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Lewis CM, Hoffmann A, Helmchen F. Linking brain activity across scales with simultaneous opto- and electrophysiology. NEUROPHOTONICS 2024; 11:033403. [PMID: 37662552 PMCID: PMC10472193 DOI: 10.1117/1.nph.11.3.033403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 07/19/2023] [Accepted: 07/24/2023] [Indexed: 09/05/2023]
Abstract
The brain enables adaptive behavior via the dynamic coordination of diverse neuronal signals across spatial and temporal scales: from fast action potential patterns in microcircuits to slower patterns of distributed activity in brain-wide networks. Understanding principles of multiscale dynamics requires simultaneous monitoring of signals in multiple, distributed network nodes. Combining optical and electrical recordings of brain activity is promising for collecting data across multiple scales and can reveal aspects of coordinated dynamics invisible to standard, single-modality approaches. We review recent progress in combining opto- and electrophysiology, focusing on mouse studies that shed new light on the function of single neurons by embedding their activity in the context of brain-wide activity patterns. Optical and electrical readouts can be tailored to desired scales to tackle specific questions. For example, fast dynamics in single cells or local populations recorded with multi-electrode arrays can be related to simultaneously acquired optical signals that report activity in specified subpopulations of neurons, in non-neuronal cells, or in neuromodulatory pathways. Conversely, two-photon imaging can be used to densely monitor activity in local circuits while sampling electrical activity in distant brain areas at the same time. The refinement of combined approaches will continue to reveal previously inaccessible and under-appreciated aspects of coordinated brain activity.
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Affiliation(s)
| | - Adrian Hoffmann
- University of Zurich, Brain Research Institute, Zurich, Switzerland
- University of Zurich, Neuroscience Center Zurich, Zurich, Switzerland
| | - Fritjof Helmchen
- University of Zurich, Brain Research Institute, Zurich, Switzerland
- University of Zurich, Neuroscience Center Zurich, Zurich, Switzerland
- University of Zurich, University Research Priority Program, Adaptive Brain Circuits in Development and Learning, Zurich, Switzerland
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2
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Sánchez-Bellot C, de la Prida LM. Brain oscillations: Hippocampal-prefrontal ripples unfolded. Curr Biol 2024; 34:R637-R639. [PMID: 38981432 DOI: 10.1016/j.cub.2024.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
Memory consolidation is the process of translating memory traces from the hippocampus to the cortex. Hippocampal ripples are key in driving this transfer. A new study now shows that independent cortical ripples can suppress this communication. What could be the underlying mechanisms?
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Gonzales DL, Khan HF, Keri HVS, Yadav S, Steward C, Muller LE, Pluta SR, Jayant K. A Translaminar Spacetime Code Supports Touch-Evoked Traveling Waves. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593381. [PMID: 38766232 PMCID: PMC11100787 DOI: 10.1101/2024.05.09.593381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Linking sensory-evoked traveling waves to underlying circuit patterns is critical to understanding the neural basis of sensory perception. To form this link, we performed simultaneous electrophysiology and two-photon calcium imaging through transparent NeuroGrids and mapped touch-evoked cortical traveling waves and their underlying microcircuit dynamics. In awake mice, both passive and active whisker touch elicited traveling waves within and across barrels, with a fast early component followed by a variable late wave that lasted hundreds of milliseconds post-stimulus. Strikingly, late-wave dynamics were modulated by stimulus value and correlated with task performance. Mechanistically, the late wave component was i) modulated by motor feedback, ii) complemented by a sparse ensemble pattern across layer 2/3, which a balanced-state network model reconciled via inhibitory stabilization, and iii) aligned to regenerative Layer-5 apical dendritic Ca 2+ events. Our results reveal a translaminar spacetime pattern organized by cortical feedback in the sensory cortex that supports touch-evoked traveling waves. GRAPHICAL ABSTRACT AND HIGHLIGHTS Whisker touch evokes both early- and late-traveling waves in the barrel cortex over 100's of millisecondsReward reinforcement modulates wave dynamics Late wave emergence coincides with network sparsity in L23 and time-locked L5 dendritic Ca 2+ spikes Experimental and computational results link motor feedback to distinct translaminar spacetime patterns.
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4
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Ramezani M, Kim JH, Liu X, Ren C, Alothman A, De-Eknamkul C, Wilson MN, Cubukcu E, Gilja V, Komiyama T, Kuzum D. High-density transparent graphene arrays for predicting cellular calcium activity at depth from surface potential recordings. NATURE NANOTECHNOLOGY 2024; 19:504-513. [PMID: 38212523 DOI: 10.1038/s41565-023-01576-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 11/16/2023] [Indexed: 01/13/2024]
Abstract
Optically transparent neural microelectrodes have facilitated simultaneous electrophysiological recordings from the brain surface with the optical imaging and stimulation of neural activity. A remaining challenge is to scale down the electrode dimensions to the single-cell size and increase the density to record neural activity with high spatial resolution across large areas to capture nonlinear neural dynamics. Here we developed transparent graphene microelectrodes with ultrasmall openings and a large, transparent recording area without any gold extensions in the field of view with high-density microelectrode arrays up to 256 channels. We used platinum nanoparticles to overcome the quantum capacitance limit of graphene and to scale down the microelectrode diameter to 20 µm. An interlayer-doped double-layer graphene was introduced to prevent open-circuit failures. We conducted multimodal experiments, combining the recordings of cortical potentials of microelectrode arrays with two-photon calcium imaging of the mouse visual cortex. Our results revealed that visually evoked responses are spatially localized for high-frequency bands, particularly for the multiunit activity band. The multiunit activity power was found to be correlated with cellular calcium activity. Leveraging this, we employed dimensionality reduction techniques and neural networks to demonstrate that single-cell and average calcium activities can be decoded from surface potentials recorded by high-density transparent graphene arrays.
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Affiliation(s)
- Mehrdad Ramezani
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, USA
| | - Jeong-Hoon Kim
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, USA
| | - Xin Liu
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, USA
| | - Chi Ren
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
| | - Abdullah Alothman
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, USA
| | - Chawina De-Eknamkul
- Department of NanoEngineering, University of California San Diego, La Jolla, CA, USA
| | - Madison N Wilson
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, USA
| | - Ertugrul Cubukcu
- Department of NanoEngineering, University of California San Diego, La Jolla, CA, USA
| | - Vikash Gilja
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, USA
| | - Takaki Komiyama
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
| | - Duygu Kuzum
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, USA.
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5
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De Koninck Y, Alonso J, Bancelin S, Béïque JC, Bélanger E, Bouchard C, Canossa M, Chaniot J, Choquet D, Crochetière MÈ, Cui N, Danglot L, De Koninck P, Devor A, Ducros M, Getz AM, Haouat M, Hernández IC, Jowett N, Keramidis I, Larivière-Loiselle C, Lavoie-Cardinal F, MacGillavry HD, Malkoç A, Mancinelli M, Marquet P, Minderler S, Moreaud M, Nägerl UV, Papanikolopoulou K, Paquet ME, Pavesi L, Perrais D, Sansonetti R, Thunemann M, Vignoli B, Yau J, Zaccaria C. Understanding the nervous system: lessons from Frontiers in Neurophotonics. NEUROPHOTONICS 2024; 11:014415. [PMID: 38545127 PMCID: PMC10972537 DOI: 10.1117/1.nph.11.1.014415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
The Frontiers in Neurophotonics Symposium is a biennial event that brings together neurobiologists and physicists/engineers who share interest in the development of leading-edge photonics-based approaches to understand and manipulate the nervous system, from its individual molecular components to complex networks in the intact brain. In this Community paper, we highlight several topics that have been featured at the symposium that took place in October 2022 in Québec City, Canada.
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Affiliation(s)
- Yves De Koninck
- CERVO Brain Research Centre, Québec City, Québec, Canada
- Laval University, Department of Psychiatry and Neurosciences, Faculty of Medicine, Québec City, Québec, Canada
| | - Johanna Alonso
- CERVO Brain Research Centre, Québec City, Québec, Canada
| | - Stéphane Bancelin
- University of Bordeaux, Interdisciplinary Institute for Neuroscience, National Centre for Scientific Research (CNRS), Bordeaux, France
| | - Jean-Claude Béïque
- University of Ottawa, Brain and Mind Research Institute, Centre of Neural Dynamics, Ottawa, Ontario, Canada
| | - Erik Bélanger
- CERVO Brain Research Centre, Québec City, Québec, Canada
- Laval University, Department of Psychiatry and Neurosciences, Faculty of Medicine, Québec City, Québec, Canada
- Laval University, Département de physique, de génie physique et d’optique, Québec City, Québec, Canada
| | - Catherine Bouchard
- CERVO Brain Research Centre, Québec City, Québec, Canada
- Laval University, Institute Intelligence and Data, Québec City, Québec, Canada
| | - Marco Canossa
- University of Trento, Department of Cellular Computational and Integrative Biology, Trento, Italy
| | - Johan Chaniot
- CERVO Brain Research Centre, Québec City, Québec, Canada
- Laval University, Department of Psychiatry and Neurosciences, Faculty of Medicine, Québec City, Québec, Canada
| | - Daniel Choquet
- University of Bordeaux, Interdisciplinary Institute for Neuroscience, National Centre for Scientific Research (CNRS), Bordeaux, France
- University of Bordeaux, CNRS, Institut national de la santé et de la recherche médicale (INSERM), Bordeaux Imaging Center (BIC), Bordeaux, France
| | | | - Nanke Cui
- Harvard Medical School, Surgical Photonics & Engineering Laboratory, Mass Eye and Ear, Boston, Massachusetts, United States
| | - Lydia Danglot
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris, INSERM U1266, Paris, France
| | - Paul De Koninck
- CERVO Brain Research Centre, Québec City, Québec, Canada
- Laval University, Department of Biochemistry, Microbiology, and Bioinformatics, Faculty of Science and Engineering, Québec City, Québec, Canada
| | - Anna Devor
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
- Massachusetts General Hospital, Athinoula A. Martinos Center for Biomedical Imaging, Charlestown, Massachusetts, United States
| | - Mathieu Ducros
- University of Bordeaux, CNRS, Institut national de la santé et de la recherche médicale (INSERM), Bordeaux Imaging Center (BIC), Bordeaux, France
| | - Angela M. Getz
- University of Bordeaux, Interdisciplinary Institute for Neuroscience, National Centre for Scientific Research (CNRS), Bordeaux, France
- University of Bordeaux, CNRS, Institut national de la santé et de la recherche médicale (INSERM), Bordeaux Imaging Center (BIC), Bordeaux, France
| | - Mohamed Haouat
- CERVO Brain Research Centre, Québec City, Québec, Canada
- Laval University, Department of Psychiatry and Neurosciences, Faculty of Medicine, Québec City, Québec, Canada
| | - Iván Coto Hernández
- Harvard Medical School, Surgical Photonics & Engineering Laboratory, Mass Eye and Ear, Boston, Massachusetts, United States
| | - Nate Jowett
- Harvard Medical School, Surgical Photonics & Engineering Laboratory, Mass Eye and Ear, Boston, Massachusetts, United States
| | | | - Céline Larivière-Loiselle
- CERVO Brain Research Centre, Québec City, Québec, Canada
- Laval University, Département de physique, de génie physique et d’optique, Québec City, Québec, Canada
| | - Flavie Lavoie-Cardinal
- CERVO Brain Research Centre, Québec City, Québec, Canada
- Laval University, Department of Psychiatry and Neurosciences, Faculty of Medicine, Québec City, Québec, Canada
- Laval University, Institute Intelligence and Data, Québec City, Québec, Canada
| | - Harold D. MacGillavry
- Utrecht University, Faculty of Science, Division of Cell Biology, Neurobiology and Biophysics, Department of Biology, Utrecht, The Netherlands
| | - Asiye Malkoç
- University of Trento, Department of Cellular Computational and Integrative Biology, Trento, Italy
- University of Trento, Department of Physics, Trento, Italy
| | | | - Pierre Marquet
- CERVO Brain Research Centre, Québec City, Québec, Canada
- Laval University, Department of Psychiatry and Neurosciences, Faculty of Medicine, Québec City, Québec, Canada
- Laval University, Centre d’optique, photonique et laser (COPL), Québec City, Québec, Canada
| | - Steven Minderler
- Harvard Medical School, Surgical Photonics & Engineering Laboratory, Mass Eye and Ear, Boston, Massachusetts, United States
| | - Maxime Moreaud
- CERVO Brain Research Centre, Québec City, Québec, Canada
- IFP Energies nouvelles, Solaize, France
| | - U. Valentin Nägerl
- University of Bordeaux, Interdisciplinary Institute for Neuroscience, National Centre for Scientific Research (CNRS), Bordeaux, France
| | - Katerina Papanikolopoulou
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center Alexander Fleming, Vari, Greece
| | | | - Lorenzo Pavesi
- University of Trento, Department of Physics, Trento, Italy
| | - David Perrais
- University of Bordeaux, Interdisciplinary Institute for Neuroscience, National Centre for Scientific Research (CNRS), Bordeaux, France
| | | | - Martin Thunemann
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Beatrice Vignoli
- University of Trento, Department of Cellular Computational and Integrative Biology, Trento, Italy
- University of Trento, Department of Physics, Trento, Italy
| | - Jenny Yau
- Harvard Medical School, Surgical Photonics & Engineering Laboratory, Mass Eye and Ear, Boston, Massachusetts, United States
| | - Clara Zaccaria
- University of Trento, Department of Physics, Trento, Italy
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Jeong H, Namboodiri VMK, Jung MW, Andermann ML. Sensory cortical ensembles exhibit differential coupling to ripples in distinct hippocampal subregions. Curr Biol 2023; 33:5185-5198.e4. [PMID: 37995696 PMCID: PMC10842729 DOI: 10.1016/j.cub.2023.10.073] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 08/29/2023] [Accepted: 10/31/2023] [Indexed: 11/25/2023]
Abstract
Cortical neurons activated during recent experiences often reactivate with dorsal hippocampal CA1 ripples during subsequent rest. Less is known about cortical interactions with intermediate hippocampal CA1, whose connectivity, functions, and ripple events differ from dorsal CA1. We identified three clusters of putative excitatory neurons in mouse visual cortex that are preferentially excited together with either dorsal or intermediate CA1 ripples or suppressed before both ripples. Neurons in each cluster were evenly distributed across primary and higher visual cortices and co-active even in the absence of ripples. These ensembles exhibited similar visual responses but different coupling to thalamus and pupil-indexed arousal. We observed a consistent activity sequence preceding and predicting ripples: (1) suppression of ripple-suppressed cortical neurons, (2) thalamic silence, and (3) activation of intermediate CA1-ripple-activated cortical neurons. We propose that coordinated dynamics of these ensembles relay visual experiences to distinct hippocampal subregions for incorporation into different cognitive maps.
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Affiliation(s)
- Huijeong Jeong
- Department of Neurology, University of California, San Francisco, 1651 4th Street, San Francisco, CA 94158, USA; Center for Synaptic Brain Dysfunctions, Institute for Basic Science, 291 Daehak-ro, Daejeon 34141, Republic of Korea; Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Daejeon 34141, Republic of Korea
| | - Vijay Mohan K Namboodiri
- Department of Neurology, University of California, San Francisco, 1651 4th Street, San Francisco, CA 94158, USA; Neuroscience Graduate Program, University of California, San Francisco, 1651 4th Street, San Francisco, CA 94158, USA; Weill Institute for Neuroscience, Kavli Institute for Fundamental Neuroscience, Center for Integrative Neuroscience, University of California, San Francisco, 1651 4th Street, San Francisco, CA 94158, USA.
| | - Min Whan Jung
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science, 291 Daehak-ro, Daejeon 34141, Republic of Korea; Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Daejeon 34141, Republic of Korea.
| | - Mark L Andermann
- Division of Endocrinology, Metabolism, and Diabetes, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Avenue, Boston, MA 02215, USA; Department of Neurobiology, Harvard Medical School, 220 Longwood Avenue, Boston, MA 02115, USA.
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7
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Sebastian ER, Quintanilla JP, Sánchez-Aguilera A, Esparza J, Cid E, de la Prida LM. Topological analysis of sharp-wave ripple waveforms reveals input mechanisms behind feature variations. Nat Neurosci 2023; 26:2171-2181. [PMID: 37946048 PMCID: PMC10689241 DOI: 10.1038/s41593-023-01471-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 09/22/2023] [Indexed: 11/12/2023]
Abstract
The reactivation of experience-based neural activity patterns in the hippocampus is crucial for learning and memory. These reactivation patterns and their associated sharp-wave ripples (SWRs) are highly variable. However, this variability is missed by commonly used spectral methods. Here, we use topological and dimensionality reduction techniques to analyze the waveform of ripples recorded at the pyramidal layer of CA1. We show that SWR waveforms distribute along a continuum in a low-dimensional space, which conveys information about the underlying layer-specific synaptic inputs. A decoder trained in this space successfully links individual ripples with their expected sinks and sources, demonstrating how physiological mechanisms shape SWR variability. Furthermore, we found that SWR waveforms segregated differently during wakefulness and sleep before and after a series of cognitive tasks, with striking effects of novelty and learning. Our results thus highlight how the topological analysis of ripple waveforms enables a deeper physiological understanding of SWRs.
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Affiliation(s)
| | | | - Alberto Sánchez-Aguilera
- Instituto Cajal. CSIC, Madrid, Spain
- Department of Physiology, Faculty of Medicine, Universidad Complutense de Madrid, Madrid, Spain
| | | | - Elena Cid
- Instituto Cajal. CSIC, Madrid, Spain
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8
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Xiao D, Yan Y, Murphy TH. Mesotrode chronic simultaneous mesoscale cortical imaging and subcortical or peripheral nerve spiking activity recording in mice. eLife 2023; 12:RP87691. [PMID: 37962180 PMCID: PMC10645427 DOI: 10.7554/elife.87691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2023] Open
Abstract
Brain function originates from hierarchical spatial-temporal neural dynamics distributed across cortical and subcortical networks. However, techniques available to assess large-scale brain network activity with single-neuron resolution in behaving animals remain limited. Here, we present Mesotrode that integrates chronic wide-field mesoscale cortical imaging and compact multi-site cortical/subcortical cellular electrophysiology in head-fixed mice that undergo self-initiated running or orofacial movements. Specifically, we harnessed the flexibility of chronic multi-site tetrode recordings to monitor single-neuron activity in multiple subcortical structures while simultaneously imaging the mesoscale activity of the entire dorsal cortex. A mesoscale spike-triggered averaging procedure allowed the identification of cortical activity motifs preferentially associated with single-neuron spiking. Using this approach, we were able to characterize chronic single-neuron-related functional connectivity maps for up to 60 days post-implantation. Neurons recorded from distinct subcortical structures display diverse but segregated cortical maps, suggesting that neurons of different origins participate in distinct cortico-subcortical pathways. We extended the capability of Mesotrode by implanting the micro-electrode at the facial motor nerve and found that facial nerve spiking is functionally associated with the PTA, RSP, and M2 network, and optogenetic inhibition of the PTA area significantly reduced the facial movement of the mice. These findings demonstrate that Mesotrode can be used to sample different combinations of cortico-subcortical networks over prolonged periods, generating multimodal and multi-scale network activity from a single implant, offering new insights into the neural mechanisms underlying specific behaviors.
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Affiliation(s)
- Dongsheng Xiao
- University of British Columbia, Department of Psychiatry, Kinsmen Laboratory of Neurological ResearchVancouverCanada
- Djavad Mowafaghian Centre for Brain Health, University of British ColumbiaVancouverCanada
| | - Yuhao Yan
- University of British Columbia, Department of Psychiatry, Kinsmen Laboratory of Neurological ResearchVancouverCanada
- Djavad Mowafaghian Centre for Brain Health, University of British ColumbiaVancouverCanada
| | - Timothy H Murphy
- University of British Columbia, Department of Psychiatry, Kinsmen Laboratory of Neurological ResearchVancouverCanada
- Djavad Mowafaghian Centre for Brain Health, University of British ColumbiaVancouverCanada
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9
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Juska VB, Maxwell G, Estrela P, Pemble ME, O'Riordan A. Silicon microfabrication technologies for biology integrated advance devices and interfaces. Biosens Bioelectron 2023; 237:115503. [PMID: 37481868 DOI: 10.1016/j.bios.2023.115503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 06/25/2023] [Accepted: 06/26/2023] [Indexed: 07/25/2023]
Abstract
Miniaturization is the trend to manufacture ever smaller devices and this process requires knowledge, experience, understanding of materials, manufacturing techniques and scaling laws. The fabrication techniques used in semiconductor industry deliver an exceptionally high yield of devices and provide a well-established platform. Today, these miniaturized devices are manufactured with high reproducibility, design flexibility, scalability and multiplexed features to be used in several applications including micro-, nano-fluidics, implantable chips, diagnostics/biosensors and neural probes. We here provide a review on the microfabricated devices used for biology driven science. We will describe the ubiquity of the use of micro-nanofabrication techniques in biology and biotechnology through the fabrication of high-aspect-ratio devices for cell sensing applications, intracellular devices, probes developed for neuroscience-neurotechnology and biosensing of the certain biomarkers. Recently, the research on micro and nanodevices for biology has been progressing rapidly. While the understanding of the unknown biological fields -such as human brain- has been requiring more research with advanced materials and devices, the development protocols of desired devices has been advancing in parallel, which finally meets with some of the requirements of biological sciences. This is a very exciting field and we aim to highlight the impact of micro-nanotechnologies that can shed light on complex biological questions and needs.
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Affiliation(s)
- Vuslat B Juska
- Tyndall National Institute, University College Cork, T12R5CP, Ireland.
| | - Graeme Maxwell
- Tyndall National Institute, University College Cork, T12R5CP, Ireland
| | - Pedro Estrela
- Department of Electronic and Electrical Engineering, University of Bath, Bath, BA2 7AY, United Kingdom; Centre for Bioengineering & Biomedical Technologies (CBio), University of Bath, Bath, BA2 7AY, United Kingdom
| | | | - Alan O'Riordan
- Tyndall National Institute, University College Cork, T12R5CP, Ireland
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10
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Feliciano-Ramos PA, Galazo M, Penagos H, Wilson M. Hippocampal memory reactivation during sleep is correlated with specific cortical states of the retrosplenial and prefrontal cortices. Learn Mem 2023; 30:221-236. [PMID: 37758288 PMCID: PMC10547389 DOI: 10.1101/lm.053834.123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 08/25/2023] [Indexed: 10/03/2023]
Abstract
Episodic memories are thought to be stabilized through the coordination of cortico-hippocampal activity during sleep. However, the timing and mechanism of this coordination remain unknown. To investigate this, we studied the relationship between hippocampal reactivation and slow-wave sleep up and down states of the retrosplenial cortex (RTC) and prefrontal cortex (PFC). We found that hippocampal reactivations are strongly correlated with specific cortical states. Reactivation occurred during sustained cortical Up states or during the transition from up to down state. Interestingly, the most prevalent interaction with memory reactivation in the hippocampus occurred during sustained up states of the PFC and RTC, while hippocampal reactivation and cortical up-to-down state transition in the RTC showed the strongest coordination. Reactivation usually occurred within 150-200 msec of a cortical Up state onset, indicating that a buildup of excitation during cortical Up state activity influences the probability of memory reactivation in CA1. Conversely, CA1 reactivation occurred 30-50 msec before the onset of a cortical down state, suggesting that memory reactivation affects down state initiation in the RTC and PFC, but the effect in the RTC was more robust. Our findings provide evidence that supports and highlights the complexity of bidirectional communication between cortical regions and the hippocampus during sleep.
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Affiliation(s)
- Pedro A Feliciano-Ramos
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Maria Galazo
- Neuroscience Program, Tulane Brain Institute, Tulane University, New Orleans, Louisana 70118, USA
- Department of Cell and Molecular Biology, Tulane Brain Institute, Tulane University, New Orleans, Louisana 70118, USA
| | - Hector Penagos
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Center for Brains, Minds, and Machines, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Matthew Wilson
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Center for Brains, Minds, and Machines, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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11
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Surinach D, Rynes ML, Saxena K, Ko E, Redish AD, Kodandaramaiah SB. Distinct mesoscale cortical dynamics encode search strategies during spatial navigation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.27.534480. [PMID: 37034682 PMCID: PMC10081171 DOI: 10.1101/2023.03.27.534480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Spatial navigation is a complex cognitive process that involves neural computations in distributed regions of the brain. Little is known about how cortical regions are coordinated when animals navigate novel spatial environments or how that coordination changes as environments become familiar. We recorded mesoscale calcium (Ca2+) dynamics across large swathes of the dorsal cortex in mice solving the Barnes maze, a 2D spatial navigation task where mice used random, serial, and spatial search strategies to navigate to the goal. Cortical dynamics exhibited patterns of repeated calcium activity with rapid and abrupt shifts between cortical activation patterns at sub-second time scales. We used a clustering algorithm to decompose the spatial patterns of cortical calcium activity in a low dimensional state space, identifying 7 states, each corresponding to a distinct spatial pattern of cortical activation, sufficient to describe the cortical dynamics across all the mice. When mice used serial or spatial search strategies to navigate to the goal, the frontal regions of the cortex were reliably activated for prolonged durations of time (> 1s) shortly after trial initiation. These frontal cortex activation events coincided with mice approaching the edge of the maze from the center and were preceded by temporal sequences of cortical activation patterns that were distinct for serial and spatial search strategies. In serial search trials, frontal cortex activation events were preceded by activation of the posterior regions of the cortex followed by lateral activation of one hemisphere. In spatial search trials, frontal cortical events were preceded by activation of posterior regions of the cortex followed by broad activation of the lateral regions of the cortex. Our results delineated cortical components that differentiate goal- and non-goal oriented spatial navigation strategies.
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Affiliation(s)
- Daniel Surinach
- Department of Mechanical Engineering, University of Minnesota, Twin Cities
| | - Mathew L Rynes
- Department of Biomedical Engineering, University of Minnesota, Twin Cities
| | - Kapil Saxena
- Department of Mechanical Engineering, University of Minnesota, Twin Cities
| | - Eunsong Ko
- Department of Mechanical Engineering, University of Minnesota, Twin Cities
- Department of Biomedical Engineering, University of Minnesota, Twin Cities
| | - A David Redish
- Department of Neuroscience, University of Minnesota, Twin Cities
| | - Suhasa B Kodandaramaiah
- Department of Mechanical Engineering, University of Minnesota, Twin Cities
- Department of Biomedical Engineering, University of Minnesota, Twin Cities
- Department of Neuroscience, University of Minnesota, Twin Cities
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12
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Jeong H, Namboodiri VMK, Jung MW, Andermann ML. Sensory cortical ensembles exhibit differential coupling to ripples in distinct hippocampal subregions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.17.533028. [PMID: 36993665 PMCID: PMC10055189 DOI: 10.1101/2023.03.17.533028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Cortical neurons activated during recent experiences often reactivate with dorsal hippocampal CA1 sharp-wave ripples (SWRs) during subsequent rest. Less is known about cortical interactions with intermediate hippocampal CA1, whose connectivity, functions, and SWRs differ from those of dorsal CA1. We identified three clusters of visual cortical excitatory neurons that are excited together with either dorsal or intermediate CA1 SWRs, or suppressed before both SWRs. Neurons in each cluster were distributed across primary and higher visual cortices and co-active even in the absence of SWRs. These ensembles exhibited similar visual responses but different coupling to thalamus and pupil-indexed arousal. We observed a consistent activity sequence: (i) suppression of SWR-suppressed cortical neurons, (ii) thalamic silence, and (iii) activation of the cortical ensemble preceding and predicting intermediate CA1 SWRs. We propose that the coordinated dynamics of these ensembles relay visual experiences to distinct hippocampal subregions for incorporation into different cognitive maps.
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Affiliation(s)
- Huijeong Jeong
- Department of Neurology, University of California, San Francisco, CA 94158, USA
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science, Daejeon 34141, Korea
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Vijay Mohan K Namboodiri
- Department of Neurology, University of California, San Francisco, CA 94158, USA
- Neuroscience Graduate Program, University of California, San Francisco, CA 94158, USA
- Weill Institute for Neuroscience, Kavli Institute for Fundamental Neuroscience, Center for Integrative Neuroscience, University of California, San Francisco 94158, CA, USA
| | - Min Whan Jung
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science, Daejeon 34141, Korea
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Mark L. Andermann
- Division of Endocrinology, Metabolism, and Diabetes, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115 USA
- Lead contact
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13
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Liang Q, Shen Z, Sun X, Yu D, Liu K, Mugo SM, Chen W, Wang D, Zhang Q. Electron Conductive and Transparent Hydrogels for Recording Brain Neural Signals and Neuromodulation. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2211159. [PMID: 36563409 DOI: 10.1002/adma.202211159] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Indexed: 06/17/2023]
Abstract
Recording brain neural signals and optogenetic neuromodulations open frontiers in decoding brain neural information and neurodegenerative disease therapeutics. Conventional implantable probes suffer from modulus mismatch with biological tissues and an irreconcilable tradeoff between transparency and electron conductivity. Herein, a strategy is proposed to address these tradeoffs, which generates conductive and transparent hydrogels with polypyrrole-decorated microgels as cross-linkers. The optical transparency of the electrodes can be attributed to the special structures that allow light waves to bypass the microgel particles and minimize their interaction. Demonstrated by probing the hippocampus of rat brains, the biomimetic electrode shows a prolonged capacity for simultaneous optogenetic neuromodulation and recording of brain neural signals. More importantly, an intriguing brain-machine interaction is realized, which involves signal input to the brain, brain neural signal generation, and controlling limb behaviors. This breakthrough work represents a significant scientific advancement toward decoding brain neural information and developing neurodegenerative disease therapies.
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Affiliation(s)
- Quanduo Liang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, P. R. China
| | - Zhenzhen Shen
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, P. R. China
| | - Xiguang Sun
- Department of Hand Surgery, Public Research Platform, The First Hospital of Jilin University, Changchun, 130061, P. R. China
| | - Dehai Yu
- Department of Hand Surgery, Public Research Platform, The First Hospital of Jilin University, Changchun, 130061, P. R. China
| | - Kewei Liu
- State Key Laboratory of Luminescence and Applications, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, 130033, P. R. China
| | - Samuel M Mugo
- Department of Physical Sciences, MacEwan University, Edmonton, ABT5J4S2, Canada
| | - Wei Chen
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, P. R. China
| | - Dong Wang
- Key Laboratory of Biomedical Engineering of Hainan Province, School of Biomedical Engineering, Hainan University, Haikou, 570228, China
| | - Qiang Zhang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, P. R. China
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14
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Fekete Z, Zátonyi A, Kaszás A, Madarász M, Slézia A. Transparent neural interfaces: challenges and solutions of microengineered multimodal implants designed to measure intact neuronal populations using high-resolution electrophysiology and microscopy simultaneously. MICROSYSTEMS & NANOENGINEERING 2023; 9:66. [PMID: 37213820 PMCID: PMC10195795 DOI: 10.1038/s41378-023-00519-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 02/03/2023] [Accepted: 03/01/2023] [Indexed: 05/23/2023]
Abstract
The aim of this review is to present a comprehensive overview of the feasibility of using transparent neural interfaces in multimodal in vivo experiments on the central nervous system. Multimodal electrophysiological and neuroimaging approaches hold great potential for revealing the anatomical and functional connectivity of neuronal ensembles in the intact brain. Multimodal approaches are less time-consuming and require fewer experimental animals as researchers obtain denser, complex data during the combined experiments. Creating devices that provide high-resolution, artifact-free neural recordings while facilitating the interrogation or stimulation of underlying anatomical features is currently one of the greatest challenges in the field of neuroengineering. There are numerous articles highlighting the trade-offs between the design and development of transparent neural interfaces; however, a comprehensive overview of the efforts in material science and technology has not been reported. Our present work fills this gap in knowledge by introducing the latest micro- and nanoengineered solutions for fabricating substrate and conductive components. Here, the limitations and improvements in electrical, optical, and mechanical properties, the stability and longevity of the integrated features, and biocompatibility during in vivo use are discussed.
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Affiliation(s)
- Z. Fekete
- Research Group for Implantable Microsystems, Faculty of Information Technology & Bionics, Pázmány Péter Catholic University, Budapest, Hungary
- Institute of Cognitive Neuroscience & Psychology, Eotvos Lorand Research Network, Budapest, Hungary
| | - A. Zátonyi
- Research Group for Implantable Microsystems, Faculty of Information Technology & Bionics, Pázmány Péter Catholic University, Budapest, Hungary
| | - A. Kaszás
- Mines Saint-Etienne, Centre CMP, Département BEL, F - 13541 Gardanne, France
- Institut de Neurosciences de la Timone, CNRS UMR 7289 & Aix-Marseille Université, 13005 Marseille, France
| | - M. Madarász
- János Szentágothai PhD Program of Semmelweis University, Budapest, Hungary
- BrainVision Center, Budapest, Hungary
| | - A. Slézia
- Institut de Neurosciences de la Timone, CNRS UMR 7289 & Aix-Marseille Université, 13005 Marseille, France
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15
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Liu X, Wang F, Ramakrishna S. Hippocampus-guided engineering of memory prosthesis. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2022. [DOI: 10.1016/j.cobme.2022.100415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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16
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Machado TA, Kauvar IV, Deisseroth K. Multiregion neuronal activity: the forest and the trees. Nat Rev Neurosci 2022; 23:683-704. [PMID: 36192596 PMCID: PMC10327445 DOI: 10.1038/s41583-022-00634-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2022] [Indexed: 12/12/2022]
Abstract
The past decade has witnessed remarkable advances in the simultaneous measurement of neuronal activity across many brain regions, enabling fundamentally new explorations of the brain-spanning cellular dynamics that underlie sensation, cognition and action. These recently developed multiregion recording techniques have provided many experimental opportunities, but thoughtful consideration of methodological trade-offs is necessary, especially regarding field of view, temporal acquisition rate and ability to guarantee cellular resolution. When applied in concert with modern optogenetic and computational tools, multiregion recording has already made possible fundamental biological discoveries - in part via the unprecedented ability to perform unbiased neural activity screens for principles of brain function, spanning dozens of brain areas and from local to global scales.
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Affiliation(s)
- Timothy A Machado
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Isaac V Kauvar
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Electrical Engineering, Stanford University, Stanford, CA, USA
| | - Karl Deisseroth
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA.
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17
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Liu X, Terada S, Ramezani M, Kim JH, Lu Y, Grosmark A, Losonczy A, Kuzum D. E-Cannula reveals anatomical diversity in sharp-wave ripples as a driver for the recruitment of distinct hippocampal assemblies. Cell Rep 2022; 41:111453. [PMID: 36198271 PMCID: PMC9640218 DOI: 10.1016/j.celrep.2022.111453] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 07/07/2022] [Accepted: 09/14/2022] [Indexed: 11/17/2022] Open
Abstract
The hippocampus plays a critical role in spatial navigation and episodic memory. However, research on in vivo hippocampal activity dynamics mostly relies on single modalities, such as electrical recordings or optical imaging, with respectively limited spatial and temporal resolution. Here, we develop the E-Cannula, integrating fully transparent graphene microelectrodes with imaging cannula, which enables simultaneous electrical recording and two-photon calcium imaging from the exact same neural populations across an anatomically extended region of the mouse hippocampal CA1 stably across several days. The large-scale multimodal recordings show that sharp wave ripples (SWRs) exhibit spatiotemporal wave patterns along multiple axes in two-dimensional (2D) space with different spatial extents and temporal propagation modes. Notably, distinct SWR wave patterns are associated with the selective recruitment of orthogonal CA1 cell assemblies. These results demonstrate the utility of the E-Cannula as a versatile neurotechnology with the potential for future integration with other optical components.
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Affiliation(s)
- Xin Liu
- Department of Electrical and Computer Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Satoshi Terada
- Department of Neuroscience, Columbia University, New York, NY, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Mehrdad Ramezani
- Department of Electrical and Computer Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Jeong-Hoon Kim
- Department of Electrical and Computer Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Yichen Lu
- Department of Electrical and Computer Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Andres Grosmark
- Department of Neuroscience, Columbia University, New York, NY, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA; The Kavli Institute for Brain Science, Columbia University, New York, NY, USA
| | - Attila Losonczy
- Department of Neuroscience, Columbia University, New York, NY, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA; The Kavli Institute for Brain Science, Columbia University, New York, NY, USA.
| | - Duygu Kuzum
- Department of Electrical and Computer Engineering, University of California, San Diego, La Jolla, CA, USA; Halıcıoğlu Data Science Institute, University of California, San Diego, La Jolla, CA, USA.
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18
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Benisty H, Song A, Mishne G, Charles AS. Review of data processing of functional optical microscopy for neuroscience. NEUROPHOTONICS 2022; 9:041402. [PMID: 35937186 PMCID: PMC9351186 DOI: 10.1117/1.nph.9.4.041402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 07/15/2022] [Indexed: 05/04/2023]
Abstract
Functional optical imaging in neuroscience is rapidly growing with the development of optical systems and fluorescence indicators. To realize the potential of these massive spatiotemporal datasets for relating neuronal activity to behavior and stimuli and uncovering local circuits in the brain, accurate automated processing is increasingly essential. We cover recent computational developments in the full data processing pipeline of functional optical microscopy for neuroscience data and discuss ongoing and emerging challenges.
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Affiliation(s)
- Hadas Benisty
- Yale Neuroscience, New Haven, Connecticut, United States
| | - Alexander Song
- Max Planck Institute for Intelligent Systems, Stuttgart, Germany
| | - Gal Mishne
- UC San Diego, Halıcığlu Data Science Institute, Department of Electrical and Computer Engineering and the Neurosciences Graduate Program, La Jolla, California, United States
| | - Adam S. Charles
- Johns Hopkins University, Kavli Neuroscience Discovery Institute, Center for Imaging Science, Department of Biomedical Engineering, Department of Neuroscience, and Mathematical Institute for Data Science, Baltimore, Maryland, United States
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19
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Chambers AR, Berge CN, Vervaeke K. Cell-type-specific silence in thalamocortical circuits precedes hippocampal sharp-wave ripples. Cell Rep 2022; 40:111132. [PMID: 35905724 DOI: 10.1016/j.celrep.2022.111132] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 06/21/2021] [Accepted: 07/01/2022] [Indexed: 11/03/2022] Open
Abstract
Evidence suggests that the hippocampus conveys memory-related neural patterns across distributed cortical circuits during high-frequency oscillations called sharp-wave ripples (SWRs). We investigate how circuit activity in the retrosplenial cortex (RSC), a primary hippocampal target, could aid in processing SWR-related input. Using patch-clamp recordings from awake mice, we find that SWR-aligned membrane potential modulation is widespread but weak, and that spiking responses are sparse. However, using cell-type-specific two-photon Ca2+ imaging and optogenetics, we show that, 1-2 s before SWRs, superficial inhibition and thalamocortical input in RSC is reduced. We propose that pyramidal dendrites experience decreased local inhibition and subcortical interference in a seconds-long time window preceding SWRs. This may aid communication of weak and sparse SWR-aligned excitation between the hippocampus and neocortex and promote the strengthening of memory-related connections.
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Affiliation(s)
- Anna R Chambers
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.
| | - Christoffer Nerland Berge
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Koen Vervaeke
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.
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20
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Abstract
When navigating through space, we must maintain a representation of our position in real time; when recalling a past episode, a memory can come back in a flash. Interestingly, the brain's spatial representation system, including the hippocampus, supports these two distinct timescale functions. How are neural representations of space used in the service of both real-world navigation and internal mnemonic processes? Recent progress has identified sequences of hippocampal place cells, evolving at multiple timescales in accordance with either navigational behaviors or internal oscillations, that underlie these functions. We review experimental findings on experience-dependent modulation of these sequential representations and consider how they link real-world navigation to time-compressed memories. We further discuss recent work suggesting the prevalence of these sequences beyond hippocampus and propose that these multiple-timescale mechanisms may represent a general algorithm for organizing cell assemblies, potentially unifying the dual roles of the spatial representation system in memory and navigation.
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Affiliation(s)
- Wenbo Tang
- Graduate Program in Neuroscience, Brandeis University, Waltham, Massachusetts, USA;
| | - Shantanu P Jadhav
- Neuroscience Program, Department of Psychology, and Volen National Center for Complex Systems, Brandeis University, Waltham, Massachusetts, USA;
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21
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Abstract
During periods of disengagement from the environment, transient population bursts, known as sharp wave ripples (SPW-Rs), occur sporadically. While numerous experiments have characterized the bidirectional relationship between SPW-Rs and activity in chosen brain areas, the topographic relationship between different segments of the hippocampus and brain-wide target areas has not been studied at high temporal and spatial resolution. Yet, such knowledge is necessary to infer the direction of communication. We analyzed two publicly available datasets with simultaneous high-density silicon probe recordings from across the mouse forebrain. We found that SPW-Rs coincide with a transient brain-wide increase in functional connectivity. In addition, we show that the diversity in SPW-R features, such as their incidence, magnitude, and intrahippocampal topography in the septotemporal axis, are correlated with slower excitability fluctuations in cortical and subcortical areas. Further, variations in SPW-R features correlated with the timing, sign, and magnitude of downstream responses with large-amplitude SPW-Rs followed by transient silence in extrahippocampal structures. Our findings expand on previous results and demonstrate that the activity patterns in extrahippocampal structures depend both on the intrahippocampal topographic origin and magnitude of hippocampal SPW-Rs.
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22
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Multimodal, Multiscale Insights into Hippocampal Seizures Enabled by Transparent, Graphene-Based Microelectrode Arrays. eNeuro 2022; 9:ENEURO.0386-21.2022. [PMID: 35470227 PMCID: PMC9087744 DOI: 10.1523/eneuro.0386-21.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 04/14/2022] [Accepted: 04/15/2022] [Indexed: 11/21/2022] Open
Abstract
Hippocampal seizures are a defining feature of mesial temporal lobe epilepsy (MTLE). Area CA1 of the hippocampus is commonly implicated in the generation of seizures, which may occur because of the activity of endogenous cell populations or of inputs from other regions within the hippocampal formation. Simultaneously observing activity at the cellular and network scales in vivo remains challenging. Here, we present a novel technology for simultaneous electrophysiology and multicellular calcium imaging of CA1 pyramidal cells (PCs) in mice enabled by a transparent graphene-based microelectrode array (Gr MEA). We examine PC firing at seizure onset, oscillatory coupling, and the dynamics of the seizure traveling wave as seizures evolve. Finally, we couple features derived from both modalities to predict the speed of the traveling wave using bootstrap aggregated regression trees. Analysis of the most important features in the regression trees suggests a transition among states in the evolution of hippocampal seizures.
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23
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Shi Y, Ananthakrishnan A, Oh S, Liu X, Hota G, Cauwenberghs G, Kuzum D. A Neuromorphic Brain Interface based on RRAM Crossbar Arrays for High Throughput Real-time Spike Sorting. IEEE TRANSACTIONS ON ELECTRON DEVICES 2022; 69:2137-2144. [PMID: 37168652 PMCID: PMC10168101 DOI: 10.1109/ted.2021.3131116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Real-time spike sorting and processing are crucial for closed-loop brain-machine interfaces and neural prosthetics. Recent developments in high-density multi-electrode arrays with hundreds of electrodes have enabled simultaneous recordings of spikes from a large number of neurons. However, the high channel count imposes stringent demands on real-time spike sorting hardware regarding data transmission bandwidth and computation complexity. Thus, it is necessary to develop a specialized real-time hardware that can sort neural spikes on the fly with high throughputs while consuming minimal power. Here, we present a real-time, low latency spike sorting processor that utilizes high-density CuOx resistive crossbars to implement in-memory spike sorting in a massively parallel manner. We developed a fabrication process which is compatible with CMOS BEOL integration. We extensively characterized switching characteristics and statistical variations of the CuOx memory devices. In order to implement spike sorting with crossbar arrays, we developed a template matching-based spike sorting algorithm that can be directly mapped onto RRAM crossbars. By using synthetic and in vivo recordings of extracellular spikes, we experimentally demonstrated energy efficient spike sorting with high accuracy. Our neuromorphic interface offers substantial improvements in area (~1000× less area), power (~200× less power), and latency (4.8μs latency for sorting 100 channels) for real-time spike sorting compared to other hardware implementations based on FPGAs and microcontrollers.
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Affiliation(s)
- Yuhan Shi
- Electrical and Computer Engineering Department. G. Cauwenberghs is with Bioengineering Department, University of California at San Diego, San Diego, CA 92093, USA
| | - Akshay Ananthakrishnan
- Electrical and Computer Engineering Department. G. Cauwenberghs is with Bioengineering Department, University of California at San Diego, San Diego, CA 92093, USA
| | - Sangheon Oh
- Electrical and Computer Engineering Department. G. Cauwenberghs is with Bioengineering Department, University of California at San Diego, San Diego, CA 92093, USA
| | - Xin Liu
- Electrical and Computer Engineering Department. G. Cauwenberghs is with Bioengineering Department, University of California at San Diego, San Diego, CA 92093, USA
| | - Gopabandhu Hota
- Electrical and Computer Engineering Department. G. Cauwenberghs is with Bioengineering Department, University of California at San Diego, San Diego, CA 92093, USA
| | - Gert Cauwenberghs
- Electrical and Computer Engineering Department. G. Cauwenberghs is with Bioengineering Department, University of California at San Diego, San Diego, CA 92093, USA
| | - Duygu Kuzum
- Electrical and Computer Engineering Department. G. Cauwenberghs is with Bioengineering Department, University of California at San Diego, San Diego, CA 92093, USA
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24
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Abstract
In human neuroscience, studies of cognition are rarely grounded in non-task-evoked, 'spontaneous' neural activity. Indeed, studies of spontaneous activity tend to focus predominantly on intrinsic neural patterns (for example, resting-state networks). Taking a 'representation-rich' approach bridges the gap between cognition and resting-state communities: this approach relies on decoding task-related representations from spontaneous neural activity, allowing quantification of the representational content and rich dynamics of such activity. For example, if we know the neural representation of an episodic memory, we can decode its subsequent replay during rest. We argue that such an approach advances cognitive research beyond a focus on immediate task demand and provides insight into the functional relevance of the intrinsic neural pattern (for example, the default mode network). This in turn enables a greater integration between human and animal neuroscience, facilitating experimental testing of theoretical accounts of intrinsic activity, and opening new avenues of research in psychiatry.
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25
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Mourão FAG, Guarnieri LDO, Amaral Júnior PA, Carvalho VR, Mendes EMAM, Moraes MFD. A Fully Adapted Headstage With Custom Electrode Arrays Designed for Electrophysiological Experiments. Front Neurosci 2022; 15:691788. [PMID: 35309085 PMCID: PMC8928121 DOI: 10.3389/fnins.2021.691788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 09/20/2021] [Indexed: 11/20/2022] Open
Abstract
Electrophysiological recordings lead amongst the techniques that aim to investigate the dynamics of neural activity sampled from large neural ensembles. However, the financial costs associated with the state-of-the-art technology used to manufacture probes and multi-channel recording systems make these experiments virtually inaccessible to small laboratories, especially if located in developing countries. Here, we describe a new method for implanting several tungsten electrode arrays, widely distributed over the brain. Moreover, we designed a headstage system, using the Intan® RHD2000 chipset, associated with a connector (replacing the expensive commercial Omnetics connector), that allows the usage of disposable and inexpensive cranial implants. Our results showed high-quality multichannel recording in freely moving animals (detecting local field, evoked responses and unit activities) and robust mechanical connections ensuring long-term continuous recordings. Our project represents an open source and inexpensive alternative to develop customized extracellular records from multiple brain regions.
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Affiliation(s)
- Flávio Afonso Gonçalves Mourão
- Programa de Pós Graduação em Neurociências, Núcleo de Neurociências, Departamento de Fisiologia e Biofísica, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Leonardo de Oliveira Guarnieri
- Programa de Pós Graduação em Neurociências, Núcleo de Neurociências, Departamento de Fisiologia e Biofísica, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
- Programa de Pós-Graduação em Engenharia Elétrica, Departamento de Engenharia Eletrônica (DELT), Escola de Engenharia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Paulo Aparecido Amaral Júnior
- Programa de Pós Graduação em Neurociências, Núcleo de Neurociências, Departamento de Fisiologia e Biofísica, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
- Programa de Pós-Graduação em Engenharia Elétrica, Departamento de Engenharia Eletrônica (DELT), Escola de Engenharia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Vinícius Rezende Carvalho
- Programa de Pós Graduação em Neurociências, Núcleo de Neurociências, Departamento de Fisiologia e Biofísica, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
- Programa de Pós-Graduação em Engenharia Elétrica, Departamento de Engenharia Eletrônica (DELT), Escola de Engenharia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Eduardo Mazoni Andrade Marçal Mendes
- Programa de Pós Graduação em Neurociências, Núcleo de Neurociências, Departamento de Fisiologia e Biofísica, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
- Programa de Pós-Graduação em Engenharia Elétrica, Departamento de Engenharia Eletrônica (DELT), Escola de Engenharia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Márcio Flávio Dutra Moraes
- Programa de Pós Graduação em Neurociências, Núcleo de Neurociências, Departamento de Fisiologia e Biofísica, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
- Programa de Pós-Graduação em Engenharia Elétrica, Departamento de Engenharia Eletrônica (DELT), Escola de Engenharia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
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26
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Opto-electrical bimodal recording of neural activity in awake head-restrained mice. Sci Rep 2022; 12:736. [PMID: 35031630 PMCID: PMC8760260 DOI: 10.1038/s41598-021-04365-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 12/09/2021] [Indexed: 11/08/2022] Open
Abstract
Electrical and optical monitoring of neural activity is major approaches for studying brain functions. Each has its own set of advantages and disadvantages, such as the ability to determine cell types and temporal resolution. Although opto-electrical bimodal recording is beneficial by enabling us to exploit the strength of both approaches, it has not been widely used. In this study, we devised three methods of bimodal recording from a deep brain structure in awake head-fixed mice by chronically implanting a gradient-index (GRIN) lens and electrodes. First, we attached four stainless steel electrodes to the side of a GRIN lens and implanted them in a mouse expressing GCaMP6f in astrocytes. We simultaneously recorded local field potential (LFP) and GCaMP6f signal in astrocytes in the hippocampal CA1 area. Second, implanting a silicon probe electrode mounted on a custom-made microdrive within the focal volume of a GRIN lens, we performed bimodal recording in the CA1 area. We monitored LFP and fluorescent changes of GCaMP6s-expressing neurons in the CA1. Third, we designed a 3D-printed scaffold to serve as a microdrive for a silicon probe and a holder for a GRIN lens. This scaffold simplifies the implantation process and makes it easier to place the lens and probe accurately. Using this method, we recorded single unit activity and LFP electrically and GCaMP6f signals of single neurons optically. Thus, we show that these opto-electrical bimodal recording methods using a GRIN lens and electrodes are viable approaches in awake head-fixed mice.
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Abstract
Characterizing cortex-wide neural activity is essential for understanding large-scale interactions among distributed cortical regions. Here, we describe a protocol using wide-field calcium imaging to monitor the cortex-wide activity in awake, head-fixed mice. This approach provides sufficient signal-to-noise ratio and spatiotemporal resolution to capture large-scale neural activity in behaving mice on a moment-by-moment basis. The use of genetically encoded calcium indicators allows longitudinal imaging over months and can achieve cell-type specificity. We also describe a pipeline to process the imaging data. For complete details on the use and execution of this protocol, please refer to Makino et al. (2017) and Liu et al. (2021).
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Affiliation(s)
- Chi Ren
- Neurobiology Section, Center for Neural Circuits and Behavior, Department of Neurosciences, and Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla, CA 92093, USA
| | - Takaki Komiyama
- Neurobiology Section, Center for Neural Circuits and Behavior, Department of Neurosciences, and Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla, CA 92093, USA
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Liu X, Ren C, Huang Z, Wilson M, Kim JH, Lu Y, Ramezani M, Komiyama T, Kuzum D. Decoding of cortex-wide brain activity from local recordings of neural potentials. J Neural Eng 2021; 18. [PMID: 34706356 DOI: 10.1088/1741-2552/ac33e7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 10/27/2021] [Indexed: 11/11/2022]
Abstract
Objective. Electrical recordings of neural activity from brain surface have been widely employed in basic neuroscience research and clinical practice for investigations of neural circuit functions, brain-computer interfaces, and treatments for neurological disorders. Traditionally, these surface potentials have been believed to mainly reflect local neural activity. It is not known how informative the locally recorded surface potentials are for the neural activities across multiple cortical regions.Approach. To investigate that, we perform simultaneous local electrical recording and wide-field calcium imaging in awake head-fixed mice. Using a recurrent neural network model, we try to decode the calcium fluorescence activity of multiple cortical regions from local electrical recordings.Main results. The mean activity of different cortical regions could be decoded from locally recorded surface potentials. Also, each frequency band of surface potentials differentially encodes activities from multiple cortical regions so that including all the frequency bands in the decoding model gives the highest decoding performance. Despite the close spacing between recording channels, surface potentials from different channels provide complementary information about the large-scale cortical activity and the decoding performance continues to improve as more channels are included. Finally, we demonstrate the successful decoding of whole dorsal cortex activity at pixel-level using locally recorded surface potentials.Significance. These results show that the locally recorded surface potentials indeed contain rich information of the large-scale neural activities, which could be further demixed to recover the neural activity across individual cortical regions. In the future, our cross-modality inference approach could be adapted to virtually reconstruct cortex-wide brain activity, greatly expanding the spatial reach of surface electrical recordings without increasing invasiveness. Furthermore, it could be used to facilitate imaging neural activity across the whole cortex in freely moving animals, without requirement of head-fixed microscopy configurations.
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Affiliation(s)
- Xin Liu
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, United States of America
| | - Chi Ren
- Neurobiology Section, Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States of America.,Center for Neural Circuits and Behavior, University of California San Diego, La Jolla, CA, United States of America.,Department of Neurosciences, University of California San Diego, La Jolla, CA, United States of America
| | - Zhisheng Huang
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, United States of America
| | - Madison Wilson
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, United States of America
| | - Jeong-Hoon Kim
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, United States of America
| | - Yichen Lu
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, United States of America
| | - Mehrdad Ramezani
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, United States of America
| | - Takaki Komiyama
- Neurobiology Section, Division of Biological Sciences, University of California San Diego, La Jolla, CA, United States of America.,Center for Neural Circuits and Behavior, University of California San Diego, La Jolla, CA, United States of America.,Department of Neurosciences, University of California San Diego, La Jolla, CA, United States of America.,Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla, CA, United States of America
| | - Duygu Kuzum
- Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, United States of America.,Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla, CA, United States of America
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The diversity and specificity of functional connectivity across spatial and temporal scales. Neuroimage 2021; 245:118692. [PMID: 34751153 DOI: 10.1016/j.neuroimage.2021.118692] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 01/01/2023] Open
Abstract
Macroscopic neuroimaging modalities in humans have revealed the organization of brain-wide activity into distributed functional networks that re-organize according to behavioral demands. However, the inherent coarse-graining of macroscopic measurements conceals the diversity and specificity in responses and connectivity of many individual neurons contained in each local region. New invasive approaches in animals enable recording and manipulating neural activity at meso- and microscale resolution, with cell-type specificity and temporal precision down to milliseconds. Determining how brain-wide activity patterns emerge from interactions across spatial and temporal scales will allow us to identify the key circuit mechanisms contributing to global brain states and how the dynamic activity of these states enables adaptive behavior.
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30
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Ren C, Komiyama T. Characterizing Cortex-Wide Dynamics with Wide-Field Calcium Imaging. J Neurosci 2021; 41:4160-4168. [PMID: 33893217 PMCID: PMC8143209 DOI: 10.1523/jneurosci.3003-20.2021] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/26/2021] [Accepted: 03/30/2021] [Indexed: 12/27/2022] Open
Abstract
The brain functions through coordinated activity among distributed regions. Wide-field calcium imaging, combined with improved genetically encoded calcium indicators, allows sufficient signal-to-noise ratio and spatiotemporal resolution to afford a unique opportunity to capture cortex-wide dynamics on a moment-by-moment basis in behaving animals. Recent applications of this approach have been uncovering cortical dynamics at unprecedented scales during various cognitive processes, ranging from relatively simple sensorimotor integration to more complex decision-making tasks. In this review, we will highlight recent scientific advances enabled by wide-field calcium imaging in behaving mice. We then summarize several technical considerations and future opportunities for wide-field imaging to uncover large-scale circuit dynamics.
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Affiliation(s)
- Chi Ren
- Neurobiology Section, Center for Neural Circuits and Behavior, Department of Neurosciences, and Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla, California 92093
| | - Takaki Komiyama
- Neurobiology Section, Center for Neural Circuits and Behavior, Department of Neurosciences, and Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla, California 92093
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