laboratoire de physique statistique
 
 
laboratoire de physique statistique

Publications

Rechercher
 
2016
Time-invariant feed-forward inhibition of Purkinje cells in the cerebellar cortex in vivo - Blot, Antonin and de Solages, Camille and Ostojic, Srdjan and Szapiro, German and Hakim, Vincent and Lena, Clement
JOURNAL OF PHYSIOLOGY-LONDON 5942729-2749 (2016) 
LPS


Abstract : Cerebellar molecular layer interneurons are considered to control the firing rate and spike timing of Purkinje cells. However, interactions between these cell types are largely unexplored in vivo. Using tetrodes, we performed simultaneous extracellular recordings of neighbouring Purkinje cells and molecular layer interneurons, presumably basket cells, in adult rats in vivo. The high levels of afferent synaptic activity encountered in vivo yield irregular spiking and reveal discharge patterns characteristic of feed-forward inhibition, thus suggesting an overlap of the afferent excitatory inputs between Purkinje cells and basket cells. Under conditions of intense background synaptic inputs, interneuron spikes exert a short-lasting inhibitory effect, delaying the following Purkinje cell spike by an amount remarkably independent of the Purkinje cell firing cycle. This effect can be explained by the short memory time of the Purkinje cell potential as a result of the intense incoming synaptic activity. Finally, we found little evidence for any involvement of the interneurons that we recorded with the cerebellar high-frequency oscillations promoting Purkinje cell synchrony. The rapid interactions between interneurons and Purkinje cells might be of particular importance in fine motor control because the inhibitory action of interneurons on Purkinje cells leads to deep cerebellar nuclear disinhibition and hence increased cerebellar output.
MyoD reprogramming requires Six1 and Six4 homeoproteins: genome-wide cis-regulatory module analysis - Santolini, Marc and Sakakibara, Iori and Gauthier, Morgane and Ribas-Aulinas, Francesc and Takahashi, Hirotaka and Sawasaki, Tatsuya and Mouly, Vincent and Concordet, Jean-Paul and Defossez, Pierre-Antoine and Hakim, Vincent and Maire, Pascal
NUCLEIC ACIDS RESEARCH 448621-8640 (2016) 
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Abstract : Myogenic regulatory factors of the MyoD family have the ability to reprogram differentiated cells toward a myogenic fate. In this study, we demonstrate that Six1 or Six4 are required for the reprogramming by MyoD of mouse embryonic fibroblasts (MEFs). Using microarray experiments, we found 761 genes under the control of both Six and MyoD. Using MyoD ChIPseq data and a genome-wide search for Six1/4 MEF3 binding sites, we found significant co-localization of binding sites for MyoD and Six proteins on over a thousand mouse genomic DNA regions. The combination of both datasets yielded 82 genes which are synergistically activated by Six and MyoD, with 96 associated MyoD+MEF3 putative cis-regulatory modules (CRMs). Fourteen out of 19 of the CRMs that we tested demonstrated in Luciferase assays a synergistic action also observed for their cognate gene. We searched putative binding sites on these CRMs using available databases and de novo search of conserved motifs and demonstrated that the Six/MyoD synergistic activation takes place in a feedforward way. It involves the recruitment of these two families of transcription factors to their targets, together with partner transcription factors, encoded by genes that are themselves activated by Six and MyoD, including Mef2, Pbx-Meis and EBF.
Sustained Rhythmic Brain Activity Underlies Visual Motion Perception in Zebrafish - Perez-Schuster, Veronica and Kulkarni, Anirudh and Nouvian, Morgane and Romano, Sebastian A. and Lygdas, Konstantinos and Jouary, Adrien and Dippopa, Mario and Pietri, Thomas and Haudrechy, Mathieu and Candat, Virginie and Boulanger-Weill, Jonathan and Hakim, Vincent and Sumbre, German
CELL REPORTS 171098-1112 (2016) 
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Abstract : Following moving visual stimuli (conditioning stimuli, CS), many organisms perceive, in the absence of physical stimuli, illusory motion in the opposite direction. This phenomenon is known as the motion aftereffect (MAE). Here, we use MAE as a tool to study the neuronal basis of visual motion perception in zebrafish larvae. Using zebrafish eye movements as an indicator of visual motion perception, we find that larvae perceive MAE. Blocking eye movements using optogenetics during CS presentation did not affect MAE, but tectal ablation significantly weakened it. Using two-photon calcium imaging of behaving GCaMP3 larvae, we find post-stimulation sustained rhythmic activity among direction-selective tectal neurons associated with the perception of MAE. In addition, tectal neurons tuned to the CS direction habituated, but neurons in the retina did not. Finally, a model based on competition between direction-selective neurons reproduced MAE, suggesting a neuronal circuit capable of generating perception of visual motion.
 
2015
Modeling the finger instability in an expanding cell monolayer - Tarle, Victoria and Ravasio, Andrea and Hakim, Vincent and Gov, Nir S.
INTEGRATIVE BIOLOGY 71218-1227 (2015) 
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Abstract : Collective motion occurs in many biological processes, such as wound healing, tumor invasion and embryogenesis. Experiments of cell monolayer migration have revealed the spontaneous formation of finger-like instabilities, with leader cells at their tips. We present a particle-based model for collective cell migration, based on several elements that have been found experimentally to influence cellular movement. Inside the bulk we include velocity alignment interactions between neighboring cells. At the border contour of the layer we introduce the following additional forces: surface-elasticity restoring force, curvature-dependent positive feedback, and contractile acto-myosin cables. We find that the curvature-driven instability at the layer edge is necessary and sufficient for the formation of cellular fingers, which are in good agreement with experimental observations.
Neuronal Morphology Generates High-Frequency Firing Resonance - Ostojic, Srdjan and Szapiro, German and Schwartz, Eric and Barbour, Boris and Brunel, Nicolas and Hakim, Vincent
JOURNAL OF NEUROSCIENCE 357056-7068 (2015) 
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Abstract : The attenuation of neuronal voltage responses to high-frequency current inputs by the membrane capacitance is believed to limit single-cell bandwidth. However, neuronal populations subject to stochastic fluctuations can follow inputs beyond this limit. We investigated this apparent paradox theoretically and experimentally using Purkinje cells in the cerebellum, a motor structure that benefits from rapid information transfer. We analyzed the modulation of firing in response to the somatic injection of sinusoidal currents. Computational modeling suggested that, instead of decreasing with frequency, modulation amplitude can increase up to high frequencies because of cellular morphology. Electrophysiological measurements in adult rat slices confirmed this prediction and displayed a marked resonance at 200 Hz. We elucidated the underlying mechanism, showing that the two-compartment morphology of the Purkinje cell, interacting with a simple spiking mechanism and dendritic fluctuations, is sufficient to create high-frequency signal amplification. This mechanism, which we term morphology-induced resonance, is selective for somatic inputs, which in the Purkinje cell are exclusively inhibitory. The resonance sensitizes Purkinje cells in the frequency range of population oscillations observed in vivo.
From Discrete to Continuum Models of Three-Dimensional Deformations in Epithelial Sheets - Murisic, Nebojsa and Hakim, Vincent and Kevrekidis, Ioannis G. and Shvartsman, Stanislav Y. and Audoly, Basile
BIOPHYSICAL JOURNAL 109154-163 (2015) 
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Abstract : Epithelial tissue, in which cells adhere tightly to each other and to the underlying substrate, is one of the four major tissue types in adult organisms. In embryos, epithelial sheets serve as versatile substrates during the formation of developing organs. Some aspects of epithelial morphogenesis can be adequately described using vertex models, in which the two-dimensional arrangement of epithelial cells is approximated by a polygonal lattice with an energy that has contributions reflecting the properties of individual cells and their interactions. Previous studies with such models have largely focused on dynamics confined to two spatial dimensions and analyzed them numerically. We show how these models can be extended to account for three-dimensional deformations and studied analytically. Starting from the extended model, we derive a continuum plate description of cell sheets, in which the effective tissue properties, such as bending rigidity, are related explicitly to the parameters of the vertex model. To derive the continuum plate model, we duly take into account a microscopic shift between the two sub-lattices of the hexagonal network, which has been ignored in previous work. As an application of the continuum model, we analyze tissue buckling by a line tension applied along a circular contour, a simplified set-up relevant to several situations in the developmental contexts. The buckling thresholds predicted by the continuum description are in good agreement with the results of stability calculations based on the vertex model. Our results establish a direct connection between discrete and continuum descriptions of cell sheets and can be used to probe a wide range of morphogenetic processes in epithelial tissues.
 
2014
Imogene: identification of motifs and cis-regulatory modules underlying gene co-regulation - Rouault, Herve and Santolini, Marc and Schweisguth, Francois and Hakim, Vincent
NUCLEIC ACIDS RESEARCH 426128-6145 (2014) 
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Abstract : Cis-regulatory modules (CRMs) and motifs play a central role in tissue and condition-specific gene expression. Here we present Imogene, an ensemble of statistical tools that we have developed to facilitate their identification and implemented in a publicly available software. Starting from a small training set of mammalian or fly CRMs that drive similar gene expression profiles, Imogene determines de novo cis-regulatory motifs that underlie this co-expression. It can then predict on a genome-wide scale other CRMs with a regulatory potential similar to the training set. Imogene bypasses the need of large datasets for statistical analyses by making central use of the information provided by the sequenced genomes of multiple species, based on the developed statistical tools and explicit models for transcription factor binding site evolution. We test Imogene on characterized tissue-specific mouse developmental CRMs. Its ability to identify CRMs with the same specificity based on its de novo created motifs is comparable to that of previously evaluated `motif-blind' methods. We further show, both in flies and in mammals, that Imogene de novo generated motifs are sufficient to discriminate CRMs related to different developmental programs. Notably, purely relying on sequence data, Imogene performs as well in this discrimination task as a previously reported learning algorithm based on Chromatin Immunoprecipitation (ChIP) data for multiple transcription factors at multiple developmental stages.
Single neuron dynamics and computation - Brunel, Nicolas and Hakim, Vincent and Richardson, Magnus J. E.
CURRENT OPINION IN NEUROBIOLOGY 25149-155 (2014) 
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Abstract : At the single neuron level, information processing involves the transformation of input spike trains into an appropriate output spike train. Building upon the classical view of a neuron as a threshold device, models have been developed in recent years that take into account the diverse electrophysiological make-up of neurons and accurately describe their input-output relations. Here, we review these recent advances and survey the computational roles that they have uncovered for various electrophysiological properties, for dendritic arbor anatomy as well as for short-term synaptic plasticity.
Six Homeoproteins and a Iinc-RNA at the Fast MYH Locus Lock Fast Myofiber Terminal Phenotype - Sakakibara, Iori and Santolini, Marc and Ferry, Arnaud and Hakim, Vincent and Maire, Pascal
PLOS GENETICS 10 (2014) 
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Abstract : Thousands of long intergenic non-coding RNAs (lincRNAs) are encoded by the mammalian genome. However, the function of most of these lincRNAs has not been identified in vivo. Here, we demonstrate a role for a novel lincRNA, linc-MYH, in adult fast-type myofiber specialization. Fast myosin heavy chain (MYH) genes and linc-MYH share a common enhancer, located in the fast MYH gene locus and regulated by Six1 homeoproteins. linc-MYH in nuclei of fast-type myofibers prevents slow-type and enhances fast-type gene expression. Functional fast-sarcomeric unit formation is achieved by the coordinate expression of fast MYHs and linc-MYH, under the control of a common Six-bound enhancer.
DOI
10
Emergence of collective modes and tri-dimensional structures from epithelial confinement - Deforet, M. and Hakim, V. and Yevick, H. G. and Duclos, G. and Silberzan, P.
NATURE COMMUNICATIONS 5 (2014) 
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Abstract : Many in vivo processes, including morphogenesis or tumour maturation, involve small populations of cells within a spatially restricted region. However, the basic mechanisms underlying the dynamics of confined cell assemblies remain largely to be deciphered and would greatly benefit from well-controlled in vitro experiments. Here we show that confluent epithelial cells cultured on finite population-sized domains, exhibit collective low-frequency radial displacement modes as well as stochastic global rotation reversals. A simple mathematical model, in which cells are described as persistent random walkers that adapt their motion to that of their neighbours, captures the essential characteristics of these breathing oscillations. As these epithelia mature, a tri-dimensional peripheral cell cord develops at the domain edge by differential extrusion, as a result of the additional degrees of freedom of the border cells. These results demonstrate that epithelial confinement alone can induce morphogenesis-like processes including spontaneous collective pulsations and transition from 2D to 3D.
DOI
11
A General Pairwise Interaction Model Provides an Accurate Description of In Vivo Transcription Factor Binding Sites - Santolini, Marc and Mora, Thierry and Hakim, Vincent
PLOS ONE 9 (2014) 
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Abstract : The identification of transcription factor binding sites (TFBSs) on genomic DNA is of crucial importance for understanding and predicting regulatory elements in gene networks. TFBS motifs are commonly described by Position Weight Matrices (PWMs), in which each DNA base pair contributes independently to the transcription factor (TF) binding. However, this description ignores correlations between nucleotides at different positions, and is generally inaccurate: analysing fly and mouse in vivo ChIPseq data, we show that in most cases the PWM model fails to reproduce the observed statistics of TFBSs. To overcome this issue, we introduce the pairwise interaction model (PIM), a generalization of the PWM model. The model is based on the principle of maximum entropy and explicitly describes pairwise correlations between nucleotides at different positions, while being otherwise as unconstrained as possible. It is mathematically equivalent to considering a TF-DNA binding energy that depends additively on each nucleotide identity at all positions in the TFBS, like the PWM model, but also additively on pairs of nucleotides. We find that the PIM significantly improves over the PWM model, and even provides an optimal description of TFBS statistics within statistical noise. The PIM generalizes previous approaches to interdependent positions: it accounts for co-variation of two or more base pairs, and predicts secondary motifs, while outperforming multiple-motif models consisting of mixtures of PWMs. We analyse the structure of pairwise interactions between nucleotides, and find that they are sparse and dominantly located between consecutive base pairs in the flanking region of TFBS. Nonetheless, interactions between pairs of non-consecutive nucleotides are found to play a significant role in the obtained accurate description of TFBS statistics. The PIM is computationally tractable, and provides a general framework that should be useful for describing and predicting TFBSs beyond PWMs.
 
2013
DOI
12
Genome-wide analyses of Shavenbaby target genes reveals distinct features of enhancer organization - Menoret, Delphine and Santolini, Marc and Fernandes, Isabelle and Spokony, Rebecca and Zanet, Jennifer and Gonzalez, Ignacio and Latapie, Yvan and Ferrer, Pierre and Rouault, Herve and White, Kevin P. and Besse, Philippe and Hakim, Vincent and Aerts, Stein and Payre, Francois and Plaza, Serge
GENOME BIOLOGY 14 (2013) 
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Abstract : Background: Developmental programs are implemented by regulatory interactions between Transcription Factors (TFs) and their target genes, which remain poorly understood. While recent studies have focused on regulatory cascades of TFs that govern early development, little is known about how the ultimate effectors of cell differentiation are selected and controlled. We addressed this question during late Drosophila embryogenesis, when the finely tuned expression of the TF Ovo/Shavenbaby (Svb) triggers the morphological differentiation of epidermal trichomes. Results: We defined a sizeable set of genes downstream of Svb and used in vivo assays to delineate 14 enhancers driving their specific expression in trichome cells. Coupling computational modeling to functional dissection, we investigated the regulatory logic of these enhancers. Extending the repertoire of epidermal effectors using genome-wide approaches showed that the regulatory models learned from this first sample are representative of the whole set of trichome enhancers. These enhancers harbor remarkable features with respect to their functional architectures, including a weak or non-existent clustering of Svb binding sites. The in vivo function of each site relies on its intimate context, notably the flanking nucleotides. Two additional cis-regulatory motifs, present in a broad diversity of composition and positioning among trichome enhancers, critically contribute to enhancer activity. Conclusions: Our results show that Svb directly regulates a large set of terminal effectors of the remodeling of epidermal cells. Further, these data reveal that trichome formation is underpinned by unexpectedly diverse modes of regulation, providing fresh insights into the functional architecture of enhancers governing a terminal differentiation program.
DOI
13
Collective Cell Motion in an Epithelial Sheet Can Be Quantitatively Described by a Stochastic Interacting Particle Model - Sepulveda, Nestor and Petitjean, Laurence and Cochet, Olivier and Grasland-Mongrain, Erwan and Silberzan, Pascal and Hakim, Vincent
PLOS COMPUTATIONAL BIOLOGY 9 (2013) 
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Abstract : Modelling the displacement of thousands of cells that move in a collective way is required for the simulation and the theoretical analysis of various biological processes. Here, we tackle this question in the controlled setting where the motion of Madin-Darby Canine Kidney (MDCK) cells in a confluent epithelium is triggered by the unmasking of free surface. We develop a simple model in which cells are described as point particles with a dynamic based on the two premises that, first, cells move in a stochastic manner and, second, tend to adapt their motion to that of their neighbors. Detailed comparison to experimental data show that the model provides a quantitatively accurate description of cell motion in the epithelium bulk at early times. In addition, inclusion of model ``leader'' cells with modified characteristics, accounts for the digitated shape of the interface which develops over the subsequent hours, providing that leader cells invade free surface more easily than other cells and coordinate their motion with their followers. The previously-described progression of the epithelium border is reproduced by the model and quantitatively explained.
 
2012
DOI
14
Different Cell Fates from Cell-Cell Interactions: Core Architectures of Two-Cell Bistable Networks - Rouault, Herve and Hakim, Vincent
BIOPHYSICAL JOURNAL 102417-426 (2012) 
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Abstract : The acquisition of different fates by cells that are initially in the same state is central to development. Here, we investigate the possible structures of bistable genetic networks that can allow two identical cells to acquire different fates through cell-cell interactions. Cell-autonomous bistable networks have been previously sampled using an evolutionary algorithm. We extend this evolutionary procedure to take into account interactions between cells. We obtain a variety of simple bistable networks that we classify into major subtypes. Some have long been proposed in the context of lateral inhibition through the Notch-Delta pathway, some have been more recently considered and others appear to be new and based on mechanisms not previously considered. The results highlight the role of posttranscriptional interactions and particularly of protein complexation and sequestration, which can replace cooperativity in transcriptional interactions. Some bistable networks are entirely based on posttranscriptional interactions and the simplest of these is found to lead, upon a single parameter change, to oscillations in the two cells with opposite phases. We provide qualitative explanations as well as mathematical analyses of the dynamical behaviors of various created networks. The results should help to identify and understand genetic structures implicated in cell-cell interactions and differentiation.
 
2010
DOI
15
Genome-wide identification of cis-regulatory motifs and modules underlying gene coregulation using statistics and phylogeny - Rouault, Herve and Mazouni, Khalil and Couturier, Lydie and Hakim, Vincent and Schweisguth, Francois
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 10714615-14620 (2010) 
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Abstract : Cell fate determination depends in part on the establishment of specific transcriptional programs of gene expression. These programs result from the interpretation of the genomic cis-regulatory information by sequence-specific factors. Decoding this information in sequenced genomes is an important issue. Here, we developed statistical analysis tools to computationally identify the cis-regulatory elements that control gene expression in a set of coregulated genes. Starting with a small number of validated and/or predicted cis-regulatory modules (CRMs) in a reference species as a training set, but with no a priori knowledge of the factors acting in trans, we computationally predicted transcription factor binding sites (TFBSs) and genomic CRMs underlying coregulation. This method was applied to the gene expression program active in Drosophila melanogaster sensory organ precursor cells (SOPs), a specific type of neural progenitor cells. Mutational analysis showed that four, including one newly characterized, out of the five top-ranked families of predicted TFBSs were required for SOP-specific gene expression. Additionaly, 19 out of the 29 top-ranked predicted CRMs directed gene expression in neural progenitor cells, i.e., SOPs or larval brain neuroblasts, with a notable fraction active in SOPs (11/29). We further identified the lola gene as the target of two SOP-specific CRMs and found that the lola gene contributed to SOP specification. The statistics and phylogeny-based tools described here can be more generally applied to identify the cis-regulatory elements of specific gene regulatory networks in any family of related species with sequenced genomes.
 
2009
DOI
16
Electrical Coupling Mediates Tunable Low-Frequency Oscillations and Resonance in the Cerebellar Golgi Cell Network - Dugue, Guillaume P. and Brunel, Nicolas and Hakim, Vincent and Schwartz, Eric and Chat, Mireille and Levesque, Maxime and Courtemanche, Richard and Lena, Clement and Dieudonne, Stephane
NEURON 61126-139 (2009) 
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Abstract : Tonic motor control involves oscillatory synchronization of activity at low frequency (5-30 Hz) throughout the sensorimotor system, including cerebellar areas. We investigated the mechanisms underpinning cerebellar oscillations. We found that Golgi interneurons, which gate information transfer in the cerebellar cortex input layer, are extensively coupled through electrical synapses. When depolarized in vitro, these neurons displayed low-frequency oscillatory synchronization, imposing rhythmic inhibition onto granule cells. Combining experiments and modeling, we show that electrical transmission of the spike afterhyperpolarization is the essential component for oscillatory population synchronization. Rhythmic firing arises in spite of strong heterogeneities, is frequency tuned by the mean excitatory input to Golgi cells, and displays pronounced resonance when the modeled network is driven by oscillating inputs. In vivo, unitary Golgi cell activity was found to synchronize with low-frequency LFP oscillations occurring during quiet waking. These results suggest a major role for Golgi cells in coordinating cerebellar sensorimotor integration during oscillatory interactions.
DOI
17
Laws of crack motion and phase-field models of fracture - Hakim, Vincent and Karma, Alain
JOURNAL OF THE MECHANICS AND PHYSICS OF SOLIDS 57342-368 (2009) 
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Abstract : Recently proposed phase-field models offer self-consistent descriptions of brittle fracture. Here, we analyze these theories in the quasistatic regime of crack propagation. We show how to derive the laws of crack motion either by using solvability conditions in a perturbative treatment for slight departure from the Griffith threshold or by generalizing the Eshelby tensor to phase-field models. The analysis provides a simple physical interpretation of the second component of the classic Eshelby integral in the limit of vanishing crack propagation velocity: it gives the elastic torque on the crack tip that is needed to balance the Herring torque arising from the anisotropic surface energy. This force-balance condition can be interpreted physically based on energetic considerations in the traditional framework of continuum fracture mechanics, in support of its general validity for real systems beyond the scope of phase-field models. The obtained law of crack motion reduces in the quasistatic limit to the principle of local symmetry in isotropic media and to the principle of maximum energy-release-rate for smooth curvilinear cracks in anisotropic media. Analytical predictions of crack paths in anisotropic media are validated by numerical simulations. interestingly, for kinked cracks in anisotropic media, force-balance gives significantly different predictions from the principle of maximum energy-release-rate and the difference between the two criteria can be numerically tested. Simulations also show that predictions obtained from force-balance hold even if the phase-field dynamics is modified to make the failure process irreversible. Finally, the role of dissipative forces on the process zone scale as well as the extension of the results to motion of planar cracks under pure antiplane shear are discussed. (c) 2008 Elsevier Ltd. All rights reserved.
DOI
18
Synchronization properties of networks of electrically coupled neurons in the presence of noise and heterogeneities - Ostojic, Srdjan and Brunel, Nicolas and Hakim, Vincent
JOURNAL OF COMPUTATIONAL NEUROSCIENCE 26369-392 (2009) 
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Abstract : We investigate how synchrony can be generated or induced in networks of electrically coupled integrate-and-fire neurons subject to noisy and heterogeneous inputs. Using analytical tools, we find that in a network under constant external inputs, synchrony can appear via a Hopf bifurcation from the asynchronous state to an oscillatory state. In a homogeneous net work, in the oscillatory state all neurons fire in synchrony, while in a heterogeneous network synchrony is looser, many neurons skipping cycles of the oscillation. If the transmission of action potentials via the electrical synapses is effectively excitatory, the Hopf bifurcation is supercritical, while effectively inhibitory transmission due to pronounced hyperpolarization leads to a subcritical bifurcation. In the latter case, the network exhibits bistability between an asynchronous state and an oscillatory state where all the neurons fire in synchrony. Finally we show that for time-varying external inputs, electrical coupling enhances the synchronization in an asynchronous network via a resonance at the firing-rate frequency.
DOI
19
Irregular firing, quasi-stationary state and spike-time dependent response - Ostojic, Srdjan and de Solages, Camille and Szapiro, German and Lena, Clement and Hakim, Vincent
BMC NEUROSCIENCE 10 (2009) 
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DOI
20
How Connectivity, Background Activity, and Synaptic Properties Shape the Cross-Correlation between Spike Trains - Ostojic, Srdjan and Brunel, Nicolas and Hakim, Vincent
JOURNAL OF NEUROSCIENCE 2910234-10253 (2009) 
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Abstract : Functional interactions between neurons in vivo are often quantified by cross-correlation functions (CCFs) between their spike trains. It is therefore essential to understand quantitatively how CCFs are shaped by different factors, such as connectivity, synaptic parameters, and background activity. Here, we study the CCF between two neurons using analytical calculations and numerical simulations. We quantify the role of synaptic parameters, such as peak conductance, decay time, and reversal potential, and analyze how various patterns of connectivity influence CCF shapes. In particular, we find that the symmetry of the CCF distinguishes in general, but not always, the case of shared inputs between two neurons from the case in which they are directly synaptically connected. We systematically examine the influence of background synaptic inputs from the surrounding network that set the baseline firing statistics of the neurons and modulate their response properties. We find that variations in the background noise modify the amplitude of the cross-correlation function as strongly as variations of synaptic strength. In particular, we show that the postsynaptic neuron spiking regularity has a pronounced influence on CCF amplitude. This suggests an efficient and flexible mechanism for modulating functional interactions.