3D model of the olfactory bulb (Migliore et al. 2014)

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Accession:151681
This entry contains a link to a full HD version of movie 1 and the NEURON code of the paper: "Distributed organization of a brain microcircuit analysed by three-dimensional modeling: the olfactory bulb" by M Migliore, F Cavarretta, ML Hines, and GM Shepherd.
Reference:
1 . Migliore M, Cavarretta F, Hines ML, Shepherd GM (2014) Distributed organization of a brain microcircuit analysed by three-dimensional modeling: the olfactory bulb Front. Comput. Neurosci. 8:50
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network; Channel/Receptor; Dendrite;
Brain Region(s)/Organism: Olfactory bulb;
Cell Type(s): Olfactory bulb main mitral cell; Olfactory bulb main interneuron granule MC cell;
Channel(s): I Na,t; I A; I K;
Gap Junctions:
Receptor(s): NMDA; Glutamate; Gaba;
Gene(s):
Transmitter(s):
Simulation Environment: NEURON;
Model Concept(s): Pattern Recognition; Activity Patterns; Bursting; Temporal Pattern Generation; Oscillations; Synchronization; Active Dendrites; Detailed Neuronal Models; Synaptic Plasticity; Action Potentials; Synaptic Integration; Unsupervised Learning;
Implementer(s): Hines, Michael [Michael.Hines at Yale.edu]; Migliore, Michele [Michele.Migliore at Yale.edu]; Cavarretta, Francesco [francesco.cavarretta at unimi.it];
Search NeuronDB for information about:  Olfactory bulb main mitral cell; Olfactory bulb main interneuron granule MC cell; NMDA; Glutamate; Gaba; I Na,t; I A; I K;

Migliore M, Cavarretta F, Hines ML, Shepherd GM (2014) Distributed organization of a brain microcircuit analysed by three-dimensional modeling: the olfactory bulb Front. Comput. Neurosci. 8:50

References and models cited by this paper

References and models that cite this paper

Cang J, Isaacson JS (2003) In vivo whole-cell recording of odor-evoked synaptic transmission in the rat olfactory bulb. J Neurosci 23:4108-16 [PubMed]

Chen WR, Shen GY, Shepherd GM, Hines ML, Midtgaard J (2002) Multiple Modes of Action-Potential Initiation and Propagation in Mitral Cell Primary Dendrite. J Neurophysiol 88:2755-64 [Journal] [PubMed]

   Olfactory Mitral cell: AP initiation modes (Chen et al 2002) [Model]

Chen WR, Shepherd GM (1997) Membrane and synaptic properties of mitral cells in slices of rat olfactory bulb. Brain Res 745:189-96 [PubMed]

Cleland TA, Linster C (2005) Computation in the olfactory system. Chem Senses 30:801-13 [PubMed]

Cleland TA, Linster C (2012) On-Center-Inhibitory-Surround Decorrelation via Intraglomerular Inhibition in the Olfactory Bulb Glomerular Layer. Front Integr Neurosci 6:5 [PubMed]

Cuntz H, Forstner F, Borst A, Hausser M (2010) One rule to grow them all: a general theory of neuronal branching and its practical application. PLoS Comput Biol [PubMed]

Davison AP, Feng J, Brown D (2003) Dendrodendritic inhibition and simulated odor responses in a detailed olfactory bulb network model. J Neurophysiol 90:1921-1935 [Journal] [PubMed]

   Olfactory Bulb Network (Davison et al 2003) [Model]

Debarbieux F, Audinat E, Charpak S (2003) Action potential propagation in dendrites of rat mitral cells in vivo. J Neurosci 23:5553-60 [PubMed]

Donohue DE, Ascoli GA (2008) A comparative computer simulation of dendritic morphology. PLoS Comput Biol 4:e1000089 [Journal] [PubMed]

   A comparative computer simulation of dendritic morphology (Donohue and Ascoli 2008) [Model]

Egaña JI, Aylwin ML, Maldonado PE (2005) Odor response properties of neighboring mitral-tufted cells in the rat olfactory bulb. Neuroscience 134:1069-80 [PubMed]

Elsaesser R, Paysan J (2007) The sense of smell, its signalling pathways, and the dichotomy of cilia and microvilli in olfactory sensory cells. BMC Neurosci 8 Suppl 3:S1

Hines M, Kumar S, Schuermann F (2011) Comparison of neuronal spike exchange methods on a Blue Gene/P supercomputer. Frontiers in Computational Neuroscience 5:49 [Journal]

   Spike exchange methods for a Blue Gene/P supercomputer (Hines et al., 2011) [Model]

Hines ML, Carnevale NT (1997) The NEURON simulation environment. Neural Comput 9:1179-209 [PubMed]

Hines ML, Markram H, Schuermann F (2008) Fully Implicit Parallel Simulation of Single Neurons J Comp Neurosci 25:439-448 [Journal] [PubMed]

   Fully Implicit Parallel Simulation of Single Neurons (Hines et al. 2008) [Model]

Hovis KR, Padmanabhan K, Urban NN (2010) A simple method of in vitro electroporation allows visualization, recording, and calcium imaging of local neuronal circuits. J Neurosci Methods 191:1-10

Igarashi KM, Ieki N, An M, Yamaguchi Y, Nagayama S, Kobayakawa K, Kobayakawa R, Tanifuji M, S (2012) Parallel mitral and tufted cell pathways route distinct odor information to different targets in the olfactory cortex. J Neurosci 32:7970-85

Junek S, Kludt E, Wolf F, Schild D (2010) Olfactory coding with patterns of response latencies. Neuron 67:872-84 [PubMed]

Kepecs A, Uchida N, Mainen ZF (2007) Rapid and precise control of sniffing during olfactory discrimination in rats. J Neurophysiol 98:205-13 [PubMed]

Linster C, Cleland TA (2009) Glomerular microcircuits in the olfactory bulb. Neural Netw 22:1169-73 [PubMed]

Luo SX, Axel R, Abbott LF (2010) Generating sparse and selective third-order responses in the olfactory system of the fly. Proc Natl Acad Sci U S A 107:10713-8 [PubMed]

McTavish TS, Migliore M, Shepherd GM, Hines ML (2012) Mitral cell spike synchrony modulated by dendrodendritic synapse location Frontiers in Computational Neuroscience 6:3 [Journal] [PubMed]

   Synchrony by synapse location (McTavish et al. 2012) [Model]

Migliore M, Cavarretta F, Hines ML, Shepherd GM (2013) Functional neurology of a brain system: a 3D olfactory bulb model to process natural odorants. Funct Neurol 28:241-3

Migliore M, Hines M, McTavish TS, Shepherd GM (2010) Functional roles of distributed synaptic clusters in the mitral-granule cell network of the olfactory bulb Frontiers in Integrative Neuroscience 4:122 [Journal] [PubMed]

   Olfactory bulb cluster formation (Migliore et al. 2010) [Model]

Migliore M, Inzirillo C, Shepherd GM (2007) Learning mechanism for column formation in the olfactory bulb. Front Integr Neurosci 1:12 [Journal] [PubMed]

   Olfactory bulb mitral and granule cell column formation (Migliore et al. 2007) [Model]

Migliore M, Shepherd GM (2008) Dendritic action potentials connect distributed dendrodendritic microcircuits J Comp Neurosci 24(2):207-221 [Journal] [PubMed]

   Olfactory bulb mitral and granule cell: dendrodendritic microcircuits (Migliore and Shepherd 2008) [Model]

Mori K, Takagi SF (1975) Spike generation in the mitral cell dendrite of the rabbit olfactory bulb. Brain Res 100:685-9 [PubMed]

Mori K, Takahashi YK, Igarashi KM, Yamaguchi M (2006) Maps of odorant molecular features in the Mammalian olfactory bulb. Physiol Rev 86:409-33

Murthy VN (2011) Olfactory maps in the brain. Annu Rev Neurosci 34:233-58

O'Connor S, Angelo K, Jacob TJ (2012) Burst firing versus synchrony in a gap junction connected olfactory bulb mitral cell network model. Front Comput Neurosci 6:75-84 [PubMed]

Rall W, Shepherd GM (1968) Theoretical reconstruction of field potentials and dendrodendritic synaptic interactions in olfactory bulb. J Neurophysiol 31:884-915 [Journal] [PubMed]

   Theoretical reconstrucion of field potentials and dendrodendritic synaptic...(Rall & Shepherd 1968) [Model]

Rall W, Shepherd GM, Reese TS, Brightman MW (1966) Dendrodendritic synaptic pathway for inhibition in the olfactory bulb. Exp Neurol 14:44-56 [PubMed]

Royet JP, Souchier C, Jourdan F, Ploye H (1988) Morphometric study of the glomerular population in the mouse olfactory bulb: numerical density and size distribution along the rostrocaudal axis. J Comp Neurol 270:559-68

Shepherd GM, Chen WR, Greer CA (2004) Olfactory bulb The Synaptic Organization of the Brain, Shepherd GM, ed. pp.165

Sholl DA (1953) Dendritic organization in the neurons of the visual and motor cortices of the cat J Anat 87:387-406

Shusterman R, Smear MC, Koulakov AA, Rinberg D (2011) Precise olfactory responses tile the sniff cycle. Nat Neurosci 14:1039-44 [PubMed]

Smear M, Shusterman R, O'Connor R, Bozza T, Rinberg D (2011) Perception of sniff phase in mouse olfaction. Nature 479:397-400

Soucy ER, Albeanu DF, Fantana AL, Murthy VN, Meister M (2009) Precision and diversity in an odor map on the olfactory bulb. Nat Neurosci 12:210-20 [PubMed]

Stewart WB, Kauer JS, Shepherd GM (1979) Functional organization of rat olfactory bulb analysed by the 2-deoxyglucose method. J Comp Neurol 185:715-34 [PubMed]

Vincis R, Gschwend O, Bhaukaurally K, Beroud J, Carleton A (2012) Dense representation of natural odorants in the mouse olfactory bulb. Nat Neurosci 15:537-9

Wachowiak M, Shipley MT (2006) Coding and synaptic processing of sensory information in the glomerular layer of the olfactory bulb. Semin Cell Dev Biol 17:411-23 [PubMed]

Whitman MC, Greer CA (2007) Synaptic integration of adult-generated olfactory bulb granule cells: basal axodendritic centrifugal input precedes apical dendrodendritic local circuits. J Neurosci 27:9951-61 [PubMed]

Willhite DC, Nguyen KT, Masurkar AV, Greer CA, Shepherd GM, Chen WR (2006) Viral tracing identifies distributed columnar organization in the olfactory bulb. Proc Natl Acad Sci U S A 103:12592-7 [PubMed]

Wolf S, Grein S, Queisser G (2013) Employing NeuGen 2.0 to automatically generate realistic morphologies of hippocampal neurons and neural networks in 3D. Neuroinformatics 11:137-48 [PubMed]

Yokoi M, Mori K, Nakanishi S (1995) Refinement of odor molecule tuning by dendrodendritic synaptic inhibition in the olfactory bulb. Proc Natl Acad Sci U S A 92:3371-5 [PubMed]

Yu Y, McTavish TS, Valenti C, Hines ML, Shepherd GM, Migliore M (2013) Sparse distributed representation of odors in a large-scale olfactory bulb circuit PLoS Comput. Biol. 9(3):e1003014 [Journal] [PubMed]

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Zubler F, Douglas R (2009) A framework for modeling the growth and development of neurons and networks. Front Comput Neurosci 3:25-74 [PubMed]

McDougal RA, Bulanova AS, Lytton WW (2016) Reproducibility in computational neuroscience models and simulations Transactions on Biomedical Engineering, online before print [Journal]

McDougal RA, Shepherd GM (2015) 3D-printer visualization of neuron models. Front Neuroinform 9:18 [Journal] [PubMed]

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Migliore M, Cavarretta F, Marasco A, Tulumello E, Hines ML, Shepherd GM (2015) Synaptic clusters function as odor operators in the olfactory bulb PNAS 112:8499-8504 [Journal] [PubMed]

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Simoes_De_Souza FM, Antunes G, Roque AC (2014) Electrical responses of three classes of Granule Neurons of the Olfactory Bulb to synaptic Inputs in Different Dendritic Locations Front. Comput. Neurosci. 8:128 [Journal]

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