Advances in Engineering and Application of Optogenetic Indicators for Neuroscience

A genetically encoded near-infrared fluorescent calcium ion indicator

(2019) Yong Qian et al.   NATURE METHODS

Functional Synaptic Architecture of Callosal Inputs in Mouse Primary Visual Cortex

(2019) Kuo-Sheng Lee et al.   NEURON

Genetically Encoded Glutamate Indicators with Altered Color and Topology

(2018) Jiahui Wu et al.   ACS Chemical Biology

A genetically encoded Ca2+ indicator based on circularly permutated sea anemone red fluorescent protein eqFP578

(2018) Yi Shen et al.   BMC BIOLOGY

Genetically encoded calcium indicator with NTnC-like design and enhanced fluorescence contrast and kinetics

(2018) D. A. Doronin et al.   BMC BIOTECHNOLOGY

A Genetically Encoded Fluorescent Sensor Enables Rapid and Specific Detection of Dopamine in Flies, Fish, and Mice

(2018) Fangmiao Sun et al.   CELL

A Suite of Transgenic Driver and Reporter Mouse Lines with Enhanced Brain-Cell-Type Targeting and Functionality

(2018) Tanya L. Daigle et al.   CELL

Mitochondrial and endoplasmic reticulum calcium homeostasis and cell death

(2018) Saverio Marchi et al.   CELL CALCIUM

A bioluminescent Ca2+ indicator based on a topological variant of GCaMP6s

(2018) Yong Qian et al.   CHEMBIOCHEM

A genetically encoded fluorescent acetylcholine indicator for in vitro and in vivo studies

(2018) Miao Jing et al.   NATURE BIOTECHNOLOGY

A robotic multidimensional directed evolution approach applied to fluorescent voltage reporters

(2018) Kiryl D. Piatkevich et al.   Nature Chemical Biology

Ultrafast glutamate sensors resolve high-frequency release at Schaffer collateral synapses

(2018) Nordine Helassa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ultrafast neuronal imaging of dopamine dynamics with designed genetically encoded sensors

(2018) Tommaso Patriarchi et al.   SCIENCE

Improved calcium sensor GCaMP-X overcomes the calcium channel perturbations induced by the calmodulin in GCaMP

(2018) Yaxiong Yang et al.   Nature Communications

Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS

(2018) William H. Zhang et al.   Nature Chemical Biology

All-optical synaptic electrophysiology probes mechanism of ketamine-induced disinhibition

(2018) Linlin Z. Fan et al.   NATURE METHODS

In vivo measurement of afferent activity with axon-specific calcium imaging

(2018) Gerard Joey Broussard et al.   NATURE NEUROSCIENCE

Simultaneous dendritic voltage and calcium imaging and somatic recording from Purkinje neurons in awake mice

(2018) Christopher J. Roome et al.   Nature Communications

NTnC-like genetically encoded calcium indicator with a positive and enhanced response and fast kinetics

(2018) Natalia V. Barykina et al.   Scientific Reports

Genetically Encoded Fluorescent Biosensors Illuminate the Spatiotemporal Regulation of Signaling Networks

(2018) Eric C. Greenwald et al.   CHEMICAL REVIEWS

The whither of bacteriophytochrome-based near-infrared fluorescent proteins: Insights from two-photon absorption spectroscopy

(2018) Aleksandr A. Lanin et al.   Journal of Biophotonics

Fast, in vivo voltage imaging using a red fluorescent indicator

(2018) Madhuvanthi Kannan et al.   NATURE METHODS

Expansion microscopy: principles and uses in biological research

(2018) Asmamaw T. Wassie et al.   NATURE METHODS

Stability, affinity, and chromatic variants of the glutamate sensor iGluSnFR

(2018) Jonathan S. Marvin et al.   NATURE METHODS

An Inconvenient Truth: Calcium Sensors Are Calcium Buffers

(2018) Shane M. McMahon et al.   TRENDS IN NEUROSCIENCES

Improved methods for marking active neuron populations

(2018) Benjamien Moeyaert et al.   Nature Communications

In Vivo Two-Photon Voltage Imaging with Sulfonated Rhodamine Dyes

(2018) Rishikesh U. Kulkarni et al.   ACS Central Science

Temporally precise labeling and control of neuromodulatory circuits in the mammalian brain

(2017) Dongmin Lee et al.   NATURE METHODS

The central amygdala controls learning in the lateral amygdala

(2017) Kai Yu et al.   NATURE NEUROSCIENCE

Temporally precise single-cell-resolution optogenetics

(2017) Or A. Shemesh et al.   NATURE NEUROSCIENCE

Novel genetically encoded fluorescent probes enable real-time detection of potassium in vitro and in vivo

(2017) Helmut Bischof et al.   Nature Communications

Fast two-photon imaging of subcellular voltage dynamics in neuronal tissue with genetically encoded indicators

(2017) Simon Chamberland et al.   eLife

Green fluorescent genetically encoded calcium indicator based on calmodulin/M13-peptide from fungi

(2017) Natalia V. Barykina et al.   PLoS One

Subcellular Imaging of Voltage and Calcium Signals Reveals Neural Processing In Vivo

(2016) Helen H. Yang et al.   CELL

Genetically Targeted All-Optical Electrophysiology with a Transgenic Cre-Dependent Optopatch Mouse

(2016) S. Lou et al.   JOURNAL OF NEUROSCIENCE

Protein-retention expansion microscopy of cells and tissues labeled using standard fluorescent proteins and antibodies

(2016) Paul W Tillberg et al.   NATURE BIOTECHNOLOGY

Genetically encoded indicators of neuronal activity

(2016) Michael Z Lin et al.   NATURE NEUROSCIENCE

Superpriming of synaptic vesicles as a common basis for intersynapse variability and modulation of synaptic strength

(2016) Holger Taschenberger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cellular resolution circuit mapping with temporal-focused excitation of soma-targeted channelrhodopsin

(2016) Christopher A Baker et al.   eLife

Sensitive red protein calcium indicators for imaging neural activity

(2016) Hod Dana et al.   eLife

A new design for a green calcium indicator with a smaller size and a reduced number of calcium-binding sites

(2016) Natalia V. Barykina et al.   Scientific Reports

Distinct Mechanisms Underlie Quiescence during Two Caenorhabditis elegans Sleep-Like States

(2015) N. F. Trojanowski et al.   JOURNAL OF NEUROSCIENCE

A general method to improve fluorophores for live-cell and single-molecule microscopy

(2015) Jonathan B Grimm et al.   NATURE METHODS

A naturally monomeric infrared fluorescent protein for protein labeling in vivo

(2015) Dan Yu et al.   NATURE METHODS

Dendritic integration: 60 years of progress

(2015) Greg J Stuart et al.   NATURE NEUROSCIENCE

Methods for the directed evolution of proteins

(2015) Michael S. Packer et al.   NATURE REVIEWS GENETICS

Transgenic Mice for Intersectional Targeting of Neural Sensors and Effectors with High Specificity and Performance

(2015) Linda Madisen et al.   NEURON

Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction

(2015) Jason H. Whitfield et al.   PROTEIN SCIENCE

High-speed recording of neural spikes in awake mice and flies with a fluorescent voltage sensor

(2015) Y. Gong et al.   SCIENCE

Labeling of active neural circuits in vivo with designed calcium integrators

(2015) B. F. Fosque et al.   SCIENCE

Ten Years of Maintaining and Expanding a Microbial Genome and Metagenome Analysis System

(2015) Victor M. Markowitz et al.   TRENDS IN MICROBIOLOGY

Minimal domain of bacterial phytochrome required for chromophore binding and fluorescence

(2015) Konstantin A. Rumyantsev et al.   Scientific Reports

Microfluidic cell sorter-aided directed evolution of a protein-based calcium ion indicator with an inverted fluorescent response

(2014) Yongxin Zhao et al.   Integrative Biology

Calcium transient prevalence across the dendritic arbour predicts place field properties

(2014) Mark E. J. Sheffield et al.   NATURE

Independent optical excitation of distinct neural populations

(2014) Nathan C Klapoetke et al.   NATURE METHODS

All-optical electrophysiology in mammalian neurons using engineered microbial rhodopsins

(2014) Daniel R Hochbaum et al.   NATURE METHODS

Cell-based reporters reveal in vivo dynamics of dopamine and norepinephrine release in murine cortex

(2014) Arnaud Muller et al.   NATURE METHODS

Rational design of a high-affinity, fast, red calcium indicator R-CaMP2

(2014) Masatoshi Inoue et al.   NATURE METHODS

High-fidelity optical reporting of neuronal electrical activity with an ultrafast fluorescent voltage sensor

(2014) François St-Pierre et al.   NATURE NEUROSCIENCE

Engineering an improved light-induced dimer (iLID) for controlling the localization and activity of signaling proteins

(2014) Gurkan Guntas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bright and fast multicoloured voltage reporters via electrochromic FRET

(2014) Peng Zou et al.   Nature Communications

A long Stokes shift red fluorescent Ca2+ indicator protein for two-photon and ratiometric imaging

(2014) Jiahui Wu et al.   Nature Communications

Imaging neural spiking in brain tissue using FRET-opsin protein voltage sensors

(2014) Yiyang Gong et al.   Nature Communications

A photochromic and thermochromic fluorescent protein

(2014) Y. Shen et al.   RSC Advances

Monitoring activity in neural circuits with genetically encoded indicators

(2014) Gerard J. Broussard et al.   Frontiers in Molecular Neuroscience

Improved Orange and Red Ca2+ Indicators and Photophysical Considerations for Optogenetic Applications

(2013) Jiahui Wu et al.   ACS Chemical Neuroscience

Genetically encoded Ca2+ indicators: Properties and evaluation

(2013) Vadim Pérez Koldenkova et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

New insights into the function and regulation of mitochondrial fission

(2013) Hidenori Otera et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

Genetically Targeted Optical Electrophysiology in Intact Neural Circuits

(2013) Guan Cao et al.   CELL

Engineering of bacterial phytochromes for near-infrared imaging, sensing, and light-control in mammals

(2013) Kiryl D. Piatkevich et al.   CHEMICAL SOCIETY REVIEWS

Spermatogonial stem cell preservation and transplantation: from research to clinic

(2013) E. Goossens et al.   HUMAN REPRODUCTION

Ultrasensitive fluorescent proteins for imaging neuronal activity

(2013) Tsai-Wen Chen et al.   NATURE

Whole-brain functional imaging at cellular resolution using light-sheet microscopy

(2013) Misha B Ahrens et al.   NATURE METHODS

An optimized fluorescent probe for visualizing glutamate neurotransmission

(2013) Jonathan S Marvin et al.   NATURE METHODS

Long-term dynamics of CA1 hippocampal place codes

(2013) Yaniv Ziv et al.   NATURE NEUROSCIENCE

Chronic Cellular Imaging of Entire Cortical Columns in Awake Mice Using Microprisms

(2013) Mark L. Andermann et al.   NEURON

Neurotransmitter Release: The Last Millisecond in the Life of a Synaptic Vesicle

(2013) Thomas C. Südhof   NEURON

Mechanism of voltage-sensitive fluorescence in a microbial rhodopsin

(2013) D. Maclaurin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Far-red light photoactivatable near-infrared fluorescent proteins engineered from a bacterial phytochrome

(2013) Kiryl D. Piatkevich et al.   Nature Communications

Fast GCaMPs for improved tracking of neuronal activity

(2013) Xiaonan R. Sun et al.   Nature Communications

Genetically encoded calcium indicators for multi-color neural activity imaging and combination with optogenetics

(2013) Jasper Akerboom et al.   Frontiers in Molecular Neuroscience

A Fluorescent Sensor for GABA and Synthetic GABAB Receptor Ligands

(2012) Anastasiya Masharina et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Multiple dynamic representations in the motor cortex during sensorimotor learning

(2012) D. Huber et al.   NATURE

Reorganization of cortical population activity imaged throughout long-term sensory deprivation

(2012) David J Margolis et al.   NATURE NEUROSCIENCE

Imaging Calcium in Neurons

(2012) Christine Grienberger et al.   NEURON

An Improved Genetically Encoded Red Fluorescent Ca2+ Indicator for Detecting Optically Evoked Action Potentials

(2012) Masamichi Ohkura et al.   PLoS One

NMDA Receptor-Dependent Long-Term Potentiation and Long-Term Depression (LTP/LTD)

(2012) C. Luscher et al.   Cold Spring Harbor Perspectives in Biology

Luminescent proteins for high-speed single-cell and whole-body imaging

(2012) Kenta Saito et al.   Nature Communications

Mitochondrial calcium homeostasis as potential target for mitochondrial medicine

(2011) Carlotta Giorgi et al.   MITOCHONDRION

Bright and stable near-infrared fluorescent protein for in vivo imaging

(2011) Grigory S Filonov et al.   NATURE BIOTECHNOLOGY

Optical recording of action potentials in mammalian neurons using a microbial rhodopsin

(2011) Joel M Kralj et al.   NATURE METHODS

Directed molecular evolution to design advanced red fluorescent proteins

(2011) Fedor V Subach et al.   NATURE METHODS

Principles for applying optogenetic tools derived from direct comparative analysis of microbial opsins

(2011) Joanna Mattis et al.   NATURE METHODS

Miniaturized integration of a fluorescence microscope

(2011) Kunal K Ghosh et al.   NATURE METHODS

Imaging Voltage in Neurons

(2011) Darcy S. Peterka et al.   NEURON

Ultrasensitive Measurements of Microbial Rhodopsin Photocycles Using Photochromic FRET

(2011) Halil Bayraktar et al.   PHOTOCHEMISTRY AND PHOTOBIOLOGY

Circular Permutation of Red Fluorescent Proteins

(2011) Bo Shui et al.   PLoS One

Electrical Spiking in Escherichia coli Probed with a Fluorescent Voltage-Indicating Protein

(2011) Joel M. Kralj et al.   SCIENCE

An Expanded Palette of Genetically Encoded Ca2+ Indicators

(2011) Y. Zhao et al.   SCIENCE

FRET-based sensors for the human M1-, M3-, and M5-acetylcholine receptors

(2010) Nicole Ziegler et al.   BIOORGANIC & MEDICINAL CHEMISTRY

A Fluorescence Resonance Energy Transfer-based M2Muscarinic Receptor Sensor Reveals Rapid Kinetics of Allosteric Modulation

(2010) Monika Maier-Peuschel et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A Conserved Mechanism of GABA Binding and Antagonism Is Revealed by Structure-Function Analysis of the Periplasmic Binding Protein Atu2422 inAgrobacterium tumefaciens

(2010) Sara Planamente et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Toward the Second Generation of Optogenetic Tools

(2010) T. Knopfel et al.   JOURNAL OF NEUROSCIENCE

High-performance genetically targetable optical neural silencing by light-driven proton pumps

(2010) Brian Y. Chow et al.   NATURE

Microprisms for In Vivo Multilayer Cortical Imaging

(2009) Thomas H. Chia et al.   JOURNAL OF NEUROPHYSIOLOGY

Determining the Neurotransmitter Concentration Profile at Active Synapses

(2009) Annalisa Scimemi et al.   MOLECULAR NEUROBIOLOGY

Imaging neural activity in worms, flies and mice with improved GCaMP calcium indicators

(2009) Lin Tian et al.   NATURE METHODS

An in vivo biosensor for neurotransmitter release and in situ receptor activity

(2009) Quoc-Thang Nguyen et al.   NATURE NEUROSCIENCE

Crystal structure of opsin in its G-protein-interacting conformation

(2008) Patrick Scheerer et al.   NATURE

Crystal structure of the ligand-free G-protein-coupled receptor opsin

(2008) Jung Hee Park et al.   NATURE

The enzyme mechanism of nitrite reductase studied at single-molecule level

(2008) S. Kuznetsova et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Optical measurement of synaptic glutamate spillover and reuptake by linker optimized glutamate-sensitive fluorescent reporters

(2008) S. A. Hires et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Construction of a fluorescent biosensor family

(2002) Robert M. De Lorimier et al.   PROTEIN SCIENCE