细胞信号转导网络的建模

细胞信号转导网络的组织和调控是十分复杂的。目前,结合试验数据,借助计算机建模的方法,进行信号转导网络的研究颤受关注。介绍了信号通路数学建模的步骤、方法,描述了当前信号转导网络建模的不同类型的模型及各自的优缺点。此外,还以G蛋白偶联受体模型为例,详细阐述了模型的层次问题,探讨了信号转导建模所面临的挑战及其未来的发展趋势。     

Transfer Functions for Protein Signal Transduction: Application to a Model of Striatal Neural Plasticity

We present a novel formulation for biochemical reaction networks in the context of protein signal transduction. The model consists of input-output transfer functions, which are derived from differential equations, using stable equilibria. We select a set of “source” species, which are interpreted as input signals. Signals are transmitted to all other species in the system (the “target” species) with a specific delay and with a specific transmission strength. The delay is computed as the maximal reaction time until a stable equilibrium for the target species is reached, in the context of all other reactions in the system. The transmission strength is the concentration change of the target species. The computed input-output transfer functions can be stored in a matrix, fitted with parameters, and even recalled to build dynamical models on the basis of state changes. By separating the temporal and the magnitudinal domain we can greatly simplify the computational model, circumventing typical problems of complex dynamical systems. The transfer function transformation of biochemical reaction systems can be applied to mass-action kinetic models of signal transduction. The paper shows that this approach yields significant novel insights while remaining a fully testable and executable dynamical model for signal transduction. In particular we can deconstruct the complex system into local transfer functions between individual species. As an example, we examine modularity and signal integration using a published model of striatal neural plasticity. The modularizations that emerge correspond to a known biological distinction between calcium-dependent and cAMP-dependent pathways. Remarkably, we found that overall interconnectedness depends on the magnitude of inputs, with higher connectivity at low input concentrations and significant modularization at moderate to high input concentrations. This general result, which directly follows from the properties of individual transfer functions, contradicts notions of ubiquitous complexity by showing input-dependent signal transmission inactivation.     

Spike Timing-Dependent Synaptic Plasticity in Visual Cortex: A Modeling Study

Recent studies show that synaptic modification depends critically on the relative spike timing of pre- and postsynaptic neurons. Here we explore the functional implications of spike timing-dependent synaptic plasticity in the visual cortex using a model circuit with modifiable intracortical excitatory connections. First we simulated the experiments using two-point stimuli, in which two visual stimuli in a topographically represented feature space were repeatedly presented in quick succession, and found that tuning of the cortical neurons was modified in a manner similar to that observed experimentally. We then explored the dependence of results on the model parameter and identified the intracortical parameters that were critical for the magnitude of the shifts and obtained a simple relationship between the amount of shift and (S = (_EXTC^rec_exc)/_INHC^rec_inh). Finally we investigated the effects of moving stimuli in a topographically represented visual space and found that they can effectively induce spike timing-dependent modification of the intracortical connections. It suggests the importance of moving stimuli in dynamic modification of the cortical maps through spike timing-dependent synaptic plasticity.     

AMPA受体的磷酸化与突触可塑性

突触可塑性在学习记忆中发挥了重要作用,AMPA(α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid,AMPA)受体功能和运输的调节是突触可塑性机制研究的重要环节。在突触可塑性发生过程中,激酶和磷酸酶能够调节AMPA受体C末端的磷酸化水平,进而影响AMPA受体运输。对于AMPA受体磷酸化的研究能够加深我们对突触可塑性机制的理解。     

Synaptic Plasticity in Medial Vestibular Nucleus Neurons: Comparison with Computational Requirements of VOR Adaptation

Background

Vestibulo-ocular reflex (VOR) gain adaptation, a longstanding experimental model of cerebellar learning, utilizes sites of plasticity in both cerebellar cortex and brainstem. However, the mechanisms by which the activity of cortical Purkinje cells may guide synaptic plasticity in brainstem vestibular neurons are unclear. Theoretical analyses indicate that vestibular plasticity should depend upon the correlation between Purkinje cell and vestibular afferent inputs, so that, in gain-down learning for example, increased cortical activity should induce long-term depression (LTD) at vestibular synapses.

Methodology/Principal Findings

Here we expressed this correlational learning rule in its simplest form, as an anti-Hebbian, heterosynaptic spike-timing dependent plasticity interaction between excitatory (vestibular) and inhibitory (floccular) inputs converging on medial vestibular nucleus (MVN) neurons (input-spike-timing dependent plasticity, iSTDP). To test this rule, we stimulated vestibular afferents to evoke EPSCs in rat MVN neurons in vitro. Control EPSC recordings were followed by an induction protocol where membrane hyperpolarizing pulses, mimicking IPSPs evoked by flocculus inputs, were paired with single vestibular nerve stimuli. A robust LTD developed at vestibular synapses when the afferent EPSPs coincided with membrane hyperpolarisation, while EPSPs occurring before or after the simulated IPSPs induced no lasting change. Furthermore, the iSTDP rule also successfully predicted the effects of a complex protocol using EPSP trains designed to mimic classical conditioning.

Conclusions

These results, in strong support of theoretical predictions, suggest that the cerebellum alters the strength of vestibular synapses on MVN neurons through hetero-synaptic, anti-Hebbian iSTDP. Since the iSTDP rule does not depend on post-synaptic firing, it suggests a possible mechanism for VOR adaptation without compromising gaze-holding and VOR performance in vivo.     

Thematic Minireview Series: Molecular Mechanisms of Synaptic Plasticity

The human brain contains ∼86 billion neurons, which are precisely organized in specific brain regions and nuclei. High fidelity synaptic communication between subsets of neurons in specific circuits is required for most human behaviors, and is often disrupted in neuropsychiatric disorders. The presynaptic axon terminals of one neuron release neurotransmitters that activate receptors on multiple postsynaptic neuron targets to induce electrical and chemical responses. Typically, postsynaptic neurons integrate signals from multiple presynaptic neurons at thousands of synaptic inputs to control downstream communication to the next neuron in the circuit. Importantly, the strength (or efficiency) of signal transmission at each synapse can be modulated on time scales ranging up to the lifetime of the organism. This “synaptic plasticity” leads to changes in overall neuronal circuit activity, resulting in behavioral modifications. This series of minireviews will focus on recent advances in our understanding of the molecular and cellular mechanisms that control synaptic plasticity.     

Regulation of AMPA Receptor Activity, Synaptic Targeting and Recycling: Role in Synaptic Plasticity

The alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors for the neurotransmitter glutamate are oligomeric structures responsible for most fast excitatory responses in the central nervous system. The activity of AMPA receptors can be directly regulated by protein phosphorylation, which may also affect the interaction with intracellular proteins and, consequently, their recycling and localization to defined postsynaptic sites. This review focuses on recent advances in understanding the dynamic regulation of AMPA receptors, on a short- and long-term basis, and its implications in synaptic plasticity.     

Structural Components of Synaptic Plasticity and Memory Consolidation

Consolidation of implicit memory in the invertebrate Aplysia and explicit memory in the mammalian hippocampus are associated with remodeling and growth of preexisting synapses and the formation of new synapses. Here, we compare and contrast structural components of the synaptic plasticity that underlies these two distinct forms of memory. In both cases, the structural changes involve time-dependent processes. Thus, some modifications are transient and may contribute to early formative stages of long-term memory, whereas others are more stable, longer lasting, and likely to confer persistence to memory storage. In addition, we explore the possibility that trans-synaptic signaling mechanisms governing de novo synapse formation during development can be reused in the adult for the purposes of structural synaptic plasticity and memory storage. Finally, we discuss how these mechanisms set in motion structural rearrangements that prepare a synapse to strengthen the same memory and, perhaps, to allow it to take part in other memories as a basis for understanding how their anatomical representation results in the enhanced expression and storage of memories in the brain.Santiago Ramón y Cajal (1894) used the insights provided by his remarkable light microscopic observations of neurons selectively stained with the Golgi method to propose the first cellular theory of memory storage as an anatomical change in the functional connections between nerve cells, later called synapses (Sherrington 1897). For most of the last century, chemical synapses were thought to convey information in only one direction—from the presynaptic to the postsynaptic neuron. It now is clear that synaptic transmission is a bidirectional and self-modifiable form of cell–cell communication (Peters et al. 1976; Jessell and Kandel 1993). This appreciation of reciprocal signaling between pre- and postsynaptic elements is consistent with other forms of intercellular communication and provides a conceptual framework for understanding memory-induced changes in the structure of the synapse. Indeed, an increasing body of evidence suggests that trans-synaptic signaling and coordinated recruitment of pre- and postsynaptic mechanisms underlie consolidation of both implicit and explicit forms of memory storage (Marrone 2005; Hawkins et al. 2006; Bailey et al. 2008).Studies in a variety of systems have found that molecular mechanisms of consolidation and long-term storage of memory begin at the level of the synapse. Existing proteins are modified, signals are sent back to the nucleus so that specific genes are expressed, and gene products are transported back to the synapse where the local synthesis of new protein is triggered to allow for the remodeling, addition, and elimination of synapses (Bailey and Kandel 1985; Bailey et al. 1996; Kandel 2001; Bourne and Harris 2008, 2012). These structural components of synaptic plasticity are thought to represent a cellular change that contributes to both implicit and explicit memory consolidation (Greenough and Bailey 1988; Bailey and Kandel 1993; Bailey et al. 2005; Bourne and Harris 2008, 2012). The association between alterations in the structure and/or number of synapses and memory storage has led to numerous studies regarding the signaling pathways that might couple molecular changes to structural changes. In addition, parallel homeostatic mechanisms have been identified that can trigger synaptic scaling, which serves to stabilize the strengthened synapses while weakening or eliminating other synapses, thus providing specificity during memory consolidation (Bourne and Harris 2011; Schacher and Hu 2014).In this review, we compare and contrast structural changes at the synapse during both implicit and explicit memory consolidation, as well as the molecular signaling pathways that initiate the learning-induced structural changes versus those that serve to maintain these changes over time. Toward that end, we will focus on two experimental model systems and several prototypic forms of synaptic plasticity that we have worked on and that have been extensively studied as representative examples of memory storage: long-term habituation and sensitization of the gill-withdrawal reflex in Aplysia. These are examples of implicit memory consolidation and hippocampal-based long-term potentiation (LTP) and long-term depression (LTD), as candidate mechanisms for the synaptic plasticity underlying explicit memory storage in mammals. These will serve as useful points of comparison to consider similarities, differences, and still-existing limitations in our understanding of the functional significance of the structural synaptic plasticity recruited during the consolidation of both implicit and explicit forms of memory.     

Ethylene Receptors: Ethylene Perception and Signal Transduction

Ethylene is sensed by a family of receptors that can be divided into two subfamilies based on phylogenetic analysis and some shared structural features. In this review we focus on the mechanistic aspects of how the receptors function in plants to transduce the ethylene signal. Recent work has led to new insights into how ethylene binds to the receptors and how this binding may induce a conformational change to regulate signaling. Additional studies point to several possible mechanisms for signal output by the receptors, which may involve changes in enzymatic activity and/or conformational changes. Other studies indicate the importance of interactions, both physical and genetic, between the receptors and early components of the signaling pathway, in particular, the Raf-like kinase CTR1, which functions as an integral component of the ethylene receptor signaling complex. The current model for signaling in Arabidopsis supports differing contributions from the receptors, with subfamily-1 receptors playing a more significant role than the subfamily-2 receptors in transmitting the ethylene signal.     

Precise-Spike-Driven Synaptic Plasticity: Learning Hetero-Association of Spatiotemporal Spike Patterns

A new learning rule (Precise-Spike-Driven (PSD) Synaptic Plasticity) is proposed for processing and memorizing spatiotemporal patterns. PSD is a supervised learning rule that is analytically derived from the traditional Widrow-Hoff rule and can be used to train neurons to associate an input spatiotemporal spike pattern with a desired spike train. Synaptic adaptation is driven by the error between the desired and the actual output spikes, with positive errors causing long-term potentiation and negative errors causing long-term depression. The amount of modification is proportional to an eligibility trace that is triggered by afferent spikes. The PSD rule is both computationally efficient and biologically plausible. The properties of this learning rule are investigated extensively through experimental simulations, including its learning performance, its generality to different neuron models, its robustness against noisy conditions, its memory capacity, and the effects of its learning parameters. Experimental results show that the PSD rule is capable of spatiotemporal pattern classification, and can even outperform a well studied benchmark algorithm with the proposed relative confidence criterion. The PSD rule is further validated on a practical example of an optical character recognition problem. The results again show that it can achieve a good recognition performance with a proper encoding. Finally, a detailed discussion is provided about the PSD rule and several related algorithms including tempotron, SPAN, Chronotron and ReSuMe.     

乙烯信号的接受与转导

对乙烯信号转导途径的相关组分、乙烯信号的转导途径以及乙烯信号感知和转导的可能机制研究的最新进展进行了简要介绍,并对今后这一领域的研究方向和在农业上的应用前景进行了探讨.     

植物水分胁迫信号识别与转导

植物对水分胁迫信号作出反应,需要经过信号的识别,转导和胞间信使传递等过程,该文从胁迫感觉,第二信使系统及蛋白质可逆磷酸化等方面,介绍了植物细胞对水分胁迫（原初 ）信号和胁迫信号分子（脱落酸）识别转导的研究进展。     

Coordination of Protein Phosphorylation and Dephosphorylation in Synaptic Plasticity

A central theme in nervous system function is equilibrium: synaptic strengths wax and wane, neuronal firing rates adjust up and down, and neural circuits balance excitation with inhibition. This push/pull regulatory theme carries through to the molecular level at excitatory synapses, where protein function is controlled through phosphorylation and dephosphorylation by kinases and phosphatases. However, these opposing enzymatic activities are only part of the equation as scaffolding interactions and assembly of multi-protein complexes are further required for efficient, localized synaptic signaling. This review will focus on coordination of postsynaptic serine/threonine kinase and phosphatase signaling by scaffold proteins during synaptic plasticity.     

Modulation of Hippocampus-Dependent Learning and Synaptic Plasticity by Nicotine

A long-standing relationship between nicotinic acetylcholine receptors (nAChRs) and cognition exists. Drugs that act at nAChRs can have cognitive-enhancing effects and diseases that disrupt cognition such as Alzheimer's disease and schizophrenia are associated with altered nAChR function. Specifically, hippocampus-dependent learning is particularly sensitive to the effects of nicotine. However, the effects of nicotine on hippocampus-dependent learning vary not only with the doses of nicotine used and whether nicotine is administered acutely, chronically, or withdrawn after chronic nicotine treatment but also vary across different hippocampus-dependent tasks such as the Morris water maze, the radial arm maze, and contextual fear conditioning. In addition, nicotine has variable effects across different types of hippocampal long-term potentiation (LTP). Because different types of hippocampus-dependent learning and LTP involve different neural and molecular substrates, comparing the effects of nicotine across these paradigms can yield insights into the mechanisms that may underlie the effects of nicotine on learning and memory and aid in understanding the variable effects of nicotine on cognitive processes. This review compares and contrasts the effects of nicotine on hippocampus-dependent learning and LTP and briefly discusses how the effects of nicotine on learning could contribute to nicotine addiction.     

Signal Transduction: From the Atomic Age to the Post-Genomic Era

We have come a long way in the 55 years since Edmond Fischer and the late Edwin Krebs discovered that the activity of glycogen phosphorylase is regulated by reversible protein phosphorylation. Many of the fundamental molecular mechanisms that operate in biological signaling have since been characterized and the vast web of interconnected pathways that make up the cellular signaling network has been mapped in considerable detail. Nonetheless, it is important to consider how fast this field is still moving and the issues at the current boundaries of our understanding. One must also appreciate what experimental strategies have allowed us to attain our present level of knowledge. We summarize here some key issues (both conceptual and methodological), raise unresolved questions, discuss potential pitfalls, and highlight areas in which our understanding is still rudimentary. We hope these wide-ranging ruminations will be useful to investigators who carry studies of signal transduction forward during the rest of the 21st century.     

Cell Volume-Induced Hormone Secretion: Signal Transduction and Specificity

Maintenance of the cell volume within physiological limits under anisosmotic conditions is an important prerequisite for survival and functioning of the cell. Cell volume alterations are also involved in numerous cellular events and are recently considered to be integrated into a physiological signal transduction network. Cell swelling induced by anisosmotic environment, hormones, oxidative stress, or substrate uptake evokes an immediate secretory burst of the material (peptide hormones, enzymes) stored in secretory vesicles from various types of cells (endocrine cells, neurons, leukocytes, exocrine pancreatic cells). The dynamics of this secretion are indistinguishable from those induced by specific secretagogues. This regulated secretion does not require a rise in the intracellular Ca²⁺. Using various tissues (pituitary, pancreatic islets, brain structures), hormones (prolactin, insulin, thyrotropin - releasing hormone - TRH, oxytocin), and inhibitors, we found that hormone secretion induced by cell swelling is not depressed by inhibition of stretch-activated channels (GdCl₃), mercury-sensitive aquaporins, protein kinase C (bisindolylmaleimide), microtubules and microfilaments (colchicine, cytochalasin)and does not involve arachidonic acid metabolites, prostaglandins and leukotrienes (indomethacin, NDGA). The blockade of Na⁺-K⁺-dependent ATPase, that of Na⁺ channels, or that of K⁺ channels exerted no effect on hyposmolarity-induced hormone secretion in pituitary cells. Norepinephrine, a physiological inhibitor of secretion of insulin, did not inhibit hypotonicity-induced secretion from pancreatic islets. The participation of such a general biophysical phenomenon in physiological reactions raises a question of its specificity. Cell swelling induced by an isosmotic ethanol-containing medium evoked release of TRH from hypothalamic paraventricular nucleus and posterior pituitary, while oxytocin (known to be engaged in the water and salt regulation) release was not stimulated. Neirofiziologiya/Neurophysiology, Vol. 37, No. 2, pp. 177–180, March–April, 2005.