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PubMed2006

Spatiotemporal dynamics of actin-rich adhesion microdomains: influence of substrate flexibility.

In this study we analyse the formation and dynamics of specific actin-rich structures called podosomes. Podosomes are very dynamic punctual adhesion sites tightly linked to the actin cytoskeleton. Mechanical properties of substrates are emerging as important physical modulators of anchorage-dependent processes involved in the cellular response. We investigate the influence of substrate flexibility on the dynamic properties of podosomes. We used mouse NIH-3T3 fibroblasts, transfected with GFP-actin and cultured on polyacrylamide collagen-coated substrates of varying stiffness. Static and dynamic features of cell morphologies associated with an optical flow analysis of the dynamics of podosomes revealed that: (1) they have constant structural properties, i.e. their shape factor and width do not change with the substrate flexibility; (2) the lifespan of podosomes and mean minimum distance between them depend on the substrate flexibility; (3) there is a variation in the displacement speed of the rosette of podosomes. Moreover, the rosettes sometimes appear as periodically emergent F-actin structures, which suggests that a two-level self-organisation process may drive first, the formation of clusters of podosomes and second, the organisation of these clusters into oscillating rings. Such dynamic features give new perspectives regarding the potential function of podosomes as mechanosensory structures.

Actins↗
PubMed1996

Dynamic properties of nucleated microtubules: GTP utilisation in the subcritical concentration regime.

Microtubule assembly kinetics have been studied quantitatively under solution conditions supporting microtubule dynamic instability. Purified GTP-tubulin (Tu-GTP) and covalently cross-linked short microtubule seeds (EGS-seeds; Koshland et al. (1988) Nature 331, 499) were used with and without biotinylation. Under sub-critical concentration conditions ([Tu-GTP] < 5.3 microM), significant microtubule growth of limited length was observed on a proportion of the EGS-seeds by immuno-electron microscopy. A sensitive fluorescence assay for microtubule GDP production was developed for parallel assessment of GTP utilisation. This revealed a correlation between the detected microtubule growth and the production of tubulin-GDP, deriving from the shortening phase of the dynamic microtubules. This correlation was confirmed by the action of nocodazole, a specific inhibitor of microtubule assembly, that was found to abolish the GDP release. The variation of the GDP release with tubulin concentration (Jh(c) plot) was determined below the critical concentration (Cc). The GDP production observed was consistent with the elongation of the observed seeded microtubules with an apparent rate constant of 1.5 x 10(6) M-1 second-1 above a threshold of approximately 1 microM tubulin. The form of this Jh(c) plot for elongation below Cc is reproduced by the Lateral Cap model for microtubule dynamic instability adapted for seeded assembly. The behaviour of the system is contrasted with that previously studied in the absence of detectable microtubule elongation (Caplow and Shanks (1990) J. Biol. Chem. 265, 8935-8941). The approach provides a means of monitoring microtubule dynamics at concentrations inaccessible to optical microscopy, and shows that essentially the same dynamic mechanisms apply at all concentrations. Numerical simulation of the subcritical concentration regime shows dynamic growth features applicable to the initiation of microtubule growth in vivo.

Animals↗
PubMed2000

Exploring dynamic similarity in human running using simulated reduced gravity.

The Froude number (a ratio of inertial to gravitational forces) predicts the occurrence of dynamic similarity in legged animals over a wide range of sizes and velocities for both walking and running gaits at Earth gravity. This is puzzling because the Froude number ignores elastic forces that are crucial for understanding running gaits. We used simulated reduced gravity as a tool for exploring dynamic similarity in human running. We simulated reduced gravity by applying a nearly constant upward force to the torsos of our subjects while they ran on a treadmill. We found that at equal Froude numbers, achieved through different combinations of velocity and levels of gravity, our subjects did not run in a dynamically similar manner. Thus, the inertial and gravitational forces that comprise the Froude number were not sufficient to characterize running in reduced gravity. Further, two dimensionless numbers that incorporate elastic forces, the Groucho number and the vertical Strouhal number, also failed to predict dynamic similarity in reduced-gravity running. To better understand the separate effects of velocity and gravity, we also studied running mechanics at fixed absolute velocities under different levels of gravity. The effects of velocity and gravity on the requirements of dynamic similarity differed in both magnitude and direction, indicating that there are no two velocity and gravity combinations at which humans will prefer to run in a dynamically similar manner. A comparison of walking and running results demonstrated that reduced gravity had different effects on the mechanics of each gait. This suggests that a single unifying hypothesis for the effects of size, velocity and gravity on both walking and running gaits will not be successful.

Animals↗
PubMed2005

Comprehensive analysis of dynamics of histone H4 acetylation in mitotic barley cells.

Nucleosomal histones are covalently modified at specific amino acid residues. In the case of histone H4, four lysines (K5, K8, K12, and K16) are acetylated. In the current studies, we examined the dynamics of histone H4 acetylation at K8 and K12 in mitotic barley cells using a three-dimensional immunofluorescent method. Based on the results and previous studies on the dynamics of K5 and K16 acetylation, we provide a comprehensive view of the dynamics of H4 acetylation. Interphase nuclei exhibit strong acetylation in the centromeric region at K5, K8 and K12. In the case of K12, strong acetylation at nucleolar organizing regions was observed from prophase to anaphase. The dynamics of K12 were closely related to those of K5. On the other hand, K8 exhibited a pattern of almost uniform acetylation from prophase to telophase and strong acetylation in distal regions of chromosomes at both metaphase and anaphase, which is very similar to the dynamics of K16 acetylation. Thus, it appears that there is pair-wise acetylation of K12 and K5 in the nucleolar organizing regions and of K8 and K16 in the gene-rich regions. Together, these results suggest that pair-wise dynamics of H4 acetylation regulate chromosomal structure and function during the cell cycle.

Acetylation↗
PubMed1990

Diastolic time during static and dynamic exercise in myocardial infarction.

To evaluate the difference in the response of DT in the early phase of static (sustained weight load) and dynamic (treadmill) exercise, the relation of DT and HR was studied by ear densitography in 11 patients with myocardial infarction. None of the patients had an ischemic electrocardiographic response during exercise. Despite an increase in HR and the pressure-HR product with both types of exercise, the pressure-HR product was significantly higher at three minutes of dynamic exercise, which was associated with a significant lengthening of left ventricular ejection time. Diastolic blood pressure rose significantly during static exercise, but it remained unchanged with dynamic exercise. Electromechanical systole and HR had a linear inverse relation at three minutes of exercise, and DT and HR had a nonlinear inverse relation (DT = e7.29-0.0156 x HR, and DT = e7.07-0.0142 x HR for static and dynamic exercises, respectively). A significant prolongation of QS2 with a consequent shortening of DT (p less than 0.05) was observed in dynamic exercise. In addition to a higher pressure-HR product, the disproportionate shortening of diastole in the early phase of dynamic exercise has a potential for initiating imbalance of myocardial oxygen supply and demand.

Blood Pressure↗
PubMed2004

Connectivity and dynamics of neural information processing.

In this article, we systematically review the current literature on neural connectivity and dynamics, or equivalently, structure and function. In particular, we discuss how changes in the connectivity of a neural network affect the spatiotemporal network dynamics qualitatively. The three major criteria of comparison are, first, the local dynamics at the network nodes which includes fixed point dynamics, oscillatory and chaotic dynamics; second, the presence of time delays via propagation along connecting pathways; and third, the properties of the connectivity matrix such as its statistics, symmetry, and translational invariance. Since the connection topology changes when anatomical scales are traversed, so will the corresponding network dynamics change. As a consequence different types of networks are encountered on different levels of neural organization.

Animals↗
PubMed2003

Two dynamic morphotypes of sarcoma cells, asymmetric stellate and triangle with leading lamella, are related to malignancy.

A notion of the dynamic morphotype was developed as a conjunction between cell shape and migration. This enabled the investigation of the relationship between malignancy and patterns of dynamic morphology in neoplastic cells in vitro. Time-lapse cinemicroscopy was used to analyse the cell behaviour of three rat neoplastic cell lines (K2, T15, and A8), differing in metastatic potential, that were instrumental in revealing a coincidence between high migratory activity and appearance of the 3D structure of actin cables in high-malignant A8 cells (Pokorná et al., 1994). A set of criteria was established for visual classification of cell morphology. Matching the pattern of cell morphology with locomotory activity led to identification of four dynamic morphotypes. Cell speed was determined by tracking and the dynamic morphotypes assigned by the operator. All the three cell populations were studied for incidence of the dynamic morphotypes in culture media differing in pH: 6.6 simulating acid extracellular condition in tumours, physiological 7.4, and alkaline 8.2. The results showed that acid pH stimulated motile activity in the intermediate-malignant T15 and most malignant A8 cells. The T15 and A8 cells also manifested a prolonged continuation of fast locomotion in the early G1 phase and displayed a prevalence of two fast moving dynamic morphotypes: asymmetric stellate and triangle with leading lamella.

Animals↗
PubMed2006

Temporal dynamics and latency patterns of receptor neuron input to the olfactory bulb.

Odorants are first represented in the brain by distributed patterns of activity in the olfactory bulb (OB). Although neurons downstream of sensory inputs respond to odorants with temporally structured activity, sensory inputs to glomeruli are typically described as static maps. Here, we imaged the temporal dynamics of receptor neuron input to the OB with a calcium-sensitive dye in the olfactory receptor nerve terminals in anesthetized mice. We found that diverse, glomerulus- and odorant-dependent temporal dynamics are present even at this initial input stage. Instantaneous spatial patterns of receptor input to glomeruli changed both within and between respiration cycles. Glomerular odorant responses differed in amplitude, latency, rise time, and degree of modulation by sniffing in an odorant-specific manner. Pattern dynamics within the first respiration cycle recurred in a similar manner during consecutive cycles. When sniff rate was increased artificially, pattern dynamics were preserved in the first sniff but were attenuated during subsequent sniffs. Temporal response properties were consistent across individuals on a coarse regional scale and on a fine scale of individual glomeruli. Latency and magnitude of glomerular inputs were only weakly correlated and might therefore convey independent odorant information. These data demonstrate that glomerular maps of primary sensory input to the OB are temporally dynamic. These dynamics may contribute to the representation of odorant information and affect information processing in the central olfactory system of rodents.

Animals↗
PubMed2004

(1)H/(15)N heteronuclear NMR spectroscopy shows four dynamic domains for phospholamban reconstituted in dodecylphosphocholine micelles.

We report the backbone dynamics of monomeric phospholamban in dodecylphosphocholine micelles using (1)H/(15)N heteronuclear NMR spectroscopy. Phospholamban is a 52-amino acid membrane protein that regulates Ca-ATPase in cardiac muscle. Phospholamban comprises three structural domains: a transmembrane domain from residues 22 to 52, a connecting loop from 17 to 21, and a cytoplasmic domain from 1 to 16 that is organized in an "L"-shaped structure where the transmembrane and the cytoplasmic domain form an angle of approximately 80 degrees (Zamoon et al., 2003; Mascioni et al., 2002). T(1), T(2), and (1)H/(15)N nuclear Overhauser effect values measured for the amide backbone resonances were interpreted using the model-free approach of Lipari and Szabo. The results point to the existence of four dynamic domains, revealing the overall plasticity of the cytoplasmic helix, the flexible loop, and part of the transmembrane domain (residues 22-30). In addition, using Carr-Purcell-Meiboom-Gill-based experiments, we have characterized phospholamban dynamics in the micros-ms timescale. We found that the majority of the residues in the cytoplasmic domain, the flexible loop, and the first ten residues of the transmembrane domain undergo dynamics in the micros-ms range, whereas minimal dynamics were detected for the transmembrane domain. Hydrogen/deuterium exchange factors measured at different temperatures support the existence of slow motion in both the loop and the cytoplasmic helix. We propose that these dynamic properties are critical factors in the biomolecular recognition of phospholamban by Ca-ATPase and other interacting proteins such as protein kinase A and protein phosphatase 1.

Calcium-Binding Proteins↗
PubMed2004

Neutron frequency windows and the protein dynamical transition.

Proteins undergo an apparent dynamical transition on temperature variation that has been correlated with the onset of function. The transition in the mean-square displacement, , that is observed using a spectrometer or computer simulation, depends on the relationship between the timescales of the relaxation processes activated and the timescale accessible to the instrument or simulation. Models are described of two extreme situations---an "equilibrium" model, in which the long-time dynamics changes with temperature and all motions are resolved by the instrument used; and a "frequency window" model, in which there is no change in the long-time dynamics but as the temperature increases, the relaxation frequencies move into the instrumental range. Here we demonstrate that the latter, frequency-window model can describe the temperature and timescale dependences of both the intermediate neutron scattering function and derived from molecular dynamics simulations of a small protein in a cryosolution. The frequency-window model also describes the energy-resolution and temperature-dependences of obtained from experimental neutron scattering on glutamate dehydrogenase in the same solvent. Although equilibrium effects should also contribute to dynamical transitions in proteins, the present results suggests that frequency-window effects can play a role in the simulations and experiments examined. Finally, misquotations of previous findings are discussed in the context of solvent activation of protein dynamics and the possible relationship of this to activity.

Biophysics↗
PubMed2005

Molecular dynamics simulations of C2F6 effects on gramicidin A: implications of the mechanisms of general anesthesia.

It was recently postulated that the effects of general anesthetics on protein global dynamics might underlie a unitary molecular mechanism of general anesthesia. To verify that the specific dynamics effects caused by general anesthetics were not shared by nonanesthetic molecules, two parallel 8-ns all-atom molecular dynamics simulations were performed on a gramicidin A (gA) channel in a fully hydrated dimyristoylphosphatidylcholine membrane in the presence and absence of hexafluoroethane (HFE), which structurally resembles the potent anesthetic molecule halothane but produces no anesthesia. Similar to halothane, HFE had no measurable effects on the gA channel structure. In contrast to halothane, HFE produced no significant changes in the gA channel dynamics. The difference between halothane and HFE on channel dynamics can be attributed to their distinctly different distributions within the lipid bilayer and consequently to the different interactions of the anesthetic and the nonanesthetic molecules with the channel-anchoring tryptophan residues. The study further supports the notion that anesthetic-induced changes in protein global dynamics may play an important role in mediating anesthetic actions on proteins.

Anesthesia, General↗
PubMed2005

Simulation of fluorescence anisotropy experiments: probing protein dynamics.

Time-resolved fluorescence anisotropy decay experiments on a protein-attached dye can probe local protein dynamics and steric restrictions, but are difficult to interpret at the structural level. Aiming at an atomistic description, we have carried out molecular dynamics simulations of such experiments. Our simulations describe an Alexa488 fluorescent dye maleimide derivative covalently attached via a single cysteine to the AB-loop of bacteriorhodopsin. Fluorescence anisotropy decay curves obtained from the simulations agree well with the measured ones. Three anisotropy decay components were resolved and assigned to: 1), the fast dynamics of the attached dye on the picosecond timescale; 2), the slower dynamics of the loop at the one nanosecond timescale; and 3), the overall tumbling of the molecule. For the biologically relevant 1-ns component we identified two processes from simulations, the motion of the flexible loop as well as slow conformational dynamics of the dye. These two processes are not separable by experiment alone. Furthermore, analysis of the correlation between the dye and the protein motion revealed which part and which motion of the protein is actually probed by the experiment. Finally, our simulations allowed us to test the usual and inevitable assumption underlying these types of spectroscopic measurements that the attached dye probe does not severely perturb the protein dynamics. For the case at hand, by comparison with a simulation of the dye-free protein, the perturbation was quantified and found to be small.

Anisotropy↗
PubMed2006

Multiscale modeling of nucleosome dynamics.

Nucleosomes form the fundamental building blocks of chromatin. Subtle modifications of the constituent histone tails mediate chromatin stability and regulate gene expression. For this reason, it is important to understand structural dynamics of nucleosomes at atomic levels. We report a novel multiscale model of the fundamental chromatin unit, a nucleosome, using a simplified model for rapid discrete molecular dynamics simulations and an all-atom model for detailed structural investigation. Using a simplified structural model, we perform equilibrium simulations of a single nucleosome at various temperatures. We further reconstruct all-atom nucleosome structures from simulation trajectories. We find that histone tails bind to nucleosomal DNA via strong salt-bridge interactions over a wide range of temperatures, suggesting a mechanism of chromatin structural organization whereby histone tails regulate inter- and intranucleosomal assemblies via binding with nucleosomal DNA. We identify specific regions of the histone core H2A/H2B-H4/H3-H3/H4-H2B/H2A, termed "cold sites", which retain a significant fraction of contacts with adjoining residues throughout the simulation, indicating their functional role in nucleosome organization. Cold sites are clustered around H3-H3, H2A-H4 and H4-H2A interhistone interfaces, indicating the necessity of these contacts for nucleosome stability. Essential dynamics analysis of simulation trajectories shows that bending across the H3-H3 is a prominent mode of intranucleosomal dynamics. We postulate that effects of salts on mononucleosomes can be modeled in discrete molecular dynamics by modulating histone-DNA interaction potentials. Local fluctuations in nucleosomal DNA vary significantly along the DNA sequence, suggesting that only a fraction of histone-DNA contacts make strong interactions dominating mononucleosomal dynamics. Our findings suggest that histone tails have a direct functional role in stabilizing higher-order chromatin structure, mediated by salt-bridge interactions with adjacent DNA.

Chromatin↗
PubMed2006

Dynamic contour tonometry and goldman applanation tonometry in eyes with keratoconus.

PURPOSE: The dynamic contour tonometer is a nonapplanation contact tonometer designed to be largely independent of the structural properties of the cornea. Theoretically, it may measure intraocular pressure most accurately in abnormally thinner corneas. This study compares intraocular pressure measurements by dynamic contour tonometry with Goldman applanation tonometry in eyes with normal corneas and eyes with advanced keratoconus. METHODS: A comparative case series. Subjects underwent intraocular pressure measurements by dynamic contour tonometry, Goldman applanation tonometry, ultrasonic pachymetry, and slit scanning topography. EXCLUSION CRITERIA: any ocular pathology other than keratoconus, previous corneal or refractive surgery, stromal scarring due to acute hydrops, or any other corneal opacities. RESULTS: Ten patients with keratoconus were included in Group A, and 12 normal patients composed Group B according to the pre-established criteria. The mean Goldman tonometry measurement in group A was 10.3 +/- 1.8 mm Hg and group B was 14.3 +/- 0.75 mm Hg. (P = 0.024). In group A, the mean measurement with the dynamic contour tonometer was 14.6 +/- 2.09 mm Hg, and in group B, it was 17.4 +/- 3.1 mm Hg (P = 0.026). The difference between both methods of measurement in group A was statistically significant (P < 0.0002). CONCLUSION: Intraocular pressure readings with dynamic contour tonometry in the keratoconus group were significantly higher than Goldman measurements and lower when compared to the control group. As there are no published manometric studies in eyes with keratoconus, these lower intra-ocular readings with the dynamic contour tonometry could be related to the discrepancy between the radius of corneal curvature and its tip, the significant thinning of the cornea, or other corneal biomechanical abnormalities related to advanced keratoconus.

Adult↗
PubMed2006

Testing the irruptive paradigm of large-herbivore dynamics.

A dominant paradigm in understanding and managing large herbivores is that, after introduction to new range or release from harvesting, the herbivore population increases to peak abundance, crashes to a lower abundance, and then increases to a carrying capacity lower than peak abundance. However, support for the paradigm has been largely anecdotal. We first developed two mathematical models to better describe irruptive dynamics. The models differed in the form of the postcrash growth toward carrying capacity: the "Caughley model" included a time lag that generated dampening oscillations, and the "Leopold model" did not. We then evaluated which of four models (theta-logistic, delayed-logistic, Leopold, and Caughley) best described the dynamics of seven ungulate populations either introduced to new range (n = 5 populations) or released from harvesting (n = 2). The dynamics of six of the populations were best described by irruptive models (two by the Leopold, one by the Caughley, and three by the delayed-logistic), and one of the populations did not display irruptive dynamics (theta-logistic model). The limited data thus support the widespread existence of irruptive dynamics, and we encourage the consideration of irruptive models in studies of large-herbivore dynamics.

Animals↗
PubMed2003

Differential diagnosis of adrenal masses by chemical shift and dynamic gadolinium enhanced MR imaging.

Chemical shift MRI is widely used for identifying adenomas, but it is not a perfect method. We determined whether combined dynamic MRI methods can lead to improved diagnostic accuracy. Fifty-seven adrenal masses were examined by chemical shift and dynamic MR imaging using 2 MR systems. The masses included 38 adenomas and 19 non-adenomas. In chemical shift MRI studies, the signal intensity index (SI) was calculated, and the lesions classified into 5 types in the dynamic MRI studies. Of the 38 adenomas studied, 37 had an SI greater than 0. In the dynamic MRI, 34 of 38 adenomas showed a benign pattern (type 1). If the SI for the adenomas in the chemical shift MRI was considered to be greater than 0, the positive predictive value was 0.9, and the negative predictive value was 0.94 and kappa = 0.79. If type 1 was considered to indicate adenomas in the dynamic MRI, the corresponding values were 0.94, 0.81 and kappa = 0.77 respectively. The results obtained when the 2 methods were combined were 1, 0.95 and kappa = 0.96 respectively. The chemical shift MRI was found to be useful for identifying adenomas in most cases. If the adrenal mass had a low SI (0 < SI < 5), dynamic MRI was also found to be helpful for making a differential diagnosis.

Adenoma↗
PubMed2006

Measurement and evaluation of dynamic joint stability of the knee and ankle after injury.

Injuries to the lower extremity, specifically the knee and ankle joints of the human body can occur in any athletic event and are most prevalent in sports requiring cutting and jumping manoeuvres. These joints are forced to rely on the dynamic restraints to maintain joint stability, due to the lack of bony congruence and the inability of the static restraints to handle the forces generated during functional tasks. Numerous variables (proprioception, postural control, electromyography, kinetics/kinematics, dynamic stability protocols) have been measured to better understand how the body maintains joint stability during a wide range of activities from static standing to dynamic cutting or landing from a jump. While the importance of dynamic restraints is not questioned, a recent impetus to conduct more functional or sport-specific testing has emerged and placed a great deal of emphasis on dynamic joint stability and how it is affected by lower extremity injuries. Evidence suggests that surgery and aggressive rehabilitation will not necessarily restore the deficits in dynamic joint stability caused by injury to the anterior cruciate ligament or lateral ankle ligaments. In today's athletic society, there is a major push to return athletes to play as quickly as possible. However, the ramifications of those decisions have not been fully grasped. If an athlete is not fully recovered, a quick return to play could start a vicious cycle of chronic injuries or permanent disability.

Ankle Injuries↗
PubMed1995

Neurohumoral factor responses to mental (arithmetic) stress and dynamic exercise in normal subjects.

We examined the responses of plasma catecholamine and plasma renin activity (PRA) during mental (arithmetic) stress and dynamic exercise in 15 normal subjects. Compared to rest values, there was a significant increase in the plasma epinephrine concentration (E), but not in the plasma norepinephrine concentration (NE) or PRA during mental arithmetic. During dynamic exercise, there were significant increases in both NE and E and in PRA. The ratio of E to NE was significantly higher during mental arithmetic than during dynamic exercise. NE was significantly correlated with PRA at rest, during mental arithmetic and dynamic exercise. No significant correlations were observed between E and PRA. Dynamic exercise primarily induces a sympathetic nervous response, and mental (arithmetic) stress mainly induces an adrenal response. The renin-angiotensin-aldosterone system response may in part be regulated by sympathetic nervous activity during both mental (arithmetic) stress and dynamic exercise.

Adult↗