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Biosynthetic site-specific (13) C labeling of the light-harvesting 2 protein complex: a model for solid state NMR structure determination of transmembrane proteins.

Partly biosynthetic site-directed isotopically (13)C enriched photosynthetic light-harvesting 2(LH2) complexes have been prepared from Rhodopseudomonas acidophila strain 10050 by using chemically labeled [1,2,3,4-(13)C], [1,4-(13)C] and [2,3-(13)C] succinic acid as a precursor in the growth medium. Two-dimensional proton driven spin diffusion (PDSD) solid state NMR correlation spectroscopy has been used to trace each individual (13)C isotope from the labeled succinic acid precursor to its destination into the protein and into the embedded major light-absorbing bacteriochlorophyll cofactors. For both the residues of the protein and for the cofactors distinct labeling patterns have been deduced, for protein complexes prepared from [1,4-(13)C]-succinic acid or [2,3-(13)C]-succinic labeled media. All residues, except isoleucine and leucine, have been labeled almost homogeneously by the succinic acid precursor. Carbonyl carbons in the protein backbone were labeled by [1,4-(13)C]-succinic acid, while the Calpha and Cbeta carbons of the residues were labeled by [2,3 (13)C]-succinic acid. Leucine and isoleucine residues were labeled using a uniformly labeled amino acid mixture in the medium. The pattern labeling yields an increase of the resolution and less spectral crowding. The partial labeling technique in combination with conventional solid state NMR methods at ultra high magnetic fields provides an attractive route to resolve chemical shifts for alpha-helical transmembrane protein structures.

Amino Acids↗

Diffusion-controlled reactions on spherical surfaces. Application to bacteriophage tail fiber attachment.

We have explored the kinetic implications of a model that may account for the acceleration of tail fiber (F) attachment to baseplates (B) by whiskers (W) on bacteriophage T4. The model assumes that a W-F complex is formed initially, and that the tethered fiber then undergoes rotational diffusion until a B-F encounter takes place. In the absence of whiskers, B-F complexes must form unassisted. Formation of a W-F intermediate will accelerate F attachment to B if (a) the bimolecular rate constant for W-F complex formation is larger than that for direct B-F interaction and (b) subsequent rotational diffusion of the tip of F to B is not much slower than the dissociation of W-F. Condition a was investigated by applying a recent theory of orientational effects on translational diffusion-controlled reactions. This theory suggests that substantial rate enhancement is expected if the reaction half-angle theta 0 is larger for W-F than for B-F complex formation. Condition b was investigated by calculating the mean and the variance of the time required for the diffusion of a molecule (the proximal tip of the fiber) on a spherical surface (whose radius is the distance from the tip to the whisker tethering point) into a circular sink (the baseplate site). The mean time is on the order of the inverse rotational diffusion coefficient, DR, of the fiber, but is sensitive to theta 0. Both conditions are satisfied for plausible choices of parameters. The solution to the diffusion equation we have obtained should have application to other physical situations, such as the rate of quenching of a fluorophore as it diffuses on the surface of a spherical membrane into proximity with a quencher.

Diffusion↗

Elucidating competitive adsorption mechanisms of atrazine and NOM using model compounds.

Based on the relative adsorbability of natural organic matter (NOM) fractions with different molecular weights (MWs), two model compounds, poly(styrene sulfonate) (PSS) (nominal MW=1800 Dalton) and p-dichlorobenzene (DCB), were chosen to study the competitive effect of large and small NOM molecules on atrazine adsorption by two powdered activated carbons (PACs) with different pore size distributions. Both isotherm and kinetic tests of atrazine adsorption were conducted using fresh PAC and PAC preloaded with the model compounds. The model compounds were found to affect atrazine adsorption through two different mechanisms due to their size difference: direct competition for sites by p-DCB and pore constriction/blockage by PSS-1.8k. p-DCB was found to significantly reduce atrazine adsorption capacity but to have no effect on atrazine adsorption kinetics. In contrast, the effect of PSS-1.8k on atrazine adsorption capacity was very small. Furthermore, during simultaneous adsorption, PSS-1.8k had no effect on atrazine surface diffusion. However, preloading PAC with PSS-1.8k lowered the atrazine surface diffusion coefficient, D(s), by more than three orders of magnitude; D(s) decreased with increasing solid phase PSS-1.8k concentration. The pore size distribution of the PAC was found to play an important role in competitive adsorption. A high mesopore surface area could alleviate pore blockage significantly.

Adsorption↗

The relative contribution of sewage and diffuse phosphorus sources in the River Avon catchment, southern England: implications for nutrient management.

In order to effectively manage nutrient river load reductions and target remediation strategies, it is important to determine the relative contributions of diffuse and point sources across the river catchment. This study used a geographical information system (GIS) to apply phosphorus (P) export coefficients (obtained from the literature) to 58 water quality monitoring sites across a large, urbanised, mixed land use catchment, typical of southern lowland England (the River Avon, Warwickshire, UK). These coefficients were used to estimate the annual P load at each monitoring site, and also the relative contribution of point source (from sewage treatment works (STW)) and diffuse input (from both livestock and agricultural land use). The estimated annual P loads showed very close agreement (r2=0.98) with the measured total phosphorus (TP) loads. Sites with the highest proportion of P derived from STW had the highest TP concentrations and loads, and also had greater variations between seasons, with elevated P concentrations occurring during the summer months. The GIS model was re-run to determine the effect of an 80% reduction in P output from STW serving over 10,000 people, thereby assessing the effect of implementing the European Union's Urban Waste Water Treatment Directive (UWWTD). The exported TP load was reduced by 52%, but the sites with the highest TP concentrations were still those with the highest proportion of P derived from STW. The GIS model was re-run to estimate the impact of 80% P reductions at a further 11 STW of varying sizes. This reduced the total TP load by only 29 tonnes year-1, but greatly reduced the P concentrations in many highly nutrient contaminated tributaries. The number of sites with P concentrations greater than 1 mg l-1 was cut from 15 (before UWWTD implementation) to 2. These findings suggest that after UWWTD implementation, resources should focus on introducing tertiary sewage treatment at the remaining large STW, before targeting diffuse inputs. This conclusion is also likely to apply to other lowland river catchments in southern England, most of which have similar population densities to the River Avon.

Diffusion↗

The influence of a protein on water dynamics in its vicinity investigated by molecular dynamics simulation.

A system containing the globular protein ubiquitin and 4,197 water molecules has been used for the analysis of the influence exerted by a protein on solvent dynamics in its vicinity. Using Voronoi polyhedra, the solvent has been divided into three subsets, i.e., the first and second hydration shell, and the remaining bulk, which is hardly affected by the protein. Translational motion in the first shell is retarded by a factor of 3 in comparison to bulk. Several molecules in the first shell do not reach the diffusive regime within 100 ps. Shell-averaged orientational autocorrelation functions, which are also subject to a retardation effect, cannot be modeled by a single exponential time law, but are instead well-described by a Kohlrausch-Williams-Watts (KWW) function. The underlying distribution of single-molecule rotational correlation times is both obtained directly from the simulation and derived theoretically. The temperature dependence of reorientation is characterized by a strongly varying correlation time, but a virtually temperature-independent KWW exponent. Thus, the coupling of water structure relaxation with the respective environment, which is characteristic of each solvation shell, is hardly affected by temperature. In other words, the functional form of the distributions of single-molecule rotational correlation times is not subject to a temperature effect. On average, a correlation between reorientation and lifetimes of neighborhood relations is observed.

Proteins↗

Tailor-made agarose-based reactive beads for hemoperfusion and plasma perfusion.

Composite beads of approximately 1 mm diameter, made of crosslinked agarose and containing Fuller's Earth or zirconium oxide powders, were prepared and used in extracorporeal systems for blood detoxification. The former was used for the removal of Paraquat, while the latter was used to remove inorganic phosphate from hyperphosphatemic animals with or without acute renal failure. The high surface area of the powder, combined with the low resistance to diffusion in the crosslinked agarose matrix, are highly advantageous. The crosslinking provides high mechanical strength, heat stability, prolonged shelf life, good blood flow characteristics, and prevents the release of fine particles into the blood. Crosslinked agarose beads of 1 mm diameter, containing chemically-bound heparin were also prepared, and used as a model for direct contact removal of LDL-cholesterol from the blood of familial hypercholesterolemic patients by hemoperfusion. The high capacity of these beads (over 5 mg LDL/mL beads) indicates that this clinical modality can replace the highly expensive plasmapheresis procedure presently used.

Animals↗

Noninvasive quantitation of myocardial blood flow in human subjects with oxygen-15-labeled water and positron emission tomography.

Noninvasive measurement of myocardial blood flow in absolute terms (i.e., milliliters per gram per min) has been difficult to accomplish despite the intrinsically quantitative power of positron emission tomography because of the nonphysiologic nature of tracers that have been employed conventionally as well as the limited spatial resolution of currently available instruments. It was previously demonstrated that myocardial blood flow in animals can be quantitated accurately with the diffusible tracer oxygen-15-labeled water (H2(15)O) when the arterial input function and myocardial radiotracer concentration were measured directly. To extend the approach for completely noninvasive measurement of blood flow, a parameter estimation procedure was developed whereby effects of limited tomographic spatial resolution and cardiac motion were compensated for within the operational flow model. In validation studies in 18 dogs, myocardial blood flow measured with positron emission tomography after intravenously administered H2(15)O correlated closely with flow measured with concomitantly administered radiolabeled microspheres over the range of 0.29 to 5.04 ml/g per min (r = 0.95). Although regional ischemia was clearly identifiable tomographically, absolute flow could not be determined accurately in ischemic regions in four dogs because of poor count statistics related to wall thinning. Subsequently, myocardial blood flow was measured in 11 normal human subjects. Flow was homogeneous throughout the myocardium, averaged 0.90 +/- 0.22 ml/g per min at rest and increased to 3.55 +/- 1.15 ml/g per min after intravenous administration of dipyridamole. Therefore, positron emission tomography with H2 15O and the approach developed permits noninvasive measurement of myocardial blood flow in absolute terms in humans and should facilitate objective assessment of interventions designed to enhance nutritive perfusion.

Adult↗

Making waves: pattern formation by a cell-surface-associated signal.

Starving Myxococcus xanthus cells organize into two strikingly different spatio-temporal patterns, either rippling or aggregation of cells into fruiting bodies. Formation of both patterns depends on a cell-surface-associated, non-diffusible signal, the C-signal. A key motility parameter modulated by the C-signal during pattern formation is the frequency at which cells reverse their gliding direction, with low and high levels of C-signalling causing an increase and a decrease in the reversal frequency, respectively. Recently, a simple yet elegant mathematical model was proposed to explain the mechanism underlying the non-linear dependence of the reversal frequency on C-signalling levels. The mathematical solution hinges on the introduction of a negative feedback loop into the biochemical circuit that regulates the reversal frequency. This system displays an oscillatory behaviour in which the oscillation frequency depends in a non-monotonic manner on the level of C-signalling. Thus, the biochemical oscillator recapitulates the effect of the C-signal on the reversal frequency. The challenge for biologists now is to test the mathematical model experimentally.

Bacterial Proteins↗

Three-component competitive adsorption model for flow-through PAC systems. 2. Model application to a PAC/membrane system.

A three-component competitive adsorption kinetic model, developed and validated in part 1 of this study, was applied to a continuous-flow PAC/membrane system to study the effects of various system and operating parameters on organic removal. The model quantitatively describes the two competitive adsorption mechanisms that occur during adsorption of trace organic compounds by powdered activated carbon (PAC) in flow-through systems where the PAC is retained in the system: pore blockage and direct competition for adsorption sites. Model simulations were conducted to investigate the effects of influent water composition, membrane cleaning water quality, PAC pore size distribution, and system operation conditions such as hydraulic retention time, membrane cleaning interval, and PAC dosing method on treatment efficiency. Effects of these factors on adsorption capacity as well as surface diffusion rate and consequent removal of the trace organic compound were discussed. It was found that optimal operating conditions for maximum trace organic compound removal must be determined on the basis of the adsorption properties and concentrations of the competing compounds in the influent. For the conditions investigated in this study, the small strongly competing compound, p-DCB, had greater impact on atrazine removal than the large pore-blocking compound, PSS-1.8k. Various process design and operating parameters had complex and interrelated effects on the impact of competitive adsorption and corresponding trace contaminant removal efficiency in hybrid PAC/membrane systems.

Adsorption↗

Inactivation of the alamethicin-induced conductance caused by quaternary ammonium ions and local anesthetics.

Long alkyl chain quaternary ammonium ions (QA), the local anesthetics (LA) tetracaine and lidocaine, imipramine, and pancuronium cause inactivation of the alamethicin-induced conductance in lipid bilayer membranes. The alamethicin-induced conductance undergoes inactivation only when these amphipathic compounds are added to the side containing alamethicin. The concentration of QA required to cause a given amount of inactivation depends on the length of the hydrocarbon chain and follows the sequence C9 greater than C10 greater than C12 greater than C16. LA and imipramine, in contrast to QA or pancuronium, are able to promote appreciable inactivation only if the pH of the alamethicin-free side is equal to or lower than the pK of these compounds. The membrane permeability to QA, LA, or imipramine is directly proportional to the alamethicin-induced conductance and is larger than the one for potassium. The observed steady state and time-course of the inactivation are well described by a model similar to that proposed by Heyer et al. (1976. J. Gen. Physiol. 67:703--729) and extended for any value of the diffuse double layer potential and for LA and imipramine. In this model QA, LA, or imipramine are able to permeate through the membrane only when the alamethicin-induced conductance is turned on. The amphipathic compounds then bind to the other membrane surface, changing the transmembrane potential and turning the conductance off. For a given concentration of QA, LA, or imipramine the extent of inactivation depends on two factors: first, the binding characteristics of these compounds to the membrane surface and second, their ability to permeate through the membrane when the alamethicin-induced conductance is turned on. The several possible mechanisms of permeation of the amphipathic molecules tested are discussed.

Alamethicin↗

Anisotropic domain growth of the axial next-nearest-neighbor Ising model at low temperatures.

We investigate the ordering kinetics for the axial next-nearest-neighbor Ising (ANNNI) model in one and two dimensions by the multispin heat bath dynamical simulation. This dynamics enables us to overcome the pinning effect and to observe the dynamical scaling law for domain growth in the ANNNI model at zero temperature. The domain growth exponent is 1/2 isotropically both in the ferromagnetic and the dry (commensurate) antiphase. In the wet (commensurate) antiphase, however, it is approximately 1/3 in the modulated direction, whereas it remains 1/2 in the nonmodulated direction. We suggest that these exponent values are dictated by 3- and 4-body diffusion-reaction processes of domain walls.

Journal Article↗

Virtual reality neurosurgery: a simulator blueprint.

OBJECTIVE: This article details preliminary studies undertaken to integrate the most relevant advancements across multiple disciplines in an effort to construct a highly realistic neurosurgical simulator based on a distributed computer architecture. Techniques based on modified computational modeling paradigms incorporating finite element analysis are presented, as are current and projected efforts directed toward the implementation of a novel bidirectional haptic device. METHODS: Patient-specific data derived from noninvasive magnetic resonance imaging sequences are used to construct a computational model of the surgical region of interest. Magnetic resonance images of the brain may be coregistered with those obtained from magnetic resonance angiography, magnetic resonance venography, and diffusion tensor imaging to formulate models of varying anatomic complexity. RESULTS: The majority of the computational burden is encountered in the presimulation reduction of the computational model and allows realization of the required threshold rates for the accurate and realistic representation of real-time visual animations. CONCLUSION: Intracranial neurosurgical procedures offer an ideal testing site for the development of a totally immersive virtual reality surgical simulator when compared with the simulations required in other surgical subspecialties. The material properties of the brain as well as the typically small volumes of tissue exposed in the surgical field, coupled with techniques and strategies to minimize computational demands, provide unique opportunities for the development of such a simulator. Incorporation of real-time haptic and visual feedback is approached here and likely will be accomplished soon.

Computer Simulation↗

Light transport in chiral and magnetochiral random media.

We present a microscopic approach to study electromagnetic wave propagation in media with broken mirror symmetry. We introduce and calculate the transport mean free path l*C associated with the residual polarization of diffuse light in chiral systems. In chiral media subject to an external magnetic field B, all symmetry requirements exist to create a macroscopic "super" light current in the direction of B that persists even in the absence of a spatial photon density gradient. However, we show that such a current is identically zero in our model. We finally show the existence of a linear magnetotransmission in magnetochiral media.

Journal Article↗

Evaluation of the performance of controlled release dosage forms of ticlopidine using in vitro intestinal permeability and computer simulations.

Prototype controlled release formulations of ticlopidine hydrochloride were developed, but when administered to humans, these formulations significantly reduced the bioavailability of intact drug in plasma. In order to examine the intestinal permeability characteristics and gastrointestinal metabolism of 14C-ticlopidine, we employed an in vitro diffusion cell system to directly measure the permeation of ticlopidine across various segments of monkey and rabbit intestine. High pressure liquid chromatography was used to determine the amount of intact ticlopidine on both the mucosal and serosal sides of the intestinal tissue. Simulations based upon the known pharmacokinetics of ticlopidine were conducted using STELLA, a modeling program, to provide insight as to the nature of the decreased bioavailability of these ticlopidine CR dosage forms. These simulations indicate that the absorption of intact ticlopidine is a non-linear phenomena, with inordinately large increases in absorbed intact drug with increases in dose. Conversely, decreases in drug available for immediate absorption, as with the controlled release dosage forms, lead to non-linear decreases in bioavailability. Such a finding is very consistent with the extensive first-pass metabolism suggested from the tissue permeability studies.

Animals↗

Cell death in age-related macular degeneration.

The cellular and molecular mechanisms underlying the death of photoreceptors and other retinal cells in age-related macular degeneration (AMD) remain poorly understood. Some of the questions for which answers need to be sought, and which are explicitly or implicitly addressed in this article include: (1) how do patterns of cell death in AMD compare, qualitatively and quantitatively, with "normal" cell death in aging retinas, and with cell death in retinitis pigmentosa (RP) and its animal models; (2) is apoptosis involved in AMD; (3) is there any evidence that rods are necessary for cone survival; (4) if the answer is yes, is there evidence that rods produce one or more survival-promoting factor(s) that act directly on cones; (5) are the effects of rods upon cones exclusively mediated by diffusible factors, or do they also involve contact-mediated interactions; (6) is there any evidence that photoreceptors regulate the survival and/or function of RPE and Müller cells, as well as the interactions between these cells and cones; (7) are trophic factors and their receptors in the macula different from those in other parts of the retina; and (8) are toxic mechanisms involved in the onset and progression of cell death in AMD? Clear cut answers to most of these (and related) questions about cell death in AMD are not yet available. The goal of this article is to summarize discussion that should help in the formulation of suitable hypotheses, amenable to experimental analysis. To provide a platform for such discussion, we present an overview of progress made in recent years in the analysis of other retinal degenerations and of neuronal degenerations in other regions of the CNS. We conclude with an overview of concepts and speculation derived from our current research.

Aging↗

[The study on three-dimensional laser scanning of dental model and computer aided set-up].

A new laser scanning and measurement method was introduced for dental model three-dimensional form. A laser diode was used as scanning light source, two CCDs (they were fixed specially) received the diffused light reflected from the dental model. The dental model rotating-moved back and forth, and horizontal moved from one side to another along horizontal axis simultaneously. Whole dental model can be scanned in 3 minutes, general precision was up to 0.03 mm. The computer can display distinctly three-dimensional images of dental model in different directions and give three-dimensional coordinate data, distance, angle, and remove teeth and make set-up after scanning. With advantages of high precision, fast speed and excellent object, the new method can be of an important applied value in orthodontic clinic.

Computer Simulation↗

Histogenesis of symmetrical 1,2-dimethylhydrazine-induced neoplasms of the colon in the mouse.

CF-1 female adult mice were given weekly sc injections of 20 mg symmetrical 1,2-dimethylhydrazine (DMH)-2HCl/kg body weight and killed at various intervals after commencement of the injection. [3H]thymidine (TdR) was given before the animals were killed. The histogenesis of colon neoplasms was investigated by means of autoradiographs prepared from sections of Epon-embedded descending colon, which were stained with periodic acid-Schiff reaction and iron hematoxylin. By 9 weeks after initiation of DMH treatment, the distal 5 cm of the colon became enlarged, the mucosa thickened, and the crypts were elongated and hyperplastic. In the hyperplastic crypts, the number of proliferating cells increased, but the distribution of these cells followed a previously discussed slow cut-off model of Cairnie et al. as for the normal crypts. Differentiation and transformation of epithelial cells occurred, but somewhat aberrantly. Hyperplasia of the crypts occurred diffusely, but neoplastic lesions that began to appear by 9 weeks after the intiial treatment were isolated. An isolated crypt from which a neoplasm developed was first repopulated by what appeared to be altered, undifferentiated "stem" cells. These cells did not differentiate, continued to divide, and eventually upon migration accumulated in the upper part of the crypts, where an earliest identifiable neoplastic lesion was observed. Once such a lesion was formed, it expanded in various directions, depending on the local environments, and formed a polypoid or discoid lesion. The biologic behavior of the neoplasm seemed to be determined by the downward progression of its leading edge. When it penetrated the muscularis mucosae, the neoplasm became highly invasive. In the murine model, the invasive adenocarcinomas were observed by 26 weeks after commencement of DMH treatment.

Adenocarcinoma↗

Mechanistic aspects of iontophoresis in human epidermal membrane.

A large number of factors are involved in the movement of ions and molecules across human epidermal membrane (HEM) under the influence of an electric field. These factors and their interplay need to be understood if our knowledge of iontophoretic transport of drugs across HEM is to reach a point where physical models and strategies may be employed for useful quantitative predictions. In a typical in vitro experiment, the fully hydrated HEM is positioned between aqueous compartments of a two-chamber diffusion cell. When a low electric field is applied across the HEM under these conditions, the transport enhancement of ions in the pre-existing pores of the stratum corneum is the result of, (a) the direct interaction of the electric field with the charge of the ion in question, and (b) convective solvent flow (electroosmosis); in the case where the permeant is non-ionic under these circumstances, transport enhancement is by convective solvent flow only. At moderate-to-high voltage iontophoresis (> or = around 1.0 V applied across a single HEM), in addition to the direct field effect and convective solvent flow in the pre-existing pores, there can generally be a significant (e.g. 10- to 100-fold enhancement) contribution to transport enhancement arising from new pore induction (electroporation). Much of the recent work in our laboratory has been devoted to defining and quantifying HEM electroporation, and an especially difficult aspect has been that of dealing with the large HEM membrane-to-membrane variabilities with regard to, (a) the extent of new pore induction, and (b) the characteristics of the newly induced pores. Recently we discovered that the extent of relevant (i.e. permeant accessible) pore induction may be correlated to the change in HEM electrical conductance (and quantifiable) if an appropriate matching background electrolyte can be selected having ion sizes comparable to that of the permeant. For example, employing tetraethylammonium (TEA) pivalate (PIV) for which the ion sizes are approximately 3.5 A, but not KCl (ion sizes approximately 1.9 A), as the background electrolyte for TEA (as the permeant) gave very good results; in this example, the sizable contribution of pore induction to iontophoresis was quantitatively factored out from the total iontophoretic enhancement. Experiments with a large number of HEM samples gave good agreement with the Nernst-Planck (N-P) predictions of the direct field effect when TEA-PIV was used as the background electrolyte for TEA transport, but large variations (up to 300%) between N-P predictions and experimental results were observed with KCl as the background electrolyte. Another area of recent effort has been HEM pore size determinations, both at low voltages (i.e. for pre-existing pores) and at voltages where the newly induced pores dominate HEM permeability. The sizes of pre-existing pores of HEM have been determined with the hindered diffusion theory (using experimental fluxes of several probe permeants of different known molecular sizes) to be generally in the range, 10-20 A, by a number of investigators in our laboratory for a large number HEM samples. Deducing pore sizes of electric field induced pores under steady electroporation conditions has been a more challenging task. We succeeded recently in developing a novel method for 'passively' determining pore sizes (i.e. by passive diffusion with hindered diffusion theory) under steady electroporation conditions: by using low frequency (12.5 Hz) a.c. at 2-5 V. We have been able to sustain electroporation at a nearly constant state of electroporation long enough to carry out a set of 'passive' diffusion experiments with relatively good precision to obtain the sizes of the newly induced pores. Studies to date have revealed that the sizes of pores induced with 2-5 V are of the same order of magnitude as those of the pre-existing pores (i.e. 10-20 A). Finally, another research question of interest has been that of pore charge

Biological Transport↗