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Johnsen KA, Cruzado NA, Menard ZC, Willats AA, Charles AS, Markowitz JE, Rozell CJ. Bridging model and experiment in systems neuroscience with Cleo: the Closed-Loop, Electrophysiology, and Optophysiology simulation testbed. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.01.27.525963. [PMID: 39026717 PMCID: PMC11257437 DOI: 10.1101/2023.01.27.525963] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Systems neuroscience has experienced an explosion of new tools for reading and writing neural activity, enabling exciting new experiments such as all-optical or closed-loop control that effect powerful causal interventions. At the same time, improved computational models are capable of reproducing behavior and neural activity with increasing fidelity. Unfortunately, these advances have drastically increased the complexity of integrating different lines of research, resulting in the missed opportunities and untapped potential of suboptimal experiments. Experiment simulation can help bridge this gap, allowing model and experiment to better inform each other by providing a low-cost testbed for experiment design, model validation, and methods engineering. Specifically, this can be achieved by incorporating the simulation of the experimental interface into our models, but no existing tool integrates optogenetics, two-photon calcium imaging, electrode recording, and flexible closed-loop processing with neural population simulations. To address this need, we have developed Cleo: the Closed-Loop, Electrophysiology, and Optophysiology experiment simulation testbed. Cleo is a Python package enabling injection of recording and stimulation devices as well as closed-loop control with realistic latency into a Brian spiking neural network model. It is the only publicly available tool currently supporting two-photon and multi-opsin/wavelength optogenetics. To facilitate adoption and extension by the community, Cleo is open-source, modular, tested, and documented, and can export results to various data formats. Here we describe the design and features of Cleo, validate output of individual components and integrated experiments, and demonstrate its utility for advancing optogenetic techniques in prospective experiments using previously published systems neuroscience models.
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Affiliation(s)
- Kyle A. Johnsen
- Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | | | - Zachary C. Menard
- Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Adam A. Willats
- Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Adam S. Charles
- Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, MD, USA
| | - Jeffrey E. Markowitz
- Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
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2
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Zhang J, Newman J, Wang Z, Qian Y, Feliciano-Ramos P, Guo W, Honda T, Chen ZS, Linghu C, Etienne-Cummings R, Fossum E, Boyden E, Wilson M. Pixel-wise programmability enables dynamic high-SNR cameras for high-speed microscopy. Nat Commun 2024; 15:4480. [PMID: 38802338 DOI: 10.1038/s41467-024-48765-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 04/30/2024] [Indexed: 05/29/2024] Open
Abstract
High-speed wide-field fluorescence microscopy has the potential to capture biological processes with exceptional spatiotemporal resolution. However, conventional cameras suffer from low signal-to-noise ratio at high frame rates, limiting their ability to detect faint fluorescent events. Here, we introduce an image sensor where each pixel has individually programmable sampling speed and phase, so that pixels can be arranged to simultaneously sample at high speed with a high signal-to-noise ratio. In high-speed voltage imaging experiments, our image sensor significantly increases the output signal-to-noise ratio compared to a low-noise scientific CMOS camera (~2-3 folds). This signal-to-noise ratio gain enables the detection of weak neuronal action potentials and subthreshold activities missed by the standard scientific CMOS cameras. Our camera with flexible pixel exposure configurations offers versatile sampling strategies to improve signal quality in various experimental conditions.
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Affiliation(s)
- Jie Zhang
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA.
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA.
| | - Jonathan Newman
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
| | - Zeguan Wang
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA
| | - Yong Qian
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA
| | - Pedro Feliciano-Ramos
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
| | - Wei Guo
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
| | - Takato Honda
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
| | - Zhe Sage Chen
- Department of Psychiatry, NYU Grossman School of Medicine, New York, NY, USA
| | - Changyang Linghu
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Ralph Etienne-Cummings
- Department of Electrical and Computer Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Eric Fossum
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
| | - Edward Boyden
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA
| | - Matthew Wilson
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
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Zhang J, Newman J, Wang Z, Qian Y, Feliciano-Ramos P, Guo W, Honda T, Chen ZS, Linghu C, Etienne-Cummings R, Fossum E, Boyden E, Wilson M. Pixel-wise programmability enables dynamic high-SNR cameras for high-speed microscopy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.27.546748. [PMID: 37425952 PMCID: PMC10327006 DOI: 10.1101/2023.06.27.546748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
High-speed wide-field fluorescence microscopy has the potential to capture biological processes with exceptional spatiotemporal resolution. However, conventional cameras suffer from low signal-to-noise ratio at high frame rates, limiting their ability to detect faint fluorescent events. Here, we introduce an image sensor where each pixel has individually programmable sampling speed and phase, so that pixels can be arranged to simultaneously sample at high speed with a high signal-to-noise ratio. In high-speed voltage imaging experiments, our image sensor significantly increases the output signal-to-noise ratio compared to a low-noise scientific CMOS camera (~2-3 folds). This signal-to-noise ratio gain enables the detection of weak neuronal action potentials and subthreshold activities missed by the standard scientific CMOS cameras. Our camera with flexible pixel exposure configurations offers versatile sampling strategies to improve signal quality in various experimental conditions.
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Affiliation(s)
- Jie Zhang
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
| | - Jonathan Newman
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
| | - Zeguan Wang
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA
| | - Yong Qian
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA
| | - Pedro Feliciano-Ramos
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
| | - Wei Guo
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
| | - Takato Honda
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
| | - Zhe Sage Chen
- Department of Psychiatry, NYU Grossman School of Medicine, New York, NY, USA
| | - Changyang Linghu
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Ralph Etienne-Cummings
- Department of Electrical and Computer Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Eric Fossum
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
| | - Edward Boyden
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA
| | - Matthew Wilson
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
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Kc E, Islam J, Lee G, Park YS. Optogenetic Approach in Trigeminal Neuralgia and Potential Concerns: Preclinical Insights. Mol Neurobiol 2024; 61:1769-1780. [PMID: 37775720 DOI: 10.1007/s12035-023-03652-w] [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: 03/15/2023] [Accepted: 09/11/2023] [Indexed: 10/01/2023]
Abstract
The integration of optogenetics in the trigeminal pain circuitry broadens and reinforces existing pain investigations. Similar to research on spinal neuropathic pain, the exploration of the underlying determinants of orofacial pain is expanding. Optogenetics facilitates more direct, specific, and subtle investigations of the neuronal circuits involved in orofacial pain. One of the most significant concerns of both dentistry and medicine is trigeminal neuralgia (TN) management due to its substantial impact on a patient's quality of life. Our objective is to gather insights from preclinical studies conducted in TN employing an optogenetic paradigm, thereby extending the prospects for in-depth neurobiological research. This review highlights optogenetic research in trigeminal pain circuitry involving TN. We outline the central and peripheral regions associated with pain-that have been investigated using optogenetics in the trigeminal pain circuitry. The study further reports its scope and limitations as well as its potential for future applications from bench to bedside.
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Affiliation(s)
- Elina Kc
- Program in Neuroscience, Department of Medicine, College of Medicine, Chungbuk National University, Cheongju, Republic of Korea
| | - Jaisan Islam
- Program in Neuroscience, Department of Medicine, College of Medicine, Chungbuk National University, Cheongju, Republic of Korea
| | - Gabsang Lee
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- The Solomon H. Snyder, Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Young Seok Park
- Program in Neuroscience, Department of Medicine, College of Medicine, Chungbuk National University, Cheongju, Republic of Korea.
- Department of Neurosurgery, Chungbuk National University Hospital, Cheongju, Republic of Korea.
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Ajieren H, Fox A, Biggs E, Albors G, Llebaria A, Irazoqui P. Design and validation of a low-cost photomodulator for in vivo photoactivation of a mGluR5 inhibitor. Biomed Eng Lett 2024; 14:245-254. [PMID: 38374907 PMCID: PMC10874351 DOI: 10.1007/s13534-023-00334-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 02/21/2024] Open
Abstract
Purpose: Severe side effects prevent the utilization of otherwise promising drugs in treatments. These side effects arise when drugs affect untargeted tissues due to poor target specificity. In photopharmacology, light controls the timing and the location of drug delivery, improving treatment specificity and pharmacokinetic control. Photopharmaceuticals have not seen widespread adoption in part because researchers do not always have access to reliable and reproducible light delivery devices at prices which fit within the larger research budget. Method: In this work, we present a customizable photomodulator for use in both wearable and implantable devices. For experimental validation of the photomodulator, we photolyse JF-NP-26 in rats. Results: We successfully drive in vivo photopharmacology with a tethered photomodulator and demonstrate modifications which enable the photomodulator to operate wirelessly. Conclusion: By documenting our photomodulator development, we hope to introduce researchers to a simple solution which significantly lowers the engineering barriers to photopharmacology research. Graphical abstract Researchers present a photomodulator, a device designed to facilitate in vivo photopharmacology. They demonstrate the in vivo capabilities of the photomodulator by photoreleasing raseglurant, an mGluR5 inhibitor, to treat pain in an acute rat model and follow this study by showing how to reconfigure the photomodulator to work wirelessly and interface with other biomedical devices. Supplementary Information The online version contains supplementary material available at 10.1007/s13534-023-00334-3.
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Affiliation(s)
- Hans Ajieren
- Department of Electrical Engineering, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218 USA
| | - Andrew Fox
- Indiana University School of Medicine, Indianapolis, IN 46202 USA
| | - Ethan Biggs
- Indiana University School of Medicine, Indianapolis, IN 46202 USA
| | - Gabriel Albors
- The Margolis Center for Health Policy, Duke University, Durham, NC 27708 USA
| | - Amadeu Llebaria
- Institute for Advanced Chemistry of Catalonia, Spanish National Research Council, Jordi Girona, 18-26, 08034 Barcelona, Spain
| | - Pedro Irazoqui
- Department of Electrical Engineering, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218 USA
- Department of Biomedical Engineering, Johns Hopkins School of Medicine, 733 N. Broadway, Baltimore, MD 21205 USA
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Ördög B, De Coster T, Dekker SO, Bart CI, Zhang J, Boink GJJ, Bax WH, Deng S, den Ouden BL, de Vries AAF, Pijnappels DA. Opto-electronic feedback control of membrane potential for real-time control of action potentials. CELL REPORTS METHODS 2023; 3:100671. [PMID: 38086387 PMCID: PMC10753386 DOI: 10.1016/j.crmeth.2023.100671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 10/09/2023] [Accepted: 11/19/2023] [Indexed: 12/21/2023]
Abstract
To unlock new research possibilities by acquiring control of action potential (AP) morphologies in excitable cells, we developed an opto-electronic feedback loop-based system integrating cellular electrophysiology, real-time computing, and optogenetic approaches and applied it to monolayers of heart muscle cells. This allowed accurate restoration and preservation of cardiac AP morphologies in the presence of electrical perturbations of different origin in an unsupervised, self-regulatory manner, without any prior knowledge of the disturbance. Moreover, arbitrary AP waveforms could be enforced onto these cells. Collectively, these results set the stage for the refinement and application of opto-electronic control systems to enable in-depth investigation into the regulatory role of membrane potential in health and disease.
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Affiliation(s)
- Balázs Ördög
- Laboratory of Experimental Cardiology, Department of Cardiology, Heart Lung Center Leiden, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands.
| | - Tim De Coster
- Laboratory of Experimental Cardiology, Department of Cardiology, Heart Lung Center Leiden, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Sven O Dekker
- Laboratory of Experimental Cardiology, Department of Cardiology, Heart Lung Center Leiden, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Cindy I Bart
- Laboratory of Experimental Cardiology, Department of Cardiology, Heart Lung Center Leiden, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Juan Zhang
- Laboratory of Experimental Cardiology, Department of Cardiology, Heart Lung Center Leiden, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Gerard J J Boink
- Amsterdam Cardiovascular Sciences, Department of Cardiology, Amsterdam UMC, Location AMC, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands; Department of Medical Biology, Amsterdam UMC, Location AMC, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Wilhelmina H Bax
- Laboratory of Experimental Cardiology, Department of Cardiology, Heart Lung Center Leiden, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Shanliang Deng
- Laboratory of Experimental Cardiology, Department of Cardiology, Heart Lung Center Leiden, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Department of Microelectronics, Delft University of Technology, 2628 CD Delft, the Netherlands
| | - Bram L den Ouden
- Laboratory of Experimental Cardiology, Department of Cardiology, Heart Lung Center Leiden, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Department of Microelectronics, Delft University of Technology, 2628 CD Delft, the Netherlands
| | - Antoine A F de Vries
- Laboratory of Experimental Cardiology, Department of Cardiology, Heart Lung Center Leiden, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Daniël A Pijnappels
- Laboratory of Experimental Cardiology, Department of Cardiology, Heart Lung Center Leiden, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands.
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Wu Y, Li BZ, Wang L, Fan S, Chen C, Li A, Lin Q, Wang P. An unsupervised real-time spike sorting system based on optimized OSort. J Neural Eng 2023; 20:066015. [PMID: 37972395 DOI: 10.1088/1741-2552/ad0d15] [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: 05/29/2023] [Accepted: 11/15/2023] [Indexed: 11/19/2023]
Abstract
Objective. The OSort algorithm, a pivotal unsupervised spike sorting method, has been implemented in dedicated hardware devices for real-time spike sorting. However, due to the inherent complexity of neural recording environments, OSort still grapples with numerous transient cluster occurrences during the practical sorting process. This leads to substantial memory usage, heavy computational load, and complex hardware architectures, especially in noisy recordings and multi-channel systems.Approach. This study introduces an optimized OSort algorithm (opt-OSort) which utilizes correlation coefficient (CC), instead of Euclidean distance as classification criterion. TheCCmethod not only bolsters the robustness of spike classification amidst the diverse and ever-changing conditions of physiological and recording noise environments, but also can finish the entire sorting procedure within a fixed number of cluster slots, thus preventing a large number of transient clusters. Moreover, the opt-OSort incorporates two configurable validation loops to efficiently reject cluster outliers and track recording variations caused by electrode drifting in real-time.Main results. The opt-OSort significantly reduces transient cluster occurrences by two orders of magnitude and decreases memory usage by 2.5-80 times in the number of pre-allocated transient clusters compared with other hardware implementations of OSort. The opt-OSort maintains an accuracy comparable to offline OSort and other commonly-used algorithms, with a sorting time of 0.68µs as measured by the hardware-implemented system in both simulated datasets and experimental data. The opt-OSort's ability to handle variations in neural activity caused by electrode drifting is also demonstrated.Significance. These results present a rapid, precise, and robust spike sorting solution suitable for integration into low-power, portable, closed-loop neural control systems and brain-computer interfaces.
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Affiliation(s)
- Yingjiang Wu
- School of Biomedical Engineering, Guangdong Medical University, Dongguan, People's Republic of China
- Songshan Lake Innovation Center of Medicine and Engineering, Guangdong Medical University, Dongguan, People's Republic of China
- Dongguan Key Laboratory of Medical Electronics and Medical Imaging Equipment, Dongguan, People's Republic of China
| | - Ben-Zheng Li
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States of America
- Department of Electrical Engineering, University of Colorado Denver, Denver, CO, United States of America
| | - Liyang Wang
- State Key Laboratory of Analog and Mixed Signal VLSI, University of Macau, Macau, People's Republic of China
- Department of Electrical and Computer Engineering, University of Macau, Macau, People's Republic of China
| | - Shaocan Fan
- School of Electronics and Communication Engineering, Sun Yat-sen University-Shenzhen Campus, Shenzhen, People's Republic of China
| | - Changhao Chen
- Zhuhai Hokai Medical Instruments Co., Ltd, Zhuhai, People's Republic of China
| | - Anan Li
- Jiangsu Key Laboratory of Brain Disease and Bioinformation, Research Center for Biochemistry and Molecular Biology, Xuzhou Medical University, Xuzhou, People's Republic of China
| | - Qin Lin
- School of Biomedical Engineering, Guangdong Medical University, Dongguan, People's Republic of China
- Songshan Lake Innovation Center of Medicine and Engineering, Guangdong Medical University, Dongguan, People's Republic of China
- Dongguan Key Laboratory of Medical Electronics and Medical Imaging Equipment, Dongguan, People's Republic of China
| | - Panke Wang
- School of Biomedical Engineering, Guangdong Medical University, Dongguan, People's Republic of China
- Songshan Lake Innovation Center of Medicine and Engineering, Guangdong Medical University, Dongguan, People's Republic of China
- Dongguan Key Laboratory of Medical Electronics and Medical Imaging Equipment, Dongguan, People's Republic of China
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Triplett MA, Gajowa M, Adesnik H, Paninski L. Bayesian target optimisation for high-precision holographic optogenetics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.25.542307. [PMID: 37292661 PMCID: PMC10246014 DOI: 10.1101/2023.05.25.542307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Two-photon optogenetics has transformed our ability to probe the structure and function of neural circuits. However, achieving precise optogenetic control of neural ensemble activity has remained fundamentally constrained by the problem of off-target stimulation (OTS): the inadvertent activation of nearby non-target neurons due to imperfect confinement of light onto target neurons. Here we propose a novel computational approach to this problem called Bayesian target optimisation. Our approach uses nonparametric Bayesian inference to model neural responses to optogenetic stimulation, and then optimises the laser powers and optical target locations needed to achieve a desired activity pattern with minimal OTS. We validate our approach in simulations and using data from in vitro experiments, showing that Bayesian target optimisation considerably reduces OTS across all conditions we test. Together, these results establish our ability to overcome OTS, enabling optogenetic stimulation with substantially improved precision.
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Affiliation(s)
- Marcus A. Triplett
- Department of Statistics, Columbia University
- Zuckerman Mind Brain Behavior Institute, Columbia University
| | - Marta Gajowa
- Department of Molecular and Cell Biology, UC Berkeley
| | | | - Liam Paninski
- Department of Statistics, Columbia University
- Zuckerman Mind Brain Behavior Institute, Columbia University
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Ocampo-Espindola JL, Nikhil KL, Li JS, Herzog ED, Kiss IZ. Synchronization, clustering, and weak chimeras in a densely coupled transcription-based oscillator model for split circadian rhythms. CHAOS (WOODBURY, N.Y.) 2023; 33:083105. [PMID: 37535024 PMCID: PMC10403273 DOI: 10.1063/5.0156135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 07/08/2023] [Indexed: 08/04/2023]
Abstract
The synchronization dynamics for the circadian gene expression in the suprachiasmatic nucleus is investigated using a transcriptional circadian clock gene oscillator model. With global coupling in constant dark (DD) conditions, the model exhibits a one-cluster phase synchronized state, in dim light (dim LL), bistability between one- and two-cluster states and in bright LL, a two-cluster state. The two-cluster phase synchronized state, where some oscillator pairs synchronize in-phase, and some anti-phase, can explain the splitting of the circadian clock, i.e., generation of two bouts of daily activities with certain species, e.g., with hamsters. The one- and two-cluster states can be reached by transferring the animal from DD or bright LL to dim LL, i.e., the circadian synchrony has a memory effect. The stability of the one- and two-cluster states was interpreted analytically by extracting phase models from the ordinary differential equation models. In a modular network with two strongly coupled oscillator populations with weak intragroup coupling, with appropriate initial conditions, one group is synchronized to the one-cluster state and the other group to the two-cluster state, resulting in a weak-chimera state. Computational modeling suggests that the daily rhythms in sleep-wake depend on light intensity acting on bilateral networks of suprachiasmatic nucleus (SCN) oscillators. Addition of a network heterogeneity (coupling between the left and right SCN) allowed the system to exhibit chimera states. The simulations can guide experiments in the circadian rhythm research to explore the effect of light intensity on the complexities of circadian desynchronization.
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Affiliation(s)
| | - K. L. Nikhil
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, Missouri 63130-4899, USA
| | - Jr-Shin Li
- Department of Electrical and Systems Engineering, Washington University in St Louis, 1 Brookings Drive, St. Louis, Missouri 63130, USA
| | - Erik D. Herzog
- Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, Missouri 63130-4899, USA
| | - István Z. Kiss
- Department of Chemistry, Saint Louis University, 3501 Laclede Ave., St. Louis, Missouri 63103, USA
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10
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Gerson J, Erdal MK, McDonough MH, Ploense KL, Dauphin-Ducharme P, Honeywell KM, Leung KK, Arroyo-Curras N, Gibson JM, Emmons NA, Meiring W, Hespanha JP, Plaxco KW, Kippin TE. High-precision monitoring of and feedback control over drug concentrations in the brains of freely moving rats. SCIENCE ADVANCES 2023; 9:eadg3254. [PMID: 37196087 PMCID: PMC10191434 DOI: 10.1126/sciadv.adg3254] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 04/12/2023] [Indexed: 05/19/2023]
Abstract
Knowledge of drug concentrations in the brains of behaving subjects remains constrained on a number of dimensions, including poor temporal resolution and lack of real-time data. Here, however, we demonstrate the ability of electrochemical aptamer-based sensors to support seconds-resolved, real-time measurements of drug concentrations in the brains of freely moving rats. Specifically, using such sensors, we achieve <4 μM limits of detection and 10-s resolution in the measurement of procaine in the brains of freely moving rats, permitting the determination of the pharmacokinetics and concentration-behavior relations of the drug with high precision for individual subjects. In parallel, we have used closed-loop feedback-controlled drug delivery to hold intracranial procaine levels constant (±10%) for >1.5 hours. These results demonstrate the utility of such sensors in (i) the determination of the site-specific, seconds-resolved neuropharmacokinetics, (ii) enabling the study of individual subject neuropharmacokinetics and concentration-response relations, and (iii) performing high-precision control over intracranial drug levels.
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Affiliation(s)
- Julian Gerson
- Department of Psychological and Brain Sciences, University of California, Santa Barbara, CA 93106, USA
- Neuroscience Research Institute, University of California, Santa Barbara, CA 93106, USA
- Institute for Collaborative Biotechnologies, University of California, Santa Barbara, CA 93106, USA
| | - Murat Kaan Erdal
- Department of Electrical and Computer Engineering, University of California, Santa Barbara, CA 93106, USA
| | - Matthew H. McDonough
- Department of Statistics and Applied Probability, University of California, Santa Barbara, CA 93106, USA
| | - Kyle L. Ploense
- Department of Psychological and Brain Sciences, University of California, Santa Barbara, CA 93106, USA
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106, USA
| | | | - Kevin M. Honeywell
- Department of Psychological and Brain Sciences, University of California, Santa Barbara, CA 93106, USA
| | - Kaylyn K. Leung
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106, USA
| | - Netzahualcoyotl Arroyo-Curras
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jenny M. Gibson
- Department of Psychological and Brain Sciences, University of California, Santa Barbara, CA 93106, USA
| | - Nicole A. Emmons
- Department of Psychological and Brain Sciences, University of California, Santa Barbara, CA 93106, USA
| | - Wendy Meiring
- Department of Statistics and Applied Probability, University of California, Santa Barbara, CA 93106, USA
| | - Joao P. Hespanha
- Department of Electrical and Computer Engineering, University of California, Santa Barbara, CA 93106, USA
| | - Kevin W. Plaxco
- Institute for Collaborative Biotechnologies, University of California, Santa Barbara, CA 93106, USA
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106, USA
| | - Tod E. Kippin
- Department of Psychological and Brain Sciences, University of California, Santa Barbara, CA 93106, USA
- Neuroscience Research Institute, University of California, Santa Barbara, CA 93106, USA
- Department of Molecular Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, USA
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11
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Bergs ACF, Liewald JF, Rodriguez-Rozada S, Liu Q, Wirt C, Bessel A, Zeitzschel N, Durmaz H, Nozownik A, Dill H, Jospin M, Vierock J, Bargmann CI, Hegemann P, Wiegert JS, Gottschalk A. All-optical closed-loop voltage clamp for precise control of muscles and neurons in live animals. Nat Commun 2023; 14:1939. [PMID: 37024493 PMCID: PMC10079764 DOI: 10.1038/s41467-023-37622-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 03/24/2023] [Indexed: 04/08/2023] Open
Abstract
Excitable cells can be stimulated or inhibited by optogenetics. Since optogenetic actuation regimes are often static, neurons and circuits can quickly adapt, allowing perturbation, but not true control. Hence, we established an optogenetic voltage-clamp (OVC). The voltage-indicator QuasAr2 provides information for fast, closed-loop optical feedback to the bidirectional optogenetic actuator BiPOLES. Voltage-dependent fluorescence is held within tight margins, thus clamping the cell to distinct potentials. We established the OVC in muscles and neurons of Caenorhabditis elegans, and transferred it to rat hippocampal neurons in slice culture. Fluorescence signals were calibrated to electrically measured potentials, and wavelengths to currents, enabling to determine optical I/V-relationships. The OVC reports on homeostatically altered cellular physiology in mutants and on Ca2+-channel properties, and can dynamically clamp spiking in C. elegans. Combining non-invasive imaging with control capabilities of electrophysiology, the OVC facilitates high-throughput, contact-less electrophysiology in individual cells and paves the way for true optogenetic control in behaving animals.
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Affiliation(s)
- Amelie C F Bergs
- Buchmann Institute for Molecular Life Sciences, Goethe University, Max-von-Laue-Strasse 15, 60438, Frankfurt, Germany
- Institute of Biophysical Chemistry, Goethe University, Max-von-Laue-Strasse 9, 60438, Frankfurt, Germany
| | - Jana F Liewald
- Buchmann Institute for Molecular Life Sciences, Goethe University, Max-von-Laue-Strasse 15, 60438, Frankfurt, Germany
- Institute of Biophysical Chemistry, Goethe University, Max-von-Laue-Strasse 9, 60438, Frankfurt, Germany
| | - Silvia Rodriguez-Rozada
- Research Group Synaptic Wiring and Information Processing, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, 20251, Hamburg, Germany
| | - Qiang Liu
- Lulu and Anthony Wang Laboratory of Neural Circuits and Behavior, The Rockefeller University, New York, NY, 10065, USA
- Department of Neuroscience, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong, China
| | - Christin Wirt
- Buchmann Institute for Molecular Life Sciences, Goethe University, Max-von-Laue-Strasse 15, 60438, Frankfurt, Germany
- Institute of Biophysical Chemistry, Goethe University, Max-von-Laue-Strasse 9, 60438, Frankfurt, Germany
| | - Artur Bessel
- Independent Researcher, Melatener Strasse 93, 52074, Aachen, Germany
| | - Nadja Zeitzschel
- Buchmann Institute for Molecular Life Sciences, Goethe University, Max-von-Laue-Strasse 15, 60438, Frankfurt, Germany
- Institute of Biophysical Chemistry, Goethe University, Max-von-Laue-Strasse 9, 60438, Frankfurt, Germany
| | - Hilal Durmaz
- Buchmann Institute for Molecular Life Sciences, Goethe University, Max-von-Laue-Strasse 15, 60438, Frankfurt, Germany
- Institute of Biophysical Chemistry, Goethe University, Max-von-Laue-Strasse 9, 60438, Frankfurt, Germany
| | - Adrianna Nozownik
- Research Group Synaptic Wiring and Information Processing, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, 20251, Hamburg, Germany
| | - Holger Dill
- Buchmann Institute for Molecular Life Sciences, Goethe University, Max-von-Laue-Strasse 15, 60438, Frankfurt, Germany
- Institute of Biophysical Chemistry, Goethe University, Max-von-Laue-Strasse 9, 60438, Frankfurt, Germany
| | - Maëlle Jospin
- Université Claude Bernard Lyon 1, Institut NeuroMyoGène, 8 Avenue Rockefeller, 69008, Lyon, France
| | - Johannes Vierock
- Institute for Biology, Experimental Biophysics, Humboldt University, 10115, Berlin, Germany
| | - Cornelia I Bargmann
- Lulu and Anthony Wang Laboratory of Neural Circuits and Behavior, The Rockefeller University, New York, NY, 10065, USA
- Chan Zuckerberg Initiative, Palo Alto, CA, USA
| | - Peter Hegemann
- Institute for Biology, Experimental Biophysics, Humboldt University, 10115, Berlin, Germany
| | - J Simon Wiegert
- Research Group Synaptic Wiring and Information Processing, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, 20251, Hamburg, Germany
- Medical Faculty Mannheim, University of Heidelberg, Ludolf-Krehl-Strasse 13-17, 68167, Mannheim, Germany
| | - Alexander Gottschalk
- Buchmann Institute for Molecular Life Sciences, Goethe University, Max-von-Laue-Strasse 15, 60438, Frankfurt, Germany.
- Institute of Biophysical Chemistry, Goethe University, Max-von-Laue-Strasse 9, 60438, Frankfurt, Germany.
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12
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Moraes JT, Trejo EJA, Camargo S, Ferreira SC, Chialvo DR. Self-tuned criticality: Controlling a neuron near its bifurcation point via temporal correlations. Phys Rev E 2023; 107:034204. [PMID: 37072953 DOI: 10.1103/physreve.107.034204] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/28/2023] [Indexed: 04/20/2023]
Abstract
Previous work showed that the collective activity of large neuronal networks can be tamed to remain near its critical point by a feedback control that maximizes the temporal correlations of the mean-field fluctuations. Since such correlations behave similarly near instabilities across nonlinear dynamical systems, it is expected that the principle should control also low-dimensional dynamical systems exhibiting continuous or discontinuous bifurcations from fixed points to limit cycles. Here we present numerical evidence that the dynamics of a single neuron can be controlled in the vicinity of its bifurcation point. The approach is tested in two models: a two-dimensional generic excitable map and the paradigmatic FitzHugh-Nagumo neuron model. The results show that in both cases, the system can be self-tuned to its bifurcation point by modifying the control parameter according to the first coefficient of the autocorrelation function.
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Affiliation(s)
- Juliane T Moraes
- Departamento de Física, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil
| | - Eyisto J Aguilar Trejo
- Center for Complex Systems and Brain Sciences (CEMSC3), Instituto de Ciencias Físicas (ICIFI), Universidad Nacional de San Martín, Campus Miguelete, 1650 San Martín, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científcas y Tecnológicas (CONICET), 1425 Buenos Aires, Argentina
| | - Sabrina Camargo
- Center for Complex Systems and Brain Sciences (CEMSC3), Instituto de Ciencias Físicas (ICIFI), Universidad Nacional de San Martín, Campus Miguelete, 1650 San Martín, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científcas y Tecnológicas (CONICET), 1425 Buenos Aires, Argentina
| | - Silvio C Ferreira
- Departamento de Física, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil
- National Institute of Science and Technology for Complex Systems, 22290-180 Rio de Janeiro, Brazil
| | - Dante R Chialvo
- Center for Complex Systems and Brain Sciences (CEMSC3), Instituto de Ciencias Físicas (ICIFI), Universidad Nacional de San Martín, Campus Miguelete, 1650 San Martín, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científcas y Tecnológicas (CONICET), 1425 Buenos Aires, Argentina
- Mark Kac Center for Complex Systems Research and Institute for Theoretical Physics, Jagiellonian University, 30-348 Kraków, Poland
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13
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Intertwining Neuropathogenic Impacts of Aberrant Circadian Rhythm and Impaired Neuroregenerative Plasticity in Huntington’s Disease: Neurotherapeutic Significance of Chemogenetics. JOURNAL OF MOLECULAR PATHOLOGY 2022. [DOI: 10.3390/jmp3040030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Huntington’s disease (HD) is a progressive neurodegenerative disorder characterized by abnormal progressive involuntary movements, cognitive deficits, sleep disturbances, and psychiatric symptoms. The onset and progression of the clinical symptoms have been linked to impaired adult neurogenesis in the brains of subjects with HD, due to the reduced neurogenic potential of neural stem cells (NSCs). Among various pathogenic determinants, an altered clock pathway appears to induce the dysregulation of neurogenesis in neurodegenerative disorders. Notably, gamma-aminobutyric acid (GABA)-ergic neurons that express the vasoactive intestinal peptide (VIP) in the brain play a key role in the regulation of circadian rhythm and neuroplasticity. While an abnormal clock gene pathway has been associated with the inactivation of GABAergic VIP neurons, recent studies suggest the activation of this neuronal population in the brain positively contributes to neuroplasticity. Thus, the activation of GABAergic VIP neurons in the brain might help rectify the irregular circadian rhythm in HD. Chemogenetics refers to the incorporation of genetically engineered receptors or ion channels into a specific cell population followed by its activation using desired chemical ligands. The recent advancement of chemogenetic-based approaches represents a potential scientific tool to rectify the aberrant circadian clock pathways. Considering the facts, the defects in the circadian rhythm can be rectified by the activation of VIP-expressing GABAergic neurons using chemogenetics approaches. Thus, the chemogenetic-based rectification of an abnormal circadian rhythm may facilitate the neurogenic potentials of NSCs to restore the neuroregenerative plasticity in HD. Eventually, the increased neurogenesis in the brain can be expected to mitigate neuronal loss and functional deficits.
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14
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Huszár R, Zhang Y, Blockus H, Buzsáki G. Preconfigured dynamics in the hippocampus are guided by embryonic birthdate and rate of neurogenesis. Nat Neurosci 2022; 25:1201-1212. [PMID: 35995878 PMCID: PMC10807234 DOI: 10.1038/s41593-022-01138-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 07/12/2022] [Indexed: 02/08/2023]
Abstract
The incorporation of new information into the hippocampal network is likely to be constrained by its innate architecture and internally generated activity patterns. However, the origin, organization and consequences of such patterns remain poorly understood. In the present study we show that hippocampal network dynamics are affected by sequential neurogenesis. We birthdated CA1 pyramidal neurons with in utero electroporation over 4 embryonic days, encompassing the peak of hippocampal neurogenesis, and compared their functional features in freely moving adult mice. Neurons of the same birthdate displayed distinct connectivity, coactivity across brain states and assembly dynamics. Same-birthdate neurons exhibited overlapping spatial representations, which were maintained across different environments. Overall, the wiring and functional features of CA1 pyramidal neurons reflected a combination of birthdate and the rate of neurogenesis. These observations demonstrate that sequential neurogenesis during embryonic development shapes the preconfigured forms of adult network dynamics.
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Affiliation(s)
- Roman Huszár
- Neuroscience Institute, New York University, New York, NY, USA.
- Center for Neural Science, New York University, New York, NY, USA.
| | - Yunchang Zhang
- Neuroscience Institute, New York University, New York, NY, USA
- Center for Neural Science, New York University, New York, NY, USA
| | - Heike Blockus
- Department of Neuroscience, Columbia University, New York, NY, USA
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - György Buzsáki
- Neuroscience Institute, New York University, New York, NY, USA.
- Center for Neural Science, New York University, New York, NY, USA.
- Department of Neurology, Langone Medical Center, New York, NY, USA.
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15
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Bayat FK, Alp Mİ, Bostan S, Gülçür HÖ, Öztürk G, Güveniş A. An improved platform for cultured neuronal network electrophysiology: multichannel optogenetics integrated with MEAs. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2022; 51:503-514. [PMID: 35930029 DOI: 10.1007/s00249-022-01613-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/11/2022] [Accepted: 07/24/2022] [Indexed: 06/15/2023]
Abstract
Cultured neuronal networks (CNNs) are powerful tools for studying how neuronal representation and adaptation emerge in networks of controlled populations of neurons. To ensure the interaction of a CNN and an artificial setting, reliable operation in both open and closed loops should be provided. In this study, we integrated optogenetic stimulation with microelectrode array (MEA) recordings using a digital micromirror device and developed an improved research tool with a 64-channel interface for neuronal network control and data acquisition. We determined the ideal stimulation parameters including light intensity, frequency, and duty cycle for our configuration. This resulted in robust and reproducible neuronal responses. We also demonstrated both open and closed loop configurations in the new platform involving multiple bidirectional channels. Unlike previous approaches that combined optogenetic stimulation and MEA recordings, we did not use binary grid patterns, but assigned an adjustable-size, non-binary optical spot to each electrode. This approach allowed simultaneous use of multiple input-output channels and facilitated adaptation of the stimulation parameters. Hence, we advanced a 64-channel interface in that each channel can be controlled individually in both directions simultaneously without any interference or interrupts. The presented setup meets the requirements of research in neuronal plasticity, network encoding and representation, closed-loop control of firing rate and synchronization. Researchers who develop closed-loop control techniques and adaptive stimulation strategies for network activity will benefit much from this novel setup.
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Affiliation(s)
- F Kemal Bayat
- Institute of Biomedical Engineering, Bogazici University, Istanbul, Turkey.
| | - M İkbal Alp
- Regenerative and Restorative Medicine Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey
| | - Sevginur Bostan
- Regenerative and Restorative Medicine Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey
| | - H Özcan Gülçür
- Institute of Biomedical Engineering, Bogazici University, Istanbul, Turkey
| | - Gürkan Öztürk
- Regenerative and Restorative Medicine Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey
| | - Albert Güveniş
- Institute of Biomedical Engineering, Bogazici University, Istanbul, Turkey
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16
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Papaioannou S, Medini P. Advantages, Pitfalls, and Developments of All Optical Interrogation Strategies of Microcircuits in vivo. Front Neurosci 2022; 16:859803. [PMID: 35837124 PMCID: PMC9274136 DOI: 10.3389/fnins.2022.859803] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 05/30/2022] [Indexed: 12/03/2022] Open
Abstract
The holy grail for every neurophysiologist is to conclude a causal relationship between an elementary behaviour and the function of a specific brain area or circuit. Our effort to map elementary behaviours to specific brain loci and to further manipulate neural activity while observing the alterations in behaviour is in essence the goal for neuroscientists. Recent advancements in the area of experimental brain imaging in the form of longer wavelength near infrared (NIR) pulsed lasers with the development of highly efficient optogenetic actuators and reporters of neural activity, has endowed us with unprecedented resolution in spatiotemporal precision both in imaging neural activity as well as manipulating it with multiphoton microscopy. This readily available toolbox has introduced a so called all-optical physiology and interrogation of circuits and has opened new horizons when it comes to precisely, fast and non-invasively map and manipulate anatomically, molecularly or functionally identified mesoscopic brain circuits. The purpose of this review is to describe the advantages and possible pitfalls of all-optical approaches in system neuroscience, where by all-optical we mean use of multiphoton microscopy to image the functional response of neuron(s) in the network so to attain flexible choice of the cells to be also optogenetically photostimulated by holography, in absence of electrophysiology. Spatio-temporal constraints will be compared toward the classical reference of electrophysiology methods. When appropriate, in relation to current limitations of current optical approaches, we will make reference to latest works aimed to overcome these limitations, in order to highlight the most recent developments. We will also provide examples of types of experiments uniquely approachable all-optically. Finally, although mechanically non-invasive, all-optical electrophysiology exhibits potential off-target effects which can ambiguate and complicate the interpretation of the results. In summary, this review is an effort to exemplify how an all-optical experiment can be designed, conducted and interpreted from the point of view of the integrative neurophysiologist.
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17
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Discovering sparse control strategies in neural activity. PLoS Comput Biol 2022; 18:e1010072. [PMID: 35622828 PMCID: PMC9140285 DOI: 10.1371/journal.pcbi.1010072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 04/01/2022] [Indexed: 11/19/2022] Open
Abstract
Biological circuits such as neural or gene regulation networks use internal states to map sensory input to an adaptive repertoire of behavior. Characterizing this mapping is a major challenge for systems biology. Though experiments that probe internal states are developing rapidly, organismal complexity presents a fundamental obstacle given the many possible ways internal states could map to behavior. Using C. elegans as an example, we propose a protocol for systematic perturbation of neural states that limits experimental complexity and could eventually help characterize collective aspects of the neural-behavioral map. We consider experimentally motivated small perturbations—ones that are most likely to preserve natural dynamics and are closer to internal control mechanisms—to neural states and their impact on collective neural activity. Then, we connect such perturbations to the local information geometry of collective statistics, which can be fully characterized using pairwise perturbations. Applying the protocol to a minimal model of C. elegans neural activity, we find that collective neural statistics are most sensitive to a few principal perturbative modes. Dominant eigenvalues decay initially as a power law, unveiling a hierarchy that arises from variation in individual neural activity and pairwise interactions. Highest-ranking modes tend to be dominated by a few, “pivotal” neurons that account for most of the system’s sensitivity, suggesting a sparse mechanism of collective control.
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18
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Wei Q, Han L, Zhang T. Spiking Adaptive Dynamic Programming Based on Poisson Process for Discrete-Time Nonlinear Systems. IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS 2022; 33:1846-1856. [PMID: 34143743 DOI: 10.1109/tnnls.2021.3085781] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
In this article, a new iterative spiking adaptive dynamic programming (SADP) method based on the Poisson process is developed to solve optimal impulsive control problems. For a fixed time interval, combining the Poisson process and the maximum likelihood estimation (MLE), the three-tuple of state, spiking interval, and probability of Poisson distribution can be computed, and then, the iterative value functions and iterative control laws can be obtained. A property analysis method is developed to show that the value functions converge to optimal performance index function as the iterative index increases from zero to infinity. Finally, two simulation examples are given to verify the effectiveness of the developed algorithm.
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19
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Pfeiffer P, Barreda Tomás FJ, Wu J, Schleimer JH, Vida I, Schreiber S. A dynamic clamp protocol to artificially modify cell capacitance. eLife 2022; 11:75517. [PMID: 35362411 PMCID: PMC9135398 DOI: 10.7554/elife.75517] [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: 11/12/2021] [Accepted: 03/17/2022] [Indexed: 11/13/2022] Open
Abstract
Dynamics of excitable cells and networks depend on the membrane time constant, set by membrane resistance and capacitance. Whereas pharmacological and genetic manipulations of ionic conductances of excitable membranes are routine in electrophysiology, experimental control over capacitance remains a challenge. Here, we present capacitance clamp, an approach that allows electrophysiologists to mimic a modified capacitance in biological neurons via an unconventional application of the dynamic clamp technique. We first demonstrate the feasibility to quantitatively modulate capacitance in a mathematical neuron model and then confirm the functionality of capacitance clamp in in vitro experiments in granule cells of rodent dentate gyrus with up to threefold virtual capacitance changes. Clamping of capacitance thus constitutes a novel technique to probe and decipher mechanisms of neuronal signaling in ways that were so far inaccessible to experimental electrophysiology.
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Affiliation(s)
- Paul Pfeiffer
- Institute for Theoretical Biology, Department of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Jiameng Wu
- Institute for Integrative Neuroanatomy, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Jan-Hendrik Schleimer
- Institute of Theoretical Biology, Department of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Imre Vida
- Institute for Integrative Neuroanatomy, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Susanne Schreiber
- Institute of Theoretical Biology, Department of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
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20
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Noguchi A, Huszár R, Morikawa S, Buzsáki G, Ikegaya Y. Inhibition allocates spikes during hippocampal ripples. Nat Commun 2022; 13:1280. [PMID: 35277500 PMCID: PMC8917132 DOI: 10.1038/s41467-022-28890-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 02/15/2022] [Indexed: 12/16/2022] Open
Abstract
Sets of spikes emitted sequentially across neurons constitute fundamental pulse packets in neural information processing, including offline memory replay during hippocampal sharp-wave ripples (SWRs). The relative timing of neuronal spikes is fine-tuned in each spike sequence but can vary between different sequences. However, the microcircuitry mechanism that enables such flexible spike sequencing remains unexplored. We recorded the membrane potentials of multiple hippocampal CA1 pyramidal cells in mice and found that the neurons were transiently hyperpolarized prior to SWRs. The pre-SWR hyperpolarizations were spatiotemporally heterogeneous, and larger hyperpolarizations were associated with later spikes during SWRs. Intracellular blockade of Cl--mediated inhibition reduced pre-SWR hyperpolarizations and advanced spike times. Single-unit recordings also revealed that the pre-SWR firing rates of inhibitory interneurons predicted the SWR-relevant spike times of pyramidal cells. Thus, pre-SWR inhibitory activity determines the sequential spike times of pyramidal cells and diversifies the repertoire of sequence patterns.
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Affiliation(s)
- Asako Noguchi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Roman Huszár
- Center for Neural Science, New York University, 4 Washington Place, New York, NY, 10003, USA
| | - Shota Morikawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan
- Institute for AI and Beyond, The University of Tokyo, Tokyo, 113-0033, Japan
| | - György Buzsáki
- Center for Neural Science, New York University, 4 Washington Place, New York, NY, 10003, USA.
- Neuroscience Institute, Department of Neurology, NYU Langone Medical Center and Center for Neural Science, New York, NY, USA.
| | - Yuji Ikegaya
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan.
- Institute for AI and Beyond, The University of Tokyo, Tokyo, 113-0033, Japan.
- Center for Information and Neural Networks, National Institute of Information and Communications Technology, Suita City, Osaka, 565-0871, Japan.
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21
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Wang C, Pesaran B, Shanechi MM. Modeling multiscale causal interactions between spiking and field potential signals during behavior. J Neural Eng 2022; 19. [DOI: 10.1088/1741-2552/ac4e1c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 01/24/2022] [Indexed: 11/12/2022]
Abstract
Abstract
Objective. Brain recordings exhibit dynamics at multiple spatiotemporal scales, which are measured with spike trains and larger-scale field potential signals. To study neural processes, it is important to identify and model causal interactions not only at a single scale of activity, but also across multiple scales, i.e. between spike trains and field potential signals. Standard causality measures are not directly applicable here because spike trains are binary-valued but field potentials are continuous-valued. It is thus important to develop computational tools to recover multiscale neural causality during behavior, assess their performance on neural datasets, and study whether modeling multiscale causalities can improve the prediction of neural signals beyond what is possible with single-scale causality. Approach. We design a multiscale model-based Granger-like causality method based on directed information and evaluate its success both in realistic biophysical spike-field simulations and in motor cortical datasets from two non-human primates (NHP) performing a motor behavior. To compute multiscale causality, we learn point-process generalized linear models that predict the spike events at a given time based on the history of both spike trains and field potential signals. We also learn linear Gaussian models that predict the field potential signals at a given time based on their own history as well as either the history of binary spike events or that of latent firing rates. Main results. We find that our method reveals the true multiscale causality network structure in biophysical simulations despite the presence of model mismatch. Further, models with the identified multiscale causalities in the NHP neural datasets lead to better prediction of both spike trains and field potential signals compared to just modeling single-scale causalities. Finally, we find that latent firing rates are better predictors of field potential signals compared with the binary spike events in the NHP datasets. Significance. This multiscale causality method can reveal the directed functional interactions across spatiotemporal scales of brain activity to inform basic science investigations and neurotechnologies.
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22
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An Y, Nam Y. Closed-loop control of neural spike rate of cultured neurons using a thermoplasmonics-based photothermal neural stimulation. J Neural Eng 2021; 18. [PMID: 34678786 DOI: 10.1088/1741-2552/ac3265] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 10/22/2021] [Indexed: 11/12/2022]
Abstract
Objective.Photothermal neural stimulation has been developed in a variety of interfaces as an alternative technology that can perturb neural activity. The demonstrations of these techniques have heavily relied on open-loop stimulation or complete suppression of neural activity. To extend the controllability of photothermal neural stimulation, combining it with a closed-loop system is required. In this work, we investigated whether photothermal suppression mechanism can be used in a closed-loop system to reliably modulate neural spike rate to non-zero setpoints.Approach. To incorporate the photothermal inhibition mechanism into the neural feedback system, we combined a thermoplasmonic stimulation platform based on gold nanorods (GNRs) and near-infrared illuminations (808 nm, spot size: 2 mm or 200μm in diameter) with a proportional-integral (PI) controller. The closed-loop feedback control system was implemented to track predetermined target spike rates of hippocampal neuronal networks cultured on GNR-coated microelectrode arrays.Main results. The closed-loop system for neural spike rate control was successfully implemented using a PI controller and the thermoplasmonic neural suppression platform. Compared to the open-loop control, the target-channel spike rates were precisely modulated to remain constant or change in a sinusoidal form in the range below baseline spike rates. The spike rate response behaviors were affected by the choice of the controller gain. We also demonstrated that the functional connectivity of a synchronized bursting network could be altered by controlling the spike rate of one of the participating channels.Significance.The thermoplasmonic feedback controller proved that it can precisely modulate neural spike rate of neural activityin vitro. This technology can be used for studying neuronal network dynamics and might provide insights in developing new neuromodulation techniques in clinical applications.
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Affiliation(s)
- Yujin An
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Yoonkey Nam
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.,KAIST Institute for Health Science and Technology, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
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23
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Adesnik H, Abdeladim L. Probing neural codes with two-photon holographic optogenetics. Nat Neurosci 2021; 24:1356-1366. [PMID: 34400843 PMCID: PMC9793863 DOI: 10.1038/s41593-021-00902-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 06/30/2021] [Indexed: 02/07/2023]
Abstract
Optogenetics ushered in a revolution in how neuroscientists interrogate brain function. Because of technical limitations, the majority of optogenetic studies have used low spatial resolution activation schemes that limit the types of perturbations that can be made. However, neural activity manipulations at finer spatial scales are likely to be important to more fully understand neural computation. Spatially precise multiphoton holographic optogenetics promises to address this challenge and opens up many new classes of experiments that were not previously possible. More specifically, by offering the ability to recreate extremely specific neural activity patterns in both space and time in functionally defined ensembles of neurons, multiphoton holographic optogenetics could allow neuroscientists to reveal fundamental aspects of the neural codes for sensation, cognition and behavior that have been beyond reach. This Review summarizes recent advances in multiphoton holographic optogenetics that substantially expand its capabilities, highlights outstanding technical challenges and provides an overview of the classes of experiments it can execute to test and validate key theoretical models of brain function. Multiphoton holographic optogenetics could substantially accelerate the pace of neuroscience discovery by helping to close the loop between experimental and theoretical neuroscience, leading to fundamental new insights into nervous system function and disorder.
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Affiliation(s)
- Hillel Adesnik
- Department of Molecular and Cell Biology and the Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA.
| | - Lamiae Abdeladim
- Department of Molecular and Cell Biology and the Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA
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Wong Fong Sang IE, Schroer J, Halbhuber L, Warm D, Yang JW, Luhmann HJ, Kilb W, Sinning A. Optogenetically Controlled Activity Pattern Determines Survival Rate of Developing Neocortical Neurons. Int J Mol Sci 2021; 22:6575. [PMID: 34205237 PMCID: PMC8235092 DOI: 10.3390/ijms22126575] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 06/16/2021] [Accepted: 06/16/2021] [Indexed: 12/29/2022] Open
Abstract
A substantial proportion of neurons undergoes programmed cell death (apoptosis) during early development. This process is attenuated by increased levels of neuronal activity and enhanced by suppression of activity. To uncover whether the mere level of activity or also the temporal structure of electrical activity affects neuronal death rates, we optogenetically controlled spontaneous activity of synaptically-isolated neurons in developing cortical cultures. Our results demonstrate that action potential firing of primary cortical neurons promotes neuronal survival throughout development. Chronic patterned optogenetic stimulation allowed to effectively modulate the firing pattern of single neurons in the absence of synaptic inputs while maintaining stable overall activity levels. Replacing the burst firing pattern with a non-physiological, single pulse pattern significantly increased cell death rates as compared to physiological burst stimulation. Furthermore, physiological burst stimulation led to an elevated peak in intracellular calcium and an increase in the expression level of classical activity-dependent targets but also decreased Bax/BCL-2 expression ratio and reduced caspase 3/7 activity. In summary, these results demonstrate at the single-cell level that the temporal pattern of action potentials is critical for neuronal survival versus cell death fate during cortical development, besides the pro-survival effect of action potential firing per se.
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Affiliation(s)
| | | | | | | | | | | | | | - Anne Sinning
- Institute of Physiology, University Medical Center Mainz, Johannes Gutenberg University, Duesbergweg 6, 55128 Mainz, Germany; (I.E.W.F.S.); (J.S.); (L.H.); (D.W.); (J.-W.Y.); (H.J.L.); (W.K.)
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25
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Perrino G, Napolitano S, Galdi F, La Regina A, Fiore D, Giuliano T, di Bernardo M, di Bernardo D. Automatic synchronisation of the cell cycle in budding yeast through closed-loop feedback control. Nat Commun 2021; 12:2452. [PMID: 33907191 PMCID: PMC8079375 DOI: 10.1038/s41467-021-22689-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 03/24/2021] [Indexed: 12/18/2022] Open
Abstract
The cell cycle is the process by which eukaryotic cells replicate. Yeast cells cycle asynchronously with each cell in the population budding at a different time. Although there are several experimental approaches to synchronise cells, these usually work only in the short-term. Here, we build a cyber-genetic system to achieve long-term synchronisation of the cell population, by interfacing genetically modified yeast cells with a computer by means of microfluidics to dynamically change medium, and a microscope to estimate cell cycle phases of individual cells. The computer implements a controller algorithm to decide when, and for how long, to change the growth medium to synchronise the cell-cycle across the population. Our work builds upon solid theoretical foundations provided by Control Engineering. In addition to providing an avenue for yeast cell cycle synchronisation, our work shows that control engineering can be used to automatically steer complex biological processes towards desired behaviours similarly to what is currently done with robots and autonomous vehicles.
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Affiliation(s)
| | - Sara Napolitano
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
- Department of Chemical, Materials and Industrial Production Engineering, University of Naples Federico II, Naples, Italy
| | - Francesca Galdi
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | | | - Davide Fiore
- Department of Mathematics and Applications "R. Caccioppoli", University of Naples Federico II, Naples, Italy
| | - Teresa Giuliano
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Mario di Bernardo
- Department of Electrical Engineering and Information Technology, University of Naples Federico II, Naples, Italy
- SSM - School for Advanced Studies, Naples, Italy
| | - Diego di Bernardo
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy.
- Department of Chemical, Materials and Industrial Production Engineering, University of Naples Federico II, Naples, Italy.
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26
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Bolus MF, Willats AA, Rozell CJ, Stanley GB. State-space optimal feedback control of optogenetically driven neural activity. J Neural Eng 2021; 18. [PMID: 32932241 DOI: 10.1088/1741-2552/abb89c] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 09/15/2020] [Indexed: 11/11/2022]
Abstract
Objective.The rapid acceleration of tools for recording neuronal populations and targeted optogenetic manipulation has enabled real-time, feedback control of neuronal circuits in the brain. Continuously-graded control of measured neuronal activity poses a wide range of technical challenges, which we address through a combination of optogenetic stimulation and a state-space optimal control framework implemented in the thalamocortical circuit of the awake mouse.Approach.Closed-loop optogenetic control of neurons was performed in real-time via stimulation of channelrhodopsin-2 expressed in the somatosensory thalamus of the head-fixed mouse. A state-space linear dynamical system model structure was used to approximate the light-to-spiking input-output relationship in both single-neuron as well as multi-neuron scenarios when recording from multielectrode arrays. These models were utilized to design state feedback controller gains by way of linear quadratic optimal control and were also used online for estimation of state feedback, where a parameter-adaptive Kalman filter provided robustness to model-mismatch.Main results.This model-based control scheme proved effective for feedback control of single-neuron firing rate in the thalamus of awake animals. Notably, the graded optical actuation utilized here did not synchronize simultaneously recorded neurons, but heterogeneity across the neuronal population resulted in a varied response to stimulation. Simulated multi-output feedback control provided better control of a heterogeneous population and demonstrated how the approach generalizes beyond single-neuron applications.Significance.To our knowledge, this work represents the first experimental application of state space model-based feedback control for optogenetic stimulation. In combination with linear quadratic optimal control, the approaches laid out and tested here should generalize to future problems involving the control of highly complex neural circuits. More generally, feedback control of neuronal circuits opens the door to adaptively interacting with the dynamics underlying sensory, motor, and cognitive signaling, enabling a deeper understanding of circuit function and ultimately the control of function in the face of injury or disease.
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Affiliation(s)
- M F Bolus
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, United States of America
| | - A A Willats
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, United States of America
| | - C J Rozell
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States of America
| | - G B Stanley
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, United States of America
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27
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Whitmire CJ, Liew YJ, Stanley GB. Thalamic state influences timing precision in the thalamocortical circuit. J Neurophysiol 2021; 125:1833-1850. [PMID: 33760642 DOI: 10.1152/jn.00261.2020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Sensory signals from the outside world are transduced at the periphery, passing through thalamus before reaching cortex, ultimately giving rise to the sensory representations that enable us to perceive the world. The thalamocortical circuit is particularly sensitive to the temporal precision of thalamic spiking due to highly convergent synaptic connectivity. Thalamic neurons can exhibit burst and tonic modes of firing that strongly influence timing within the thalamus. The impact of these changes in thalamic state on sensory encoding in the cortex, however, remains unclear. Here, we investigated the role of thalamic state on timing in the thalamocortical circuit of the vibrissa pathway in the anesthetized rat. We optogenetically hyperpolarized thalamus while recording single unit activity in both thalamus and cortex. Tonic spike-triggered analysis revealed temporally precise thalamic spiking that was locked to weak white-noise sensory stimuli, whereas thalamic burst spiking was associated with a loss in stimulus-locked temporal precision. These thalamic state-dependent changes propagated to cortex such that the cortical timing precision was diminished during the hyperpolarized (burst biased) thalamic state. Although still sensory driven, the cortical neurons became significantly less precisely locked to the weak white-noise stimulus. The results here suggests a state-dependent differential regulation of spike timing precision in the thalamus that could gate what signals are ultimately propagated to cortex.NEW & NOTEWORTHY The majority of sensory signals are transmitted through the thalamus. There is growing evidence of complex thalamic gating through coordinated firing modes that have a strong impact on cortical sensory representations. Optogenetic hyperpolarization of thalamus pushed it into burst firing that disrupted precise time-locked sensory signaling, with a direct impact on the downstream cortical encoding, setting the stage for a timing-based thalamic gate of sensory signaling.
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Affiliation(s)
- Clarissa J Whitmire
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia
| | - Yi Juin Liew
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia.,Joint PhD Program in Biomedical Engineering, Georgia Institute of Technology-Emory University-Peking University, Atlanta, Georgia
| | - Garrett B Stanley
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia
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28
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Bongard J, Levin M. Living Things Are Not (20th Century) Machines: Updating Mechanism Metaphors in Light of the Modern Science of Machine Behavior. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.650726] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
One of the most useful metaphors for driving scientific and engineering progress has been that of the “machine.” Much controversy exists about the applicability of this concept in the life sciences. Advances in molecular biology have revealed numerous design principles that can be harnessed to understand cells from an engineering perspective, and build novel devices to rationally exploit the laws of chemistry, physics, and computation. At the same time, organicists point to the many unique features of life, especially at larger scales of organization, which have resisted decomposition analysis and artificial implementation. Here, we argue that much of this debate has focused on inessential aspects of machines – classical properties which have been surpassed by advances in modern Machine Behavior and no longer apply. This emerging multidisciplinary field, at the interface of artificial life, machine learning, and synthetic bioengineering, is highlighting the inadequacy of existing definitions. Key terms such as machine, robot, program, software, evolved, designed, etc., need to be revised in light of technological and theoretical advances that have moved past the dated philosophical conceptions that have limited our understanding of both evolved and designed systems. Moving beyond contingent aspects of historical and current machines will enable conceptual tools that embrace inevitable advances in synthetic and hybrid bioengineering and computer science, toward a framework that identifies essential distinctions between fundamental concepts of devices and living agents. Progress in both theory and practical applications requires the establishment of a novel conception of “machines as they could be,” based on the profound lessons of biology at all scales. We sketch a perspective that acknowledges the remarkable, unique aspects of life to help re-define key terms, and identify deep, essential features of concepts for a future in which sharp boundaries between evolved and designed systems will not exist.
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29
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Voigts J, Deister CA, Moore CI. Layer 6 ensembles can selectively regulate the behavioral impact and layer-specific representation of sensory deviants. eLife 2020; 9:48957. [PMID: 33263283 PMCID: PMC7817180 DOI: 10.7554/elife.48957] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 12/01/2020] [Indexed: 11/21/2022] Open
Abstract
Predictive models can enhance the salience of unanticipated input. Here, we tested a key potential node in neocortical model formation in this process, layer (L) 6, using behavioral, electrophysiological and imaging methods in mouse primary somatosensory neocortex. We found that deviant stimuli enhanced tactile detection and were encoded in L2/3 neural tuning. To test the contribution of L6, we applied weak optogenetic drive that changed which L6 neurons were sensory responsive, without affecting overall firing rates in L6 or L2/3. This stimulation selectively suppressed behavioral sensitivity to deviant stimuli, without impacting baseline performance. This stimulation also eliminated deviance encoding in L2/3 but did not impair basic stimulus responses across layers. In contrast, stronger L6 drive inhibited firing and suppressed overall sensory function. These findings indicate that, despite their sparse activity, specific ensembles of stimulus-driven L6 neurons are required to form neocortical predictions, and to realize their behavioral benefit.
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Affiliation(s)
- Jakob Voigts
- Department of Neuroscience and Carney Institute for Brain Science, Brown University, Providence, United States.,Department of Brain and Cognitive Sciences, MIT, Cambridge, United States
| | - Christopher A Deister
- Department of Neuroscience and Carney Institute for Brain Science, Brown University, Providence, United States
| | - Christopher I Moore
- Department of Neuroscience and Carney Institute for Brain Science, Brown University, Providence, United States
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30
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Moulin TC, Covill LE, Itskov PM, Williams MJ, Schiöth HB. Rodent and fly models in behavioral neuroscience: An evaluation of methodological advances, comparative research, and future perspectives. Neurosci Biobehav Rev 2020; 120:1-12. [PMID: 33242563 DOI: 10.1016/j.neubiorev.2020.11.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 08/25/2020] [Accepted: 11/12/2020] [Indexed: 01/31/2023]
Abstract
The assessment of behavioral outcomes is a central component of neuroscientific research, which has required continuous technological innovations to produce more detailed and reliable findings. In this article, we provide an in-depth review on the progress and future implications for three model organisms (mouse, rat, and Drosophila) essential to our current understanding of behavior. By compiling a comprehensive catalog of popular assays, we are able to compare the diversity of tasks and usage of these animal models in behavioral research. This compilation also allows for the evaluation of existing state-of-the-art methods and experimental applications, including optogenetics, machine learning, and high-throughput behavioral assays. We go on to discuss novel apparatuses and inter-species analyses for centrophobism, feeding behavior, aggression and mating paradigms, with the goal of providing a unique view on comparative behavioral research. The challenges and recent advances are evaluated in terms of their translational value, ethical procedures, and trustworthiness for behavioral research.
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Affiliation(s)
- Thiago C Moulin
- Functional Pharmacology Unit, Department of Neuroscience, Uppsala University, Uppsala, Sweden.
| | - Laura E Covill
- Functional Pharmacology Unit, Department of Neuroscience, Uppsala University, Uppsala, Sweden; Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Pavel M Itskov
- Functional Pharmacology Unit, Department of Neuroscience, Uppsala University, Uppsala, Sweden; Department of Pharmacology, Institute of Pharmacy, Sechenov First Moscow State Medical University, Moscow, Russia; Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Michael J Williams
- Functional Pharmacology Unit, Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Helgi B Schiöth
- Functional Pharmacology Unit, Department of Neuroscience, Uppsala University, Uppsala, Sweden; Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russia
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31
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Zhao Y, Park IM. Variational Online Learning of Neural Dynamics. Front Comput Neurosci 2020; 14:71. [PMID: 33154718 PMCID: PMC7591751 DOI: 10.3389/fncom.2020.00071] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 06/25/2020] [Indexed: 11/13/2022] Open
Abstract
New technologies for recording the activity of large neural populations during complex behavior provide exciting opportunities for investigating the neural computations that underlie perception, cognition, and decision-making. Non-linear state space models provide an interpretable signal processing framework by combining an intuitive dynamical system with a probabilistic observation model, which can provide insights into neural dynamics, neural computation, and development of neural prosthetics and treatment through feedback control. This brings with it the challenge of learning both latent neural state and the underlying dynamical system because neither are known for neural systems a priori. We developed a flexible online learning framework for latent non-linear state dynamics and filtered latent states. Using the stochastic gradient variational Bayes approach, our method jointly optimizes the parameters of the non-linear dynamical system, the observation model, and the black-box recognition model. Unlike previous approaches, our framework can incorporate non-trivial distributions of observation noise and has constant time and space complexity. These features make our approach amenable to real-time applications and the potential to automate analysis and experimental design in ways that testably track and modify behavior using stimuli designed to influence learning.
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Affiliation(s)
- Yuan Zhao
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, NY, United States
- Center for Neural Circuit Dynamics, Stony Brook University, Stony Brook, NY, United States
- Institute for Advanced Computational Science, Stony Brook University, Stony Brook, NY, United States
| | - Il Memming Park
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, NY, United States
- Center for Neural Circuit Dynamics, Stony Brook University, Stony Brook, NY, United States
- Institute for Advanced Computational Science, Stony Brook University, Stony Brook, NY, United States
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32
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Newman JP, Voigts J, Borius M, Karlsson M, Harnett MT, Wilson MA. Twister3: a simple and fast microwire twister. J Neural Eng 2020; 17:026040. [PMID: 32074512 PMCID: PMC8879418 DOI: 10.1088/1741-2552/ab77fa] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Objective. Twisted wire probes (TWPs, e.g. stereotrodes and tetrodes) provide a cheap and reliable method for obtaining high quality, multiple single-unit neural recordings in freely moving animals. Despite their ubiquity, TWPs are constructed using a tedious procedure consisting of manually folding, turning, and fusing microwire. This imposes a significant labor burden on research personnel who use TWPs in their experiments. Approach. To address this issue, we created Twister3, an open-source microwire twisting machine. This machine features a quick-draw wire feeder that eliminates manual wire folding, an auto-aligning motor attachment mechanism which results in consistently straight probes, and a high speed motor for rapid probe turning. Main results. Twister3 greatly increases the speed and repeatability of constructing twisted microwire probes compared to existing options. Users with less than one hour of experience using the device were able to make ~70 tetrodes per hour, on average. It is cheap, well documented, and all associated designs and source code are open-source. Significance. Twister3 significantly reduces the labor burden of creating high-quality TWPs so electrophysiologists can spend more of their time performing recordings rather than making probes. Therefore, this device is of interest to any lab performing TWP neural recordings, for example, using microdrives.
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Affiliation(s)
- Jonathan P Newman
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, United States of America.,Picower Institute for Learning and Memory, MIT, Cambridge, MA, United States of America.,Open Ephys Inc, Cambridge, MA, United States of America.,Author to whom any correspondence should be addressed
| | - Jakob Voigts
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, United States of America.,McGovern Institute for Brain Research, MIT, Cambridge, MA, United States of America.,Open Ephys Inc, Cambridge, MA, United States of America
| | - Maxim Borius
- SpikeGadgets LLC, San Francisco, CA, United States of America
| | | | - Mark T Harnett
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, United States of America.,McGovern Institute for Brain Research, MIT, Cambridge, MA, United States of America
| | - Matthew A Wilson
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, United States of America.,Picower Institute for Learning and Memory, MIT, Cambridge, MA, United States of America.,Open Ephys Inc, Cambridge, MA, United States of America
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33
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A VTA to Basal Amygdala Dopamine Projection Contributes to Signal Salient Somatosensory Events during Fear Learning. J Neurosci 2020; 40:3969-3980. [PMID: 32277045 DOI: 10.1523/jneurosci.1796-19.2020] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 03/25/2020] [Accepted: 03/26/2020] [Indexed: 01/02/2023] Open
Abstract
The amygdala is a brain area critical for the formation of fear memories. However, the nature of the teaching signal(s) that drive plasticity in the amygdala are still under debate. Here, we use optogenetic methods to investigate the contribution of ventral tegmental area (VTA) dopamine neurons to auditory-cued fear learning in male mice. Using anterograde and retrograde labeling, we found that a sparse and relatively evenly distributed population of VTA neurons projects to the basal amygdala (BA). In vivo optrode recordings in behaving mice showed that many VTA neurons, among them putative dopamine neurons, are excited by footshocks, and acquire a response to auditory stimuli during fear learning. Combined cfos imaging and retrograde labeling in dopamine transporter (DAT) Cre mice revealed that a large majority of BA projectors (>95%) are dopamine neurons, and that BA projectors become activated by the tone-footshock pairing of fear learning protocols. Finally, silencing VTA dopamine neurons, or their axon terminals in the BA during the footshock, reduced the strength of fear memory as tested 1 d later, whereas silencing the VTA-central amygdala (CeA) projection had no effect. Thus, VTA dopamine neurons projecting to the BA contribute to fear memory formation, by coding for the saliency of the footshock event and by signaling such events to the basal amygdala.SIGNIFICANCE STATEMENT Powerful mechanisms of fear learning have evolved in animals and humans to enable survival. During fear conditioning, a sensory cue, such as a tone (the conditioned stimulus), comes to predict an innately aversive stimulus, such as a mild footshock (the unconditioned stimulus). A brain representation of the unconditioned stimulus must act as a teaching signal to instruct plasticity of the conditioned stimulus representation in fear-related brain areas. Here we show that dopamine neurons in the VTA that project to the basal amygdala contribute to such a teaching signal for plasticity, thereby facilitating the formation of fear memories. Knowledge about the role of dopamine in aversively motivated plasticity might allow further insights into maladaptive plasticities that underlie anxiety and post-traumatic stress disorders in humans.
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Das R, Moradi F, Heidari H. Biointegrated and Wirelessly Powered Implantable Brain Devices: A Review. IEEE TRANSACTIONS ON BIOMEDICAL CIRCUITS AND SYSTEMS 2020; 14:343-358. [PMID: 31944987 DOI: 10.1109/tbcas.2020.2966920] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
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35
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Fischer LF, Mojica Soto-Albors R, Buck F, Harnett MT. Representation of visual landmarks in retrosplenial cortex. eLife 2020; 9:51458. [PMID: 32154781 PMCID: PMC7064342 DOI: 10.7554/elife.51458] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 02/03/2020] [Indexed: 11/13/2022] Open
Abstract
The process by which visual information is incorporated into the brain’s spatial framework to represent landmarks is poorly understood. Studies in humans and rodents suggest that retrosplenial cortex (RSC) plays a key role in these computations. We developed an RSC-dependent behavioral task in which head-fixed mice learned the spatial relationship between visual landmark cues and hidden reward locations. Two-photon imaging revealed that these cues served as dominant reference points for most task-active neurons and anchored the spatial code in RSC. This encoding was more robust after task acquisition. Decoupling the virtual environment from mouse behavior degraded spatial representations and provided evidence that supralinear integration of visual and motor inputs contributes to landmark encoding. V1 axons recorded in RSC were less modulated by task engagement but showed surprisingly similar spatial tuning. Our data indicate that landmark representations in RSC are the result of local integration of visual, motor, and spatial information. When moving through a city, people often use notable or familiar landmarks to help them navigate. Landmarks provide us with information about where we are and where we need to go next. But despite the ease with which we – and most other animals – use landmarks to find our way around, it remains unclear exactly how the brain makes this possible. One area that seems to have a key role is the retrosplenial cortex, which is located deep within the back of the brain in humans. This area becomes more active when animals use visual landmarks to navigate. It is also one of the first brain regions to be affected in Alzheimer's disease, which may help to explain why patients with this condition can become lost and disoriented, even in places they have been many times before. To find out how the retrosplenial cortex supports navigation, Fischer et al. measured its activity in mice exploring a virtual reality world. The mice ran through simulated corridors in which visual landmarks indicated where hidden rewards could be found. The activity of most neurons in the retrosplenial cortex was most strongly influenced by the mouse’s position relative to the landmark; for example, some neurons were always active 10 centimeters after the landmark. In other experiments, when the landmarks were present but no longer indicated the location of a reward, the same neurons were much less active. Fischer et al. also measured the activity of the neurons when the mice were running with nothing shown on the virtual reality, and when they saw a landmark but did not run. Notably, the activity seen when the mice were using the landmarks to find rewards was greater than the sum of that recorded when the mice were just running or just seeing the landmark without a reward, making the “landmark response” an example of so-called supralinear processing. Fischer et al. showed that visual centers of the brain send information about landmarks to retrosplenial cortex. But only the latter adjusts its activity depending on whether the mouse is using that landmark to navigate. These findings provide the first evidence for a “landmark code” at the level of neurons and lay the foundations for studying impaired navigation in patients with Alzheimer's disease. By showing that retrosplenial cortex neurons combine different types of input in a supralinear fashion, the results also point to general principles for how neurons in the brain perform complex calculations.
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Affiliation(s)
- Lukas F Fischer
- Department of Brain and Cognitive Sciences, MGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, United States
| | - Raul Mojica Soto-Albors
- Department of Brain and Cognitive Sciences, MGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, United States
| | - Friederike Buck
- Department of Brain and Cognitive Sciences, MGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, United States
| | - Mark T Harnett
- Department of Brain and Cognitive Sciences, MGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, United States
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36
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Voigts J, Harnett MT. Somatic and Dendritic Encoding of Spatial Variables in Retrosplenial Cortex Differs during 2D Navigation. Neuron 2020; 105:237-245.e4. [PMID: 31759808 PMCID: PMC6981016 DOI: 10.1016/j.neuron.2019.10.016] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 08/14/2019] [Accepted: 10/09/2019] [Indexed: 12/21/2022]
Abstract
Active amplification of organized synaptic inputs in dendrites can endow individual neurons with the ability to perform complex computations. However, whether dendrites in behaving animals perform independent local computations is not known. Such activity may be particularly important for complex behavior, where neurons integrate multiple streams of information. Head-restrained imaging has yielded important insights into cellular and circuit function, but this approach limits behavior and the underlying computations. We describe a method for full-featured 2-photon imaging in awake mice during free locomotion with volitional head rotation. We examine head direction and position encoding in simultaneously imaged apical tuft dendrites and their respective cell bodies in retrosplenial cortex, an area that encodes multi-modal navigational information. Activity in dendrites was not determined solely by somatic activity but reflected distinct navigational variables, fulfilling the requirements for dendritic computation. Our approach provides a foundation for studying sub-cellular processes during complex behaviors.
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Affiliation(s)
- Jakob Voigts
- Department of Brain & Cognitive Sciences and McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Mark T Harnett
- Department of Brain & Cognitive Sciences and McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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37
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Abstract
Closed-loop optogenetic stimulation devices deliver optical stimulations based on real-time measurement and analysis of neural responses to stimulations. However, the use of large bench-top and tethered devices hinders the naturalistic test environment, which is crucial in pre-clinical neuroscience studies involving small rodent subjects. This paper presents a tetherless, lightweight and miniaturized head-mountable closed-loop optogenetic stimulation device. The device consists of three hardware modules: a hybrid electrode, an action potential detector, and an optogenetic stimulator. In addition, the device includes three software modules: a feature extractor, a control algorithm, and a pulse generator. The details of the design, implementation, and bench-testing of the device are presented. Furthermore, an in vitro test environment is formed using synthetic neural signals, wherein the device is validated for its closed-loop performance. During the in vitro validation, the device was able to identify abnormal neural signals, and trigger optical stimulation. On the other hand, it was able to also distinguish normal neural signals and inhibit optical stimulation. The overall power consumption of the device is 24 mW. The device measures 6 mm in radius and weighs 0.44 g excluding the power source.
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38
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Wang PK, Pun SH, Chen CH, McCullagh EA, Klug A, Li A, Vai MI, Mak PU, Lei TC. Low-latency single channel real-time neural spike sorting system based on template matching. PLoS One 2019; 14:e0225138. [PMID: 31756211 PMCID: PMC6874356 DOI: 10.1371/journal.pone.0225138] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 10/29/2019] [Indexed: 11/26/2022] Open
Abstract
Recent technical advancements in neural engineering allow for precise recording and control of neural circuits simultaneously, opening up new opportunities for closed-loop neural control. In this work, a rapid spike sorting system was developed based on template matching to rapidly calculate instantaneous firing rates for each neuron in a multi-unit extracellular recording setting. Cluster templates were first generated by a desktop computer using a non-parameter spike sorting algorithm (Super-paramagnetic clustering) and then transferred to a field-programmable gate array digital circuit for rapid sorting through template matching. Two different matching techniques–Euclidean distance (ED) and correlational matching (CM)–were compared for the accuracy of sorting and the performance of calculating firing rates. The performance of the system was first verified using publicly available artificial data and was further confirmed with pre-recorded neural spikes from an anesthetized Mongolian gerbil. Real-time recording and sorting from an awake mouse were also conducted to confirm the system performance in a typical behavioral neuroscience experimental setting. Experimental results indicated that high sorting accuracies were achieved for both template-matching methods, but CM can better handle spikes with non-Gaussian spike distributions, making it more robust for in vivo recording. The technique was also compared to several other off-line spike sorting algorithms and the results indicated that the sorting accuracy is comparable but sorting time is significantly shorter than these other techniques. A low sorting latency of under 2 ms and a maximum spike sorting rate of 941 spikes/second have been achieved with our hybrid hardware/software system. The low sorting latency and fast sorting rate allow future system developments of neural circuit modulation through analyzing neural activities in real-time.
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Affiliation(s)
- Pan Ke Wang
- State Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Macau, China
- Department of Electrical and Computer Engineering, Faculty of Science and Technology, University of Macau, Macau, China
| | - Sio Hang Pun
- State Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Macau, China
- * E-mail:
| | - Chang Hao Chen
- State Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Macau, China
| | - Elizabeth A. McCullagh
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States of America
| | - Achim Klug
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States of America
| | - Anan Li
- Jiangsu Key Laboratory of Brain Disease and Bioinformation, Research Center for Biochemistry and Molecular Biology, Xuzhou Medical University, Xuzhou, China
| | - Mang I. Vai
- State Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Macau, China
- Department of Electrical and Computer Engineering, Faculty of Science and Technology, University of Macau, Macau, China
| | - Peng Un Mak
- Department of Electrical and Computer Engineering, Faculty of Science and Technology, University of Macau, Macau, China
| | - Tim C. Lei
- State Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Macau, China
- Department of Electrical Engineering, University of Colorado, Denver, CO, United States of America
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39
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Pisarchik AN, Maksimenko VA, Hramov AE. From Novel Technology to Novel Applications: Comment on "An Integrated Brain-Machine Interface Platform With Thousands of Channels" by Elon Musk and Neuralink. J Med Internet Res 2019; 21:e16356. [PMID: 31674923 PMCID: PMC6914250 DOI: 10.2196/16356] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 10/16/2019] [Accepted: 10/20/2019] [Indexed: 01/20/2023] Open
Affiliation(s)
- Alexander N Pisarchik
- Center for Biomedical Technology, Technical University of Madrid, Pozuelo de Alarcón, Madrid, Spain.,Neuroscience and Cognitive Technology Laboratory, Center for Technologies in Robotics and Mechatronics Components, Innopolis University, Innopolis, Russian Federation
| | - Vladimir A Maksimenko
- Neuroscience and Cognitive Technology Laboratory, Center for Technologies in Robotics and Mechatronics Components, Innopolis University, Innopolis, Russian Federation
| | - Alexander E Hramov
- Neuroscience and Cognitive Technology Laboratory, Center for Technologies in Robotics and Mechatronics Components, Innopolis University, Innopolis, Russian Federation
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40
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Vila CH, Williamson RS, Hancock KE, Polley DB. Optimizing optogenetic stimulation protocols in auditory corticofugal neurons based on closed-loop spike feedback. J Neural Eng 2019; 16:066023. [PMID: 31394519 PMCID: PMC6956656 DOI: 10.1088/1741-2552/ab39cf] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
OBJECTIVE Optogenetics provides a means to probe functional connections between brain areas. By activating a set of presynaptic neurons and recording the activity from a downstream brain area, one can establish the sign and strength of a feedforward connection. One challenge is that there are virtually limitless patterns that can be used to stimulate a presynaptic brain area. Functional influences on downstream brain areas can depend not just on whether presynaptic neurons were activated, but how they were activated. Corticofugal axons from the auditory cortex (ACtx) heavily innervate the auditory tectum, the inferior colliculus (IC). Here, we sought to determine whether different modes of corticocollicular activation could titrate the strength of feedforward modulation of sound processing in IC neurons. APPROACH We used multi-channel electrophysiology and optogenetics to record from multiple regions of the IC in awake head-fixed mice while optogenetically stimulating ACtx neurons expressing Chronos, an ultra-fast channelrhodopsin. To identify cortical activation patterns associated with the strongest effects on IC firing rates, we employed a closed-loop evolutionary optimization procedure that tailored the voltage command signal sent to the laser based on spike feedback from single IC neurons. MAIN RESULTS Within minutes, our evolutionary search procedure converged on ACtx stimulation configurations that produced more effective and widespread enhancement of IC unit activity than generic activation parameters. Cortical modulation of midbrain spiking was bi-directional, as the evolutionary search procedure could be programmed to converge on activation patterns that either suppressed or enhanced sound-evoked IC firing rate. SIGNIFICANCE This study introduces a closed-loop optimization procedure to probe functional connections between brain areas. Our findings demonstrate that the influence of descending feedback projections on subcortical sensory processing can vary both in sign and degree depending on how cortical neurons are activated in time.
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Affiliation(s)
- Charles-Henri Vila
- - Eaton-Peabody Laboratories, Massachusetts Eye and Ear Infirmary, Boston MA 02114 USA
- - Bertarelli Fellows Program, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Ross S Williamson
- - Eaton-Peabody Laboratories, Massachusetts Eye and Ear Infirmary, Boston MA 02114 USA
- - Dept. Otolaryngology, Harvard Medical School, Boston MA 02114
| | - Kenneth E Hancock
- - Eaton-Peabody Laboratories, Massachusetts Eye and Ear Infirmary, Boston MA 02114 USA
- - Dept. Otolaryngology, Harvard Medical School, Boston MA 02114
| | - Daniel B Polley
- - Eaton-Peabody Laboratories, Massachusetts Eye and Ear Infirmary, Boston MA 02114 USA
- - Dept. Otolaryngology, Harvard Medical School, Boston MA 02114
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41
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Gagnon-Turcotte G, Keramidis I, Ethier C, De Koninck Y, Gosselin B. A Wireless Electro-Optic Headstage With a 0.13- μm CMOS Custom Integrated DWT Neural Signal Decoder for Closed-Loop Optogenetics. IEEE TRANSACTIONS ON BIOMEDICAL CIRCUITS AND SYSTEMS 2019; 13:1036-1051. [PMID: 31352352 DOI: 10.1109/tbcas.2019.2930498] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We present a wireless electro-optic headstage that uses a 0.13- μm CMOS custom integrated circuit (IC) implementing a digital neural decoder (ND-IC) for enabling real-time closed-loop (CL) optogenetics. The ND-IC processes the neural activity data using three digital cores: 1) the detector core detects and extracts the action potential (AP) of individual neurons by using an adaptive threshold; 2) the data compression core compresses the detected AP by using an efficient Symmlet-2 discrete wavelet transform (DWT) processor for decreasing the amount of data to be transmitted by the low-power wireless link; and 3) the classification core sorts the compressed AP into separated clusters on the fly according to their wave shapes. The ND-IC encompasses several innovations: 1) the compression core decreases the complexity from O(n 2) to O(n · log(n)) compared to the previous solutions, while using two times less memory, thanks to the use of a new coefficient sorting tree; and 2) the AP classification core reuses both the compressed DWT coefficients to perform implicit dimensionality reduction, which allows for performing intensive signal processing on-chip, while increasing power and hardware efficiency. This core also reuses the signal standard deviation already computed by the AP detector core as threshold for performing automatic AP sorting. The headstage also introduces innovations by enabling a new wireless CL scheme between the neural data acquisition module and the optical stimulator. Our CL scheme uses the AP sorting and timing information produced by the ND-IC for detecting complex firing patterns within the brain. The headstage is also smaller (1.13 cm 3), lighter (3.0 g with a 40 mAh battery) and less invasive than the previous solutions, while providing a measured autonomy of 2h40, with the ND-IC. The whole system and the ND-IC are first validated in vivo in the LD thalamus of a Long-Evans rat, and then in freely-moving CL experiments involving a mouse virally expressing ChR2-mCherry in inhibitory neurons of the prelimbic cortex, and the results show that our system works well within an in vivo experimental setting with a freely moving mouse.
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42
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Bolus MF, Willats AA, Whitmire CJ, Rozell CJ, Stanley GB. Design strategies for dynamic closed-loop optogenetic neurocontrol in vivo. J Neural Eng 2019; 15:026011. [PMID: 29300002 DOI: 10.1088/1741-2552/aaa506] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
OBJECTIVE Controlling neural activity enables the possibility of manipulating sensory perception, cognitive processes, and body movement, in addition to providing a powerful framework for functionally disentangling the neural circuits that underlie these complex phenomena. Over the last decade, optogenetic stimulation has become an increasingly important and powerful tool for understanding neural circuit function, owing to the ability to target specific cell types and bidirectionally modulate neural activity. To date, most stimulation has been provided in open-loop or in an on/off closed-loop fashion, where previously-determined stimulation is triggered by an event. Here, we describe and demonstrate a design approach for precise optogenetic control of neuronal firing rate modulation using feedback to guide stimulation continuously. APPROACH Using the rodent somatosensory thalamus as an experimental testbed for realizing desired time-varying patterns of firing rate modulation, we utilized a moving average exponential filter to estimate firing rate online from single-unit spiking measured extracellularly. This estimate of instantaneous rate served as feedback for a proportional integral (PI) controller, which was designed during the experiment based on a linear-nonlinear Poisson (LNP) model of the neuronal response to light. MAIN RESULTS The LNP model fit during the experiment enabled robust closed-loop control, resulting in good tracking of sinusoidal and non-sinusoidal targets, and rejection of unmeasured disturbances. Closed-loop control also enabled manipulation of trial-to-trial variability. SIGNIFICANCE Because neuroscientists are faced with the challenge of dissecting the functions of circuit components, the ability to maintain control of a region of interest in spite of changes in ongoing neural activity will be important for disambiguating function within networks. Closed-loop stimulation strategies are ideal for control that is robust to such changes, and the employment of continuous feedback to adjust stimulation in real-time can improve the quality of data collected using optogenetic manipulation.
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Affiliation(s)
- M F Bolus
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, United States of America
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43
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Mohammadi Z, Kincaid JM, Pun SH, Klug A, Liu C, Lei TC. Computationally inexpensive enhanced growing neural gas algorithm for real-time adaptive neural spike clustering. J Neural Eng 2019; 16:056007. [DOI: 10.1088/1741-2552/ab208c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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44
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Nair A, Chauhan P, Saha B, Kubatzky KF. Conceptual Evolution of Cell Signaling. Int J Mol Sci 2019; 20:E3292. [PMID: 31277491 PMCID: PMC6651758 DOI: 10.3390/ijms20133292] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 06/26/2019] [Accepted: 06/28/2019] [Indexed: 12/27/2022] Open
Abstract
During the last 100 years, cell signaling has evolved into a common mechanism for most physiological processes across systems. Although the majority of cell signaling principles were initially derived from hormonal studies, its exponential growth has been supported by interdisciplinary inputs, e.g., from physics, chemistry, mathematics, statistics, and computational fields. As a result, cell signaling has grown out of scope for any general review. Here, we review how the messages are transferred from the first messenger (the ligand) to the receptor, and then decoded with the help of cascades of second messengers (kinases, phosphatases, GTPases, ions, and small molecules such as cAMP, cGMP, diacylglycerol, etc.). The message is thus relayed from the membrane to the nucleus where gene expression ns, subsequent translations, and protein targeting to the cell membrane and other organelles are triggered. Although there are limited numbers of intracellular messengers, the specificity of the response profiles to the ligands is generated by the involvement of a combination of selected intracellular signaling intermediates. Other crucial parameters in cell signaling are its directionality and distribution of signaling strengths in different pathways that may crosstalk to adjust the amplitude and quality of the final effector output. Finally, we have reflected upon its possible developments during the coming years.
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Affiliation(s)
- Arathi Nair
- National Center for Cell Science (NCCS), Ganeshkhind, Pune 411007, India
| | - Prashant Chauhan
- National Center for Cell Science (NCCS), Ganeshkhind, Pune 411007, India
| | - Bhaskar Saha
- National Center for Cell Science (NCCS), Ganeshkhind, Pune 411007, India.
| | - Katharina F Kubatzky
- Zentrum für Infektiologie, Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany.
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45
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Wang C, Shanechi MM. Estimating Multiscale Direct Causality Graphs in Neural Spike-Field Networks. IEEE Trans Neural Syst Rehabil Eng 2019; 27:857-866. [DOI: 10.1109/tnsre.2019.2908156] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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46
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Shapiro LP, Kietzman HW, Guo J, Rainnie DG, Gourley SL. Rho-kinase inhibition has antidepressant-like efficacy and expedites dendritic spine pruning in adolescent mice. Neurobiol Dis 2019; 124:520-530. [PMID: 30593834 PMCID: PMC6365018 DOI: 10.1016/j.nbd.2018.12.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 11/15/2018] [Accepted: 12/21/2018] [Indexed: 12/29/2022] Open
Abstract
Adolescence represents a critical period of neurodevelopment, defined by structural and synaptic pruning within the prefrontal cortex. While characteristic of typical development, this structural instability may open a window of vulnerability to developing neuropsychiatric disorders, including depression. Thus, therapeutic interventions that support or expedite neural remodeling in adolescence may be advantageous. Here, we inhibited the neuronally-expressed cytoskeletal regulatory factor Rho-kinase (ROCK), focusing primarily on the clinically-viable ROCK inhibitor fasudil. ROCK inhibition had rapid antidepressant-like effects in adolescent mice, and its efficacy was comparable to ketamine and fluoxetine. It also modified levels of the antidepressant-related signaling factors, tropomyosin/tyrosine receptor kinase B and Akt, as well as the postsynaptic marker PSD-95, in the ventromedial prefrontal cortex (vmPFC). Meanwhile, adolescent-typical dendritic spine pruning on excitatory pyramidal neurons in the vmPFC was expedited. Further, vmPFC-specific shRNA-mediated reduction of ROCK2, the dominant ROCK isoform in the brain, had antidepressant-like consequences. We cautiously suggest that ROCK inhibitors may have therapeutic potential for adolescent-onset depression.
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Affiliation(s)
- Lauren P Shapiro
- Molecular and Systems Pharmacology, Emory University, Atlanta, GA, United States; Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, United States; Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States
| | - Henry W Kietzman
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, United States; Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States; Graduate Program in Neuroscience, Emory University, Atlanta, GA, United States
| | - Jidong Guo
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States; Department of Psychiatry, Emory University School of Medicine, Atlanta, GA, United States
| | - Donald G Rainnie
- Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States; Department of Psychiatry, Emory University School of Medicine, Atlanta, GA, United States
| | - Shannon L Gourley
- Molecular and Systems Pharmacology, Emory University, Atlanta, GA, United States; Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, United States; Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States; Graduate Program in Neuroscience, Emory University, Atlanta, GA, United States; Department of Psychiatry, Emory University School of Medicine, Atlanta, GA, United States.
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47
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Hocker D, Park IM. Myopic control of neural dynamics. PLoS Comput Biol 2019; 15:e1006854. [PMID: 30856171 PMCID: PMC6428347 DOI: 10.1371/journal.pcbi.1006854] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 03/21/2019] [Accepted: 02/07/2019] [Indexed: 01/29/2023] Open
Abstract
Manipulating the dynamics of neural systems through targeted stimulation is a frontier of research and clinical neuroscience; however, the control schemes considered for neural systems are mismatched for the unique needs of manipulating neural dynamics. An appropriate control method should respect the variability in neural systems, incorporating moment to moment “input” to the neural dynamics and behaving based on the current neural state, irrespective of the past trajectory. We propose such a controller under a nonlinear state-space feedback framework that steers one dynamical system to function as through it were another dynamical system entirely. This “myopic” controller is formulated through a novel variant of a model reference control cost that manipulates dynamics in a short-sighted manner that only sets a target trajectory of a single time step into the future (hence its myopic nature), which omits the need to pre-calculate a rigid and computationally costly neural feedback control solution. To demonstrate the breadth of this control’s utility, two examples with distinctly different applications in neuroscience are studied. First, we show the myopic control’s utility to probe the causal link between dynamics and behavior for cognitive processes by transforming a winner-take-all decision-making system to operate as a robust neural integrator of evidence. Second, an unhealthy motor-like system containing an unwanted beta-oscillation spiral attractor is controlled to function as a healthy motor system, a relevant clinical example for neurological disorders. Stimulating a neural system and observing its effect through simultaneous observation offers the promise to better understand how neural systems perform computations, as well as for the treatment of neurological disorders. A powerful perspective for understanding a neural system’s behavior undergoing stimulation is to conceptualize them as dynamical systems, which considers the global effect that stimulation has on the brain, rather than only assessing what impact it has on the recorded signal from the brain. With this more comprehensive perspective comes a central challenge of determining what requirements need to be satisfied to harness neural observations and then stimulate to make one dynamical system function as another one entirely. This could lead to applications such as neural stimulators that make a diseased brain behave like its healthy counterpart, or to make a neural system previously capable of only hasty decision making to wait and accumulate more evidence for a more informed decision. In this work we explore the implications of this new perspective on neural stimulation and derive a simple prescription for using neural observations to inform stimulation protocol that makes one neural system behave like another one.
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Affiliation(s)
- David Hocker
- Department of Neurobiology and Behavior Stony Brook University, Stony Brook, New York, United States of America
| | - Il Memming Park
- Department of Neurobiology and Behavior Stony Brook University, Stony Brook, New York, United States of America
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, United States of America
- Institute for Advanced Computational Science, Stony Brook University, Stony Brook, New York, United States of America
- * E-mail:
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48
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Battefeld A, Popovic MA, van der Werf D, Kole MHP. A Versatile and Open-Source Rapid LED Switching System for One-Photon Imaging and Photo-Activation. Front Cell Neurosci 2019; 12:530. [PMID: 30705622 PMCID: PMC6344383 DOI: 10.3389/fncel.2018.00530] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 12/21/2018] [Indexed: 01/12/2023] Open
Abstract
Combining fluorescence and transmitted light sources for microscopy is an invaluable method in cellular neuroscience to probe the molecular and cellular mechanisms of cells. This approach enables the targeted recording from fluorescent reporter protein expressing neurons or glial cells in brain slices and fluorescence-assisted electrophysiological recordings from subcellular structures. However, the existing tools to mix multiple light sources in one-photon microscopy are limited. Here, we present the development of several microcontroller devices that provide temporal and intensity control of light emitting diodes (LEDs) for computer controlled microscopy illumination. We interfaced one microcontroller with μManager for rapid and dynamic overlay of transmitted and fluorescent images. Moreover, on the basis of this illumination system we implemented an electronic circuit to combine two pulsed LED light sources for fast (up to 1 kHz) ratiometric calcium (Ca2+) imaging. This microcontroller enabled the calibration of intracellular Ca2+ concentration and furthermore the combination of Ca2+ imaging with optogenetic activation. The devices are based on affordable components and open-source hardware and software. Integration into existing bright-field microscope systems will take ∼1 day. The microcontroller based LED imaging substantially advances conventional illumination methods by limiting light exposure and adding versatility and speed.
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Affiliation(s)
- Arne Battefeld
- Department of Axonal Signaling, Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, Amsterdam, Netherlands.,Grass Laboratory, Marine Biological Laboratory, Woods Holem, MA, United States
| | - Marko A Popovic
- Department of Axonal Signaling, Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, Amsterdam, Netherlands
| | - Dirk van der Werf
- Department of Mechatronics, Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, Amsterdam, Netherlands
| | - Maarten H P Kole
- Department of Axonal Signaling, Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, Amsterdam, Netherlands.,Cell Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
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49
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Abstract
The firing rate of neuronal spiking in vitro and in vivo significantly varies over extended timescales, characterized by long-memory processes and complex statistics, and appears in spontaneous as well as evoked activity upon repeated stimulus presentation. These variations in response features and their statistics, in face of repeated instances of a given physical input, are ubiquitous in all levels of brain-behavior organization. They are expressed in single neuron and network response variability but even appear in variations of subjective percepts or psychophysical choices and have been described as stemming from history-dependent, stochastic, or rate-determined processes.But what are the sources underlying these temporally rich variations in firing rate? Are they determined by interactions of the nervous system as a whole, or do isolated, single neurons or neuronal networks already express these fluctuations independent of higher levels? These questions motivated the application of a method that allows for controlled and specific long-term activation of a single neuron or neuronal network, isolated from higher levels of cortical organization.This chapter highlights the research done in cultured cortical networks to study (1) the inherent non-stationarity of neuronal network activity, (2) single neuron response fluctuations and underlying processes, and (3) the interface layer between network and single cell, the non-stationary efficacy of the ensemble of synapses impinging onto the observed neuron.
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50
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Zhang Z, Russell LE, Packer AM, Gauld OM, Häusser M. Closed-loop all-optical interrogation of neural circuits in vivo. Nat Methods 2018; 15:1037-1040. [PMID: 30420686 PMCID: PMC6513754 DOI: 10.1038/s41592-018-0183-z] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 09/04/2018] [Indexed: 11/09/2022]
Abstract
Understanding the causal relationship between neural activity and behavior requires the ability to perform rapid and targeted interventions in ongoing activity. Here we describe a closed-loop all-optical strategy for dynamically controlling neuronal activity patterns in awake mice. We rapidly tailored and delivered two-photon optogenetic stimulation based on online readout of activity using simultaneous two-photon imaging, thus enabling the manipulation of neural circuit activity 'on the fly' during behavior.
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Affiliation(s)
- Zihui Zhang
- Wolfson Institute for Biomedical Research, University College London, London, UK
- Department of Electronic & Electrical Engineering, University College London, London, UK
| | - Lloyd E Russell
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Adam M Packer
- Wolfson Institute for Biomedical Research, University College London, London, UK.
- Oxford University, Oxford, UK.
| | - Oliver M Gauld
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Michael Häusser
- Wolfson Institute for Biomedical Research, University College London, London, UK.
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