Model Calcium Sensors for Network Homeostasis: Sensor and Readout Parameter Analysis from a Database of Model Neuronal Networks

In activity-dependent homeostatic regulation (ADHR) of neuronal and network properties, the intracellular Ca2+ concentration is a good candidate for sensing activity levels because it is correlated with the electrical activity of the cell. Previous ADHR models, developed with abstract activity sensors for model pyloric neurons and networks of the crustacean stomatogastric ganglion, showed that functional activity can be maintained by a regulation mechanism that senses activity levels solely from Ca2+. At the same time, several intracellular pathways have been discovered for Ca2+-dependent regulation of ion channels. To generate testable predictions for dynamics of these signaling pathways, we undertook a parameter study of model Ca2+ sensors across thousands of model pyloric networks. We found that an optimal regulation signal can be generated for 86% of model networks with a sensing mechanism that activates with a time constant of 1 ms and that inactivates within 1 s. The sensor performed robustly around this optimal point and did not need to be specific to the role of the cell. When multiple sensors with different time constants were used, coverage extended to 88% of the networks. Without changing the sensors, it extended to 95% of the networks by letting the sensors affect the readout nonlinearly. Specific to this pyloric network model, the sensor of the follower pyloric constrictor cell was more informative than the pacemaker anterior burster cell for producing a regulatory signal. Conversely, a global signal indicating network activity that was generated by summing the sensors in individual cells was less informative for regulation.

[1]  Kenneth Levenberg A METHOD FOR THE SOLUTION OF CERTAIN NON – LINEAR PROBLEMS IN LEAST SQUARES , 1944 .

[2]  A. Hodgkin,et al.  A quantitative description of membrane current and its application to conduction and excitation in nerve , 1952, The Journal of physiology.

[3]  F ROSENBLATT,et al.  The perceptron: a probabilistic model for information storage and organization in the brain. , 1958, Psychological review.

[4]  D. Marquardt An Algorithm for Least-Squares Estimation of Nonlinear Parameters , 1963 .

[5]  Geoffrey E. Hinton,et al.  Learning representations by back-propagating errors , 1986, Nature.

[6]  James L. McClelland,et al.  Parallel distributed processing: explorations in the microstructure of cognition, vol. 1: foundations , 1986 .

[7]  W. N. Ross,et al.  Changes in intracellular calcium during neuron activity. , 1989, Annual review of physiology.

[8]  T. Murphy,et al.  L-type voltage-sensitive calcium channels mediate synaptic activation of immediate early genes , 1991, Neuron.

[9]  D. McCormick,et al.  Simulation of the currents involved in rhythmic oscillations in thalamic relay neurons. , 1992, Journal of neurophysiology.

[10]  R. Harris-Warrick,et al.  Physiological role of the transient potassium current in the pyloric circuit of the lobster stomatogastric ganglion. , 1992, Journal of neurophysiology.

[11]  L. F. Abbott,et al.  Analysis of Neuron Models with Dynamically Regulated Conductances , 1993, Neural Computation.

[12]  E. Marder,et al.  Activity-dependent regulation of conductances in model neurons. , 1993, Science.

[13]  W. R. Foster,et al.  Significance of conductances in Hodgkin-Huxley models. , 1993, Journal of neurophysiology.

[14]  E Marder,et al.  Activity-dependent current distributions in model neurons. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[15]  E. Marder,et al.  Activity-dependent changes in the intrinsic properties of cultured neurons. , 1994, Science.

[16]  G. Kane Parallel Distributed Processing: Explorations in the Microstructure of Cognition, vol 1: Foundations, vol 2: Psychological and Biological Models , 1994 .

[17]  J. Bower,et al.  An active membrane model of the cerebellar Purkinje cell. I. Simulation of current clamps in slice. , 1994, Journal of neurophysiology.

[18]  E. Marder,et al.  Selective regulation of current densities underlies spontaneous changes in the activity of cultured neurons , 1995, The Journal of neuroscience : the official journal of the Society for Neuroscience.

[19]  P. Linsdell,et al.  Electrical activity and calcium influx regulate ion channel development in embryonic Xenopus skeletal muscle , 1995, The Journal of neuroscience : the official journal of the Society for Neuroscience.

[20]  M. Greenberg,et al.  Calcium regulation of gene expression in neurons: the mode of entry matters , 1995, Current Opinion in Neurobiology.

[21]  E. Marder,et al.  Principles of rhythmic motor pattern generation. , 1996, Physiological reviews.

[22]  Karl Deisseroth,et al.  Ca2+-dependent regulation in neuronal gene expression , 1997, Current Opinion in Neurobiology.

[23]  E. Marder,et al.  A Model Neuron with Activity-Dependent Conductances Regulated by Multiple Calcium Sensors , 1998, The Journal of Neuroscience.

[24]  J. Simmers,et al.  Neuromodulatory Inputs Maintain Expression of a Lobster Motor Pattern-Generating Network in a Modulation-Dependent State: Evidence from Long-Term Decentralization In Vitro , 1998, The Journal of Neuroscience.

[25]  Niraj S. Desai,et al.  Activity-dependent scaling of quantal amplitude in neocortical neurons , 1998, Nature.

[26]  E. Marder,et al.  Activity-Dependent Regulation of Potassium Currents in an Identified Neuron of the Stomatogastric Ganglion of the Crab Cancer borealis , 1999, The Journal of Neuroscience.

[27]  Chris I. De Zeeuw,et al.  GATA-3 Is Involved in the Development of Serotonergic Neurons in the Caudal Raphe Nuclei , 1999, The Journal of Neuroscience.

[28]  H. Eng,et al.  Synthesis of β-Tubulin, Actin, and Other Proteins in Axons of Sympathetic Neurons in Compartmented Cultures , 1999, The Journal of Neuroscience.

[29]  Eve Marder,et al.  Network Stability from Activity-Dependent Regulation of Neuronal Conductances , 1999, Neural Computation.

[30]  Britt Mellström,et al.  DREAM is a Ca2+-regulated transcriptional repressor , 1999, Nature.

[31]  J. Simmers,et al.  Transition to endogenous bursting after long-term decentralization requires De novo transcription in a critical time window. , 2000, Journal of neurophysiology.

[32]  K. Rhodes,et al.  Modulation of A-type potassium channels by a family of calcium sensors , 2000, Nature.

[33]  F. E.,et al.  A Relational Model of Data Large Shared Data Banks , 2000 .

[34]  K. Deisseroth,et al.  Critical Dependence of cAMP Response Element-Binding Protein Phosphorylation on L-Type Calcium Channels Supports a Selective Response to EPSPs in Preference to Action Potentials , 2000, The Journal of Neuroscience.

[35]  Michael Bate,et al.  Altered Electrical Properties in DrosophilaNeurons Developing without Synaptic Transmission , 2001, The Journal of Neuroscience.

[36]  E. Marder,et al.  Central pattern generators and the control of rhythmic movements , 2001, Current Biology.

[37]  Bartlett W. Mel,et al.  Impact of Active Dendrites and Structural Plasticity on the Memory Capacity of Neural Tissue , 2001, Neuron.

[38]  B. Rudy,et al.  A role for frequenin, a Ca2+-binding protein, as a regulator of Kv4 K+-currents , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[39]  E. Marder,et al.  Global Structure, Robustness, and Modulation of Neuronal Models , 2001, The Journal of Neuroscience.

[40]  Britt Mellström,et al.  Mechanisms of Ca2+-dependent transcription , 2001, Current Opinion in Neurobiology.

[41]  E. Marder,et al.  Activity-dependent modification of inhibitory synapses in models of rhythmic neural networks , 2001, Nature Neuroscience.

[42]  B. Mellström,et al.  Mechanisms of Ca(2+)-dependent transcription. , 2001, Current opinion in neurobiology.

[43]  E. Marder,et al.  Failure of averaging in the construction of a conductance-based neuron model. , 2002, Journal of neurophysiology.

[44]  John Simmers,et al.  Long-term neuromodulatory regulation of a motor pattern-generating network: maintenance of synaptic efficacy and oscillatory properties. , 2002, Journal of neurophysiology.

[45]  Eve Marder,et al.  Alternative to hand-tuning conductance-based models: construction and analysis of databases of model neurons. , 2003, Journal of neurophysiology.

[46]  C. Sekirnjak,et al.  Long-Lasting Increases in Intrinsic Excitability Triggered by Inhibition , 2003, Neuron.

[47]  M. Leighton,et al.  Residues within the myristoylation motif determine intracellular targeting of the neuronal Ca2+ sensor protein KChIP1 to post-ER transport vesicles and traffic of Kv4 K+ channels , 2003, Journal of Cell Science.

[48]  R. Harris-Warrick,et al.  KChIP1 and frequenin modify shal-evoked potassium currents in pyloric neurons in the lobster stomatogastric ganglion. , 2003, Journal of neurophysiology.

[49]  Bruce R. Johnson,et al.  Activity-Independent Homeostasis in Rhythmically Active Neurons , 2003, Neuron.

[50]  E. Marder,et al.  Similar network activity from disparate circuit parameters , 2004, Nature Neuroscience.

[51]  G. Viana di Prisco,et al.  Quantitative investigation of calcium signals for locomotor pattern generation in the lamprey spinal cord. , 2004, Journal of neurophysiology.

[52]  J. Ames,et al.  Dimerization of Neuronal Calcium Sensor Proteins , 2018, Front. Mol. Neurosci..

[53]  Rajarshi Guha,et al.  Interpreting Computational Neural Network Quantitative Structure-Activity Relationship Models: A Detailed Interpretation of the Weights and Biases , 2005, J. Chem. Inf. Model..

[54]  Philipp Slusallek,et al.  Introduction to real-time ray tracing , 2005, SIGGRAPH Courses.

[55]  John Guckenheimer,et al.  Activity-independent coregulation of IA and Ih in rhythmically active neurons. , 2005, Journal of neurophysiology.

[56]  E. Marder,et al.  Variable channel expression in identified single and electrically coupled neurons in different animals , 2006, Nature Neuroscience.

[57]  M. Ronjat,et al.  Transient loss of voltage control of Ca2+ release in the presence of maurocalcine in skeletal muscle. , 2006, Biophysical journal.

[58]  Idan Segev,et al.  The Endurance and Selectivity of Spatial Patterns of Long-Term Potentiation/Depression in Dendrites under Homeostatic Synaptic Plasticity , 2006, The Journal of Neuroscience.

[59]  Erik De Schutter,et al.  Complex Parameter Landscape for a Complex Neuron Model , 2006, PLoS Comput. Biol..

[60]  R. Dolmetsch,et al.  The C Terminus of the L-Type Voltage-Gated Calcium Channel CaV1.2 Encodes a Transcription Factor , 2006, Cell.

[61]  R. Malenka,et al.  Synaptic scaling mediated by glial TNF-α , 2006, Nature.

[62]  Eve Marder,et al.  Structure and visualization of high-dimensional conductance spaces. , 2006, Journal of neurophysiology.

[63]  R. Malenka,et al.  Synaptic scaling mediated by glial TNF-alpha. , 2006, Nature.

[64]  Jean-Marc Goaillard,et al.  Quantitative expression profiling of identified neurons reveals cell-specific constraints on highly variable levels of gene expression , 2007, Proceedings of the National Academy of Sciences.

[65]  Robert J Calin-Jageman,et al.  Parameter space analysis suggests multi-site plasticity contributes to motor pattern initiation in Tritonia. , 2007, Journal of neurophysiology.

[66]  Allen I. Selverston,et al.  Artificial synaptic modification reveals a dynamical invariant in the pyloric CPG , 2008, European Journal of Applied Physiology.

[67]  R. Calabrese,et al.  Using constraints on neuronal activity to reveal compensatory changes in neuronal parameters. , 2007, Journal of neurophysiology.

[68]  Jorge Golowasch,et al.  Neuromodulators, Not Activity, Control Coordinated Expression of Ionic Currents , 2007, The Journal of Neuroscience.

[69]  P. Wenner,et al.  GABAA transmission is a critical step in the process of triggering homeostatic increases in quantal amplitude , 2008, Proceedings of the National Academy of Sciences.

[70]  G. Turrigiano,et al.  Rapid Synaptic Scaling Induced by Changes in Postsynaptic Firing , 2008, Neuron.

[71]  Cengiz Günay,et al.  Channel Density Distributions Explain Spiking Variability in the Globus Pallidus: A Combined Physiology and Computer Simulation Database Approach , 2008, The Journal of Neuroscience.

[72]  David T. Yue,et al.  Mechanism of Local and Global Ca2+ Sensing by Calmodulin in Complex with a Ca2+ Channel , 2008, Cell.

[73]  Gidon Felsen,et al.  Neural Substrates of Sensory-Guided Locomotor Decisions in the Rat Superior Colliculus , 2008, Neuron.

[74]  Erik De Schutter,et al.  Frontiers in Computational Neuroscience Calcium, Synaptic Plasticity and Intrinsic Homeostasis in Purkinje Neuron Models Materials and Methods Original Pc Model , 2022 .

[75]  Cengiz Günay,et al.  Finding sensors for homeostasis of biological neuronal networks using artificial neural networks , 2009, 2009 International Joint Conference on Neural Networks.

[76]  Cengiz Günay,et al.  Database Analysis of Simulated and Recorded Electrophysiological Datasets with PANDORA’s Toolbox , 2009, Neuroinformatics.

[77]  E. Marder,et al.  How Multiple Conductances Determine Electrophysiological Properties in a Multicompartment Model , 2009, The Journal of Neuroscience.

[78]  J. Golowasch,et al.  Activity and neuromodulatory input contribute to the recovery of rhythmic output after decentralization in a central pattern generator. , 2009, Journal of neurophysiology.

[79]  Astrid A. Prinz,et al.  Geometry and dynamics of activity-dependent homeostatic regulation in neurons , 2009, BMC Neuroscience.

[80]  Ah Chung Tsoi,et al.  Neural Network Classification and Prior Class Probabilities , 1996, Neural Networks: Tricks of the Trade.