Dynamic rheology of agar gels: theory and experiments. Part I. Development of a rheological model

A theoretical rheological model for agar gels is proposed, based on the bead and spring model for linear flexible random coils and the model for crosslinked polymers. The model introduces the concept of a temperature dependence of the monomeric friction coefficient, ζ₀, of the agar molecule. The model has a random coil-like behavior at high temperatures (close to 373 K), and contributions from a three-dimensional network at low temperatures (close to 273 K). A proposed temperature dependence of the net association rate allows the calculation of the fraction of associated molecules as a function of time and temperature. The proposed model predicts the gelation behavior of agar gels utilizing time–temperature data (cooling curves).     

Effect of temperature and concentration on rheological behavior of xanthan-carob mixed gels

The gelation and melting behavior of 1∶1, 1∶3 xanthan-carob mixed gels were evaluated at isothermal and non-isothermal states, as a function of total polymer concentrations of 0.1, 0.5 and 1%. A thermal hysteresis was observed between gelation and melting. The higher the polymer concentration, the higher the melting temperature. The gelation points were determined by three criteria. Depending on the criterion used the gelation temperature was different (52 to 70°C). Pseudoequilibrium modulus and elastic active network chain (EANC) concentration were calculated from the plateau modulus in the frequency spectrum. Temperature dependence of the monomeric friction coefficient was estimated from the relaxation time and EANC. Time-temperature superposition theory was not applicable due to dramatic phase transitions occurring during the gelation of X/C mixture.     

“Melt-in-the-mouth” gels from mixtures of xanthan and konjac glucomannan under acidic conditions: A rheological and calorimetric study of the mechanism of synergistic gelation

The effect of acidification on a typical commercial xanthan and on pyruvate-free xanthan (PFX), alone and in gelling mixtures with konjac glucomannan (KGM), has been studied by differential scanning calorimetry (DSC) and small-deformation oscillatory measurements of storage modulus (G′) and loss modulus (G″). For both xanthan samples, progressive reduction in pH caused a progressive increase in temperature of the disorder–order transition in DSC, and a progressive reduction in gelation temperature with KGM. This inverse correlation is interpreted as showing that synergistic gelation involves disruption of the xanthan 5-fold helix, probably by attachment of KGM to the cellulosic backbone of the xanthan molecule (as proposed previously by a research group in the Institute of Food Research, Norwich, UK). Higher transition temperature accompanied by lower gelation temperature for PFX in comparison with commercial xanthan at neutral pH is explained in the same way. However, an additional postulate from the Norwich group, that attachment of KGM (or galactomannans) can occur only when the xanthan molecule is disordered, is inconsistent with the observation that gelation of acidified mixtures of KGM with PFX can occur at temperatures more than 60 °C below completion of conformational ordering of the PFX component (as characterised by DSC). Increase in G′ on cooling for mixtures of commercial xanthan with KGM at pH values of 4.5 and 4.25 occurred in two discrete steps, the first following the temperature-course observed for the same mixtures at neutral pH and the second occurring over the lower temperatures observed for mixtures of KGM with PFX at the same values of pH. These two “waves” of gel formation are attributed to interaction of KGM with, respectively, xanthan sequences that had retained a high content of pyruvate substituents, and sequences depleted in pyruvate by acid hydrolysis. At pH values of 4.0 and lower, gelation of mixtures of KGM with commercial xanthan followed essentially the same temperature-course as for mixtures with PFX, indicating extensive loss of pyruvate under these more strongly acidic conditions. Mixtures prepared at pH values in the range 4.0–3.5 gave comparable moduli at room temperature (20 °C) to those obtained at neutral pH, but showed substantial softening on heating to body temperature, suggesting possible applications in replacement of gelatin in products where “melt-in-the-mouth” characteristics are important for acceptability to the consumer.     

Molecular structure of potassium kappa carrageenate gels: a rheological and pulsed electric birefringence study

Measurements have been made of the shear modulus as a function of biopolymer concentration for pure potassium kappa carrageenate gels. The results have been discussed on the basis of rubber elasticity theory to investigate the free polymer linkages between junction zones within the gels. Pulsed electric birefringence studies have been made on segmented kappa carrageenan as a model for the junction zones of the gel.     

The influence of headgroup structure and fatty acyl chain saturation of phospholipids on monolayer behavior: a comparative rheological study

This paper compares six phospholipidic monolayers at the water/chloroform interface by performing dilational rheological measurements with a drop tensiometer apparatus. The chosen lipids differ both in their headgroup structure and fatty acyl chain saturation or symmetry. The study concentrated on monolayers formed with DPPC, DPPE, DOPC, DOPE, POPC and POPE. Using a generalized Maxwell rheological model, transposed at the interface, the intimate intermolecular interactions between amphiphilic molecules are studied on and off the monolayer plane. The equilibrium and nonequilibrium phenomena are analyzed and, respectively, correlated with monolayer cohesion and with monolayer/sub-surface interactions. The purpose of this work is to gain further insights into the influences (as slight as they are) of the weak changes in phospholipid structure and on the behavior of the monolayers. The results, widely described, provide further details on nuances existing between very similar molecules, and likewise, on the synergies created between the different effects.     

Positional behavior and body size of arboreal primates: a theoretical framework for field studies and an illustration of its application.

The rationale for most field studies of the positional behavior of arboreal primates has been the need to document natural behaviors quantitatively in order to infer the functional significance of morphological configurations. This focus on interactions of morphology with behavior is justifiable, but there exists another important level of biological relationships, that of the animal with its structural habitat, which it must negotiate to find food and avoid being preyed on. Recently it has become apparent that body size is likely to affect relationships of positional behavior with habitat structure, as well as with morphology. Here I offer a framework for research on functional relationships of positional behavior, body size, and habitat structure, with the ultimate objective of elucidating the aptive significance of the great diversity exhibited by arboreal primates. This approach specifies several distinct problems that animals solve, and indicates how research might be directed at revealing the relative effectiveness with which different primates solve them. A preliminary application of the framework examines sympatric north Sumatran primates.     

Dynamic games and field experiments examining intra- and intersexual conflict: explaining counterintuitive mating behavior in a Mediterranean wrasse, Symphodus ocellatus

Intersexual conflict and intrasexual competition are widelyrecognized as playing critical roles in determining mating systems.Although they occur simultaneously in populations, these processesare usually treated independently. In reality, the fitness ofreproductive strategies will depend on the outcome of both within-and between-sex conflicts. Using a modeling approach based onmultiple, linked, dynamic state variable models, we examined thereproductive behavior of a Mediterranean wrasse, Symphodus ocellatus.We compared the predictions of models that examine only a singleconflict interaction with those that consider multiple within-and between-sex conflicts simultaneously. The observed distributionof sneaker males and females among nests was compared with thosepredicted by the models. We found that the closest fit withempirical observations and experiments is given by the modelthat examines conflict between females, sneakers, and nestingmales simultaneously. Removal of successful nests indicatedthat females join nests with few or no sneakers present, whereassneakers join these nests only later, even though this leadsto lower sneaker mating success. This behavior can be explainedby observing that although sneakers would have higher fitnessat nests where the spawning rate is greater, females would notbe willing to spawn at these nests in the presence of sneakers. Presumably,once the nests have achieved high past success, females are willingto spawn in the presence of sneakers because of the associated decreasedchance of nesting male desertion.     

Crenation and cupping of the red cell: A new theoretical approach. Part II. Cupping

Typical, axisymmetrical cup shaped cells have been carefully measured and the shapes analyzed mathematically. The results show that the strain energy of a cup shaped cell is always higher than that of a biconcave cell except when the two layers of the membrane involved in resistance to bending are free to slide over one another. This is true whether intrinsic curvature of the membrane is positive, negative or zero. If the two layers can slide over one another, the cup shape becomes the lower energy form. Shear resistance, if appreciable, must cause the cup cell to buckle. Photomicrographs of cup shaped cells show buckled configurations characteristic of those of a partly deflated thin-walled rubber ball, which is a similar object having a low ratio of bending/shear strength.In light of these findings, the cup shape of the red cell can no longer be considered as evidence of intrinsic membrane curvature of opposite sign to that of the crenated cell, but appears to indicate a phase change either in the hydrophobic interior of the bimolecular membrane or in some equivalent interface.     

A community model of ciliateTetrahymena and bacteriaE. coli: Part II. Interactions in a batch system

Premised on relatively simple assumptions, mathematical models like those of Monod, Pirt or Droop inadequately explain the complex transient behavior of microbial populations. In particular, these models fail to explain many aspects of the dynamics of aTetrahymena pyriformis-Escherichia coli community. In this study an alternative approach, an individual-based model, is employed to investigate the growth and interactions ofTetrahymena pyriformis andE. coli in a batch culture. Due to improved representation of physiological processes, the model provides a better agreement with experimental data of bacterial density and ciliate biomass than previous modeling studies. It predicts a much larger coexistence domain than rudimentary models, dependence of biomass dynamics on initial conditions (bacteria to ciliate biomasses ratio) and appropriate timing of minimal bacteria density. Moreover, it is found that accumulation ofE. coli sized particles andE. coli toxic metabolites has a stabilizing effect on the system.     

Development of a variational scheme for model inversion of multi-area model of brain. Part II: VBEM method

In Part I and Part II of these two companion papers (henceforth called Part I and Part II), we develop and evaluate a variational Bayesian expectation maximization (VBEM) method for model inversion of our multi-area extended neural mass model (MEN). In this paper, we develop the VBEM method to estimate posterior distributions of parameters of MEN. We choose suitable prior distributions for the model parameters in order to use properties of a conjugate-exponential model in implementing VBEM. Consequently, VBEM leads to analytically tractable forms. The proposed VBEM algorithm starts with initialization and consists of repeated iterations of a variational Bayesian expectation step (VB E-step) and a variational Bayesian maximization step (VB M-step). Posterior distributions of the model parameters are updated in the VB M-step. Distribution of the hidden state is updated in the VB E-step. We develop a variational extended Kalman smoother (VEKS) to infer the distribution of the hidden state in the VB E-step and derive the forward and backward passes of VEKS, analogous to the Kalman smoother. In Part I, we evaluate and validate the VBEM method using simulation studies.     

Water flow controls distribution and feeding behavior of two co-occurring coral reef fishes: II. Laboratory experiments

The chaenopsid blenny Acanthemblemaria spinosa occupies topographically high locations on coral reefs where flow speeds and turbulence are frequently greater than those experienced by its congener, A. aspera, which occupies locations close to the reef surface. To investigate the adaptive mechanisms resulting in this microhabitat differentiation, the foraging effort and success of these fishes were determined in laboratory flumes that produced flow conditions approximating those experienced in the field. Individual fish were subjected to unidirectional (smooth and turbulent) and oscillatory flows while they fed on calanoid copepods, Acartia tonsa, whose vulnerability to predation varies with water flow. In unidirectional flow both blenny species had their greatest foraging success at intermediate flow speeds (ca. 10 cm s⁻¹) and under turbulent flow. Under all conditions, Acanthemblemaria spinosa exhibited greater foraging effort and attacked at greater distances, greater mean water speeds, and in oscillatory flow, over a greater proportion of the wave cycle than did A. aspera. A. spinosa also exhibited greater foraging success under turbulent flow conditions. These differences in feeding patterns allow A. spinosa, with its higher metabolic rate, to occupy the more energetic higher locations in corals where planktonic food is more abundant. A. aspera occupies the poorer quality habitat in terms of planktonic food availability but its lower metabolic rate allows it to thrive there. Consequently, these species divide the resource in short supply, i.e., shelter holes, based on their differing abilities to capture prey in energetic water conditions in conjunction with their differing food energy requirements. Communicated by Biology Editor Dr. Mark McCormick     

Specificity space,the structure and evolution of metabolic pathways: Part II of a general theory

Biomolecular structures are interacting in terms of their force fields. These force fields define the specificity surfaces of the molecules. Specificity surfaces are represented by specificity vectors in a multidimensional specificity space. A quantitative analytical expression is developed for biochemical reactions and the evolution of metabolic pathways in the specificity space. This leads to detailed identification of various biomolecular processes with individual terms in the equation. This theoretical analysis permits defining detailed function and resolution requirement of enzymes, as well as, how these fit into the overall metabolic pattern of the cell. This paper is Part II of a general theory of the physical basis of the biological state of matter.     

Comparison of instantaneous and locomotor bout sampling methods: a case study of adult male chimpanzee locomotor behavior and substrate use.

Currently two methods, instantaneous and locomotor bout sampling, are used most commonly in studies of locomotor behavior. To date, no study has addressed how comparable the results of the two methods are. This paper considers whether different sampling methods of locomotor behavior produce different results. Continuous locomotor bout and instantaneous sampling were carried out simultaneously on each focal animal during a seven month study of chimpanzee positional behavior in the Tai Forest of the Ivory Coast. Results provide two independent sets of data which describe the same events. Results indicate that as locomotor bouts are frequently presented (the percentage of bouts spent in an activity), they overrepresent the frequencies of activities that occur relatively often, but for short distances, and underrepresent activities that have a relatively large mean distance per bout. However, when bouts are weighted with distance, as originally defined by Fleagle (1976b), there are no significant differences in the results obtained by the two methods. Both provide similar results for the frequencies of locomotor activities, frequency of substrate use, and the relationship between substrate and locomotor activity. The advantage of instantaneous sampling is that because it is done at regular intervals, it can easily be carried out in conjunction with sampling other behavioral and ecological data. The advantages of locomotor bout sampling are that it permits the sampling of rare or brief locomotor events and allows for an analysis of sequences of locomotor activities. This paper demonstrates that the two methods can be conducted simultaneously and thus provide the richest return from which the effect of environment and morphology on locomotion can be addressed.     

Psychological stressors as a model of maternal adversity: diurnal modulation of corticosterone responses and changes in maternal behavior

Maternal adversity is associated with long-lasting consequences on cognitive development, behavior and physiological responses in rat offspring. Few studies have examined whether repeated maternal stress produces repeated activation of the hypothalamus-pituitary-adrenal (HPA) axis in mothers and whether it modifies maternal behavior. Here, we tested a novel model of perinatal stress using repeated exposure to "purely" psychological stressors throughout the gestation and lactation periods in rats. We first tested the diurnal influences of repeated 1-h strobe light exposure on maternal corticosterone secretion. Despite the hyporesponsiveness to stress documented in late pregnant and lactating mothers, we observed an enhanced response to strobe light in the afternoon compared to the morning in stressed mothers during lactation. Next, dams were exposed to 24-h forced foraging followed by 10-h wet bedding during the diurnal peak of corticosterone secretion. Although no corticosterone responses to forced foraging and wet bedding were observed, the combination of both stressors had a significant effect on maternal behavior. Mother-pup interactions were significantly altered during the first 8 days of lactation. Taken together, these findings suggest that lactating mothers maintain responsiveness to specific and repeated psychological stressors, in particular at the time of the diurnal peak in corticosterone secretion. Depending on the stressor applied, either neuroendocrine activation or changes in maternal behavior might be important determinants of the long-term consequences in the offspring. The combination of forced foraging, wet bedding and strobe light might represent a novel model of mild maternal adversity using "purely" psychological stressors.     

Antibiotic resistance and the evolution of group-beneficial traits. II: a metapopulation model

Inspired by the evolution of antibiotic resistance in bacteria, we have developed a model that examines the evolution of "producers" (who secrete a substance that breaks down antibiotics) and non-producers. In a previous study, we found that frequency-dependent selection could favor an intermediate frequency of producers in a single, large population. Here we develop a metapopulation model that examines the evolution of producers and non-producers. Our results indicate that in a metapopulation with many groups, each of size N, the equilibrial frequency of producers decreases with group size. Even when N is high (e.g. 150 individuals/group), however, a significant frequency of producers is still predicted. We also found that the equilibrial frequency of producers increases as the minimum numbers of producers necessary to provide protection to non-producers increases. Lastly, increasing the benefit/cost ratio (b/c) for producers increases their equilibrial frequency.     

Rise, fall and resurrection of chromosome territories: a historical perspective. Part II. Fall and resurrection of chromosome territories during the 1950s to 1980s. Part III. Chromosome territories and the functional nuclear architecture: experiments and models from the 1990s to the present

Part II of this historical review on the progress of nuclear architecture studies points out why the original hypothesis of chromosome territories from Carl Rabl and Theodor Boveri (described in part I) was abandoned during the 1950s and finally proven by compelling evidence forwarded by laser-uv-microbeam studies and in situ hybridization experiments. Part II also includes a section on the development of advanced light microscopic techniques breaking the classical Abbe limit written for readers with little knowledge about the present state of the theory of light microscopic resolution. These developments have made it possible to perform 3D distance measurements between genes or other specifically stained, nuclear structures with high precision at the nanometer scale. Moreover, it has become possible to record full images from fluorescent structures and perform quantitative measurements of their shapes and volumes at a level of resolution that until recently could only be achieved by electron microscopy. In part III we review the development of experiments and models of nuclear architecture since the 1990s. Emphasis is laid on the still strongly conflicting views about the basic principles of higher order chromatin organization. A concluding section explains what needs to be done to resolve these conflicts and to come closer to the final goal of all studies of the nuclear architecture, namely to understand the implications of nuclear architecture for nuclear functions.     

Development of a novel stall design for dairy cattle: Part II. The effect of minimal stall partitioning on lying behavior,rumination, stall cleanliness,and preference

Free-stalls for dairy cows promote cleanliness, provide cows with a defined space to lie down, and decrease labor and bedding required for maintenance. However, current stall features can restrict behavior and reduce stall use. The objective of this study was to assess the short-term effect of a novel free-stall design (flexible single-bar partition, no neck rail, increased slope) on stall cleanliness and the lying behavior, rumination, milk production, and preferences of dairy cows in comparison to standard free-stalls (metal loop partitions, neck rail). In the first experiment, 60 Holstein cows were randomly divided into two groups and switched between standard and novel stalls in a replicated crossover design with four 7-day periods. Lying behavior and rumination were recorded continuously. Milk yields were recorded 2x/day, and stall cleanliness scores were collected on the last four days of weeks 3 and 4. The second experiment was a 6-day preference test where 14 cows from experiment 1 were given free access to 16 standard and 16 novel stalls. Lying behavior was recorded continuously. On day 6, standing, perching, and intention, lying, and rising movements were recorded. In experiment 1, cows spent 12 min less time lying down (14.1 vs 14.3 ± 0.48 h/d), had one fewer lying bouts (8.8 vs 9.8 ± 0.23 bouts/d), and had longer lying bouts by 6 min (1.4 vs 1.5 ± 0.05 h/bout) in novel stalls. Rumination time (547.3 vs 548.9 ± 4.66 min/d) and milk yield (35.0 vs 35.2 ± 0.51 kg/d) did not differ between stall types. However, novel stalls were more than twice as soiled as standard stalls (32.8 vs 14.2 ± 1.38% of rear half soiled). In experiment 2, the cows most recently housed in the novel stalls showed a clear preference for lying down in those stalls, whereas cows most recently housed in standard stalls showed no preference. Intention and lying down movements were longer in standard stalls when other cows were present in diagonally opposite stalls, but were similar between stall types when not occupied. All cows preferred standing in novel stalls. Novel stalls may have improved stall use compared to standard free-stalls, and the design requires further development to address cleanliness concerns. Future work is required to provide comfortable stalls without sacrificing cleanliness.     

The response of oscillating glycolysis to perturbations in the NADH/NAD system: a comparison between experiments and a computer model.

The glycolytic pathway is described by a set of coupled non linear differential equations of first order with respect to time. The individual terms of these equations consist of enzyme velocities assuming a steady state hypothesis for the enzymatic forms. These are specified and the system is solved numerically. Oscillations are explained by interaction of PFK with the adenylate system. The conditions for the occurrence of oscillations are tested in a series of computer runs. The phase relations between intermediates of the model agree with those found in yeast cells. As an application of the model the disturbation of oscillations by the addition of acetaldehyde is simulated. The predictions of the model agree with experimental results.     

广义Rothermel模型预测平地无风条件下红松-蒙古栎林地表混合可燃物的火行为

以帽儿山地区红松-蒙古栎林下地表混合可燃物为材料,进行不同含水率、载量和混合比例的室内点烧试验,观测得到蔓延速率、驻留时间、反应强度、火线强度和火焰长度,并与采用表面积加权法和载量加权法的广义Rothermel模型预测值进行比较.结果表明:广义Rothermel模型对红松-蒙古栎林下地表混合可燃物的林火蔓延速率、反应强度的预测平均绝对误差分别为0.04 m·min-1、77 kW·m-2,预测平均相对误差分别为16％、22％;对驻留时间、火线强度和火焰长度的预测偏低,预测平均绝对误差分别为15.5 s、17.3 kW·m-1和9.7 cm,预测平均相对误差分别为55.5％、48.7％和24％.这些误差可以看成是用该模型预测同类可燃物相应火行为的误差下限.两种加权算法对模型预测精度影响差异不大,当红松可燃物所占比重较小时,表面积加权法得到的蔓延速率和反应强度预测值精度较高,载量加权法得到的火线强度和火焰长度预测值精度较高;当红松可燃物所占比重较大时,结果则相反.     

Use of a structured kinetic model of antibody synthesis and secretion for optimization of antibody production systems: II. Transient analysis

The dynamic behavior of the monoclonal antibody (MAb) secretory pathway is studied by transient simulations using our previously developed structured kinetic model for antibody synthesis and secretion by hybridoma cells. The response of the secretory pathway to blocks in specific pathway steps and step changes in characteristic pathway parameters is presented in order to gain a better understanding of pathway dynamics and identify possible ratelimiting steps in the pathway. Model simulations suggest that the step of antibody assembly in the endoplasmic reticulum (ER) is a very good candidate for a rate-limiting step in the antibody secretory pathway in fast-growing hybridoma cells, whereas translation of the heavy and light chains is most likely rate-limiting in slowly growing or stationary phase cells. Transient simulation results are compared with experimentally observed transient changes in specific antibody secretion rates and used to suggest strategies for optimizing antibody secretion in large-scale production systems.