Colored Petri net modeling and simulation of signal transduction pathways

Presented herein is a methodology for quantitatively analyzing the complex signaling network by resorting to colored Petri nets (CPN). The mathematical as well as Petri net models for two basic reaction types were established, followed by the extension to a large signal transduction system stimulated by epidermal growth factor (EGF) in an application study. The CPN models based on the Petri net representation and the conservation and kinetic equations were used to examine the dynamic behavior of the EGF signaling pathway. The usefulness of Petri nets is demonstrated for the quantitative analysis of the signal transduction pathway. Moreover, the trade-offs between modeling capability and simulation efficiency of this pathway are explored, suggesting that the Petri net model can be invaluable in the initial stage of building a dynamic model.     

A model for signal transduction in suspension cultures of Taxus chinensis var. mairei induced by an oligosaccharide from Fusarium oxysporum

A non-linear cascade model is proposed to describe the signal transduction pathway in suspension cultures of Taxus chinensis var. mairei induced by an oligosaccharide from Fusarium oxysporum. The oxidative burst intensity, which was defined as the amount of the free radicals including superoxide anion (O² ), H₂O₂ and OH^– and measured by ESR spectrometry, was used as the signal characteristic and the theory of electronic signal transduction cascade was then applied to derive the initial model. The model shows that the signal transduction cascade process is composed of three cascade nets, represented by the phosphorylation of a G-protein, activation of an ion channel and phospholipase C, and phosphorylation of protein kinase C. The three reactions were calculated as beginning at 30.5, 48.8 and 141.4 min after elicitation, and the maximum variation rates of the signal intensity in the three nets occurred at 43.2, 80.6 and 192.6 min, respectively. The validity of the model predictions was verified by experimental data.     

Sound production and mating in a waterboatman, Palmacorixa nana (Heteroptera: Corixidae)

Both male and female Palmacorixa nana stridulate by rubbing fields of pegs on the fore femora over thickened flanges on the maxillary plates. I sugges that the head is the sound-radiating structure and is driven into oscillation when its edges are plucked by rows of femoral pegs. P. nana males produce spontaneous, courtship, mounting and copulatory signals. The latter tow signals are produced by a new mechanism which constitutes only the third record of inter-individual stridulation in insects. The known acoustic behaviour of the female is limited to a signal indicating readiness to mate. Mating behaviour was observed and copulatory success found not to rely on a complete exchange of acoustic signals. Comparison of data from several sources indicates that corixids capable of singing can either have an obligatory or optional exchange of signals.     

Transfer of light-induced electron-spin polarization from the intermediary acceptor to the prereduced primary acceptor in the reaction center of photosynthetic bacteria.

In reaction centers and chromatophores of photosynthetic bacteria strong light-induced emissive ESR signals have been found, not only after a flash but also under continuous illumination. The signal, with g = 2.0048 and delta Hpp = 7.6 G, is only present under reducing conditions in material in which the primary acceptor, ubiquinone, U and its associated high-spin ferrous ion are magnetically uncoupled. its amplitude under continuous illumination is strongly dependent on light intensity and on microwave power. The emissive signal is attributed to the prereduced primary acceptor, U-, which becomes polarized through transfer of spin polarization by a magnetic exchange interaction with the photoreduced, spin polarized intermediary acceptor, I-. A kinetic model is presented which explains the observed dependence of emissivity on light intensity and microwave power. Applying this analysis to the light saturation data, a value of the exchange rate between I- and U- of 4.10(8) s-1 is derived, corresponding to an exchange interaction of 3--5 G.     

Sensor fusion with on-line gas emission multisensor arrays and standard process measuring devices in baker's yeast manufacturing process

The use of a multisensor array for measuring the emission from a production-scale baker's yeast manufacturing process is reported. The sensor array, containing 14 different gas-sensitive semiconductor devices and an infrared gas sensor, was used to monitor the gas emission from a yeast culture bioreactor during fed-batch operation. The signal pattern from the sensors was evaluated in relation to two key process variables, the cell mass and the ethanol concentrations. Fusion with the on-line sensor signals for reactor weight and aeration rate made it possible to estimate cell mass and ethanol concentration using computation with backpropagating artificial neural nets. Identification of process states with the same fusion of sensor signals was realized using principal component analysis. (c) 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 55: 427-438, 1997.     

Homogeneous nets of neuron-like elements

Propagation and reverberation of excitation patterns are investigated for 1-dimensional and 2-dimensional homogeneous nets of neuron-like elements. A 1-dimensional net has a proper set of excitation patterns which only can be conducted in the net. Such a net has an ability of discriminating and shaping stimulus signals. Two types of self-reproducing reverberatory excitation patterns are shown for 2-dimensional homogeneous nets. An algebraic theory of general homogeneous nets is also developed.     

Estimation of Instantaneous Gas Exchange in Flow-Through Respirometry Systems: A Modern Revision of Bartholomew's Z-Transform Method

Flow-through respirometry systems provide accurate measurement of gas exchange over long periods of time. However, these systems have limitations in tracking rapid changes. When an animal infuses a metabolic gas into the respirometry chamber in a short burst, diffusion and airflow in the chamber gradually alter the original signal before it arrives at the gas analyzer. For single or multiple bursts, the recorded signal is smeared or mixed, which may result in dramatically altered recordings compared to the emitted signal. Recovering the original metabolic signal is a difficult task because of the inherent ill conditioning problem. Here, we present two new methods to recover the fast dynamics of metabolic patterns from recorded data. We first re-derive the equations of the well-known Z-transform method (ZT method) to show the source of imprecision in this method. Then, we develop a new model of analysis for respirometry systems based on the experimentally determined impulse response, which is the response of the system to a very short unit input. As a result, we present a major modification of the ZT method (dubbed the ‘EZT method’) by using a new model for the impulse response, enhancing its precision to recover the true metabolic signals. The second method, the generalized Z-transform (GZT) method, was then developed by generalizing the EZT method; it can be applied to any flow-through respirometry system with any arbitrary impulse response. Experiments verified that the accuracy of recovering the true metabolic signals is significantly improved by the new methods. These new methods can be used more broadly for input estimation in variety of physiological systems.     

A structured approach for the engineering of biochemical network models, illustrated for signalling pathways

Quantitative models of biochemical networks (signal transduction cascades, metabolic pathways, gene regulatory circuits) are a central component of modern systems biology. Building and managing these complex models is a major challenge that can benefit from the application of formal methods adopted from theoretical computing science. Here we provide a general introduction to the field of formal modelling, which emphasizes the intuitive biochemical basis of the modelling process, but is also accessible for an audience with a background in computing science and/or model engineering. We show how signal transduction cascades can be modelled in a modular fashion, using both a qualitative approach--qualitative Petri nets, and quantitative approaches--continuous Petri nets and ordinary differential equations (ODEs). We review the major elementary building blocks of a cellular signalling model, discuss which critical design decisions have to be made during model building, and present a number of novel computational tools that can help to explore alternative modular models in an easy and intuitive manner. These tools, which are based on Petri net theory, offer convenient ways of composing hierarchical ODE models, and permit a qualitative analysis of their behaviour. We illustrate the central concepts using signal transduction as our main example. The ultimate aim is to introduce a general approach that provides the foundations for a structured formal engineering of large-scale models of biochemical networks.     

Distinct roles of electric and hydraulic signals on the reaction of leaf gas exchange upon re-irrigation in Zea mays L

The hypothesis that electric and hydraulic long-distance signals modify photosynthesis and stomatal aperture upon re-irrigation in intact drought-stressed plants was examined. Maize plants (Zea mays L.) were exposed to drought conditions by decreasing the soil water content to 40-50% of field capacity. The decrease in water content resulted in a decline in stomatal conductance to 50-60% of the level in well-watered plants. Re-irrigation of the plants initiated both hydraulic and electric signals, followed by a two-phase response of the net CO2 uptake rate and stomatal conductance of leaves. The transitional first phase (phase 1) is characterized by a rapid decrease in both levels. In the second phase (phase 2), both parameters gradually increase to levels above those of drought-stressed plants. Elimination of either the hydraulic signal by compensatory pressure application to the root system, or of the electric signal by cooling of the leaf blade gave evidence that the two signals (1) propagated independently from each other and (2) triggered the two-phase response in leaf gas exchange. The results provided evidence that the hydraulic signal initiated a hydropassive decrease in stomatal aperture and for the involvement of electric signals in the regulation of photosynthesis of drought-stressed plants.     

Reaction of bovine cytochrome c oxidase with hydrogen peroxide produces a tryptophan cation radical and a porphyrin cation radical

Oxidized bovine cytochrome c oxidase reacts with hydrogen peroxide to generate two electron paramagnetic resonance (EPR) free radical signals (Fabian, M., and Palmer, G. (1995) Biochemistry 34, 13802-13810). These radicals are associated with the binuclear center and give rise to two overlapped EPR signals, one signal being narrower in line width (DeltaHptp = 12 G) than the other (DeltaHptp = 45 G). We have used electron nuclear double resonance (ENDOR) spectrometry to identify the two different chemical species giving rise to these two EPR signals. Comparison of the ENDOR spectrum associated with the narrow signal with that of compound I of horseradish peroxidase (formed by reaction of that enzyme with hydrogen peroxide) demonstrates that the two species are virtually identical. The chemical species giving rise to the narrow signal is therefore identified as an exchange-coupled porphyrin cation radical similar to that formed in horseradish peroxidase compound I. Comparison of the ENDOR spectrum of compound ES (formed by the reaction of hydrogen peroxide with cytochrome c peroxidase) with that of the broad signal indicates that the chemical species giving rise to the broad EPR signal in cytochrome c oxidase is probably an exchange coupled tryptophan cation radical. This is substantiated using H(2)O/D(2)O solvent exchange experiments where the ENDOR difference spectrum of the broad EPR signal of cytochrome c oxidase shows a feature consistent with hyperfine coupling to the exchangeable N(1) proton of a tryptophan cation radical.     

Transfer of light-induced electron-spin polarization from the intermediary acceptor to the prereduced primary acceptor in the reaction center of photosynthetic bacteria

In reaction centers and chromatophores of photosynthetic bacteria strong light-induced emissive ESR signals have been found, not only after a flash, but also under continuous illumination. The signal, with g = 2.0048 and ΔH_pp = 7.6 G, is only present under reducing conditions in material in which the primary acceptor, ubiquinone, U and its associated high-spin ferrous ion are magnetically uncoupled. Its amplitude under continuous illumination is strongly dependent on light intensity and on microwave power.

The emissive signal is attributed to the prereduced primary acceptor, U⁻, which becomes polarized through transfer of spin polarization by a magnetic exchange interaction with the photoreduced, spin polarized intermediary acceptor, I⁻. A kinetic model is presented which explains the observed dependence of emissivity on light intensity and microwave power. Applying this analysis to the light saturation data, a value of the exchange rate between I⁻ and U⁻ of 4 · 10⁸ s⁻¹ is derived, corresponding to an exchange interaction of 3–5 G.     

Saccade control in a simulated robot camera-head system: neural net architectures for efficient learning of inverse kinematics

The high speed of saccades means that they cannot be guided by visual feedback, so that any saccadic control system must know in advance the correct output signals to fixate a particular retinal position. To investigate neural-net architectures for learning this inverse-kinematics problem we simulated a 4 deg-of-freedom robot camera-head system, in which the head could pan and tilt and the cameras pan and verge. The main findings were: (1) Linear nets, multilayer perceptrons (MLPs) trained by backpropagation, and cerebellar model arithmetic computers (CMACs) all learnt rapidly to 5–10% accuracy when given perfect error feedback. (2) For additional accuracy (down to 2%) two-layer nets learnt much faster than a single MLP or CMAC: the best combination tried was to have a CMAC learn the errors of a trained linear net. (3) Imperfect error signals were provided by a crude controller whose output was simply proportional to retinal input in the relevant axis, thereby providing a mechanism for (a) controlling the camera-head system when the feedforward neural net controller was wrong or inoperative, and (b) converting sensory error signals into motor error signals as required in supervised learning. It proved possible to train neural-net controllers using these imperfect error signals over a range of learning rates and crude-controller gains. These results suggest that appropriate neural-net architectures can provide practical, accurate and robust adaptive control for saccadic movements. In addition, the arrangement of a crude controller teaching a sophisticated one may be similar to that used by the primate saccadic system, with brainstem circuitry teaching the cerebellum.     

Calcium signal communication in the central nervous system

The communication of calcium signals between cells is known to be operative between neurons where these signals integrate intimately with electrical and chemical signal communication at synapses. Recently, it has become clear that glial cells also exchange calcium signals between each other in cultures and in brain slices. This communication pathway has received utmost attention since it is known that astrocytic calcium signals can be induced by neuronal stimulation and can be communicated back to the neurons to modulate synaptic transmission. In addition to this, cells that are generally not considered as brain cells become progressively incorporated in the picture, as astrocytic calcium signals are reported to be communicated to endothelial cells of the vessel wall and can affect smooth muscle cell tone to influence the vessel diameter and thus blood flow. We review the available evidence for calcium signal communication in the central nervous system, taking into account a basic functional unit -the brain cell tripartite- consisting of neurons, glial cells and vascular cells and with emphasis on glial-vascular calcium signaling aspects.     

Characteristics and plasticity of electrical synaptic transmission

Electrical synapses are an omnipresent feature of nervous systems, from the simple nerve nets of cnidarians to complex brains of mammals. Formed by gap junction channels between neurons, electrical synapses allow direct transmission of voltage signals between coupled cells. The relative simplicity of this arrangement belies the sophistication of these synapses. Coupling via electrical synapses can be regulated by a variety of mechanisms on times scales ranging from milliseconds to days, and active properties of the coupled neurons can impart emergent properties such as signal amplification, phase shifts and frequency-selective transmission. This article reviews the biophysical characteristics of electrical synapses and some of the core mechanisms that control their plasticity in the vertebrate central nervous system.     

Quaternary structure changes in a second Per-Arnt-Sim domain mediate intramolecular redox signal relay in the NifL regulatory protein

Per-Arnt-Sim (PAS) domains play a critical role in signal transduction in multidomain proteins by sensing diverse environmental signals and regulating the activity of output domains. Multiple PAS domains are often found within a single protein. The NifL regulatory protein from Azotobacter vinelandii contains tandem PAS domains, the most N-terminal of which, PAS1, contains a FAD cofactor and is responsible for redox sensing, whereas the second PAS domain, PAS2, has no apparent cofactor and its function is unknown. Amino acid substitutions in PAS2 were identified that either lock NifL in a form that constitutively inhibits NifA or that fail to respond to the redox status, suggesting that PAS2 plays a pivotal role in transducing the redox signal from PAS1 to the C-terminal output domains. The isolated PAS2 domain is a homodimer in solution and the subunits are in rapid exchange. PAS2 dimerization is maintained in the redox signal transduction mutants, but is inhibited by substitutions in PAS2 that lock NifL in the inhibitory conformer. Our results support a model for signal transduction in NifL, whereby redox-dependent conformational changes in PAS1 are relayed to the C-terminal domains via changes in the quaternary structure of the PAS2 domain.     

Two-H-bonded and one-H-bonded structure alternations in collagen

This paper concerns the conformational variability of collagen as related to the concrete tripeptides (GXY)n constituting its primary structure. The previously elaborated model (V.G.Tumanyan, N.G.Esipova, Biophysics 28, 1021-1025, 1983) with two nets of hydrogen bonds is useful for tripeptides where X is an amino acid. If X is an imino acid, the common one-bonded Rich & Crick model is valid. In this work, compound sequences including tripeptides of different types are considered. Molecular mechanics is used to assess the conformations of the junction regions when a structure with two nets of hydrogen bonds precedes the structure with one net, and vice versa. Thus, all types of sequences typical for natural collagen are covered. It is shown that the combined model representing an alternation of the two-H-bonded model and the one-H-bonded Rich & Crick model is satisfactory stereochemically, and provides more favorable energy in comparison with the continuous one-H-bonded model. Besides, a more favorable hydration of the molecule occures in this case. Some conclusions are made about interchain and intrachain ionic bonds. Thus, it is deduced for the concrete fibrillar protein how a one-dimensional structure determines three-dimensional structure. The macromolecular structure thus suggested is in accord with the experimental data on hydrogen exchange.     

Proton NMR detection of porphyrins and cytochrome C in small unilamellar vesicles: role of the dissociation kinetic constant

The molecular tumbling of small unilamellar vesicles is not fast enough to enable the detection of (1)H NMR signals of molecules associated with phospholipids. We show that relatively fast kinetic exchange of the interacting molecules is able to induce a strong decrease of the residual homonuclear dipolar coupling, allowing the acquisition of sharp signals. At low molecule/lipids molecular ratio, this can be lead to signal broadening due to exchange at intermediate rates on the NMR chemical timescale. However, proton resonances can be easily detected when sufficient lipids are added to prevent the occurrence of any free compounds in solution. This is demonstrated, using lipid signal suppression, in the case of paramagnetic porphyrin derivatives as well as diamagnetic hematoporphyrin. Since several peptides and proteins are expected to be associated with lipids having relatively fast dynamics, this study addresses, as a first example, the interaction of cytochrome c.     

Trans-kingdom Cross-Talk: Small RNAs on the Move

This review focuses on the mobility of small RNA (sRNA) molecules from the perspective of trans-kingdom gene silencing. Mobility of sRNA molecules within organisms is a well-known phenomenon, facilitating gene silencing between cells and tissues. sRNA signals are also transmitted between organisms of the same species and of different species. Remarkably, in recent years many examples of RNA-signal exchange have been described to occur between organisms of different kingdoms. These examples are predominantly found in interactions between hosts and their pathogens, parasites, and symbionts. However, they may only represent the tip of the iceberg, since the emerging picture suggests that organisms in biological niches commonly exchange RNA-silencing signals. In this case, we need to take this into account fully to understand how a given biological equilibrium is obtained. Despite many observations of trans-kingdom RNA signal transfer, several mechanistic aspects of these signals remain unknown. Such RNA signal transfer is already being exploited for practical purposes, though. Pathogen genes can be silenced by plant-produced sRNAs designed to affect these genes. This is also known as Host-Induced Genes Silencing (HIGS), and it has the potential to become an important disease-control method in the future.     

核定位信号及其在病毒感染机制中的研究进展

核定位信号介导的蛋白入核是细胞内信号传递网络中核内外物质信息交流的重要一环,绝大多数病毒蛋白进入细胞核均需要核质转运受体识别和结合入核蛋白携带的核定位信号序列。病毒蛋白的入核转运机制在病毒感染过程中起着至关重要的作用,对于病毒的复制、毒力具有重要意义,针对该机制的研究有利于新的抗病毒靶点的发现。本文对核定位信号的分类信息进行了总结,并对不同的核质转运受体及其介导的入核机制进行了比较分析,概述了病毒入核蛋白及其核定位信号在病毒感染机制中的研究发现。