Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “dynamics”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

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

At least 1,747 records · Page 97Linked to original sources
PubMed2003

In vivo imaging of human retinal flow dynamics by color Doppler optical coherence tomography.

BACKGROUND: Color Doppler optical coherence tomography (CDOCT) combines laser Doppler velocimetry and optical coherence tomography for simultaneous micron-scale resolution cross-sectional imaging of tissue microstructure and blood flow. Recently, CDOCT was adapted to a slitlamp biomicroscope for imaging structure and blood flow in the human retina. OBJECTIVE: To demonstrate feasibility of CDOCT for imaging retinal hemodynamics. DESIGN: Enabling CDOCT to measure retinal blood flow pulsatility in humans. SETTING: Laboratory. MAIN OUTCOME MEASURES: Time-resolved flow profiles and images of retinal blood flow dynamics for measurement of pulsatility within retinal vessels. RESULTS: Rapid sequences of images were acquired over selected vessels near the optic nerve head. From these images, retinal blood flow profiles were extracted and synchronized to an external reference obtained with a photoplethysmograph. Each profile was acquired in less than 10 milliseconds. CONCLUSIONS: Our results indicate that CDOCT provides laser Doppler information in addition to conventional optical coherence tomography, allowing the observation of blood flow dynamics simultaneous to imaging retinal structure. CDOCT is a promising technology for research and clinical studies of retinal blood flow dynamics. CLINICAL RELEVANCE: Blood flow dynamics, such as pulsatility and autoregulation, have been shown to change throughout the progression of diabetic retinopathy and glaucoma. Enabling CDOCT to observe retinal dynamics improves its potential as a clinical diagnostic tool.

Blood Flow Velocity↗
PubMed1996

Stimulation of microtubule dynamic turnover in living cells treated with okadaic acid.

We have examined the effects of okadaic acid, an inhibitor of protein phosphatases type 1 and 2A, on the dynamic instability behavior of individual microtubules in living cells. Addition of 1 microM okadaic acid to PtK1 epithelial cells induced ruffling of lamellar regions; after 50 min in okadaic acid, many cells were observed to round up. Confocal microscopy of okadaic acid-treated cells stained with an antibody to tubulin showed that microtubules were more densely packed near the periphery of the rounded cells, and in many cells, a reduction in the density of microtubules near the microtubule-organizing center was observed. The dynamic behavior of individual microtubules in cells previously injected with rhodamine-labeled tubulin was quantified by tracking individual microtubules from image sequences. Microtubule dynamic turnover was markedly stimulated in cells treated with 1 microM okadaic acid for 50-60 min: The average rates of both microtubule growing and shortening increased, and the average duration of pause, or attenuation, a phase in which neither growth nor shortening could be detected, was significantly decreased. Further, okadaic acid induced an approximately twofold increase in the frequency of catastrophe transitions and a threefold decrease in the frequency of rescue transitions. Dynamicity, a measure of the net gain and loss of polymer at microtubule plus ends, increased nearly threefold in okadaic acid-treated cells. These results demonstrate that microtubule turnover is stimulated in okadaic acid-treated cells and suggest that phosphorylation of molecules which interact with microtubules may result in increased microtubule dynamic turnover in vivo.

Animals↗
PubMed1996

Differences in the regulation of microtubule dynamics by microtubule-associated proteins MAP1B and MAP2.

The regulation of microtubule dynamics in vitro by microtubule-associated proteins (MAPs) was examined, using purified porcine MAP1B and MAP2. MAP1B has a significantly smaller effect on the observed critical concentration for microtubule assembly than MAP2. Assembly is faster in the presence of either MAP, and the resulting microtubules are shorter, indicating that nucleation is substantially promoted by the MAPs. Both MAPs stabilise the microtubule lattice as observed from podophyllotoxin-induced disassembly, but the effect of MAP1B is weaker than the effect of MAP2. At steady-state of assembly MAP1B still allows microtubule dynamic instability to occur as inferred from microtubule length changes. The comparison of the effects of MAP1B and MAP2 indicates that the reduction of the observed critical concentration is attributable to the reduction of the depolymerisation rate and correlates with the extent of suppression of dynamic instability. Numerical simulations illustrate that microtubule dynamics are strongly influenced by relatively small changes in the strength of a limited subset of subunit interactions in the lattice. The observed characteristic differences between the MAPs may be important for the regulation of distinct populations of microtubules which coexist in the same cell, where differences in stability and dynamics may be essential for their different spatial roles as, for example, in developing neurons.

Animals↗
PubMed1996

Microtubule dynamic turnover is suppressed during polarization and stimulated in hepatocyte growth factor scattered Madin-Darby canine kidney epithelial cells.

The dynamic behavior of microtubules has been measured in non-polarized, polarized, and hepatocyte growth factor treated Madin-Darby canine kidney epithelial cells. In a nocodazole disassembly assay, microtubules in polarized cells were more resistant to depolymerization than microtubules in non-polarized cells; microtubules in scattered cells were nearly completely disassembled. Analysis of fluorescent microtubules in living cells further revealed that individual microtubules in polarized cells were kinetically stabilized and microtubules in scattered cells were highly dynamic. Individual microtubule behavior in polarized cells was characterized by a suppression of the average rate of shortening, an increase in the average duration of pause, a decrease in the frequency of catastrophe transitions, and an increase in the frequency of rescue transitions, when compared with microtubules in non-polarized cells. In contrast, microtubule behavior in epithelial cells treated with hepatocyte growth factor was characterized by increase in the average rates of microtubule growth and shortening, a decrease in the frequency of rescue transitions, and an increase in the frequency of catastrophe transitions, when compared with polarized cells. Dynamicity, a measure of the gain and loss of subunits from microtubule plus ends, was 2.7 microns/min in polarized cells and 11.1 microns/min in scattered cells. These results demonstrate that individual microtubule dynamic behavior is markedly suppressed in polarized epithelial cells. Our results further demonstrate that in addition to its previously characterized effects on cell locomotion, hepatocyte growth factor stimulates microtubule dynamic turnover in lamellar regions of living cells.

Animals↗
PubMed1999

Stimulation-induced changes in filopodial dynamics determine the action radius of growth cones in the snail Helisoma trivolvis.

Filopodia on neuronal growth cones constantly extend and retract, thereby functioning as both sensory probes and structural devices during neuronal pathfinding. To better understand filopodial dynamics and their regulation by encounters with molecules in the environment, we investigated filopodial dynamics of identified B5 neurons from the buccal ganglion of the snail Helisoma trivolvis before and after treatment with nitric oxide (NO). We have previously demonstrated that treatment with several NO-donors caused a transient, cGMP-mediated elevation in [Ca(2+)](i), which was causally related to an increase in filopodial length and a reduction in the number of filopodia on growth cones. We demonstrate here that these effects were the result of distinct changes in filopodial dynamics. The NO-donor SIN-1 induced a general increase in filopodial motility. Filopodial elongation after treatment with SIN-1 resulted from a significant increase in the rate at which filopodia extended, as well as a significant increase in the time filopodia spent elongating. The reduction in filopodial number was caused by a significant decrease in the frequency with which new filopodia were inserted into the growth cone. With the exception of the back where filopodia appeared less motile, filopodial dynamics appeared to be mostly independent of the location on the growth cone. These results suggest that NO can regulate filopodial dynamics on migrating growth cones and might function as a messenger to adjust the action radius of a growth cone during pathfinding.

Animals↗
PubMed1999

600 ps molecular dynamics reveals stable substructures and flexible hinge points in cAMP dependent protein kinase.

Molecular dynamics simulations of the catalytic subunit of cAMP dependent protein kinase (cAPK) have been performed in an aqueous environment. The relations among the protein hydrogen-bonding network, secondary structural elements, and the internal motions of rigid domains were examined. The values of fluctuations of protein dihedral angles during dynamics show quite distinct maxima in the regions of loops and minima in the regions of alpha-helices and beta-strands. Analyses of conformation snapshots throughout the run show stable subdomains and indicate that these rigid domains are constrained during the dynamics by a stable network of hydrogen bonds. The most stable subdomain during the dynamics was in the small lobe including part of the carboxy-terminal tail. The most significant flexible region was the highly conserved glycine-rich loop between beta strands 1 and 2 in the small lobe. Many of the main chain dihedral angle changes measured in a comparison of the crystallographic structures of "open" and "closed" conformations of cAPK correspond to the highly flexible residues found during dynamics.

Animals↗
PubMed1997

Association of human growth hormone and calcium phosphate by dynamic compaction: in vitro biocompatibility and bioactivity.

The association of therapeutic agents with biomaterials has been achieved through various techniques, such as coating of the ceramic block surface or drug incorporation into ceramics. The dynamic compaction method recently was developed to consolidate drug-loaded calcium phosphate powder without a sintering step. In the present work, human recombinant growth hormone was loaded on biphasic calcium phosphate powder and consolidated by a specific process of cold sintering (dynamic compaction). Analyses of the biocompatibility of compacted pellets (mouse L929 fibroblastic cell culture) and the bioactivity of the drugs released by them (growth hormone bioassay) were performed. This report demonstrates the biocompatibility of the compacts prepared by dynamic compaction. L929 cell proliferation was maintained and the capacity to secrete fibronectin was conserved in the presence of compacted materials. Comparison of released growth hormone integrity, revealed by radioimmunoassay and eluted stain bioassay, has shown that the biological activity of growth hormone was totally preserved after dynamic compaction. However, 35% of loaded growth hormone was not released in our experimental conditions, probably because of the inaccessibility of growth hormone within the granulated compacts. Dynamic compaction shows good potential for the production of biomaterials capable of releasing therapeutic agents in situ.

Animals↗
PubMed2000

Breast cancer in dense breast: detection with contrast-enhanced dynamic MR imaging.

The purpose of this study was to identify contrast enhancement patterns of dense breast parenchyma and to investigate the ability of dynamic magnetic resonance imaging (MRI) to detect cancer in the dense breast. Thirty-two patients with breast cancer in dense breast underwent gadolinium-enhanced dynamic MRI. The detectability of cancer by dynamic MRI, mammography, and physical examination was compared. Two parenchymal enhancement patterns could be identified. One was increasingly multiple patchy enhancement found predominantly in the periphery (type A), and the other was faint enhancement without any nodular opacification (type B). Type A was thought to reflect severe proliferative fibrocystic change (PFC). For both patterns, the detection rate of primary cancers by dynamic MRI was found to be superior to that by other modalities. Dynamic MRI also could detect multifocal cancers, which could not be found with other modalities, although the detectability of these small cancers might be reduced in patients with severe PFC.

Adenocarcinoma↗
PubMed2000

Partial-FOV reconstruction in dynamic spiral imaging.

In many applications of dynamic MR imaging, only a portion of the field-of-view (FOV) exhibits considerable variations in time. In such cases, a prior knowledge of the static part of the image allows a partial-FOV reconstruction of the dynamic section using only a fraction of the raw data. This method of reconstruction generally results in higher temporal resolution, because the scan time for partial-FOV data is shorter. The fidelity of this reconstruction technique depends, among other factors, on the accuracy of the prior information of the static section. This information is usually derived from the reconstructed images at previous time frames. This data, however, is normally corrupted by the motion artifact Because the temporal frequency contents of the motion artifact is very similar to that of the dynamic section, a temporal low-pass filter can efficiently remove this artifact from the static data. The bandwidth of the filter can be obtained from the rate of variations inside and outside the dynamic area. In general, when the temporal bandwidth is not spatially uniform, a bank of low-pass filters can provide a proper suppression of the motion artifact outside the dynamic section. This reconstruction technique is adapted for spiral acquisition and is successfully applied to cardiac fluoroscopy, doubling the temporal resolution.

Algorithms↗
PubMed2001

Power Doppler ultrasonography for assessment of synovitis in the metacarpophalangeal joints of patients with rheumatoid arthritis: a comparison with dynamic magnetic resonance imaging.

OBJECTIVE: To evaluate the effectiveness of power Doppler ultrasonography (PDUS) for assessing inflammatory activity in the metacarpophalangeal (MCP) joints of patients with rheumatoid arthritis (RA), using dynamic magnetic resonance imaging (MRI) as a reference method. METHODS: PDUS and dynamic MRI were performed on 54 MCP joints of 15 patients with active RA and on 12 MCP joints of 3 healthy controls. PDUS was performed with a LOGIQ 500 unit by means of a 7-13-MHz linear array transducer. Later the same day, MRI was performed with a 1.0T MR unit. A series of 24 coronal T1-weighted images of the second through the fifth MCP joints was obtained, with intravenous injection of gadolinium diethylenetriaminepentaacetic acid after the fourth image (dynamic MRI). From the MR images, the rate of early synovial enhancement (RESE; defined as the relative enhancement per second during the first 55 seconds postinjection) was calculated and compared with the flow signal on PDUS, which was scored as present or absent. RESULTS: In RA patients, flow signal on PDUS was detected in 17 of 54 MCP joints examined. Postcontrast MR images revealed an RESE of > or = 1.0%/second in 18 of 54 RA MCP joints. PDUS showed no flow in 47 of 48 MCP joints with an RESE of <1.0%/second and revealed flow in 16 of 18 MCP joints with an RESE of > or = 1.0%/second. Using dynamic MRI as a reference, PDUS had a sensitivity of 88.8% and a specificity of 97.9%. CONCLUSION: PDUS was reliable for assessing inflammatory activity in the MCP joints of RA patients, using dynamic MRI as the standard. PDUS and clinical assessment of joint swelling/tenderness were only weakly correlated.

Adult↗
PubMed1993

Mechanical hyperalgesias in neuropathic pain patients: dynamic and static subtypes.

Two behavioral kinds of mechanical hyperalgesia can be clearly discerned by clinical criteria in patients with neuropathic syndromes, i.e., a dynamic type, elicitable by lightly stroking the symptomatic skin, and a static type, elicitable by steadily applying gentle pressure on it. Of 28 patients studied, 19 had dynamic and 18 had static type mechanical hyperalgesia (9 expressed both types). Experimental compression-ischemia nerve block totally abolished the dynamic hyperalgesia in all patients except in 2, in whom it was markedly diminished. Disappearance of dynamic hyperalgesia occurred contemporaneously with block of myelinated A fibers, as expressed by abolition of the sensations of touch and cold, monitored quantitatively. Static hyperalgesia, however, outlasted A-fiber block in 15 of 18 patients; the phenomenon persisted during the stage when only unmyelinated fibers were available for impulse conduction. It is thus concluded that, at the primary afferent level, dynamic hyperalgesia is mediated by myelinated fibers, whereas static hyperalgesia depends on unmyelinated afferents. These two kinds of hyperalgesia represent discrete pathophysiological entities with distinct clinical connotations.

Adult↗
PubMed2004

Hydration dependence of backbone and side chain polylysine dynamics: a 13C solid-state NMR and IR spectroscopy study.

The molecular dynamics of solid poly-L-lysine has been studied by the following natural abundance (13)C-NMR relaxation methods: measurements of the relaxation times T(1) at two resonance frequencies, off-resonance T(1rho) at two spin-lock frequencies, and proton-decoupled T(1rho). Experiments were performed at different temperatures and hydration levels (up to 17% H(2)O by weight). The natural abundance (13)C-CPMAS spectrum of polylysine provides spectral resolution of all types of backbone and side chain carbons and thus, dynamic parameters could be determined separately for each of them. At the same time, the conformational properties of polylysine were investigated by Fourier transform infrared spectroscopy. The data obtained from the different NMR experiments were simultaneously analyzed using the correlation function formalism and model-free approach. The results indicate that in dry polylysine both backbone and side chains take part in two low amplitude motions with correlation times of the order of 10(-4) s and 10(-9) s. Upon hydration, the dynamic parameters of the backbone remain almost constant except for the amplitude of the slower process that increases moderately. The side chain dynamics reveals a much stronger hydration response: the amplitudes of both slow and fast motions increase significantly and the correlation time of the slow motion shortens by about five orders of magnitude, and at hydration levels of more than 10% H(2)O fast and slow side chain motions are experimentally indistinguishable. These changes in the molecular dynamics cannot be ascribed to any hydration-dependent conformational transitions of polylysine because IR spectra reveal almost no hydration dependence in either backbone or side chain absorption domains. The physical nature of the fast and slow motions, their correlation time distributions, and hydration dependence of microdynamic parameters are discussed.

Magnetic Resonance Spectroscopy↗
PubMed1990

Conformational sampling using high-temperature molecular dynamics.

High-temperature molecular dynamics as a method for conformational search was explored on the antigen combining site of McPC 603, a phosphorylcholine binding immunoglobulin. Simulations at temperatures of 500, 800, and 1500 K were run for 111.5, 101.7, and 76.3 ps, respectively. The effectiveness of the search was assessed using a variety of methods. For the shorter hypervariable loops, molecular dynamics explored an appreciable fraction of the conformational space as evidenced by a comparison to a simple theoretical model of the size of the conformational space. However, for the longer loops and the antigen combining site as a whole, the simulation times were too short for a complete search. The simulations at 500 and 800 K both generated conformations that minimized to energies 200 kcal/mole lower than the crystal structure. However, the 1500 K simulation produced higher energy structures, even after minimization; in addition, this highest temperature run had many cis-trans peptide isomerizations. This suggests that 1500 K is too high a temperature for unconstrained conformational sampling. Comparison of the results of high temperature molecular dynamics with a direct conformational search method, [R. E. Bruccoleri & M. Karplus (1987) Biopolymers 26, 137-168]. showed that the two methods did not overlap much in conformational space. Simple geometric measures of the conformational space indicated that the direct method covered more space than molecular dynamics at the lower temperature, but not at 1500 K. The results suggest that high-temperature molecular dynamics can aid in conformational searches.

Amino Acid Sequence↗
PubMed1992

Langevin dynamics of peptides: the frictional dependence of isomerization rates of N-acetylalanyl-N'-methylamide.

The rate constant for the transition between the equatorial and axial conformations of N-acetylalanyl-N'-methylamide has been determined from Langevin dynamics (LD) simulations with no explicit solvent. The isomerization rate is maximum at collision frequency gamma = 2 ps-1, shows diffusive character for gamma greater than or equal to 10 ps-1, but does not approach zero even at gamma = 0.01 ps-1. This behavior differs from that found for a one-dimensional bistable potential and indicates that both collisional energy transfer with solvent and vibrational energy transfer between internal modes are important in the dynamics of barrier crossing for this system. It is suggested that conformational searches of peptides be carried out using LD with a collision frequency that maximizes the isomerization rate (i.e., gamma approximately 2 ps-1). This method is expected to be more efficient than either molecular dynamics in vacuo (which corresponds to LD with gamma = 0) or molecular dynamics in solvent (where dynamics is largely diffusive).

Alanine↗
PubMed2005

NMR methods for studying the structure and dynamics of RNA.

Proper functioning of RNAs requires the formation of complex three-dimensional structures combined with the ability to rapidly interconvert between multiple functional states. This review covers recent advances in isotope-labeling strategies and NMR experimental approaches that have promise for facilitating solution structure determinations and dynamics studies of biologically active RNAs. Improved methods for the production of isotopically labeled RNAs combined with new multidimensional heteronuclear NMR experiments make it possible to dramatically reduce spectral crowding and simplify resonance assignments for RNAs. Several novel applications of experiments that directly detect hydrogen-bonding interactions are discussed. These studies demonstrate how NMR spectroscopy can be used to distinguish between possible secondary structures and identify mechanisms of ligand binding in RNAs. A variety of recently developed methods for measuring base and sugar residual dipolar couplings are described. NMR residual dipolar coupling techniques provide valuable data for determining the long-range structure and orientation of helical regions in RNAs. A number of studies are also presented where residual dipolar coupling constraints are used to determine the global structure and dynamics of RNAs. NMR relaxation data can be used to probe the dynamics of macromolecules in solution. The power dependence of transverse rotating-frame relaxation rates was used here to study dynamics in the minimal hammerhead ribozyme. Improved methods for isotopically labeling RNAs combined with new types of structural data obtained from a growing repertoire of NMR experiments are facilitating structural and dynamic studies of larger RNAs.

Hydrogen Bonding↗
PubMed2003

Gas-phase activation and reaction dynamics of chiral ion-dipole complexes.

A family of enantiomerically pure oxonium ions, that is O-protonated 1-aryl-1-methoxyethanes, has been generated in the gas phase by the (CH(3))(2)Cl(+) methylation of the corresponding 1-arylethanols. Some information on their reaction dynamics was obtained from a detailed kinetic study of their inversion of configuration and dissociation. The activation parameters of the inversion reaction are found to obey two different isokinetic relationships depending upon the nature and the position of the substituents in the oxonium ions. In contrast, the activation parameters of the dissociation reaction obey a single isokinetic relationship. The inversion and dissociation rate constants do not follow simple linear free-energy relationships. This complicated kinetic picture has been rationalized in terms of different activation dynamics in gaseous CH(3)Cl, which, in turn, determine the reaction dynamics of the oxonium ion. When the predominant activation of the oxonium ion involves resonant energy exchange from the 1015 cm(-1) CH(3) rocking mode of unperturbed CH(3)Cl, the inversion reaction proceeds through the dynamically most favored TS, characterized by the unassisted C(alpha)bond;O bond elongation. When, instead, the activation of the oxonium ions requires the formation of an intimate encounter complex with CH(3)Cl, the inversion reaction takes place via the energetically most favored TS, characterized by multiple coordination of the CH(3)OH moiety with the H(alpha) and H(ortho) atoms of the benzylic residue. The activation dynamics operating in the intimate encounter complex with CH(3)Cl is also responsible for the dissociation of most selected oxonium ions.

Journal Article↗
PubMed2004

Microtubules become more dynamic but not shorter during preprophase band formation: a possible "search-and-capture" mechanism for microtubule translocation.

The dynamic behavior of the microtubule cytoskeleton plays a crucial role in cellular organization, but the physical mechanisms underlying microtubule (re)organization in plant cells are poorly understood. We investigated microtubule dynamics in tobacco BY-2 suspension cells during interphase and during the formation of the preprophase band (PPB), the cytoskeletal structure that defines the site of cytokinesis. Here we show that after 2 h of microtubule accumulation in the PPB and concurrent disappearance elsewhere in the cortex, the PPB is completed and starts to breakdown exponentially already 20 min before the onset of prometaphase. During formation of the PPB, the dynamic instability, i.e., the stochastic alternating between growing and shrinking phases, of the cortical microtubules outside the PPB increases significantly, but the microtubules do not become shorter. Based on this, as well as on the cross-linking of microtubules in the PPB and the lack of evidence for motor involvement, we propose a "search-and-capture" mechanism for PPB formation, in which the regulation of dynamic instability causes the cortical microtubules to become more dynamic and possibly longer, while the microtubule cross-linking activity of the developing PPB preferentially stabilizes these "searching" microtubules. Thus, microtubules gradually disappear from the cortex outside the PPB and aggregate to the forming PPB.

Algorithms↗
PubMed1988

Microtubule dynamics in the chromosomal spindle fiber: analysis by fluorescence and high-resolution polarization microscopy.

We describe preliminary results from two studies exploring the dynamics of microtubule assembly and organization within chromosomal spindle fibers. In the first study, we microinjected fluorescently labeled tubulin into mitotic PtK1 cells and measured fluorescence redistribution after photobleaching (FRAP) to determine the assembly dynamics of the microtubules within the chromosomal fibers in metaphase cells depleted of nonkinetochore microtubules by cooling to 23-24 degrees C. FRAP measurements showed that the tubulin throughout at least 72% of the microtubules within the chromosomal fibers exchanges with the cellular tubulin pool with a half-time of 77 sec. There was no observable poleward flux of subunits. If the assembly of the kinetochore microtubules is governed by dynamic instability, our results indicate that the half-life of microtubule attachment to the kinetochore is less than several min at 23-24 degrees C. In the second study, we used high-resolution polarization microscopy to observe microtubule dynamics during mitosis in newt lung epithelial cells. We obtained evidence from 150-nm-thick optical sections that microtubules throughout the spindle laterally associate for several sec into "rods" composed of a few microtubules. These transient lateral associations between microtubules appeared to produce the clustering of nonkinetochore and kinetochore microtubules into the chromosomal fibers. Our results indicate that the chromosomal fiber is a dynamic structure, because microtubule assembly is transient, lateral interactions between microtubules are transient, and the attachment of the kinetochores to microtubules may also be transient.

Animals↗