Neuronal Network Analysis

From brain slice to freely moving mouse, optical methods are being used to probe single neuron physiology and neural circuit function. Efforts in physics, engineering, and genetics have resulted in novel techniques that permit more refined optical interrogation of brain function. The field of optogenetics has enabled neural activity to be driven by light, while optical read-out of neural activity has been improved in terms of speed, spatial resolution, and imaging depth. Genetically encoded sensors and activators of neural activity can now be expressed in cell subtypes helping us to understand neural circuits with unprecedented detail and specificity. In this chapter, we discuss some of the currently available optical methods while highlighting their relative strengths and weaknesses.

[1]  G. Loeb,et al.  R. Lemon , 1985, Neuroscience.

[2]  G. L. Masson,et al.  Feedback inhibition controls spike transfer in hybrid thalamic circuits , 2002, Nature.

[3]  S. Retterer,et al.  Dexamethasone treatment reduces astroglia responses to inserted neuroprosthetic devices in rat neocortex , 2005, Experimental Neurology.

[4]  Donald W. Bouldin,et al.  A Cluster Separation Measure , 1979, IEEE Transactions on Pattern Analysis and Machine Intelligence.

[5]  P. Somogyi,et al.  Neuronal Diversity and Temporal Dynamics: The Unity of Hippocampal Circuit Operations , 2008, Science.

[6]  C. Wilson,et al.  Capacitance compensation and bridge balance adjustment in intracellular recording from dendritic neurons , 1989, Journal of Neuroscience Methods.

[7]  J. Glowinski,et al.  Influence of the hippocampus on interneurons of the rat prefrontal cortex , 2004, The European journal of neuroscience.

[8]  A. Bacci,et al.  Enhancement of Spike-Timing Precision by Autaptic Transmission in Neocortical Inhibitory Interneurons , 2006, Neuron.

[9]  D. Szarowski,et al.  Cerebral Astrocyte Response to Micromachined Silicon Implants , 1999, Experimental Neurology.

[10]  D. Dijk,et al.  Effect of unilateral somatosensory stimulation prior to sleep on the sleep EEG in humans , 1994, Journal of sleep research.

[11]  P. Achermann,et al.  Mathematical models of sleep regulation. , 2003, Frontiers in bioscience : a journal and virtual library.

[12]  Andrew B. Schwartz,et al.  Brain-Controlled Interfaces: Movement Restoration with Neural Prosthetics , 2006, Neuron.

[13]  Vincenzo Crunelli,et al.  NeuReal: An interactive simulation system for implementing artificial dendrites and large hybrid networks , 2008, Journal of Neuroscience Methods.

[14]  Farzan Nadim,et al.  Synaptic Dynamics Do Not Determine Proper Phase of Activity in a Central Pattern Generator , 2005, The Journal of Neuroscience.

[15]  Arnaud Delorme,et al.  EEGLAB: an open source toolbox for analysis of single-trial EEG dynamics including independent component analysis , 2004, Journal of Neuroscience Methods.

[16]  Sean L. Hill,et al.  Sleep homeostasis and cortical synchronization: I. Modeling the effects of synaptic strength on sleep slow waves. , 2007, Sleep.

[17]  Paul H M Kullmann,et al.  Implementation of a fast 16-Bit dynamic clamp using LabVIEW-RT. , 2004, Journal of neurophysiology.

[18]  大村 友博.  Society for Neuroscience 39^ Annual Meeting に参加して , 2010 .

[19]  Andrew B Schwartz,et al.  Cortical neural prosthetics. , 2004, Annual review of neuroscience.

[20]  L. Geddes.  Electrodes and the measurement of bioelectric events , 1972 .

[21]  Alexander S. Ecker,et al.  Recording chronically from the same neurons in awake, behaving primates. , 2007, Journal of neurophysiology.

[22]  Randy M Bruno,et al.  Feedforward Mechanisms of Excitatory and Inhibitory Cortical Receptive Fields , 2002, The Journal of Neuroscience.

[23]  H. Robinson,et al.  Injection of digitally synthesized synaptic conductance transients to measure the integrative properties of neurons , 1993, Journal of Neuroscience Methods.

[24]  Giulio Tononi,et al.  Exploratory behavior, cortical BDNF expression, and sleep homeostasis. , 2007, Sleep.

[25]  Sharad Ramanathan,et al.  Optical interrogation of neural circuits in Caenorhabditis elegans , 2009, Nature Methods.

[26]  Johannes J. Letzkus,et al.  Axon Initial Segment Kv1 Channels Control Axonal Action Potential Waveform and Synaptic Efficacy , 2007, Neuron.

[27]  K. Deisseroth,et al.  Parvalbumin neurons and gamma rhythms enhance cortical circuit performance , 2009, Nature.

[28]  V. Vyazovskiy,et al.  Handedness leads to interhemispheric EEG asymmetry during sleep in the rat. , 2008, Journal of neurophysiology.

[29]  S. Royer,et al.  Cell-type-specific GABA responses and chloride homeostasis in the cortex and amygdala. , 2001, Journal of neurophysiology.

[30]  F. A. Wilson,et al.  Functional stability of dorsolateral prefrontal neurons. , 2004, Journal of neurophysiology.

[31]  B. Connors,et al.  Intrinsic firing patterns of diverse neocortical neurons , 1990, Trends in Neurosciences.

[32]  Radford M. Neal.  Pattern Recognition and Machine Learning , 2007, Technometrics.

[33]  Michele Giugliano,et al.  The Impact of Input Fluctuations on the Frequency–Current Relationships of Layer 5 Pyramidal Neurons in the Rat Medial Prefrontal Cortex , 2007, The Journal of Neuroscience.

[34]  Y. Kubota,et al.  GABAergic cell subtypes and their synaptic connections in rat frontal cortex. , 1997, Cerebral cortex.

[35]  J. Lacaille,et al.  Interneuron Diversity series: Hippocampal interneuron classifications – making things as simple as possible, not simpler , 2003, Trends in Neurosciences.

[36]  G. Tamás,et al.  Excitatory Effect of GABAergic Axo-Axonic Cells in Cortical Microcircuits , 2006, Science.

[37]  T. Murphy,et al.  Automated light-based mapping of motor cortex by photoactivation of channelrhodopsin-2 transgenic mice , 2009, Nature Methods.

[38]  P. Celada,et al.  Activation of pyramidal cells in rat medial prefrontal cortex projecting to ventral tegmental area by a 5-HT1A receptor agonist , 2006, European Neuropsychopharmacology.

[39]  A. Borbély.  A two process model of sleep regulation. , 1982, Human neurobiology.

[40]  Anthony A Grace,et al.  Entorhinal cortex inhibits medial prefrontal cortex and modulates the activity states of electrophysiologically characterized pyramidal neurons in vivo. , 2009, Cerebral cortex.

[41]  P. Jonas,et al.  Shunting Inhibition Improves Robustness of Gamma Oscillations in Hippocampal Interneuron Networks by Homogenizing Firing Rates , 2006, Neuron.

[42]  A. Zaitsev,et al.  Properties of excitatory synaptic responses in fast-spiking interneurons and pyramidal cells from monkey and rat prefrontal cortex. , 2006, Cerebral cortex.

[43]  Romain Brette,et al.  High-Resolution Intracellular Recordings Using a Real-Time Computational Model of the Electrode , 2007, Neuron.

[44]  David A Lewis,et al.  Functional properties of fast spiking interneurons and their synaptic connections with pyramidal cells in primate dorsolateral prefrontal cortex. , 2005, Journal of neurophysiology.

[45]  A. Prinz,et al.  Phase resetting and phase locking in hybrid circuits of one model and one biological neuron. , 2004, Biophysical journal.

[46]  A. Nieder,et al.  Complementary Contributions of Prefrontal Neuron Classes in Abstract Numerical Categorization , 2008, The Journal of Neuroscience.

[47]  Stéphane Charpier,et al.  Feedforward Inhibition of Projection Neurons by Fast-Spiking GABA Interneurons in the Rat Striatum In Vivo , 2005, The Journal of Neuroscience.

[48]  Astrid A Prinz,et al.  Predictions of phase-locking in excitatory hybrid networks: excitation does not promote phase-locking in pattern-generating networks as reliably as inhibition. , 2009, Journal of neurophysiology.

[49]  A. Destexhe.  Kinetic Models of Synaptic Transmission , 1997 .

[50]  M. Stecker,et al.  Classification of the extracellular fields produced by activated neural structures , 2005, Biomedical engineering online.

[51]  E. P. Gardner,et al.  Petilla terminology: nomenclature of features of GABAergic interneurons of the cerebral cortex , 2008, Nature Reviews Neuroscience.

[52]  Tamás F Freund,et al.  Interneuron Diversity series: Rhythm and mood in perisomatic inhibition , 2003, Trends in Neurosciences.

[53]  Giulio Tononi,et al.  Modeling sleep and wakefulness in the thalamocortical system. , 2005, Journal of neurophysiology.

[54]  P. Somogyi,et al.  Brain-state- and cell-type-specific firing of hippocampal interneurons in vivo , 2003, Nature.

[55]  T. Freund,et al.  Cholinergic synapses in the rat brain: a correlated light and electron microscopic immunohistochemical study employing a monoclonal antibody against choline acetyltransferase , 1984, Brain Research.

[56]  V. Vyazovskiy,et al.  Fast track:Unilateral vibrissae stimulation during waking induces interhemispheric EEG asymmetry during subsequent sleep in the rat , 2000, Journal of sleep research.

[57]  H. Markram,et al.  Redistribution of synaptic efficacy between neocortical pyramidal neurons , 1996, Nature.

[58]  Y. Kawaguchi,et al.  Two distinct activity patterns of fast-spiking interneurons during neocortical UP states , 2008, Proceedings of the National Academy of Sciences.

[59]  C. Gray,et al.  Chattering Cells: Superficial Pyramidal Neurons Contributing to the Generation of Synchronous Oscillations in the Visual Cortex , 1996, Science.

[60]  Matthew J Nelson,et al.  Do electrode properties create a problem in interpreting local field potential recordings? , 2010, Journal of neurophysiology.

[61]  G. Buzsáki,et al.  Characterization of neocortical principal cells and interneurons by network interactions and extracellular features. , 2004, Journal of neurophysiology.

[62]  D. Prince,et al.  Major Differences in Inhibitory Synaptic Transmission onto Two Neocortical Interneuron Subclasses , 2003, The Journal of Neuroscience.

[63]  Juha Voipio,et al.  GABAergic Depolarization of the Axon Initial Segment in Cortical Principal Neurons Is Caused by the Na–K–2Cl Cotransporter NKCC1 , 2008, The Journal of Neuroscience.

[64]  O. Paulsen,et al.  Spike Timing of Distinct Types of GABAergic Interneuron during Hippocampal Gamma Oscillations In Vitro , 2004, The Journal of Neuroscience.

[65]  Stefano Fusi,et al.  The dynamical response properties of neocortical neurons to temporally modulated noisy inputs in vitro. , 2008, Cerebral cortex.

[66]  Michael Okun,et al.  The Subthreshold Relation between Cortical Local Field Potential and Neuronal Firing Unveiled by Intracellular Recordings in Awake Rats , 2010, The Journal of Neuroscience.

[67]  P. Tresco,et al.  Response of brain tissue to chronically implanted neural electrodes , 2005, Journal of Neuroscience Methods.

[68]  P. Jonas,et al.  Synaptic mechanisms of synchronized gamma oscillations in inhibitory interneuron networks , 2007, Nature Reviews Neuroscience.

[69]  G. Tononi,et al.  Sleep and synaptic homeostasis: a hypothesis , 2003, Brain Research Bulletin.

[70]  R. Segev,et al.  A method for spike sorting and detection based on wavelet packets and Shannon's mutual information , 2002, Journal of Neuroscience Methods.

[71]  Allen I. Selverston,et al.  StdpC: A modern dynamic clamp , 2006, Journal of Neuroscience Methods.

[72]  Arnold R Kriegstein,et al.  Blind patch clamp recordings in embryonic and adult mammalian brain slices , 2006, Nature Protocols.

[73]  Ravi V. Bellamkonda,et al.  Dexamethasone-coated neural probes elicit attenuated inflammatory response and neuronal loss compared to uncoated neural probes , 2007, Brain Research.

[74]  G. Buzsáki,et al.  Interneurons of the hippocampus , 1998, Hippocampus.

[75]  A.J. Preyer,et al.  Causes of Transient Instabilities in the Dynamic Clamp , 2009, IEEE Transactions on Neural Systems and Rehabilitation Engineering.

[76]  R. Quian Quiroga,et al.  Unsupervised Spike Detection and Sorting with Wavelets and Superparamagnetic Clustering , 2004, Neural Computation.

[77]  F. A. Seiler,et al.  Numerical Recipes in C: The Art of Scientific Computing , 1989 .

[78]  B. Gähwiler,et al.  Target cell-specific modulation of transmitter release at terminals from a single axon. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[79]  Michael Grätzel,et al.  Photoelectrochemical cells , 2001, Nature.

[80]  P. Somogyi,et al.  Target-cell-specific facilitation and depression in neocortical circuits , 1998, Nature Neuroscience.

[81]  Jerald D. Kralik,et al.  Chronic, multisite, multielectrode recordings in macaque monkeys , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[82]  J. Borst,et al.  In vivo dynamic clamp study of I(h) in the mouse inferior colliculus. , 2010, Journal of neurophysiology.

[83]  A. Destexhe,et al.  The high-conductance state of neocortical neurons in vivo , 2003, Nature Reviews Neuroscience.

[84]  Peter Jonas,et al.  Patch-clamp recording from mossy fiber terminals in hippocampal slices , 2006, Nature Protocols.

[85]  A. Destexhe,et al.  Synaptic background activity controls spike transfer from thalamus to cortex , 2005, Nature Neuroscience.

[86]  William W. Lytton.  Optimizing Synaptic Conductance Calculation for Network Simulations , 1996, Neural Computation.

[87]  Jerald D. Kralik,et al.  Techniques for long-term multisite neuronal ensemble recordings in behaving animals. , 2001, Methods.

[88]  Kuei Yuan Tseng,et al.  Excitatory response of prefrontal cortical fast‐spiking interneurons to ventral tegmental area stimulation in vivo , 2006, Synapse.

[89]  G. Tononi,et al.  Effects of skilled training on sleep slow wave activity and cortical gene expression in the rat. , 2009, Sleep.

[90]  Geoffrey E. Hinton,et al.  SMEM Algorithm for Mixture Models , 1998, Neural Computation.

[91]  W. Gerstner,et al.  Dynamic I-V curves are reliable predictors of naturalistic pyramidal-neuron voltage traces. , 2008, Journal of neurophysiology.

[92]  L. Mukhametov,et al.  Unihemispheric sleep deprivation in bottlenose dolphins , 1992, Journal of sleep research.

[93]  Sten Grillner,et al.  Global Neuroinformatics: The International Neuroinformatics Coordinating Facility , 2007, The Journal of Neuroscience.

[94]  T. Freund,et al.  Differences between Somatic and Dendritic Inhibition in the Hippocampus , 1996, Neuron.

[95]  K. Honda,et al.  Dawn of the evolution of photoelectrochemistry , 2004 .

[96]  J. Bezdek,et al.  FCM: The fuzzy c-means clustering algorithm , 1984 .

[97]  Michele Giugliano,et al.  Fast Calculation of Short-Term Depressing Synaptic Conductances , 1999, Neural Computation.

[98]  Tim Gollisch,et al.  From response to stimulus: adaptive sampling in sensory physiology , 2007, Current Opinion in Neurobiology.

[99]  D. Dijk,et al.  Frontal predominance of a relative increase in sleep delta and theta EEG activity after sleep loss in humans. , 1999, Sleep research online : SRO.

[100]  D. McCormick,et al.  Comparative electrophysiology of pyramidal and sparsely spiny stellate neurons of the neocortex. , 1985, Journal of neurophysiology.

[101]  Richard Miles,et al.  Interneuron Diversity series: Fast in, fast out – temporal and spatial signal processing in hippocampal interneurons , 2004, Trends in Neurosciences.

[102]  Matthew Fellows,et al.  On the variability of manual spike sorting , 2004, IEEE Transactions on Biomedical Engineering.

[103]  K. Svoboda,et al.  The subcellular organization of neocortical excitatory connections , 2009, Nature.

[104]  Gillespie,et al.  Exact numerical simulation of the Ornstein-Uhlenbeck process and its integral. , 1996, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[105]  Eve Marder,et al.  The dynamic clamp comes of age , 2004, Trends in Neurosciences.

[106]  Eve Marder,et al.  Animal-to-Animal Variability in Motor Pattern Production in Adults and during Growth , 2005, The Journal of Neuroscience.

[107]  B. Connors,et al.  Two dynamically distinct inhibitory networks in layer 4 of the neocortex. , 2003, Journal of neurophysiology.

[108]  G. Tononi,et al.  Molecular and electrophysiological evidence for net synaptic potentiation in wake and depression in sleep , 2008, Nature Neuroscience.

[109]  Lorin S Milescu,et al.  Real-time kinetic modeling of voltage-gated ion channels using dynamic clamp. , 2008, Biophysical journal.

[110]  Robert J Butera,et al.  MRCI: a flexible real-time dynamic clamp system for electrophysiology experiments , 2004, Journal of Neuroscience Methods.

[111]  Arnold R Kriegstein,et al.  GABA Regulates Excitatory Synapse Formation in the Neocortex via NMDA Receptor Activation , 2008, The Journal of Neuroscience.

[112]  T. Sejnowski,et al.  Fluctuating synaptic conductances recreate in vivo-like activity in neocortical neurons , 2001, Neuroscience.

[113]  B. McNaughton,et al.  Firing characteristics of deep layer neurons in prefrontal cortex in rats performing spatial working memory tasks. , 1998, Cerebral cortex.

[114]  Ronald Wilders,et al.  Dynamic clamp: a powerful tool in cardiac electrophysiology , 2006, The Journal of physiology.

[115]  Johannes J. Letzkus,et al.  Dendritic patch-clamp recording , 2006, Nature Protocols.

[116]  P. Somogyi,et al.  Defined types of cortical interneurone structure space and spike timing in the hippocampus , 2005, The Journal of physiology.

[117]  S. Shoham,et al.  Patterned Optical Activation of Retinal Ganglion Cells , 2007, 2007 29th Annual International Conference of the IEEE Engineering in Medicine and Biology Society.

[118]  Pierre Giraud,et al.  Paired-recordings from synaptically coupled cortical and hippocampal neurons in acute and cultured brain slices , 2008, Nature Protocols.

[119]  Yi Zhou,et al.  Spike sorting based on automatic template reconstruction with a partial solution to the overlapping problem , 2004, Journal of Neuroscience Methods.

[120]  G. Tononi,et al.  Sleep function and synaptic homeostasis. , 2006, Sleep medicine reviews.

[121]  A. Borbély,et al.  Sleep EEG in the rat as a function of prior waking. , 1986, Electroencephalography and clinical neurophysiology.

[122]  E. Marder,et al.  Dynamic clamp: computer-generated conductances in real neurons. , 1993, Journal of neurophysiology.