We present in vivo evidence that, when growth is arrested by nutrient deprivation, cells induce rapid clearance of Pol I-Rrn3 complexes, followed by the assembly of inactive Pol I homodimers. This dual repressive mechanism reverts upon nutrient addition, thus restoring cell growth. Moreover, Pol I dimers also form after inhibition of either ribosome biogenesis or protein synthesis. Our mutational analysis, based on the electron cryomicroscopy structures of monomeric Pol I alone and in complex with Rrn3, underscores the central role of subunits A43 and A14 in the regulation of differential Pol I complexes assembly and subsequent promoter association.

Exonuclease of human DNA polymerase gamma disengages its strand displacement function.

PubMed

He, Quan; Shumate, Christie K; White, Mark A; Molineux, Ian J; Yin, Y Whitney

2013-11-01

Pol γ, the only DNA polymerase found in human mitochondria, functions in both mtDNA repair and replication. During mtDNA base-excision repair, gaps are created after damaged base excision. Here we show that Pol γ efficiently gap-fills except when the gap is only a single nucleotide. Although wild-type Pol γ has very limited ability for strand displacement DNA synthesis, exo(-) (3'-5' exonuclease-deficient) Pol γ has significantly high activity and rapidly unwinds downstream DNA, synthesizing DNA at a rate comparable to that of the wild-type enzyme on a primer-template. The catalytic subunit Pol γA alone, even when exo(-), is unable to synthesize by strand displacement, making this the only known reaction of Pol γ holoenzyme that has an absolute requirement for the accessory subunit Pol γB. © 2013. Published by Elsevier B.V.

Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells.

PubMed

Moqtaderi, Zarmik; Wang, Jie; Raha, Debasish; White, Robert J; Snyder, Michael; Weng, Zhiping; Struhl, Kevin

2010-05-01

Genome-wide occupancy profiles of five components of the RNA polymerase III (Pol III) machinery in human cells identified the expected tRNA and noncoding RNA targets and revealed many additional Pol III-associated loci, mostly near short interspersed elements (SINEs). Several genes are targets of an alternative transcription factor IIIB (TFIIIB) containing Brf2 instead of Brf1 and have extremely low levels of TFIIIC. Strikingly, expressed Pol III genes, unlike nonexpressed Pol III genes, are situated in regions with a pattern of histone modifications associated with functional Pol II promoters. TFIIIC alone associates with numerous ETC loci, via the B box or a novel motif. ETCs are often near CTCF binding sites, suggesting a potential role in chromosome organization. Our results suggest that human Pol III complexes associate preferentially with regions near functional Pol II promoters and that TFIIIC-mediated recruitment of TFIIIB is regulated in a locus-specific manner.

Genomic Binding Profiles of Functionally Distinct RNA Polymerase III Transcription Complexes in Human Cells

PubMed Central

Moqtaderi, Zarmik; Wang, Jie; Raha, Debasish; White, Robert J.; Snyder, Michael; Weng, Zhiping; Struhl, Kevin

2012-01-01

Genome-wide occupancy profiles of five components of the RNA Polymerase III (Pol III) machinery in human cells identified the expected tRNA and non-coding RNA targets and revealed many additional Pol III-associated loci, mostly near SINEs. Several genes are targets of an alternative TFIIIB containing Brf2 instead of Brf1 and have extremely low levels of TFIIIC. Strikingly, expressed Pol III genes, unlike non-expressed Pol III genes, are situated in regions with a pattern of histone modifications associated with functional Pol II promoters. TFIIIC alone associates with numerous ETC loci, via the B box or a novel motif. ETCs are often near CTCF binding sites, suggesting a potential role in chromosome organization. Our results suggest that human Pol III complexes associate preferentially with regions near functional Pol II promoters and that TFIIIC-mediated recruitment of TFIIIB is regulated in a locus-specific manner. PMID:20418883

Role for the MED21-MED7 Hinge in Assembly of the Mediator-RNA Polymerase II Holoenzyme*

PubMed Central

Sato, Shigeo; Tomomori-Sato, Chieri; Tsai, Kuang-Lei; Yu, Xiaodi; Sardiu, Mihaela; Saraf, Anita; Washburn, Michael P.; Florens, Laurence; Asturias, Francisco J.; Conaway, Ronald C.

2016-01-01

Mediator plays an integral role in activation of RNA polymerase II (Pol II) transcription. A key step in activation is binding of Mediator to Pol II to form the Mediator-Pol II holoenzyme. Here, we exploit a combination of biochemistry and macromolecular EM to investigate holoenzyme assembly. We identify a subset of human Mediator head module subunits that bind Pol II independent of other subunits and thus probably contribute to a major Pol II binding site. In addition, we show that binding of human Mediator to Pol II depends on the integrity of a conserved “hinge” in the middle module MED21-MED7 heterodimer. Point mutations in the hinge region leave core Mediator intact but lead to increased disorder of the middle module and markedly reduced affinity for Pol II. These findings highlight the importance of Mediator conformation for holoenzyme assembly. PMID:27821593

Eukaryotic DNA polymerase ζ

PubMed Central

Makarova, Alena V.; Burgers, Peter M.

2015-01-01

This review focuses on eukaryotic DNA polymerase ζ (Pol ζ), the enzyme responsible for the bulk of mutagenesis in eukaryotic cells in response to DNA damage. Pol ζ is also responsible for a large portion of mutagenesis during normal cell growth, in response to spontaneous damage or to certain DNA structures and other blocks that stall DNA replication forks. Novel insights in mutagenesis have been derived from recent advances in the elucidation of the subunit structure of Pol ζ. The lagging strand DNA polymerase δ shares the small Pol31 and Pol32 subunits with the Rev3-Rev7 core assembly giving a four subunit Pol ζ complex that is the active form in mutagenesis. Furthermore, Pol ζ forms essential interactions with the mutasome assembly factor Rev1 and with proliferating cell nuclear antigen (PCNA). These interactions are modulated by posttranslational modifications such as ubiquitination and phosphorylation that enhance translesion synthesis (TLS) and mutagenesis. PMID:25737057

Interpreting the rational addiction model.

PubMed

Ferguson, B S

2000-10-01

The rational addiction (RA) model of Becker and Murphy (Becker GS, Murphy KM. A theory of rational addiction. J Pol Econ 1988; 96(4): 675-700) has rapidly become one of the standard models in the literature on addictive behaviour. This paper reviews some theoretical issues surrounding its use, and indicates areas in which caution should be used in applying this model.

Inpatient Admissions and Costs Associated with Persistent Use of Dalfampridine Extended-Release in Multiple Sclerosis: A Claims Database Analysis.

PubMed

Guo, Amy; Niyazov, Alexander; Macaulay, Dendy; Terasawa, Emi; Schmerold, Luke; Wu, Eric Q; Krieger, Stephen

2017-07-01

While the clinical benefits of dalfampridine extended-release (D-ER) have been established in patients with multiple sclerosis (MS) through multiple clinical trials, there is limited real-world data on D-ER use, in particular the persistent use of D-ER, and associated acute care resource utilization and costs. To examine the real-world association of D-ER use and inpatient admissions and costs among patients with MS. This study was a retrospective observational claims analysis of the MarketScan database (April 2009-March 2014). Eligible patients consisted of adult enrollees aged 18-64 years who had (a) 12 months of continuous private plan enrollment preceding (baseline) and following (follow-up) the first D-ER claim; (b) ≥ 2 MS diagnosis codes with ≥ 1 during the baseline period; (c) ≥ 2 consecutive D-ER claims; and (d) no alternate gait-impairing etiologies during the baseline and follow-up periods. Patients were separated into 2 D-ER cohorts in the main analysis: persistent (≥ 360 days of D-ER supply) and nonpersistent (< 360 days of supply) users. Sensitivity analyses were conducted, examining additional breakdowns of days of supply within the nonpersistent cohort. Inpatient admissions (all-cause and MS-related) and health care expenditures were calculated and compared between the cohorts during follow-up using Wilcoxon rank-sum and chi-square tests. Regression models were conducted, controlling for age, sex, MS relapses, comorbidities, disease-modifying therapy use, and other baseline factors, including inpatient admissions and costs. Of 1,598 eligible patients, 719 (45.0%) were persistent D-ER users, and 879 (55.0%) were nonpersistent D-ER users. The 2 cohorts had similar demographic and clinical characteristics, with mean (SD) ages of 51.0 (8.4) and 50.6 (8.6) years and were 71.3% and 66.6% female, respectively. Compared with nonpersistent D-ER use, persistent D-ER use was associated with lower odds of all-cause inpatient admissions (OR = 0.58, P = 0.010) and MS-related inpatient admissions (OR = 0.50, P = 0.004). Persistent use was also associated with lower inpatient expenditures for all-cause admissions ($669 vs. $1,515, P = 0.002) and MS-related admissions ($388 vs. $891, P = 0.008). Persistent D-ER use was associated with significantly lower rates of all-cause and MS-related inpatient admissions and costs. Funding for this research and medical writing assistance was provided by Acorda Therapeutics. The study sponsor was involved in all stages of the study research and manuscript preparation. Guo and Niyazov were employees of Acorda Therapeutics at the time of this study and may own stock/stock options. Wu, Macaulay, Terasawa, and Schmerold are employees of Analysis Group, which received consultancy fees from Acorda Therapeutics for this project. Krieger was a consultant for Acorda Therapeutics for this project and has the following additional financial interests to report: consulting/advisory board work with Bayer, Biogen, EMD Serono, Novartis, Genentech, Genzyme, and Teva. Study concept and design were contributed by Guo, Niyazov, Macaulay, and Wu. Macaulay, Terasawa, Schmerold, and Wu helped prepare the data, and data interpretation was performed by Krieger, Guo, Niyazov, and Macaulay, along with Terasawa and Wu. The manuscript was written by Terasawa and Schmerold, along with Macaulay, and revised by all the authors. A portion of the current research was presented in poster format at the 2106 American Academy of Neurology Annual Meeting, which took place in Vancouver, BC, Canada, on April 15-21, 2016.

Stufenweise Integration von eLearning an der Technischen Universität München

NASA Astrophysics Data System (ADS)

Pätzold, Sebastian; Graf, Stephan; Gergintchev, Ivan; Pongratz, Hans; Rathmayer, Sabine

Der vorliegende Beitrag beschreibt als Best Practice Beispiel die stufenweise Integration eines Learning Management Systems (LMS) in die Infrastruktur von Information und Kommunikation (IuK) der Technischen Universität München (TUM). Dabei wird sowohl die Konsolidierung mehrfach angebotener Funktionalitäten und Dienste in den verschiedenen Portalen der Universität als auch die sukzessive Optimierung der Abläufe aufgezeigt. Gleichzeitig wird auf zukünftige weitere Entwicklungen hin zu einer vollständigen Integration der IuK, aber auch auf die Probleme in den unterschiedlichen Stadien der Entwicklung eingegangen.

Meilensteine in der Erforschung der kompakten Objekte

NASA Astrophysics Data System (ADS)

Camenzind, Max

Kompakte Objekte besitzen zum einen eine sehr hohe Dichte, und zum anderen sind sie durch die Tatsache charakterisiert, dass keine nuklearen Reaktionen mehr in ihrem Inneren stattfinden können. Aus diesem Grund können sie im Unterschied zu gewöhnlichen Sternen der Gravitation nicht mehr mit dem Druck des thermischen Gases widerstehen. In den Weißen Zwergen bzw. Neutronensternen wird der Gravitation der Quantendruck eines Elektronengases bzw. einer Neutronenflüssigkeit entgegengesetzt. Ein solches Gas besteht aus Elektronen bzw. Neutronen, die auf ihr niedrigstes Energieniveau zusammengepresst wurden. Durch die daraus resultierende hohe Bewegungsenergie der Fermionen wird der sogenannte Quantendruck erzeugt.

Extrusion & Compoundierung

NASA Astrophysics Data System (ADS)

Collin, Heinz; Schulze, Verena

Unter Extrusion wird das kontinuierliche Fördern von formbaren Massen verstanden. Dies können Kunststoffe, Teigwaren in der Lebensmittelindustrie oder auch keramische Massen sein. In der chemischen Industrie werden ebenfalls hochviskose (schwerfließende) Stoffe oder Pasten dosiert, gefördert und extrudiert. Früher waren vorzugsweise Kolbenstrangpressen im Einsatz, bis sich ab 1950 in steigendem Maße die Schneckenmaschinen durchgesetzt haben. Der weltweite Siegeszug der Kunststoffe ist zu einem erheblichen Teil auf die stetige technologische Weiterentwicklung im Bereich der Extrusionstechnik zurückzuführen. Der Markt der weltweit produzierten Maschinen für die Kunststoffverarbeitung erreichte im Jahr 2006 einen Wert von 20 Milliarden Euro und somit zählt dieser Bereich mittlerweile zu einem der großen Industriezweige [1].

Implantate in der Augenheilkunde

NASA Astrophysics Data System (ADS)

Dresp, Joachim H.

Im Bereich der Augenheilkunde findet sich die weltweit am häufigsten ausgeführte chirurgische Massnahme, die operative Behandlung des Grauen Stars: die Katarakt. Bei der Katarakt handelt es sich um eine Eintrübung der natürlichen Augenlinse, die sich je nach Stadium der Erkrankung leicht opak, über milchig bis zu bräunlich präsentiert. Mit dieser Zunahme der Undurchlässigkeit für das sichtbare Licht geht eine Abnahme des Sehvermögens einher, die bis zur totalen Erblindung führen kann. Bedingt durch die sehr eingeschränkten chirurgischen Möglichkeiten in den Ländern der Dritten Welt ist die Katarakt die Erblindungsursache Nummer 1 in der Welt. Ganz im Gegensatz hierzu ist in den industrialisierten Ländern Europas, Amerikas und Asiens die Katarakt-OP die sicherste chirurgische Intervention. In der Augenheilkunde werden Implantate aller drei Aggregatszustände verwendet.

Medizintechnik in der Tumororthopädie

NASA Astrophysics Data System (ADS)

Burgkart, Rainer; Gollwitzer, Hans; Holzapfel, Boris; Rudert, Maximilian; Rechl, Hans; Gradinger, Reiner

Die Behandlung der Knochentumoren unterlag in den letzten 20 Jahren einem raschen und stetigen Wandel, was zum einen auf die verbesserten Therapieerfolge durch den Einsatz von neoadjuvanten Therapieformen zurückzuführen ist, und andererseits von medizintechnischen Entwicklungen bezüglich moderner Schnittbilddiagnostik, neuer 3D Operationsplanungsverfahren wie das Rapid Prototyping und adaptiv modularer Tumorendoprothesensystemen u. a. begleitet wurde. Gerade die technischen Entwicklungen haben dazu geführt, daß im Bereich der Extremitäten und der Wirbelsäule radikalere Eingriffe durchgeführt werden können, was die lokale Tumorkontrolle wesentlich verbessert hat. In zunehmenden Maße werden deshalb nicht nur Kurzzeiterfolge sondern auch mittel- und langfristige Fortschritte bei der Behandlung der malignen Knochentumoren einschließlich der Metastasenbehandlung erreicht. Grundlage der Therapie ist dabei immer primär die Sicherung der Diagnose mittels Biopsie und die bildgebende sowie histologische Stadieneinteilung des malignen Tumors. Nach der Tumorresektion kann die Rekonstruktion biologisch oder mit Endoprothesensystemen erfolgen. Gerade die weiterentwickelten modularen Systeme führen zu guten funktionellen Ergebnissen mit langen Standzeiten und einer reduzierten Komplikationsrate. Individuell angefertigte Implantate sind vor allem im Bereich der Rekonstruktion komplexer Beckentumoren von großer klinischer Bedeutung.

Lesion bypass by S. cerevisiae Pol ζ alone

PubMed Central

Stone, Jana E.; Kumar, Dinesh; Binz, Sara K.; Inase, Aki; Iwai, Shigenori; Chabes, Andrei; Burgers, Peter M.; Kunkel, Thomas A.

2011-01-01

DNA polymerase zeta (Pol ζ) participates in translesion synthesis (TLS) of DNA adducts that stall replication fork progression. Previous studies have led to the suggestion that the primary role of Pol ζ in TLS is to extend primers created when another DNA polymerase inserts nucleotides opposite lesions. Here we test the non-exclusive possibility that Pol ζ can sometimes perform TLS in the absence of any other polymerase. To do so, we quantified the efficiency with which S. cerevisiae Pol ζ bypasses abasic sites, cis-syn cyclobutane pyrimidine dimers and (6-4) photoproducts. In reactions containing dNTP concentrations that mimic those induced by DNA damage, a Pol ζ derivative with phenylalanine substituted for leucine 979 at the polymerase active site bypasses all three lesions at efficiencies between 27–73%. Wild-type Pol ζ also bypasses these lesions, with efficiencies that are lower and depend on the sequence context in which the lesion resides. The results are consistent with the hypothesis that, in addition to extending aberrant termini created by other DNA polymerases, Pol ζ has the potential to be the sole DNA polymerase involved in TLS. PMID:21622032

Involvement of the Reparative DNA Polymerase Pol X of African Swine Fever Virus in the Maintenance of Viral Genome Stability In Vivo

PubMed Central

Redrejo-Rodríguez, Modesto; Rodríguez, Javier M.; Suárez, Cristina; Salas, José

2013-01-01

The function of the African swine fever virus (ASFV) reparative DNA polymerase, Pol X, was investigated in the context of virus infection. Pol X is a late structural protein that localizes at cytoplasmic viral factories during DNA replication. Using an ASFV deletion mutant lacking the Pol X gene, we have shown that Pol X is not required for virus growth in Vero cells or swine macrophages under one-step growth conditions. However, at a low multiplicity of infection, when multiple rounds of replication occur, the growth of the mutant virus is impaired in swine macrophages but not in Vero cells, suggesting that Pol X is needed to repair the accumulated DNA damage. The replication of the mutant virus in Vero cells presents sensitivity to oxidative damage, and mutational analysis of viral DNA shows that deletion of Pol X results in an increase in the mutation frequency in macrophages. Therefore, our data reveal a biological role for ASFV Pol X in the context of the infected cell in the preservation of viral genetic information. PMID:23824796

Structure of the initiation-competent RNA polymerase I and its implication for transcription

NASA Astrophysics Data System (ADS)

Pilsl, Michael; Crucifix, Corinne; Papai, Gabor; Krupp, Ferdinand; Steinbauer, Robert; Griesenbeck, Joachim; Milkereit, Philipp; Tschochner, Herbert; Schultz, Patrick

2016-07-01

Eukaryotic RNA polymerase I (Pol I) is specialized in rRNA gene transcription synthesizing up to 60% of cellular RNA. High level rRNA production relies on efficient binding of initiation factors to the rRNA gene promoter and recruitment of Pol I complexes containing initiation factor Rrn3. Here, we determine the cryo-EM structure of the Pol I-Rrn3 complex at 7.5 Å resolution, and compare it with Rrn3-free monomeric and dimeric Pol I. We observe that Rrn3 contacts the Pol I A43/A14 stalk and subunits A190 and AC40, that association re-organizes the Rrn3 interaction interface, thereby preventing Pol I dimerization; and Rrn3-bound and monomeric Pol I differ from the dimeric enzyme in cleft opening, and localization of the A12.2 C-terminus in the active centre. Our findings thus support a dual role for Rrn3 in transcription initiation to stabilize a monomeric initiation competent Pol I and to drive pre-initiation complex formation.

Characterization of a Y-Family DNA Polymerase eta from the Eukaryotic Thermophile Alvinella pompejana

DOE PAGES

Kashiwagi, Sayo; Kuraoka, Isao; Fujiwara, Yoshie; ...

2010-01-01

Humore » man DNA polymerase η (HsPol η ) plays an important role in translesion synthesis (TLS), which allows for replication past DNA damage such as UV-induced cis-syn cyclobutane pyrimidine dimers (CPDs). Here, we characterized ApPol η from the thermophilic worm Alvinella pompejana , which inhabits deep-sea hydrothermal vent chimneys. ApPol η shares sequence homology with HsPol η and contains domains for binding ubiquitin and proliferating cell nuclear antigen. Sun-induced UV does not penetrate Alvinella's environment; however, this novel DNA polymerase catalyzed efficient and accurate TLS past CPD, as well as 7,8-dihydro-8-oxoguanine and isomers of thymine glycol induced by reactive oxygen species. In addition, we found that ApPol η is more thermostable than HsPol η , as expected from its habitat temperature. Moreover, the activity of this enzyme was retained in the presence of a higher concentration of organic solvents. Therefore, ApPol η provides a robust, human-like Pol η that is more active after exposure to high temperatures and organic solvents.« less

Characterization of a Y-Family DNA Polymerase eta from the Eukaryotic Thermophile Alvinella pompejana

PubMed Central

Kashiwagi, Sayo; Kuraoka, Isao; Fujiwara, Yoshie; Hitomi, Kenichi; Cheng, Quen J.; Fuss, Jill O.; Shin, David S.; Masutani, Chikahide; Tainer, John A.; Hanaoka, Fumio; Iwai, Shigenori

2010-01-01

Human DNA polymerase η (HsPolη) plays an important role in translesion synthesis (TLS), which allows for replication past DNA damage such as UV-induced cis-syn cyclobutane pyrimidine dimers (CPDs). Here, we characterized ApPolη from the thermophilic worm Alvinella pompejana, which inhabits deep-sea hydrothermal vent chimneys. ApPolη shares sequence homology with HsPolη and contains domains for binding ubiquitin and proliferating cell nuclear antigen. Sun-induced UV does not penetrate Alvinella's environment; however, this novel DNA polymerase catalyzed efficient and accurate TLS past CPD, as well as 7,8-dihydro-8-oxoguanine and isomers of thymine glycol induced by reactive oxygen species. In addition, we found that ApPolη is more thermostable than HsPolη, as expected from its habitat temperature. Moreover, the activity of this enzyme was retained in the presence of a higher concentration of organic solvents. Therefore, ApPolη provides a robust, human-like Polη that is more active after exposure to high temperatures and organic solvents. PMID:20936172

Analytical theory of the hydrophobic effect of solutes in water.

PubMed

Urbic, Tomaz; Dill, Ken A

2017-09-01

We develop an analytical statistical-mechanical model for hydrophobic solvation in water. In this three-dimensional Mercedes-Benz-like model, two neighboring waters have three possible interaction states: a radial van der Waals interaction, a tetrahedral orientation-dependent hydrogen-bonding interaction, or no interaction. Nonpolar solutes are modeled as van der Waals particles of different radii. The model is sufficiently simple that we can calculate the partition function and thermal and volumetric properties of solvation versus temperature, pressure, and solute radius. Predictions are in good agreement with results of Monte Carlo simulations. And their trends agree with experiments on hydrophobic solute insertion. The theory shows that first-shell waters are more highly structured than bulk waters, because of hydrogen bonding, and that that structure melts out faster with temperature than it does in bulk waters. Because the theory is analytical, it can explore a broad range of solvation properties and anomalies of water, at minimal computational expense.

Analytical theory of the hydrophobic effect of solutes in water

NASA Astrophysics Data System (ADS)

Urbic, Tomaz; Dill, Ken A.

2017-09-01

We develop an analytical statistical-mechanical model for hydrophobic solvation in water. In this three-dimensional Mercedes-Benz-like model, two neighboring waters have three possible interaction states: a radial van der Waals interaction, a tetrahedral orientation-dependent hydrogen-bonding interaction, or no interaction. Nonpolar solutes are modeled as van der Waals particles of different radii. The model is sufficiently simple that we can calculate the partition function and thermal and volumetric properties of solvation versus temperature, pressure, and solute radius. Predictions are in good agreement with results of Monte Carlo simulations. And their trends agree with experiments on hydrophobic solute insertion. The theory shows that first-shell waters are more highly structured than bulk waters, because of hydrogen bonding, and that that structure melts out faster with temperature than it does in bulk waters. Because the theory is analytical, it can explore a broad range of solvation properties and anomalies of water, at minimal computational expense.

Nuclear DNA polymerase beta from Leishmania infantum. Cloning, molecular analysis and developmental regulation

PubMed Central

Taladriz, Soraya; Hanke, Tobias; Ramiro, María J.; García-Díaz, Miguel; Lacoba, Mario García de; Blanco, Luis; Larraga, Vicente

2001-01-01

We have identified a novel polymerase beta (Pol β)-like enzyme from Leishmania infantum, a parasite protozoon causing disease in humans. This protein, named Li Pol β, shows a nuclear localization that contrasts with the mitochondrial localization of Pol β from Crithidia fasciculata, a closely related parasite, the only polymerase β described so far in Trypanosomatidae. Li Pol β, that belongs to the DNA polymerase X family, displays an evolutionarily conserved Pol β-type DNA polymerase core, in which most of the key residues involved in DNA binding, nucleotide binding, dRPase and polymerization catalysis are conserved. In agreement with this, Li Pol β, overproduced in Escherichia coli, displayed intrinsic DNA polymerase activity. Cell synchronization experiments showed a correlation between both Li Pol β mRNA and protein levels along the parasite cell cycle. Analysis of these parameters at the different growth phases of the parasite, from the proliferative (non-infective) logarithmic phase to the non-dividing (highly infectious) stationary phase, showed high levels of Li Pol β at the infective phase of the parasite. The data suggest a role of Li Pol β in base excision repair in L.infantum, a parasite usually affected by oxygen stress environments into the macrophage host cells. PMID:11557814

Foamy virus reverse transcriptase is expressed independently from the Gag protein.

PubMed Central

Enssle, J; Jordan, I; Mauer, B; Rethwilm, A

1996-01-01

In the foamy virus (FV) subgroup of retroviruses the pol genes are located in the +1 reading frame relative to the gag genes and possess potential ATG initiation codons in their 5' regions. This genome organization suggests either a + 1 ribosomal frameshift to generate a Gag-Pol fusion protein, similar to all other retroviruses studied so far, or new initiation of Pol translation, as used by pararetroviruses, to express the Pol protein. By using a genetic approach we have ruled out the former possibility and provide evidence for the latter. Two down-mutations (M53 and M54) of the pol ATG codon were found to abolish replication and Pol protein expression of the human FV isolate. The introduction of a new ATG in mutation M55, 3' to the down-mutated ATG of mutation M53, restored replication competence, indicating that the pol ATG functions as a translational initiation codon. Two nonsense mutants (M56 and M57), which functionally separated gag and pol with respect to potential frame-shifting sites, were also replication-competent, providing further genetic evidence that FVs express the Pol protein independently from Gag. Our results show that during a particular step of the replication cycle, FVs differ fundamentally from all other retroviruses. Images Fig. 3 PMID:8633029

ASSESSING POPULATION EXPOSURES TO MULTIPLE AIR POLLUTANTS USING A MECHANISTIC SOURCE-TO-DOSE MODELING FRAMEWORK

EPA Science Inventory

The Modeling Environment for Total Risks studies (MENTOR) system, combined with an extension of the SHEDS (Stochastic Human Exposure and Dose Simulation) methodology, provide a mechanistically consistent framework for conducting source-to-dose exposure assessments of multiple pol...

Human cytomegalovirus and Herpes Simplex type I virus can engage RNA polymerase I for transcription of immediate early genes

PubMed Central

Kostopoulou, Ourania N.; Wilhelmi, Vanessa; Raiss, Sina; Ananthaseshan, Sharan; Lindström, Mikael S.; Bartek, Jiri; Söderberg-Naucler, Cecilia

2017-01-01

Human cytomegalovirus (HCMV) utilizes RNA polymerase II to transcribe viral genes and produce viral mRNAs. It can specifically target the nucleolus to facilitate viral transcription and translation. As RNA polymerase I (Pol I)-mediated transcription is active in the nucleolus, we investigated the role of Pol I, along with relative contributions of the human Pol II and Pol III, to early phases of viral transcription in HCMV infected cells, compared with Herpes Simplex Virus-1 (HSV-1) and Murine cytomegalovirus (MCMV). Inhibition of Pol I with siRNA or the Pol I inhibitors CX-5461 or Actinomycin D (5nM) resulted in significantly decreased IE and pp65 mRNA and protein levels in human fibroblasts at early times post infection. This initially delayed replication was compensated for later during the replication process, at which stage it didn’t significantly affect virus production. Pol I inhibition also reduced HSV-1 ICP0 and gB transcripts, suggesting that some herpesviruses engage Pol I for their early transcription. In contrast, inhibition of Pol I failed to affect MCMV transcription. Collectively, our results contribute to better understanding of the functional interplay between RNA Pol I-mediated nucleolar events and the Herpes viruses, particularly HCMV whose pathogenic impact ranges from congenital malformations and potentially deadly infections among immunosuppressed patients, up to HCMV’s emerging oncomodulatory role in human tumors. PMID:29228551

Uniform Free-Energy Profiles of the P-O Bond Formation and Cleavage Reactions Catalyzed by DNA Polymerases β and λ.

PubMed

Klvaňa, Martin; Bren, Urban; Florián, Jan

2016-12-29

Human X-family DNA polymerases β (Polβ) and λ (Polλ) catalyze the nucleotidyl-transfer reaction in the base excision repair pathway of the cellular DNA damage response. Using empirical valence bond and free-energy perturbation simulations, we explore the feasibility of various mechanisms for the deprotonation of the 3'-OH group of the primer DNA strand, and the subsequent formation and cleavage of P-O bonds in four Polβ, two truncated Polλ (tPolλ), and two tPolλ Loop1 mutant (tPolλΔL1) systems differing in the initial X-ray crystal structure and nascent base pair. The average calculated activation free energies of 14, 18, and 22 kcal mol -1 for Polβ, tPolλ, and tPolλΔL1, respectively, reproduce the trend in the observed catalytic rate constants. The most feasible reaction pathway consists of two successive steps: specific base (SB) proton transfer followed by rate-limiting concerted formation and cleavage of the P-O bonds. We identify linear free-energy relationships (LFERs) which show that the differences in the overall activation and reaction free energies among the eight studied systems are determined by the reaction free energy of the SB proton transfer. We discuss the implications of the LFERs and suggest pK a of the 3'-OH group as a predictor of the catalytic rate of X-family DNA polymerases.

Uniform Free-Energy Profiles of the P–O Bond Formation and Cleavage Reactions Catalyzed by DNA Polymerases β and λ

PubMed Central

2016-01-01

Human X-family DNA polymerases β (Polβ) and λ (Polλ) catalyze the nucleotidyl-transfer reaction in the base excision repair pathway of the cellular DNA damage response. Using empirical valence bond and free-energy perturbation simulations, we explore the feasibility of various mechanisms for the deprotonation of the 3′-OH group of the primer DNA strand, and the subsequent formation and cleavage of P–O bonds in four Polβ, two truncated Polλ (tPolλ), and two tPolλ Loop1 mutant (tPolλΔL1) systems differing in the initial X-ray crystal structure and nascent base pair. The average calculated activation free energies of 14, 18, and 22 kcal mol–1 for Polβ, tPolλ, and tPolλΔL1, respectively, reproduce the trend in the observed catalytic rate constants. The most feasible reaction pathway consists of two successive steps: specific base (SB) proton transfer followed by rate-limiting concerted formation and cleavage of the P–O bonds. We identify linear free-energy relationships (LFERs) which show that the differences in the overall activation and reaction free energies among the eight studied systems are determined by the reaction free energy of the SB proton transfer. We discuss the implications of the LFERs and suggest pKa of the 3′-OH group as a predictor of the catalytic rate of X-family DNA polymerases. PMID:27992186

Quantum mechanical force field for hydrogen fluoride with explicit electronic polarization.

PubMed

Mazack, Michael J M; Gao, Jiali

2014-05-28

The explicit polarization (X-Pol) theory is a fragment-based quantum chemical method that explicitly models the internal electronic polarization and intermolecular interactions of a chemical system. X-Pol theory provides a framework to construct a quantum mechanical force field, which we have extended to liquid hydrogen fluoride (HF) in this work. The parameterization, called XPHF, is built upon the same formalism introduced for the XP3P model of liquid water, which is based on the polarized molecular orbital (PMO) semiempirical quantum chemistry method and the dipole-preserving polarization consistent point charge model. We introduce a fluorine parameter set for PMO, and find good agreement for various gas-phase results of small HF clusters compared to experiments and ab initio calculations at the M06-2X/MG3S level of theory. In addition, the XPHF model shows reasonable agreement with experiments for a variety of structural and thermodynamic properties in the liquid state, including radial distribution functions, interaction energies, diffusion coefficients, and densities at various state points.

Understanding the Physical and Molecular Basis of Stability of Arabidopsis DNA Pol λ under UV-B and High NaCl Stress.

PubMed

Roy, Sujit; Banerjee, Victor; Das, Kali Pada

2015-01-01

Here, we have investigated the physical and molecular basis of stability of Arabidopsis DNA Pol λ, the sole X family DNA polymerase member in plant genome, under UV-B and salinity stress in connection with the function of the N-terminal BRCT (breast cancer-associated C terminus) domain and Ser-Pro rich region in the regulation of the overall structure of this protein. Tryptophan fluorescence studies, fluorescence quenching and Bis-ANS binding experiments using purified recombinant full length Pol λ and its N-terminal deletion forms have revealed UV-B induced conformational change in BRCT domain deficient Pol λ. On the other hand, the highly conserved C-terminal catalytic core PolX domain maintained its tertiary folds under similar condition. Circular dichroism (CD) and fourier transform infrared (FT-IR) spectral studies have indicated appreciable change in the secondary structural elements in UV-B exposed BRCT domain deficient Pol λ. Increased thermodynamic stability of the C-terminal catalytic core domain suggested destabilizing effect of the N-terminal Ser-Pro rich region on the protein structure. Urea-induced equilibrium unfolding studies have revealed increased stability of Pol λ and its N-terminal deletion mutants at high NaCl concentration. In vivo aggregation studies using transient expression systems in Arabidopsis and tobacco indicated possible aggregation of Pol λ lacking the BRCT domain. Immunoprecipitation assays revealed interaction of Pol λ with the eukaryotic molecular chaperone HSP90, suggesting the possibility of regulation of Pol λ stability by HSP90 in plant cell. Overall, our results have provided one of the first comprehensive information on the biophysical characteristics of Pol λ and indicated the importance of both BRCT and Ser-Pro rich modules in regulating the stability of this protein under genotoxic stress in plants.

Replicative DNA Polymerase δ but Not ε Proofreads Errors in Cis and in Trans

PubMed Central

Flood, Carrie L.; Rodriguez, Gina P.; Bao, Gaobin; Shockley, Arthur H.; Kow, Yoke Wah; Crouse, Gray F.

2015-01-01

It is now well established that in yeast, and likely most eukaryotic organisms, initial DNA replication of the leading strand is by DNA polymerase ε and of the lagging strand by DNA polymerase δ. However, the role of Pol δ in replication of the leading strand is uncertain. In this work, we use a reporter system in Saccharomyces cerevisiae to measure mutation rates at specific base pairs in order to determine the effect of heterozygous or homozygous proofreading-defective mutants of either Pol ε or Pol δ in diploid strains. We find that wild-type Pol ε molecules cannot proofread errors created by proofreading-defective Pol ε molecules, whereas Pol δ can not only proofread errors created by proofreading-defective Pol δ molecules, but can also proofread errors created by Pol ε-defective molecules. These results suggest that any interruption in DNA synthesis on the leading strand is likely to result in completion by Pol δ and also explain the higher mutation rates observed in Pol δ-proofreading mutants compared to Pol ε-proofreading defective mutants. For strains reverting via AT→GC, TA→GC, CG→AT, and GC→AT mutations, we find in addition a strong effect of gene orientation on mutation rate in proofreading-defective strains and demonstrate that much of this orientation dependence is due to differential efficiencies of mispair elongation. We also find that a 3′-terminal 8 oxoG, unlike a 3′-terminal G, is efficiently extended opposite an A and is not subject to proofreading. Proofreading mutations have been shown to result in tumor formation in both mice and humans; the results presented here can help explain the properties exhibited by those proofreading mutants. PMID:25742645

DNA polymerase θ (POLQ) can extend from mismatches and from bases opposite a (6–4) photoproduct

PubMed Central

Seki, Mineaki; Wood, Richard D.

2007-01-01

DNA polymerase θ (pol θ) is a nuclear A-family DNA polymerase encoded by the POLQ gene in vertebrate cells. The biochemical properties of pol θ and of Polq-defective mice have suggested that pol θ participates in DNA damage tolerance. For example, pol θ was previously found to be proficient not only in incorporation of a nucleotide opposite a thymine glycol or an abasic site, but also extends a polynucleotide chain efficiently from the base opposite the lesion. We carried out experiments to determine whether this ability to extend from non-standard termini is a more general property of the enzyme. Pol θ extended relatively efficiently from matched termini as well as termini with A:G, A:T, and A:C mismatches, with less descrimination than a well-studied A family DNA polymerase, exonuclease-free pol I from E. coli. Although pol θ was unable to, by itself, bypass a cyclobutane pyrimidine dimer or a (6–4) photoproduct, it could perform some extension from primers with bases placed across from these lesions. When pol θ was combined with DNA polymerase ι , an enzyme that can insert a base opposite a UV-induced (6–4) photoproduct, complete bypass of a (6–4) photoproduct was possible. These data show that in addition to its ability to insert nucleotides opposite some DNA lesions, pol θ is proficient at extension of unpaired termini. These results show the potential of pol θ to act as an extender after incorporation of nucleotides by other DNA polymerases, and aid in understanding the role of pol θ in somatic mutagenesis and genome instability. PMID:17920341

DNA polymerase theta (POLQ) can extend from mismatches and from bases opposite a (6-4) photoproduct.

PubMed

Seki, Mineaki; Wood, Richard D

2008-01-01

DNA polymerase theta (pol theta) is a nuclear A-family DNA polymerase encoded by the POLQ gene in vertebrate cells. The biochemical properties of pol theta and of Polq-defective mice have suggested that pol theta participates in DNA damage tolerance. For example, pol theta was previously found to be proficient not only in incorporation of a nucleotide opposite a thymine glycol or an abasic site, but also extends a polynucleotide chain efficiently from the base opposite the lesion. We carried out experiments to determine whether this ability to extend from non-standard termini is a more general property of the enzyme. Pol theta extended relatively efficiently from matched termini as well as termini with A:G, A:T and A:C mismatches, with less descrimination than a well-studied A-family DNA polymerase, exonuclease-free pol I from E. coli. Although pol theta was unable to, by itself, bypass a cyclobutane pyrimidine dimer or a (6-4) photoproduct, it could perform some extension from primers with bases placed across from these lesions. When pol theta was combined with DNA polymerase iota, an enzyme that can insert a base opposite a UV-induced (6-4) photoproduct, complete bypass of a (6-4) photoproduct was possible. These data show that in addition to its ability to insert nucleotides opposite some DNA lesions, pol theta is proficient at extension of unpaired termini. These results show the potential of pol theta to act as an extender after incorporation of nucleotides by other DNA polymerases, and aid in understanding the role of pol theta in somatic mutagenesis and genome instability.

Alteration of BRCA1 expression affects alcohol-induced transcription of RNA Pol III-dependent genes.

PubMed

Zhong, Qian; Shi, Ganggang; Zhang, Yanmei; Lu, Lei; Levy, Daniel; Zhong, Shuping

2015-02-01

Emerging evidence has indicated that alcohol consumption is an established risk factor for breast cancer. Deregulation of RNA polymerase III (Pol III) transcription enhances cellular Pol III gene production, leading to an increase in translational capacity to promote cell transformation and tumor formation. We have reported that alcohol intake increases Pol III gene transcription to promote cell transformation and tumor formation in vitro and in vivo. Studies revealed that tumor suppressors, pRb, p53, PTEN and Maf1 repress the transcription of Pol III genes. BRCA1 is a tumor suppressor and its mutation is tightly related to breast cancer development. However, it is not clear whether BRCA1 expression affects alcohol-induced transcription of Pol III genes. At the present studies, we report that restoring BRCA1 in HCC 1937 cells, which is a BRCA1 deficient cell line, represses Pol III gene transcription. Expressing mutant or truncated BRCA1 in these cells does not affect the ability of repression on Pol III genes. Our analysis has demonstrated that alcohol induces Pol III gene transcription. More importantly, overexpression of BRCA1 in estrogen receptor positive (ER+) breast cancer cells (MCF-7) decreases the induction of tRNA(Leu) and 5S rRNA genes by alcohol, whereas reduction of BRCA1 by its siRNA slightly increases the transcription of the class of genes. This suggests that BRCA1 is associated with alcohol-induced deregulation of Pol III genes. These studies for the first time demonstrate the role of BRCA1 in induction of Pol III genes by alcohol and uncover a novel mechanism of alcohol-associated breast cancer. Copyright © 2014 Elsevier B.V. All rights reserved.

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

Poore, WP

The vision of the Distributed Energy Research Program (DER) program of the U.S. Department of Energy (DOE) is that the United States will have the cleanest and most efficient and reliable energy system in the world by maximizing the use of affordable distributed energy resources. Electricity consumers will be able to choose from a diverse number of efficient, cost-effective, and environmentally friendly distributed energy options and easily connect them into the nation's energy infrastructure while providing benefits to their owners and other stakeholders. The long-term goal of this vision is that DER will achieve a 20% share of new electricmore » capacity additions in the United States by 2010, thereby helping to make the nation's electric power generation and delivery system more efficient, reliable, secure, clean, economical, and diverse in terms of fuel use (oil, natural gas, solar, hydroelectric, etc.) and prime mover resource (solar, wind, gas turbines, etc.). Near- and mid-term goals are to develop new technologies for implementing and operating DER and address barriers associated with DER usage and then to reduce costs and emissions and improve the efficiency and reliability of DER. Numerous strategies for meeting these goals have been developed into a research, development, and demonstration (RD&D) program that supports generation and delivery systems architecture, including modeling and simulation tools. The benefits associated with DER installations are often significant and numerous. They almost always provide tangible economic benefits, such as energy savings or transmission and distribution upgrade deferrals, as well as intangible benefits, such as power quality improvements that lengthen maintenance or repair intervals for power equipment. Also, the benefits routinely are dispersed among end users, utilities, and the public. For instance, an end user may use the DER to reduce their peak demand and save money due to lower demand charges. Reduced end user peak demand, in turn, may lower a distribution system peak load such that upgrades are deferred or avoided. This could benefit other consumers by providing them with higher reliability and power quality as well as avoiding their cost share of a distribution system upgrade. In this example, the costs of the DER may be born by the end user, but that user reaps only a share of the benefits. This report, the first product of a study to quantify the value of DER, documents initial project efforts to develop an assessment methodology. The focus of currently available site-specific DER assessment techniques are typically limited to two parties, the owner/user and the local utility. Rarely are the impacts on other stakeholders, including interconnected distribution utilities, transmission system operators, generating system operators, other local utility customers, local and regional industry and business, various levels of government, and the environment considered. The goal of this assessment is to quantify benefits and cost savings that accrue broadly across a region, recognizing that DER installations may have local, regional, or national benefits.« less

UVB Induces a Genome-Wide Acting Negative Regulatory Mechanism That Operates at the Level of Transcription Initiation in Human Cells

PubMed Central

Gyenis, Ákos; Umlauf, David; Újfaludi, Zsuzsanna; Boros, Imre; Ye, Tao; Tora, Làszlò

2014-01-01

Faithful transcription of DNA is constantly threatened by different endogenous and environmental genotoxic effects. Transcription coupled repair (TCR) has been described to stop transcription and quickly remove DNA lesions from the transcribed strand of active genes, permitting rapid resumption of blocked transcription. This repair mechanism has been well characterized in the past using individual target genes. Moreover, numerous efforts investigated the fate of blocked RNA polymerase II (Pol II) during DNA repair mechanisms and suggested that stopped Pol II complexes can either backtrack, be removed and degraded or bypass the lesions to allow TCR. We investigated the effect of a non-lethal dose of UVB on global DNA-bound Pol II distribution in human cells. We found that the used UVB dose did not induce Pol II degradation however surprisingly at about 93% of the promoters of all expressed genes Pol II occupancy was seriously reduced 2–4 hours following UVB irradiation. The presence of Pol II at these cleared promoters was restored 5–6 hours after irradiation, indicating that the negative regulation is very dynamic. We also identified a small set of genes (including several p53 regulated genes), where the UVB-induced Pol II clearing did not operate. Interestingly, at promoters, where Pol II promoter clearance occurs, TFIIH, but not TBP, follows the behavior of Pol II, suggesting that at these genes upon UVB treatment TFIIH is sequestered for DNA repair by the TCR machinery. In agreement, in cells where the TCR factor, the Cockayne Syndrome B protein, was depleted UVB did not induce Pol II and TFIIH clearance at promoters. Thus, our study reveals a UVB induced negative regulatory mechanism that targets Pol II transcription initiation on the large majority of transcribed gene promoters, and a small subset of genes, where Pol II escapes this negative regulation. PMID:25058334

Basis of Miscoding of the DNA Adduct N2,3-Ethenoguanine by Human Y-family DNA Polymerases*

PubMed Central

Zhao, Linlin; Pence, Matthew G.; Christov, Plamen P.; Wawrzak, Zdzislaw; Choi, Jeong-Yun; Rizzo, Carmelo J.; Egli, Martin; Guengerich, F. Peter

2012-01-01

N2,3-Ethenoguanine (N2,3-ϵG) is one of the exocyclic DNA adducts produced by endogenous processes (e.g. lipid peroxidation) and exposure to bioactivated vinyl monomers such as vinyl chloride, which is a known human carcinogen. Existing studies exploring the miscoding potential of this lesion are quite indirect because of the lability of the glycosidic bond. We utilized a 2′-fluoro isostere approach to stabilize this lesion and synthesized oligonucleotides containing 2′-fluoro-N2,3-ϵ-2′-deoxyarabinoguanosine to investigate the miscoding potential of N2,3-ϵG by Y-family human DNA polymerases (pols). In primer extension assays, pol η and pol κ replicated through N2,3-ϵG, whereas pol ι and REV1 yielded only 1-base incorporation. Steady-state kinetics revealed that dCTP incorporation is preferred opposite N2,3-ϵG with relative efficiencies in the order of pol κ > REV1 > pol η ≈ pol ι, and dTTP misincorporation is the major miscoding event by all four Y-family human DNA pols. Pol ι had the highest dTTP misincorporation frequency (0.71) followed by pol η (0.63). REV1 misincorporated dTTP and dGTP with much lower frequencies. Crystal structures of pol ι with N2,3-ϵG paired to dCTP and dTTP revealed Hoogsteen-like base pairing mechanisms. Two hydrogen bonds were observed in the N2,3-ϵG:dCTP base pair, whereas only one appears to be present in the case of the N2,3-ϵG:dTTP pair. Base pairing mechanisms derived from the crystal structures explain the slightly favored dCTP insertion for pol ι in steady-state kinetic analysis. Taken together, these results provide a basis for the mutagenic potential of N2,3-ϵG. PMID:22910910

DNA Polymerase λ Inactivation by Oxidized Abasic Sites&

PubMed Central

Stevens, Adam J.; Guan, Lirui; Bebenek, Katarzyna; Kunkel, Thomas A.; Greenberg, Marc M.

2013-01-01

Base excision repair plays a vital role in maintaining genomic integrity in mammalian cells. DNA polymerase λ is believed to play a backup role to DNA polymerase β in base excision repair. Two oxidized abasic lesions that are produced by a variety of DNA damaging agents, including several antitumor antibiotics, the C4′-oxidized abasic site following Ape1 incision (pC4-AP) and 5′-(2-phosphoryl-1,4-dioxobutane) (DOB), irreversibly inactivate Pol β and Pol λ. The interactions of DOB and pC4-AP with Pol λ are examined in detail using DNA substrates containing these lesions at defined sites. Single turnover kinetic experiments show that Pol λ excises DOB almost 13-times more slowly than a 5′-phosphorylated 2-deoxyribose (dRP). pC4-AP is excised approximately twice as fast as DOB. The absolute rate constants are considerably slower than those reported for Pol β at the respective reactions, suggesting that Pol λ may be an inefficient backup in BER. DOB inactivates Pol λ approximately 3-fold less efficiently than it does Pol β and the difference is attributable to a higher KI (33 ± 7 nM). Inactivation of Pol λ’s lyase activity by DOB also prevents the enzyme from carrying out polymerization following preincubation of the protein and DNA. Mass spectral analysis of GluC digested Pol λ inactivated by DOB shows that Lys324 is modified. There is inferential support that Lys312 may also be modified. Both residues are within the Pol λ lyase active site. Protein modification involves reaction with released but-2-ene-1,4-dial. When acting on pC4-AP, Pol λ achieves approximately 4 turnovers on average before being inactivated. Lyase inactivation by pC4-AP is also accompanied by loss of polymerase activity and mass spectrometry indicates that Lys312 and Lys324 are modified by the lesion. The ability of DOB and pC4-AP to inactivate Pol λ provides additional evidence that these lesions are significant sources of the cytotoxicity of DNA damaging agents that produce them. PMID:23330920

Gammaretroviral pol sequences act in cis to direct polysome loading and NXF1/NXT-dependent protein production by gag-encoded RNA.

PubMed

Bartels, Hanni; Luban, Jeremy

2014-09-12

All retroviruses synthesize essential proteins via alternatively spliced mRNAs. Retrovirus genera, though, exploit different mechanisms to coordinate the synthesis of proteins from alternatively spliced mRNAs. The best studied of these retroviral, post-transcriptional effectors are the trans-acting Rev protein of lentiviruses and the cis-acting constitutive transport element (CTE) of the betaretrovirus Mason-Pfizer monkey virus (MPMV). How members of the gammaretrovirus genus translate protein from unspliced RNA has not been elucidated. The mechanism by which two gammaretroviruses, XMRV and MLV, synthesize the Gag polyprotein (Pr65Gag) from full-length, unspliced mRNA was investigated here. The yield of Pr65Gag from a gag-only expression plasmid was found to be at least 30-fold less than that from an otherwise isogenic gag-pol expression plasmid. A frameshift mutation disrupting the pol open reading frame within the gag-pol expression plasmid did not decrease Pr65Gag production and 398 silent nucleotide changes engineered into gag rendered Pr65Gag synthesis pol-independent. These results are consistent with pol-encoded RNA acting in cis to promote Pr65Gag translation. Two independently-acting pol fragments were identified by screening 17 pol deletion mutations. To determine the mechanism by which pol promoted Pr65Gag synthesis, gag RNA in total and cytoplasmic fractions was quantitated by northern blot and by RT-PCR. The pol sequences caused, maximally, three-fold increase in total or cytoplasmic gag mRNA. Instead, pol sequences increased gag mRNA association with polyribosomes ~100-fold, a magnitude sufficient to explain the increase in Pr65Gag translation efficiency. The MPMV CTE, an NXF1-binding element, substituted for pol in promoting Pr65Gag synthesis. A pol RNA stem-loop resembling the CTE promoted Pr65Gag synthesis. Over-expression of NXF1 and NXT, host factors that bind to the MPMV CTE, synergized with pol to promote gammaretroviral gag RNA loading onto polysomes and to increase Pr65Gag synthesis. Conversely, Gag polyprotein synthesis was decreased by NXF1 knockdown. Finally, overexpression of SRp20, a shuttling protein that binds to NXF1 and promotes NXF1 binding to RNA, also increased gag RNA loading onto polysomes and increased Pr65Gag synthesis. These experiments demonstrate that gammaretroviral pol sequences act in cis to recruit NXF1 and SRp20 to promote polysome loading of gag RNA and, thereby license the synthesis of Pr65Gag from unspliced mRNA.

Zeitlicher Verlauf der avaskulären Nekrose des Hüftkopfes bei Patienten mit Pemphigus vulgaris.

PubMed

Balighi, Kamran; Daneshpazhooh, Maryam; Aghazadeh, Nessa; Saeidi, Vahide; Shahpouri, Farzam; Hejazi, Pardis; Chams-Davatchi, Cheyda

2016-10-01

Pemphigus vulgaris (PV) wird in der Regel mit systemischen Corticosteroiden und Immunsuppressiva behandelt. Avaskuläre Nekrose (AVN) des Hüftkopfes ist eine gut bekannte schwerere Komplikation einer Corticosteroid-Therapie. Die Charakteristika dieser schweren Komplikation bei PV sind nach wie vor unbekannt. Nicht kontrollierte, retrospektive Untersuchung aller PV-bedingten AVN-Fälle, die in einer iranischen Klinik für bullöse Autoimmunerkrankungen zwischen 1985 und 2013 diagnostiziert wurden. Anhand der Krankenakten von 2321 untersuchten PV-Patienten wurden 45 Fälle (1,93 %) von femoraler AVN identifiziert. Dreißig davon waren Männer. Das mittlere Alter bei der Diagnose der AVN betrug 47,4 ± 14,2 Jahre. Der mittlere Zeitraum zwischen der Diagnose des PV und dem Einsetzen der AVN lag bei 25,3 ± 18,3 Monaten. Mit Ausnahme von acht Fällen (17,8 %) setzte die AVN bei der Mehrheit der Patienten innerhalb von drei Jahren nach Diagnose des PV ein. Die mittlere kumulative Dosis von Prednisolon bei Patienten mit AVN betrug 13.115,8 ± 7041,1 mg. Zwischen der Prednisolon-Gesamtdosis und dem Zeitraum bis zum Einsetzen der AVN bestand eine starke Korrelation (p = 0,001). Bei Patienten mit Alendronateinnahme in der Vorgeschichte war dieser Zeitraum signifikant kürzer (p = 0,01). Die AVN ist eine schwere Komplikation einer Corticosteroid-Behandlung bei Patienten mit PV. Sie wird bei 2 % der Patienten beobachtet und tritt vor allem in den ersten drei Behandlungsjahren auf. Bei Patienten, die höhere Dosen von Prednisolon erhalten, setzt die AVN tendenziell früher ein. © 2016 Deutsche Dermatologische Gesellschaft (DDG). Published by John Wiley & Sons Ltd.

Umsetzung der Unternehmensstrategie mit der Balanced Scorecard

NASA Astrophysics Data System (ADS)

Crespo, Isabel; Bergmann, Lars; Portmann, Stefan; Lacker, Thomas; Lacker, Michael; Fleischmann, Jürgen; Kozó, Hans

Die Balanced Scorecard (BSC) ist ein Ansatz zum strategischen Management, der neben der Ausrichtung des Unternehmens auf finanzielle Zielwerte ebenso großes Gewicht auf so genannte weiche Faktoren legt, die den wirtschaftlichen Erfolg eines Unternehmens erst ermöglichen. Das entscheidende Merkmal der Balanced Scorecard ist dabei, dass sie ein ausgewogenes System strategischer Ziele herstellt, welches das Unternehmen hinsichtlich der vier Perspektiven Finanzen, Kunden, interne Prozesse und Mitarbeiter und Potenziale strategisch ausrichtet (Kaplan u. Norton 1997).

Lentivirus-mediated bifunctional cell labeling for in vivo melanoma study

PubMed Central

Day, Chi-Ping; Carter, John; Bonomi, Carrie; Esposito, Dominic; Crise, Bruce; Ortiz-Conde, Betty; Hollingshead, Melinda; Merlino, Glenn

2009-01-01

SUMMARY Lentiviral vectors (LVs) are capable of labeling a broad spectrum of cell types, achieving stable expression of transgenes. However, for in vivo studies, the duration of marker gene expression has been highly variable. We have developed a series of LVs harboring different promoters for expressing reporter gene in mouse cells. Long-term culture and colony formation of several LV-labeled mouse melanoma cells showed that promoters derived from mammalian house-keeping genes, especially those encoding RNA polymerase II (Pol2) and ferritin (FerH), provided the highest consistency for reporter expression. For in vivo studies, primary B16BL6 mouse melanoma were infected with LVs whose luciferase-GFP fusion gene (Luc/GFP) was driven by either Pol2 or FerH promoters. When transplanted into syngeneic C57BL/6 mice, Luc/GFP-labeled B16BL6 mouse melanoma cells can be monitored by bioluminescence imaging in vivo, and GFP-positive cells can be isolated from the tumors by FACS. Pol2-Luc/GFP labeling, while lower in activity, was more sustainable than FerH-Luc/GFP labeling in B16BL6 over consecutive passages into mice. We conclude that Pol-2-Luc/GFP labeling allows long-term in vivo monitoring and tumor cell isolation in immunocompetent mouse melanoma models. SIGNIFICANCE In this study we have developed and identified lentiviral vectors that allow labeled mouse melanoma cells to maintain long-term and consistent expression of a bifunctional luciferase-GFP marker gene, even in syngeneic mice with an intact immune function. This cell-labeling system can be used to build immunocompetent mouse melanoma models that permit both tumor monitoring and FACS-based tumor cell isolation from tissues, greatly facilitating the in vivo study of melanoma. PMID:19175523

Transcription initiation complex structures elucidate DNA opening.

PubMed

Plaschka, C; Hantsche, M; Dienemann, C; Burzinski, C; Plitzko, J; Cramer, P

2016-05-19

Transcription of eukaryotic protein-coding genes begins with assembly of the RNA polymerase (Pol) II initiation complex and promoter DNA opening. Here we report cryo-electron microscopy (cryo-EM) structures of yeast initiation complexes containing closed and open DNA at resolutions of 8.8 Å and 3.6 Å, respectively. DNA is positioned and retained over the Pol II cleft by a network of interactions between the TATA-box-binding protein TBP and transcription factors TFIIA, TFIIB, TFIIE, and TFIIF. DNA opening occurs around the tip of the Pol II clamp and the TFIIE 'extended winged helix' domain, and can occur in the absence of TFIIH. Loading of the DNA template strand into the active centre may be facilitated by movements of obstructing protein elements triggered by allosteric binding of the TFIIE 'E-ribbon' domain. The results suggest a unified model for transcription initiation with a key event, the trapping of open promoter DNA by extended protein-protein and protein-DNA contacts.

Difficulties with Emotion Regulation and Psychopathology Interact to Predict Early Smoking Cessation Lapse.

PubMed

Farris, Samantha G; Zvolensky, Michael J; Schmidt, Norman B

2016-06-01

There is little knowledge about how emotion regulation difficulties interplay with psychopathology in terms of smoking cessation. Participants ( n = 250; 53.2 % female, M age = 39.5, SD = 13.85) were community-recruited daily smokers (≥8 cigarettes per day) who self-reported motivation to quit smoking; 38.8 % of the sample met criteria for a current (past 12-month) psychological disorder. Emotion regulation deficits were assessed pre-quit using the Difficulties with Emotion Regulation Scale (DERS; Gratz and Roemer in J Psychopathol Behav Assess 26(1):41-54, 2004) and smoking behavior in the 28 days post-quit was assessed using the Timeline Follow-Back (TLFB; Sobell and Sobell in Measuring alcohol consumption: psychosocial and biochemical methods. Humana Press, Totowa, 1992). A Cox proportional-hazard regression analysis was used to model the effects of past-year psychopathology, DERS (total score), and their interaction, in terms of time to lapse post-quit day. After adjusting for the effects of gender, age, pre-quit level of nicotine dependence, and treatment condition, the model revealed a non-significant effect of past-year psychopathology ( OR = 1.14, CI 95 % = 0.82-1.61) and difficulties with emotion regulation ( OR = 1.01, CI 95 % = 1.00-1.01) on likelihood of lapse rate. However, the interactive effect of psychopathology status and difficulties with emotion regulation was significant ( OR = 0.98, CI 95 % = 0.97-0.99). Specifically, there was a significant conditional effect of psychopathology status on lapse rate likelihood at low, but not high, levels of emotion regulation difficulties. Plots of the cumulative survival functions indicated that for smokers without a past-year psychological disorder, those with lower DERS scores relative to elevated DERS scores had significantly lower likelihood of early smoking lapse, whereas for smokers with past-year psychopathology, DERS scores did not differentially impact lapse rate likelihood. Smokers with emotion regulation difficulties may have challenges quitting, and not having such difficulties, especially without psychopathology, decreases the potential likelihood of early lapse.

Beitrag zum mechanismus der oxydation von freiblei in bleiakkumulatorpaste bei der reifung

NASA Astrophysics Data System (ADS)

Duc Hung, Nguyen; Garche, J.; Wiesener, K.

The kinetics of lead oxidation during curing was studied by chemical analysis of the free lead content as well as by the gas volumetry of oxygen. The difference in the results in this research lies in the evolution of hydrogen as a curing reaction. This agrees with the results of curing the paste The optimal water content of the paste for lead oxidation was determined. A model for the electrolyte film during curing has been developed, which allows the results to be interpreted satisfactorily.

An ATP-dependent ligase with substrate flexibility involved in assembly of the peptidyl nucleoside antibiotic polyoxin

USDA-ARS?s Scientific Manuscript database

Polyoxin (POL) is an unusual nucleoside antibiotic, in which peptidyl moiety and nucleoside skeleton are linked by an amide bond. However, their biosynthesis remains poorly understood. Here, we report the deciphering of PolG as an ATP-dependent ligase responsible for the assembly of POL. A polG muta...

Refolding Active Human DNA Polymerase ν from Inclusion Bodies

PubMed Central

Arana, Mercedes E.; Powell, Gary K.; Edwards, Lori L.; Kunkel, Thomas A.; Petrovich, Robert M.

2017-01-01

Human DNA polymerase ν (Pol ν) is a conserved family A DNA polymerase of uncertain biological function. Physical and biochemical characterization aimed at understanding Pol ν function is hindered by the fact that, when over-expressed in E. coli, Pol ν is largely insoluble, and the small amount of soluble protein is difficult to purify. Here we describe the use of high hydrostatic pressure to refold Pol ν from inclusion bodies, in soluble and active form. The refolded Pol ν has properties comparable to those of the small amount of Pol ν that was purified from the soluble fraction. The approach described here may be applicable to other DNA polymerases that are expressed as insoluble inclusion bodies in E. coli. PMID:19853037

Einsatz molekularer Methoden für Starterkulturen

NASA Astrophysics Data System (ADS)

Ehrmann, Matthias A.; Pavlovic, Melanie

Unter Starterkulturen versteht man Mikroorganismen (Bakterien, Hefen, Pilze), die pflanzlichen bzw. tierischen Rohstoffen zur gezielten Veränderung ihrer chemischen Zusammensetzung zugesetzt werden. Sie dienen im Wesentlichen der Aromabildung, der Strukturveränderung und der Konservierung der Lebensmittel und werden aufgrund spezieller, funktioneller Eigenschaften selektiert. Die Zugabe von Starterkulturen erfolgt in der Regel in relativ hohen Keimzahlen in Form von Rein- oder Mischkulturen. Die zum Einsatz kommenden Mikroorganismen sind ebenso zahlreich wie die daraus resultierenden Produkte und reichen von der Fermentation von Milchprodukten, Fleisch und Gemüse durch Milchsäurebakterien über die Essigsäureherstellung bis hin zum Einsatz von Hefen in der Brau- und Weinindustrie. Hieraus ergibt sich auch eine zunehmende Bedeutung schneller und zuverlässiger Methoden zur taxonomischen Identifizierung, aber auch zur Charakterisierung des genetischen Potenzials der jeweiligen Starterkulturen.

Satellitenbewegung, band III: Natiirliche und gesteuerte bewegung.

NASA Astrophysics Data System (ADS)

Jochim, E. F.

2014-12-01

Im dritten Band der Satellitenbewegung werden in fortlaufender Nummerierung einige für Untersuchungen der Bewegung der künstlichen Satelliten wichtige Grundlagen der Astrodynamik mit ausführlichen mathematischen Formelsystemen behandelt. Dazu zählen die unterschiedlichen Aspekte der Bewegung der natürlichen Himmelskörper, die Steuerung und Kontrolle von künstlichen Objekten, und insbesondere die für eine Satellitenbahnanalyse wichtigen physikalischen Beeinflussungen einer Satellitenbewegung. Mathematisch entscheidend ist die Wahl geeigneter Bahnparameter, die ein bestimmtes Bewegungsproblem widerspruchsfrei und singularitätenfrei zu behandeln gestatten. Für die Behandlung routinemäßiger Aufgabenstellungen der Satellitenbewegung, in erster Linie einer präzisen Bahnbestimmung und Bahnverbesserung, kann auf eine Fülle von lehrbuchartigen Monographien verwiesen werden, so dass diese Problematik in der vorliegenden Arbeit nur angedeutet werden soll.

Dynamical analysis of an n‑H‑T cosmological quintessence real gas model with a general equation of state

NASA Astrophysics Data System (ADS)

Ivanov, Rossen I.; Prodanov, Emil M.

2018-01-01

The cosmological dynamics of a quintessence model based on real gas with general equation of state is presented within the framework of a three-dimensional dynamical system describing the time evolution of the number density, the Hubble parameter and the temperature. Two global first integrals are found and examples for gas with virial expansion and van der Waals gas are presented. The van der Waals system is completely integrable. In addition to the unbounded trajectories, stemming from the presence of the conserved quantities, stable periodic solutions (closed orbits) also exist under certain conditions and these represent models of a cyclic Universe. The cyclic solutions exhibit regions characterized by inflation and deflation, while the open trajectories are characterized by inflation in a “fly-by” near an unstable critical point.

Was leistet ein Sportler? Kraft, Leistung und Energie im Muskel

NASA Astrophysics Data System (ADS)

Thaller, Sigrid; Mathelitsch, Leopold

2006-01-01

Der Leistungsbegriff ist im Sport weiter gefasst als in der Physik. In beiden Fällen liegt der Fokus jedoch auf einer pro Zeiteinheit erfolgten Energieumsetzung. Allerdings gibt die rein physikalische Leistung nicht immer Auskunft über den Energieumsatz der Muskeln. Die Muskelkraft hängt von der Kontraktionsgeschwindigkeit des Muskels ab. Ein Muskel verhält sich also anders als eine Feder. Für den Hochleistungssport müssen die Energieumsätze der Muskeln durch spezielle Trainings- und Nahrungsprogramme optimiert werden.

Sterblichkeit: der paradoxe Kunstgriff des Lebens - Eine Betrachtung vor dem Hintergrund der modernen Biologie

NASA Astrophysics Data System (ADS)

Verbeek, Bernhard

Leben gibt es auf der Erde seit fast 4 Mio. Jahren, trotz allen Katastrophen. Die Idee des Lebens scheint unsterblich. Der Tod aber offenbar auch. Jedes Lebewesen ist davon bedroht, ja für Menschen und andere "höhere“ Lebewesen ist er im Lebensprogramm eingebaut - todsicher. Diese Tatsache ist alles andere als selbstverständlich. Ist sie überhaupt kompatibel mit dem Prinzip der Evolution, nach dem der am besten Angepasste überlebt?

Borderline personality disorder features, emotion dysregulation and non-suicidal self-injury: Preliminary findings in a sample of community-dwelling Italian adolescents.

PubMed

Somma, Antonella; Sharp, Carla; Borroni, Serena; Fossati, Andrea

2017-02-01

In order to assess the relationships among borderline personality disorder features, non-suicidal self-injury (NSSI) and emotion dysregulation, 122 community-dwelling Italian adolescents were administered by the Italian translations of the Borderline Personality Features Scale for Children-11, the Deliberate Self-Harm Inventory and the Difficulties in Emotion Regulation Scale (DERS). Regression models showed that both Deliberate Self-Harm Inventory (DSHI) and DERS scores significantly predicted Borderline Personality Features Scale for Children-11 total score; moreover, the DSHI total score significantly predicted the DERS total score. Our findings suggest that borderline personality features in adolescence are moderately, albeit significantly related to NSSI, and that emotion dysregulation does not completely account for the association between borderline personality features and NSSI, although it seems to explain a non-trivial proportion of this relationship. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Control Strategies for Distributed Energy Resources to Maximize the Use of Wind Power in Rural Microgrids

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

Lu, Shuai; Elizondo, Marcelo A.; Samaan, Nader A.

2011-10-10

The focus of this paper is to design control strategies for distributed energy resources (DERs) to maximize the use of wind power in a rural microgrid. In such a system, it may be economical to harness wind power to reduce the consumption of fossil fuels for electricity production. In this work, we develop control strategies for DERs, including diesel generators, energy storage and demand response, to achieve high penetration of wind energy in a rural microgrid. Combinations of centralized (direct control) and decentralized (autonomous response) control strategies are investigated. Detailed dynamic models for a rural microgrid are built to conductmore » simulations. The system response to large disturbances and frequency regulation are tested. It is shown that optimal control coordination of DERs can be achieved to maintain system frequency while maximizing wind power usage and reducing the wear and tear on fossil fueled generators.« less

Spin-Flavor van der Waals Forces and NN interaction

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

Alvaro Calle Cordon, Enrique Ruiz Arriola

A major goal in Nuclear Physics is the derivation of the Nucleon-Nucleon (NN) interaction from Quantum Chromodynamics (QCD). In QCD the fundamental degrees of freedom are colored quarks and gluons which are confined to form colorless strongly interacting hadrons. Because of this the resulting nuclear forces at sufficiently large distances correspond to spin-flavor excitations, very much like the dipole excitations generating the van der Waals (vdW) forces acting between atoms. We study the Nucleon-Nucleon interaction in the Born-Oppenheimer approximation at second order in perturbation theory including the Delta resonance as an intermediate state. The potential resembles strongly chiral potentials computedmore » either via soliton models or chiral perturbation theory and has a van der Waals like singularity at short distances which is handled by means of renormalization techniques. Results for the deuteron are discussed.« less

Multiwalled Carbon Nanotube Deposition on Model Environmental Surfaces

EPA Science Inventory

Deposition of multiwalled carbon nanotubes (MWNTs) on model environmental surfaces was investigated using a quartz crystal microbalance with dissipation monitoring (QCM-D). Deposition behaviors of MWNTs on positively and negatively charged surfaces were in good agreement with Der...

Calculations of the free energy of interaction of the c-Fos-c-Jun coiled coil: effects of the solvation model and the inclusion of polarization effects.

PubMed

Zuo, Zhili; Gandhi, Neha S; Mancera, Ricardo L

2010-12-27

The leucine zipper region of activator protein-1 (AP-1) comprises the c-Jun and c-Fos proteins and constitutes a well-known coiled coil protein-protein interaction motif. We have used molecular dynamics (MD) simulations in conjunction with the molecular mechanics/Poisson-Boltzmann generalized-Born surface area [MM/PB(GB)SA] methods to predict the free energy of interaction of these proteins. In particular, the influence of the choice of solvation model, protein force field, and water potential on the stability and dynamic properties of the c-Fos-c-Jun complex were investigated. Use of the AMBER polarizable force field ff02 in combination with the polarizable POL3 water potential was found to result in increased stability of the c-Fos-c-Jun complex. MM/PB(GB)SA calculations revealed that MD simulations using the POL3 water potential give the lowest predicted free energies of interaction compared to other nonpolarizable water potentials. In addition, the calculated absolute free energy of binding was predicted to be closest to the experimental value using the MM/GBSA method with independent MD simulation trajectories using the POL3 water potential and the polarizable ff02 force field, while all other binding affinities were overestimated.

Stenting und technische Stentumgebung

NASA Astrophysics Data System (ADS)

Hoffstetter, Marc; Pfeifer, Stefan; Schratzenstaller, Thomas; Wintermantel, Erich

In hoch entwickelten Industrieländern stehen laut Weltgesundheitsorganisation (WHO) Herz-Kreislauf-Erkrankungen und speziell die Koronare Herzkrankheit (KHK) an erster Stelle der Todesursachen. In Deutschland betrug die Zahl der erfassten, an KHK erkrankten Personen ohne Berücksichtigung der Dunkelziffer allein im Jahre 2001 über 473.000. Die KHK war im Jahre 2003 mit 92.673 erfassten Todesfällen immer noch die häufigste Todesursache, obgleich in Deutschland die Häufigkeit der Koronarinterventionen zur Behandlung der KHK zwischen 1984 und 2003 um fast das 80fache von 2.809 auf 221.867 Eingriffe pro Jahr gestiegen ist [1]. Neben der hohen Zahl an Todesfällen haben die betroffenen Personen durch chronische Schmerzen und eingeschränkte körperliche Leistungsfähigkeit zusätzlich eine starke Beeinträchtigung der Lebensqualität [2].In Folge dessen wird die erkrankte Person häufig zum Pflegefall was neben den gesundheitlichen Aspekten auch eine sozioökonomische Komponente in Form der fehlenden Arbeitskraft und den auftretenden Pflegekosten nach sich zieht. Die Kosten für die Behandlung der KHK in Deutschland beliefen sich im Jahre 2002 laut Statistischem Bundesamt auf rund 6,9 Mrd. €. Verglichen mit ähnlichen Zahlen der USA dürfte sich der entstandene Schaden für die deutsche Volkswirtschaft im zwei- bis dreistelligen Milliardenbereich bewegen [3].