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PubMed2003

Anomalous fluctuations of active polar filaments.

Using a simple model, we study the fluctuating dynamics of inextensible, semiflexible polar filaments interacting with active and directed force generating centers such as molecular motors. Taking into account the fact that the activity occurs on time scales comparable to the filament relaxation time, we obtain some unexpected differences between both the steady-state and dynamical behaviors of active as compared to passive filaments. For the statics, the filaments have a length-scale-dependent rigidity. Dynamically, we find strongly enhanced anomalous diffusion.

Actin Cytoskeleton↗
PubMedDate not supplied

Quantification of in vivo anaerobic metabolism in the normal cat retina through intraretinal pH measurements.

We examined intraretinal [H+] in the intact retina of anesthetized cats using H+-sensitive microelectrodes to obtain spatial profiles of extracellular [H+]. One H+ is produced when an anaerobically generated ATP is utilized. We theorized that H+ production directly reflects anaerobic glucose consumption. From the choroid (pH approximately 7.40), [H+]o steadily increased to a maximum concentration in the proximal portion of the outer nuclear layer (pH approximately 7.20). The shape of the profile was always concave down, indicating that a net production of H+ occurred across the avascular outer retina. A three-layer diffusion model of the outer retina was developed and fitted to the data to quantify photoreceptor H+ extrusion into the extracellular space (Q(OR-H+)). It was determined that the outer segment (OS) layer had negligible H+ extrusion. The data were then refitted to a special three-layer model in which the OS layer Q(H+) was set equal to zero, but in which the inner segments and outer nuclear layer produced H+. The resulting Q(OR-H+) was several orders of magnitude lower than previous measurements of Q(OR-lactate), which were based on choroidal mass balances of lactate. Stoichiometrically, one H+ is produced for each lactate produced, so we concluded that Q(OR-H+) is a measure of net rather than total H+ production. Because retinal acid production is so high, the retina must contain efficient H+ clearance and/or neutralization mechanisms that prevent severe acidosis. The effect of light on retinal extracellular [H+] and Q(OR-H+) was also examined. As expected, light adaptation caused a retinal alkalinization that resulted from a 52% reduction in Q(OR-H+). This is in agreement with previous studies that have shown that both oxidative (e.g. Haugh et al., 1990) and glycolytic metabolism (Wang et al., 1997a,c) in the photoreceptor are decreased by a factor of 2 during light adaptation. Although we could not obtain absolute values for outer retinal glycolysis, changes in Q(OR-H+) appear to directly reflect changes in glycolytic metabolism.

Adaptation, Ocular↗
PubMed1997

Assessment of protein solution versus crystal structure determination using spin-diffusion-suppressed NOE and heteronuclear relaxation data.

A spin-diffusion-suppressed NOE buildup series has been measured for E. coli thioredoxin. The extensive 13C and 15N relaxation data previously reported for this protein allow for direct interpretation of dynamical contributions to the 1H-1H cross-relaxation rates for a large proportion of the NOE cross peaks. Estimates of the average accuracy for these derived NOE distances are bounded by 4% and 10%, based on a comparison to the corresponding X-ray distances. An independent fluctuation model is proposed for prediction of the dynamical corrections to 1H-1H cross-relaxation rates, based solely on experimental structural and heteronuclear relaxation data. This analysis is aided by the demonstration that heteronuclear order parameters greater than 0.6 depend only on the variance of the H-X bond orientation, independent of the motional model in either one- or two-dimensional diffusion (i.e., 1-S2 = 3/4 sin2 2 theta sigma). The combination of spin-diffusion-suppressed NOE data and analysis of dynamical corrections to 1H-1H cross-relaxation rates based on heteronuclear relaxation data has allowed for a detailed interpretation of various discrepancies between the reported solution and crystal structures.

Crystallography, X-Ray↗
PubMed2004

B factor dependence of the temporal characteristics of brain activation using dynamic apparent diffusion coefficient contrast.

Functional MRI studies to date have been generally performed using the blood oxygenation level dependent (BOLD) contrast mechanism. Recently, it has been proposed that dynamic change in the apparent diffusion coefficient (ADC), measured using intravoxel incoherent motion (IVIM) weighting, can be used as a robust functional contrast mechanism. Based on the differences in the timing characteristics compared to the BOLD activation, the ADC contrast can be selectively sensitized to upstream vascular pools (e.g., arterial networks). In this study we further investigated the timing characteristics of the functional ADC contrast using multiple degrees of IVIM weighting. It was found that the time course in the high b factor range lagged behind that of the low b factor range, indicating that the low b factor ADC contrast included contributions from the larger and faster moving arteries, and the smaller arterioles and capillaries downstream were reflected in the high b factor changes. These changes help confirm the arterial origin of the ADC contrast and offer a direction to improve the localization of activity to small vessel networks.

Brain Mapping↗
PubMed2006

Theoretical and experimental exploration of rules for combining transport parameters in laminar membranes.

Permeabilities, time lags, and mean first passage times were measured in silastic (Sil) and ethylene vinyl acetate copolymer (EVAc) membranes and in the series composites Sil/EVAc and EVAc/Sil. These measurements were used to test phenomenological rules derived previously [R. A. Siegel, J. Phys. Chem. 95, 2556 (1991)] relating the parameters of the constituent membranes to the same parameters for the membrane composites. Reasonable agreement was found between experimental results and these rules. As predicted, permeability and time lag are the same in either direction of transport through the series composite, while mean first passage time is direction dependent. In addition to the experimental results, the combination rules are rederived using the partition/diffusion model of membrane transport, and certain new theoretical connections are noted.

Biological Transport↗
PubMed1995

Studies of the bound conformations of methyl alpha-lactoside and methyl beta-allolactoside to ricin B chain using transferred NOE experiments in the laboratory and rotating frames, assisted by molecular mechanics and dynamics calculations.

The conformation in solution of methyl beta-galactopyranosyl-(1-->4)-alpha-glucopyranoside (methyl alpha-lactoside) and methyl beta-galactopyranosyl-(1-->6)-beta-glucopyranoside (methyl beta-allolactoside) has been studied through NMR spectroscopy and molecular mechanics calculations. NOE measurements both in the laboratory and rotating frames, have been interpreted in terms of an ensemble average distribution of conformers. Molecular mechanics calculations have been performed to estimate the probability distribution of conformers from the steric energy maps. The experimental results indicate that methyl alpha-lactoside spends about 90% of its time in a broad low-energy region close to the global minimum, while methyl beta-allolactoside presents much higher flexibility. The conformational changes that occur when both disaccharides are bound to the ricin B chain in aqueous solution have been studied using transferred NOE experiments at several protein/ligand ratios. The observed data indicate that the protein causes a conformational variation in the torsion angles of methyl alpha-lactoside changing towards smaller angle values (phi/psi approximately -20/-20), although the recognized conformer is still within the lowest energy region. In particular, the torsional changes separate Gal H1 from Glc H3 and Glc H6 protons, with a noticeable decrease in the intensities of the corresponding NOE cross-peaks, which were clearly observed for the free disaccharide. On the other hand, different conformations around the phi, psi, and omega glycosidic bonds of methyl beta-allolactoside are recognized by the lectin. In fact, for the methyl-beta-allolactoside-ricin-B complex, only the NOESY cross-peaks corresponding to the protons of the galactose residue are negative, as expected for a molecule in the slow motion regime. In contrast, the corresponding cross peaks for the glucose residue were about zero, as expected for a molecule whose motion is practically independent of the protein. However, for the methyl-alpha-lactoside-ricin-B complex, all the NOESY cross-peaks for both the galactose and glucose moieties were clearly negative. From the NMR experimental point of view, it is demonstrated that the comparison of longitudinal and transversal transferred NOEs allows one to clearly differentiate direct enhancements from spin diffusion effects, which are of major concern when analysing NOE spectra of macromolecules.(ABSTRACT TRUNCATED AT 250 WORDS)

Magnetic Resonance Spectroscopy↗
PubMedDate not supplied

Health services organizations computer innovation. Ready or not?

Health services organizations (HSOs) have expanded into increasingly integrated delivery systems requiring more sophisticated health information systems (HISs) to support decision making. Computer innovations are required in most HSOs to support these HISs. Health services organizations decision makers are faced with many complex decisions during the computer innovation process. One of their most important decisions is judging HSO innovation readiness. Accurate judgments about HSO innovation readiness will have a direct impact on how successful decision makers are as computer innovators.

Automation↗
PubMed1990

Quantitative relationships between single-cell and cell-population model parameters for chemosensory migration responses of alveolar macrophages to C5a.

Phenomenological parameters from a mathematical model of cell motility are used to quantitatively characterize chemosensory migration responses of rat alveolar macrophages migrating to C5a in the linear under-agarose assay, simultaneously at the levels of both single cells and cell populations. This model provides theoretical relationships between single-cell and cell-population motility parameters. Our experiments offer a critical test of these theoretical linking relationships, by comparison of results obtained at the cell population level to results obtained at the single-cell level. Random motility of a cell population is characterized by the random motility coefficient, mu (analogous to a particle diffusion coefficient), whereas single-cell random motility is described by cell speed, s, and persistence time, P (related to the period of time that a cell moves in one direction before changing direction). Population chemotaxis is quantified by the chemotactic sensitivity, chi 0, which provides a measure of the minimum attractant gradient necessary to elicit a specified chemotactic response. Single-cell chemotaxis is characterized by the chemotactic index, CI, which ranges from 0 for purely random motility to 1 for perfectly directed motility. Measurements of cell number versus migration distance were analyzed in conjunction with the phenomenological model to determine the population parameters while paths of individual cells in the same experiment were analyzed in order to determine the single-cell parameters. The parameter mu shows a biphasic dependence on C5a concentration with a maximum of 1.9 x 10(-8) cm2/sec at 10(-11) M C5a and relative minima of 0.86 x 10(-8) cm2/sec at 10(-7) M C5a and 1.1 x 10(-8) cm2/sec in the absence of Ca; s and P remain fairly constant with C5a concentration, with s ranging from 2.1 to 2.5 microns/min and P varying from 22 to 32 min. chi 0 is equal to 1.0 x 10(-6) cm/receptor for all C5a concentrations tested, corresponding to 60% correct orientation for a difference of 500 bound C5a receptors across a 20 microns cell length. The maximum CI measured was 0.2. Values for the population parameters mu and chi 0 were calculated from single-cell parameter values using the aforementioned theoretical linking relationships. The values of mu and chi 0 calculated from single-cell parameters agreed with values of mu and chi 0 determined independently from population migrations, over the full range of C5a concentrations, confirming the validity of the linking equations. Experimental confirmation of such relationships between single-cell and cell-population parameters has not previously been reported.

Animals↗
PubMed2000

Quantitative measurements of airflow inside a nuclear laboratory.

Dispersion dynamics of accidentally released radioactive aerosols or gases through laboratory workrooms are determined primarily by airflow, which impacts the level of human exposure and the response of air monitoring instrumentation. Therefore, applying conclusions derived from measurements of the fundamental aspects of airflow (velocity, direction, and turbulence) can lead to better protection of workers by suggesting appropriate locations for air monitoring and sampling. Historically, it has been very difficult to quantitatively measure these fundamental aspects of indoor airflow because of the low flow rates (often <10 cm s(-1)) and difficulties in quantitative measurement of three-dimensional airflow. Recent advances in sonic anemometry have enabled such measurements. For this study, a sonic anemometer was used that was capable of measuring airflow velocities with a sensitivity of about 0.5 cm s(-1) for each of the three-directional components. A sampling frequency of 1 Hz was selected to measure the fluctuations in the air velocity associated with turbulence and expressed in terms of "turbulence intensity." Point measurements of airflow velocities, directions, and turbulence intensities were made at 69 locations in a mechanically ventilated plutonium laboratory located at Los Alamos National Laboratory. Although the measurements were not made with workers present, all measurements were made at a height of 1.5 m, approximately the height of a worker's breathing zone (BZ). Velocities ranged from 8 cm s(-1) to 41 cm s(-1), with a median velocity of 18 cm s(-1). Percent turbulence intensities ranged from 13% to 57% with a median of 34%. The measured velocities and turbulence intensities in the laboratory showed that forced convective flows and turbulent eddy diffusion drive dispersion of released aerosols or gases. Results show that after an airborne release, mixing within the room can take minutes and may not always be complete. This is contrary to simplifying assumptions made by some risk modeling of accidentally released materials in a room. Our results also suggest that the mixing pattern would not be omnidirectional at most release locations, especially in the early stages of the release. Finally, airflow directions were upwards in breathing zones at most workstations. Because most releases in the plutonium laboratory occur at a height immediately below the BZ, the concentrated aerosol could be lifted into the BZ, followed by dispersal to the air monitor with the initiation of alarm.

Air Pollution, Radioactive↗
PubMed2000

The infection of human skin by schistosome cercariae: studies using Franz cells.

Franz cells (2-chambered, air/fluid phase static diffusion devices, previously used for the study of drugs across viable human skin) are utilized for the first time to investigate the process of infection of human skin by Schistosoma mansoni cercariae. Skin obtained from cosmetic surgery sources was used in the Franz cells to describe the temporal dynamics of the early interaction of cercariae with skin. At 38 degrees C, about 50% of cercariae applied in water to the epidermal surface of the skin were irreversibly attached within 1 min and after 5 min about 85%, were similarly irrecoverable. The technique also provides the means of following the early penetration path of cercariae by histological methods. Franz cell results on the dynamics of attachment/early penetration have been compared with those obtained using artificial skin equivalents and non-human mammalian skin models in the context of the physical and chemical differences between these systems and viable human skin. It is concluded that Franz cells provide a convenient system for directly investigating the early phases of S. mansoni cercariae interaction with human skin.

Animals↗
PubMed2000

Oxygen supply to contracting skeletal muscle at the microcirculatory level: diffusion vs. convection.

An adequate supply of oxygen is essential for the normal function of all cells. Because skeletal muscle cells have the ability to vary their oxygen demand by over an order of magnitude on going from rest to vigorous contraction, it is important that mechanisms be in place to ensure that the supply of oxygen is maintained at sufficient levels. Microcirculation plays a critical role in this process, as the terminal branches of this intricate network of blood vessels determine the distribution of perfusion, as well as the structural framework for diffusion. The oxygen supply depends on proper functioning of both the convective and diffusive components of the transport system. Convection is responsible for the long-range, rapid transport of oxygen by bulk flow of the blood and diffusion is the efficient mechanism for transport over the short distances between capillaries and muscle cells. Convective transport is dominated by the movement of red blood cells, as virtually all the oxygen at normal haematocrit is carried inside them, reversibly bound to haemoglobin. Over the years, specialized techniques, many of them video-based, have been developed for use in intravital microscopy to measure the parameters needed to quantify convection and diffusion in both capillaries and the larger microvessels, arterioles and venules. Most of our knowledge of oxygen transport in the microcirculation of muscle pertains to the resting condition, because one must be able to visualize the structures of interest, such as microvessels and muscle cells, and the large tissue movements that occur during contraction preclude measurements during that time. In resting muscle it has been found that the arterioles are the primary site of the diffusion of oxygen from the circulation, where the oxygen is utilized by nearby muscle cells or diffuses directly to nearby venules or capillaries. Diffusive interactions among neighbouring capillaries have also been observed. In contracting muscles, microvessels observed immediately following the period of stimulation exhibit enhancements of both convective (increased flow of red blood cells) and diffusive (increased perfused capillary surface area) transport. The use of computational models in the interpretation of experimental studies is leading to an increased understanding of the processes that underlie the oxygen transport system in skeletal muscle.

Animals↗
PubMed2000

Water-protein interactions in the molten-globule state of carbonic anhydrase b: an NMR spin-diffusion study.

We have used the homonuclear Overhauser effect (NOE) to characterize a model protein: carbonic anhydrase B. We have obtained NOE difference spectra for this protein, centering the on-resonance signals either at the methyl-proton or at the water-proton signals. The spin-diffusion spectra obtained as a function of protein concentration and temperature provide direct evidence of much greater protein-water interaction in the molten-globule state than in the native and denatured states. Furthermore, although the protein loses its gross tertiary structure in both the molten-globule and denatured states, it remains almost as compact in its molten-globule state as it is in the native state. The spin-diffusion spectra, obtained as a function of a variable delay time after the saturation pulse, allowed us to measure the relaxation times of several types of proton in the solution. These spectra contain enough information to distinguish between those water molecules solvating the protein and the free ones present as bulk water.

Animals↗
PubMed2005

Toward a theory of wave energy transport in large irregular structures.

An ansatz is proposed by which the energy transport behavior observed at early times in a direct numerical simulation (DNS) of a large irregular structure may be extrapolated to arbitrary times. In the slow-transport limit, this ansatz leads to a diffusion-like equation, similar to that of time-domain statistical energy analysis (SEA), but it does not require substructuring. The model is successfully used to extract diffusion parameters from simulated data of unambiguously diffusive character. The model is then successfully used to extract diffusion parameters from data obtained in a DNS of a simple undamped two-room structure of a kind typically analyzed by SEA or room acoustics.

Journal Article↗
PubMed2005

Surface-sensitive polarized Raman spectroscopy of biological tissue.

In a two-layer diffusing medium, polarized light directly backscattering off the superficial layer will partially retain its sense of polarization, whereas deeper-probing light will be increasingly depolarized by diffusion. This effect has been studied in both elastic scattering and fluorescence contexts. We apply this method to Raman scattering in two two-layer models with a highly diffusing lower layer of glucose powder and an upper layer of either clear plastic or chicken skin. We employ detection of orthogonal polarization states to generate a Raman spectrum of only the superficial layer by combining the orthogonal signals.

Animals↗
PubMed2004

The role of hydrogen bonding in the enzymatic reaction catalyzed by HIV-1 protease.

The hydrogen-bond network in various stages of the enzymatic reaction catalyzed by HIV-1 protease was studied through quantum-classical molecular dynamics simulations. The approximate valence bond method was applied to the active site atoms participating directly in the rearrangement of chemical bonds. The rest of the protein with explicit solvent was treated with a classical molecular mechanics model. Two possible mechanisms were studied, general-acid/general-base (GA/GB) with Asp 25 protonated at the inner oxygen, and a direct nucleophilic attack by Asp 25. Strong hydrogen bonds leading to spontaneous proton transfers were observed in both reaction paths. A single-well hydrogen bond was formed between the peptide nitrogen and outer oxygen of Asp 125. The proton was diffusely distributed with an average central position and transferred back and forth on a picosecond scale. In both mechanisms, this interaction helped change the peptide-bond hybridization, increased the partial charge on peptidyl carbon, and in the GA/GB mechanism, helped deprotonate the water molecule. The inner oxygens of the aspartic dyad formed a low-barrier, but asymmetric hydrogen bond; the proton was not positioned midway and made a slightly elongated covalent bond, transferring from one to the other aspartate. In the GA/GB mechanism both aspartates may help deprotonate the water molecule. We observed the breakage of the peptide bond and found that the protonation of the peptidyl amine group was essential for the peptide-bond cleavage. In studies of the direct nucleophilic mechanism, the peptide carbon of the substrate and oxygen of Asp 25 approached as close as 2.3 A.

Binding Sites↗
PubMed2002

Autocrine loops with positive feedback enable context-dependent cell signaling.

We describe a mechanism for context-dependent cell signaling mediated by autocrine loops with positive feedback. We demonstrate that the composition of the extracellular medium can critically influence the intracellular signaling dynamics induced by extracellular stimuli. Specifically, in the epidermal growth factor receptor (EGFR) system, amplitude and duration of mitogen-activated protein kinase (MAPK) activation are modulated by the positive-feedback loop formed by the EGFR, the Ras-MAPK signaling pathway, and a ligand-releasing protease. The signaling response to a transient input is short-lived when most of the released ligand is lost to the cellular microenvironment by diffusion and/or interaction with an extracellular ligand-binding component. In contrast, the response is prolonged or persistent in a cell that is efficient in recapturing the endogenous ligand. To study functional capabilities of autocrine loops, we have developed a mathematical model that accounts for ligand release, transport, binding, and intracellular signaling. We find that context-dependent signaling arises as a result of dynamic interaction between the parts of an autocrine loop. Using the model, we can directly interpret experimental observations on context-dependent responses of autocrine cells to ionizing radiation. In human carcinoma cells, MAPK signaling patterns induced by a short pulse of ionizing radiation can be transient or sustained, depending on cell type and composition of the extracellular medium. On the basis of our model, we propose that autocrine loops in this, and potentially other, growth factor and cytokine systems may serve as modules for context-dependent cell signaling.

Autocrine Communication↗
PubMed1997

Transgenic rats as models for studying the role of ornithine decarboxylase expression in permanent middle cerebral artery occlusion.

BACKGROUND AND PURPOSE: Cerebral ischemia causes activation of ornithine decarboxylase (ODC) gene and subsequent accumulation of putrescine, which might either directly or indirectly affect the outcome of cerebral infarct. We developed a transgenic rat overexpressing human ODC, which was used to explore the effect of abnormally high putrescine concentration in the brain on the infarct volume after permanent middle cerebral artery (MCA) occlusion. METHODS: The transgenic rats were produced by the pronuclear injection technique with the use of cloned human ODC gene. The right MCA was permanently occluded through craniotomy. ODC activity and polyamines were assayed in the infarcted and contralateral hemispheres. MRI was used to quantify T2 relaxation time, apparent diffusion constant (ADC), and infarct volume, which was also determined by 2,3,5-triphenyltetrazolium chloride. RESULTS: Permanent MCA occlusion resulted in extensive activation of ODC, which was approximately sevenfold greater than in syngenic animals at 20 hours after occlusion. Consequently, putrescine increased from approximately 10 and 230 pmol/mg to 160 and 410 pmol/mg in the infarcted hemisphere of syngenic and transgenic animals, respectively, but all the other polyamines were unchanged. This high putrescine in the transgenic rats did not influence infarct size evolution, as determined by MRI, T2, ADC, or the infarct volume by 2,3,5-triphenyltetrazolium chloride at 48 hours. CONCLUSIONS: Data from the ODC transgenic rat model show that the development of brain infarct after permanent MCA occlusion was not influenced by extensive levels of putrescine, indicating that this endogenous amine is not involved in maturation and spread of stroke lesion in vivo. Thus, it seems that ODC activation reflects an endogenous adaptation of neural cells to a noxious stimulus that does not directly influence lesion development.

Animals↗
PubMed2000

Sarcomeric Ca2+ gradients during activation of frog skeletal muscle fibres imaged with confocal and two-photon microscopy.

Intra-sarcomeric gradients of [Ca2+] during activation of action potential stimulated frog single fibres were investigated with the Ca2+ indicator fluo-3 and confocal and two-photon microscopy. The object of these experiments was to look for evidence of extra-junctional Ca2+ release and examine the microscopic diffusion of Ca2+ within the sarcomere. By exploiting the spatial periodicity of sarcomeres within the fibre, we could achieve a high effective line-scanning rate ( approximately 8000 lines s-1), although the laser scanning microscope was limited to < 1000 lines s-1. At this high time resolution, the time course of fluorescence changes was very different at the z- and m-lines, with a significant delay ( approximately 1 ms; 22 C) between the rise of fluorescence at the z-line and the m-line. To calculate the expected fluorescence changes, we used a multi-compartment model of Ca2+ movements in the half-sarcomere in which Ca2+ release was restricted to triadic junctions (located at z-lines). Optical blurring by the microscope was simulated to generate fluorescence signals which could be compared directly to experimental data. The model which reproduced our experimental findings most accurately included Ca2+ binding by ATP, as well as indicator binding to immobile sarcomeric proteins. After taking sarcomeric misregistration within the fibre into account, there was very good agreement between the model and experimental results. We conclude that there is no experimental evidence for Ca2+ release at locations other than at z-lines. In addition, our calculations support the conclusion that rapidly diffusing Ca2+ buffers (such as ATP) are important in shaping the Ca2+ transient and that the details of intracellular indicator binding need to be considered to explain correctly the time course of fluorescence change in the fibre.

Adenosine Triphosphate↗