Designing Tools for Assumption-Proof Brain Mapping

Can we develop technologies to systematically map classical mechanisms throughout the brain, while retaining the flexibility to investigate new mechanisms as they are discovered? We discuss principles of scalable, flexible technologies that could yield comprehensive maps of brain function.

[1]  R. MacKinnon,et al.  Phospholipids and the origin of cationic gating charges in voltage sensors , 2006, Nature.

[2]  C. Nicholson,et al.  Biophysical Properties of Brain Extracellular Space Explored with Ion-Selective Microelectrodes, Integrative Optical Imaging and Related Techniques , 2007 .

[3]  S. Hestrin,et al.  A network of fast-spiking cells in the neocortex connected by electrical synapses , 1999, Nature.

[4]  P. Scheiffele,et al.  SAM68 Regulates Neuronal Activity-Dependent Alternative Splicing of Neurexin-1 , 2011, Cell.

[5]  Arthur R. Houweling,et al.  Behavioural report of single neuron stimulation in somatosensory cortex , 2008, Nature.

[6]  Andreas Lüthi,et al.  Perineuronal Nets Protect Fear Memories from Erasure , 2009, Science.

[7]  R. Nicoll,et al.  Endogenous cannabinoids mediate retrograde signalling at hippocampal synapses , 2001, Nature.

[8]  Henry H. Yin,et al.  Dopaminergic Control of Corticostriatal Long-Term Synaptic Depression in Medium Spiny Neurons Is Mediated by Cholinergic Interneurons , 2006, Neuron.

[9]  Suhasa B. Kodandaramaiah,et al.  Automated whole-cell patch clamp electrophysiology of neurons in vivo , 2012, Nature Methods.

[10]  Shannon Saszik,et al.  A Mammalian Retinal Bipolar Cell Uses Both Graded Changes in Membrane Voltage and All-or-Nothing Na+ Spikes to Encode Light , 2012, The Journal of Neuroscience.

[11]  S. Nelson,et al.  Cell-type–based model explaining coexpression patterns of genes in the brain , 2011, Proceedings of the National Academy of Sciences.

[12]  Roger Y Tsien,et al.  Very long-term memories may be stored in the pattern of holes in the perineuronal net , 2013, Proceedings of the National Academy of Sciences.

[13]  Allan R. Jones,et al.  Genome-wide atlas of gene expression in the adult mouse brain , 2007, Nature.

[14]  E. Kandel,et al.  Nitric Oxide Acts Directly in the Presynaptic Neuron to Produce Long-Term Potentiationin Cultured Hippocampal Neurons , 1996, Cell.

[15]  Eve Marder,et al.  Plasticity in the Neurotransmitter Repertoire , 2013, Science.

[16]  D. Johnston,et al.  Regulation of Synaptic Efficacy by Coincidence of Postsynaptic APs and EPSPs , 1997 .

[17]  J. Fiala,et al.  Dendritic spines disappear with chilling but proliferate excessively upon rewarming of mature hippocampus , 2004, Neuroscience.

[18]  Hannah Monyer,et al.  Gap Junctions between Interneurons Are Required for Normal Spatial Coding in the Hippocampus and Short-Term Spatial Memory , 2011, The Journal of Neuroscience.

[19]  Alan Carleton,et al.  Long term functional plasticity of sensory inputs mediated by olfactory learning , 2014, eLife.

[20]  Josef Spacek,et al.  Extracellular sheets and tunnels modulate glutamate diffusion in hippocampal neuropil , 2013, The Journal of comparative neurology.

[21]  Boris Barbour,et al.  Ultra-rapid axon-axon ephaptic inhibition of cerebellar Purkinje cells by the pinceau , 2014, Nature Neuroscience.

[22]  M. Bear,et al.  Regulation of distinct AMPA receptor phosphorylation sites during bidirectional synaptic plasticity , 2000, Nature.

[23]  Daniel J. R. Christensen,et al.  Sleep Drives Metabolite Clearance from the Adult Brain , 2013, Science.

[24]  G. G. Stokes "J." , 1890, The New Yale Book of Quotations.

[25]  Pramod K Dash,et al.  Disruption of the perineuronal net in the hippocampus or medial prefrontal cortex impairs fear conditioning. , 2013, Learning & memory.

[26]  Eric R Kandel,et al.  The molecular biology of memory: cAMP, PKA, CRE, CREB-1, CREB-2, and CPEB , 2012, Molecular Brain.

[27]  M. Larkum,et al.  NMDA spikes enhance action potential generation during sensory input , 2014, Nature Neuroscience.

[28]  Eve Marder,et al.  Correlations in ion channel expression emerge from homeostatic tuning rules , 2013, Proceedings of the National Academy of Sciences.

[29]  O. Prospero-Garcia,et al.  Reliability of Spike Timing in Neocortical Neurons , 1995 .

[30]  Anthony M Zador,et al.  Differences in Sensitivity to Neural Timing among Cortical Areas , 2012, The Journal of Neuroscience.

[31]  E. Kandel,et al.  A Neuronal Isoform of the Aplysia CPEB Has Prion-Like Properties , 2003, Cell.

[32]  Yuriy Mishchenko On optical detection of densely labeled synapses in neuropil and mapping connectivity with combinatorially multiplexed fluorescent synaptic markers , 2010 .

[33]  Srinivas C. Turaga,et al.  Connectomic reconstruction of the inner plexiform layer in the mouse retina , 2013, Nature.

[34]  Jan M. Rabaey,et al.  Physical principles for scalable neural recording , 2013, Front. Comput. Neurosci..

[35]  H. Markram,et al.  Neuropeptide and calcium‐binding protein gene expression profiles predict neuronal anatomical type in the juvenile rat , 2005, The Journal of physiology.

[36]  P. Detwiler,et al.  Directionally selective calcium signals in dendrites of starburst amacrine cells , 2002, Nature.

[37]  Stephen J. Smith,et al.  Deep molecular diversity of mammalian synapses: why it matters and how to measure it , 2012, Nature Reviews Neuroscience.

[38]  P. Negulescu,et al.  Characterization of voltage-gated sodium-channel blockers by electrical stimulation and fluorescence detection of membrane potential , 2006, Nature Biotechnology.

[39]  R. Segev,et al.  How silent is the brain: is there a “dark matter” problem in neuroscience? , 2006, Journal of Comparative Physiology A.

[40]  Stefan R. Pulver,et al.  Ultra-sensitive fluorescent proteins for imaging neuronal activity , 2013, Nature.

[41]  J. D. Sweatt,et al.  Epigenetic mechanisms in memory formation , 2010, International Journal of Developmental Neuroscience.

[42]  Srinivas C. Turaga,et al.  Space-time wiring specificity supports direction selectivity in the retina , 2014, Nature.

[43]  Thomas J Younts,et al.  Endogenous cannabinoid signaling at inhibitory interneurons , 2014, Current Opinion in Neurobiology.

[44]  Stefan Leutgeb,et al.  Neurotransmitter Switching in the Adult Brain Regulates Behavior , 2013, Science.

[45]  J. Sanes,et al.  Can molecules explain long-term potentiation? , 1999, Nature Neuroscience.

[46]  M. Kramer,et al.  Beyond the Connectome: The Dynome , 2014, Neuron.

[47]  John R. Carlson,et al.  Non-synaptic inhibition between grouped neurons in an olfactory circuit , 2012, Nature.

[48]  Stephen J. Smith,et al.  Array Tomography: A New Tool for Imaging the Molecular Architecture and Ultrastructure of Neural Circuits , 2007, Neuron.

[49]  Hongkui Zeng,et al.  Correlated gene expression and target specificity demonstrate excitatory projection neuron diversity. , 2015, Cerebral cortex.

[50]  Hassana K. Oyibo,et al.  Sequencing the Connectome , 2012, PLoS biology.

[51]  B. Connors,et al.  Two networks of electrically coupled inhibitory neurons in neocortex , 1999, Nature.

[52]  E. Callaway,et al.  Excitatory cortical neurons form fine-scale functional networks , 2005, Nature.

[53]  Kristina D. Micheva,et al.  Array Tomography: A New Tool for Imaging the Molecular Architecture and Ultrastructure of Neural Circuits , 2007, Neuron.

[54]  K. Deisseroth,et al.  Millisecond-timescale, genetically targeted optical control of neural activity , 2005, Nature Neuroscience.

[55]  R. Tsien,et al.  Synergies and Coincidence Requirements between NO, cGMP, and Ca2+ in the Induction of Cerebellar Long-Term Depression , 1997, Neuron.

[56]  D. McCormick,et al.  Modulation of intracortical synaptic potentials by presynaptic somatic membrane potential , 2006, Nature.

[57]  M. Wilson,et al.  Coordinated memory replay in the visual cortex and hippocampus during sleep , 2007, Nature Neuroscience.

[58]  M. Bear,et al.  A Cholinergic Mechanism for Reward Timing within Primary Visual Cortex , 2013, Neuron.

[59]  Jeff W Lichtman,et al.  Why not connectomics? , 2013, Nature Methods.

[60]  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.

[61]  A. J. Castiglioni,et al.  Cell-Specific Alternative Splicing Increases Calcium Channel Current Density in the Pain Pathway , 2004, Neuron.

[62]  Louis K. Scheffer,et al.  A visual motion detection circuit suggested by Drosophila connectomics , 2013, Nature.

[63]  E. Miller,et al.  Different time courses of learning-related activity in the prefrontal cortex and striatum , 2005, Nature.

[64]  Joseph E. LeDoux,et al.  Cardiovascular responses elicited by stimulation of neurons in the central amygdaloid nucleus in awake but not anesthetized rats resemble conditioned emotional responses , 1987, Brain Research.

[65]  G. E. Vates,et al.  A Paravascular Pathway Facilitates CSF Flow Through the Brain Parenchyma and the Clearance of Interstitial Solutes, Including Amyloid β , 2012, Science Translational Medicine.

[66]  E. Boyden,et al.  Simultaneous whole-animal 3D-imaging of neuronal activity using light-field microscopy , 2014, Nature Methods.

[67]  K. Mullis,et al.  Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. , 1985, Science.

[68]  Cori Bargmann Beyond the connectome: How neuromodulators shape neural circuits , 2012, BioEssays : news and reviews in molecular, cellular and developmental biology.

[69]  Kristen M. Harris,et al.  Warmer preparation of hippocampal slices prevents synapse proliferation that might obscure LTP-related structural plasticity , 2007, Neuropharmacology.

[70]  Spencer L. Smith,et al.  Dendritic spikes enhance stimulus selectivity in cortical neurons in vivo , 2013, Nature.

[71]  Eric R. Kandel,et al.  Aplysia CPEB Can Form Prion-like Multimers in Sensory Neurons that Contribute to Long-Term Facilitation , 2010, Cell.

[72]  C. Schroeder,et al.  Neuronal Oscillations and Multisensory Interaction in Primary Auditory Cortex , 2007, Neuron.

[73]  Sen Song,et al.  Highly Nonrandom Features of Synaptic Connectivity in Local Cortical Circuits , 2005, PLoS biology.

[74]  Anatol C. Kreitzer,et al.  Retrograde Inhibition of Presynaptic Calcium Influx by Endogenous Cannabinoids at Excitatory Synapses onto Purkinje Cells , 2001, Neuron.

[75]  Rosa Cao,et al.  The hemo-neural hypothesis: on the role of blood flow in information processing. , 2008, Journal of neurophysiology.

[76]  Z. J. Zhou,et al.  Starburst amacrine cells change from spiking to nonspiking neurons during retinal development. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[77]  M. Carandini,et al.  Inhibition dominates sensory responses in awake cortex , 2012, Nature.

[78]  K. Fox,et al.  The role of nitric oxide in pre-synaptic plasticity and homeostasis , 2013, Front. Cell. Neurosci..

[79]  Hajime Hirase,et al.  Astrocyte calcium signaling transforms cholinergic modulation to cortical plasticity in vivo , 2011, Neuroscience Research.

[80]  Yuriy Mishchenko,et al.  Automation of 3D reconstruction of neural tissue from large volume of conventional serial section transmission electron micrographs , 2009, Journal of Neuroscience Methods.

[81]  J. Lisman,et al.  The molecular basis of CaMKII function in synaptic and behavioural memory , 2002, Nature Reviews Neuroscience.

[82]  K. Harris,et al.  Slices Have More Synapses than Perfusion-Fixed Hippocampus from both Young and Mature Rats , 1999, The Journal of Neuroscience.

[83]  Thomas C. Südhof,et al.  Presynaptic Neurexin-3 Alternative Splicing trans-Synaptically Controls Postsynaptic AMPA Receptor Trafficking , 2013, Cell.

[84]  D. Pinkel,et al.  Supporting Online Material Materials and Methods Figs. S1 and S2 Tables S1 and S2 References Combined Analog and Action Potential Coding in Hippocampal Mossy Fibers , 2022 .

[85]  E Marder,et al.  Modulators with Convergent Cellular Actions Elicit Distinct Circuit Outputs , 2001, The Journal of Neuroscience.

[86]  Mu-ming Poo,et al.  Self-Control in Decision-Making Involves Modulation of the vmPFC Valuation System , 2012 .

[87]  Christof Koch,et al.  Ephaptic coupling of cortical neurons , 2011, Nature Neuroscience.

[88]  K. Svoboda,et al.  Estimating intracellular calcium concentrations and buffering without wavelength ratioing. , 2000, Biophysical journal.

[89]  Terrence J. Sejnowski,et al.  Astrocytes contribute to gamma oscillations and recognition memory , 2014, Proceedings of the National Academy of Sciences.

[90]  H. Markram,et al.  Interneurons of the neocortical inhibitory system , 2004, Nature Reviews Neuroscience.

[91]  B. Giepmans,et al.  Immunolabeling artifacts and the need for live-cell imaging , 2012, Nature Methods.

[92]  A. Araque,et al.  Tripartite synapses: glia, the unacknowledged partner , 1999, Trends in Neurosciences.

[93]  Henry Markram,et al.  Combinatorial Expression Rules of Ion Channel Genes in Juvenile Rat (Rattus norvegicus) Neocortical Neurons , 2012, PloS one.

[94]  L. Acsády,et al.  Serotonergic control of the hippocampus via local inhibitory interneurons. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[95]  N. Spitzer,et al.  Illumination controls differentiation of dopamine neurons regulating behaviour , 2008, Nature.

[96]  Mriganka Sur,et al.  Nucleus basalis-enabled stimulus-specific plasticity in the visual cortex is mediated by astrocytes , 2012, Proceedings of the National Academy of Sciences.

[97]  John S. Satterlee,et al.  Molecular neuroanatomy: a generation of progress , 2014, Trends in Neurosciences.

[98]  G Büldt,et al.  Photoactive mitochondria: in vivo transfer of a light-driven proton pump into the inner mitochondrial membrane of Schizosaccharomyces pombe. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[99]  R. Huganir,et al.  PKM-ζ is not required for hippocampal synaptic plasticity, learning and memory , 2013, Nature.

[100]  C. Koch,et al.  The origin of extracellular fields and currents — EEG, ECoG, LFP and spikes , 2012, Nature Reviews Neuroscience.

[101]  G. Perea,et al.  Tripartite synapses: astrocytes process and control synaptic information , 2009, Trends in Neurosciences.

[102]  M. Bear,et al.  Reward Timing in the Primary Visual Cortex , 2006, Science.

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

[104]  H. Khorana,et al.  Studies on polynucleotides. XCVI. Repair replications of short synthetic DNA's as catalyzed by DNA polymerases. , 1971, Journal of molecular biology.

[105]  R. Yuste,et al.  The Brain Activity Map Project and the Challenge of Functional Connectomics , 2012, Neuron.

[106]  D. Black,et al.  A CaMK IV responsive RNA element mediates depolarization-induced alternative splicing of ion channels , 2001, Nature.

[107]  P. Scheiffele,et al.  Alternative Splicing Controls Selective Trans-Synaptic Interactions of the Neuroligin-Neurexin Complex , 2006, Neuron.

[108]  J. Kauer,et al.  Hippocampal interneurons are excited via serotonin-gated ion channels. , 1997, Journal of neurophysiology.

[109]  Philipp J. Keller,et al.  Light-sheet functional imaging in fictively behaving zebrafish , 2014, Nature Methods.

[110]  S. Hestrin,et al.  Cell-type identity: a key to unlocking the function of neocortical circuits , 2009, Current Opinion in Neurobiology.

[111]  N. Spitzer Activity-dependent neurotransmitter respecification , 2012, Nature Reviews Neuroscience.

[112]  J. McGann,et al.  Fear Learning Enhances Neural Responses to Threat-Predictive Sensory Stimuli , 2013, Science.

[113]  R. Llinás,et al.  Uniform olivocerebellar conduction time underlies Purkinje cell complex spike synchronicity in the rat cerebellum. , 1993, The Journal of physiology.