Dynamics of endotoxin fever in the rabbit

To analyze the dynamic properties of body temperature and effector mechanisms during endotoxin fever, both experimental and mathematical procedures were applied. Experiments were carried out on rabbits in a climatic chamber at various ambient temperatures. Salmonella typhosa endotoxin (0.1 microgram/kg) was injected into an ear vein. A biphasic core temperature increase evoked by different effector mechanisms depending on ambient temperature was observed. A mathematical model based on experimental results with nonfebrile rabbits predicts the effector behavior at all ambient temperatures. From a comparison of experimental results with the model prediction, it is concluded that the increase of core temperature during fever is essentially caused by a dynamic shift of the controller characteristics. The effect of the pyrogen may be simulated by a resultant fever-controlling signal that is biphasic but increases more steeply than does core temperature. The analysis suggests that the three possible fever-driving effectors, metabolism, ear blood flow, and respiratory evaporative heat loss, should be controlled by the same resultant signal, although the time courses of the effectors and of core temperature vary distinctly at different air temperatures. The model uses an additive controller structure.     

Regulation of ATP supply in mammalian skeletal muscle during resting state-->intensive work transition

In the present debating paper, the problem how the rate of ATP supply by oxidative phosphorylation in mitochondria is adjusted to meet a greatly increased demand for ATP during intensive exercise of skeletal muscle is discussed. Different experimental results are collected from different positions of the literature and confronted with five conceptual models of the regulation of the oxidative phosphorylation system. The previously performed computer simulations using a dynamic model of oxidative phosphorylation are also discussed in this context. The possible regulatory mechanisms considered in the present article are: (A) output activation: an external effector activates directly only the output of the system (ATP turnover); (B) input/output activation: an external effector activates directly the output (ATP usage) and input (substrate dehydrogenation) of the system; (C) removal of substrate shortage: only ATP consumption and substrate supply by blood are directly activated; (D) removal of oxygen shortage: only ATP consumption and oxygen supply by blood are directly activated; (E) each step activation: an external effector activates both the ATP-consuming subsystem and all the steps in the ATP-producing subsystem (particular enzymes/carriers/blocks of oxidative phosphorylation, substrate supply, oxygen supply). The performed confrontation of the considered mechanisms with the presented results leads to the conclusion that only the each step activation model is quantitatively consistent with the whole set of experimental data discussed. It is therefore postulated that a universal effector/regulatory mechanism of a still unknown nature which activates all steps of oxidative phosphorylation should exist and be discovered. A possible nature of such an effector is shortly discussed.     

Recent advances in temperature regulation during exercise in humans

This paper describes first the dynamics of heat transfer from active muscle to the body core and then the physiological regulatory mechanisms that act to modify the rates of heat transfer from core to skin and from skin to environment. After this, nonthermal factors influencing the regulatory mechanisms are described, emphasizing the importance of body fluid status and its influence on the temperature regulatory mechanisms. The control of cutaneous vasomotor and venomotor tone is the shared effector loop of both the blood pressure and temperature regulatory systems; during exercise these systems interact, with the former system predominating when mutually exclusive demands exist. The importance of blood volume is emphasized again in a final discussion of the effects of improved physical condition on the temperature regulatory system.     

Stimulus design for model selection and validation in cell signaling

Mechanism-based chemical kinetic models are increasingly being used to describe biological signaling. Such models serve to encapsulate current understanding of pathways and to enable insight into complex biological processes. One challenge in model development is that, with limited experimental data, multiple models can be consistent with known mechanisms and existing data. Here, we address the problem of model ambiguity by providing a method for designing dynamic stimuli that, in stimulus–response experiments, distinguish among parameterized models with different topologies, i.e., reaction mechanisms, in which only some of the species can be measured. We develop the approach by presenting two formulations of a model-based controller that is used to design the dynamic stimulus. In both formulations, an input signal is designed for each candidate model and parameterization so as to drive the model outputs through a target trajectory. The quality of a model is then assessed by the ability of the corresponding controller, informed by that model, to drive the experimental system. We evaluated our method on models of antibody–ligand binding, mitogen-activated protein kinase (MAPK) phosphorylation and de-phosphorylation, and larger models of the epidermal growth factor receptor (EGFR) pathway. For each of these systems, the controller informed by the correct model is the most successful at designing a stimulus to produce the desired behavior. Using these stimuli we were able to distinguish between models with subtle mechanistic differences or where input and outputs were multiple reactions removed from the model differences. An advantage of this method of model discrimination is that it does not require novel reagents, or altered measurement techniques; the only change to the experiment is the time course of stimulation. Taken together, these results provide a strong basis for using designed input stimuli as a tool for the development of cell signaling models.     

Determination of feature relevance for the grouping of motor unit action potentials through a generative mixture model

The study of motor unit action potential (MUAP) activity from electromyographic signals is important for neurological investigations aiming to understand the state of the neuromuscular system. In this context, the identification and clustering of MUAPs that exhibit common characteristics, and the assessment of which data features are most relevant for the definition of such cluster structure, are central issues. In this paper, we propose the application of an unsupervised feature relevance determination (FRD) method to the analysis of experimental MUAPs. This method is embedded in a constrained mixture of distributions model that simultaneously performs data clustering and visualization. The experimental results of the analysis of a data set consisting of MUAPs measured from the First Dorsal Interosseous, a hand muscle, indicate that the features corresponding to the hyperpolarization period in the physiological process of generating muscle fibre action potentials are consistently estimated to be the most relevant. Moreover, the MUAP cluster structure of the data is shown to be only partially attributable to inter-subject differences, with the hyperpolarization period providing the best discrimination of the data by subject.     

Model of human/liquid cooling garment interaction for space suit automatic thermal control

The Wissler human thermoregulation model was augmented to incorporate simulation of a space suit thermal control system that includes interaction with a liquid cooled garment (LCG) and ventilation gas flow through the suit. The model was utilized in the design process of an automatic controller intended to maintain thermal neutrality of an exercising subject wearing a liquid cooling garment. An experimental apparatus was designed and built to test the efficacy of specific physiological state measurements to provide feedback data for input to the automatic control algorithm. Control of the coolant inlet temperature to the LCG was based on evaluation of transient physiological parameters that describe the thermal state of the subject, including metabolic rate, skin temperatures, and core temperature. Experimental evaluation of the control algorithm function was accomplished in an environmental chamber under conditions that simulated the thermal environment of a space suit and transient metabolic work loads typical of astronaut extravehicular activity (EVA). The model was also applied to analyze experiments to evaluate performance of the automatic control system in maintaining thermal comfort during extensive transient metabolic profiles for a range of environmental temperatures. Finally, the model was used to predict the efficacy of the LCG thermal controller for providing thermal comfort for a variety of regiments that may be encountered in future space missions. Simulations with the Wissler model accurately predicted the thermal interaction between the subject and LCG for a wide range of metabolic profiles and environmental conditions and matched the function of the automatic temperature controller for inlet cooling water to the LCG.     

A balance control model of quiet upright stance based on an optimal control strategy

Models of balance control can aid in understanding the mechanisms by which humans maintain balance. A balance control model of quiet upright stance based on an optimal control strategy is presented here. In this model, the human body was represented by a simple single-segment inverted pendulum during upright stance, and the neural controller was assumed to be an optimal controller that generates ankle control torques according to a certain performance criterion. This performance criterion was defined by several physical quantities relevant to sway. In order to accurately simulate existing experimental data, an optimization procedure was used to specify the set of model parameters to minimize the scalar error between experimental and simulated sway measures. Thirty-two independent simulations were performed for both younger and older adults. The model's capabilities, in terms of reflecting sway behaviors and identifying aging effects, were then analyzed based on the simulation results. The model was able to accurately predict center-of-pressure-based sway measures, and identify potential changes in balance control mechanisms caused by aging. Correlations between sway measures and model parameters are also discussed.     

Heat balance of the human body: influence of variations of locally distributed parameters

Human body temperature control is characterized by a local dependence of system variables and parameters. Essential properties regarding inhomogeneity of the passive system have been investigated using mathematical methods. The general diffusion-equation has been solved using implicit finite difference methods with nonlinear boundary conditions. In order to allow comparison with experimental results, a simple ideal controller has been defined. On the basis of an inhomogeneous cylinder model with four concentric layers, influences of variations due to differences between tissues and individuals or measurements of parameters such as basal metabolism and conductivity have been studied. Stationary temperature profiles calculated for homogeneous and inhomogeneous conditions have been compared. Finally, the influence of blood flow has been discussed, as well as the stationary behaviour of profiles due to blood flow and blood flow control. The change of sign of curvature of temperature profile is possible only if blood flow mechanisms and the local distribution of metabolism are taken into account.     

Threshold dissociation of thermoregulatory effector responses in febrile rabbits

When the core temperature stabilizes at a hyperthermic level after iv injection of lipopolysaccharide (LPS), the threshold core temperature for cutaneous vasoconstriction (Thcv) is significantly increased in hot and neutral environments, while the threshold core temperature for shivering (Thsh) is not significantly altered in hot or cold environments but is significantly reduced at thermoneutrality. This type of dissociated threshold alterations of thermoregulatory effector responses seems to be typical for the febrile response of rabbits to LPS. Because the same threshold dissociation can be demonstrated after icv injection of LPS, the systemic and the central effects of LPS in the generation of fever seem to be mediated by identical mechanisms. Prostaglandins of the E series (PGE), one of the mediators considered as important in fever generation, cause parallel increases in Thcv and Thsh when injected icv. This indicates that the mode of action of PGE on the central targets producing hyperthermia differs from that of the ensemble of mediators involved in the generation of LPS fever in rabbits. In rabbits pretreated with aspirin, the threshold dissociation after iv LPS injection still occurs. This indicates that factors other than PGE play an important role in the generation of the threshold dissociation of thermoregulatory effector responses, which is typical for LPS fever. These data indicate also that the states of activity of the thermoregulatory effectors involved in the febrile responses can be altered individually and that the activities of these effectors during LPS fever are quite different from their activities in the control state.     

Modelling hand skin temperature in relation to body composition

Skin temperature is a challenging parameter to predict due to the complex interaction of physical and physiological variations. Previous studies concerning the correlation of regional physiological characteristics and body composition showed that obese people have higher hand skin temperature compared to the normal weight people. To predict hand skin temperature in a different environment, a two-node hand thermophysiological model was developed and validated with published experimental data. In addition, a sensitivity analysis was performed which showed that the variations in skin blood flow and blood temperature are most influential on hand skin temperature. The hand model was applied to simulate the hand skin temperature of the obese and normal weight subgroup in different ambient conditions. Higher skin blood flow and blood temperature were used in the simulation of obese people. The results showed a good agreement with experimental data from the literature, with the maximum difference of 0.31 °C. If the difference between blood flow and blood temperature of obese and normal weight people was not taken into account, the hand skin temperature of obese people was predicted with an average deviation of 1.42 °C. In conclusion, when modelling hand skin temperatures, it should be considered that regional skin temperature distribution differs in obese and normal weight people.     

Fc gamma receptors play a dominant role in protective tumor immunity against a virus-encoded tumor-specific antigen in a murine model of experimental pulmonary metastases

Simian virus 40 (SV40) large tumor antigen (Tag) represents a virus-encoded tumor-specific antigen expressed in many types of human cancers and a potential immunologic target for antitumor responses. Fc receptors are important mediators in the regulation and execution of host effector mechanisms against conditions including infectious diseases, autoimmunity, and cancer. By examining tumor protection in SV40 Tag-immunized wild-type BALB/c mice using an experimental pulmonary metastasis model, we attempted to address whether engagement of the immunoglobulin G Fc receptors (FcgammaRs) on effector cells is necessary to mediate antitumor responses. All immunized BALB/c FcgammaR-/- knockout mice developed anti-SV40 Tag antibody responses prior to experimental challenge with a tumorigenic cell line expressing SV40 Tag. However, all mice deficient in the activating FcgammaRI (CD64) and FcgammaRIII (CD16) were unable to mount protective immunologic responses against tumor challenge and developed tumor lung foci. In contrast, mice lacking the inhibitory receptor FcgammaRII (CD32) demonstrated resistance to tumorigenesis. These results underscore the importance of effector cell populations expressing FcgammaRI/III within this murine tumor model system, and along with the production of a specific humoral immune response, antibody-dependent cell-mediated cytotoxicity (ADCC) may be a functioning mechanism of tumor clearance. Additionally, these data demonstrate the potential utility of ADCC as a viable approach for targeting vaccination strategies that promote FcgammaRI/III scavenging pathways against cancer.     

Molecular mechanisms of T-cell anergy

Anergy is a long-term stable state of T-lymphocyte unresponsiveness to antigenic stimulation associated with the blockade of IL-2 production and proliferation. Anergy is a pathway of peripheral tolerance formation. In this review, mechanisms underlying T-cell tolerization are considered in a classical in vitro model of clonal anergy, and these mechanisms are compared with different pathways of anergy induction in vivo. Special attention is given to regulatory T-lymphocytes because, on one hand, anergy is a specific feature of these cells, and on the other hand anergy is also a mechanism of their action on target cells — effector T-lymphocytes. The role of this phenomenon in the differentiation of regulatory T-cells and also in the development of activation-induced apoptosis in effector T-lymphocytes is discussed.     

Connecting nanoscale images of proteins with their genetic sequences

We present a technique for reconstructing biomolecular structures from scanning force microscope data. The technique works by iteratively refining model molecules by comparison of simulated and experimental images. It can remove instrument artifacts to yield accurate dimensional measurements from tip-broadened data. The result of the reconstruction is a model that can be chosen to include the physically significant parameters for the system at hand. We demonstrate this by reconstructing scanning force microscope images of the cartilage proteoglycan aggrecan. By explicitly including the protein backbone in the model, we are able to associate measured three-dimensional structures with sites in the protein primary structure. The distribution of aggrecan core protein lengths that we measure suggests that 48% of aggrecan molecules found in vivo have been partially catabolized at either the E(1480)-(1481)G or E(1667)-(1668)G aggrecanase cleavage site.     

Hierarchical analysis of large-scale two-dimensional gel electrophoresis experiments

Large-scale two-dimensional gel experiments have the potential to identify proteins that play an important role in elucidating cell mechanisms and in various stages of drug discovery. Such experiments, typically including hundreds or even thousands of related gels, are notoriously difficult to perform, and analysis of the gel images has until recently been virtually impossible. In this paper we describe a scalable computational model that permits the organization and analysis of a large gel collection. The model is implemented in Compugen's Z4000 system. Gels are organized in a hierarchical, multidimensional data structure that allow the user to view a large-scale experiment as a tree of numerous simpler experiments, and carry out the analysis one step at a time. Analyzed sets of gels form processing units that can be combined into higher level units in an iterative framework. The different conditions at the core of the experiment design, termed the dimensions of the experiment, are transformed from a multidimensional structure to a single hierarchy. The higher level comparison is performed with the aid of a synthetic "adaptor" gel image, called a Raw Master Gel (RMG). The RMG allows the inclusion of data from an entire set of gels to be presented as a gel image, thereby enabling the iterative process. Our model includes a flexible experimental design approach that allows the researcher to choose the condition to be analyzed a posteriori. It also enables data reuse, the performing of several different analysis designs on the same experimental data. The stability and reproducibility of a protein can be analyzed by tracking it up or down the hierarchical dimensions of the experiment.     

Stabilization of halophilic malate dehydrogenase

Malate dehydrogenase from the extreme halophile, Halobacterium marismortui, is stable only in highly concentrated solutions of certain salts. Previous work has established that its physiological environment is saturated in KCl; it remains soluble is saturated NaCl or KCl solutions; also it unfolds in solutions containing less than 2.5 M-NaCl or -KCl, salt concentrations which are still relatively high. New data show that the structure of this enzyme can be stabilized in a range of high concentrations of Mg2+ or other "salting-in" ions, also with exceptional protein-solvent interactions. "Salting-in" ions, contrary to stabilizing protein structure, usually favour unfolding. These, and most other results concerning the structure, stability and solvent interactions of the protein cannot be understood in terms of the usual effects of salts on protein structure. In this paper, a novel stabilization model is proposed for halophilic malate dehydrogenase that can account for all observations so far. The model results from experiments on the protein in salt solutions chosen for their different effects on protein stability (potassium phosphate, a strongly "salting-out" agent, and MgCl2, which is "salting-in"), and previously published data from NaCl and KCl solutions (mildly "salting-out"). Enzymic activity and stability measurements were combined with neutron scattering, ultracentrifugation and quasi-elastic light-scattering experiments. The analysis showed that the structure of the protein in solution as well as the dominant stabilization mechanisms were different in different salt solutions in which this enzyme is active. Thus, in molar concentrations of phosphate ions, stabilization and hydration are similar to those of non-halophilic soluble proteins, in which the hydrophobic effect dominates. In high concentrations of KCl, NaCl or MgCl2, on the other hand, solution particles are formed in which the protein dimer interacts with large numbers of salt and water molecules (the mass of solvent molecules involved depends on the nature of the salt but it is approximately equivalent to the protein mass). It is proposed that, under these conditions, the hydrophobicity of the protein core is too weak to stabilize the folded structure and the main stabilization mechanism is the formation of co-operative hydrate bonds between the protein and hydrated salt ions. Model predictions are in agreement with all experimental results, such as the different numbers of solvent molecules found in the solution particles formed with different salts, the loss of the exceptional solvent interactions concomitant with unfolding at non-physiological salt concentrations, and the different temperature denaturation curves observed for different salt solutions.(ABSTRACT TRUNCATED AT 400 WORDS)     

Identifying Optimal Models to Represent Biochemical Systems

Biochemical systems involving a high number of components with intricate interactions often lead to complex models containing a large number of parameters. Although a large model could describe in detail the mechanisms that underlie the system, its very large size may hinder us in understanding the key elements of the system. Also in terms of parameter identification, large models are often problematic. Therefore, a reduced model may be preferred to represent the system. Yet, in order to efficaciously replace the large model, the reduced model should have the same ability as the large model to produce reliable predictions for a broad set of testable experimental conditions. We present a novel method to extract an “optimal” reduced model from a large model to represent biochemical systems by combining a reduction method and a model discrimination method. The former assures that the reduced model contains only those components that are important to produce the dynamics observed in given experiments, whereas the latter ensures that the reduced model gives a good prediction for any feasible experimental conditions that are relevant to answer questions at hand. These two techniques are applied iteratively. The method reveals the biological core of a model mathematically, indicating the processes that are likely to be responsible for certain behavior. We demonstrate the algorithm on two realistic model examples. We show that in both cases the core is substantially smaller than the full model.     

Cybernetic model predictive control of a continuous bioreactor with cell recycle

The control of poly-beta-hydroxybutyrate (PHB) productivity in a continuous bioreactor with cell recycle is studied by simulation. A cybernetic model of PHB synthesis in Alcaligenes eutrophus is developed. Model parameters are identified using experimental data, and simulation results are presented. The model is interfaced to a multirate model predictive control (MPC) algorithm. PHB productivity and concentration are controlled by manipulating dilution rate and recycle ratio. Unmeasured time varying disturbances are imposed to study regulatory control performance, including unreachable setpoints. With proper controller tuning, the nonlinear MPC algorithm can track productivity and concentration setpoints despite a change in the sign of PHB productivity gain with respect to dilution rate. It is shown that the nonlinear MPC algorithm is able to track the maximum achievable productivity for unreachable setpoints under significant process/model mismatch. The impact of model uncertainty upon controller performance is explored. The multirate MPC algorithm is tested using three controllers employing models that vary in complexity of regulation. It is shown that controller performance deteriorates as a function of decreasing biological complexity.     

Closed loop control of human body temperature: results from a one-dimensional model

A one-dimensional model of human thermoregulation is used to solve a variety of basic problems in determining an adequate structure of the controller for metabolic heat production, skin blood flow and sweat production. Assuming one integrated central and one integrated peripheral afferent signal the controller parameters are evaluated by analysis of the control performance. Based on a validation by experimental results this allows the determination of a first optimized set of values for controller gains and weight of skin temperature feedback. Furthermove we analyse the effect of inhomogeneous distribution of heat production and blood flow, the influence of body fat content, of controller gains, of weight of skin temperature feedback and of depth of peripheral receptors on the dynamic performance. Increase of peripheral blood flow in particular evokes essentially both an increase of energy requirement in the cold and a quicker system response. Differing rates of increase of metabolic heat production are the consequence of differing body fat content. The weight of skin temperature feedback can be limited to 5...20%, because values outside this range evoke dynamic responses incompatible with the experiments. The actual value can only be determined if there is a correct assumption for the depth of the skin receptors. The use of measured superficial skin temperatures brings about an underestimation of the peripheral afferent signal. Of the controller gains it is primarily the gain of the metabolic controller which affects the dynamic response of the system. The experimental fact of a delayed onset of sweat production after a transition from cold to heat is the consequence of a high gain of the vasomotor system.     

Motor control of voluntary arm movements

The motor control of pointing and reaching-to-grasp movements was investigated using two different approaches (kinematic and modelling) in order to establish whether the type of control varies according to modifications of arm kinematics. Kinematic analysis of arm movements was performed on subjects' hand trajectories directed to large and small stimuli located at two different distances. The subjects were required either to grasp and to point to each stimulus. The kinematics of the subsequent movement, during which subject's hand came back to the starting position, were also studied. For both movements, kinematic analysis was performed on hand linear trajectories as well as on joint angular trajectories of shoulder and elbow. The second approach consisted in the parametric identification of the black box (ARMAX) model of the controller driving the arm movement. Such controller is hypothesized to work for the correct execution of the motor act. The order of the controller ARMAX model was analyzed with respect to the different experimental conditions (distal task, stimulus size and distance). Results from kinematic analysis showed that target distance and size influenced kinematic parameters both of angular and linear displacements. Nevertheless, the structure of the motor program was found to remain constant with distane and distal task, while it varied with precision requirements due to stimulus size. The estimated model order of the controller confirmed the invariance of the control law with regard to movement amplitude, whereas it was sensitive to target size.     

Control of vertebrate intraflagellar transport by the planar cell polarity effector Fuz

Cilia play key roles in development and homeostasis, and defects in cilia structure or function lead to an array of human diseases. Ciliogenesis is accomplished by the intraflagellar transport (IFT) system, a set of proteins governing bidirectional transport of cargoes within ciliary axonemes. In this paper, we present a novel platform for in vivo analysis of vertebrate IFT dynamics. Using this platform, we show that the planar cell polarity (PCP) effector Fuz was required for normal IFT dynamics in vertebrate cilia, the first evidence directly linking PCP to the core machinery of ciliogenesis. Further, we show that Fuz played a specific role in trafficking of retrograde, but not anterograde, IFT proteins. These data place Fuz in the small group of known IFT effectors outside the core machinery and, additionally, identify Fuz as a novel cytoplasmic effector that differentiates between the retrograde and anterograde IFT complexes.