Optogenetic Investigation of Neural Circuits Underlying Brain Disease in Animal Models
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Neural Coding and the Statistical Modeling of Neuronal Responses By
Neural coding and the statistical modeling of neuronal responses by Jonathan Pillow A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy Center for Neural Science New York University Jan 2005 Eero P. Simoncelli TABLE OF CONTENTS LIST OF FIGURES v INTRODUCTION 1 1 Characterization of macaque retinal ganglion cell responses using spike-triggered covariance 5 1.1NeuralCharacterization.................... 9 1.2One-DimensionalModelsandtheSTA............ 12 1.3Multi-DimensionalModelsandSTCAnalysis........ 16 1.4 Separability and Subspace STC ................ 21 1.5 Subunit model . ....................... 23 1.6ModelValidation........................ 25 1.7Methods............................. 28 2 Estimation of a Deterministic IF model 37 2.1Leakyintegrate-and-firemodel................. 40 2.2Simulationresultsandcomparison............... 41 ii 2.3Recoveringthelinearkernel.................. 42 2.4Recoveringakernelfromneuraldata............. 44 2.5Discussion............................ 46 3 Estimation of a Stochastic, Recurrent IF model 48 3.1TheModel............................ 52 3.2TheEstimationProblem.................... 54 3.3ComputationalMethodsandNumericalResults....... 57 3.4TimeRescaling......................... 60 3.5Extensions............................ 61 3.5.1 Interneuronalinteractions............... 62 3.5.2 Nonlinear input ..................... 63 3.6Discussion............................ 64 AppendixA:ProofofLog-ConcavityofModelLikelihood..... 65 AppendixB:ComputingtheLikelihoodGradient........ -
Neural Oscillations As a Signature of Efficient Coding in the Presence of Synaptic Delays Matthew Chalk1*, Boris Gutkin2,3, Sophie Dene` Ve2
RESEARCH ARTICLE Neural oscillations as a signature of efficient coding in the presence of synaptic delays Matthew Chalk1*, Boris Gutkin2,3, Sophie Dene` ve2 1Institute of Science and Technology Austria, Klosterneuburg, Austria; 2E´ cole Normale Supe´rieure, Paris, France; 3Center for Cognition and Decision Making, National Research University Higher School of Economics, Moscow, Russia Abstract Cortical networks exhibit ’global oscillations’, in which neural spike times are entrained to an underlying oscillatory rhythm, but where individual neurons fire irregularly, on only a fraction of cycles. While the network dynamics underlying global oscillations have been well characterised, their function is debated. Here, we show that such global oscillations are a direct consequence of optimal efficient coding in spiking networks with synaptic delays and noise. To avoid firing unnecessary spikes, neurons need to share information about the network state. Ideally, membrane potentials should be strongly correlated and reflect a ’prediction error’ while the spikes themselves are uncorrelated and occur rarely. We show that the most efficient representation is when: (i) spike times are entrained to a global Gamma rhythm (implying a consistent representation of the error); but (ii) few neurons fire on each cycle (implying high efficiency), while (iii) excitation and inhibition are tightly balanced. This suggests that cortical networks exhibiting such dynamics are tuned to achieve a maximally efficient population code. DOI: 10.7554/eLife.13824.001 *For correspondence: Introduction [email protected] Oscillations are a prominent feature of cortical activity. In sensory areas, one typically observes Competing interests: The ’global oscillations’ in the gamma-band range (30–80 Hz), alongside single neuron responses that authors declare that no are irregular and sparse (Buzsa´ki and Wang, 2012; Yu and Ferster, 2010). -
Neural Dust: Ultrasonic Biological Interface
Neural Dust: Ultrasonic Biological Interface Dongjin (DJ) Seo Electrical Engineering and Computer Sciences University of California at Berkeley Technical Report No. UCB/EECS-2018-146 http://www2.eecs.berkeley.edu/Pubs/TechRpts/2018/EECS-2018-146.html December 1, 2018 Copyright © 2018, by the author(s). All rights reserved. Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. To copy otherwise, to republish, to post on servers or to redistribute to lists, requires prior specific permission. Neural Dust: Ultrasonic Biological Interface by Dongjin Seo A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Engineering - Electrical Engineering and Computer Sciences in the Graduate Division of the University of California, Berkeley Committee in charge: Professor Michel M. Maharbiz, Chair Professor Elad Alon Professor John Ngai Fall 2016 Neural Dust: Ultrasonic Biological Interface Copyright 2016 by Dongjin Seo 1 Abstract Neural Dust: Ultrasonic Biological Interface by Dongjin Seo Doctor of Philosophy in Engineering - Electrical Engineering and Computer Sciences University of California, Berkeley Professor Michel M. Maharbiz, Chair A seamless, high density, chronic interface to the nervous system is essential to enable clinically relevant applications such as electroceuticals or brain-machine interfaces (BMI). Currently, a major hurdle in neurotechnology is the lack of an implantable neural interface system that remains viable for a patient's lifetime due to the development of biological response near the implant. -
Perceiving Invisible Light Through a Somatosensory Cortical Prosthesis
ARTICLE Received 24 Aug 2012 | Accepted 15 Jan 2013 | Published 12 Feb 2013 DOI: 10.1038/ncomms2497 Perceiving invisible light through a somatosensory cortical prosthesis Eric E. Thomson1,2, Rafael Carra1,w & Miguel A.L. Nicolelis1,2,3,4,5 Sensory neuroprostheses show great potential for alleviating major sensory deficits. It is not known, however, whether such devices can augment the subject’s normal perceptual range. Here we show that adult rats can learn to perceive otherwise invisible infrared light through a neuroprosthesis that couples the output of a head-mounted infrared sensor to their soma- tosensory cortex (S1) via intracortical microstimulation. Rats readily learn to use this new information source, and generate active exploratory strategies to discriminate among infrared signals in their environment. S1 neurons in these infrared-perceiving rats respond to both whisker deflection and intracortical microstimulation, suggesting that the infrared repre- sentation does not displace the original tactile representation. Hence, sensory cortical prostheses, in addition to restoring normal neurological functions, may serve to expand natural perceptual capabilities in mammals. 1 Department of Neurobiology, Duke University, Box 3209, 311 Research Drive, Bryan Research, Durham, North Carolina 27710, USA. 2 Edmond and Lily Safra International Institute for Neuroscience of Natal (ELS-IINN), Natal 01257050, Brazil. 3 Department of Biomedical Engineering, Duke University, Durham, North Carolina 27710, USA. 4 Department of Psychology and Neuroscience, Duke University, Durham, North Carolina 27710, USA. 5 Center for Neuroengineering, Duke University, Durham, North Carolina 27710, USA. w Present address: University of Sao Paulo School of Medicine, Sao Paulo 01246-000, Brazil. Correspondence and requests for materials should be addressed to M.A.L.N. -
Optogenetics Controlling Neurons with Photons
Valerie C. Coffey Optogenetics Controlling Neurons with Photons An advancing field of neuroscience uses light to understand how the brain works and to create new tools to treat disease. Wireless optogenetics tools like these tiny implants in live mice are enabling scientists to map the stimulation of certain neurons of the brain to specific responses. J. Rogers/Northwestern Univ. 24 OPTICS & PHOTONICS NEWS APRIL 2018 APRIL 2018 OPTICS & PHOTONICS NEWS 25 In just over a decade, the discovery of numerous opsins with different specializations has allowed scientists and engineers to make rapid progress in mapping brain activity. wo thousand years ago, ancient Egyptians halorhodopsin can silence the neurons in the hypo- knew that the electrical shocks of torpedo thalamus, inducing sleep in living mice. fish, applied to the body, could offer pain In just over a decade, the discovery of numerous relief. Two hundred years ago, physicians opsins with different specializations has allowed scien- understood that electrical stimulation of a tists and engineers to make rapid progress in mapping Tfrog’s spine could control muscle contraction. Today, brain activity, motivated by the hope of solving intrac- electrical therapy underlies many treatments, from table neurological conditions. And it doesn’t hurt that pacemakers to pain control. investment in neuroscience research has grown at the But neuroscience has long awaited a more precise same time. tool for controlling specific types of neurons. Electrical In 2013, the Obama administration announced a stimulation (e-stim) approaches stimulate a large area collaborative public-private effort, the Brain Research without precise spatial control, and can’t distinguish through Advancing Innovative Neurotechnologies between different cell types. -
Computational Neuroscience Meets Optogenetics: Unlocking the Brain’S Secrets
Health & Medicine ︱ Prof Simon Schultz and Dr Konstantin Nikolic Computational neuroscience meets optogenetics: Unlocking the brain’s secrets Working at the interface omposed of billions of specialised responsible for perception, action Simplified models allow researchers to study how the geometry of a neuron’s “dendritic tree” affects its ability to process information. between engineering and nerve cells (called neurons) wired and memory. But this is changing. neuroscience, Professor Simon C together in complex, intricate Schultz and Dr Konstantin webs, the brain is inherently challenging LET THERE BE LIGHT Nikolic at Imperial College to study. Neurons communicate with A powerful new tool (invented by Boyden of Neurotechnology and Director of SHEDDING LIGHT ON THE BRAIN AN INSIGHT INTO NEURONAL GAIN London are developing tools each other by transmitting electrical and and Deisseroth just a little over a decade the Imperial Centre of Excellence in Their innovative approach uses Using two biophysical models of to help us understand the chemical signals along neural circuits: ago) allows researchers to map the brain’s Neurotechnology, Dr Konstantin Nikolic, sophisticated two-photon microscopy, neurons, genetically-modified to include intricate workings of the brain. signals that vary both in space and time. connections, giving unprecedented Associate Professor in the Department optogenetics and electrophysiology two distinct light-sensitive proteins Combining a revolutionary Until now, technical limitations in the access to the workings of the brain. Its of Electrical and Electronic Engineering, to measure (and disturb) patterns of (called opsins): channelrhodopsin-2 technology – optogenetics available research methods to study the impressive resolution enables precise and Dr Sarah Jarvis are taking a unique neuronal activity in vivo (in living tissue). -
Mousecircuits.Org: an Online Repository to Guide the Circuit Era of Disordered Affect
bioRxiv preprint doi: https://doi.org/10.1101/2020.02.16.951608; this version posted February 17, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. MouseCircuits.org: An online repository to guide the circuit era of disordered affect Kristin R. Anderson ID 1,2 and Dani Dumitriu ID 1,2 1Columbia University, Departments of Pediatrics and Psychiatry, New York State Psychiatric Institute, 1051 Riverside Drive, New York, NY 10032 2Columbia University, Zuckerman Institute, 3227 Broadway, New York, NY 10027 Affective disorders rank amongst the most disruptive and tem and the gut microbiome (2,3). However, the mysteries of prevalent psychiatric diseases, resulting in enormous societal the brain, a structure with idiosyncratic and interconnected and economic burden, and immeasurable personal costs. Novel architecture, are unlikely to be revealed solely on the basis of therapies are urgently needed but have remained elusive. The this type of sledgehammer approach. era of circuit-mapping in rodent models of disordered affect, ushered in by recent technological advancements allowing for Enter the era of circuit dissection. In the last precise and specific neural control, has reenergized the hope for decade, groundbreaking technological advances have al- precision psychiatry. Here, we present a novel whole-brain cu- lowed neuroscientists to take control of neural firing with mulative network and critically access the progress made to- impressive precision and specificity (Figure 1) (4–7). -
Maria Barthmes, Andre Bazzone, Ulrich Thomas, Andrea Brüggemann, Michael George, Niels Fertig, Alison Obergrussberger
Label-free analysis of Na+/Ca2+- exchanger (NCX) isolated from iPSC-derived cardiomyocytes Maria Barthmes, Andre Bazzone, Ulrich Thomas, Andrea Brüggemann, Michael George, Niels Fertig, Alison Obergrussberger Nanion Technologies GmbH, Ganghoferstr. 70A, 80339 Munich, Germany, contact: [email protected] Abstract Measuring NCX activity in human iPSC derived The Sodium-Calcium Exchangers (NCX) play an To drive the progress in pharmacological NCX cardiomyocytes important role in the cellular calcium research, new methods to measure NCX Human iPSC derived cardiomyocytes are being with high fluidic speed, the cells detached homeostasis under physiological and function are needed. At the current time, investigated as a model for cardiac safety again, but a sheet of the cell membrane pathological conditions. NCX has been of functional investigation of NCX range from assessment. To measure native NCX in these remains on the sensor. NCX currents can be interest as a pharmacological target for many patch-clamp, calcium flux assays, Langendorff- cardiomyocytes a cell based assay was evoked in these sheets. For a higher NCX signal years, in particular because clinical trials perfused hearts to studies in whole animals. We developed. Cardiomyocytes were detached female cardiomyocytes were used. This method involving inhibitors of the sodium-proton have developed an electrophysiological from the culture dish and added to the lipid enables the efficient investigation of the isolated exchanger, NHE, have delivered mixed results. method to investigate NCX function which is coated SSM sensor. Where the cell connected cardiac NCX current in a native membrane. Inhibition of the reversed mode of NCX is based on the solid supported membrane (SSM) with the lipid layer. -
Early-Stage Dynamics of Chloride Ion–Pumping Rhodopsin Revealed by a Femtosecond X-Ray Laser
Early-stage dynamics of chloride ion–pumping rhodopsin revealed by a femtosecond X-ray laser Ji-Hye Yuna,1, Xuanxuan Lib,c,1, Jianing Yued, Jae-Hyun Parka, Zeyu Jina, Chufeng Lie, Hao Hue, Yingchen Shib,c, Suraj Pandeyf, Sergio Carbajog, Sébastien Boutetg, Mark S. Hunterg, Mengning Liangg, Raymond G. Sierrag, Thomas J. Laneg, Liang Zhoud, Uwe Weierstalle, Nadia A. Zatsepine,h, Mio Ohkii, Jeremy R. H. Tamei, Sam-Yong Parki, John C. H. Spencee, Wenkai Zhangd, Marius Schmidtf,2, Weontae Leea,2, and Haiguang Liub,d,2 aDepartment of Biochemistry, College of Life Sciences and Biotechnology, Yonsei University, Seodaemun-gu, 120-749 Seoul, South Korea; bComplex Systems Division, Beijing Computational Science Research Center, Haidian, 100193 Beijing, People’s Republic of China; cDepartment of Engineering Physics, Tsinghua University, 100086 Beijing, People’s Republic of China; dDepartment of Physics, Beijing Normal University, Haidian, 100875 Beijing, People’s Republic of China; eDepartment of Physics, Arizona State University, Tempe, AZ 85287; fPhysics Department, University of Wisconsin, Milwaukee, Milwaukee, WI 53201; gLinac Coherent Light Source, Stanford Linear Accelerator Center National Accelerator Laboratory, Menlo Park, CA 94025; hDepartment of Chemistry and Physics, Australian Research Council Centre of Excellence in Advanced Molecular Imaging, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia; and iDrug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, 230-0045 Yokohama, Japan Edited by Nicholas K. Sauter, Lawrence Berkeley National Laboratory, Berkeley, CA, and accepted by Editorial Board Member Axel T. Brunger February 21, 2021 (received for review September 30, 2020) Chloride ion–pumping rhodopsin (ClR) in some marine bacteria uti- an acceptor aspartate (13–15). -
An Optogenetic Approach to Understanding the Neural Circuits of Fear Joshua P
Controlling the Elements: An Optogenetic Approach to Understanding the Neural Circuits of Fear Joshua P. Johansen, Steffen B.E. Wolff, Andreas Lüthi, and Joseph E. LeDoux Neural circuits underlie our ability to interact in the world and to learn adaptively from experience. Understanding neural circuits and how circuit structure gives rise to neural firing patterns or computations is fundamental to our understanding of human experience and behavior. Fear conditioning is a powerful model system in which to study neural circuits and information processing and relate them to learning and behavior. Until recently, technological limitations have made it difficult to study the causal role of specific circuit elements during fear conditioning. However, newly developed optogenetic tools allow researchers to manipulate individual circuit components such as anatom- ically or molecularly defined cell populations, with high temporal precision. Applying these tools to the study of fear conditioning to control specific neural subpopulations in the fear circuit will facilitate a causal analysis of the role of these circuit elements in fear learning and memory. By combining this approach with in vivo electrophysiological recordings in awake, behaving animals, it will also be possible to determine the functional contribution of specific cell populations to neural processing in the fear circuit. As a result, the application of optogenetics to fear conditioning could shed light on how specific circuit elements contribute to neural coding and to fear learning and memory. Furthermore, this approach may reveal general rules for how circuit structure and neural coding within circuits gives rise to sensory experience and behavior. Key Words: Electrophysiology, fear conditioning, learning and circuits and the identification of sites of neural plasticity in these memory, neural circuits, neural plasticity, optogenetics circuits. -
6 Optogenetic Actuation, Inhibition, Modulation and Readout for Neuronal Networks Generating Behavior in the Nematode Caenorhabditis Elegans
Mario de Bono, William R. Schafer, Alexander Gottschalk 6 Optogenetic actuation, inhibition, modulation and readout for neuronal networks generating behavior in the nematode Caenorhabditis elegans 6.1 Introduction – the nematode as a genetic model in systems neurosciencesystems neuroscience Elucidating the mechanisms by which nervous systems process information and gen- erate behavior is among the fundamental problems of biology. The complexity of our brain and plasticity of our behaviors make it challenging to understand even simple human actions in terms of molecular mechanisms and neural activity. However the molecular machines and operational features of our neural circuits are often found in invertebrates, so that studying flies and worms provides an effective way to gain insights into our nervous system. Caenorhabditis elegans offers special opportunities to study behavior. Each of the 302 neurons in its nervous system can be identified and imaged in live animals [1, 2], and manipulated transgenically using specific promoters or promoter combinations [3, 4, 5, 6]. The chemical synapses and gap junctions made by every neuron are known from electron micrograph reconstruction [1]. Importantly, forward genetics can be used to identify molecules that modulate C. elegans’ behavior. Forward genetic dis- section of behavior is powerful because it requires no prior knowledge. It allows mol- ecules to be identified regardless of in vivo concentration, and focuses attention on genes that are functionally important. The identity and expression patterns of these molecules then provide entry points to study the molecular mechanisms and neural circuits controlling the behavior. Genetics does not provide the temporal resolution required to study neural circuit function directly. -
Exploring the Function of Neural Oscillations in Early Sensory Systems
FOCUSED REVIEW published: 15 May 2010 doi: 10.3389/neuro.01.010.2010 Exploring the function of neural oscillations in early sensory systems Kilian Koepsell1*, Xin Wang 2, Judith A. Hirsch 2 and Friedrich T. Sommer1* 1 Redwood Center for Theoretical Neuroscience, University of California, Berkeley, CA, USA 2 Neuroscience Graduate Program, University of Southern California, Los Angeles, CA, USA Neuronal oscillations appear throughout the nervous system, in structures as diverse as the cerebral cortex, hippocampus, subcortical nuclei and sense organs. Whether neural rhythms contribute to normal function, are merely epiphenomena, or even interfere with physiological processing are topics of vigorous debate. Sensory pathways are ideal for investigation of oscillatory activity because their inputs can be defined. Thus, we will focus on sensory systems Edited by: S. Murray Sherman, as we ask how neural oscillations arise and how they might encode information about the University of Chicago, USA stimulus. We will highlight recent work in the early visual pathway that shows how oscillations Reviewed by: can multiplex different types of signals to increase the amount of information that spike trains Michael J. Friedlander, Baylor College of Medicine, USA encode and transmit. Last, we will describe oscillation-based models of visual processing and Jose-Manuel Alonso, Sociedad Espanola explore how they might guide further research. de Neurociencia, Spain; University of Connecticut, USA; State University Keywords: LGN, retina, visual coding, oscillations, multiplexing of New York, USA Naoum P. Issa, University of Chicago, USA NEURAL OSCILLATIONS IN EARLY However, the autocorrelograms are subject to *Correspondence: SENSORY SYSTEMS confounds caused by the refractory period and Oscillatory neural activity has been observed spectral peaks often fail to reveal weak rhythms.