Studies with Composite Membranes: III. Measurement of Water Permeability

The permeability of tritiated water (THO) across simple and layer-type composite membranes of collodion containing different amounts of polystyrenesulfonic acid has been measured and corrected for the effects of aqueous stationary layers present at the membrane-solution interfaces. It was found that the water permeabilities in the two opposite directions across the composite membranes were different, whereas they were the same across simple membranes. The theoretical permeability value for the composite membrane (formed by putting one simple membrane on top of another simple membrane of increasing charge density and gently pressing them together), calculated from the values due to simple membranes, was found to be always greater than the two measured values. It was shown that the aqueous layers trapped between membranes were not responsible for the low measured values. The factor causing this was ascribed to the mechanism which produced rectification of water flow in the composite membranes. Establishment of the THO concentration profile in the layered membranes showed that accumulation and depletion of THO in the membrane phase when the THO was flowing from the high charge density side to the low charge density side and vice versa, respectively, were responsible for the unequal flows observed across the composite membrane in the two directions.     

Alternative forms of competition and predation dramatically affect habitat selection under foraging--predation-risk trade-offs

Habitat selection under foraging—predation-risk trade-offshas been a frequent topic of interest to theoretical behavioraland evolutionary ecologists. However, most habitat selectionmodels assume that individuals compete exploitatively for resourcesand that predation is either density independent or dilutedcompletely by competitor number, despite empirical evidencethat other forms of competition and predation also occur innature. I developed an individual-based model for studyingthe effects of alternative forms of competition and predationon the process of habitat selection under foraging—predation-risktrade-offs. To make the model more relevant to natural populations,I assumed that individuals vary continuously in traits relatedto competitive ability and vulnerability to predation and allowed resources and predators to be distributed across more than twohabitats. The results of my investigation demonstrate thatthe predicted pattern of habitat selection can be affecteddramatically by the form predation is assumed to take. Whenpredation is density dependent or frequency dependent, individuals will tend to be distributed across habitats according to theirabsolute vulnerability to predation. In contrast, when predationis density dependent or vulnerability dependent, individualswill tend to segregate by competitive ability. Whether oneassumes that individuals compete for resources via exploitationor interference also influences the predicted pattern of habitat selection. In general, interference competition results in amore even distribution of competitors across habitats.     

Multilamellarity, structure and hydration of extruded POPC vesicles by SANS

The small-angle neutron scattering (SANS) data of 12 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) dispersions at low lipid concentration (1 mg per 100-mg heavy water) prepared by 5, 9 and 29 extrusions through filters of pores with 50, 100, 200 and 400 nm diameter are presented. They were analyzed within a theory that permits the determination of both structural and hydration parameters of the bilayers as well as the portions of multilamellar vesicles in dispersions with negligible long-range order between the vesicles. The scattering length density profile across the bilayers is approximated by assuming a central hydrocarbon core surrounded by a water-accessible coat. It is modeled by two different forms of functions. In the boat model, the scattering length density of the coat changes linearly from core to water, whereas in the strip model it is constant across the water-accessible coat. It was found that the boat model reflects the reality better than the strip model. The decrease of the multilamellar vesicle portions, either with increasing the number of extrusions at same filter size and with decreasing the filter size, was characterized quantitatively.     

Epithelial Fluid Transport: Protruding Macromolecules and Space Charges Can Bring about Electro-Osmotic Coupling at the Tight Junctions

The purpose of the present work is to investigate whether the idea of epithelial fluid transport based on electro-osmotic coupling at the level of the leaky tight junction (TJ) can be further supported by a plausible theoretical model. We develop a model for fluid transport across epithelial layers based on electro-osmotic coupling at leaky tight junctions (TJ) possessing protruding macromolecules and fixed electrical charges. The model embodies systems of electro-hydrodynamic equations for the intercellular pathway, namely the Brinkman and the Poisson-Boltzmann differential equations applied to the TJ. We obtain analytical solutions for a system of these two equations, and are able to derive expressions for the fluid velocity profile and the electrostatic potential. We illustrate the model by employing geometrical parameters and experimental data from the corneal endothelium, for which we have previously reported evidence for a central role for electro-osmosis in translayer fluid transport. Our results suggest that electro-osmotic coupling at the TJ can account for fluid transport by the corneal endothelium. We conclude that electro-osmotic coupling at the tight junctions could represent one of the basic mechanisms driving fluid transport across some leaky epithelia, a process that remains unexplained.     

Epithelial fluid transport: protruding macromolecules and space charges can bring about electro-osmotic coupling at the tight junctions

The purpose of the present work is to investigate whether the idea of epithelial fluid transport based on electro-osmotic coupling at the level of the leaky tight junction (TJ) can be further supported by a plausible theoretical model. We develop a model for fluid transport across epithelial layers based on electro-osmotic coupling at leaky tight junctions (TJ) possessing protruding macromolecules and fixed electrical charges. The model embodies systems of electro-hydrodynamic equations for the intercellular pathway, namely the Brinkman and the Poisson-Boltzmann differential equations applied to the TJ. We obtain analytical solutions for a system of these two equations, and are able to derive expressions for the fluid velocity profile and the electrostatic potential. We illustrate the model by employing geometrical parameters and experimental data from the corneal endothelium, for which we have previously reported evidence for a central role for electro-osmosis in translayer fluid transport. Our results suggest that electro-osmotic coupling at the TJ can account for fluid transport by the corneal endothelium. We conclude that electro-osmotic coupling at the tight junctions could represent one of the basic mechanisms driving fluid transport across some leaky epithelia, a process that remains unexplained.     

Determination of contact angle by molecular simulation using number and atomic density contours

The contact angles of Lennard-Jones fluid droplets on a structureless solid surface, simulated using Monte Carlo simulation, are calculated by fitting isochoric surfaces and making a number of assumptions about the droplet. The results show that there are significant uncertainties in the calculated contact angles due to the choice of these assumptions, such as the grid size used in tracking the isochoric density profile, the omission of isochoric data points near the surface and the function used to fit the isochoric profile. In this study, we propose a new method of calculating density contours based on atomic density instead of number density. This method results in a much smaller variation in contact angle when applying different assumptions than using number density for isochoric contours. The most consistent results, across a range of assumptions about the droplet and the contact angle, come from averaging the contact angle from several isochoric density profiles. In addition, this gives a measurement of the variation due to the choice of isochoric density.     

Theory of propagation of ordinary surface cyclotron waves

The dispersion properties of ordinary surface cyclotron waves in a semiinfinite nonuniform plasma are investigated. The waves propagate across the external magnetic field directed along the plasma surface in a metal waveguide the internal surface of which is covered with a dielectric. The problem is solved analytically in the framework of a kinetic model for plasma particles under the assumption of weak spatial dispersion. The influence of the parameters of the dielectric layer separating the plasma from the metal wall, the shape of the plasma density profile, and the value of the external magnetic field on the dispersion properties of surface cyclotron waves is studied both numerically and analytically.     

Clustering of the DNA sequences complementary to repetitive nuclear RNA of HeLa cells.

We have studied the hybridization profile of heterogeneous nuclear RNA from HeLa cells across DNA density gradients, and found that components in the high molecular weight fraction of heterogeneous nuclear RNA of HeLa cells hybridize to discrete density fractions on the light and heavy sides of the DNA. The conditions used for hybridization in this work allowed the detection of only those components in the RNA complementary to reiterated sequences in the DNA. These sequences in HnRNA are known to include double-stranded regions, which can be isolated readily. The double-stranded RNA shows a pattern of hybridization across a DNA density gradient which is similar to that of total HnRNA. It is concluded that the repeated sequences in HnRNA are complementary to clusters of repeated sequences in the DNA.     

Scaling of root length density of maize in the field profile

Root length density is an important parameter in crop growth simulation and in evaluating consequences of root pattern on crop water and nutrient uptake. In this study, a scaling model was presented for estimating the profile distribution of root length density of maize (Zea mays L.). The model inputs are root length data of a reference profile and bulk densities of soil layers, as well as root length data in the first soil layer of a field profile to be investigated. Using the root length data of 10 soil profiles investigated over 2 years, the model was examined. The results show that the proposed scaling approach is effective in estimating the root length density of each layer of soil in the field profile. The relative root mean square error (RRMSE) of the developed scaling model was 25.28%, while that of the traditional exponential model was 39.53%. The scaling approach would facilitate determination of heterogeneous distributions of root length densities in the field.     

Direct proof of a "more-than-single-layered" peptidoglycan architecture of Escherichia coli W7: a neutron small-angle scattering study

A neutron small-angle scattering study was performed to determine the thickness and the scattering density profile of isolated peptidoglycan sacculi of Escherichia coli W7 in aqueous suspension (D2O). The maximum thickness (7 +/- 0.5 nm) of the sacculus from the exponential-phase cells was large enough to suggest the existence of a more-than-single-layered architecture. The experimental density profile across the thickness of the sacculus did not allow an unambiguous differentiation between a single-layered architecture characterized by completely extended peptide side chains projecting from the sugar strands or, alternatively, a partially triple layered structure. To resolve this ambiguity, sacculi were labeled with deuterated wall peptides. Comparison of the two experimental profiles indicated that the sacculus is more than single layered across its surface, with about 75 to 80% of its surface single layered and 20 to 25% triple layered.     

Location of high-affinity metal binding sites in the profile structure of the Ca+2-ATPase in the sarcoplasmic reticulum by resonance x-ray diffraction.

Resonance x-ray diffraction measurements on the lamellar diffraction from oriented multilayers of isolated sarcoplasmic reticulum (SR) membranes containing a small concentration of lanthanide (III) ions (lanthanide/protein molar ratio approximately 4) have allowed us to calculate both the electron density profile of the SR membrane and the separate electron density profile of the resonant lanthanide atoms bound to the membrane to a relatively low spatial resolution of approximately 40 A. Analysis of the membrane electron density profile and modeling of the separate low resolution lanthanide atom profile, using step-function electron density models based on the assumption that metal binding sites in the membrane profile are discrete and localized, resulted in the identification of a minimum of three such binding sites in the membrane profile. Two of these sites are low-affinity, low-occupancy sites identified with the two phospholipid polar headgroup regions of the lipid bilayer within the membrane profile. Up to 20% of the total lanthanide (III) ions bind to these low-affinity sites. The third site has relatively high affinity for lanthanide ion binding; its Ka is roughly an order of magnitude larger than that for the lower affinity polar headgroup sites. Approximately 80% of the total lanthanide ions present in the sample are bound to this high-affinity site, which is located in the "stalk" portion of the "headpiece" within the profile structure of the Ca+2 ATPase protein, approximately 12 A outside of the phospholipid polar headgroups on the extravesicular side of the membrane profile. Based on the nature of our results and on previous reports in the literature concerning the ability of lanthanide (III) ions to function as Ca+2 analogues for the Ca+2 ATPase we suggest that we have located a high-affinity metal binding site in the membrane profile which is involved in the active transport of Ca+2 ions across the SR membrane by the Ca+2 ATPase.     

Deuterium isotope effects in the unusual addition of toluene to fumarate catalyzed by benzylsuccinate synthase

The first step in the anaerobic metabolism of toluene is a highly unusual reaction: the addition of toluene across the double bond of fumarate to produce (R)-benzylsuccinate, which is catalyzed by benzylsuccinate synthase. Benzylsuccinate synthase is a member of the glycyl radical-containing family of enzymes, and the reaction is initiated by abstraction of a hydrogen atom from the methyl group of toluene. To gain insight into the free energy profile of this reaction, we have measured the kinetic isotope effects on Vmax and Vmax/Km when deuterated toluene is the substrate. At 30 degrees C the isotope effects are 1.7 +/- 0.2 and 2.9 +/- 0.1 on Vmax and Vmax/Km, respectively; at 4 degrees C they increase slightly to 2.2 +/- 0.2 and 3.1 +/- 0.1, respectively. We compare these results with the theoretical isotope effects on Vmax and Vmax/Km that are predicted from the free energy profile for the uncatalyzed reaction, which has previously been computed using density functional theory [Himo, F. (2002) J. Phys. Chem. B 106, 7688-7692]. The comparison allows us to draw some conclusions on how the enzyme may catalyze this unusual reaction.     

Effect of ring width, cambial age, and climatic variables on the within-ring wood density profile of Norway spruce Picea abies (L.) Karst.

Studying the effects of dendrometric and climatic variables on within-ring density variations needs flexible and interpretable models. We described the within-ring density profile using a piecewise linear regression and studied its dependence on (1) dendrometric variables such as cambial age (CA) and ring width (RW), and (2) climatic variables. Based on X-ray analysis of 5,191 Norway spruce rings, a six-parameter three-segmented model was fitted on each within-ring density profile. Each model parameter was related to dendrometric and climatic variables using multiple linear regressions. Then, these models were assembled in two models relating the within-ring density profile to (1) RW and CA (model M1), and (2) climatic variables (model M2). M1 showed an R ² of 83.4 % and a residual standard error of 68.5 kg m^?3. Larger rings were associated with a decrease of latewood proportion and mean ring density. Rings with high CA were characterised by high maximum ring density. M2 showed an R ² of 60.9 % and a residual standard error of 94.9 kg m^?3. Warm summers increased the maximum ring density. Years with favourable water status decreased mean ring density. The piecewise linear models allowed the classification of within-ring density profiles in three types. Considering CA and RW led to the most explicative model since RW described many processes such as silviculture or climate. Earlywood density was impacted by water status while latewood density was conditioned by both temperatures and water status. Our approach may be used for the identification of within-ring density fluctuations or to assess the effects of silviculture or global change on the within-ring density profile.     

Mathematical modeling of oxygen transport in skeletal muscle

Inhomogeneous perfusion of capillary beds can result in large-scale diffusion of oxygen between distant portions of an organ. The conceptual model of a single capillary supplying oxygen to a surrounding concentric cylinder of tissue is not applicable to a consideration of such processes. An entirely different approach to the modeling of oxygen transport to tissue, with specific reference to the capillary beds of skeletal muscle, is presented here. This approach is intended to replace the theoretical Krogh cylinder model of capillary-tissue oxygen transport with a much more realistic model that takes into account inhomogeneities of capillary density, blood flow velocity, and oxygen concentration inherent in the micro-vasculature. The oxygen distribution in inhomogeneously perfused skeletal muscle is analyzed mathematically by defining an averaged concentration profile that neglects the fine-scale variation from capillary to capillary.     

Spatiotemporal dynamics in marginal populations

Population dynamics across a mortality gradient at an ecological margin are investigated using a novel modeling approach that allows direct comparison of stochastic spatially explicit simulation results with deterministic mean field models. The results show that demographic stochasticity has a large effect at population margins such that density profiles fall off more sharply than predicted by mean field models. Substantial spatial structure emerges at the margin, and spatial correlations (measured parallel to the margin) exhibit a sharp maximum in the tail of the density profile, indicating that spatial substructuring is greatest at an intermediate point across the ecological gradient. Such substructuring may have a substantial impact on Allee effects and evolutionary processes in marginal populations.     

Optical properties of P3HT and N2200 polymers: a performance study of an optimally tuned DFT functional

The optical properties of systems composed of the polymers PolyeraActivInk? N2200 and P3HT are experimentally and theoretically investigated using UV-Vis spectroscopy and time-dependent density functional theory calculations, respectively. From a theoretical point of view, we carried out an analysis considering several functionals and model oligomers of different sizes to mimic the polymers. As our studies were performed with and without solvents, a first important result regards the fact that, by considering solvent effects, a better agreement between theoretical and experimental results could be achieved. Our findings also show that an optimally tuned functional is better suited to describe the experimental absorption profile than a hybrid one for the flexible polymer (P3HT). For the almost rigid polymer considered here (N2200), on the other hand, hybrid functionals may perform better than tuned functionals.     

Phenotype‐dependent selection underlies patterns of sorting across habitats: the case of stream‐fishes

Spatial and temporal heterogeneity within landscapes influences the distribution and phenotypic diversity of individuals both within and across populations. Phenotype–habitat correlations arise either through phenotypes within an environment altering through the process of natural selection or plasticity, or phenotypes remaining constant but individuals altering their distribution across environments. The mechanisms of non‐random movement and phenotype‐dependent habitat choice may account for associations within highly heterogeneous systems, such as streams, where local adaptation may be negated, plasticity too costly and movement is particularly important. Despite growing attention, however, few empirical tests have yet to be conducted. Here we provide a test of phenotype‐dependent habitat choice and ask: 1) if individuals collected from a single habitat type continue to select original habitat; 2) if decisions are phenotype‐dependent and functionally related to habitat requirements; and 3) if phenotypic‐sorting continues despite increasing population density. To do so we both conducted experimental trials manipulating the density of four stream‐fish species collected from either a single riffle or pool and developed a game‐theoretical model exploring the influence of individuals’ growth rate, sampling and competitive abilities as well as interference on distribution across two habitats as a function of density. Our experimental trials show individuals selecting original versus alternative habitats differed in their morphologies, that morphologies were functionally related to habitat‐type swimming demands, and that phenotypic‐sorting remained significant (although decreased) as density increased. According to our model this only occurs when phenotypes have contrasting habitat preferences and only one phenotype disperses (i.e. selects alternatives) in response to density pressures. This supports our explanation that empirical habitat selection was due to a combination of collecting a fraction of mobile individuals with different habitat preferences and the exclusion of individuals via scramble competition at increased densities. Phenotype‐dependent habitat choice can thereby account for observed patterns of natural stream‐fish distribution.     

Architecture of bacterial lipid A in solution. A neutron small-angle scattering study

The phase structure of isolated bacterial lipid A, the lipid anchor of the lipopolysaccharides of the outer membrane of Gram-negative bacteria, has been investigated by neutron small-angle scattering. The shape of the scattering curves obtained at different H2O/2H2O ratios revealed a lamellar organisation of the lipid A at neutral pH both above and below its main phase temperature (approximately 40-45 degrees C). Analysis of the scattering curves and interpretation of the corresponding thickness distance distribution functions of the lamellar aggregates led to a model in which the lipid A molecules form a bilayer of about 5 nm in thickness. This value for the thickness of the bilayer, as well as the neutron-scattering density profile across the bilayer, can be explained by a molecular model which shows interdigitation of the fatty acid chains of the lipid A.     

Relationship between resource selection, distribution, and abundance: a test with implications to theory and conservation

Much of applied and theoretical ecology is concerned with the interactions of habitat quality, animal distribution, and population abundance. We tested a technique that uses resource selection functions (RSF) to scale animal density to the relative probability of selecting a patch of habitat. Following an accurate survey of a reference block, the habitat-based density estimator can be used to predict population abundance for other areas with no or unreliable survey data. We parameterized and tested the technique using multiple years of radiotelemetry locations and survey data collected for woodland caribou across four landscape-level survey blocks. The habitat-based density estimator performed poorly. Predictions were no better than those of a simple area estimator and in some cases deviated from the observed by a factor of 10. We developed a simulation model to investigate factors that might influence prediction success. We experimentally manipulated population density, caribou distribution, ability of animals to track carrying capacity, and precision of the estimation equation. Our simulations suggested that interactions between population density, the size of the reference block, and the pattern of distribution can lead to large discrepancies between observed and predicted population numbers. Over- or undermatching patch carrying capacity and precision of the estimator can influence predictions, but the effect is much less extreme. Although there is some empirical and theoretical evidence to support a relationship between animal abundance and resource selection, our study suggests that a number of factors can seriously confound these relationships. Habitat-based density estimators might be effective where a stable, isolated population at equilibrium is used to generate predictions for areas with similar population parameters and ecological conditions.     

Effect of experimental methodology on estimation of density at sex initiation in cyclically parthenogenetic rotifers

Sexual reproduction is density-dependent in several cyclically parthenogenetic rotifer species and induced by a chemical signal produced by the rotifers. As population density increases, the chemical accumulates in the medium until reaching a threshold that triggers sex. The density threshold for sex initiation is of ecological and evolutionary importance due to the large impact that timing of sex has on fitness in cyclical parthenogenetic rotifers. Here we study the effects of experimental methodology in combination with intrinsic features of the biological system on the estimation of the density required to produce enough of this chemical to initiate sex (i.e., density threshold). We have developed a theoretical model describing the dynamics of both population density and the concentration of the chemical signal. Model analysis showed that the time at which sex is recorded in an experiment, the initial density (i.e., experimental volume) and the population growth rate can affect the estimation of density thresholds. Results from an experiment in which density at sex initiation was tested for 29 clones of Brachionus plicatilis at two culture volumes, revealed that density threshold is negatively dependent on the experimental volume. We conclude that in order to estimate density thresholds so that they are comparable across studies, experimental methodology should be standardized.