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Buffer conditions and non-tubulin factors critically affect the microtubule dynamic instability of sea urchin egg tubulin.

The dynamic instability of individual microtubules (Mts) in cytoplasmic extracts or assembled from highly purified sea urchin egg tubulin was examined using video-enhanced, differential-interference contrast (VE-DIC) light microscopy. Extract Mts (endogenous tubulin = 12.1 microM) displayed only plus-ended growth. The elongation velocity was 7.8 microns/min for an average duration of 1.3 min before switching (catastrophe) to rapid shortening, which occurred at 13.0 microns/min for an average duration of 0.5 min before switching (rescue) back to the elongation phase. These parameters are typical of interphase Mt dynamic instability. Surprisingly, Mts assembled from purified urchin egg tubulin in standard buffers were less dynamic that those reported for purified brain tubulin or Mts in the extract. Buffer parameters were changed in an attempt to mimic the extract Mt results. The pH buffer itself, Hepes or Pipes, drastically altered Mt dynamics but could not achieve high elongation velocity with high catastrophe frequencies. Calcium at 1 microM had negligible effects, while increasing pH from 6.9 to 7.2 stimulated elongation velocity. Finally, Mt dynamics of purified egg tubulin (11.9 microM) were assayed in ultrafiltrates (MW cut-off less than 30 kD) of the cytoplasmic extracts. Mts elongated slowly at 1.2 microns/min for 26 min before a catastrophe and rapid shortening at 11.8 microns/min. Rescue was less frequent than unfiltered extracts, minus-ended growth was observed, and self-assembly occurred at slightly higher tubulin concentrations. Therefore, the egg extracts and cytoplasm must contain non-buffer factors which stimulate elongation velocity by 6.5-fold without self-assembly, increase catastrophe frequency by 20-fold, and block minus-ended growth.

Animals↗

Computer simulation of nerve growth cone filopodial dynamics for visualization and analysis.

The neuronal growth cone plays a fundamental role in nerve development and regeneration. A sensory-motile structure, it determines the path of axonal extension through its interactions with the extracellular environment, ultimately directing the formation of functional connections in the nervous system. Though several mechanisms of interaction have been proposed, these have been difficult to describe quantitatively due to the complexity of growth cone behavior, as manifested in the randomly and rapidly changing shape of the growth cone. The application of mathematical techniques to model growth cone shape and motility in terms of underlying processes represents a promising approach with untapped potential for helping to unravel this complexity while revealing new insights into axonal pathfinding events. This paper presents a simulation model for filopodial dynamics, a primary feature of the motile growth cone. The model produces realizations of dynamic filopodial structure on representative growth cones for a given set of model parameters, which include the rates of filopodial initiation, extension, and retraction, filopodial length at maximum extension, and angular orientation. These parameters are based on recent experimental characterization of filopodial dynamics [Buettner et al., 1994: Dev. Biol. 163:407-422]. The mathematical relationship between the model parameters and average filopodial number and length per growth cone is described, and the contribution of individual parameters to overall filopodial morphology is illustrated both visually and numerically. In addition, the model is used to simulate filopodial encounter with a target for various conditions of filopodial dynamics. The result is characterized in terms of a mean encounter time for a population of growth cones and provides an indication of the effect of individual parameters of filopodial dynamics on the encounter process. Future experimental testing will be required to develop the model further. However, in its current form, the model enables a first approximation analysis of many hypothesis of growth cone migration and pathfinding and offers insight into the the underlying mechanisms of nerve growth and regeneration.

Cell Size↗

Direct measurement of dynamic frequency shift induced by cross-correlations in 15N-enriched proteins.

We describe a new NMR experimental scheme that allows the direct determination of the dynamic frequency shift induced by chemical shift anisotropy/dipolar interaction (CSA/DD) cross-correlations in 15N-enriched proteins. Its principle consists of comparing two rates of polarisation transfer between the amide proton and nitrogen. The first rate, which is independent of the dynamic frequency shift, is based on a selective Hartmann-Hahn coherence transfer. The second rate, which depends on the dynamic frequency shift, is based on a free evolution of the transverse magnetisation. We report experimental validation of this approach by measuring the average dynamic frequency shift due to CSA/DD cross-correlations in the calcium-binding protein D9k. The method may also be applicable to the measurement of dynamic frequency shift induced by cross-correlations between the Curie spin and dipolar interactions.

Magnetic Resonance Spectroscopy↗

Dynamic pH junction-sweeping capillary electrophoresis for online preconcentration of toxic pyrrolizidine alkaloids in Chinese herbal medicine.

There is a need to develop simple yet effective preconcentration methods to enhance concentration sensitivity for CE analysis of trace level analytes in real samples, particularly when commonly available but less sensitive detection methods, e.g., UV detection, are used. In this report, a hyphenated online preconcentration strategy combining dynamic pH junction with sweeping (i.e., dynamic pH junction-sweeping) was employed for the analysis of four toxic pyrrolizidine alkaloids (PAs) of senkirkine, senecionine, retrorsine, and seneciphylline in Chinese herbal medicine (Kuan donghua). Direct electrokinetically focusing of a large sample volume injection (up to 20% of capillary length) on the capillary was performed using the dynamic pH junction-sweeping method. A sample matrix consisting of 10 mM phosphate with 20% methanol at pH 4.0 and a BGE containing 20 mM borate, 30 mM SDS, and 20% methanol at pH 9.1 were utilized to realize dynamic pH junction-sweeping for PAs. This online preconcentration strategy resulted in sensitivity enhancement factors ranging from 23.8- to 90.0-fold for the four toxic PAs, giving an LOD as low as 30 ppb for the PAs. Critical factors such as sample matrix type, pH, and salt concentration were also examined to achieve higher sensitivity enhancement, shorter analysis time, and better resolution. The results indicate that the proposed dynamic pH junction-sweeping technique is a powerful alternative approach for identification and determination of trace levels of these toxic PAs and other hydrophobic, protonatable compounds in real samples.

Chromatography, Micellar Electrokinetic Capillary↗

Adsorption/desorption phenomena on pure and Teflon AF-coated titania surfaces studied by dynamic contact angle analysis.

As a result of inflammatory processes, plaque formation on dental titanium implants often leads to clinically pathogenic situations. This special biofilm formation on (bio)materials in contact with saliva is initiated by ionic and protein interactions. In this interfacial process, albumin becomes a main constituent of dental pellicle. Interfacial reactions change the surface characteristics. They determine the following steps of macromolecular adsorption and bacterial adhesion. This work focuses on the dynamic contact angle analysis (DCA), which is a tool for online measurements of dynamic changes of wettability without disturbing the interface during detection. Repeatability of the DCA method has been assessed according to the Bland and Altman method. The kinetics and equilibrium data of shifts in the wetting tension hysteresis indicate ionic influences at the titanium/bovine serum albumin (BSA) interface: the Ca-mediated increase of the BSA adsorption on titanium and the adsorption maximum at the isoelectric point (IEP) of BSA. Ti was surface modified by Teflon AF polymeric coatings. The result of the assessment gives reason to consider Teflon AF as a reference material for DCA repeatability studies. This surface modification caused drastic changes in the dynamic interfacial reactions. Shifts in the wetting tensions during DCA adsorption-desorption experiments clearly demonstrated the partially irreversible adsorption of BSA on Teflon AF. In contrast, reversible adsorption behavior was detected on pure Ti surfaces. These findings strengthen the hypothesis that the analysis of dynamic changes in wetting tension and wetting tension hysteresis is a sensitive analytical method for the detection of dynamic interfacial changes at biomaterial/biosystem interfaces during the initial steps of biofilm formation.

Adsorption↗

Fluctuating charge normal modes: An algorithm for implementing molecular dynamics simulations with polarizable potentials.

A new method for performing molecular dynamics simulations with fluctuating charge polarizable potentials is introduced. In fluctuating charge models, polarizability is treated by allowing the partial charges to be variables, with values that are coupled to charges on the same molecule as well as those on other molecules. The charges can be efficiently propagated in a molecular dynamics simulation using extended Lagrangian dynamics. By making a coordinate change from the charge variables to a set of normal mode charge coordinates for each molecule, a new method is constructed in which the normal mode charge variables uncouple from those on the same molecule. The method is applied to the TIP4P-FQ model of water and compared to other methods for implementing the dynamics. The methods are compared using different molecular dynamics time steps.

Journal Article↗

Force field validation for nucleic acid simulations: comparing energies and dynamics of a DNA dodecamer.

Important questions exist regarding the quality of force fields used in molecular dynamics (MD) simulations and their interoperable use with other available MD implementations. NAMD is one of the most efficient and scalable parallel molecular dynamics codes for large-scale biomolecular simulations in the open source domain. It is the aim of this article to analyze and compare the dynamics of a benchmark DNA dodecamer d(CTTTTGCAAAAG)2 system, including its binding to a specific drug molecule arising from the use of various simulation protocols in NAMD using Amber98, with the dynamics arising from simulations of the same dodecamer using Amber98 in the AMBER package, one of the most well-established simulation codes for nucleic acids. Based upon a set of validation benchmarks, the details of which are discussed, we find that nucleic acid simulations using NAMD give meaningful results and that the essential features of the resulting dynamics are similar to those arising from the AMBER package. This sets the stage for reliable large-scale simulations of nucleic acids using NAMD.

Computer Simulation↗

Purinergic pathway suppresses the release of .NO and stimulates proteoglycan synthesis in chondrocyte/agarose constructs subjected to dynamic compression.

Mechanical loading plays a fundamental role in the physiological and pathological processes of articular cartilage. The application of dynamic compression to chondrocytes cultured in agarose, downregulates the release of nitric oxide (NO) and enhances cell proliferation and proteoglycan synthesis. We hypothesize that the observed metabolic changes in response to dynamic compression involve a purinergic signaling pathway. Chondrocyte/agarose constructs were subjected to dynamic compression (15%, 1 Hz, 48 h) in the presence of antagonists for the purinergic pathway. Gadolinium was used as a putative inhibitor of stretch-activated calcium ion channels including adenosine 5'-triphosphate (ATP) release channels; suramin was employed as a P2 receptor antagonist and apyrase was used to catalyze the hydrolysis of extracellular ATP. The data presented demonstrate that in the absence of the inhibitor, dynamic compression suppressed .NO release. Treatment with gadolinium and suramin caused a compression-induced upregulation of .NO release, a response abolished with apyrase. Compression-induced stimulation of cell proliferation was reversed with gadolinium, suramin, or apyrase. By contrast, compression-induced stimulation of proteoglycan synthesis was abolished under all treatment conditions. Thus, the purinergic pathway is important in suppressing the release of .NO and stimulation of proteoglycan synthesis. Indeed, high levels of .NO could trigger a downstream catabolic response and mediate the compression-induced inhibition of cell proliferation. The current study demonstrates for the first time the importance of a purinergic pathway in mediating the metabolic response to dynamic compression and suppressing an inflammatory effect.

Adenosine Triphosphate↗

Nonuniform flow dynamics in the aorta of normal children: a simplified approach to measurement using magnetic resonance velocity mapping.

PURPOSE: To determine regional flow dynamics in the normal aorta (Ao) in children. Understanding flow dynamics in children is important in cardiovascular energetics, in designing improved aortic reconstructions by crafting the surgery to mimic normal aortic flow, and in Doppler flow calculations. The objective of this study was to determine regional flow dynamics in the normal Ao in children. MATERIALS AND METHODS: We performed magnetic resonance velocity mapping on 13 subjects (ages 7.2 +/- 6.2 years) with normal Aos to determine flow dynamics in four equal quadrants in the ascending (AAo) and descending aorta (DAo) aligned along the long axis of the Ao. Statistical significance was set at P <.05. RESULTS: In the AAo, the left posterior quadrant displayed significantly less blood flow (16% +/- 5%) than the other quadrants (26-29%) over the cardiac cycle. In the DAo, both anterior quadrants carried significantly less blood flow (20% and 21%) than the posterior quadrants (27% and 32%). At maximum flow (15% +/- 5% into the cardiac cycle for the AAo; 27% +/- 15% for the DAo), there was significantly more flow in the right posterior quadrant (28% +/- 2%) than other quadrants (22-23%) in the AAo. In the DAo, both posterior quadrants had significantly higher flow rates (27% and 30%) than the anterior quadrants (21% and 22%). Maximum velocity in both the AAo and the DAo occurred in the left posterior quadrant in 10/13 at 16-24% into the cardiac cycle. At end-systole, a short flow reversal was noted in the posterior quadrants in the AAo in 11/13; in the DAo, this occurred in the anterior quadrants in 10/13. CONCLUSION: Flow dynamics in the normal Ao in children are not symmetrical; the flow distributions are asymmetric in both the AAo and the DAo throughout systole, including flow reversal related to the dicrotic notch. These results may help improve Ao surgery.

Analysis of Variance↗

Pain dynamics observed by functional magnetic resonance imaging: differential regression analysis technique.

PURPOSE: To observe the dynamic responses of the cortical areas related to the pain processing by using the differential regression analysis (DRA) technique in functional magnetic resonance imaging (fMRI) and investigation of pain mechanisms. MATERIALS AND METHODS: For pain studies, thermal stimulation was applied by immersing the index finger into a hot bath of water with a temperature of 50-52 degrees C. Motor (finger tapping) and visual (flickering light) stimulation experiments were conducted to elucidate the physiological differences between the simple sensory tasks and pain tasks. To obtain dynamic responses, T values (regression analysis) were sequentially estimated by using a series of shifted differential window functions (narrow width). RESULTS: By using the DRA technique, well-defined prompt responses were observed for both motor and visual stimuli. On the other hand, in the pain experiment, a set of sequentially varying responses was observed for the thalamus (Thal), the dorsal anterior cingulate cortex (dACC), the caudal ACC (cACC), and the rostral ACC (rACC). This time-dependent response suggests the dynamics of pain signal processing in cortical areas. CONCLUSION: The results support the hypothesis that the activated areas are similar to the previously reported pain processing areas; however, new sequential responses were observed, suggesting that the technique may reveal dynamics of pain perception and their pathway, important elements in understanding the mechanism of pain. The DRA technique can provide a new opportunity for many spatiotemporal analyses, for example, the physiologically complex and little-studied physiological phenomena, such as pain dynamics.

Cerebral Cortex↗

Spin-echo and dynamic gadolinium-enhanced FLASH MR imaging of hepatocellular carcinoma: correlation with histopathologic findings.

Evaluation of histologic subtype and degree of differentiation in hepatocellular carcinoma (HCC) is essential because it affects patient prognosis and treatment planning. To evaluate the histologic subtype of HCC with magnetic resonance (MR) imaging, conventional spin-echo and dynamic studies were correlated with histopathologic and angiographic findings in 72 HCCs. Dynamic MR imaging was performed with the fast low-angle shot (FLASH) technique after administration of gadopentetate dimeglumine. There was considerable overlap in signal intensity between various tumor grades on both T1- and T2-weighted images. On dynamic MR images, the peak contrast enhancement ratio correlated with tumor grade (well-differentiated, 29.5 +/- 24.7; moderately differentiated, 63.5 +/- 24.1; poorly differentiated, 86.9 +/- 26.4) or degree of dilatation of the sinusoidlike vascular space between tumor cells. The maximum contrast-to-noise ratio in tumor (relative to surrounding liver) was achieved within 60 seconds in 45 HCCs (mostly of the trabecular or pseudoglandular type). Enhancement was slight or minimal in 17 tumors (mostly small, well-differentiated tumors). In 10 tumors, the degree of enhancement increased with time, with maximum enhancement in the delayed phase (most frequently in scirrhous HCC). These dynamic patterns correlated with angiographic findings. These data indicate that the degree and pattern of enhancement on dynamic MR images reflect tumor differentiation and architecture of HCC.

Angiography, Digital Subtraction↗

Dual dynamic contrast-enhanced MR imaging.

A method was devised for obtaining dynamic contrast-enhanced T1-weighted and relaxation rate (delta R2*) images simultaneously to evaluate regional hemodynamics of the brain tumors. On a 1.5-T MR system, dual dynamic contrast-enhanced images were obtained using a gradient echo (dual echo fast field echo) pulse sequence with the keyhole technique to improve temporal and spatial resolution during a rapid bolus injection of gadopentetate dimeglumine. The dynamic T1 contrast images were obtained from the first echo: moreover. integral delta R2*dt values were calculated from the first and the second echo images. The dynamic T1 contrast images provided information about characteristic enhancement pattern (vascularization and disruption of blood-brain barrier), and the integral delta R2*dt values provided a map of regional blood pool in tumor site, peritumoral edema, and other surrounding regions of the brain. The ability to obtain dynamic contrast-enhanced T1 contrast and delta R2* imaging at the same time allows optimization of the advantages of each and thereby more information about the microvascular circulation of the brain lesions.

Brain↗

Differentiation between completely hyalinized uterine leiomyomas and ordinary leiomyomas: three-phase dynamic magnetic resonance imaging (MRI) vs. diffusion-weighted MRI with very small b-factors.

PURPOSE: To assess the possibility of differentiating between completely hyalinized leiomyomas and ordinary leiomyomas by using diffusion-weighted (DW) magnetic resonance imaging (MRI) (DWI) employing very small b-factors (b = 1.51 and 55.3 seconds/mm(2)) in comparison with three-phase dynamic MRI. MATERIALS AND METHODS: The subjects were 25 patients with 52 histopathologically confirmed uterine leiomyomas. All leiomyomas were divided into two histopathologic subtypes (5 completely hyalinized leiomyomas and 47 ordinary leiomyomas). For each leiomyoma, the enhancement index (EI) at three-phase dynamic MRI and apparent diffusion coefficient (ADC) were obtained and then compared. RESULTS: The EIs at second and third dynamic phases clearly differentiated the two types of leiomyomas without overlap of values. ADCs also clearly differentiated the two types of leiomyomas without overlap of values. Moreover, there were significant positive correlations between ADCs and EIs at all dynamic phases (r = 0.41-0.50, P < 0.01). CONCLUSION: Not only three-phase dynamic MRI but also DWI with very small b-factors could be useful for differentiating completely hyalinized leiomyomas from ordinary leiomyomas.

Adult↗

Dynamic MR venography: an intrinsic benefit of time-resolved MR angiography.

PURPOSE: To investigate the possibility of obtaining dynamic contrast-enhanced magnetic resonance venography (DCE-MRV) images of the lower extremities. MATERIALS AND METHODS: Peripheral contrast-enhanced magnetic resonance angiography (CE-MRA) was performed on 20 patients using a time-resolved sequence that combined undersampled projection reconstruction (PR) in-plane and Cartesian slice encoding through-plane. The contrast dynamics of distal vessels were depicted. An automated segmentation algorithm based on a contrast arrival time (CAT) threshold was used to generate contrast dynamics in the venous system. The signal difference between the vein and artery was measured to evaluate the effectiveness of this technique in isolating the venous contrast dynamics. RESULTS: The automatically generated image series depicted the contrast dynamics of both the arterial and venous systems, including asymmetric venous enhancement and background tissue enhancement. Quantitative measurement showed a mean venous/arterial signal ratio increase from 1.58 to 4.82 for the peak venous frame after arterial signal suppression. CONCLUSION: DCE-MRV is a minimally invasive technique for evaluating the venous side of the systemic vascular anatomy. Time-resolved MRA has the potential clinical benefit of enabling both arterial and venous disease to be detected in patients undergoing CE-MRA.

Contrast Media↗

Crossing the phase boundary to study protein dynamics and function: combination of amide hydrogen exchange in solution and ion fragmentation in the gas phase.

Protein dynamics are the key to understanding their behavior. The static protein structure alone in most cases is insufficient to describe the vast array of complex functions they perform in vivo. Until recently there were relatively few techniques available to investigate the dynamic nature of these proteins. Mass spectrometry has recently emerged as a powerful biophysical method, capable of providing both structural and dynamic information. By utilizing the labile nature of amide hydrogens as a marker of the backbone dynamics in solution, combined with gas-phase dissociation techniques, we now have a high-resolution tool to locate these exchanging hydrogens within the sequence of the protein and to probe the functional importance of its structural elements. In this paper we describe several applications of these methodologies to illustrate the importance of dynamics to the biological functions of proteins.

Amides↗

Dynamic stress response of the implant/cement interface: an axisymmetric analysis of a knee tibial component.

To determine the adverse effects on the implant/cement interface stresses caused by a dynamic load on the implant, an axisymmetric dynamic finite element analysis was performed for an idealized knee tibial component assuming perfect bonding at the interface. The component, consisting of a metal plate with a central stem, was subjected to a compressive load that varied with time as a terminated ramp function. At first, the reliability of the interface stress predictions was assessed by computing the effects of a number of method-related parameters, viz., the finite element mesh density, the assumed bone properties. Analysis was then performed considering the stem length, cement mantle thickness, and the type of implant metal as design variables. The analysis predicts high-frequency (600 Hz) stress oscillations of significant amplitude at those locations of the interface that are also subjected to high static stresses: near the stem-plate junction and the stem tip for normal stress, and at the stem tip for shear stress. However, the predicted stress amplitude has been found to be particularly sensitive to the assumed rise time of the input load function. With a rise time of 2.0 ms, an input condition considered to be severe enough to represent the most vigorous dynamic activity, the maximum stress augmentation, because of stress oscillations, is predicted to be less than 25%. In general, the design variables have been found to affect the static stresses much more than the dynamic ones. It has been concluded that for the cases studied, dynamic effects are relatively small and a static analysis is sufficient to characterize the interface stress condition.

Aged↗

Value of a dynamic MR scan in predicting vascular ingrowth from free vascularized scapular transplant used for treatment of avascular femoral head necrosis.

We have treated three patients with avascular osteonecrosis using vascularized scapular bone graft. To predict blood perfusion in both the diseased femoral head and the transferred bone, all the hips were followed up using dynamic magnetic resonance (MR) scans, performed 1 and 7 months after surgery. In the present cases, it was shown that conventional enhanced MR imaging sometimes depicts increased intensity in bone marrow without blood perfusion due to the leakage of gadolinium-DTPA (Gd-DTPA) from the capillaries surrounding the avascular tissue. It was found that Gd-DTPA remaining in the dead bone marrow resulted in a false-positive image. By contrast, the dynamic MR scan evaluated only those images taken before the leakage. This is one of the advantages of the dynamic study, which reflects actual blood flow in the bone. The fast rise in the time-intensity curve following bolus injection of Gd-DTPA indicates that there is fast blood perfusion in the bone. The dynamic MR scan has demonstrated that there is little blood perfusion in the diseased bone 1 month after the operation and that vascular ingrowth from the transferred bone flap proceeds gradually between 1 and 7 months after surgery. These findings indicate that the dynamic MR scan is very useful in demonstrating vascular ingrowth after surgery in avascular necrosis of the femoral head and can be a reliable monitoring technique for anastomotic patency of the vascularized bone flap.

Adolescent↗

Dynamic range compression in MRI by means of a nonlinear gradient pulse.

In current magnetic resonance imaging (MRI), valuable information must often be discarded because the NMR signal has greater dynamic range than the analog-to-digital converter (ADC) hardware. Typically, a small set of high-intensity data points near the center of the spin echo is responsible for most of the MRI data dynamic range. We predict that it is possible to reduce the dynamic range of the MRI spin echo by incorporating an identical nonlinear gradient pulse into each repetition of the imaging pulse sequence, prior to data sampling. This pulse converts the phase distribution of the subject, ordinarily a linear function of image coordinates, into a nonlinear function. A nonlinear phase distribution can have a negligible impact on image magnitude and yet a profound impact on spin-echo magnitude. Given a nonlinear phase distribution, there will no longer be a single data point at which all of the protons have an identical phase (the echo center). Instead, the protons become phase coherent on a piecemeal basis, the echo peak is smoothed out, and its maximum amplitude and dynamic range are greatly diminished. Using gradient pulses of quadratic spatial variation, we estimate that maximum echo amplitude and dynamic range can be reduced in most cases by an order of magnitude.

Analog-Digital Conversion↗