SEARCH · PubMed Health

Results for “DAMPs”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 289 records · Page 16Linked to original sources

PubMed2003

Damped elastic recoil of the titin spring in myofibrils of human myocardium.

The giant protein titin functions as a molecular spring in muscle and is responsible for most of the passive tension of myocardium. Because the titin spring is extended during diastolic stretch, it will recoil elastically during systole and potentially may influence the overall shortening behavior of cardiac muscle. Here, titin elastic recoil was quantified in single human heart myofibrils by using a high-speed charge-coupled device-line camera and a nanonewtonrange force sensor. Application of a slack-test protocol revealed that the passive shortening velocity (Vp) of nonactivated cardiomyofibrils depends on: (i) initial sarcomere length, (ii) release-step amplitude, and (iii) temperature. Selective digestion of titin, with low doses of trypsin, decelerated myofibrillar passive recoil and eventually stopped it. Selective extraction of actin filaments with a Ca2+-independent gelsolin fragment greatly reduced the dependency of Vp on release-step size and temperature. These results are explained by the presence of viscous forces opposing myofibrillar passive recoil that are caused mainly by weak actin-titin interactions. Thus, Vp is determined by two distinct factors: titin elastic recoil and internal viscous drag forces. The recoil could be modeled as that of a damped entropic spring consisting of independent worm-like chains. The functional importance of myofibrillar elastic recoil was addressed by comparing instantaneous Vp to unloaded shortening velocity, which was measured in demembranated, fully Ca2+-activated, human cardiac fibers. Titin-driven passive recoil was much faster than active unloaded shortening velocity in early phases of isotonic contraction. Damped myofibrillar elastic recoil could help accelerate active contraction speed of human myocardium during early systolic shortening.

Actins↗

PubMed2003

Circadian gene expression in mammalian fibroblasts revealed by real-time luminescence reporting: temperature compensation and damping.

Mammalian cells such as rat-1 fibroblasts have been shown to exhibit daily oscillations in the expression of several gene transcripts in culture. After induction, these oscillations persist with a period of approximately 24 h for several days. This characteristic suggests that the oscillations are controlled by a circadian clock, but the crucial criterion of temperature compensation has not been demonstrated for rat-1 fibroblasts. We have developed an automated assay of circadian expression of the mPer1 promoter in rat-1 fibroblasts that have been stably transfected with a luciferase reporter. Using this cell culture-based in vitro luminescent reporter assay, we found that the daily oscillation of mPer1 promoter activity in rat-1 cells is temperature compensated over the range of 28.5-36.5 degrees C. This finding means that these oscillations are bona fide circadian rhythms. Moreover, the circadian clock of these homeothermic mammalian cells not only is temperature compensated but also is overcompensated such that it runs faster at cooler temperatures (Q10 of 0.85-0.88). The oscillations in rat-1 fibroblasts damp more rapidly at cooler temperatures, and damping is not due to cells becoming unhealthy because a second stimulus will reinitiate a robust rhythm. These data show that rat-1 cell cultures that are stably transfected with luminescence reporters are an excellent model system for studying circadian clocks at the cellular level in mammals.

Animals↗

PubMed2003

Cortical damping: analysis of thalamocortical response transformations in rodent barrel cortex.

In the whisker-barrel system, layer IV excitatory neurons respond preferentially to high-velocity deflections of their principal whisker, and these responses are inhibited by deflections of adjacent whiskers. Thalamic input neurons are amplitude and velocity sensitive and have larger excitatory and weaker inhibitory receptive fields than cortical neurons. Computational models based on known features of barrel circuitry capture these and other differences between thalamic and cortical neuron response properties. The models' responses are highly sensitive to thalamic firing synchrony, a finding subsequently confirmed in real barrels by in vivo experiments. Here, we use dynamic systems analysis to examine how barrel circuitry attains its sensitivity to input timing, and how this sensitivity explains the transformation of receptive fields between thalamus and cortex. We find that strong inhibition renders the net effect of intracortical connections suppressive or damping, distinguishing it from previous amplifying models of cortical microcircuits. In damping circuits, recurrent excitation enhances response tuning not by amplifying responses to preferred inputs, but by enabling them to better withstand strong inhibitory influences. Dense interconnections among barrel neurons result in considerable response homogeneity. Neurons outside the barrel layer respond more heterogeneously, possibly reflecting diverse networks and multiple transformations within the cortical output layers.

Afferent Pathways↗

PubMed1983

Factors involved in the initiation of phage phi 29 DNA replication in vitro: requirement of the gene 2 product for the formation of the protein p3-dAMP complex.

To study the requirements for the in vitro formation of the protein p3-dAMP complex, the first step in phi29 DNA replication, extracts from B. subtilis infected with phi29 mutants in genes 2, 3, 5, 6 and 17, involved in DNA synthesis, have been used. The formation of the initiation complex is completely dependent on the presence of a functional gene 2 product, in addition to protein p3 and phi29 DNA-protein p3 as template. ATP is also required, although it can be replaced by other nucleotides. The products of genes 5, 6 and 17 do not seem to be needed in the formation of the initiation complex. Inhibitors of the host DNA polymerase III, DNA gyrase or RNA polymerase had no effect on the formation of the protein p3-dAMP complex, suggesting that these proteins are not involved in the initiation of phi29 DNA replication. ddATP or aphidicolin, inhibitors of DNA chain elongation, had also no effect on the formation of the initiation complex.

Adenosine Diphosphate↗

PubMed1999

Insertion of dGMP and dAMP during in vitro DNA synthesis opposite an oxidized form of 7,8-dihydro-8-oxoguanine.

Oxidative damage to DNA bases commonly resultsin the formation of oxidized purines, particularly 7,8-dihydro-8-oxoguanine (8-oxoG) and 7,8-dihydro-8-oxoadenine (8-oxoA), the former being a well-known mutagenic lesion. Since 8-oxoG is readily subject to further oxidation compared with normal bases, the insertion of a base during DNA synthesis opposite an oxidized form of 8-oxoG was investigated in vitro. A synthetic template containing a single 8-oxoG lesion was first treated with different one-electron oxidants or under singlet oxygen conditions and then subjected to primer extension catalyzed by Klenow fragment exo- (Kf exo-), calf thymus DNA polymerase alpha (pol alpha) or human DNA polymerase beta (pol beta). Consistent with previous reports, dAMP and dCMP are inserted selectively opposite 8-oxoG with all three DNA polymerases. Interestingly, oxidation of 8-oxoG was found to induce dAMP and dGMP insertion opposite the lesion by Kf exo- with transient inhibition of primer extension occurring at the site of the modified base. Furthermore, the lesion constitutes a block during DNA synthesis by pol alpha and pol beta. Experiments with an 8-oxoA-modified template oligonucleotide show that both 8-oxoA and an oxidized form of 8-oxoA direct insertion of dTMP by Kf exo-. Mass spectrometric analysis of 8-oxoG-containing oligonucleotides before and after oxidation with IrCl62-are consistent with oxidation of primarily the 8-oxoG site, resulting in formation of a guanidinohydantoin moiety as the major product. No evidence for formation of abasic sites was obtained. These results demonstrate that an oxidized form of 8-oxoG, possibly guanidinohydantoin, may direct misreading and misinsertion of dNTPs during DNA synthesis. If such a process occurred in vivo, it would represent a point mutagenic lesion leading to G-->T and G-->C transversions. However, the corresponding oxidized form of 8-oxoA primarily shows correct insertion of T during DNA synthesis with Kf exo-.

Animals↗

PubMed2000

Low frequency damped oscillations of cat visual cortical neurones.

A synchronizing volley of excitation was delivered to cells from the primary visual cortex of the anaesthetized cat by an electrical pulse stimulation of the optic radiations. In intracellular records, this resulted in an initial, fast depolarization of the membrane potential followed by a longer lasting (266 ms) hyperpolarization, and then to small amplitude damped oscillations of the membrane potential. In different cells the number of peaks ranged from 3 to 6, and the amplitude of the first oscillation averaged 3.5 mV. If the pulse stimulation was repeated during visual drive with an optimal bar stimulus, the membrane potential fluctuations were non-linearly enhanced with spike bursts recorded during the depolarized states of the membrane potential. The amplitude of the first oscillation in these cases averaged 6.9 mV. The mean frequency of damped oscillations was 9.9 Hz. The results suggest that these oscillations are mediated by the waxing and waning of the excitatory drive to the recorded neurone.

Action Potentials↗

PubMed2006

Quasi-mode damping in two-dimensional fully non-uniform coronal loops.

Resonantly damped fast kink quasi-modes are computed in fully resistive magnetohydrodynamics for fully non-uniform two-dimensional equilibrium models. The equilibrium model is a straight cylindrically symmetric flux tube with a plasma density that is non-uniform both across and along the loop. The variation of density across the loop can cover the whole loop. Our results indicate that the period and damping of coronal loop oscillations mainly depend on the density contrast and the inhomogeneity length-scale and are independent of the details of longitudinal stratification. This study extends previous studies on coronal loop oscillations, and allows for a better comparison between observations and theory.

Journal Article↗

PubMed2006

Excitation and damping of disturbances in cylindrical coronal loops.

The excitation and damping of transversal coronal loop oscillations is studied using one-and two-dimensional models of line-tied cylindrical loops. By solving the time-dependent magnetohydrodynamic equations it is shown how an initial disturbance generated in the solar corona induces kink mode oscillations. We investigate the effect of the disturbance on a loop with a non-uniform boundary layer. In particular, a strong damping of transversal oscillations due to resonant absorption is found, such as predicted by previous works based on normal mode analysis.

Journal Article↗

PubMed2003

Oscillations of plants' stems and their damping: theory and experimentation.

Free oscillations of upright plants' stems, or in technical terms slender tapered rods with one end free, can be modelled by considering the equilibrium between bending moments and moments resulting from inertia. For stems with apical loads and negligible mass of the stem and for stems with finite mass but without top loading, analytical solutions of the differential equations with appropriate boundary conditions are available for a finite number of cases. For other cases approximations leading to an upper and a lower estimate of the frequency of oscillation omega can be derived. For the limiting case of omega = 0, the differential equations are identical with Greenhill's equations for the stability against Euler buckling of slender poles. To illustrate, the oscillation frequencies of 25 spruce trees (Picea sitchensis (Bong.) Carr.) were compared with those calculated on the basis of their morphology, their density and their static elasticity modulus. For Arundo donax L. and Cyperus alternifolius L. the observed oscillation frequency was used in turn to calculate the dynamic elasticity modulus, which was compared with that determined in three-point bending. Oscillation damping was observed for A. donax and C. alternifolius for plants' stems with and without leaves or inflorescence. In C. alternifolius the difference can be attributed to the aerodynamic resistance of the leaves, whereas in A. donax structural damping in addition plays a major role.

Biomechanical Phenomena↗

PubMed1999

Landau damping of an electron plasma wave in a plasma with modulated density.

The collisionless Landau damping is analyzed for a homogeneous plasma with a sinusoidal density perturbation. The exact damping values are obtained by numerically solving the kinetic dispersion relation of the electron plasma mode. Quantitative results are provided on the influence of the amplitude and the wave vector of the density modulation. Within a simplified fluid framework, a fit is given to these data.

Journal Article↗

PubMed2001

Ermakov-Lewis angles for one-parameter supersymmetric families of Newtonian free damping modes.

We apply the Ermakov-Lewis procedure to the one-parameter damped modes y recently introduced by Rosu and Reyes, which are related to the common Newtonian free damping modes y by the general Riccati solution [H. C. Rosu and M. Reyes, Phys. Rev. E 57, 4850 (1998)]. In particular, we calculate and plot the angle quantities of this approach that can help to distinguish these modes from the common y modes.

Journal Article↗

PubMed2002

Diffusion in a periodically driven damped and undamped pendulum.

We study the diffusion process in a periodically driven damped and undamped pendulum. The effect of angular frequency omega of the external periodic force on the diffusion process is investigated. We show the occurrence of normal and anomalous diffusions in the undamped system. In the presence of damping, normal chaotic diffusion is found. Near certain bifurcation points, the phase velocity is found to be intermittent and the diffusion coefficient is found to exhibit power-law divergence. We argue that the divergence of the diffusion coefficient near the bifurcation points is similar to that of the average laminar lengths near them. The effect of bias on the dynamics is also discussed.

Journal Article↗

PubMed2003

Classical acoustic waves in damped media.

A Green function technique is employed to investigate the propagation of classical damped acoustic waves in complex media. The calculations are based on the linear response function approach, which is very convenient to deal with this kind of problem. Both the displacement and the gradient displacement Green functions are determined. All deformations in the media are supposed to be negligible, so the motions considered here are purely acoustic waves. The damping term gamma is included in a phenomenological way into the wave vector expression. By using the fluctuation-dissipation theorem, the power spectrum of the acoustic waves is also derived and has interesting properties, the most important of them being a possible relation with the analysis of seismic reflection data.

Journal Article↗

PubMed2005

Magnetic-field effects on nonlinear electrostatic-wave Landau damping.

A numerical code, which solves the Vlasov-Poisson system of equations for an electron magnetized plasma with motionless ions, is presented. The numerical integration of the Vlasov equation has been performed using the "splitting method" and the cylindric geometry in the velocity space is used to describe the motion of the particles around the external field. The time evolution of an electrostatic wave, propagating perpendicularly to the background magnetic field, is numerically studied in both the linear and nonlinear regimes, for different values of the ratio gamma between the electron oscillation time in a sinusoidal potential well and the electron cyclotron period. It is shown that the external magnetic field plays very different roles, depending on the values of the initial wave amplitude. When the initial amplitude is less than some threshold, the magnetic field prevents the Landau damping of the electrostatic wave (Bernstein-Landau paradox). When the wave amplitude is above the threshold, for intermediate values of gamma the presence of a background magnetic field allows for the electric energy dissipation at variance with the behavior of electrostatic wave in unmagnetized plasma, while for high gamma values once again the magnetic field prevents the damping.

Journal Article↗

PubMed2005

Damping of electromagnetic waves due to electron-positron pair production.

The problem of the back reaction during the process of electron-positron pair production by a circularly polarized electromagnetic wave propagating in a plasma is investigated. A model based on the relativistic Boltzmann-Vlasov equation with a source term representing the Schwinger formula for the pair creation rate is used. The damping of the wave, the nonlinear up-shift of its frequency due to the plasma density increase, and the effect of the damping on the wave polarization and on the background plasma acceleration are investigated as a function of the wave amplitude.

Journal Article↗

PubMed2006

Envelope solitons on anharmonic damped atomic chains.

We investigate the influence of dissipation on envelope solitons on anharmonic chains. We consider both Stokes and hydrodynamical damping and derive the evolution equations for the envelope in both the continuum and the quasi-continuum approximation of the chain. We introduce an appropriate collective variable ansatz for the envelope in order to describe the effect of damping on the soliton shape. We derive ordinary differential equations for the evolution of the three collective variables amplitude, width, and chirp which describe the spatial modulation of the envelope. The analytical results are in good agreement with the simulations of the discrete system for high-energy excitations on the chain. Our results derived from the quasi-continuum approximation show significant improvements compared to the continuum approximation.

Journal Article↗

PubMed2006

Modification of the damping rate of the oscillations of a dust particle levitating in a plasma due to the delayed charging effect.

Dependence of the damping rate of the oscillations of the dust particles levitating in the sheath on the plasma parameters is investigated both theoretically and experimentally. Significant deviations of the damping rate from the values predicted by the Epstein formula are found in the experiment. The delayed charging effect is applied for the theoretical explanation of the experimental results. Qualitative agreement between the theoretical and experimental data is obtained.

Journal Article↗

PubMed2000

Exact linearization of the radiation-damped spin system

Nonlinear evolution of the Landau-Lifshitz type can be exactly linearized. Special cases include the radiation-damped spin system and the superradiant system in the semiclassical regime, in the presence of time-varying driving fields. For these, the resultant linear system is simply that of a spin 1 / 2 particle, with the radiation damping rate, or superradiant characteristic time, manifested as an imaginary addition to the spin's resonance frequency. Consequently, methods from inverse scattering theory can be used to design driving fields. The behavior of these systems under stochastic excitation can be determined exactly.

Journal Article↗