@article {70248, title = {Connectivity underlying motor cortex activity during goal-directed behaviour.}, journal = {Nature}, volume = {649}, year = {2026}, month = {2026 Jan 01}, pages = {416-422}, abstract = {

Neural representations of information are shaped by long-range input and local network interactions. Previous studies linking neural coding and cortical connectivity have focused on input-driven activity in the sensory cortex. Here we studied neural activity in the motor cortex while mice gathered rewards with multidirectional tongue reaching. This behaviour does not require training, allowing us to probe neural coding and connectivity before activity is shaped by extended learning. Motor cortex neurons were tuned to target location and reward outcome, and typically responded during and after movements. We studied the underlying network interactions in vivo by estimating causal neural connections using an all-optical method. Mapping connectivity between more than 20,000,000 excitatory neuron pairs showed a multi-scale columnar architecture in layer 2/3 of the motor cortex. Neurons displayed local (less than 100 {\textmu}m) like-to-like excitatory connectivity according to target-location tuning, and inhibition over longer spatial scales. Connectivity patterns comprised a continuum, with abundant sparsely connected neurons and rare densely connected neurons that function as network hubs. Hub neurons were weakly tuned to target location and reward outcome but influenced more neighbouring neurons. This network of neurons, encoding location and outcome of movements to different motor goals, may be a general substrate for rapid learning of complex, goal-directed behaviours.

}, keywords = {Animals, Female, Goals, Learning, Male, Mice, Mice, Inbred C57BL, Motor Cortex, Movement, Neural Pathways, Neurons, Reward, Tongue}, issn = {1476-4687}, doi = {10.1038/s41586-025-09758-6}, url = {https://doi.org/10.1038/s41586-025-09758-6}, author = {Finkelstein, Arseny and Daie, Kayvon and Rozsa, Marton and Darshan, Ran and Svoboda, Karel} } @article {69841, title = {DELTA: A method for brain-wide measurement of synaptic protein turnover reveals localized plasticity during learning.}, journal = {Nat Neurosci}, year = {2025}, month = {2025 Mar 31}, abstract = {

Synaptic plasticity alters neuronal connections in response to experience, which is thought to underlie learning and memory. However, the loci of learning-related synaptic plasticity, and the degree to which plasticity is localized or distributed, remain largely unknown. Here we describe a new method, DELTA, for mapping brain-wide changes in synaptic protein turnover with single-synapse resolution, based on Janelia Fluor dyes and HaloTag knock-in mice. During associative learning, the turnover of the ionotropic glutamate receptor subunit GluA2, an indicator of synaptic plasticity, was enhanced in several brain regions, most markedly hippocampal area CA1. More broadly distributed increases in the turnover of synaptic proteins were observed in response to environmental enrichment. In CA1, GluA2 stability was regulated in an input-specific manner, with more turnover in layers containing input from CA3 compared to entorhinal cortex. DELTA will facilitate exploration of the molecular and circuit basis of learning and memory and other forms of plasticity at scales ranging from single synapses to the entire brain.

}, issn = {1546-1726}, doi = {10.1038/s41593-025-01923-4}, url = {https://doi.org/10.1038/s41593-025-01923-4}, author = {Mohar, Boaz and Michel, Gabriela and Wang, Yi-Zhi and Hernandez, Veronica and Grimm, Jonathan B and Park, Jin-Yong and Patel, Ronak and Clarke, Morgan and Brown, Timothy A and Bergmann, Cornelius and Gebis, Kamil K and Wilen, Anika P and Liu, Bian and Johnson, Richard and Graves, Austin and Tchumatchenko, Tatjana and Savas, Jeffrey N and Fornasiero, Eugenio F and Huganir, Richard L and Tillberg, Paul W and Lavis, Luke D and Svoboda, Karel and Spruston, Nelson} } @article {69833, title = {Glutamate indicators with increased sensitivity and tailored deactivation rates}, journal = {Nat Methods}, year = {2025}, month = {2025 Dec 23}, abstract = {

Understanding how neurons integrate signals from thousands of input synapses requires methods to monitor neurotransmission across many sites simultaneously. The fluorescent protein glutamate indicator iGluSnFR enables visualization of synaptic signaling, but the sensitivity, scale and speed of such measurements are limited by existing variants. Here we developed two highly sensitive fourth-generation iGluSnFR variants with fast activation and tailored deactivation rates: iGluSnFR4f for tracking rapid dynamics, and iGluSnFR4s for recording from large populations of synapses. These indicators detect glutamate with high spatial specificity and single-vesicle sensitivity in vivo. We used them to record natural patterns of synaptic transmission across multiple experimental contexts in mice, including two-photon imaging in cortical layers 1{\textendash}4 and hippocampal CA1, and photometry in the midbrain. The iGluSnFR4 variants extend the speed, sensitivity and scalability of glutamate imaging, enabling direct observation of information flow through neural networks in the intact brain.

}, doi = {10.1038/s41592-025-02965-z}, url = {https://doi.org/10.1038/s41592-025-02965-z}, author = {Aggarwal, Abhi and Negrean, Adrian and Chen, Yang and Iyer, Rishyashring and Reep, Daniel and Liu, Anyi and Palutla, Anirudh and Xie, Michael E. and MacLennan, Bryan J. and Hagihara, Kenta M. and Kinsey, Lucas W. and Sun, Julianna L. and Yao, Pantong and Zheng, Jihong and Tsang, Arthur and Tsegaye, Getahun and Zhang, Yonghai and Patel, Ronak H. and Arthur, Benjamin J. and Hiblot, Julien and Leippe, Philipp and Tarnawski, Miroslaw and Marvin, Jonathan S. and Vevea, Jason D. and Turaga, Srinivas C. and Tebo, Alison G. and Carandini, Matteo and Rossi, L. F. and Kleinfeld, David and Konnerth, Arthur and Svoboda, Karel and Turner, Glenn C. and Hasseman, Jeremy and Podgorski, Kaspar} } @article {70201, title = {Neural dynamics outside task-coding dimensions drive decision trajectories through transient amplification}, journal = {bioRxiv}, year = {2025}, month = {2025 Nov 22}, abstract = {

Most behaviors involve neural dynamics in high-dimensional activity spaces. A common approach is to extract dimensions that capture task-related variability, such as those separating stimuli or choices, yielding low-dimensional, task-aligned neural activity subspaces ({\textquotedblleft}coding dimensions{\textquotedblright}). However, whether these dimensions actively drive decisions or merely reflect underlying computations remains unclear. Moreover, neural activity outside these coding subspaces ({\textquotedblleft}residual dimensions{\textquotedblright}) is often ignored, though it could also causally shape neural dynamics driving behavior. We developed a recurrent neural network model that fits population activity and uncovers the dynamic interactions between coding and residual subspaces on single trials. Applied to electrophysiological recordings from the anterior lateral motor cortex (ALM) and motor thalamus in mice performing a delayed response task, our model demonstrates that perturbations of residual dimensions reliably alter behavioral choices, whereas perturbations of the choice dimension, which strongly encodes the animal{\textquoteright}s upcoming decision, are largely ineffective. These perturbation effects arise because residual dimensions drive transient amplification across an intermediate number of coding and residual dimensions (\~10), before the dynamics collapse into discrete attractor states corresponding to the animal{\textquoteright}s choice. By dissecting the low-dimensional variability underlying error trials, we find that it primarily shifts trajectories along residual dimensions, biasing single decisions. Residual activity in thalamus shapes cortical decision dynamics, implicating weakly selective thalamic populations in the emergence of cortical selectivity. Our findings challenge the conventional focus on low-dimensional coding subspaces as sufficient framework for understanding neural computations, demonstrating that dimensions previously considered task-irrelevant and accounting for little variance can have a critical role in driving behavior.

}, doi = {10.1101/2025.11.20.689599}, url = {https://www.biorxiv.org/content/early/2025/11/22/2025.11.20.689599}, author = {Pereira-Obilinovic, Ulises and Daie, Kayvon and Chen, Susu and Svoboda, Karel and Darshan, Ran} } @article {69774, title = {Neuropixels Opto: Combining high-resolution electrophysiology and optogenetics}, journal = {bioRxiv}, year = {2025}, month = {2025 Feb 06}, abstract = {

High-resolution extracellular electrophysiology is the gold standard for recording spikes from distributed neural populations, and is especially powerful when combined with optogenetics for manipulation of specific cell types with high temporal resolution. We integrated these approaches into prototype Neuropixels Opto probes, which combine electronic and photonic circuits. These devices pack 960 electrical recording sites and two sets of 14 light emitters onto a 1 cm shank, allowing spatially addressable optogenetic stimulation with blue and red light. In mouse cortex, Neuropixels Opto probes delivered high-quality recordings together with spatially addressable optogenetics, differentially activating or silencing neurons at distinct cortical depths. In mouse striatum and other deep structures, Neuropixels Opto probes delivered efficient optotagging, facilitating the identification of two cell types in parallel. Neuropixels Opto probes represent an unprecedented tool for recording, identifying, and manipulating neuronal populations.

}, doi = {10.1101/2025.02.04.636286}, url = {https://www.biorxiv.org/content/early/2025/02/06/2025.02.04.636286}, author = {Lakunina, Anna and Socha, Karolina Z and Ladd, Alexander and Bowen, Anna J and Chen, Susu and Colonell, Jennifer and Doshi, Anjal and Karsh, Bill and Krumin, Michael and Kulik, Pavel and Li, Anna and Neutens, Pieter and O{\textquoteright}Callaghan, John and Olsen, Meghan and Putzeys, Jan and Tilmans, Harrie AC and Ye, Zhiwen and Welkenhuysen, Marleen and H{\"a}usser, Michael and Koch, Christof and Ting, Jonathan T. and Neuropixels Opto Consortium and Dutta, Barun and Harris, Timothy D and Steinmetz, Nicholas A and Svoboda, Karel and Siegle, Joshua H and Carandini, Matteo} } @article {69185, title = {Brain-wide neural activity underlying memory-guided movement.}, journal = {Cell}, volume = {187}, year = {2024}, month = {2024 Feb 01}, pages = {676-691.e16}, abstract = {

Behavior relies on activity in structured neural circuits that are distributed across the brain, but most experiments probe neurons in a single area at a time. Using multiple Neuropixels probes, we recorded from multi-regional loops connected to the anterior lateral motor cortex (ALM), a circuit node mediating memory-guided directional licking. Neurons encoding sensory stimuli, choices, and actions were distributed across the brain. However, choice coding was concentrated in the ALM and subcortical areas receiving input from the ALM in an ALM-dependent manner. Diverse orofacial movements were encoded in the hindbrain; midbrain; and, to a lesser extent, forebrain. Choice signals were first detected in the ALM and the midbrain, followed by the thalamus and other brain areas. At movement initiation, choice-selective activity collapsed across the brain, followed by new activity patterns driving specific actions. Our experiments provide the foundation for neural circuit models of decision-making and movement initiation.

}, keywords = {Brain, Memory, Movement, Neurons, Thalamus}, issn = {1097-4172}, doi = {10.1016/j.cell.2023.12.035}, author = {Chen, Susu and Liu, Yi and Wang, Ziyue Aiden and Colonell, Jennifer and Liu, Liu D and Hou, Han and Tien, Nai-Wen and Wang, Tim and Harris, Timothy and Druckmann, Shaul and Li, Nuo and Svoboda, Karel} } @article {69611, title = {Sub-threshold neuronal activity and the dynamical regime of cerebral cortex.}, journal = {Nat Commun}, volume = {15}, year = {2024}, month = {2024 Sep 11}, pages = {7958}, abstract = {

Cortical neurons exhibit temporally irregular spiking patterns and heterogeneous firing rates. These features arise in model circuits operating in a {\textquoteright}fluctuation-driven regime{\textquoteright}, in which fluctuations in membrane potentials emerge from the network dynamics. However, it is still debated whether the cortex operates in such a regime. We evaluated the fluctuation-driven hypothesis by analyzing spiking and sub-threshold membrane potentials of neurons in the frontal cortex of mice performing a decision-making task. We showed that while standard fluctuation-driven models successfully account for spiking statistics, they fall short in capturing the heterogeneity in sub-threshold activity. This limitation is an inevitable outcome of bombarding single-compartment neurons with a large number of pre-synaptic inputs, thereby clamping the voltage of all neurons to more or less the same average voltage. To address this, we effectively incorporated dendritic morphology into the standard models. Inclusion of dendritic morphology in the neuronal models increased neuronal selectivity and reduced error trials, suggesting a functional role for dendrites during decision-making. Our work suggests that, during decision-making, cortical neurons in high-order cortical areas operate in a fluctuation-driven regime.

}, keywords = {Action Potentials, Animals, Cerebral Cortex, Decision Making, Dendrites, Frontal Lobe, Male, Membrane Potentials, Mice, Mice, Inbred C57BL, Models, Neurological, Neurons}, issn = {2041-1723}, doi = {10.1038/s41467-024-51390-x}, url = {https://doi.org/10.1038/s41467-024-51390-x}, author = {Amsalem, Oren and Inagaki, Hidehiko and Yu, Jianing and Svoboda, Karel and Darshan, Ran} } @article {68786, title = {Distributing task-related neural activity across a cortical network through task-independent connections.}, journal = {Nature Communications}, volume = {14}, year = {2023}, month = {2023 May 18}, pages = {2851}, abstract = {

Task-related neural activity is widespread across populations of neurons during goal-directed behaviors. However, little is known about the synaptic reorganization and circuit mechanisms that lead to broad activity changes. Here we trained a subset of neurons in a spiking network with strong synaptic interactions to reproduce the activity of neurons in the motor cortex during a decision-making task. Task-related activity, resembling the neural data, emerged across the network, even in the untrained neurons. Analysis of trained networks showed that strong untrained synapses, which were independent of the task and determined the dynamical state of the network, mediated the spread of task-related activity. Optogenetic perturbations suggest that the motor cortex is strongly-coupled, supporting the applicability of the mechanism to cortical networks. Our results reveal a cortical mechanism that facilitates distributed representations of task-variables by spreading the activity from a subset of plastic neurons to the entire network through task-independent strong synapses.

}, keywords = {Action Potentials, Models, Neurological, Neurons, Synapses}, issn = {2041-1723}, doi = {10.1038/s41467-023-38529-y}, author = {Kim, Christopher M and Finkelstein, Arseny and Chow, Carson C and Svoboda, Karel and Darshan, Ran} } @article {68665, title = {Fast and sensitive GCaMP calcium indicators for imaging neural populations.}, journal = {Nature}, year = {2023}, month = {2023 Mar 15}, abstract = {

Calcium imaging with protein-based indicators is widely used to follow neural activity in intact nervous systems, but current protein sensors report neural activity at timescales much slower than electrical signalling and are limited by trade-offs between sensitivity and kinetics. Here we used large-scale screening and structure-guided mutagenesis to develop and optimize several fast and sensitive GCaMP-type indicators. The resulting {\textquoteright}jGCaMP8{\textquoteright} sensors, based on the calcium-binding protein calmodulin and a fragment of endothelial nitric oxide synthase, have ultra-fast kinetics (half-rise times of 2 ms) and the highest sensitivity for neural activity reported for a protein-based calcium sensor. jGCaMP8 sensors will allow tracking of large populations of neurons on timescales relevant to neural computation.

}, issn = {1476-4687}, doi = {10.1038/s41586-023-05828-9}, author = {Zhang, Yan and Rozsa, Marton and Liang, Yajie and Bushey, Daniel and Wei, Ziqiang and Zheng, Jihong and Reep, Daniel and Broussard, Gerard Joey and Tsang, Arthur and Tsegaye, Getahun and Narayan, Sujatha and Obara, Christopher J and Lim, Jing-Xuan and Patel, Ronak and Zhang, Rongwei and Ahrens, Misha B and Turner, Glenn C and Wang, Samuel S-H and Korff, Wyatt L and Schreiter, Eric R and Svoboda, Karel and Hasseman, Jeremy P and Kolb, Ilya and Looger, Loren L} } @article {68708, title = {Predictive and robust gene selection for spatial transcriptomics.}, journal = {Nature Communications}, volume = {14}, year = {2023}, month = {2023 Apr 12}, pages = {2091}, abstract = {

A prominent trend in single-cell transcriptomics is providing spatial context alongside a characterization of each cell{\textquoteright}s molecular state. This typically requires targeting an a priori selection of genes, often covering less than 1\% of the genome, and a key question is how to optimally determine the small gene panel. We address this challenge by introducing a flexible deep learning framework, PERSIST, to identify informative gene targets for spatial transcriptomics studies by leveraging reference scRNA-seq data. Using datasets spanning different brain regions, species, and scRNA-seq technologies, we show that PERSIST reliably identifies panels that provide more accurate prediction of the genome-wide expression profile, thereby capturing more information with fewer genes. PERSIST can be adapted to specific biological goals, and we demonstrate that PERSIST{\textquoteright}s binarization of gene expression levels enables models trained on scRNA-seq data to generalize with to spatial transcriptomics data, despite the complex shift between these technologies.

}, keywords = {Gene Expression Profiling, Sequence Analysis, RNA, Single-Cell Analysis, Transcriptome}, issn = {2041-1723}, doi = {10.1038/s41467-023-37392-1}, author = {Covert, Ian and Gala, Rohan and Wang, Tim and Svoboda, Karel and S{\"u}mb{\"u}l, Uygar and Lee, Su-In} } @article {68690, title = {Sensitivity optimization of a rhodopsin-based fluorescent voltage indicator}, journal = {Neuron}, volume = {111}, year = {2023}, month = {2023 May 17}, pages = {1547-1563}, abstract = {

The ability to optically image cellular transmembrane voltages at millisecond-timescale resolutions can offer unprecedented insight into the function of living brains in behaving animals. Here, we present a\ point mutation\ that increases the sensitivity of Ace2 opsin-based voltage indicators. We use the mutation to develop Voltron2, an improved chemigeneic voltage indicator that has a 65\% higher sensitivity to single APs and 3-fold higher sensitivity to subthreshold potentials than Voltron. Voltron2 retained the sub-millisecond kinetics and photostability of its predecessor, although with lower baseline fluorescence. In multiple\ in\ vitro\ and\ in\ vivo\ comparisons with its predecessor across multiple species, we found Voltron2 to be more sensitive to APs and subthreshold fluctuations. Finally, we used Voltron2 to study and evaluate the possible mechanisms of\ interneuron\ synchronization in the mouse hippocampus. Overall, we have discovered a generalizable mutation that significantly increases the sensitivity of Ace2 rhodopsin-based sensors, improving their voltage reporting capability.

}, issn = {08966273}, doi = {10.1016/j.neuron.2023.03.009}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0896627323002052}, author = {Abdelfattah, Ahmed S. and Zheng, Jihong and Singh, Amrita and Huang, Yi-Chieh and Reep, Daniel and Tsegaye, Getahun and Tsang, Arthur and Arthur, Benjamin J. and Rehorova, Monika and Olson, Carl V.L. and Shuai, Yichun and Zhang, Lixia and Fu, Tian-Ming and Milkie, Daniel E. and Moya, Maria V. and Weber, Timothy D. and Lemire, Andrew L. and Baker, Christopher A. and Falco, Natalie and Zheng, Qinsi and Grimm, Jonathan B. and Yip, Mighten C. and Walpita, Deepika and Chase, Martin and Campagnola, Luke and Murphy, Gabe J. and Wong, Allan M. and Forest, Craig R. and Mertz, Jerome and Economo, Michael N. and Turner, Glenn C. and Koyama, Minoru and Lin, Bei-Jung and Betzig, Eric and Novak, Ondrej and Lavis, Luke D. and Svoboda, Karel and Korff, Wyatt and Chen, Tsai-Wen and Schreiter, Eric R. and Hasseman, Jeremy P. and Kolb, Ilya} } @article {67951, title = {A midbrain-thalamus-cortex circuit reorganizes cortical dynamics to initiate movement.}, journal = {Cell}, volume = {185}, year = {2022}, month = {2022 Mar 17}, pages = {1065}, abstract = {

Motor behaviors are often planned long before execution but only released after specific sensory events. Planning and execution are each associated with distinct patterns of motor cortex activity. Key questions are how these dynamic activity patterns are generated and how they relate to behavior. Here, we investigate the multi-regional neural circuits that link an auditory "Go cue" and the transition from planning to execution of directional licking. Ascending glutamatergic neurons in the midbrain reticular and pedunculopontine nuclei show short latency and phasic changes in spike rate that are selective for the Go cue. This signal is transmitted via the thalamus to the motor cortex, where it triggers a rapid reorganization of motor cortex state from planning-related activity to a motor command, which in turn drives appropriate movement. Our studies show how midbrain can control cortical dynamics via the thalamus for rapid and precise motor behavior.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2022.02.006}, author = {Inagaki, Hidehiko K and Chen, Susu and Ridder, Margreet C and Sah, Pankaj and Li, Nuo and Yang, Zidan and Hasanbegovic, Hana and Gao, Zhenyu and Gerfen, Charles R and Svoboda, Karel} } @article {67965, title = {Neural Algorithms and Circuits for Motor Planning.}, journal = {Annual Reviews Neuroscience}, year = {2022}, month = {2022 Feb 22}, abstract = {

The brain plans and executes volitional movements. The underlying patterns of neural population activity have been explored in the context of movements of the eyes, limbs, tongue, and head in nonhuman primates and rodents. How do networks of neurons produce the slow neural dynamics that prepare specific movements and the fast dynamics that ultimately initiate these movements? Recent work exploits rapid and calibrated perturbations of neural activity to test specific dynamical systems models that are capable of producing the observed neural activity. These joint experimental and computational studies show that cortical dynamics during motor planning reflect fixed points of neural activity (attractors). Subcortical control signals reshape and move attractors over multiple timescales, causing commitment to specific actions and rapid transitions to movement execution. Experiments in rodents are beginning to reveal how these algorithms are implemented at the level of brain-wide neural circuits. Expected final online publication date for the , Volume 45 is July 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

}, issn = {1545-4126}, doi = {10.1146/annurev-neuro-092021-121730}, author = {Inagaki, Hidehiko K and Chen, Susu and Daie, Kayvon and Finklestein, Arseny and Fontolan, Lorenzo and Romani, Sandro and Svoboda, Karel} } @article {68224, title = {Neural Algorithms and Circuits for Motor Planning.}, journal = {Annual Review Neuroscience}, volume = {45}, year = {2022}, month = {2022 Jul 08}, pages = {249-271}, abstract = {

The brain plans and executes volitional movements. The underlying patterns of neural population activity have been explored in the context of movements of the eyes, limbs, tongue, and head in nonhuman primates and rodents. How do networks of neurons produce the slow neural dynamics that prepare specific movements and the fast dynamics that ultimately initiate these movements? Recent work exploits rapid and calibrated perturbations of neural activity to test specific dynamical systems models that are capable of producing the observed neural activity. These joint experimental and computational studies show that cortical dynamics during motor planning reflect fixed points of neural activity (attractors). Subcortical control signals reshape and move attractors over multiple timescales, causing commitment to specific actions and rapid transitions to movement execution. Experiments in rodents are beginning to reveal how these algorithms are implemented at the level of brain-wide neural circuits.

}, keywords = {Algorithms, Animals, Brain, Motor Cortex, Movement, Neurons}, issn = {1545-4126}, doi = {10.1146/annurev-neuro-092021-121730}, author = {Inagaki, Hidehiko K and Chen, Susu and Daie, Kayvon and Finkelstein, Arseny and Fontolan, Lorenzo and Romani, Sandro and Svoboda, Karel} } @article {68379, title = {The Neurodata Without Borders ecosystem for neurophysiological data science.}, journal = {eLife}, volume = {11}, year = {2022}, month = {2022 Oct 04}, abstract = {

The neurophysiology of cells and tissues are monitored electrophysiologically and optically in diverse experiments and species, ranging from flies to humans. Understanding the brain requires integration of data across this diversity, and thus these data must be findable, accessible, interoperable, and reusable (FAIR). This requires a standard language for data and metadata that can coevolve with neuroscience. We describe design and implementation principles for a language for neurophysiology data. Our open-source software (Neurodata Without Borders, NWB) defines and modularizes the interdependent, yet separable, components of a data language. We demonstrate NWB{\textquoteright}s impact through unified description of neurophysiology data across diverse modalities and species. NWB exists in an ecosystem, which includes data management, analysis, visualization, and archive tools. Thus, the NWB data language enables reproduction, interchange, and reuse of diverse neurophysiology data. More broadly, the design principles of NWB are generally applicable to enhance discovery across biology through data FAIRness.

}, keywords = {Data Science, Ecosystem, Humans, Metadata, Neurophysiology, Software}, issn = {2050-084X}, doi = {10.7554/eLife.78362}, author = {Rubel, Oliver and Tritt, Andrew and Ly, Ryan and Dichter, Benjamin K and Ghosh, Satrajit and Niu, Lawrence and Baker, Pamela and Soltesz, Ivan and Ng, Lydia and Svoboda, Karel and Frank, Loren and Bouchard, Kristofer E} } @article {65319, title = {Accurate localization of linear probe electrodes across multiple brains.}, journal = {eNeuro}, volume = {8}, year = {2021}, month = {2021 Nov 12}, pages = {ENEURO.0241-21.2021}, author = {Liu, Liu D. and Chen, Susu and Economo, Michael N. and Li, Nuo and Svoboda, Karel} } @article {67231, title = {Attractor dynamics gate cortical information flow during decision-making.}, journal = {Nature Neuroscience}, volume = {24}, year = {2021}, month = {2021 Jun 1}, pages = {843-50}, abstract = {

Decisions are held in memory until enacted, which makes them potentially vulnerable to distracting sensory input. Gating of information flow from sensory to motor areas could protect memory from interference during decision-making, but the underlying network mechanisms are not understood. Here, we trained mice to detect optogenetic stimulation of the somatosensory cortex, with a delay separating sensation and action. During the delay, distracting stimuli lost influence on behavior over time, even though distractor-evoked neural activity percolated through the cortex without attenuation. Instead, choice-encoding activity in the motor cortex became progressively less sensitive to the impact of distractors. Reverse engineering of neural networks trained to reproduce motor cortex activity revealed that the reduction in sensitivity to distractors was caused by a growing separation in the neural activity space between attractors that encode alternative decisions. Our results show that communication between brain regions can be gated via attractor dynamics, which control the degree of commitment to an action.

}, issn = {1546-1726}, doi = {10.1038/s41593-021-00840-6}, author = {Finkelstein, Arseny and Fontolan, Lorenzo and Economo, Michael N and Li, Nuo and Romani, Sandro and Svoboda, Karel} } @article {67815, title = {EASI-FISH for thick tissue defines lateral hypothalamus spatio-molecular organization.}, journal = {Cell}, volume = {184}, year = {2021}, month = {2021 Dec 01}, pages = {6361}, abstract = {

Determining the spatial organization and morphological characteristics of molecularly defined cell types is a major bottleneck for characterizing the architecture underpinning brain function. We developed Expansion-Assisted Iterative Fluorescence In Situ Hybridization (EASI-FISH) to survey gene expression in brain tissue, as well as a turnkey computational pipeline to rapidly process large EASI-FISH image datasets. EASI-FISH was optimized for thick brain sections (300\ μm) to facilitate reconstruction of spatio-molecular domains that generalize across brains. Using the EASI-FISH pipeline, we investigated the spatial distribution of dozens of molecularly defined cell types in the lateral hypothalamic area (LHA), a brain region with poorly defined anatomical organization. Mapping cell types in the LHA revealed nine spatially and molecularly defined subregions. EASI-FISH also facilitates iterative reanalysis of scRNA-seq datasets to determine marker-genes that further dissociated spatial and morphological heterogeneity. The EASI-FISH pipeline democratizes mapping molecularly defined cell types, enabling discoveries about brain organization.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2021.11.024}, author = {Wang, Yuhan and Eddison, Mark and Fleishman, Greg and Weigert, Martin and Xu, Shengjin and Wang, Tim and Rokicki, Konrad and Goina, Cristian and Henry, Fredrick E and Lemire, Andrew L and Schmidt, Uwe and Yang, Hui and Svoboda, Karel and Myers, Eugene W and Saalfeld, Stephan and Korff, Wyatt and Sternson, Scott M and Tillberg, Paul W} } @article {67211, title = {High-fidelity estimates of spikes and subthreshold waveforms from 1-photon voltage imaging in~vivo.}, journal = {Cell Reports}, volume = {35}, year = {2021}, month = {2021 Apr 06}, pages = {108954}, abstract = {

The ability to probe the membrane potential of multiple genetically defined neurons simultaneously would have a profound impact on neuroscience research. Genetically encoded voltage indicators are a promising tool for this purpose, and recent developments have achieved a high signal-to-noise ratio in\ vivo with 1-photon fluorescence imaging. However, these recordings exhibit several sources of noise and signal extraction remains a challenge. We present an improved signal extraction pipeline, spike-guided penalized matrix decomposition-nonnegative matrix factorization (SGPMD-NMF), which resolves supra- and subthreshold voltages in\ vivo. The method incorporates biophysical and optical constraints. We validate the pipeline with simultaneous patch-clamp and optical recordings from mouse layer 1 in\ vivo and with simulated and composite datasets with realistic noise. We demonstrate applications to mouse hippocampus expressing paQuasAr3-s or SomArchon1, mouse cortex expressing SomArchon1 or Voltron, and zebrafish spines expressing zArchon1.

}, issn = {2211-1247}, doi = {10.1016/j.celrep.2021.108954}, author = {Xie, Michael E and Adam, Yoav and Fan, Linlin Z and B{\"o}hm, Urs L and Kinsella, Ian and Zhou, Ding and Rozsa, Marton and Singh, Amrita and Svoboda, Karel and Paninski, Liam and Cohen, Adam E} } @article {67232, title = {Neuropixels 2.0: A miniaturized high-density probe for stable, long-term brain recordings.}, journal = {Science}, volume = {372}, year = {2021}, month = {2021 Apr 16}, abstract = {

Measuring the dynamics of neural processing across time scales requires following the spiking of thousands of individual neurons over milliseconds and months. To address this need, we introduce the Neuropixels 2.0 probe together with newly designed analysis algorithms. The probe has more than 5000 sites and is miniaturized to facilitate chronic implants in small mammals and recording during unrestrained behavior. High-quality recordings over long time scales were reliably obtained in mice and rats in six laboratories. Improved site density and arrangement combined with newly created data processing methods enable automatic post hoc correction for brain movements, allowing recording from the same neurons for more than 2 months. These probes and algorithms enable stable recordings from thousands of sites during free behavior, even in small animals such as mice.

}, issn = {1095-9203}, doi = {10.1126/science.abf4588}, author = {Steinmetz, Nicholas A and Ayd{\i}n, {\c C}a{\u g}atay and Lebedeva, Anna and Okun, Michael and Pachitariu, Marius and Bauza, Marius and Beau, Maxime and Bhagat, Jai and B{\"o}hm, Claudia and Broux, Martijn and Chen, Susu and Colonell, Jennifer and Gardner, Richard J and Karsh, Bill and Kloosterman, Fabian and Kostadinov, Dimitar and Mora-Lopez, Carolina and O{\textquoteright}Callaghan, John and Park, Junchol and Putzeys, Jan and Sauerbrei, Britton and van Daal, Rik J J and Vollan, Abraham Z and Wang, Shiwei and Welkenhuysen, Marleen and Ye, Zhiwen and Dudman, Joshua T and Dutta, Barundeb and Hantman, Adam W and Harris, Kenneth D and Lee, Albert K and Moser, Edvard I and O{\textquoteright}Keefe, John and Renart, Alfonso and Svoboda, Karel and H{\"a}usser, Michael and Haesler, Sebastian and Carandini, Matteo and Harris, Timothy D} } @article {66007, title = {Targeted photostimulation uncovers circuit motifs supporting short-term memory.}, journal = {Nature Neuroscience}, volume = {24}, year = {2021}, month = {2021 Jan 25}, pages = {259-265}, abstract = {

Short-term memory is associated with persistent neural activity that is maintained by positive feedback between neurons. To explore the neural circuit motifs that produce memory-related persistent activity, we measured coupling between functionally characterized motor cortex neurons in mice performing a memory-guided response task. Targeted two-photon photostimulation of small (\<10) groups of neurons produced sparse calcium responses in coupled neurons over approximately 100 μm. Neurons with similar task-related selectivity were preferentially coupled. Photostimulation of different groups of neurons modulated activity in different subpopulations of coupled neurons. Responses of stimulated and coupled neurons persisted for seconds, far outlasting the duration of the photostimuli. Photostimuli produced behavioral biases that were predictable based on the selectivity of the perturbed neuronal population, even though photostimulation preceded the behavioral response by seconds. Our results suggest that memory-related neural circuits contain intercalated, recurrently connected modules, which can independently maintain selective persistent activity.

}, issn = {1546-1726}, doi = {10.1038/s41593-020-00776-3}, author = {Daie, Kayvon and Svoboda, Karel and Druckmann, Shaul} } @article {65726, title = {A comparison of neuronal population dynamics measured with calcium imaging and electrophysiology.}, journal = {PLoS Computational Biology}, volume = {16}, year = {2020}, month = {2020 Sep 15}, pages = {e1008198}, abstract = {

Calcium imaging with fluorescent protein sensors is widely used to record activity in neuronal populations. The transform between neural activity and calcium-related fluorescence involves nonlinearities and low-pass filtering, but the effects of the transformation on analyses of neural populations are not well understood. We compared neuronal spikes and fluorescence in matched neural populations in behaving mice. We report multiple discrepancies between analyses performed on the two types of data, including changes in single-neuron selectivity and population decoding. These were only partially resolved by spike inference algorithms applied to fluorescence. To model the relation between spiking and fluorescence we simultaneously recorded spikes and fluorescence from individual neurons. Using these recordings we developed a model transforming spike trains to synthetic-imaging data. The model recapitulated the differences in analyses. Our analysis highlights challenges in relating electrophysiology and imaging data, and suggests forward modeling as an effective way to understand differences between these data.

}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1008198}, author = {Wei, Ziqiang and Lin, Bei-Jung and Chen, Tsai-Wen and Daie, Kayvon and Svoboda, Karel and Druckmann, Shaul} } @article {65972, title = {High throughput instrument to screen fluorescent proteins under two-photon excitation.}, journal = {Biomedical Optics Express}, volume = {11}, year = {2020}, month = {2020 Dec 01}, pages = {7192-7203}, abstract = {

Two-photon microscopy together with fluorescent proteins and fluorescent protein-based biosensors are commonly used tools in neuroscience. To enhance their experimental scope, it is important to optimize fluorescent proteins for two-photon excitation. Directed evolution of fluorescent proteins under one-photon excitation is common, but many one-photon properties do not correlate with two-photon properties. A simple system for expressing fluorescent protein mutants is colonies on an agar plate. The small focal volume of two-photon excitation makes creating a high throughput screen in this system a challenge for a conventional point-scanning approach. We present an instrument and accompanying software that solves this challenge by selectively scanning each colony based on a colony map captured under one-photon excitation. This instrument, called the GIZMO, can measure the two-photon excited fluorescence of 10,000 colonies in 7 hours. We show that the GIZMO can be used to evolve a fluorescent protein under two-photon excitation.

}, issn = {2156-7085}, doi = {10.1364/BOE.409353}, author = {Molina, Rosana S and King, Jonathan and Franklin, Jacob and Clack, Nathan and McRaven, Christopher and Goncharov, Vasily and Flickinger, Daniel and Svoboda, Karel and Drobizhev, Mikhail and Hughes, Thomas E} } @article {65738, title = {The mind of a mouse.}, journal = {Cell}, volume = {182}, year = {2020}, month = {2020 Sep 17}, pages = {1372-1376}, abstract = {

Large scientific projects in genomics and astronomy are influential not because they answer any single question but because they enable investigation of continuously arising new questions from the same data-rich sources. Advances in automated mapping of the brain{\textquoteright}s synaptic connections (connectomics) suggest that the complicated circuits underlying brain function are ripe for analysis. We discuss benefits of mapping a mouse brain at the level of synapses.

}, issn = {1097-4172}, doi = {10.1016/j.cell.2020.08.010}, author = {Abbott, Larry F and Bock, Davi D and Callaway, Edward M and Denk, Winfried and Dulac, Catherine and Fairhall, Adrienne L and Fiete, Ila and Harris, Kristen M and Helmstaedter, Moritz and Jain, Viren and Kasthuri, Narayanan and LeCun, Yann and Lichtman, Jeff W and Littlewood, Peter B and Luo, Liqun and Maunsell, John H R and Reid, R Clay and Rosen, Bruce R and Rubin, Gerald M and Sejnowski, Terrence J and Seung, H Sebastian and Svoboda, Karel and Tank, David W and Tsao, Doris and Van Essen, David C} } @article {65321, title = {Rapid mesoscale volumetric imaging of neural activity with synaptic resolution.}, journal = {Nature Methods}, volume = {17}, year = {2020}, month = {2020 Mar 02}, pages = {291-4}, abstract = {

Imaging neurons and neural circuits over large volumes at high speed and subcellular resolution is a difficult task. Incorporating a Bessel focus module into a two-photon fluorescence mesoscope, we achieved rapid volumetric imaging of neural activity over the mesoscale with synaptic resolution. We applied the technology to calcium imaging of entire dendritic spans of neurons as well as neural ensembles within multiple cortical regions over two hemispheres of the awake mouse brain.

}, issn = {1548-7105}, doi = {10.1038/s41592-020-0760-9}, author = {Lu, Rongwen and Liang, Yajie and Meng, Guanghan and Zhou, Pengcheng and Svoboda, Karel and Paninski, Liam and Ji, Na} } @article {65364, title = {Recurrent interactions in local cortical circuits.}, journal = {Nature}, volume = {579}, year = {2020}, month = {2020 Mar 04}, pages = {256-59}, abstract = {

Most cortical synapses are local and excitatory. Local recurrent circuits could implement amplification, allowing pattern completion and other computations. Cortical circuits contain subnetworks that consist of neurons with similar receptive fields and increased connectivity relative to the network average. Cortical neurons that encode different types of information are spatially intermingled and distributed over large brain volumes, and this complexity has hindered attempts to probe the function of these subnetworks by perturbing them individually. Here we use computational modelling, optical recordings and manipulations to probe the function of recurrent coupling in layer 2/3 of the mouse vibrissal somatosensory cortex during active tactile discrimination. A neural circuit model of layer 2/3 revealed that recurrent excitation enhances sensory signals by amplification, but only for subnetworks with increased connectivity. Model networks with high amplification were sensitive to damage: loss of a few members of the subnetwork degraded stimulus encoding. We tested this prediction by mapping neuronal selectivity and photoablating neurons with specific selectivity. Ablation of a small proportion of layer 2/3 neurons (10-20, less than 5\% of the total) representing touch markedly reduced responses in the spared touch representation, but not in other representations. Ablations most strongly affected neurons with stimulus responses that were similar to those of the ablated population, which is also consistent with network models. Recurrence among cortical neurons with similar selectivity therefore drives input-specific amplification during behaviour.

}, issn = {1476-4687}, doi = {10.1038/s41586-020-2062-x}, author = {Peron, Simon and Pancholi, Ravi and Voelcker, Bettina and Wittenbach, Jason D and {\'O}lafsd{\'o}ttir, H Freyja and Freeman, Jeremy and Svoboda, Karel} } @article {65081, title = {Bright and photostable chemigenetic indicators for extended in vivo voltage imaging.}, journal = {Science}, volume = {365}, year = {2019}, month = {2019 Aug 13}, pages = {699-704}, abstract = {

Imaging changes in membrane potential using genetically encoded fluorescent voltage indicators (GEVIs) has great potential for monitoring neuronal activity with high spatial and temporal resolution. Brightness and photostability of fluorescent proteins and rhodopsins have limited the utility of existing GEVIs. We engineered a novel GEVI, "Voltron", that utilizes bright and photostable synthetic dyes instead of protein-based fluorophores, extending the combined duration of imaging and number of neurons imaged simultaneously by more than tenfold relative to existing GEVIs. We used Voltron for in vivo voltage imaging in mice, zebrafish, and fruit flies. In mouse cortex, Voltron allowed single-trial recording of spikes and subthreshold voltage signals from dozens of neurons simultaneously, over 15 min of continuous imaging. In larval zebrafish, Voltron enabled the precise correlation of spike timing with behavior.

}, issn = {1095-9203}, doi = {10.1126/science.aav6416}, author = {Abdelfattah, Ahmed S and Kawashima, Takashi and Singh, Amrita and Novak, Ondrej and Liu, Hui and Shuai, Yichun and Huang, Yi-Chieh and Campagnola, Luke and Seeman, Stephanie C and Yu, Jianing and Zheng, Jihong and Grimm, Jonathan B and Patel, Ronak and Friedrich, Johannes and Mensh, Brett D and Paninski, Liam and Macklin, John J and Murphy, Gabe J and Podgorski, Kaspar and Lin, Bei-Jung and Chen, Tsai-Wen and Turner, Glenn C and Liu, Zhe and Koyama, Minoru and Svoboda, Karel and Ahrens, Misha B and Lavis, Luke D and Schreiter, Eric R} } @article {64781, title = {Discrete attractor dynamics underlies persistent activity in the frontal cortex.}, journal = {Nature}, volume = {566}, year = {2019}, month = {2019 Feb 06}, pages = {212-7}, abstract = {

Short-term memories link events separated in time, such as past sensation and future actions. Short-term memories are correlated with slow neural dynamics, including selective persistent activity, which can be maintained over seconds. In a delayed response task that requires short-term memory, neurons in the mouse anterior lateral motor cortex (ALM) show persistent activity that instructs future actions. To determine the principles that underlie this persistent activity, here we combined intracellular and extracellular electrophysiology with optogenetic perturbations and network modelling. We show that during the delay epoch, the activity of ALM neurons moved towards discrete end points that correspond to specific movement directions. These end points were robust to transient shifts in ALM activity caused by optogenetic perturbations. Perturbations occasionally switched the population dynamics to the other end point, followed by incorrect actions. Our results show that discrete attractor dynamics underlie short-term memory related to motor planning.

}, issn = {1476-4687}, doi = {10.1038/s41586-019-0919-7}, author = {Inagaki, Hidehiko K and Fontolan, Lorenzo and Romani, Sandro and Svoboda, Karel} } @article {65205, title = {Functional clustering of dendritic activity during decision-making.}, journal = {Elife}, volume = {8}, year = {2019}, month = {2019 Oct 30}, abstract = {

The active properties of dendrites can support local nonlinear operations, but previous imaging and electrophysiological measurements have produced conflicting views regarding the prevalence and selectivity of local nonlinearities in vivo. We imaged calcium signals in pyramidal cell dendrites in the motor cortex of mice performing a tactile decision task. A custom microscope allowed us to image the soma and up to 300 μm of contiguous dendrite at 15 Hz, while resolving individual spines. New analysis methods were used to estimate the frequency and spatial scales of activity in dendritic branches and spines. The majority of dendritic calcium transients were coincident with global events. However, task-associated calcium signals in dendrites and spines were compartmentalized by dendritic branching and clustered within branches over approximately 10 μm. Diverse behavior-related signals were intermingled and distributed throughout the dendritic arbor, potentially supporting a large learning capacity in individual neurons.

}, issn = {2050-084X}, doi = {10.7554/eLife.46966}, author = {Kerlin, Aaron and Boaz, Mohar and Flickinger, Daniel and MacLennan, Bryan J and Dean, Matthew B and Davis, Courtney and Spruston, Nelson and Svoboda, Karel} } @article {64986, title = {High-performance calcium sensors for imaging activity in neuronal populations and microcompartments.}, journal = {Nature Methods}, volume = {16}, year = {2019}, month = {2019 Jun 17}, pages = {649-57}, abstract = {

Calcium imaging with genetically encoded calcium indicators (GECIs) is routinely used to measure neural activity in intact nervous systems. GECIs are frequently used in one of two different modes: to track activity in large populations of neuronal cell bodies, or to follow dynamics in subcellular compartments such as axons, dendrites and individual synaptic compartments. Despite major advances, calcium imaging is still limited by the biophysical properties of existing GECIs, including affinity, signal-to-noise ratio, rise and decay kinetics and dynamic range. Using structure-guided mutagenesis and neuron-based screening, we optimized the green fluorescent protein-based GECI GCaMP6 for different modes of in vivo imaging. The resulting jGCaMP7 sensors provide improved detection of individual spikes (jGCaMP7s,f), imaging in neurites and neuropil (jGCaMP7b), and may allow tracking larger populations of neurons using two-photon (jGCaMP7s,f) or wide-field (jGCaMP7c) imaging.

}, issn = {1548-7105}, doi = {10.1038/s41592-019-0435-6}, author = {Dana, Hod and Sun, Yi and Mohar, Boaz and Hulse, Brad K and Kerlin, Aaron M and Hasseman, Jeremy P and Tsegaye, Getahun and Tsang, Arthur and Wong, Allan and Patel, Ronak and Macklin, John J and Chen, Yang and Konnerth, Arthur and Jayaraman, Vivek and Looger, Loren L and Schreiter, Eric R and Svoboda, Karel and Kim, Douglas S} } @article {59912, title = {NWB:N 2.0: An accessible data standard for neurophysiology.}, journal = {bioRxiv}, year = {2019}, month = {2019 Jan 17}, abstract = {

Neurodata Without Borders: Neurophysiology (NWB:N) is a data standard for neurophysiology, providing neuroscientists with a common standard to share, archive, use, and build common analysis tools for neurophysiology data. With NWB:N version 2.0 (NWB:N 2.0) we made significant advances towards creating a usable standard, software ecosystem, and vibrant community for standardizing neurophysiology data. In this manuscript we focus in particular on the NWB:N data standard schema and present advances towards creating an accessible data standard for neurophysiology.

}, doi = {10.1101/523035}, author = {Rubel, Oliver and Tritt, Andrew and Dichter, Benjamin and Braun, Thomas and Cain, Nicholas and Clack, Nathan G and Davidson, Thomas J and Dougherty, Max and Fillion-Rubin, Jean-Christophe and Graddis, Nile and Grauer, Michael and Kiggins, Justin T and Niu, Lawrence and Ozturk, Doruk and Schroeder, William and Soltesz, Ivan and Sommer, Friedrich T and Svoboda, Karel and Ng, Lydia and et al} } @article {51792, title = {An orderly single-trial organization of population dynamics in premotor cortex predicts behavioral variability.}, journal = {Nature Communications}, volume = {10}, year = {2019}, month = {2019 Jan 15}, pages = {216}, abstract = {

Animals are not simple input-output machines. Their responses to even very similar stimuli are variable. A key, long-standing question in neuroscience is to understand the neural correlates of such behavioral variability. To reveal these correlates, behavior and neural population activity must be related to one another on single trials. Such analysis is challenging due to the dynamical nature of brain function (e.g., in decision making), heterogeneity across neurons and limited sampling of the relevant neural population. By analyzing population recordings from mouse frontal cortex in perceptual decision-making tasks, we show that an analysis approach tailored to the coarse grain features of the dynamics is able to reveal previously unrecognized structure in the organization of population activity. This structure is similar on error and correct trials, suggesting dynamics that may be constrained by the underlying circuitry, is able to predict multiple aspects of behavioral variability and reveals long time-scale modulation of population activity.

}, issn = {2041-1723}, doi = {10.1038/s41467-018-08141-6}, author = {Wei, Ziqiang and Inagaki, Hidehiko and Li, Nuo and Svoboda, Karel and Druckmann, Shaul} } @article {64832, title = {Prediction of choice from competing mechanosensory and choice-memory cues during active tactile decision making.}, journal = {The Journal of Neuroscience : the official journal of the Society for Neuroscience}, volume = {39}, year = {2019}, month = {2019 May 15}, pages = {3921-33}, abstract = {

Perceptual decision making is an active process where animals move their sense organs to extract task-relevant information. To investigate how the brain translates sensory input into decisions during active sensation, we developed a mouse active touch task where the mechanosensory input can be precisely measured and that challenges animals to use multiple mechanosensory cues. Male mice were trained to localise a pole using a single whisker and to report their decision by selecting one of three choices. Using high-speed imaging and machine vision we estimated whisker-object mechanical forces at millisecond resolution. Mice solved the task by a sensory-motor strategy where both the strength and direction of whisker bending were informative cues to pole location. We found competing influences of immediate sensory input and choice memory on mouse choice. On correct trials, choice could be predicted from the direction and strength of whisker bending, but not from previous choice. In contrast, on error trials, choice could be predicted from previous choice but not from whisker bending. This study shows that animal choices during active tactile decision making can be predicted from mechanosenory and choice-memory signals; and provides a new task, well-suited for future study of the neural basis of active perceptual decisions.Due to the difficulty of measuring the sensory input to moving sense organs, active perceptual decision making remains poorly understood. The whisker system provides a way forward since it is now possible to measure the mechanical forces due to whisker-object contact during behaviour. Here we train mice in a novel behavioural task that challenges them to use rich mechanosensory cues, but can be performed using one whisker and enables task-relevant mechanical forces to be precisely estimated. This approach enables rigorous study of how sensory cues translate into action during active, perceptual decision making. Our findings provide new insight into active touch and how sensory/internal signals interact to determine behavioural choices.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.2217-18.2019}, author = {Campagner, Dario and Evans, Mathew H and Chlebikova, Katarina and Colins-Rodriguez, Andrea and Loft, Michaela S E and Fox, Sarah and Pettifer, David and Humphries, Mark D and Svoboda, Karel and Petersen, Rasmus S} } @article {64813, title = {Principles governing the dynamics of GABAergic interneurons in the barrel cortex.}, journal = {bioRxiv}, year = {2019}, month = {2019 Feb 21}, abstract = {

Information processing in the neocortex is performed by GABAergic interneurons that are integrated with excitatory neurons into precisely structured circuits. To reveal how each neuron type shapes sensory representations, we measured spikes and membrane potential of specific types of neurons in the barrel cortex while mice performed an active, whisker-dependent object localization task. Whiskers were tracked with millisecond precision. Fast-spiking (FS) neurons were activated by touch with short latency and by whisking. FS neurons track thalamic input and provide feedforward inhibition. Somatostatin (SOM)-expressing neurons were also excited by touch, but with a delay (5 ms) compared to excitatory (E) and FS neurons. SOM neurons monitor local excitation and provide feedback inhibition. Vasoactive intestinal polypeptide (VIP)-expressing neurons were not driven by touch but elevated their spike rate during whisking, disinhibiting E and FS neurons. Our data reveal rules of recruitment for specific interneuron types, providing foundations for understanding cortical computations.

}, doi = {10.1101/554949}, author = {Yu, Jianing and Hu, Hang and Agmon, Ariel and Svoboda, Karel} } @article {65138, title = {Reconstruction of 1,000 projection neurons reveals new cell types and organization of long-range connectivity in the mouse brain.}, journal = {Cell}, volume = {179}, year = {2019}, month = {2019 Sep 19}, pages = {268-81}, abstract = {

Neuronal\ cell\ types\ are the nodes of neural circuits that determine the flow of information within the\ brain. Neuronal morphology, especially the shape of the axonal arbor, provides an essential descriptor of\ cell\ type and\ reveals\ how individual\ neurons\ route their output across the\ brain. Despite the importance of morphology, few\ projection\ neurons\ in the\ mouse\ brain\ have been reconstructed in their entirety. Here we present a robust and efficient platform for imaging and reconstructing complete neuronal morphologies, including axonal arbors that span substantial portions of the\ brain. We used this platform to reconstruct more than\ 1,000\ projection\ neurons\ in the motor cortex, thalamus, subiculum, and hypothalamus. Together, the reconstructed\ neurons\ constitute more than 85\ meters of axonal length and are available in a searchable online database. Axonal shapes revealed previously unknown subtypes of\ projection\ neurons\ and suggest organizational principles of\ long-range\ connectivity.

}, issn = {00928674}, doi = {10.1016/j.cell.2019.07.042}, author = {Winnubst, Johan and Bas, Erhan and Ferreira, Tiago A. and Wu, Zhuhao and Economo, Michael N. and Edson, Patrick and Arthur, Ben J. and Bruns, Christopher and Rokicki, Konrad and Schauder, David and Olbris, Donald J. and Murphy, Sean D. and Ackerman, David G. and Arshadi, Cameron and Baldwin, Perry and Blake, Regina and Elsayed, Ahmad and Hasan, Mashtura and Ramirez, Daniel and Dos Santos, Bruno and Weldon, Monet and Zafar, Amina and Dudman, Joshua T. and Gerfen, Charles R. and Hantman, Adam W. and Korff, Wyatt and Sternson, Scott M. and Spruston, Nelson and Svoboda, Karel and Chandrashekar, Jayaram} } @article {65129, title = {Recruitment of GABAergic interneurons in the barrel cortex during active tactile behavior.}, journal = {Neuron}, volume = {104}, year = {2019}, month = {2019 Oct 23}, pages = {412-27}, abstract = {

Neural computation involves diverse types of GABAergic inhibitory interneurons that are integrated with excitatory (E) neurons into precisely structured circuits. To understand how each neuron type shapes sensory representations, we measured firing patterns of defined types of neurons in the barrel cortex while mice performed an active, whisker-dependent object localization task. Touch excited fast-spiking (FS) interneurons at short latency, followed by activation of E neurons and somatostatin-expressing (SST) interneurons. Touch only weakly modulated vasoactive intestinal polypeptide-expressing (VIP) interneurons. Voluntary whisker movement activated FS neurons in the ventral posteromedial nucleus (VPM) target layers, a subset of SST neurons and a majority of VIP neurons. Together, FS neurons track thalamic input, mediating feedforward inhibition. SST neurons monitor local excitation, providing feedback inhibition. VIP neurons are activated by non-sensory inputs, disinhibiting E and FS neurons. Our data reveal rules of recruitment for interneuron types during behavior, providing foundations for understanding computation in cortical microcircuits.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2019.07.027}, author = {Yu, Jianing and Hu, Hang and Agmon, Ariel and Svoboda, Karel} } @article {65080, title = {Response to "Fallacies of mice experiments".}, journal = {Neuroinformatics}, year = {2019}, month = {2019 Aug 03}, abstract = {

In a recent Editorial, De Schutter commented on our recent study on the roles of a cortico-cerebellar loop in motor planning in mice (De Schutter 2019, Neuroinformatics, 17, 181-183, Gao et al. 2018, Nature, 563, 113-116). Two issues were raised. First, De Schutter questions the involvement of the fastigial nucleus in motor planning, rather than the dentate nucleus, given previous anatomical studies in non-human primates. Second, De Schutter suggests that our study design did not delineate different components of the behavior and the fastigial nucleus might play roles in sensory discrimination rather than motor planning. These comments are based on anatomical studies in other species and homology-based arguments and ignore key anatomical data and neurophysiological experiments from our study. Here we outline our interpretation of existing data and point out gaps in knowledge where future studies are needed.

}, issn = {1559-0089}, doi = {10.1007/s12021-019-09433-y}, author = {Gao, Zhenyu and Thomas, Alyse M and Economo, Michael N and Abrego, Amada M and Svoboda, Karel and De Zeeuw, Chris I and Li, Nuo} } @article {65226, title = {Spatiotemporal constraints on optogenetic inactivation in cortical circuits.}, journal = {eLife}, volume = {8}, year = {2019}, month = {2019 Nov 18}, abstract = {

Optogenetics allows manipulations of genetically and spatially defined neuronal populations with excellent temporal control. However, neurons are coupled with other neurons over multiple length scales, and the effects of localized manipulations thus spread beyond the targeted neurons. We benchmarked several optogenetic methods to inactivate small regions of neocortex. Optogenetic excitation of GABAergic neurons produced more effective inactivation than light-gated ion pumps. Transgenic mice expressing the light-dependent chloride channel GtACR1 produced the most potent inactivation. Generally, inactivation spread substantially beyond the photostimulation light, caused by strong coupling between cortical neurons. Over some range of light intensity, optogenetic excitation of inhibitory neurons reduced activity in these neurons, together with pyramidal neurons, a signature of inhibition-stabilized neural networks ({\textquoteright}paradoxical effect{\textquoteright}). The offset of optogenetic inactivation was followed by rebound excitation in a light dose-dependent manner, limiting temporal resolution. Our data offer guidance for the design of optogenetics experiments.

}, issn = {2050-084X}, doi = {10.7554/eLife.48622}, author = {Li, Nuo and Chen, Susu and Guo, Zengcai V and Chen, Han and Huo, Yan and Inagaki, Hidehiko K and Chen, Guang and Davis, Courtney and Hansel, David and Guo, Caiying and Svoboda, Karel} } @article {49383, title = {Anterolateral motor cortex connects with a medial subdivision of ventromedial thalamus through cell-type-specific circuits, forming an excitatory thalamo-cortico-thalamic loop via layer 1 apical tuft dendrites of layer 5B pyramidal tract type neurons.}, journal = {The Journal of Neuroscience : the official journal of the Society for Neuroscience}, volume = {38}, year = {2018}, month = {2018 Aug 24}, pages = {8787-97}, abstract = {

The anterolateral motor cortex (ALM) and ventromedial (VM) thalamus are functionally linked to support persistent activity during motor planning. We analyzed the underlying synaptic interconnections using optogenetics and electrophysiology in mice (♀/♂). In cortex, thalamocortical (TC) axons from VM excited VM-projecting pyramidal-tract (PT) neurons in layer 5B of ALM. These axons also strongly excited layer 2/3 neurons (which strongly excite PT neurons, as previously shown) but not VM-projecting corticothalamic (CT) neurons in layer 6. The strongest connections in the VM{\textrightarrow}PT circuit were localized to apical-tuft dendrites of PT neurons, in layer 1. These tuft inputs were selectively augmented after blocking hyperpolarization-activated cyclic nucleotide-gated (HCN) channels. In thalamus, axons from ALM PT neurons excited ALM-projecting VM neurons, located medially in VM. These axons provided weak input to neurons in mediodorsal nucleus, and little or no input either to neurons in the GABAergic reticular thalamic nucleus or to neurons in VM projecting to primary motor cortex (M1). Conversely, M1 PT axons excited M1- but not ALM-projecting VM neurons. Our findings indicate, first, a set of cell-type-specific connections forming an excitatory thalamo-cortico-thalamic (T-C-T) loop for ALM<->VM communication and a circuit-level substrate for supporting reverberant activity in this system. Second, a key feature of this loop is the prominent involvement of layer 1 synapses onto apical dendrites, a subcellular compartment with distinct signaling properties, including HCN-mediated gain control. Third, the segregation of the ALM<->VM loop from M1-related circuits of VM adds cellular-level support for the concept of parallel pathway organization in the motor system.Anterolateral motor cortex (ALM), a higher-order motor area in the mouse, and ventromedial thalamus (VM) are anatomically and functionally linked, but their synaptic interconnections at the cellular level are unknown. Our results show that ALM pyramidal tract neurons monosynaptically excite ALM-projecting thalamocortical neurons in a medial subdivision of VM, and vice versa. The thalamo-cortico-thalamic loop formed by these recurrent connections constitutes a circuit-level substrate for supporting reverberant activity in this system.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.1333-18.2018}, author = {Guo, KuangHua and Yamawaki, Naoki and Svoboda, Karel and Shepherd, Gordon M G} } @article {49476, title = {A cortico-cerebellar loop for motor planning.}, journal = {Nature}, volume = {563}, year = {2018}, month = {2018 Oct 17}, pages = {113-6}, abstract = {

Persistent and ramping neural activity in the frontal cortex anticipates specific movements. Preparatory activity is distributed across several brain regions, but it is unclear which brain areas are involved and how this activity is mediated by multi-regional interactions. The cerebellum is thought to be primarily involved in the short-timescale control of movement; however, roles for this structure in cognitive processes have also been proposed. In humans, cerebellar damage can cause defects in planning and working memory. Here we show that persistent representation of information in the frontal cortex during motor planning is dependent on the cerebellum. Mice performed a sensory discrimination task in which they used short-term memory to plan a future directional movement. A transient perturbation in the medial deep cerebellar nucleus (fastigial nucleus) disrupted subsequent correct responses without hampering movement execution. Preparatory activity was observed in both the frontal cortex and the cerebellar nuclei, seconds before the onset of movement. The silencing of frontal cortex activity abolished preparatory activity in the cerebellar nuclei, and fastigial activity was necessary to maintain cortical preparatory activity. Fastigial output selectively targeted the behaviourally relevant part of the frontal cortex through the thalamus, thus closing a cortico-cerebellar loop. Our results support the view that persistent neural dynamics during motor planning is maintained by neural circuits that span multiple brain regions, and that cerebellar computations extend beyond online motor control.

}, issn = {1476-4687}, doi = {10.1038/s41586-018-0633-x}, author = {Gao, Zhenyu and Davis, Courtney and Thomas, Alyse M and Economo, Michael N and Abrego, Amada M and Svoboda, Karel and De Zeeuw, Chris I and Li, Nuo} } @article {49496, title = {Distinct descending motor cortex pathways and their roles in movement.}, journal = {Nature}, volume = {563}, year = {2018}, month = {2018 Nov}, pages = {79-84}, abstract = {

Activity in the motor cortex predicts movements, seconds before they are initiated. This preparatory activity has been observed across cortical layers, including in descending pyramidal tract neurons in layer 5. A key question is how preparatory activity is maintained without causing movement, and is ultimately converted to a motor command to trigger appropriate movements. Here, using single-cell transcriptional profiling and axonal reconstructions, we identify two types of pyramidal tract neuron. Both types project to several targets in the basal ganglia and brainstem. One type projects to thalamic regions that connect back to motor cortex; populations of these neurons produced early preparatory activity that persisted until the movement was initiated. The second type projects to motor centres in the medulla and mainly\ produced late preparatory activity and motor commands. These results indicate that two types of motor cortex output neurons have specialized roles in motor control.

}, issn = {1476-4687}, doi = {10.1038/s41586-018-0642-9}, author = {Economo, Michael N and Viswanathan, Sarada and Tasic, Bosiljka and Bas, Erhan and Winnubst, Johan and Menon, Vilas and Graybuck, Lucas T and Nguyen, Thuc Nghi and Smith, Kimberly A and Yao, Zizhen and Wang, Lihua and Gerfen, Charles R and Chandrashekar, Jayaram and Zeng, Hongkui and Looger, Loren L and Svoboda, Karel} } @article {49119, title = {Dynamic cues for whisker-based object localization: An analytical solution to vibration during active whisker touch.}, journal = {PLoS Computational Biology}, volume = {14}, year = {2018}, month = {2018 Mar 27}, pages = {e1006032}, abstract = {

Vibrations are important cues for tactile perception across species. Whisker-based sensation in mice is a powerful model system for investigating mechanisms of tactile perception. However, the role vibration plays in whisker-based sensation remains unsettled, in part due to difficulties in modeling the vibration of whiskers. Here, we develop an analytical approach to calculate the vibrations of whiskers striking objects. We use this approach to quantify vibration forces during active whisker touch at a range of locations along the whisker. The frequency and amplitude of vibrations evoked by contact are strongly dependent on the position of contact along the whisker. The magnitude of vibrational shear force and bending moment is comparable to quasi-static forces. The fundamental vibration frequencies are in a detectable range for mechanoreceptor properties and below the maximum spike rates of primary sensory afferents. These results suggest two dynamic cues exist that rodents can use for object localization: vibration frequency and comparison of vibrational to quasi-static force magnitude. These complement the use of quasi-static force angle as a distance cue, particularly for touches close to the follicle, where whiskers are stiff and force angles hardly change during touch. Our approach also provides a general solution to calculation of whisker vibrations in other sensing tasks.

}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1006032}, author = {Vaxenburg, Roman and Wyche, Isis and Svoboda, Karel and Efros, Alexander L and Hires, Samuel Andrew} } @article {49154, title = {Genetic dissection of neural circuits: a decade of progress}, journal = {Neuron}, volume = {98}, year = {2018}, month = {2018 Apr 18}, pages = {256-81}, abstract = {

Tremendous progress has been made since\ Neuron\ published our Primer on genetic dissection of neural circuits 10 years ago. Since then, cell-type-specific anatomical, neurophysiological, and perturbation studies have been carried out in a multitude of invertebrate and vertebrate organisms, linking neurons and circuits to behavioral functions. New methods allow systematic classification of cell types and provide genetic access to diverse neuronal types for studies of connectivity and neural coding during behavior. Here we evaluate key advances over the past decade and discuss future directions.

}, doi = {10.1016/j.neuron.2018.03.040}, author = {Luo, Liqun and Callaway, Edward M and Svoboda, Karel} } @article {49813, title = {High-performance GFP-based calcium indicators for imaging activity in neuronal populations and microcompartments.}, journal = {bioRxiv}, year = {2018}, month = {2018 Oct 3}, abstract = {

Calcium imaging with genetically encoded calcium indicators (GECIs) is routinely used to measure neural activity in intact nervous systems. GECIs are frequently used in one of two different modes: to track activity in large populations of neuronal cell bodies, or to follow dynamics in subcellular compartments such as axons, dendrites and individual synaptic compartments. Despite major advances, calcium imaging is still limited by the biophysical properties of existing GECIs, including affinity, signal-to-noise ratio, rise and decay kinetics, and dynamic range. Using structure-guided mutagenesis and neuron-based screening, we optimized the green fluorescent protein-based GECI GCaMP6 for different modes of in vivo imaging. The jGCaMP7 sensors provide improved detection of individual spikes (jGCaMP7s,f), imaging in neurites and neuropil (jGCaMP7b), and tracking large populations of neurons using 2-photon (jGCaMP7s,f) or wide-field (jGCaMP7c) imaging.

}, doi = {10.1101/434589}, author = {Dana, Hod and Sun, Yi and Mohar, Boaz and Hulse, Brad and Hasseman, Jeremy P and Tsegaye, Getahun and Tsang, Arthur and Wong, Allan and Patel, Ronak and Macklin, John J and Chen, Yang and Konnerth, Arthur and Jayaraman, Vivek and Looger, Loren L and Schreiter, Eric R and Svoboda, Karel and Kim, Douglas S} } @article {49124, title = {Low-dimensional and monotonic preparatory activity in mouse anterior lateral motor cortex.}, journal = {The Journal of Neuroscience : the official journal of the Society for Neuroscience}, volume = {38}, year = {2018}, month = {2018 Apr 25}, pages = {4163-85}, abstract = {

Neurons in multiple brain regions fire trains of action potentials anticipating specific movements, but this {\textquoteright}preparatory activity{\textquoteright} has not been systematically compared across behavioral tasks. We compared preparatory activity in auditory and tactile delayed-response tasks in male mice. Skilled, directional licking was the motor output. The anterior lateral motor cortex (ALM) is necessary for motor planning in both tasks. Multiple features of ALM preparatory activity during the delay epoch were similar across tasks. First, majority of neurons showed direction-selective activity and spatially intermingled neurons were selective for either movement direction. Second, many cells showed mixed coding of sensory stimulus and licking direction, with a bias toward licking direction. Third, delay activity was monotonic and low-dimensional. Fourth, pairs of neurons with similar direction selectivity showed high spike-count correlations. Our study forms the foundation to analyze the neural circuit mechanisms underlying preparatory activity in a genetically tractable model organism.Short-term memories link events separated in time. Neurons in frontal cortex fire trains of action potentials anticipating specific movements, often seconds before the movement. This {\textquoteright}preparatory activity{\textquoteright} has been observed in multiple brain regions, but has rarely been compared systematically across behavioral tasks in the same brain region. To identify common features of preparatory activity, we developed and compared preparatory activity in auditory and tactile delayed-response tasks in mice. The same cortical area is necessary for both tasks. Multiple features of preparatory activity, measured with high-density silicon probes, were similar across tasks. We find that preparatory activity is low-dimensional and monotonic. Our study forms the foundation to analyze the circuit mechanisms underlying preparatory activity in a genetically tractable model organism.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3152-17.2018}, author = {Inagaki, Hidehiko K and Inagaki, Miho and Romani, Sandro and Svoboda, Karel} } @article {49495, title = {Shared and distinct transcriptomic cell types across neocortical areas.}, journal = {Nature}, volume = {563}, year = {2018}, month = {2018 Nov}, pages = {72-78}, abstract = {

The neocortex contains a multitude of cell types that are segregated into layers and functionally distinct areas. To investigate the diversity of cell types across the mouse neocortex, here we analysed 23,822 cells from two areas at distant poles of the mouse neocortex: the primary visual cortex and the anterior lateral motor cortex. We define 133 transcriptomic cell types by deep, single-cell RNA sequencing. Nearly all types of GABA (γ-aminobutyric acid)-containing neurons are shared across both areas, whereas most types of glutamatergic neurons were found in one of the two areas. By combining single-cell RNA sequencing and retrograde labelling, we match transcriptomic types of glutamatergic neurons to their long-range projection specificity. Our study establishes a combined transcriptomic and projectional taxonomy of cortical cell types from functionally distinct areas of the adult mouse cortex.

}, issn = {1476-4687}, doi = {10.1038/s41586-018-0654-5}, author = {Tasic, Bosiljka and Yao, Zizhen and Graybuck, Lucas T and Smith, Kimberly A and Nguyen, Thuc Nghi and Bertagnolli, Darren and Goldy, Jeff and Garren, Emma and Economo, Michael N and Viswanathan, Sarada and Penn, Osnat and Bakken, Trygve and Menon, Vilas and Miller, Jeremy and Fong, Olivia and Hirokawa, Karla E and Lathia, Kanan and Rimorin, Christine and Tieu, Michael and Larsen, Rachael and Casper, Tamara and Barkan, Eliza and Kroll, Matthew and Parry, Sheana and Shapovalova, Nadiya V and Hirschstein, Daniel and Pendergraft, Julie and Sullivan, Heather A and Kim, Tae Kyung and Szafer, Aaron and Dee, Nick and Groblewski, Peter and Wickersham, Ian and Cetin, Ali and Harris, Julie A and Levi, Boaz P and Sunkin, Susan M and Madisen, Linda and Daigle, Tanya L and Looger, Loren and Bernard, Amy and Phillips, John and Lein, Ed and Hawrylycz, Michael and Svoboda, Karel and Jones, Allan R and Koch, Christof and Zeng, Hongkui} } @article {49470, title = {Thy1 transgenic mice expressing the red fluorescent calcium indicator jRGECO1a for neuronal population imaging in vivo.}, journal = {PloS One}, volume = {13}, year = {2018}, month = {2018}, pages = {e0205444}, abstract = {

Calcium imaging is commonly used to measure the neural activity of large groups of neurons in mice. Genetically encoded calcium indicators (GECIs) can be delivered for this purpose using non-invasive genetic methods. Compared to viral gene transfer, transgenic targeting of GECIs provides stable long-term expression and obviates the need for invasive viral injections. Transgenic mice expressing the green GECI GCaMP6 are already widely used. Here we present the generation and characterization of transgenic mice expressing the sensitive red GECI jRGECO1a, driven by the Thy1 promoter. Four transgenic lines with different expression patterns showed sufficiently high expression for cellular in vivo imaging. We used two-photon microscopy to characterize visual responses of individual neurons in the visual cortex in vivo. The signal-to-noise ratio in transgenic mice was comparable to, or better than, mice transduced with adeno-associated virus. In addition, we show that Thy1-jRGECO1a transgenic mice are useful for transcranial population imaging and functional mapping using widefield fluorescence microscopy. We also demonstrate imaging of visual responses in retinal ganglion cells in vitro. Thy1-jRGECO1a transgenic mice are therefore a useful addition to the toolbox for imaging activity in intact neural networks.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0205444}, author = {Dana, Hod and Novak, Ondrej and Guardado-Montesino, Michael and Fransen, James W and Hu, Amy and Borghuis, Bart G and Guo, Caiying and Kim, Douglas S and Svoboda, Karel} } @article {48751, title = {Circuits in the rodent brainstem that control whisking in concert with other orofacial motor actions.}, journal = {Neuroscience}, volume = {368}, year = {2017}, month = {2017 Aug 23}, pages = {152-70}, abstract = {

The world view of rodents is largely determined by sensation on two length scales. One is within the animal{\textquoteright}s peri-personal space. Sensorimotor control on this scale involves active movements of the nose, tongue, head, and vibrissa, along with sniffing to determine olfactory clues. The second scale involves the detection of more distant space through vision and audition; these detection processes also impact repositioning of the head, eyes, and ears. Here we focus on orofacial motor actions, primarily vibrissa-based touch but including nose twitching, head bobbing, and licking, that control sensation at short, peri-personal distances. The orofacial nuclei for control of the motor plants, as well as primary and secondary sensory nuclei associated with these motor actions, lie within the hindbrain. The current data support three themes: First, the position of the sensors is determined by the summation of two drive signals, i.e., a fast rhythmic component and an evolving orienting component. Second, the rhythmic component is coordinated across all orofacial motor actions and is phase-locked to sniffing as the animal explores. Reverse engineering reveals that the preB{\"o}tzinger inspiratory complex provides the reset to the relevant premotor oscillators. Third, direct feedback from somatosensory trigeminal nuclei can rapidly alter motion of the sensors. This feedback is disynaptic and can be tuned by high-level inputs. The elucidation of synergistic coordination of orofacial motor actions to form behaviors, beyond that of a common rhythmic component, represents a work in progress that encompasses feedback through the midbrain and forebrain as well as hindbrain areas.

}, issn = {1873-7544}, doi = {10.1016/j.neuroscience.2017.08.034}, author = {McElvain, Lauren E and Friedman, Beth and Karten, Harvey J and Svoboda, Karel and Wang, Fan and Desch{\^e}nes, Martin and Kleinfeld, David} } @article {48935, title = {Fully integrated silicon probes for high-density recording of neural activity.}, journal = {Nature}, volume = {551}, year = {2017}, month = {2017 Nov 08}, pages = {232-236}, abstract = {

Sensory, motor and cognitive operations involve the coordinated action of large neuronal populations across multiple brain regions in both superficial and deep structures. Existing extracellular probes record neural activity with excellent spatial and temporal (sub-millisecond) resolution, but from only a few dozen neurons per shank. Optical Ca(2+) imaging offers more coverage but lacks the temporal resolution needed to distinguish individual spikes reliably and does not measure local field potentials. Until now, no technology compatible with use in unrestrained animals has combined high spatiotemporal resolution with large volume coverage. Here we design, fabricate and test a new silicon probe known as Neuropixels to meet this need. Each probe has 384 recording channels that can programmably address 960 complementary metal-oxide-semiconductor (CMOS) processing-compatible low-impedance TiN sites that tile a single 10-mm long, 70 {\texttimes} 20-μm cross-section shank. The 6 {\texttimes} 9-mm probe base is fabricated with the shank on a single chip. Voltage signals are filtered, amplified, multiplexed and digitized on the base, allowing the direct transmission of noise-free digital data from the probe. The combination of dense recording sites and high channel count yielded well-isolated spiking activity from hundreds of neurons per probe implanted in mice and rats. Using two probes, more than 700 well-isolated single neurons were recorded simultaneously from five brain structures in an awake mouse. The fully integrated functionality and small size of Neuropixels probes allowed large populations of neurons from several brain structures to be recorded in freely moving animals. This combination of high-performance electrode technology and scalable chip fabrication methods opens a path towards recording of brain-wide neural activity during behaviour.

}, issn = {1476-4687}, doi = {10.1038/nature24636}, author = {Jun, James J and Steinmetz, Nicholas A and Siegle, Joshua H and Denman, Daniel J and Bauza, Marius and Barbarits, Brian and Lee, Albert K and Anastassiou, Costas A and Andrei, Alexandru and Ayd{\i}n, {\c C}a{\u g}atay and Barbic, Mladen and Blanche, Timothy J and Bonin, Vincent and Couto, Jo{\~a}o and Dutta, Barundeb and Gratiy, Sergey L and Gutnisky, Diego A and H{\"a}usser, Michael and Karsh, Bill and Ledochowitsch, Peter and Lopez, Carolina Mora and Mitelut, Catalin and Musa, Silke and Okun, Michael and Pachitariu, Marius and Putzeys, Jan and Rich, P Dylan and Rossant, Cyrille and Sun, Wei-Lung and Svoboda, Karel and Carandini, Matteo and Harris, Kenneth D and Koch, Christof and O{\textquoteright}Keefe, John and Harris, Timothy D} } @article {48459, title = {Maintenance of persistent activity in a frontal thalamocortical loop.}, journal = {Nature}, volume = {545}, year = {2017}, month = {2017 May 03}, pages = {181-6}, abstract = {

Persistent neural activity maintains information that connects past and future events. Models of persistent activity often invoke reverberations within local cortical circuits, but long-range circuits could also contribute. Neurons in the mouse anterior lateral motor cortex (ALM) have been shown to have selective persistent activity that instructs future actions. The ALM is connected bidirectionally with parts of the thalamus, including the ventral medial and ventral anterior-lateral nuclei. We recorded spikes from the ALM and thalamus during tactile discrimination with a delayed directional response. Here we show that, similar to ALM neurons, thalamic neurons exhibited selective persistent delay activity that predicted movement direction. Unilateral photoinhibition of delay activity in the ALM or thalamus produced contralesional neglect. Photoinhibition of the thalamus caused a short-latency and near-complete collapse of ALM activity. Similarly, photoinhibition of the ALM diminished thalamic activity. Our results show that the thalamus is a circuit hub in motor preparation and suggest that persistent activity requires reciprocal excitation across multiple brain areas.

}, issn = {1476-4687}, doi = {10.1038/nature22324}, author = {Guo, Zengcai V and Inagaki, Hidehiko K and Daie, Kayvon and Druckmann, Shaul and Gerfen, Charles R and Svoboda, Karel} } @article {48493, title = {A map of anticipatory activity in mouse motor cortex.}, journal = {Neuron}, volume = {94}, year = {2017}, month = {2017 May 17}, pages = {866-879.e4}, abstract = {

Activity in the mouse anterior lateral motor cortex (ALM) instructs directional movements, often seconds before movement initiation. It is unknown whether this preparatory activity is localized to ALM or widely distributed within motor cortex. Here we imaged activity across motor cortex while mice performed a whisker-based object localization task with a delayed, directional licking response. During tactile sensation and the delay epoch, object location was represented in motor cortex areas that are medial and posterior relative to ALM, including vibrissal motor cortex. Preparatory activity appeared first in deep layers of ALM, seconds before the behavioral response, and remained localized to ALM until the behavioral response. Later, widely distributed neurons represented the outcome of the trial. Cortical area was more predictive of neuronal selectivity than laminar location or axonal projection target. Motor cortex therefore represents sensory, motor, and outcome information in a spatially organized manner.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2017.05.005}, author = {Chen, Tsai-Wen and Li, Nuo and Daie, Kayvon and Svoboda, Karel} } @article {48560, title = {Mechanisms underlying a thalamocortical transformation during active tactile sensation.}, journal = {PLoS Computational Biology}, volume = {13}, year = {2017}, month = {2017 Jun 07}, pages = {e1005576}, abstract = {

During active somatosensation, neural signals expected from movement of the sensors are suppressed in the cortex, whereas information related to touch is enhanced. This tactile suppression underlies low-noise encoding of relevant tactile features and the brain{\textquoteright}s ability to make fine tactile discriminations. Layer (L) 4 excitatory neurons in the barrel cortex, the major target of the somatosensory thalamus (VPM), respond to touch, but have low spike rates and low sensitivity to the movement of whiskers. Most neurons in VPM respond to touch and also show an increase in spike rate with whisker movement. Therefore, signals related to self-movement are suppressed in L4. Fast-spiking (FS) interneurons in L4 show similar dynamics to VPM neurons. Stimulation of halorhodopsin in FS interneurons causes a reduction in FS neuron activity and an increase in L4 excitatory neuron activity. This decrease of activity of L4 FS neurons contradicts the "paradoxical effect" predicted in networks stabilized by inhibition and in strongly-coupled networks. To explain these observations, we constructed a model of the L4 circuit, with connectivity constrained by in vitro measurements. The model explores the various synaptic conductance strengths for which L4 FS neurons actively suppress baseline and movement-related activity in layer 4 excitatory neurons. Feedforward inhibition, in concert with recurrent intracortical circuitry, produces tactile suppression. Synaptic delays in feedforward inhibition allow transmission of temporally brief volleys of activity associated with touch. Our model provides a mechanistic explanation of a behavior-related computation implemented by the thalamocortical circuit.

}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1005576}, author = {Gutnisky, Diego Adrian and Yu, Jianing and Hires, Samuel Andrew and To, Minh-Son and Bale, Michael and Svoboda, Karel and Golomb, David} } @article {48954, title = {Neural mechanisms of movement planning: motor cortex and beyond.}, journal = {Current Opinion in Neurobiology}, volume = {49}, year = {2017}, month = {2017 Nov 20}, pages = {33-41}, abstract = {

Neurons in motor cortex and connected brain regions fire in anticipation of specific movements, long before movement occurs. This neural activity reflects internal processes by which the brain plans and executes volitional movements. The study of motor planning offers an opportunity to understand how the structure and dynamics of neural circuits support persistent internal states and how these states influence behavior. Recent advances in large-scale neural recordings are beginning to decipher the relationship of the dynamics of populations of neurons during motor planning and movements. New behavioral tasks in rodents, together with quantified perturbations, link dynamics in specific nodes of neural circuits to behavior. These studies reveal a neural network distributed across multiple brain regions that collectively supports motor planning. We review recent advances and highlight areas where further work is needed to achieve a deeper understanding of the mechanisms underlying motor planning and related cognitive processes.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2017.10.023}, author = {Svoboda, Karel and Li, Nuo} } @article {48549, title = {Neural signatures of dynamic stimulus selection in Drosophila.}, journal = {Nature Neuroscience}, volume = {20}, year = {2017}, month = {2017 Jun 12}, pages = {1104-13}, abstract = {

Many animals orient using visual cues, but how a single cue is selected from among many is poorly understood. Here we show that Drosophila ring neurons{\textemdash}central brain neurons implicated in navigation{\textemdash}display visual stimulus selection. Using\ in vivo\ two-color two-photon imaging with genetically encoded calcium indicators, we demonstrate that individual ring neurons inherit simple-cell-like receptive fields from their upstream partners. Stimuli in the contralateral visual field suppressed responses to ipsilateral stimuli in both populations. Suppression strength depended on when and where the contralateral stimulus was presented, an effect stronger in ring neurons than in their upstream inputs. This history-dependent effect on the temporal structure of visual responses, which was well modeled by a simple biphasic filter, may determine how visual references are selected for the fly{\textquoteright}s internal compass. Our approach highlights how two-color calcium imaging can help identify and localize the origins of sensory transformations across synaptically connected neural populations.

}, doi = {10.1038/nn.4581}, author = {Sun, Yi and Nern, Aljoscha and Franconville, Romain and Dana, Hod and Schreiter, Eric R and Looger, Loren L and Svoboda, Karel and Kim, Douglas S and Hermundstad, Ann M and Jayaraman, Vivek} } @inbook {48598, title = {Flow of information underlying a tactile decision in mice.}, booktitle = {Micro-, Meso- and Macro-Dynamics of the Brain}, year = {2016}, abstract = {

Motor planning allows us to conceive, plan, and initiate skilled motor behaviors. Motor planning involves activity distributed widely across the cortex. How this activity dynamically comes together to guide movement remains an unsolved problem. We study motor planning in mice performing a tactile decision behavior. Head-fixed mice discriminate object locations with their whiskers and report their choice by directional licking ({\textquotedblleft}lick left{\textquotedblright}/{\textquotedblleft}lick right{\textquotedblright}). A short-term memory component separates tactile {\textquotedblleft}sensation{\textquotedblright} and {\textquotedblleft}action{\textquotedblright} into distinct epochs. Using loss-of-function experiments, cell-type specific electrophysiology, and cellular imaging, we delineate when and how activity in specific brain areas and cell types drives motor planning in mice. Our results suggest that information flows serially from sensory to motor areas during motor planning. The motor cortex circuit maintains the motor plan during short-term memory and translates the motor plan into motor commands that drive the upcoming directional licking.

}, doi = {10.1007/978-3-319-28802-4_3}, author = {Li, Nuo and Guo, Zengcai V and Chen, Tsai-Wen and Svoboda, Karel} } @article {47551, title = {A large field of view two-photon mesoscope with subcellular resolution for in vivo imaging.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 Jun 14}, pages = {e14472}, abstract = {

Imaging is used to map activity across populations of neurons. Microscopes with cellular resolution have small (\<1 millimeter) fields of view and cannot simultaneously image activity distributed across multiple brain areas. Typical large field of view microscopes do not resolve single cells, especially in the axial dimension. We developed a 2-photon random access mesoscope (2p-RAM) that allows high-resolution imaging anywhere within a volume spanning multiple brain areas (∅ 5 mm x 1 mm cylinder). 2p-RAM resolution is near diffraction limited (lateral, 0.66 μm, axial 4.09 μm at the center; excitation wavelength = 970 nm; numerical aperture = 0.6) over a large range of excitation wavelengths. A fast three-dimensional scanning system allows efficient sampling of neural activity in arbitrary regions of interest across the entire imaging volume. We illustrate the use of the 2p-RAM by imaging neural activity in multiple, non-contiguous brain areas in transgenic mice expressing protein calcium sensors.

}, issn = {2050-084X}, doi = {10.7554/eLife.14472}, author = {Sofroniew, Nicholas James and Flickinger, Daniel and King, Jonathon and Svoboda, Karel} } @article {47974, title = {Layer 4 fast-spiking interneurons filter thalamocortical signals during active somatosensation.}, journal = {Nature Neuroscience}, volume = {19}, year = {2016}, month = {2016 Oct 17}, pages = {1647-57}, abstract = {

We rely on movement to explore the environment, for example, by palpating an object. In somatosensory cortex, activity related to movement of digits or whiskers is suppressed, which could facilitate detection of touch. Movement-related suppression is generally assumed to involve corollary discharges. Here we uncovered a thalamocortical mechanism in which cortical fast-spiking interneurons, driven by sensory input, suppress movement-related activity in layer 4 (L4) excitatory neurons. In mice locating objects with their whiskers, neurons in the ventral posteromedial nucleus (VPM) fired in response to touch and whisker movement. Cortical L4 fast-spiking interneurons inherited these responses from VPM. In contrast, L4 excitatory neurons responded mainly to touch. Optogenetic experiments revealed that fast-spiking interneurons reduced movement-related spiking in excitatory neurons, enhancing selectivity for touch-related information during active tactile sensation. These observations suggest a fundamental computation performed by the thalamocortical circuit to accentuate salient tactile information.

}, issn = {1546-1726}, doi = {10.1038/nn.4412}, author = {Yu, Jianing and Gutnisky, Diego A and Hires, S Andrew and Svoboda, Karel} } @article {47274, title = {A platform for brain-wide imaging and reconstruction of individual neurons.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 Jan 20}, abstract = {

The structure of axonal arbors controls how signals from individual neurons are routed within the mammalian brain. However, the arbors of very few long-range projection neurons have been reconstructed in their entirety, as axons with diameters as small as 100 nm arborize in target regions dispersed over many millimeters of tissue. We introduce a platform for high-resolution, three-dimensional fluorescence imaging of complete tissue volumes that enables the visualization and reconstruction of long-range axonal arbors. This platform relies on a high-speed two-photon microscope integrated with a tissue vibratome and a suite of computational tools for large-scale image data. We demonstrate the power of this approach by reconstructing the axonal arbors of multiple neurons in the motor cortex across a single mouse brain.

}, issn = {2050-084X}, doi = {10.7554/eLife.10566}, author = {Economo, Michael N and Clack, Nathan G and Lavis, Luke D and Gerfen, Charles R and Svoboda, Karel and Myers, Eugene W and Chandrashekar, Jayaram} } @article {47425, title = {Robust neuronal dynamics in premotor cortex during motor planning.}, journal = {Nature}, year = {2016}, month = {2016 Apr 13}, abstract = {

Neural activity maintains representations that bridge past and future events, often over many seconds. Network models can produce persistent and ramping activity, but the positive feedback that is critical for these slow dynamics can cause sensitivity to perturbations. Here we use electrophysiology and optogenetic perturbations in the mouse premotor cortex to probe the robustness of persistent neural representations during motor planning. We show that preparatory activity is remarkably robust to large-scale unilateral silencing: detailed neural dynamics that drive specific future movements were quickly and selectively restored by the network. Selectivity did not recover after bilateral silencing of the premotor cortex. Perturbations to one hemisphere are thus corrected by information from the other hemisphere. Corpus callosum bisections demonstrated that premotor cortex hemispheres can maintain preparatory activity independently. Redundancy across selectively coupled modules, as we observed in the premotor cortex, is a hallmark of robust control systems. Network models incorporating these principles show robustness that is consistent with data.

}, issn = {1476-4687}, doi = {10.1038/nature17643}, author = {Li, Nuo and Daie, Kayvon and Svoboda, Karel and Druckmann, Shaul} } @article {47396, title = {Sensitive red protein calcium indicators for imaging neural activity.}, journal = {eLife}, volume = {5}, year = {2016}, month = {2016 Mar 24}, abstract = {

Genetically encoded calcium indicators (GECIs) allow measurement of activity in large populations of neurons and in small neuronal compartments, over times of milliseconds to months. Although GFP-based GECIs are widely used for in vivo neurophysiology, GECIs with red-shifted excitation and emission spectra have advantages for in vivo imaging because of reduced scattering and absorption in tissue, and a consequent reduction in phototoxicity. However, current red GECIs are inferior to the state-of-the-art GFP-based GCaMP6 indicators for detecting and quantifying neural activity. Here we present improved red GECIs based on mRuby (jRCaMP1a, b) and mApple (jRGECO1a), with sensitivity comparable to GCaMP6. We characterized the performance of the new red GECIs in cultured neurons and in mouse, Drosophila, zebrafish and C. elegans in vivo. Red GECIs facilitate deep-tissue imaging, dual-color imaging together with GFP-based reporters, and the use of optogenetics in combination with calcium imaging.

}, issn = {2050-084X}, doi = {10.7554/eLife.12727}, author = {Dana, Hod and Mohar, Boaz and Sun, Yi and Narayan, Sujatha and Gordus, Andrew and Hasseman, Jeremy P and Tsegaye, Getahun and Holt, Graham T and Hu, Amy and Walpita, Deepika and Patel, Ronak and Macklin, John J and Bargmann, Cornelia I and Ahrens, Misha B and Schreiter, Eric R and Jayaraman, Vivek and Looger, Loren L and Svoboda, Karel and Kim, Douglas S} } @article {46664, title = {A cellular resolution map of barrel cortex activity during tactile behavior.}, journal = {Neuron}, volume = {86}, year = {2015}, month = {2015 Apr 21}, pages = {783-99}, abstract = {

Comprehensive measurement of neural activity remains challenging due to the large numbers of neurons in each brain area. We used volumetric two-photon imaging in mice expressing GCaMP6s and nuclear red fluorescent proteins to sample activity in 75\% of superficial barrel cortex neurons across the relevant cortical columns, approximately 12,000 neurons per animal, during performance of a single whisker object localization task. Task-related activity peaked during object palpation. An encoding model\ related activity to behavioral variables. In the column corresponding to the spared whisker, 300 layer (L) 2/3 pyramidal neurons (17\%) each encoded touch and whisker movements. Touch representation declined by half in surrounding columns; whisker movement representation was unchanged. Following the emergence of stereotyped task-related movement, sensory representations showed no measurable plasticity. Touch direction was topographically organized, with distinct organization for passive and active touch. Our work reveals sparse and spatially intermingled representations of multiple tactile features.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2015.03.027}, author = {Peron, Simon P and Freeman, Jeremy and Iyer, Vijay and Guo, Caiying and Svoboda, Karel} } @article {46590, title = {Comprehensive imaging of cortical networks.}, journal = {Current Opinion in Neurobiology}, volume = {32}, year = {2015}, month = {2015 Apr 10}, pages = {115-123}, abstract = {

Neural computations are implemented by activity in spatially distributed neural circuits. Cellular imaging fills a unique niche in linking activity of specific types of neurons to behavior, over spatial scales spanning single neurons to entire brain regions, and temporal scales from milliseconds to months. Imaging may soon make it possible to track activity of all neurons in a brain region, such as a cortical column. We review recent methodological advances that facilitate optical imaging of neuronal populations in vivo, with an emphasis on calcium imaging using protein indicators in mice. We point out areas that are particularly ripe for future developments.

}, issn = {1873-6882}, doi = {10.1016/j.conb.2015.03.016}, author = {Peron, Simon and Chen, Tsai-Wen and Svoboda, Karel} } @article {46524, title = {Dual-channel circuit mapping reveals sensorimotor convergence in the primary motor cortex.}, journal = {The Journal of Neuroscience}, volume = {35}, year = {2015}, month = {2015 Mar 11}, pages = {4418-26}, abstract = {

Cortical cells integrate synaptic input from multiple sources, but how these different inputs are distributed across individual neurons is largely unknown. Differences in input might account for diverse responses in neighboring neurons during behavior. We present a strategy for comparing the strengths of multiple types of input onto the same neuron. We developed methods for independent dual-channel photostimulation of synaptic inputs using ChR2 together with ReaChR, a red-shifted channelrhodopsin. We used dual-channel photostimulation to probe convergence of sensory information in the mouse primary motor cortex. Input from somatosensory cortex and thalamus converges in individual neurons. Similarly, inputs from distinct somatotopic regions of the somatosensory cortex are integrated at the level of single motor cortex neurons. We next developed a ReaChR transgenic mouse under the control of both Flp- and Cre-recombinases that is an effective tool for circuit mapping. Our approach to dual-channel photostimulation enables quantitative comparison of the strengths of multiple pathways across all length scales of the brain.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3741-14.2015}, author = {Hooks, Bryan M and Lin, John Y and Guo, Caiying and Svoboda, Karel} } @article {46987, title = {Low-noise encoding of active touch by layer 4 in the somatosensory cortex.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015 Aug 6}, abstract = {

Cortical spike trains often appear noisy, with the timing and number of spikes varying across repetitions of stimuli. Spiking variability can arise from internal (behavioral state, unreliable neurons, or chaotic dynamics in neural circuits) and external (uncontrolled behavior or sensory stimuli) sources. The amount of irreducible internal noise in spike trains, an important constraint on models of cortical networks, has been difficult to estimate, since behavior and brain state must be precisely controlled or tracked. We recorded from excitatory barrel cortex neurons in layer 4 during active behavior, where mice control tactile input through learned whisker movements. Touch was the dominant sensorimotor feature, with \>70\% spikes occurring in millisecond timescale epochs after touch onset. The variance of touch responses was smaller than expected from Poisson processes, often reaching the theoretical minimum. Layer 4 spike trains thus reflect the millisecond-timescale structure of tactile input with little noise.

}, issn = {2050-084X}, doi = {10.7554/eLife.06619}, author = {Andrew Hires, Samuel and Gutnisky, Diego A and Yu, Jianing and O{\textquoteright}Connor, Daniel H and Svoboda, Karel} } @article {47354, title = {Neural coding in barrel cortex during whisker-guided locomotion.}, journal = {eLife}, volume = {4}, year = {2015}, month = {2015 Dec 23}, abstract = {

Animals seek out relevant information by moving through a dynamic world, but sensory systems are usually studied under highly constrained and passive conditions that may not probe important dimensions of the neural code. Here, we explored neural coding in the barrel cortex of head-fixed mice that tracked walls with their whiskers in tactile virtual reality. Optogenetic manipulations revealed that barrel cortex plays a role in wall-tracking. Closed-loop optogenetic control of layer 4 neurons can substitute for whisker-object contact to guide behavior resembling wall tracking. We measured neural activity using two-photon calcium imaging and extracellular recordings. Neurons were tuned to the distance between the animal snout and the contralateral wall, with monotonic, unimodal, and multimodal tuning curves. This rich representation of object location in the barrel cortex could not be predicted based on simple stimulus-response relationships involving individual whiskers and likely emerges within cortical circuits.

}, issn = {2050-084X}, doi = {10.7554/eLife.12559}, author = {Sofroniew, Nicholas James and Vlasov, Yurii A and Andrew Hires, Samuel and Freeman, Jeremy and Svoboda, Karel} } @article {46314, title = {Whisking.}, journal = {Current Biology}, volume = {25}, year = {2015}, month = {2015 Feb 16}, pages = {R137-40}, abstract = {

Eyes may be {\textquoteright}the window to the soul{\textquoteright} in humans, but whiskers provide a better path to the inner lives of rodents. The brain has remarkable abilities to focus its limited resources on information that matters, while ignoring a cacophony of distractions. While inspecting a visual scene, primates foveate to multiple salient locations, for example mouths and eyes in images of people, and ignore the rest. Similar processes have now been observed and studied in rodents in the context of whisker-based tactile sensation. Rodents use their mechanosensitive whiskers for a diverse range of tactile behaviors such as navigation, object recognition and social interactions. These animals move their whiskers in a purposive manner to locations of interest. The shapes of whiskers, as well as their movements, are exquisitely adapted for tactile exploration in the dark tight burrows where many rodents live. By studying whisker movements during tactile behaviors, we can learn about the tactile information available to rodents through their whiskers and how rodents direct their attention. In this primer, we focus on how the whisker movements of rats and mice are providing clues about the logic of active sensation and the underlying neural mechanisms.

}, issn = {1879-0445}, doi = {10.1016/j.cub.2015.01.008}, author = {Sofroniew, Nicholas J and Svoboda, Karel} } @article {6879, title = {Flow of cortical activity underlying a tactile decision in mice.}, journal = {Neuron}, volume = {81}, year = {2014}, month = {2014 Jan 8}, pages = {179-94}, abstract = {

Perceptual decisions involve distributed cortical activity. Does information flow sequentially from one cortical area to another, or do networks of interconnected areas contribute at the same time? Here we delineate when and how activity in specific areas drives a whisker-based decision in mice. A short-term memory component temporally separated tactile "sensation" and "action" (licking). Using optogenetic inhibition (spatial resolution, 2 mm; temporal resolution, 100 ms), we surveyed the neocortex for regions driving behavior during specific behavioral epochs. Barrel cortex was critical for sensation. During the short-term memory, unilateral inhibition of anterior lateral motor cortex biased responses to the ipsilateral side. Consistently, barrel cortex showed stimulus-specific activity during sensation, whereas motor cortex showed choice-specific preparatory activity and movement-related activity, consistent with roles in motor planning and movement. These results suggest serial information flow from sensory to motor areas during perceptual decision making.

}, keywords = {Action Potentials, Afferent Pathways, Animals, Cerebral Cortex, Conditioning, Decision Making, Discrimination (Psychology), Female, Green Fluorescent Proteins, Male, Mice, Motion Perception, Nerve Net, Neurons, Operant, Photic Stimulation, Rhodopsin, Touch, Transgenic, Vesicular Inhibitory Amino Acid Transport Proteins, Vibrissae}, issn = {1097-4199}, doi = {10.1016/j.neuron.2013.10.020}, author = {Guo, Zengcai V and Li, Nuo and Huber, Daniel and Ophir, Eran and Gutnisky, Diego and Ting, Jonathan T and Feng, Guoping and Svoboda, Karel} } @article {45062, title = {Natural whisker-guided behavior by head-fixed mice in tactile virtual reality.}, journal = {Journal of Neuroscience}, volume = {34}, year = {2014}, month = {2014 Jul 16}, pages = {9537-50}, abstract = {

During many natural behaviors the relevant sensory stimuli and motor outputs are difficult to quantify. Furthermore, the high dimensionality of the space of possible stimuli and movements compounds the problem of experimental control. Head fixation facilitates stimulus control and movement tracking, and can be combined with techniques for recording and manipulating neural activity. However, head-fixed mouse behaviors are typically trained through extensive instrumental conditioning. Here we present a whisker-based, tactile virtual reality system for head-fixed mice running on a spherical treadmill. Head-fixed mice displayed natural movements, including running and rhythmic whisking at 16 Hz. Whisking was centered on a set point that changed in concert with running so that more protracted whisking was correlated with faster running. During turning, whiskers moved in an asymmetric manner, with more retracted whisker positions in the turn direction and protracted whisker movements on the other side. Under some conditions, whisker movements were phase-coupled to strides. We simulated a virtual reality tactile corridor, consisting of two moveable walls controlled in a closed-loop by running speed and direction. Mice used their whiskers to track the walls of the winding corridor without training. Whisker curvature changes, which cause forces in the sensory follicles at the base of the whiskers, were tightly coupled to distance from the walls. Our behavioral system allows for precise control of sensorimotor variables during natural tactile navigation.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.0712-14.2014}, author = {Sofroniew, Nicholas J and Cohen, Jeremy D and Lee, Albert K and Svoboda, Karel} } @article {6897, title = {Procedures for behavioral experiments in head-fixed mice.}, journal = {PLoS One}, volume = {9}, year = {2014}, month = {2014}, pages = {e88678}, abstract = {

The mouse is an increasingly prominent model for the analysis of mammalian neuronal circuits. Neural circuits ultimately have to be probed during behaviors that engage the circuits. Linking circuit dynamics to behavior requires precise control of sensory stimuli and measurement of body movements. Head-fixation has been used for behavioral research, particularly in non-human primates, to facilitate precise stimulus control, behavioral monitoring and neural recording. However, choice-based, perceptual decision tasks by head-fixed mice have only recently been introduced. Training mice relies on motivating mice using water restriction. Here we describe procedures for head-fixation, water restriction and behavioral training for head-fixed mice, with a focus on active, whisker-based tactile behaviors. In these experiments mice had restricted access to water (typically 1 ml/day). After ten days of water restriction, body weight stabilized at approximately 80\% of initial weight. At that point mice were trained to discriminate sensory stimuli using operant conditioning. Head-fixed mice reported stimuli by licking in go/no-go tasks and also using a forced choice paradigm using a dual lickport. In some cases mice learned to discriminate sensory stimuli in a few trials within the first behavioral session. Delay epochs lasting a second or more were used to separate sensation (e.g. tactile exploration) and action (i.e. licking). Mice performed a variety of perceptual decision tasks with high performance for hundreds of trials per behavioral session. Up to four months of continuous water restriction showed no adverse health effects. Behavioral performance correlated with the degree of water restriction, supporting the importance of controlling access to water. These behavioral paradigms can be combined with cellular resolution imaging, random access photostimulation, and whole cell recordings.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0088678}, author = {Guo, Zengcai V and Hires, S Andrew and Li, Nuo and O{\textquoteright}Connor, Daniel H and Komiyama, Takaki and Ophir, Eran and Huber, Daniel and Bonardi, Claudia and Morandell, Karin and Gutnisky, Diego and Peron, Simon and Xu, Ning-long and Cox, James and Svoboda, Karel} } @article {6963, title = {Structural plasticity within the barrel cortex during initial phases of whisker-dependent learning.}, journal = {The Journal of Neuroscience}, volume = {34}, year = {2014}, month = {2014 Apr 23}, pages = {6078-83}, abstract = {

We report learning-related structural plasticity in layer 1 branches of pyramidal neurons in the barrel cortex, a known site of sensorimotor integration. In mice learning an active, whisker-dependent object localization task, layer 2/3 neurons showed enhanced spine growth during initial skill acquisition that both preceded and predicted expert performance. Preexisting spines were stabilized and new persistent spines were formed. These findings suggest rapid changes in connectivity between motor centers and sensory cortex guide subsequent sensorimotor learning.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.4919-12.2014}, author = {Kuhlman, Sandra J and O{\textquoteright}Connor, Daniel H and Fox, Kevin and Svoboda, Karel} } @article {45353, title = {Thy1 - GCaMP6 transgenic mice for neuronal population imaging in vivo.}, journal = {PLoS One}, volume = {9}, year = {2014}, month = {2014}, pages = {e108697}, chapter = {e108697}, abstract = {

Genetically-encoded calcium indicators (GECIs) facilitate imaging activity of genetically defined neuronal populations in vivo. The high intracellular GECI concentrations required for in vivo imaging are usually achieved by viral gene transfer using adeno-associated viruses. Transgenic expression of GECIs promises important advantages, including homogeneous, repeatable, and stable expression without the need for invasive virus injections. Here we present the generation and characterization of transgenic mice expressing the GECIs GCaMP6s or GCaMP6f under the Thy1 promoter. We quantified GCaMP6 expression across brain regions and neurons and compared to other transgenic mice and AAV-mediated expression. We tested three mouse lines for imaging in the visual cortex in vivo and compared their performance to mice injected with AAV expressing GCaMP6. Furthermore, we show that GCaMP6 Thy1 transgenic mice are useful for long-term, high-sensitivity imaging in behaving mice.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0108697}, author = {Dana, Hod and Chen, Tsai-Wen and Hu, Amy and Shields, Brenda C and Cui, Guohong and Looger, Loren and Kim, Douglas S. and Svoboda, Karel} } @article {6158, title = {The mechanical variables underlying object localization along the axis of the whisker.}, journal = {The Journal of Neuroscience}, volume = {33}, year = {2013}, month = {2013 Apr 17}, pages = {6726-41}, abstract = {

Rodents move their whiskers to locate objects in space. Here we used psychophysical methods to show that head-fixed mice can localize objects along the axis of a single whisker, the radial dimension, with one-millimeter precision. High-speed videography allowed us to estimate the forces and bending moments at the base of the whisker, which underlie radial distance measurement. Mice judged radial object location based on multiple touches. Both the number of touches (1-17) and the forces exerted by the pole on the whisker (up to 573 μN; typical peak amplitude, 100 μN) varied greatly across trials. We manipulated the bending moment and lateral force pressing the whisker against the sides of the follicle and the axial force pushing the whisker into the follicle by varying the compliance of the object during behavior. The behavioral responses suggest that mice use multiple variables (bending moment, axial force, lateral force) to extract radial object localization. Characterization of whisker mechanics revealed that whisker bending stiffness decreases gradually with distance from the face over five orders of magnitude. As a result, the relative amplitudes of different stress variables change dramatically with radial object distance. Our data suggest that mice use distance-dependent whisker mechanics to estimate radial object location using an algorithm that does not rely on precise control of whisking, is robust to variability in whisker forces, and is independent of object compliance and object movement. More generally, our data imply that mice can measure the amplitudes of forces in the sensory follicles for tactile sensation.

}, keywords = {Algorithms, Animals, Biological, Computer Simulation, Corneal Topography, Cues, Decision Making, Electron, Exploratory Behavior, Functional Laterality, Inbred C57BL, Male, Mice, Microscopy, Models, Physical Stimulation, Psychophysics, Scanning, Time Factors, Touch, Vibrissae}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.4316-12.2013}, author = {Pammer, Lorenz and O{\textquoteright}Connor, Daniel H and Hires, S Andrew and Clack, Nathan G and Huber, Daniel and Myers, Eugene W and Svoboda, Karel} } @article {6146, title = {Neural coding during active somatosensation revealed using illusory touch.}, journal = {Nature Neuroscience}, volume = {16}, year = {2013}, month = {2013 Jun 2}, pages = {958-65}, abstract = {

Active sensation requires the convergence of external stimuli with representations of body movements. We used mouse behavior, electrophysiology and optogenetics to dissect the temporal interactions among whisker movement, neural activity and sensation of touch. We photostimulated layer 4 activity in single barrels in a closed loop with whisking. Mimicking touch-related neural activity caused illusory perception of an object at a particular location, but scrambling the timing of the spikes over one whisking cycle (tens of milliseconds) did not abolish the illusion, indicating that knowledge of instantaneous whisker position is unnecessary for discriminating object locations. The illusions were induced only during bouts of directed whisking, when mice expected touch, and in the relevant barrel. Reducing activity biased behavior, consistent with a spike count code for object detection at a particular location. Our results show that mice integrate coding of touch with movement over timescales of a whisking bout to produce perception of active touch.

}, issn = {1546-1726}, doi = {10.1038/nn.3419}, author = {O{\textquoteright}Connor, Daniel H and Hires, S Andrew and Guo, Zengcai V and Li, Nuo and Yu, Jianing and Sun, Qian-Quan and Huber, Daniel and Svoboda, Karel} } @article {6579, title = {A neuron-based screening platform for optimizing genetically-encoded calcium indicators.}, journal = {PLoS One}, volume = {8}, year = {2013}, month = {2013}, pages = {e77728}, abstract = {

Fluorescent protein-based sensors for detecting neuronal activity have been developed largely based on non-neuronal screening systems. However, the dynamics of neuronal state variables (e.g., voltage, calcium, etc.) are typically very rapid compared to those of non-excitable cells. We developed an electrical stimulation and fluorescence imaging platform based on dissociated rat primary neuronal cultures. We describe its use in testing genetically-encoded calcium indicators (GECIs). Efficient neuronal GECI expression was achieved using lentiviruses containing a neuronal-selective gene promoter. Action potentials (APs) and thus neuronal calcium levels were quantitatively controlled by electrical field stimulation, and fluorescence images were recorded. Images were segmented to extract fluorescence signals corresponding to individual GECI-expressing neurons, which improved sensitivity over full-field measurements. We demonstrate the superiority of screening GECIs in neurons compared with solution measurements. Neuronal screening was useful for efficient identification of variants with both improved response kinetics and high signal amplitudes. This platform can be used to screen many types of sensors with cellular resolution under realistic conditions where neuronal state variables are in relevant ranges with respect to timing and amplitude.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0077728}, author = {Wardill, Trevor J. and Chen, Tsai-Wen and Schreiter, Eric R and Hasseman, Jeremy P and Tsegaye, Getahun and Fosque, Benjamin F and Behnam, Reza and Shields, Brenda C and Ramirez, Melissa and Kimmel, Bruce E and Kerr, Rex A and Jayaraman, Vivek and Looger, Loren L and Svoboda, Karel and Kim, Douglas S.} } @article {6295, title = {Organization of cortical and thalamic input to pyramidal neurons in mouse motor cortex.}, journal = {The Journal of Neuroscience}, volume = {33}, year = {2013}, month = {2013 Jan 9}, pages = {748-60}, abstract = {

Determining how long-range synaptic inputs engage pyramidal neurons in primary motor cortex (M1) is important for understanding circuit mechanisms involved in regulating movement. We used channelrhodopsin-2-assisted circuit mapping to characterize the long-range excitatory synaptic connections made by multiple cortical and thalamic areas onto pyramidal neurons in mouse vibrissal motor cortex (vM1). Each projection innervated vM1 pyramidal neurons with a unique laminar profile. Collectively, the profiles for different sources of input partially overlapped and spanned all cortical layers. Specifically, orbital cortex (OC) inputs primarily targeted neurons in L6. Secondary motor cortex (M2) inputs excited neurons mainly in L5B, including pyramidal tract neurons. In contrast, thalamocortical inputs from anterior motor-related thalamic regions, including VA/VL (ventral anterior thalamic nucleus/ventrolateral thalamic nucleus), targeted neurons in L2/3 through L5B, but avoided L6. Inputs from posterior sensory-related thalamic areas, including POm (posterior thalamic nuclear group), targeted neurons only in the upper layers (L2/3 and L5A), similar to inputs from somatosensory (barrel) cortex. Our results show that long-range excitatory inputs target vM1 pyramidal neurons in a layer-specific manner. Inputs from sensory-related cortical and thalamic areas preferentially target the upper-layer pyramidal neurons in vM1. In contrast, inputs from OC and M2, areas associated with volitional and cognitive aspects of movements, bypass local circuitry and have direct monosynaptic access to neurons projecting to brainstem and thalamus.

}, keywords = {Animals, Cerebral Cortex, Data Interpretation, Efferent Pathways, Electric Stimulation, Electrophysiological Phenomena, Female, Inbred C57BL, Male, Mice, Motor Cortex, Neurons, Patch-Clamp Techniques, Pons, Pyramidal Tracts, Statistical, Thalamus}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.4338-12.2013}, author = {Hooks, Bryan M and Mao, Tianyi and Gutnisky, Diego A and Yamawaki, Naoki and Svoboda, Karel and Shepherd, Gordon M G} } @article {6889, title = {Tapered whiskers are required for active tactile sensation.}, journal = {eLife}, volume = {2}, year = {2013}, month = {2013 Nov 19}, pages = {e01350}, abstract = {

Many mammals forage and burrow in dark constrained spaces. Touch through facial whiskers is important during these activities, but the close quarters makes whisker deployment challenging. The diverse shapes of facial whiskers reflect distinct ecological niches. Rodent whiskers are conical, often with a remarkably linear taper. Here we use theoretical and experimental methods to analyze interactions of mouse whiskers with objects. When pushed into objects, conical whiskers suddenly slip at a critical angle. In contrast, cylindrical whiskers do not slip for biologically plausible movements. Conical whiskers sweep across objects and textures in characteristic sequences of brief sticks and slips, which provide information about the tactile world. In contrast, cylindrical whiskers stick and remain stuck, even when sweeping across fine textures. Thus the conical whisker structure is adaptive for sensor mobility in constrained environments and in feature extraction during active haptic exploration of objects and surfaces. DOI: http://dx.doi.org/10.7554/eLife.01350.001.

}, issn = {2050-084X}, doi = {10.7554/eLife.01350}, author = {Hires, Samuel Andrew and Pammer, Lorenz and Svoboda, Karel and Golomb, David} } @article {6674, title = {Thalamocortical input onto layer 5 pyramidal neurons measured using quantitative large-scale array tomography.}, journal = {Frontiers in Neural Circuits}, volume = {7}, year = {2013}, month = {2013}, pages = {177}, abstract = {

The subcellular locations of synapses on pyramidal neurons strongly influences dendritic integration and synaptic plasticity. Despite this, there is little quantitative data on spatial distributions of specific types of synaptic input. Here we use array tomography (AT), a high-resolution optical microscopy method, to examine thalamocortical (TC) input onto layer 5 pyramidal neurons. We first verified the ability of AT to identify synapses using parallel electron microscopic analysis of TC synapses in layer 4. We then use large-scale array tomography (LSAT) to measure TC synapse distribution on L5 pyramidal neurons in a 1.00 {\texttimes} 0.83 {\texttimes} 0.21 mm(3) volume of mouse somatosensory cortex. We found that TC synapses primarily target basal dendrites in layer 5, but also make a considerable input to proximal apical dendrites in L4, consistent with previous work. Our analysis further suggests that TC inputs are biased toward certain branches and, within branches, synapses show significant clustering with an excess of TC synapse nearest neighbors within 5-15 μm compared to a random distribution. Thus, we show that AT is a sensitive and quantitative method to map specific types of synaptic input on the dendrites of entire neurons. We anticipate that this technique will be of wide utility for mapping functionally-relevant anatomical connectivity in neural circuits.

}, issn = {1662-5110}, doi = {10.3389/fncir.2013.00177}, author = {Rah, Jong-Cheol and Bas, Erhan and Colonell, Jennifer and Mishchenko, Yuriy and Karsh, Bill and Fetter, Richard D and Myers, Eugene W and Chklovskii, Dmitri B and Svoboda, Karel and Harris, Timothy D and Isaac, John T R} } @article {6124, title = {Ultrasensitive fluorescent proteins for imaging neuronal activity.}, journal = {Nature}, volume = {499}, year = {2013}, month = {2013 Jul 18}, pages = {295-300}, abstract = {

Fluorescent calcium sensors are widely used to image neural activity. Using structure-based mutagenesis and neuron-based screening, we developed a family of ultrasensitive protein calcium sensors (GCaMP6) that outperformed other sensors in cultured neurons and in zebrafish, flies and mice in vivo. In layer 2/3 pyramidal neurons of the mouse visual cortex, GCaMP6 reliably detected single action potentials in neuronal somata and orientation-tuned synaptic calcium transients in individual dendritic spines. The orientation tuning of structurally persistent spines was largely stable over timescales of weeks. Orientation tuning averaged across spine populations predicted the tuning of their parent cell. Although the somata of GABAergic neurons showed little orientation tuning, their dendrites included highly tuned dendritic segments (5{\textendash}40-{\textmu}m long). GCaMP6 sensors thus provide new windows into the organization and dynamics of neural circuits over multiple spatial and temporal scales.

}, doi = {10.1038/nature12354}, author = {Chen, Tsai-Wen and Wardill, Trevor J. and Sun, Yi and Pulvar, Stefan R. and Renninger, Sabine L. and Baohan, Amy and Schreiter, Eric R and Kerr, Rex A and Orger, Michael B. and Jayaraman, Vivek and Looger, Loren L and Svoboda, Karel and Kim, Douglas S.} } @article {5162, title = {Activity in motor-sensory projections reveals distributed coding in somatosensation.}, journal = {Nature}, volume = {489}, year = {2012}, month = {2012 Sep 13}, pages = {299-303}, abstract = {

Cortical-feedback projections to primary sensory areas terminate most heavily in layer 1 (L1) of the neocortex, where they make synapses with tuft dendrites of pyramidal neurons. L1 input is thought to provide {\textquoteleft}contextual{\textquoteright} information, but the signals transmitted by L1 feedback remain uncharacterized. In the rodent somatosensory system, the spatially diffuse feedback projection from vibrissal motor cortex (vM1) to vibrissal somatosensory cortex (vS1, also known as the barrel cortex) may allow whisker touch to be interpreted in the context of whisker position to compute object location. When mice palpate objects with their whiskers to localize object features, whisker touch excites vS1 and later vM1 in a somatotopic manner. Here we use axonal calcium imaging to track activity in vM1{\textendash}\>vS1 afferents in L1 of the barrel cortex while mice performed whisker-dependent object localization. Spatially intermingled individual axons represent whisker movements, touch and other behavioural features. In a subpopulation of axons, activity depends on object location and persists for seconds after touch. Neurons in the barrel cortex thus have information to integrate movements and touches of multiple whiskers over time, key components of object identification and navigation by active touch.

}, issn = {1476-4687}, doi = {10.1038/nature11321}, author = {Petreanu, Leopoldo and Gutnisky, Diego A and Huber, Daniel and Xu, Ning-long and O{\textquoteright}Connor, Dan H and Tian, Lin and Looger, Loren and Svoboda, Karel} } @article {5200, title = {Automated tracking of whiskers in videos of head fixed rodents.}, journal = {PLoS Computational Biology}, volume = {8}, year = {2012}, month = {2012 Jul}, pages = {e1002591}, abstract = {

We have developed software for fully automated tracking of vibrissae (whiskers) in high-speed videos (\>500 Hz) of head-fixed, behaving rodents trimmed to a single row of whiskers. Performance was assessed against a manually curated dataset consisting of 1.32 million video frames comprising 4.5 million whisker traces. The current implementation detects whiskers with a recall of 99.998\% and identifies individual whiskers with 99.997\% accuracy. The average processing rate for these images was 8 Mpx/s/cpu (2.6 GHz Intel Core2, 2 GB RAM). This translates to 35 processed frames per second for a 640 px{\texttimes}352 px video of 4 whiskers. The speed and accuracy achieved enables quantitative behavioral studies where the analysis of millions of video frames is required. We used the software to analyze the evolving whisking strategies as mice learned a whisker-based detection task over the course of 6 days (8148 trials, 25 million frames) and measure the forces at the sensory follicle that most underlie haptic perception.

}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1002591}, author = {Clack, Nathan G and O{\textquoteright}Connor, Daniel H and Huber, Daniel and Petreanu, Leopoldo and Hires, Andrew and Peron, Simon and Svoboda, Karel and Myers, Eugene W} } @article {4601, title = {A Cre-dependent GCaMP3 reporter mouse for neuronal imaging in vivo.}, journal = {The Journal of Neuroscience}, volume = {32}, year = {2012}, month = {2012 Feb 29}, pages = {3131-41}, abstract = {

Fluorescent calcium indicator proteins, such as GCaMP3, allow imaging of activity in genetically defined neuronal populations. GCaMP3 can be expressed using various gene delivery methods, such as viral infection or electroporation. However, these methods are invasive and provide inhomogeneous and nonstationary expression. Here, we developed a genetic reporter mouse, Ai38, which expresses GCaMP3 in a Cre-dependent manner from the ROSA26 locus, driven by a strong CAG promoter. Crossing Ai38 with appropriate Cre mice produced robust GCaMP3 expression in defined cell populations in the retina, cortex, and cerebellum. In the primary visual cortex, visually evoked GCaMP3 signals showed normal orientation and direction selectivity. GCaMP3 signals were rapid, compared with virally expressed GCaMP3 and synthetic calcium indicators. In the retina, Ai38 allowed imaging spontaneous calcium waves in starburst amacrine cells during development, and light-evoked responses in ganglion cells in adult tissue. Our results show that the Ai38 reporter mouse provides a flexible method for targeted expression of GCaMP3.

}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.4469-11.2012}, author = {Zariwala, Hatim A and Borghuis, Bart G and Hoogland, Tycho M and Madisen, Linda and Tian, Lin and De Zeeuw, Chris I and Zeng, Hongkui and Looger, Loren L and Svoboda, Karel and Chen, Tsai-Wen} } @article {6294, title = {Nonlinear dendritic integration of sensory and motor input during an active sensing task.}, journal = {Nature}, volume = {492}, year = {2012}, month = {2012 Dec 13}, pages = {247-51}, abstract = {

Active dendrites provide neurons with powerful processing capabilities. However, little is known about the role of neuronal dendrites in behaviourally related circuit computations. Here we report that a novel global dendritic nonlinearity is involved in the integration of sensory and motor information within layer 5 pyramidal neurons during an active sensing behaviour. Layer 5 pyramidal neurons possess elaborate dendritic arborizations that receive functionally distinct inputs, each targeted to spatially separate regions. At the cellular level, coincident input from these segregated pathways initiates regenerative dendritic electrical events that produce bursts of action potential output and circuits featuring this powerful dendritic nonlinearity can implement computations based on input correlation. To examine this in vivo we recorded dendritic activity in layer 5 pyramidal neurons in the barrel cortex using two-photon calcium imaging in mice performing an object-localization task. Large-amplitude, global calcium signals were observed throughout the apical tuft dendrites when active touch occurred at particular object locations or whisker angles. Such global calcium signals are produced by dendritic plateau potentials that require both vibrissal sensory input and primary motor cortex activity. These data provide direct evidence of nonlinear dendritic processing of correlated sensory and motor information in the mammalian neocortex during active sensation.

}, keywords = {Animal, Animals, Behavior, Calcium, Dendrites, Inbred C57BL, Male, Mice, Motor Activity, Patch-Clamp Techniques, Pyramidal Cells, Sensation, Signal Transduction}, issn = {1476-4687}, doi = {10.1038/nature11601}, author = {Xu, Ning-long and Harnett, Mark T and Williams, Stephen R and Huber, Daniel and O{\textquoteright}Connor, Daniel H and Svoboda, Karel and Magee, Jeffrey C} } @article {5164, title = {Optimization of a GCaMP calcium indicator for neural activity imaging.}, journal = {The Journal of Neuroscience}, volume = {32}, year = {2012}, month = {2012 Oct 3}, pages = {13819-40}, chapter = {13819}, abstract = {

Genetically encoded calcium indicators (GECIs) are powerful tools for systems neuroscience. Recent efforts in protein engineering have significantly increased the performance of GECIs. The state-of-the art single-wavelength GECI, GCaMP3, has been deployed in a number of model organisms and can reliably detect three or more action potentials in short bursts in several systems in vivo . Through protein structure determination, targeted mutagenesis, high-throughput screening, and a battery of in vitro assays, we have increased the dynamic range of GCaMP3 by severalfold, creating a family of {\textquotedblleft}GCaMP5{\textquotedblright} sensors. We tested GCaMP5s in several systems: cultured neurons and astrocytes, mouse retina, and in vivo in Caenorhabditis chemosensory neurons, Drosophila larval neuromuscular junction and adult antennal lobe, zebrafish retina and tectum, and mouse visual cortex. Signal-to-noise ratio was improved by at least 2- to 3-fold. In the visual cortex, two GCaMP5 variants detected twice as many visual stimulus-responsive cells as GCaMP3. By combining in vivo imaging with electrophysiology we show that GCaMP5 fluorescence provides a more reliable measure of neuronal activity than its predecessor GCaMP3.GCaMP5allows more sensitive detection of neural activity in vivo andmayfind widespread applications for cellular imaging in general.

}, doi = {10.1523/​JNEUROSCI.2601-12.2012}, author = {Akerboom, Jasper and Chen, Tsai-Wen and Wardill, Trevor J. and Marvin, Jonathan S and Mutlu, Sevinc and Carreras Caldero, Nicole and Esposti, Federico and Borghuis, Bart G and Sun, Xiaonan Richard and Gordus, Andrew and Orger, Michael B. and Portugues, Ruben and Engert, Florian and Macklin, John J and Filosa, Alessandro and Aggarwal, Aman and Kerr, Rex and Takagi, Ryousuke and Kracun, Sebastian and Shigetomi, Eiji and Khakh, Baljit S. and Baier, Herwig and Lagnado, Leon and Wang, Samuel S-H and Bargmann, Cornelia and Kimmel, Bruce and Jayaraman, Vivek and Svoboda, Karel and Kim, Douglas S. and Schreiter, Eric R and Looger, Loren L} } @article {4589, title = {Regular spiking and intrinsic bursting pyramidal cells show orthogonal forms of experience-dependent plasticity in layer V of barrel cortex.}, journal = {Neuron}, volume = {73}, year = {2012}, month = {2012 Jan 26}, pages = {391-404}, abstract = {

Most functional plasticity studies in the cortex have focused on layers (L) II/III and IV, whereas relatively little is known of LV. Structural measurements of dendritic spines in\ vivo suggest some specialization among LV cell subtypes. We therefore studied experience-dependent plasticity in the barrel cortex using intracellular recordings to distinguish regular spiking (RS) and intrinsic bursting (IB) subtypes. Postsynaptic potentials and suprathreshold responses in\ vivo revealed a remarkable dichotomy in RS and IB cell plasticity; spared whisker potentiation occurred in IB but not RS cells while deprived whisker depression occurred in RS but not IB cells. Similar RS/IB differences were found in the LII/III to V connections in brain slices. Modeling studies showed that subthreshold changes predicted the suprathreshold changes. These studies demonstrate the major functional partition of plasticity within a single cortical layer and reveal the LII/III to LV connection as a major excitatory locus of cortical plasticity.

}, issn = {1097-4199}, doi = {10.1016/j.neuron.2011.11.034}, author = {Jacob, Vincent and Petreanu, Leopoldo and Wright, Nick and Svoboda, Karel and Fox, Kevin} } @article {6301, title = {A toolbox of Cre-dependent optogenetic transgenic mice for light-induced activation and silencing.}, journal = {Nature Neuroscience}, volume = {15}, year = {2012}, month = {2012 May}, pages = {793-802}, abstract = {

Cell type-specific expression of optogenetic molecules allows temporally precise manipulation of targeted neuronal activity. Here we present a toolbox of four knock-in mouse lines engineered for strong, Cre-dependent expression of channelrhodopsins ChR2-tdTomato and ChR2-EYFP, halorhodopsin eNpHR3.0 and archaerhodopsin Arch-ER2. All four transgenes mediated Cre-dependent, robust activation or silencing of cortical pyramidal neurons in vitro and in vivo upon light stimulation, with ChR2-EYFP and Arch-ER2 demonstrating light sensitivity approaching that of in utero or virally transduced neurons. We further show specific photoactivation of parvalbumin-positive interneurons in behaving ChR2-EYFP reporter mice. The robust, consistent and inducible nature of our ChR2 mice represents a significant advance over previous lines, and the Arch-ER2 and eNpHR3.0 mice are to our knowledge the first demonstration of successful conditional transgenic optogenetic silencing. When combined with the hundreds of available Cre driver lines, this optimized toolbox of reporter mice will enable widespread investigations of neural circuit function with unprecedented reliability and accuracy.

}, keywords = {Action Potentials, Animals, Archaeal Proteins, Brain, Electroporation, Halorhodopsins, Integrases, Light, Luminescent Proteins, Mice, Neurogenesis, Neurons, Optics and Photonics, Proteins, Rhodopsin, Transgenic, Wakefulness}, issn = {1546-1726}, doi = {10.1038/nn.3078}, author = {Madisen, Linda and Mao, Tianyi and Koch, Henner and Zhuo, Jia-min and Berenyi, Antal and Fujisawa, Shigeyoshi and Hsu, Yun-Wei A and Garcia, Alfredo J and Gu, Xuan and Zanella, Sebastien and Kidney, Jolene and Gu, Hong and Mao, Yimei and Hooks, Bryan M and Boyden, Edward S and Buzs{\'a}ki, Gy{\"o}rgy and Ramirez, Jan Marino and Jones, Allan R and Svoboda, Karel and Han, Xue and Turner, Eric E and Zeng, Hongkui} } @article {5379, title = {DIADEMchallenge.org: a compendium of resources fostering the continuous development of automated neuronal reconstruction.}, journal = {Neuroinformatics}, volume = {9}, year = {2011}, month = {2011 Sep}, pages = {303-4}, abstract = {

Concomitant with the publication of this Special Issue of Neuroinformatics, a substantially updated version of the DIADEM web site has been released at http://diademchallenge.org. This web site was originally designed to host the challenge for automating the digital reconstruction of axonal and dendritic morphology (hence the DIADEM acronym). This post-competition version features additional content for continued use as the access point for DIADEM-related material. From the very beginning, one of the spirits of DIADEM has been to share data and resources with the neuroscience research community at large. The resources available from or linked to the DIADEM website constitute a substantial scientific legacy of the 2009/2010 competition. The new content includes finalist algorithms, image stack data, gold standard reconstructions, an updated DIADEM metric, and a retrospective on the competition in text and images.

}, doi = {10.1007/s12021-011-9104-3}, author = {Gillette, Todd A. and Brown, Kerry M. and Svoboda, Karel and Liu, Yuan and Ascoli, Giorgio A.} } @article {4307, title = {From cudgel to scalpel: toward precise neural control with optogenetics.}, journal = {Nature Methods}, volume = {8}, year = {2011}, month = {2011 Jan}, pages = {30-4}, abstract = {

Optogenetics is routinely used to activate and inactivate genetically defined neuronal populations in vivo. A second optogenetic revolution will occur when spatially distributed and sparse neural assemblies can be precisely manipulated in behaving animals.

}, keywords = {Animals, Gene Expression Regulation, Genetic Techniques, Light, Neurons, Organ Specificity, Photic Stimulation}, issn = {1548-7105}, doi = {10.1038/nmeth.f.325}, author = {Peron, Simon and Svoboda, Karel} } @article {4303, title = {Laminar analysis of excitatory local circuits in vibrissal motor and sensory cortical areas.}, journal = {PLoS Biology}, volume = {9}, year = {2011}, month = {2011 Jan 4}, pages = {e1000572}, abstract = {

Rodents move their whiskers to locate and identify objects. Cortical areas involved in vibrissal somatosensation and sensorimotor integration include the vibrissal area of the primary motor cortex (vM1), primary somatosensory cortex (vS1; barrel cortex), and secondary somatosensory cortex (S2). We mapped local excitatory pathways in each area across all cortical layers using glutamate uncaging and laser scanning photostimulation. We analyzed these maps to derive laminar connectivity matrices describing the average strengths of pathways between individual neurons in different layers and between entire cortical layers. In vM1, the strongest projection was L2/3{\textrightarrow}L5. In vS1, strong projections were L2/3{\textrightarrow}L5 and L4{\textrightarrow}L3. L6 input and output were weak in both areas. In S2, L2/3{\textrightarrow}L5 exceeded the strength of the ascending L4{\textrightarrow}L3 projection, and local input to L6 was prominent. The most conserved pathways were L2/3{\textrightarrow}L5, and the most variable were L4{\textrightarrow}L2/3 and pathways involving L6. Local excitatory circuits in different cortical areas are organized around a prominent descending pathway from L2/3{\textrightarrow}L5, suggesting that sensory cortices are elaborations on a basic motor cortex-like plan.

}, keywords = {Animals, Brain Mapping, Mice, Motor Cortex, Nerve Net, Presynaptic Terminals, Somatosensory Cortex, Vibrissae}, issn = {1545-7885}, doi = {10.1371/journal.pbio.1000572}, author = {Hooks, B M and Hires, S Andrew and Zhang, Ying-Xin and Huber, Daniel and Petreanu, Leopoldo and Svoboda, Karel and Shepherd, Gordon M G} } @article {5283, title = {Long-range neuronal circuits underlying the interaction between sensory and motor cortex.}, journal = {Neuron}, volume = {72}, year = {2011}, month = {2011 Oct 6}, pages = {111-23}, abstract = {

In the rodent vibrissal system, active sensation and sensorimotor integration are mediated in part by connections between barrel cortex and vibrissal motor cortex. Little is known about how these structures interact at the level of neurons. We used Channelrhodopsin-2 (ChR2) expression, combined with anterograde and retrograde labeling, to map connections between barrel cortex and pyramidal neurons in mouse motor cortex. Barrel cortex axons preferentially targeted upper layer (L2/3, L5A) neurons in motor cortex; input to neurons projecting back to barrel cortex was particularly strong. Barrel cortex input to deeper layers (L5B, L6) of motor cortex, including neurons projecting to the brainstem, was weak, despite pronounced geometric overlap of dendrites with axons from barrel cortex. Neurons in different layers received barrel cortex input within stereotyped dendritic domains. The cortico-cortical neurons in superficial layers of motor cortex thus couple motor and sensory signals and might mediate sensorimotor integration and motor learning.

}, keywords = {Animals, Inbred C57BL, Membrane Potentials, Mice, Molecular Imaging, Motor Cortex, Neural Pathways, Neuroanatomical Tract-Tracing Techniques, Neurons, Somatosensory Cortex, Vibrissae}, issn = {1097-4199}, doi = {10.1016/j.neuron.2011.07.029}, author = {Mao, Tianyi and Kusefoglu, Deniz and Hooks, Bryan M and Huber, Daniel and Petreanu, Leopoldo and Svoboda, Karel} } @article {3892, title = {Multiple new site-specific recombinases for use in manipulating animal genomes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, year = {2011}, month = {2011 Aug 23}, pages = {14198-203}, abstract = {

Site-specific recombinases have been used for two decades to manipulate the structure of animal genomes in highly predictable ways and have become major research tools. However, the small number of recombinases demonstrated to have distinct specificities, low toxicity, and sufficient activity to drive reactions to completion in animals has been a limitation. In this report we show that four recombinases derived from yeast-KD, B2, B3, and R-are highly active and nontoxic in Drosophila and that KD, B2, B3, and the widely used FLP recombinase have distinct target specificities. We also show that the KD and B3 recombinases are active in mice.

}, issn = {1091-6490}, doi = {10.1073/pnas.1111704108}, author = {Nern, Aljoscha and Pfeiffer, Barret D and Svoboda, Karel and Rubin, Gerald M} } @article {4308, title = {The past, present, and future of single neuron reconstruction.}, journal = {Neuroinformatics}, volume = {9}, year = {2011}, month = {2011 Sep}, pages = {97-8}, issn = {1559-0089}, doi = {10.1007/s12021-011-9097-y}, author = {Svoboda, Karel} } @article {65007, title = {Ephus: multipurpose data acquisition software for neuroscience experiments.}, journal = {Front Neural Circuits}, volume = {4}, year = {2010}, month = {2010}, pages = {100}, abstract = {

Physiological measurements in neuroscience experiments often involve complex stimulus paradigms and multiple data channels. Ephus (http://www.ephus.org) is an open-source software package designed for general-purpose data acquisition and instrument control. Ephus operates as a collection of modular programs, including an ephys program for standard whole-cell recording with single or multiple electrodes in typical electrophysiological experiments, and a mapper program for synaptic circuit mapping experiments involving laser scanning photostimulation based on glutamate uncaging or channelrhodopsin-2 excitation. Custom user functions allow user-extensibility at multiple levels, including on-line analysis and closed-loop experiments, where experimental parameters can be changed based on recently acquired data, such as during in vivo behavioral experiments. Ephus is compatible with a variety of data acquisition and imaging hardware. This paper describes the main features and modules of Ephus and their use in representative experimental applications.

}, issn = {1662-5110}, doi = {10.3389/fncir.2010.00100}, author = {Suter, Benjamin A and O{\textquoteright}Connor, Timothy and Iyer, Vijay and Petreanu, Leopoldo T and Hooks, Bryan M and Kiritani, Taro and Svoboda, Karel and Shepherd, Gordon M G} } @article {4290, title = {The functional asymmetry of auditory cortex is reflected in the organization of local cortical circuits.}, journal = {Nature Neuroscience}, volume = {13}, year = {2010}, month = {2010 Nov}, pages = {1413-20}, abstract = {

The primary auditory cortex (A1) is organized tonotopically, with neurons sensitive to high and low frequencies arranged in a rostro-caudal gradient. We used laser scanning photostimulation in acute slices to study the organization of local excitatory connections onto layers 2 and 3 (L2/3) of the mouse A1. Consistent with the organization of other cortical regions, synaptic inputs along the isofrequency axis (orthogonal to the tonotopic axis) arose predominantly within a column. By contrast, we found that local connections along the tonotopic axis differed from those along the isofrequency axis: some input pathways to L3 (but not L2) arose predominantly out-of-column. In vivo cell-attached recordings revealed differences between the sound-responsiveness of neurons in L2 and L3. Our results are consistent with the hypothesis that auditory cortical microcircuitry is specialized to the one-dimensional representation of frequency in the auditory cortex.

}, keywords = {Acoustic Stimulation, Adjuvants, Amino Acids, Animals, Anisotropy, Auditory Cortex, Brain Mapping, Cholera Toxin, Confocal, Excitatory Postsynaptic Potentials, Functional Laterality, Glutamic Acid, Immunologic, Inbred C57BL, Inbred CBA, Long-Evans, Mice, Microscopy, Nerve Net, Neural Pathways, Neurons, Newborn, Nonparametric, Photic Stimulation, Psychoacoustics, Rats, Statistics, Time Factors}, issn = {1546-1726}, doi = {10.1038/nn.2659}, author = {Oviedo, Hysell V and Bureau, Ingrid and Svoboda, Karel and Zador, Anthony M} } @article {4296, title = {The functional properties of barrel cortex neurons projecting to the primary motor cortex.}, journal = {The Journal of Neuroscience}, volume = {30}, year = {2010}, month = {2010 Mar 24}, pages = {4256-60}, abstract = {

Nearby neurons, sharing the same locations within the mouse whisker map, can have dramatically distinct response properties. To understand the significance of this diversity, we studied the relationship between the responses of individual neurons and their projection targets in the mouse barrel cortex. Neurons projecting to primary motor cortex (MI) or secondary somatosensory area (SII) were labeled with red fluorescent protein (RFP) using retrograde viral infection. We used in vivo two-photon Ca(2+) imaging to map the responses of RFP-positive and neighboring L2/3 neurons to whisker deflections. Neurons projecting to MI displayed larger receptive fields compared with other neurons, including those projecting to SII. Our findings support the view that intermingled neurons in primary sensory areas send specific stimulus features to different parts of the brain.

}, keywords = {Afferent Pathways, Aniline Compounds, Animals, Brain Mapping, Calcium, Evoked Potentials, Functional Laterality, Genetic, Luminescent Proteins, Mice, Motor Cortex, Neurons, Newborn, Physical Stimulation, Somatosensory, Somatosensory Cortex, Transduction, Vibrissae, Xanthenes}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3774-09.2010}, author = {Sato, Takashi R and Svoboda, Karel} } @article {4288, title = {Learning-related fine-scale specificity imaged in motor cortex circuits of behaving mice.}, journal = {Nature}, volume = {464}, year = {2010}, month = {2010 Apr 22}, pages = {1182-6}, abstract = {

Cortical neurons form specific circuits, but the functional structure of this microarchitecture and its relation to behaviour are poorly understood. Two-photon calcium imaging can monitor activity of spatially defined neuronal ensembles in the mammalian cortex. Here we applied this technique to the motor cortex of mice performing a choice behaviour. Head-fixed mice were trained to lick in response to one of two odours, and to withhold licking for the other odour. Mice routinely showed significant learning within the first behavioural session and across sessions. Microstimulation and trans-synaptic tracing identified two non-overlapping candidate tongue motor cortical areas. Inactivating either area impaired voluntary licking. Imaging in layer 2/3 showed neurons with diverse response types in both areas. Activity in approximately half of the imaged neurons distinguished trial types associated with different actions. Many neurons showed modulation coinciding with or preceding the action, consistent with their involvement in motor control. Neurons with different response types were spatially intermingled. Nearby neurons (within approximately 150 mum) showed pronounced coincident activity. These temporal correlations increased with learning within and across behavioural sessions, specifically for neuron pairs with similar response types. We propose that correlated activity in specific ensembles of functionally related neurons is a signature of learning-related circuit plasticity. Our findings reveal a fine-scale and dynamic organization of the frontal cortex that probably underlies flexible behaviour.

}, keywords = {Animal, Animals, Axonal Transport, Behavior, Chemical, Choice Behavior, Inbred C57BL, Learning, Male, Mice, Motor Cortex, Motor Neurons, Neural Pathways, Odors, Pyramidal Cells, Reward, Stimulation, Time Factors, Tongue}, issn = {1476-4687}, doi = {10.1038/nature08897}, author = {Komiyama, Takaki and Sato, Takashi R and O{\textquoteright}Connor, Daniel H and Zhang, Ying-Xin and Huber, Daniel and Hooks, Bryan M and Gabitto, Mariano and Svoboda, Karel} } @article {4289, title = {Neural activity in barrel cortex underlying vibrissa-based object localization in mice.}, journal = {Neuron}, volume = {67}, year = {2010}, month = {2010 Sep 23}, pages = {1048-61}, abstract = {

Classical studies have related the spiking of selected neocortical neurons to behavior, but little is known about activity sampled from the entire neural population. We recorded from neurons selected independent of spiking, using cell-attached recordings and two-photon calcium imaging, in the barrel cortex of mice performing an object localization task. Spike rates varied across neurons, from silence to \>60 Hz. Responses were diverse, with some neurons showing large increases in spike rate when whiskers contacted the object. Nearly half the neurons discriminated object location; a small fraction of neurons discriminated perfectly. More active neurons were more discriminative. Layer (L) 4 and L5 contained the highest fractions of discriminating neurons (\~{}63\% and 79\%, respectively), but a few L2/3 neurons were also highly discriminating. Approximately 13,000 spikes per activated barrel column were available to mice for decision making. Coding of object location in the barrel cortex is therefore highly redundant.

}, keywords = {Action Potentials, Afferent Pathways, Animal, Animals, Behavior, Biological, Brain Mapping, Calcium, Discrimination (Psychology), Inbred C57BL, Male, Mice, Models, Neurons, Physical Stimulation, ROC Curve, Somatosensory Cortex, Vibrissae}, issn = {1097-4199}, doi = {10.1016/j.neuron.2010.08.026}, author = {O{\textquoteright}Connor, Daniel H and Peron, Simon P and Huber, Daniel and Svoboda, Karel} } @article {4298, title = {Structural plasticity underlies experience-dependent functional plasticity of cortical circuits.}, journal = {The Journal of Neuroscience}, volume = {30}, year = {2010}, month = {2010 Apr 7}, pages = {4927-32}, abstract = {

The stabilization of new spines in the barrel cortex is enhanced after whisker trimming, but its relationship to experience-dependent plasticity is unclear. Here we show that in wild-type mice, whisker potentiation and spine stabilization are most pronounced for layer 5 neurons at the border between spared and deprived barrel columns. In homozygote alphaCaMKII-T286A mice, which lack experience-dependent potentiation of responses to spared whiskers, there is no increase in new spine stabilization at the border between barrel columns after whisker trimming. Our data provide a causal link between new spine synapses and plasticity of adult cortical circuits and suggest that alphaCaMKII autophosphorylation plays a role in the stabilization but not formation of new spines.

}, keywords = {Animals, Cerebral Cortex, Dendritic Spines, Inbred C57BL, Learning, Male, Mice, Nerve Net, Neuronal Plasticity, Synapses, Transgenic, Vibrissae}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.6403-09.2010}, author = {Wilbrecht, Linda and Holtmaat, Anthony and Wright, Nick and Fox, Kevin and Svoboda, Karel} } @article {2329, title = {Vibrissa-based object localization in head-fixed mice.}, journal = {The Journal of Neuroscience}, volume = {30}, year = {2010}, month = {2010 Feb 3}, pages = {1947-67}, abstract = {

Linking activity in specific cell types with perception, cognition, and action, requires quantitative behavioral experiments in genetic model systems such as the mouse. In head-fixed primates, the combination of precise stimulus control, monitoring of motor output, and physiological recordings over large numbers of trials are the foundation on which many conceptually rich and quantitative studies have been built. Choice-based, quantitative behavioral paradigms for head-fixed mice have not been described previously. Here, we report a somatosensory absolute object localization task for head-fixed mice. Mice actively used their mystacial vibrissae (whiskers) to sense the location of a vertical pole presented to one side of the head and reported with licking whether the pole was in a target (go) or a distracter (no-go) location. Mice performed hundreds of trials with high performance (\>90\% correct) and localized to \<0.95 mm (\<6 degrees of azimuthal angle). Learning occurred over 1-2 weeks and was observed both within and across sessions. Mice could perform object localization with single whiskers. Silencing barrel cortex abolished performance to chance levels. We measured whisker movement and shape for thousands of trials. Mice moved their whiskers in a highly directed, asymmetric manner, focusing on the target location. Translation of the base of the whiskers along the face contributed substantially to whisker movements. Mice tended to maximize contact with the go (rewarded) stimulus while minimizing contact with the no-go stimulus. We conjecture that this may amplify differences in evoked neural activity between trial types.

}, keywords = {Animals, Exploratory Behavior, Head Movements, Inbred C57BL, Mice, Movement, Physical, Restraint, Somatosensory Cortex, Space Perception, Touch, Vibrissae}, issn = {1529-2401}, doi = {10.1523/JNEUROSCI.3762-09.2010}, author = {O{\textquoteright}Connor, Daniel H and Clack, Nathan G and Huber, Daniel and Komiyama, Takaki and Myers, Eugene W and Svoboda, Karel} } @article {4267, title = {Experience-dependent structural synaptic plasticity in the mammalian brain.}, journal = {Nature Reviews Neuroscience}, volume = {10}, year = {2009}, month = {2009 Sep}, pages = {647-58}, abstract = {

Synaptic plasticity in adult neural circuits may involve the strengthening or weakening of existing synapses as well as structural plasticity, including synapse formation and elimination. Indeed, long-term in vivo imaging studies are beginning to reveal the structural dynamics of neocortical neurons in the normal and injured adult brain. Although the overall cell-specific morphology of axons and dendrites, as well as of a subpopulation of small synaptic structures, are remarkably stable, there is increasing evidence that experience-dependent plasticity of specific circuits in the somatosensory and visual cortex involves cell type-specific structural plasticity: some boutons and dendritic spines appear and disappear, accompanied by synapse formation and elimination, respectively. This Review focuses on recent evidence for such structural forms of synaptic plasticity in the mammalian cortex and outlines open questions.

}, keywords = {Animals, Brain, Humans, Nerve Net, Neurogenesis, Neuronal Plasticity, Synapses}, issn = {1471-0048}, doi = {10.1038/nrn2699}, author = {Holtmaat, Anthony and Svoboda, Karel} } @article {1646, title = {Imaging neural activity in worms, flies and mice with improved GCaMP calcium indicators.}, journal = {Nature Methods}, volume = {6}, year = {2009}, month = {2009 Dec}, pages = {875-81}, abstract = {

Genetically encoded calcium indicators (GECIs) can be used to image activity in defined neuronal populations. However, current GECIs produce inferior signals compared to synthetic indicators and recording electrodes, precluding detection of low firing rates. We developed a single-wavelength GCaMP2-based GECI (GCaMP3), with increased baseline fluorescence (3-fold), increased dynamic range (3-fold) and higher affinity for calcium (1.3-fold). We detected GCaMP3 fluorescence changes triggered by single action potentials in pyramidal cell dendrites, with signal-to-noise ratio and photostability substantially better than those of GCaMP2, D3cpVenus and TN-XXL. In Caenorhabditis elegans chemosensory neurons and the Drosophila melanogaster antennal lobe, sensory stimulation-evoked fluorescence responses were significantly enhanced with GCaMP3 (4-6-fold). In somatosensory and motor cortical neurons in the intact mouse, GCaMP3 detected calcium transients with amplitudes linearly dependent on action potential number. Long-term imaging in the motor cortex of behaving mice revealed large fluorescence changes in imaged neurons over months.

}, keywords = {Animals, Brain, Caenorhabditis elegans, Calcium, Cell Line, Drosophila melanogaster, Fluorescence Resonance Energy Transfer, Humans, Mice, Neurons}, issn = {1548-7105}, doi = {10.1038/nmeth.1398}, author = {Tian, Lin and Hires, S Andrew and Mao, Tianyi and Huber, Daniel and Chiappe, M Eugenia and Chalasani, Sreekanth H and Petreanu, Leopoldo and Akerboom, Jasper and McKinney, Sean A and Schreiter, Eric R and Bargmann, Cornelia I and Jayaraman, Vivek and Svoboda, Karel and Looger, Loren L} } @article {4273, title = {Myosin-dependent targeting of transmembrane proteins to neuronal dendrites.}, journal = {Nature Neuroscience}, volume = {12}, year = {2009}, month = {2009 May}, pages = {568-76}, abstract = {

The distinct electrical properties of axonal and dendritic membranes are largely a result of specific transport of vesicle-bound membrane proteins to each compartment. How this specificity arises is unclear because kinesin motors that transport vesicles cannot autonomously distinguish dendritically projecting microtubules from those projecting axonally. We hypothesized that interaction with a second motor might enable vesicles containing dendritic proteins to preferentially associate with dendritically projecting microtubules and avoid those that project to the axon. Here we show that in rat cortical neurons, localization of several distinct transmembrane proteins to dendrites is dependent on specific myosin motors and an intact actin network. Moreover, fusion with a myosin-binding domain from Melanophilin targeted Channelrhodopsin-2 specifically to the somatodendritic compartment of neurons in mice in vivo. Together, our results suggest that dendritic transmembrane proteins direct the vesicles in which they are transported to avoid the axonal compartment through interaction with myosin motors.

}, keywords = {Adaptor Proteins, Animals, Cell Compartmentation, Cell Polarity, Cerebral Cortex, Cytoskeleton, Dendrites, Membrane Proteins, Mice, Microfilaments, Microtubules, Molecular Motor Proteins, Myosins, Protein Transport, Rats, Recombinant Fusion Proteins, Rhodopsin, Signal Transducing, Transport Vesicles}, issn = {1546-1726}, doi = {10.1038/nn.2318}, author = {Lewis, Tommy L and Mao, Tianyi and Svoboda, Karel and Arnold, Don B} } @article {6491, title = {A proposal for a coordinated effort for the determination of brainwide neuroanatomical connectivity in model organisms at a mesoscopic scale.}, journal = {PLoS Computational Biology}, volume = {5}, year = {2009}, month = {2009 Mar}, pages = {e1000334}, abstract = {

In this era of complete genomes, our knowledge of neuroanatomical circuitry remains surprisingly sparse. Such knowledge is critical, however, for both basic and clinical research into brain function. Here we advocate for a concerted effort to fill this gap, through systematic, experimental mapping of neural circuits at a mesoscopic scale of resolution suitable for comprehensive, brainwide coverage, using injections of tracers or viral vectors. We detail the scientific and medical rationale and briefly review existing knowledge and experimental techniques. We define a set of desiderata, including brainwide coverage; validated and extensible experimental techniques suitable for standardization and automation; centralized, open-access data repository; compatibility with existing resources; and tractability with current informatics technology. We discuss a hypothetical but tractable plan for mouse, additional efforts for the macaque, and technique development for human. We estimate that the mouse connectivity project could be completed within five years with a comparatively modest budget.

}, keywords = {Animals, Brain, Databases, Factual, Humans, Macaca, Mice, Models, Nerve Net, Neuroanatomy, Neurological, Research Design}, issn = {1553-7358}, doi = {10.1371/journal.pcbi.1000334}, author = {Bohland, Jason W and Wu, Caizhi and Barbas, Helen and Bokil, Hemant and Bota, Mihail and Breiter, Hans C and Cline, Hollis T and Doyle, John C and Freed, Peter J and Greenspan, Ralph J and Haber, Suzanne N and Hawrylycz, Michael and Herrera, Daniel G and Hilgetag, Claus C and Huang, Z Josh and Jones, Allan and Jones, Edward G and Karten, Harvey J and Kleinfeld, David and K{\"o}tter, Rolf and Lester, Henry A and Lin, John M and Mensh, Brett D and Mikula, Shawn and Panksepp, Jaak and Price, Joseph L and Safdieh, Joseph and Saper, Clifford B and Schiff, Nicholas D and Schmahmann, Jeremy D and Stillman, Bruce W and Svoboda, Karel and Swanson, Larry W and Toga, Arthur W and Van Essen, David C and Watson, James D and Mitra, Partha P} } @article {5253, title = {Rapid functional maturation of nascent dendritic spines.}, journal = {Neuron}, volume = {61}, year = {2009}, month = {2009 Jan 29}, pages = {247-58}, abstract = {

Spine growth and retraction with synapse formation and elimination plays an important role in shaping brain circuits during development and in the adult brain, yet the temporal relationship between spine morphogenesis and the formation of functional synapses remains poorly defined. We imaged hippocampal pyramidal neurons to identify spines of different ages. We then used two-photon glutamate uncaging, whole-cell recording, and Ca(2+) imaging to analyze the properties of nascent spines and their older neighbors. New spines expressed glutamate-sensitive currents that were indistinguishable from mature spines of comparable volumes. Some spines exhibited negligible AMPA receptor-mediated responses, but the occurrence of these "silent" spines was uncorrelated with spine age. In contrast, NMDA receptor-mediated Ca(2+) accumulations were significantly lower in new spines. New spines reconstructed using electron microscopy made synapses. Our data support a model in which outgrowth and enlargement of nascent spines is tightly coupled to formation and maturation of glutamatergic synapses.

}, keywords = {AMPA, Animals, Calcium, Calcium Signaling, Cell Differentiation, Confocal, Dendritic Spines, Electron, Glutamic Acid, Hippocampus, Microscopy, Neuronal Plasticity, Organ Culture Techniques, Patch-Clamp Techniques, Pyramidal Cells, Rats, Receptors, Synapses, Synaptic Membranes, Synaptic Transmission, Time Factors, Transmission}, issn = {1097-4199}, doi = {10.1016/j.neuron.2008.10.054}, author = {Zito, Karen and Scheuss, Volker and Knott, Graham and Hill, Travis and Svoboda, Karel} } @article {5249, title = {Reverse engineering the mouse brain.}, journal = {Nature}, volume = {461}, year = {2009}, month = {2009 Oct 15}, pages = {923-9}, abstract = {

Behaviour is governed by activity in highly structured neural circuits. Genetically targeted sensors and switches facilitate measurement and manipulation of activity in vivo, linking activity in defined nodes of neural circuits to behaviour. Because of access to specific cell types, these molecular tools will have the largest impact in genetic model systems such as the mouse. Emerging assays of mouse behaviour are beginning to rival those of behaving monkeys in terms of stimulus and behavioural control. We predict that the confluence of new behavioural and molecular tools in the mouse will reveal the logic of complex mammalian circuits.

}, keywords = {Action Potentials, Animal, Animals, Behavior, Brain, Mice, Neural Pathways, Somatosensory Cortex}, issn = {1476-4687}, doi = {10.1038/nature08539}, author = {O{\textquoteright}Connor, Daniel H and Huber, Daniel and Svoboda, Karel} } @article {5251, title = {Subcellular dynamics of type II PKA in neurons.}, journal = {Neuron}, volume = {62}, year = {2009}, month = {2009 May 14}, pages = {363-74}, abstract = {

Protein kinase A (PKA) plays multiple roles in neurons. The localization and specificity of PKA are largely controlled by A-kinase anchoring proteins (AKAPs). However, the dynamics of PKA in neurons and the roles of specific AKAPs are poorly understood. We imaged the distribution of type II PKA in hippocampal and cortical layer 2/3 pyramidal neurons in vitro and in vivo. PKA was concentrated in dendritic shafts compared to the soma, axons, and dendritic spines. This spatial distribution was imposed by the microtubule-binding protein MAP2, indicating that MAP2 is the dominant AKAP in neurons. Following cAMP elevation, catalytic subunits dissociated from the MAP2-tethered regulatory subunits and rapidly became enriched in nearby spines. The spatial gradient of type II PKA between dendritic shafts and spines was critical for the regulation of synaptic strength and long-term potentiation. Therefore, the localization and activity-dependent translocation of type II PKA are important determinants of PKA function.

}, keywords = {A Kinase Anchor Proteins, Animals, Cerebral Cortex, Cyclic AMP-Dependent Protein Kinases, Dendritic Spines, Hippocampus, Mice, Microtubule-Associated Proteins, Pyramidal Cells, Rats, Subcellular Fractions, Tissue Distribution, Transgenic}, issn = {1097-4199}, doi = {10.1016/j.neuron.2009.03.013}, author = {Zhong, Haining and Sia, Gek-Ming and Sato, Takashi R and Gray, Noah W and Mao, Tianyi and Khuchua, Zaza and Huganir, Richard L and Svoboda, Karel} } @article {2185, title = {The subcellular organization of neocortical excitatory connections.}, journal = {Nature}, volume = {457}, year = {2009}, month = {2009 Feb 26}, pages = {1142-5}, abstract = {

Understanding cortical circuits will require mapping the connections between specific populations of neurons, as well as determining the dendritic locations where the synapses occur. The dendrites of individual cortical neurons overlap with numerous types of local and long-range excitatory axons, but axodendritic overlap is not always a good predictor of actual connection strength. Here we developed an efficient channelrhodopsin-2 (ChR2)-assisted method to map the spatial distribution of synaptic inputs, defined by presynaptic ChR2 expression, within the dendritic arborizations of recorded neurons. We expressed ChR2 in two thalamic nuclei, the whisker motor cortex and local excitatory neurons and mapped their synapses with pyramidal neurons in layers 3, 5A and 5B (L3, L5A and L5B) in the mouse barrel cortex. Within the dendritic arborizations of L3 cells, individual inputs impinged onto distinct single domains. These domains were arrayed in an orderly, monotonic pattern along the apical axis: axons from more central origins targeted progressively higher regions of the apical dendrites. In L5 arborizations, different inputs targeted separate basal and apical domains. Input to L3 and L5 dendrites in L1 was related to whisker movement and position, suggesting that these signals have a role in controlling the gain of their target neurons. Our experiments reveal high specificity in the subcellular organization of excitatory circuits.

}, keywords = {Animals, Axons, Dendrites, Mice, Neocortex, Neural Pathways, Pyramidal Cells, Rhodopsin, Thalamic Nuclei}, issn = {1476-4687}, doi = {10.1038/nature07709}, author = {Petreanu, Leopoldo and Mao, Tianyi and Sternson, Scott M and Svoboda, Karel} } @article {4258, title = {Characterization and subcellular targeting of GCaMP-type genetically-encoded calcium indicators.}, journal = {PLoS One}, volume = {3}, year = {2008}, month = {2008 Mar 19}, pages = {e1796}, abstract = {

Genetically-encoded calcium indicators (GECIs) hold the promise of monitoring [Ca(2+)] in selected populations of neurons and in specific cellular compartments. Relating GECI fluorescence to neuronal activity requires quantitative characterization. We have characterized a promising new genetically-encoded calcium indicator-GCaMP2-in mammalian pyramidal neurons. Fluorescence changes in response to single action potentials (17+/-10\% DeltaF/F [mean+/-SD]) could be detected in some, but not all, neurons. Trains of high-frequency action potentials yielded robust responses (302+/-50\% for trains of 40 action potentials at 83 Hz). Responses were similar in acute brain slices from in utero electroporated mice, indicating that long-term expression did not interfere with GCaMP2 function. Membrane-targeted versions of GCaMP2 did not yield larger signals than their non-targeted counterparts. We further targeted GCaMP2 to dendritic spines to monitor Ca(2+) accumulations evoked by activation of synaptic NMDA receptors. We observed robust DeltaF/F responses (range: 37\%-264\%) to single spine uncaging stimuli that were correlated with NMDA receptor currents measured through a somatic patch pipette. One major drawback of GCaMP2 was its low baseline fluorescence. Our results show that GCaMP2 is improved from the previous versions of GCaMP and may be suited to detect bursts of high-frequency action potentials and synaptic currents in vivo.

}, keywords = {Action Potentials, Animals, Calcium, Hippocampus, Humans, Rats, Subcellular Fractions}, issn = {1932-6203}, doi = {10.1371/journal.pone.0001796}, author = {Mao, Tianyi and O{\textquoteright}Connor, Daniel H and Scheuss, Volker and Nakai, Junichi and Svoboda, Karel} } @article {4257, title = {Genetic dissection of neural circuits.}, journal = {Neuron}, volume = {57}, year = {2008}, month = {2008 Mar 13}, pages = {634-60}, abstract = {

Understanding the principles of information processing in neural circuits requires systematic characterization of the participating cell types and their connections, and the ability to measure and perturb their activity. Genetic approaches promise to bring experimental access to complex neural systems, including genetic stalwarts such as the fly and mouse, but also to nongenetic systems such as primates. Together with anatomical and physiological methods, cell-type-specific expression of protein markers and sensors and transducers will be critical to construct circuit diagrams and to measure the activity of genetically defined neurons. Inactivation and activation of genetically defined cell types will establish causal relationships between activity in specific groups of neurons, circuit function, and animal behavior. Genetic analysis thus promises to reveal the logic of the neural circuits in complex brains that guide behaviors. Here we review progress in the genetic analysis of neural circuits and discuss directions for future research and development.

}, keywords = {Animals, Gene Expression Regulation, Humans, Nerve Net, Neural Pathways, Neurons}, issn = {1097-4199}, doi = {10.1016/j.neuron.2008.01.002}, author = {Luo, Liqun and Callaway, Edward M and Svoboda, Karel} } @article {4254, title = {A genetically encoded fluorescent sensor of ERK activity.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, year = {2008}, month = {2008 Dec 9}, pages = {19264-9}, abstract = {

The activity of the ERK has complex spatial and temporal dynamics that are important for the specificity of downstream effects. However, current biochemical techniques do not allow for the measurement of ERK signaling with fine spatiotemporal resolution. We developed a genetically encoded, FRET-based sensor of ERK activity (the extracellular signal-regulated kinase activity reporter, EKAR), optimized for signal-to-noise ratio and fluorescence lifetime imaging. EKAR selectively and reversibly reported ERK activation in HEK293 cells after epidermal growth factor stimulation. EKAR signals were correlated with ERK phosphorylation, required ERK activity, and did not report the activities of JNK or p38. EKAR reported ERK activation in the dendrites and nucleus of hippocampal pyramidal neurons in brain slices after theta-burst stimuli or trains of back-propagating action potentials. EKAR therefore permits the measurement of spatiotemporal ERK signaling dynamics in living cells, including in neuronal compartments in intact tissues.

}, keywords = {Action Potentials, Animals, Artifacts, Bacterial Proteins, Cell Line, Dendrites, Endothelial Cells, Enzyme Activation, Extracellular Signal-Regulated MAP Kinases, Fluorescence Resonance Energy Transfer, Fluorescent Dyes, Genes, Green Fluorescent Proteins, Hippocampus, Humans, Kidney, Luminescent Proteins, MAP Kinase Signaling System, Organ Culture Techniques, Patch-Clamp Techniques, Pyramidal Cells, Rats, Reporter}, issn = {1091-6490}, doi = {10.1073/pnas.0804598105}, author = {Harvey, Christopher D and Ehrhardt, Anka G and Cellurale, Cristina and Zhong, Haining and Yasuda, Ryohei and Davis, Roger J and Svoboda, Karel} } @article {5215, title = {Sparse optical microstimulation in barrel cortex drives learned behaviour in freely moving mice.}, journal = {Nature}, volume = {451}, year = {2008}, month = {2008 Jan 3}, pages = {61-4}, abstract = {

Electrical microstimulation can establish causal links between the activity of groups of neurons and perceptual and cognitive functions. However, the number and identities of neurons microstimulated, as well as the number of action potentials evoked, are difficult to ascertain. To address these issues we introduced the light-gated algal channel channelrhodopsin-2 (ChR2) specifically into a small fraction of layer 2/3 neurons of the mouse primary somatosensory cortex. ChR2 photostimulation in vivo reliably generated stimulus-locked action potentials at frequencies up to 50 Hz. Here we show that naive mice readily learned to detect brief trains of action potentials (five light pulses, 1 ms, 20 Hz). After training, mice could detect a photostimulus firing a single action potential in approximately 300 neurons. Even fewer neurons (approximately 60) were required for longer stimuli (five action potentials, 250 ms). Our results show that perceptual decisions and learning can be driven by extremely brief epochs of cortical activity in a sparse subset of supragranular cortical pyramidal neurons.

}, keywords = {Action Potentials, Algal Proteins, Animal, Animals, Behavior, Cerebral Cortex, Electric Stimulation, Learning, Mice, Microbial, Movement, Optics and Photonics, Photic Stimulation, Pyramidal Cells, Rhodopsins}, issn = {1476-4687}, doi = {10.1038/nature06445}, author = {Huber, Daniel and Petreanu, Leopoldo and Ghitani, Nima and Ranade, Sachin and Hrom{\'a}dka, Tom{\'a}s and Mainen, Zach and Svoboda, Karel} } @article {5213, title = {The spread of Ras activity triggered by activation of a single dendritic spine.}, journal = {Science}, volume = {321}, year = {2008}, month = {2008 Jul 4}, pages = {136-40}, abstract = {

In neurons, individual dendritic spines isolate N-methyl-d-aspartate (NMDA) receptor-mediated calcium ion (Ca2+) accumulations from the dendrite and other spines. However, the extent to which spines compartmentalize signaling events downstream of Ca2+ influx is not known. We combined two-photon fluorescence lifetime imaging with two-photon glutamate uncaging to image the activity of the small guanosine triphosphatase Ras after NMDA receptor activation at individual spines. Induction of long-term potentiation (LTP) triggered robust Ca2+-dependent Ras activation in single spines that decayed in approximately 5 minutes. Ras activity spread over approximately 10 micrometers of dendrite and invaded neighboring spines by diffusion. The spread of Ras-dependent signaling was necessary for the local regulation of the threshold for LTP induction. Thus, Ca2+-dependent synaptic signals can spread to couple multiple synapses on short stretches of dendrite.

}, keywords = {Animals, Calcium, Cell Membrane, Dendritic Spines, Diffusion, Fluorescence Resonance Energy Transfer, Glutamic Acid, GTPase-Activating Proteins, Guanine Nucleotide Exchange Factors, Hippocampus, Long-Term Potentiation, N-Methyl-D-Aspartate, Pyramidal Cells, ras Proteins, Rats, Receptors, Recombinant Fusion Proteins, Signal Transduction, Synapses, Transfection}, issn = {1095-9203}, doi = {10.1126/science.1159675}, author = {Harvey, Christopher D and Yasuda, Ryohei and Zhong, Haining and Svoboda, Karel} } @article {4225, title = {Channelrhodopsin-2-assisted circuit mapping of long-range callosal projections.}, journal = {Nature Neuroscience}, volume = {10}, year = {2007}, month = {2007 May}, pages = {663-8}, abstract = {

The functions of cortical areas depend on their inputs and outputs, but the detailed circuits made by long-range projections are unknown. We show that the light-gated channel channelrhodopsin-2 (ChR2) is delivered to axons in pyramidal neurons in vivo. In brain slices from ChR2-expressing mice, photostimulation of ChR2-positive axons can be transduced reliably into single action potentials. Combining photostimulation with whole-cell recordings of synaptic currents makes it possible to map circuits between presynaptic neurons, defined by ChR2 expression, and postsynaptic neurons, defined by targeted patching. We applied this technique, ChR2-assisted circuit mapping (CRACM), to map long-range callosal projections from layer (L) 2/3 of the somatosensory cortex. L2/3 axons connect with neurons in L5, L2/3 and L6, but not L4, in both ipsilateral and contralateral cortex. In both hemispheres the L2/3-to-L5 projection is stronger than the L2/3-to-L2/3 projection. Our results suggest that laminar specificity may be identical for local and long-range cortical projections.

}, keywords = {Animals, Axons, Brain Mapping, Corpus Callosum, Embryo, Female, Functional Laterality, Inbred C57BL, Mammalian, Membrane Potentials, Mice, Nerve Net, Neural Pathways, Newborn, Patch-Clamp Techniques, Photic Stimulation, Pregnancy, Retinaldehyde, Rhodopsin, Somatosensory Cortex, Transgenic}, issn = {1097-6256}, doi = {10.1038/nn1891}, author = {Petreanu, Leopoldo and Huber, Daniel and Sobczyk, Aleksander and Svoboda, Karel} } @article {4226, title = {The functional microarchitecture of the mouse barrel cortex.}, journal = {PLoS Biology}, volume = {5}, year = {2007}, month = {2007 Jul 10}, pages = {e189}, abstract = {

Cortical maps, consisting of orderly arrangements of functional columns, are a hallmark of the organization of the cerebral cortex. However, the microorganization of cortical maps at the level of single neurons is not known, mainly because of the limitations of available mapping techniques. Here, we used bulk loading of Ca(2+) indicators combined with two-photon microscopy to image the activity of multiple single neurons in layer (L) 2/3 of the mouse barrel cortex in vivo. We developed methods that reliably detect single action potentials in approximately half of the imaged neurons in L2/3. This allowed us to measure the spiking probability following whisker deflection and thus map the whisker selectivity for multiple neurons with known spatial relationships. At the level of neuronal populations, the whisker map varied smoothly across the surface of the cortex, within and between the barrels. However, the whisker selectivity of individual neurons recorded simultaneously differed greatly, even for nearest neighbors. Trial-to-trial correlations between pairs of neurons were high over distances spanning multiple cortical columns. Our data suggest that the response properties of individual neurons are shaped by highly specific subcolumnar circuits and the momentary intrinsic state of the neocortex.

}, keywords = {Algorithms, Aniline Compounds, Animals, Brain Mapping, Evoked Potentials, Fluorescent Dyes, Inbred C57BL, Mice, Models, Neural Pathways, Neurological, Organic Chemicals, Physical Stimulation, Sensory Receptor Cells, Somatosensory, Somatosensory Cortex, Vibrissae, Xanthenes}, issn = {1545-7885}, doi = {10.1371/journal.pbio.0050189}, author = {Sato, Takashi R and Gray, Noah W and Mainen, Zachary F and Svoboda, Karel} } @article {4222, title = {Locally dynamic synaptic learning rules in pyramidal neuron dendrites.}, journal = {Nature}, volume = {450}, year = {2007}, month = {2007 Dec 20}, pages = {1195-200}, abstract = {

Long-term potentiation (LTP) of synaptic transmission underlies aspects of learning and memory. LTP is input-specific at the level of individual synapses, but neural network models predict interactions between plasticity at nearby synapses. Here we show in mouse hippocampal pyramidal cells that LTP at individual synapses reduces the threshold for potentiation at neighbouring synapses. After input-specific LTP induction by two-photon glutamate uncaging or by synaptic stimulation, subthreshold stimuli, which by themselves were too weak to trigger LTP, caused robust LTP and spine enlargement at neighbouring spines. Furthermore, LTP induction broadened the presynaptic-postsynaptic spike interval for spike-timing-dependent LTP within a dendritic neighbourhood. The reduction in the threshold for LTP induction lasted approximately 10 min and spread over approximately 10 microm of dendrite. These local interactions between neighbouring synapses support clustered plasticity models of memory storage and could allow for the binding of behaviourally linked information on the same dendritic branch.

}, keywords = {Animals, Dendrites, Excitatory Postsynaptic Potentials, Glutamic Acid, Learning, Long-Term Potentiation, Mice, Models, Neurological, Pyramidal Cells, Synapses}, issn = {1476-4687}, doi = {10.1038/nature06416}, author = {Harvey, Christopher D and Svoboda, Karel} } @article {1250, title = {Geometric and functional organization of cortical circuits.}, journal = {Nature Neuroscience}, volume = {8}, year = {2005}, month = {2005 Jun}, pages = {782-90}, abstract = {

Can neuronal morphology predict functional synaptic circuits? In the rat barrel cortex, {\textquoteright}barrels{\textquoteright} and {\textquoteright}septa{\textquoteright} delineate an orderly matrix of cortical columns. Using quantitative laser scanning photostimulation we measured the strength of excitatory projections from layer 4 (L4) and L5A to L2/3 pyramidal cells in barrel- and septum-related columns. From morphological reconstructions of excitatory neurons we computed the geometric circuit predicted by axodendritic overlap. Within most individual projections, functional inputs were predicted by geometry and a single scale factor, the synaptic strength per potential synapse. This factor, however, varied between projections and, in one case, even within a projection, up to 20-fold. Relationships between geometric overlap and synaptic strength thus depend on the laminar and columnar locations of both the pre- and postsynaptic neurons, even for neurons of the same type. A large plasticity potential appears to be incorporated into these circuits, allowing for functional {\textquoteright}tuning{\textquoteright} with fixed axonal and dendritic arbor geometry.

}, keywords = {Animals, Axons, Brain Mapping, Cell Shape, Dendrites, Electric Stimulation, Excitatory Postsynaptic Potentials, Image Cytometry, Lasers, Lysine, Neural Pathways, Neuronal Plasticity, Organ Culture Techniques, Photic Stimulation, Pyramidal Cells, Rats, Somatosensory Cortex, Sprague-Dawley, Synapses, Synaptic Transmission, Ultraviolet Rays}, issn = {1097-6256}, doi = {10.1016/j.tins.2005.05.006}, author = {Shepherd, Gordon M G and Stepanyants, Armen and Bureau, Ingrid and Chklovskii, Dmitri and Svoboda, Karel} } @article {46399, title = {Rapid and reversible chemical inactivation of synaptic transmission in genetically targeted neurons.}, journal = {Neuron}, volume = {48}, year = {2005}, month = {2005 Dec 8}, pages = {727-35}, abstract = {

Inducible and reversible silencing of selected neurons in vivo is critical to understanding the structure and dynamics of brain circuits. We have developed Molecules for Inactivation of Synaptic Transmission (MISTs) that can be genetically targeted to allow the reversible inactivation of neurotransmitter release. MISTs consist of modified presynaptic proteins that interfere with the synaptic vesicle cycle when crosslinked by small molecule "dimerizers." MISTs based on the vesicle proteins VAMP2/Synaptobrevin and Synaptophysin induced rapid ( approximately 10 min) and reversible block of synaptic transmission in cultured neurons and brain slices. In transgenic mice expressing MISTs selectively in Purkinje neurons, administration of dimerizer reduced learning and performance of the rotarod behavior. MISTs allow for specific, inducible, and reversible lesions in neuronal circuits and may provide treatment of disorders associated with neuronal hyperactivity.

}, keywords = {Animals, Cells, Cultured, Cross-Linking Reagents, Dimerization, Gene Targeting, In Vitro Techniques, Learning, Mice, Mice, Transgenic, Motor Activity, Neural Inhibition, Neurons, Neurotransmitter Agents, Purkinje Cells, Synaptic Transmission, Synaptic Vesicles, Synaptophysin, Time Factors, Vesicle-Associated Membrane Protein 2}, issn = {0896-6273}, doi = {10.1016/j.neuron.2005.11.015}, author = {Karpova, Alla Y and Tervo, Dougal G R and Gray, Noah W and Svoboda, Karel} } @article {1264, title = {Cortical rewiring and information storage.}, journal = {Nature}, volume = {431}, year = {2004}, month = {2004 Oct 14}, pages = {782-8}, abstract = {

Current thinking about long-term memory in the cortex is focused on changes in the strengths of connections between neurons. But ongoing structural plasticity in the adult brain, including synapse formation/elimination and remodelling of axons and dendrites, suggests that memory could also depend on learning-induced changes in the cortical {\textquoteright}wiring diagram{\textquoteright}. Given that the cortex is sparsely connected, wiring plasticity could provide a substantial boost in storage capacity, although at a cost of more elaborate biological machinery and slower learning.

}, issn = {1476-4687}, author = {Chklovskii, Dmitri B and Mel, B.W. and Svoboda, Karel} }