Analysis of the source of heterogeneity in the osmotic response of plant membrane vesicles

Plasma membrane vesicles have been widely employed to understand the biophysics of water movements, especially when active aquaporins are present. In general, water permeability coefficients in these preparations outcome from the analysis of the osmotic response of the vesicles by means of light scattering. As from now, this is possible by following a theoretical approach that assumes that scattered light follows a single exponential function and that this behavior is the consequence of vesicle volume changes due to an osmotic challenge. However, some experimental data do not necessarily fit to single exponentials but to double ones. It is argued that the observed double exponential behavior has two possible causes: different vesicle population in terms of permeability or in terms of size distribution. As classical models cannot identify this source of heterogeneity, a mathematical modeling approach was developed based on phenomenological equations of water transport. In the three comparative models presented here, it was assumed that water moves according to an osmotic mechanism across the vesicles, and there is no solute movement across them. Interestingly, when tested in a well described plasma membrane vesicle preparation, the application of these models indicates that the source of heterogeneity in the osmotic response is vesicles having different permeability, clearly discarding the variable size effect. In conclusion, the mathematical approach presented here allows to identify the source of heterogeneity; this information being of particular interest, especially when studying gating mechanisms triggered in water channel activity.     

Topological analysis of the major protein in isolated intact rat liver gap junctions and gap junction-derived single membrane structures

The topological organization of the major rat liver gap junction protein has been examined in intact gap junctions and gap junction-derived single membrane structures. Two methods, low pH and urea at alkaline pH, were used to "transform" or "split" double membrane gap junctions into single membrane structures. Low pH treatment "transforms" rat liver gap junctions into small single membrane vesicles which have an altered sodium dodecyl sulfate-polyacrylamide gel electrophoresis profile after digestion with L-1-to-sylamido-2-phenylethylchloromethyl ketone-trypsin. Alkaline pH treatment in the presence of 8 M urea can split isolated rat liver gap junctions into single membrane sheets which have no detectable structural alteration or altered sodium dodecyl sulfate-polyacrylamide gel electrophoresis profile after proteolytic digestion, suggesting that these single membrane sheets may be useful for topological studies of the gap junction protein. Proteolytic digestion studies have been used to localize the carboxyl terminus of the molecule on the cytoplasmic surface of the intact gap junction. However, the amino terminus does not appear to be accessible to proteases or to interaction with an antibody that is specific for the amino-terminal region of the molecule in intact or split gap junctions. Binding of antibodies, that block junctional channel conductance, can be eliminated by proteolytic digestion of intact gap junctions, suggesting that all antigenic sites for these antibodies are located on the cytoplasmic surface of the intact gap junction. In addition, calmodulin gel overlays indicate that at least two calmodulin binding sites exist on the cytoplasmic surface of the junctional protein. The information generated from these studies has been used to develop a low resolution two-dimensional model for the organization of the major rat liver gap junctional protein in the junctional membrane.     

How do species interactions affect species distribution models?

One of the most promising recent advances in biogeography has been the increased interest and understanding of species distribution models – estimates of the probability that a species is present given environmental data. Unfortunately, such analyses ignore many aspects of ecology, and so are difficult to interpret. In particular, we know that species interactions have a profound influence on distributions, but it is not usually possible to incorporate this knowledge into species distribution models. What is needed is a rigorous understanding of how unmeasured biotic interactions affect the inferences generated by species distribution models. To fill this gap, we develop a general mathematical approach that uses probability theory to determine how unmeasured biotic interactions affect inferences from species distribution models. Using this approach, we reanalyze one of the most important classes of mechanistic models of competition: models of consumer resource dynamics. We determine how measurements of one aspect of the environment – a single environmental variable – can be used to estimate the probability that an environment is suitable with species distribution models. We show that species distribution models, which ignore numerous facets of consumer resource dynamics such as the presence of a competitor or the dynamics of depletable resources, can furnish useful predictions for the probability that an environment is suitable in some circumstances. These results provide a rigorous link between complex mechanistic models of species interactions and species distribution models. In so doing they demonstrate that unmeasured biotic interactions can have strong and counterintuitive consequences on species distribution models.     

A Lagrange-based generalised formulation for the equations of motion of simple walking models

Simple 2D models of walking often approximate the human body to multi-link dynamic systems, where body segments are represented by rigid links connected by frictionless hinge joints. Performing forward dynamics on the equations of motion (EOM) of these systems can be used to simulate their movement. However, deriving these equations can be time consuming. Using Lagrangian mechanics, a generalised formulation for the EOM of n-link open-loop chains is derived. This can be used for single support walking models. This has an advantage over Newton–Euler mechanics in that it is independent of coordinate system and prior knowledge of the ground reaction force (GRF) is not required. Alternative strategies, such as optimisation algorithms, can be used to estimate joint activation and simulate motion. The application of Lagrange multipliers, to enforce motion constraints, is used to adapt this general formulation for application to closed-loop chains. This can be used for double support walking models. Finally, inverse dynamics are used to calculate the GRF for these general n-link chains. The necessary constraint forces to maintain a closed-loop chain, calculated from the Lagrange multipliers, are one solution to the indeterminate problem of GRF distribution in double support models. An example of this method’s application is given, whereby an optimiser estimates the joint moments by tracking kinematic data.     

The gap junction-like form of a vacuolar proton channel component appears not to be an artifact of isolation: An immunocytochemical localization study

Gap junctional structures containing a 16-kDa intrinsic membrane protein have been isolated from the hepatopancreas of the crustacean Nephrops norvegicus. These structures are double membranes 14-15 nm thick and composed of hexagonal arrays of particles which have a central pore that is penetrated by a cationic negative stain. Membrane preparations have also been isolated from the hepatopancreas and these contain similar gap junctional regions of uniform width. Affinity purified antibodies to the 16-kDa protein bind principally to these gap junctional regions. Antiserum raised against the isolated gap junctional structures binds strongly to the lateral surfaces of the columnar epithelial cells and in particular to gap junction-like regions.     

The correction factors for sucrose gap measurements and their practical applications.

The distribution of extracellular and intracellular potential in the sucrose gap apparatus, previously established for a single fiber using the cable equations for a core conductor model (Jirounek and Straub, Biophys. J., 11:1, 1971), is obtained for a multifiber preparation. The exact equation is derived relating the true membrane potential change to the measured potential differences across the sucrose gap, the junction potentials between sucrose and physiological solution, the membrane potential in the sucrose region, and the electrical parameters of the preparation in each region of the sucrose gap. The extracellular potential distribution has been measured using a modified sucrose gap apparatus for the frog sciatic nerve and the rabbit vagus nerve. The results indicate a hyperpolarization of the preparations in the sucrose region, of 60--75 mV. The hyperpolarization is independent of the presence of junction potentials. The calculation of the correction terms in the equation relating the actual to the measured potential change is illustrated for the case of complete depolarization by KC1 on one side of the sucrose gap. The correction terms in the equation are given for various experimental conditions, and a number of nomographic charts are presented, by means of which the correction factors can be rapidly evaluated.     

Electrical characteristics of frog atrial trabeculae in the double sucrose gap.

The electrical behavior of small single frog atrial trabeculae in the double sucrose gap has been investigated. The currents injected during voltage clamp experiments did not behave as predicted from the assumption of spatial uniformity of the voltage across a Hodgkin-Huxley membrane. Much of the difference is due to the geometrical complexities of this tissue. Nonetheless, two transient inward currents have been identified, the faster of which is blocked by tetrodotoxin (TTX). The magnitude of the slower transient varies markedly between preparations but always increases in a given preparation with increase of external calcium. The fast transient current traces, at small to intermediate depolarizations, are often marred by the presence of notches and secondary peaks due most probably to the loss of space clamp conditions. In many preparations these could be removed by reducing the current magnitude through application of a partially-blocking dose of TTX. Conversely, in the preparations whose fast transient was fully blocked by TTX, notches and secondary peaks in the slow transient could by induced through increasing calcium concentration and thereby the slow current magnitude. Previously used techniques for the measurement of the reversal potential of the fast inward transient have been shown to be invalid. In so far as they can be measured, the reversal potentials of the fast and slow inward transient are in the same neighborhood, i.e. around 120 mV from rest. The true values may be quite a bit apart. The total charge flow in the capacitive transient was measured for different sized nodes and preparations. From these data and estimates of plasma membrane area per unit trabecular volume, specific membrane capacitances of around 3 muF/cm2 were calculated for small bundles. The apparent ion current densities on this basis are approximately 1/10 of those measured in axons. The capacitive current occurring in small bundles decayed as the sum of at least three exponential functions of time. On the basis of these data and the anomalously large stable node widths, we suggest a coaxial core model of the preparation with the inner elements in series with an additional large extracellular resistance.     

Physiologically structured models – from versatile technique to ecological theory

A ubiquitous feature of natural communities is the variation in size that can be observed between organisms, a variation that to a substantial degree is intraspecific. Size variation within species by necessity implies that ecological interactions vary both in intensity and type over the life cycle of an individual. Physiologically structured population models (PSPMs) constitute a modelling approach especially designed to analyse these size‐dependent interactions as they explicitly link individual level processes such as consumption and growth to population dynamics. We discuss two cases where PSPMs have been used to analyse the dynamics of size‐structured populations. In the first case, a model of a size‐structured consumer population feeding on a non‐structured prey was successful in predicting both qualitative (mechanisms) and quantitative (individual growth, survival, cycle amplitude) aspects of the population dynamics of a planktivorous fish population. We conclude that single generation cycles as a result of intercohort competition is a general outcome of size‐structured consumer–resource interactions. In the second case, involving both cohort competition and cannibalism, we show that PSPMs may predict double asymptotic growth trajectories with individuals ending up as giants. These growth trajectories, which have also been observed in field data, could not be predicted from individual level information, but are emergent properties of the population feedback on individual processes. In contrast to the size‐structured consumer–resource model, the dynamics in this case cannot be reduced to simpler lumped stage‐based models, but can only be analysed within the domain of PSPMs. Parameter values used in PSPMs adhere to the individual level and are derived independently from the system at focus, whereas model predictions involve both population level processes and individual level processes under conditions of population feedback. This leads to an increased ability to test model predictions but also to a larger set of variables that is predicted at both the individual and population level. The results turn out to be relatively robust to specific model assumptions and thus render a higher degree of generality than purely individual‐based models. At the same time, PSPMs offer a much higher degree of realism, precision and testing ability than lumped stage‐based or non‐structured models. The results of our analyses so far suggest that also in more complex species configurations only a limited set of mechanisms determines the dynamics of PSPMs. We therefore conclude that there is a high potential for developing an individual‐based, size‐dependent community theory using PSPMs.     

Lumped and population stochastic models of skeletal muscle: Implications and predictions

Lumped models of skeletal muscle have been assumed a) in the design of experiments and the interpretation of experimental findings, b) in theoretical studies. In this paper, a population model that takes into account the differing properties and separate (independent) activation of motor units is presented as the most appropriate for muscle. A realistic (for muscle) transformation, populationlumped model, resulting in the lumping of motor unit neural signals or system responses, is proposed. On this basis, the possibility of modelling muscle as a single system is examined; and the consequences of treating muscle as a lumped system, in experiments or theoretical studies, are discussed. Also, the advantages of lumping, in models of muscle, are reviewed. Predictions of a computer population model, together with actual recordings from a hand muscle, are used to confirm the results of the analysis.     

Stochastic effects in intercellular calcium spiking in hepatocytes

We carry out a Monte Carlo simulation of stochastic effects for two models of intercellular calcium wave propagation in rat hepatocytes. Both models involve gap junction diffusion by a second messenger. We find that, in general, the stochastic effects improve agreement with experiment, for a reasonable choice of model parameters. Both stochastic models exhibit baseline fluctuations and variations in the peak heights of Ca(2+). In addition, we find for one model that there is a distribution of latency times, rather than a single latency time, with a distribution width which is comparable to the experimental observation of spike widths. We also find for the other model with low gap junction diffusion that it is possible for cell multiplets to oscillate independently initially, but to subsequently become synchronized.     

On the generality of habitat distribution models: a case study of capercaillie in three Swiss regions

Predictive habitat distribution models are normally assumed to sacrifice generality for precision and reality. Nevertheless, such models are often applied to predict the distribution of a species outside the area for which the model has been calibrated.
We investigated how the geographic extent of the data used for calibration influenced the performance of habitat distribution models applied on independent data. We took a multi-scale logistic regression approach by varying the grain size to develop six habitat models for capercaillie Tetrao urogallus in Switzerland: three regional models, for the northern Pre-Alps, eastern Central Alps and Jura mountains, respectively, and three pooled models, each using data from two of the three regions. The six models were validated with data from the region(s) not used for model building. We used Cohen's Kappa and the area under the receiver operating characteristics curve as accuracy measures. The regional models performed well in the region where they had been calibrated, but poorly to moderately well in the other regions. The pooled models classified almost as well in their calibration regions as the corresponding regional models, but generally better when validated on data from the independent region. Hence, models built with data from single regions provide less certain predictions of species' distributions in other regions. We recommend building more general models using data pooled from several regions, when the aim is to predict species' distributions in independent regions.     

Aggregation error in nonlinear ecological models

Conditions are presented for accurately representing the dynamics of several components of a nonlinear ecological system by a single state variable. For mass-balance ecosystem models, only two conditions exist that permit such aggregation without introducing error into the model. Under the first condition, components can be lumped if their environmental losses (e.g. respiration or migration) are characterized by identical linear functions. Under the second condition, the components must maintain constant proportionality throughout their transient behavior. If these conditions are violated, it is not possible to aggregate without error. However, it is shown that aggregation error can still be minimized. The theorems developed here extend related results derived for the general theory of systems and have the advantage of generality, being applicable to nonlinear models of considerable complexity.     

Computational characterization of double reduction in autotetraploid natural populations

Population genetic theory has been well developed for diploid species, but its extension to study genetic diversity, variation and evolution in autopolyploids, a class of polyploids derived from the genome doubling of a single ancestral species, requires the incorporation of multisomic inheritance. Double reduction, which is characteristic of autopolyploidy, has long been believed to shape the evolutionary consequence of organisms in changing environments. Here, we develop a computational model for testing and estimating double reduction and its genomic distribution in autotetraploids. The model is implemented with the expectation–maximization (EM) algorithm to dissect unobservable allelic recombinations among multiple chromosomes, enabling the simultaneous estimation of allele frequencies and double reduction in natural populations. The framework fills an important gap in the population genetic theory of autopolyploids.     

Selection for the α-Thalassemia Genes

Extremely high incidences of single and double deletions of α-globin genes are known among Asian populations. To study possible mechanisms for the maintenance of such deletions, mathematical analyses have been conducted. It has been shown that a stable polymorphism can be achieved easily through heterozygote advantage using deterministic models. The results strongly suggest that high incidences of single and double deletion of α-globin genes among Asian populations are maintained by some type of heterozygote advantage.     

Generation of neutralizing activity against human immunodeficiency virus type 1 in serum by antibody gene transfer

Although several human immunodeficiency virus (HIV) vaccine approaches have elicited meaningful antigen-specific T-cell responses in animal models, no single vaccine candidate has engendered antibodies that broadly neutralize primary isolates of HIV type 1 (HIV-1). Thus, there remains a significant gap in the design of HIV vaccines. To address this issue, we exploited the existence of rare human monoclonal antibodies that have been isolated from HIV-infected individuals. Such antibodies neutralize a wide array of HIV-1 field isolates and have been shown to be effective in vivo. However, practical considerations preclude the use of antibody preparations as a prophylactic passive immunization strategy in large populations. Our concept calls for an antibody gene of choice to be transferred to muscle where the antibody molecule is synthesized and distributed to the circulatory system. In these experiments, we used a recombinant adeno-associated virus (rAAV) vector to deliver the gene for the human antibody IgG1b12 to mouse muscle. Significant levels of HIV-neutralizing activity were found in the sera of mice for over 6 months after a single intramuscular administration of the rAAV vector. This approach allows for predetermination of antibody affinity and specificity prior to "immunization" and avoids the need for an active humoral immune response against the HIV envelope protein.     

THE PERMEABILITY OF ISOLATED AND IN SITU MOUSE HEPATIC GAP JUNCTIONS STUDIED WITH ENZYMATIC TRACERS

We have studied the effects of phospholipase C from Clostridium welchii on gap junctions in the intact mouse liver and in a junction-rich fraction prepared from mouse liver. Treatment of the isolated junctions results in the disappearance of both the 20 A gap and of the polygonal lattice visible with lanthanum. The junctions are morphologically unaltered, however, when whole livers are perfused with phospholipase via the portal vein. These results suggest that extracellular phospholipase cannot diffuse into the junctional area, but that the enzyme may affect structures within the gap from its cytoplasmic surfaces which become exposed in the isolated preparations. Horseradish peroxidase, which has physical dimensions similar to those of Clostridium phospholipase is also denied access to the 20 A gap in whole liver, while peroxidase reaction product can be seen in the gap in isolated preparations. Beef liver catalase, however, a tracer molecule much larger than peroxidase, cannot penetrate even in isolated fractions. If the cytoplasmic approaches to the gap junction used by peroxidase and phospholipase are available in vivo, and have not been created during the process of mechanical isolation, they may play a role in cell-to-cell passage of molecules larger than ions.     

The electrophysiology of gap junctions and gap junction channels and their mathematical modelling

In most tissues of vertebrates, gap junctions control the exchange of ions and small molecules between adjacent cells, thus co-ordinating the cellular activities. The application of the dual voltage-clamp method to cell pair preparations enables one to elucidate the electrical properties of gap junctions and gap junction channels. The conductive and kinetic data obtained at the multichannel and single channel level led to a generalised concept for the operation of gap junction channels. Based on the biological data gained in this way, a mathematical model has been developed. This model is versatile and allows to simulate the electrophysiological behaviour of different types of vertebrate gap junctions.     

A temporally explicit species distribution model for a long distance avian migrant,the common cuckoo

Modelling the distribution of migratory species has rarely been extended beyond breeding and wintering ranges despite many species showing much more complex movement patterns with multiple stopovers. We aimed to create a temporally explicit species distribution model describing the full annual distribution cycle, and use it to model the complex seasonal shifts in distribution of the common cuckoo Cuculus canorus, a declining long‐distance migrant. To do this we used full‐year satellite telemetry occurrence data, with their associated temporal information, to inform a temporally explicit species distribution model using MaxEnt. The resulting full‐year distribution model was highly predictive (AUC = 0.894) and appeared to have generality at the species‐level despite being informed by data from a single breeding population. Comparison of our methodology with seasonal distribution models describing the breeding, winter and migration ranges separately showed that our full‐year method provided more general and extensive predictions and performed better when tested with an independent dataset. When species distribution models based on a single season exclude environmental conditions experienced by birds in other parts of the annual cycle they risk underestimating niche breadth and neglecting the importance of stopover habitat. Conversely, models which simply average conditions across a season may miss the significance of finer scale within‐season movements and overestimate niche breadth. In contrast, our framework for a full‐year migrant distribution model successfully captures the finer‐scale changes expected in seasonal environments and can be used to inform conservation management at every stage of migration. The full‐year model framework appears to produce temporal distribution models generalised to the species‐level from occurrence data limited to few individuals of a single population and may have particular utility when aiming to describe the distribution of species with complex migration patterns from telemetry data.     

土壤多样性理论在欧美的实践及在我国土壤景观研究中的应用前景

介绍了土壤多样性理论的基本概念与研究方法以及在西班牙、美国等欧美国家的研究实践 ,包括在欧盟 CORINE数据库和美国 STATSGO数据库支持下进行的多样性主要指数 (多样性指数、均匀度指数和多度指数等 )的算法、主要模型 (多度分布模型、幂律模型等 )的分析、GIS和地统计学方法的应用等。通过这些研究实践 ,可以看出土壤多样性理论在研究土壤的空间可变性、土壤景观格局的相互关系 ,土地利用与城市化过程对土壤多样性的影响等方面确有独到之处 ,为解决当前我国土壤学面临的环境资源可持续发展、环境监控、基因保护、城市化过程等热点问题提供了一个崭新的研究思路 ,展现出良好的应用前景     

A comparative evaluation of the biological action of allergens and allergoids prepared from plant pollen by the double radial immunodiffusion method

Antisera to allergens and allergoids prepared from timothy, orchard grass, birch and wormwood pollen have been obtained and used in the double radial immunodiffusion test. The preparations of the allergoid row have been found capable of inducing immune response in laboratory animals (rabbits). Both forms of pollen preparations, allergens and allergoids, have been shown to possess common antigenic determinants reacting with antibodies present in antisera to allergens and allergoids. The absence of identity in the ratio of manifestations of gel precipitation reactions for allergoid with respect to the initial forms of allergens of individual pollen preparation has been noted.