Neuroscience › Cellular and Molecular Neuroscience

Photoreceptor and optogenetics research

Works Count: 66648

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Description

This cluster of papers focuses on the application of optogenetics in neuroscience and biophysics research, particularly the use of microbial rhodopsins such as Channelrhodopsin for precise control and manipulation of neural activity. It covers topics such as neural stimulation, photocycle dynamics, and in vivo control of neural circuitry using light-sensitive proteins. The research also explores the molecular mechanisms and biophysical principles underlying optogenetic tools.

Keywords

Optogenetics; Channelrhodopsin; Neural Control; Microbial Rhodopsins; Neuronal Stimulation; Photocycle Dynamics; Neural Circuitry; Proton Pump; Sensory Rhodopsin; In Vivo Control

Optogenetics: 10 years of microbial opsins in neuroscience

2015-08-26

Karl Deisseroth

Light-driven monodirectional molecular rotor

1999-09-01

Nagatoshi Koumura , Robert W. J. Zijlstra , Richard A. van Delden +2 more

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The separation of synaptic vesicles from nerve-ending particles (‘synaptosomes’)

1964-02-01

VP Whittaker , I.Arthur Michaelson , R.J. Kirkland

Research Article| February 01 1964 The separation of synaptic vesicles from nerve-ending particles (‘synaptosomes’) VP Whittaker; VP Whittaker Search for other works by this author on: This Site PubMed Google … Research Article| February 01 1964 The separation of synaptic vesicles from nerve-ending particles (‘synaptosomes’) VP Whittaker; VP Whittaker Search for other works by this author on: This Site PubMed Google Scholar IA Michaelson; IA Michaelson Search for other works by this author on: This Site PubMed Google Scholar RJA Kirkland RJA Kirkland Search for other works by this author on: This Site PubMed Google Scholar Biochem J (1964) 90 (2): 293–303. https://doi.org/10.1042/bj0900293 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn Email Cite Icon Cite Get Permissions Citation VP Whittaker, IA Michaelson, RJA Kirkland; The separation of synaptic vesicles from nerve-ending particles (‘synaptosomes’). Biochem J 1 February 1964; 90 (2): 293–303. doi: https://doi.org/10.1042/bj0900293 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Journal Search Advanced Search © 1964 The Biochemical Society1964 Article PDF first page preview Close Modal You do not currently have access to this content.

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[69] Isolation of the cell membrane of Halobacterium halobium and its fractionation into red and purple membrane

1974-01-01

Dieter Oesterhelt , Walther Stoeckenius

Chemical Nature of Synaptic Transmission in Vertebrates

1974-04-01

K. Krnjević

Regulation of parkinsonian motor behaviours by optogenetic control of basal ganglia circuitry

2010-07-01

Alexxai V. Kravitz , Benjamin Freeze , Philip R. L. Parker +4 more

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Synaptic vesicle exocytosis captured by quick freezing and correlated with quantal transmitter release.

1979-05-01

John E. Heuser , Thomas S. Reese , Michael J. Dennis +3 more

We describe the design and operation of a machine that freezes biological tissues by contact with a cold metal block, which incorporates a timing circuit that stimulates frog neuromuscular junctions … We describe the design and operation of a machine that freezes biological tissues by contact with a cold metal block, which incorporates a timing circuit that stimulates frog neuromuscular junctions in the last few milliseconds before thay are frozen. We show freeze-fracture replicas of nerve terminals frozen during transmitter discharge, which display synpatic vesicles caught in the act of exocytosis. We use 4-aminopyridine (4-AP) to increase the number of transmitter quanta discharged with each nerve impulse, and show that the number of exocytotic vesicles caught by quick-freezing increases commensurately, indicating that one vesicle undergoes exocytosis for each quantum that is discharged. We perform statistical analyses on the spatial distribution of synaptic vesicle discharge sites along the "active zones" that mark the secretory regions of these nerves, and show that individual vesicles fuse with the plasma membrane independent of one another, as expected from physiological demonstrations that quanta are discharged independently. Thus, the utility of quick-freezing as a technique to capture biological processes as evanescent as synaptic transmission has been established. An appendix describes a new capacitance method to measure freezing rates, which shows that the "temporal resolution" of our quick-freezing technique is 2 ms or better.

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A toolbox of Cre-dependent optogenetic transgenic mice for light-induced activation and silencing

2012-03-25

Linda Madisen , Tianyi Mao , Henner Koch +7 more

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THE KINETICS OF FORMATION OF NATIVE RIBONUCLEASE DURING OXIDATION OF THE REDUCED POLYPEPTIDE CHAIN

1961-09-01

Christian B. Anfinsen , E Haber , Michael Sela +1 more

In this article, Anfinsen, Haber, Sela, and White reported that there existed a considerable lag phase before enzymatic activity appeared after the sample of bovine pancreatic ribonuclease was treated with … In this article, Anfinsen, Haber, Sela, and White reported that there existed a considerable lag phase before enzymatic activity appeared after the sample of bovine pancreatic ribonuclease was treated with mercaptoethanol in urea, during which period the sulfhydrl titer and the specific optical rotation changed along a curve similar to that of a first-order reaction. The lag in enzymatic activity in vitro often took several hours, while the same process seemed to take only a few minutes in vivo. This discrepancy eventually led to the discovery of an enzyme system in the endoplasmic reticulum of cells that catalyzes the disulfide interchange reaction, and subsequently, the rapid formation of the correct, native disulfide pairing in relatively short order.

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Molecular structure determination by electron microscopy of unstained crystalline specimens

1975-05-01

P.N.T. Unwin , Richard A. Henderson

Electrogenerated Chemiluminescence and Its Biorelated Applications

2008-05-28

Wujian Miao

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTElectrogenerated Chemiluminescence and Its Biorelated ApplicationsWujian Miao†View Author Information Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, Mississippi 39406† Telephone (601) 266 4716; fax … ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTElectrogenerated Chemiluminescence and Its Biorelated ApplicationsWujian Miao†View Author Information Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, Mississippi 39406† Telephone (601) 266 4716; fax (601) 266 6075; e-mail [email protected]Cite this: Chem. Rev. 2008, 108, 7, 2506–2553Publication Date (Web):May 28, 2008Publication History Received19 November 2007Published online28 May 2008Published inissue 1 July 2008https://pubs.acs.org/doi/10.1021/cr068083ahttps://doi.org/10.1021/cr068083areview-articleACS PublicationsCopyright © 2008 American Chemical SocietyRequest reuse permissionsArticle Views21190Altmetric-Citations1786LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Electrodes,Oxidation,pH,Phosphates,Quantum mechanics Get e-Alerts

Global and target analysis of time-resolved spectra

2004-06-11

Ivo H. M. van Stokkum , Delmar S. Larsen , Rienk van Grondelle

Primary and secondary mechanisms of action of visible to near-IR radiation on cells

1999-03-01

Т. Й. Кару

Requirement of Rigid-Body Motion of Transmembrane Helices for Light Activation of Rhodopsin

1996-11-01

David Farrens , Christian Altenbach , Ke Yang +2 more

Conformational changes are thought to underlie the activation of heterotrimeric GTP-binding protein (G protein)—coupled receptors. Such changes in rhodopsin were explored by construction of double cysteine mutants, each containing one … Conformational changes are thought to underlie the activation of heterotrimeric GTP-binding protein (G protein)—coupled receptors. Such changes in rhodopsin were explored by construction of double cysteine mutants, each containing one cysteine at the cytoplasmic end of helix C and one cysteine at various positions in the cytoplasmic end of helix F. Magnetic dipolar interactions between spin labels attached to these residues revealed their proximity, and changes in their interaction upon rhodopsin light activation suggested a rigid body movement of helices relative to one another. Disulfide cross-linking of the helices prevented activation of transducin, which suggests the importance of this movement for activation of rhodopsin.

Molecular Genetics of Human Color Vision: The Genes Encoding Blue, Green, and Red Pigments

1986-04-11

Jeremy Nathans , Darcy Thomas , David S. Hogness

Human color vision is based on three light-sensitive pigments. The isolation and sequencing of genomic and complementary DNA clones that encode the apoproteins of these three pigments are described. The … Human color vision is based on three light-sensitive pigments. The isolation and sequencing of genomic and complementary DNA clones that encode the apoproteins of these three pigments are described. The deduced amino acid sequences show 41 ± 1 percent identity with rhodopsin. The red and green pigments show 96 percent mutual identity but only 43 percent identity with the blue pigment. Green pigment genes vary in number among color-normal individuals and, together with a single red pigment gene, are proposed to reside in a head-to-tail tandem array within the X chromosome.

Neuron-type-specific signals for reward and punishment in the ventral tegmental area

2012-01-18

Jeremiah Y. Cohen , Sebastian Haesler , Linh Vong +2 more

Induction by cyclic GMP of cationic conductance in plasma membrane of retinal rod outer segment

1985-01-01

Evgeniy E. Fesenko , С. С. Колесников , A.L. Lyubarsky

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

2010-01-01

Brian Y. Chow , Xue Han , Allison S. Dobry +7 more

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Parvalbumin neurons and gamma rhythms enhance cortical circuit performance

2009-04-26

Vikaas S. Sohal , Feng Zhang , Ofer Yizhar +1 more

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Three-dimensional model of purple membrane obtained by electron microscopy

1975-09-01

Richard A. Henderson , P.N.T. Unwin

Optogenetics in Neural Systems

2011-07-01

Ofer Yizhar , Lief E. Fenno , Thomas J. Davidson +2 more

Independent optical excitation of distinct neural populations

2014-02-09

Nathan C Klapoetke , Yasunobu Murata , Sung Soo Kim +7 more

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Amygdala circuitry mediating reversible and bidirectional control of anxiety

2011-03-01

Kay M. Tye , Rohit Prakash , Sung‐Yon Kim +7 more

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Rhodopsin-like Protein from the Purple Membrane of Halobacterium halobium

1971-09-01

Dieter Oesterhelt , Walther Stoeckenius

Neocortical excitation/inhibition balance in information processing and social dysfunction

2011-07-26

Ofer Yizhar , Lief E. Fenno , Matthias Prigge +7 more

The effect of sodium ions on the electrical activity of the giant axon of the squid

1949-03-01

A. L. Hodgkin , B. Katz

Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to … Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.

ROS signaling: the new wave?

2011-04-15

Ron Mittler , Sandy Vanderauwera , Nobuhiro Suzuki +6 more

A robust and high-throughput Cre reporting and characterization system for the whole mouse brain

2009-12-20

Linda Madisen , Theresa A. Zwingman , Susan M. Sunkin +7 more

Organization of the retina of the mudpuppy, Necturus maculosus. II. Intracellular recording.

1969-05-01

F. Werblin , John E. Dowling

Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy

1990-06-01

Richard A. Henderson , J.M. Baldwin , T.A. Ceska +3 more

Multimodal fast optical interrogation of neural circuitry

2007-04-01

Feng Zhang , Liping Wang , Martin Brauner +7 more

Structure of bacteriorhodopsin at 1.55 Å resolution

1999-08-01

Hartmut Luecke , Brigitte Schobert , Hans-Thomas Richter +2 more

Local anesthetics: hydrophilic and hydrophobic pathways for the drug-receptor reaction.

1977-04-01

Bertil Hille

The properties of Na channels of the node of Ranvier are altered by neutral, amine, and quaternary local anesthetic compounds. The kinetics of the Na currents are governed by a … The properties of Na channels of the node of Ranvier are altered by neutral, amine, and quaternary local anesthetic compounds. The kinetics of the Na currents are governed by a composite of voltage- and time-dependent gating processes with voltage- and time-dependent block of channels by drug. Conventional measurements of steady-state sodium inactivation by use of 50-ms prepulses show a large negative voltage shift of the inactivation curve with neutral benzocaine and with some ionizable amines like lidocaine and tetracaine, but no shift is seen with quaternary OX-572. However, when the experiment is done with repetitive application of a prepulse-testpulse waveform, a shift with the quaternary cations (applied internally) is seen as well. 1-min hyperpolarizations of lidocaine- or tetracaine-treated fibers restore two to four times as many channels to the conducting pool as 50-ms hyperpolarizations. Raising the external Ca++ concentration also has a strong unblocking effect. These manipulations do not relieve block in fibers treated with internal quaternary drugs. The results are interpreted in terms of a single receptor in Na channels for the different drug types. Lipid-soluble drug forms are thought to come and go from the receptor via a hydrophobic region of the membrane, while charged and less lipid-soluble forms pass via a hydrophilic region (the inner channel mouth). The hydrophilic pathway is open only when the gates of the channel are open. Any drug form in the channel increases the probability of closing the inactivation gate which, in effect, is equivalent to a negative shift of the voltage dependence of inactivation.

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What the Frog's Eye Tells the Frog's Brain

1959-11-01

Jerome Y. Lettvin , Humberto R. Maturana , Warren S. McCulloch +1 more

In this paper, we analyze the activity of single fibers in the optic nerve of a frog. Our method is to find what sort of stimulus causes the largest activity … In this paper, we analyze the activity of single fibers in the optic nerve of a frog. Our method is to find what sort of stimulus causes the largest activity in one nerve fiber and then what is the exciting aspect of that stimulus such that variations in everything else cause little change in the response. It has been known for the past 20 years that each fiber is connected not to a few rods and cones in the retina but to very many over a fair area. Our results show that for the most part within that area, it is not the light intensity itself but rather the pattern of local variation of intensity that is the exciting factor. There are four types of fibers, each type concerned with a different sort of pattern. Each type is uniformly distributed over the whole retina of the frog. Thus, there are four distinct parallel distributed channels whereby the frog's eye informs his brain about the visual image in terms of local pattern independent of average illumination. We describe the patterns and show the functional and anatomical separation of the channels. This work has been done on the frog, and our interpretation applies only to the frog.

CRITICAL PERIOD REGULATION

2004-06-24

Takao K. Hensch

Neuronal circuits are shaped by experience during critical periods of early postnatal life. The ability to control the timing, duration, and closure of these heightened levels of brain plasticity has … Neuronal circuits are shaped by experience during critical periods of early postnatal life. The ability to control the timing, duration, and closure of these heightened levels of brain plasticity has recently become experimentally accessible, especially in the developing visual system. This review summarizes our current understanding of known critical periods across several systems and species. It delineates a number of emerging principles: functional competition between inputs, role for electrical activity, structural consolidation, regulation by experience (not simply age), special role for inhibition in the CNS, potent influence of attention and motivation, unique timing and duration, as well as use of distinct molecular mechanisms across brain regions and the potential for reactivation in adulthood. A deeper understanding of critical periods will open new avenues to "nurture the brain"-from international efforts to link brain science and education to improving recovery from injury and devising new strategies for therapy and lifelong learning.

Deviations from michaelis-menten behaviour of plant glutamate dehydrogenase with ammonium as variable substrate

1980-01-01

Edwin Pahlich , Chr. Gerlitz

A [2]Catenane-Based Solid State Electronically Reconfigurable Switch

2000-08-18

C. Patrick Collier , Gunter Mattersteig , Eric W. M. Wong +6 more

A solid state, electronically addressable, bistable [2]catenane-based molecular switching device was fabricated from a single monolayer of the [2]catenane, anchored with phospholipid counterions, and sandwiched between an n-type polycrystalline silicon … A solid state, electronically addressable, bistable [2]catenane-based molecular switching device was fabricated from a single monolayer of the [2]catenane, anchored with phospholipid counterions, and sandwiched between an n-type polycrystalline silicon bottom electrode and a metallic top electrode. The device exhibits hysteretic (bistable) current/voltage characteristics. The switch is opened at +2 volts, closed at -2 volts, and read at approximately 0.1 volt and may be recycled many times under ambient conditions. A mechanochemical mechanism for the action of the switch is presented and shown to be consistent with temperature-dependent measurements of the device operation.

The Synaptic Organization of the Brain

2004-01-08

Abstract Synapses are the contact sites that enable neurons to form connections between each other in order to transmit and process neural information. Synaptic organization is concerned with the principles … Abstract Synapses are the contact sites that enable neurons to form connections between each other in order to transmit and process neural information. Synaptic organization is concerned with the principles by which neurons form circuits that mediate the specific functional operations of different brain regions. One of the aims of this book is to show that the study of synaptic organization—in its full multidisciplinary, multilevel, and theoretical dimension—is a powerful means of integrating brain information to give clear insights into the neural basis of behavior. This book, which has been revised in this the fifth edition, details local circuits in the different regions of the brain. The results of the mouse and human genome projects are incorporated. Also the book contains support from neuroscience databases. Among the new advances covered are 2-photon confocal laser microscopy of dendrites and dendritic spines, biochemical analyses, and dual patch and multielectrode recordings, applied together with an increasing range of behavioral and gene-targeting methods.

Crystal Structure of Rhodopsin: A G Protein-Coupled Receptor

2000-08-04

Krzysztof Palczewski , Takashi Kumasaka , Tetsuya Hori +7 more

Heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors (GPCRs) respond to a variety of different external stimuli and activate G proteins. GPCRs share many structural features, including a bundle of seven … Heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors (GPCRs) respond to a variety of different external stimuli and activate G proteins. GPCRs share many structural features, including a bundle of seven transmembrane alpha helices connected by six loops of varying lengths. We determined the structure of rhodopsin from diffraction data extending to 2.8 angstroms resolution. The highly organized structure in the extracellular region, including a conserved disulfide bridge, forms a basis for the arrangement of the seven-helix transmembrane motif. The ground-state chromophore, 11-cis-retinal, holds the transmembrane region of the protein in the inactive conformation. Interactions of the chromophore with a cluster of key residues determine the wavelength of the maximum absorption. Changes in these interactions among rhodopsins facilitate color discrimination. Identification of a set of residues that mediate interactions between the transmembrane helices and the cytoplasmic surface, where G-protein activation occurs, also suggests a possible structural change upon photoactivation.

Capsaicin: cellular targets, mechanisms of action, and selectivity for thin sensory neurons.

1991-06-01

Peter Holzer

Optogenetic stimulation of a hippocampal engram activates fear memory recall

2012-03-22

Xu Liu , Steve Ramirez , Petti T. Pang +4 more

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The Development and Application of Optogenetics

2011-03-02

Lief E. Fenno , Ofer Yizhar , Karl Deisseroth

Genetically encoded, single-component optogenetic tools have made a significant impact on neuroscience, enabling specific modulation of selected cells within complex neural tissues. As the optogenetic toolbox contents grow and diversify, … Genetically encoded, single-component optogenetic tools have made a significant impact on neuroscience, enabling specific modulation of selected cells within complex neural tissues. As the optogenetic toolbox contents grow and diversify, the opportunities for neuroscience continue to grow. In this review, we outline the development of currently available single-component optogenetic tools and summarize the application of various optogenetic tools in diverse model organisms.

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Channelrhodopsin-2, a directly light-gated cation-selective membrane channel

2003-11-13

Georg Nagel , Tanjef Szellas , Wolfram Huhn +6 more

Microbial-type rhodopsins are found in archaea, prokaryotes, and eukaryotes. Some of them represent membrane ion transport proteins such as bacteriorhodopsin, a light-driven proton pump, or channelrhodopsin-1 (ChR1), a recently identified … Microbial-type rhodopsins are found in archaea, prokaryotes, and eukaryotes. Some of them represent membrane ion transport proteins such as bacteriorhodopsin, a light-driven proton pump, or channelrhodopsin-1 (ChR1), a recently identified light-gated proton channel from the green alga Chlamydomonas reinhardtii . ChR1 and ChR2, a related microbial-type rhodopsin from C. reinhardtii , were shown to be involved in generation of photocurrents of this green alga. We demonstrate by functional expression, both in oocytes of Xenopus laevis and mammalian cells, that ChR2 is a directly light-switched cation-selective ion channel. This channel opens rapidly after absorption of a photon to generate a large permeability for monovalent and divalent cations. ChR2 desensitizes in continuous light to a smaller steady-state conductance. Recovery from desensitization is accelerated by extracellular H + and negative membrane potential, whereas closing of the ChR2 ion channel is decelerated by intracellular H + . ChR2 is expressed mainly in C. reinhardtii under low-light conditions, suggesting involvement in photoreception in dark-adapted cells. The predicted seven-transmembrane α helices of ChR2 are characteristic for G protein-coupled receptors but reflect a different motif for a cation-selective ion channel. Finally, we demonstrate that ChR2 may be used to depolarize small or large cells, simply by illumination.

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Millisecond-timescale, genetically targeted optical control of neural activity

2005-08-14

Edward S. Boyden , Feng Zhang , Ernst Bamberg +2 more

Bacterial Rhodopsin: Evidence for a New Type of Phototrophy in the Sea

2000-09-15

Oded Béjà , L. Aravind , Eugene V. Koonin +7 more

Extremely halophilic archaea contain retinal-binding integral membrane proteins called bacteriorhodopsins that function as light-driven proton pumps. So far, bacteriorhodopsins capable of generating a chemiosmotic membrane potential in response to light … Extremely halophilic archaea contain retinal-binding integral membrane proteins called bacteriorhodopsins that function as light-driven proton pumps. So far, bacteriorhodopsins capable of generating a chemiosmotic membrane potential in response to light have been demonstrated only in halophilic archaea. We describe here a type of rhodopsin derived from bacteria that was discovered through genomic analyses of naturally occuring marine bacterioplankton. The bacterial rhodopsin was encoded in the genome of an uncultivated γ-proteobacterium and shared highest amino acid sequence similarity with archaeal rhodopsins. The protein was functionally expressed in Escherichia coli and bound retinal to form an active, light-driven proton pump. The new rhodopsin exhibited a photochemical reaction cycle with intermediates and kinetics characteristic of archaeal proton-pumping rhodopsins. Our results demonstrate that archaeal-like rhodopsins are broadly distributed among different taxa, including members of the domain Bacteria . Our data also indicate that a previously unsuspected mode of bacterially mediated light-driven energy generation may commonly occur in oceanic surface waters worldwide.

Cell diversity and network dynamics in photosensitive human brain organoids

2017-04-25

Giorgia Quadrato , Tuan Nguyen , Evan Z. Macosko +7 more

Chemotaxis in Bacteria

1966-08-12

Julius Adler

Motile Escherichia coli placed at one end of a capillary tube containing an energy source and oxygen migrate out into the tube in one or two bands, which are clearly … Motile Escherichia coli placed at one end of a capillary tube containing an energy source and oxygen migrate out into the tube in one or two bands, which are clearly visible to the naked eye and can also be demonstrated by photography, microscopy, and densitometry and by assaying for bacteria throughout the tube. The formation of two bands is not due to heterogeneity among the bacteria, since the bacteria in each band, when reused, will form two more bands. If an anaerobically utilizable energy source such as galactose is present in excess over the oxygen, the first band consumes all the oxygen and a part of the sugar and the second band uses the residual sugar anaerobically. On the other hand, if oxygen is present in excess over the sugar, the first band oxidizes all the sugar and leaves behind unused oxygen, and the second band uses up the residual oxygen to oxidize an endogenous energy source. The essence of the matter is that the bacteria create a gradient of oxygen or of an energy source, and then they move preferentially in the direction of the higher concentration of the chemical. As a consequence, bands of bacteria (or rings of bacteria in the case of agar plates) form and move out. These results show that E. coli is chemotactic toward oxygen and energy sources such as galactose, glucose, aspartic acid, threonine, or serine. The full repertoire of chemotactic responses by E. coli is no doubt greater than this, and a more complete list remains to be compiled. The studies reported here demonstrate that chemotaxis allows bacteria to find that environment which provides them with the greatest supply of energy. It is clearly an advantage for bacteria to be able to carry out chemotaxis, since by this means they can avoid unfavorable conditions and seek optimum surroundings. Finally, it is necessary to acknowledge the pioneering work of Englemann, Pfeffer, and the other late-19thcentury biologists who discovered chemotaxis in bacteria, and to point out that the studies reported here fully confirm the earlier reports of Beijerinck (4) and Sherris and his collaborators (5,6) on a band of bacteria chemotactic toward oxygen. By using a chemically defined medium instead of a complex broth, it has been possible to study this band more closely and to demonstrate in addition the occurrence of a second band of bacteria chemotactic toward an energy source. Beijerinck (4) did, in fact, sometimes observe a second band, but he did not offer an explanation for it.

Optogenetics

2010-12-20

Karl Deisseroth

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The Chlamydomonas Sourcebook

1989-01-01

Elizabeth H. Harris

Professor Emil Paleček: seven decades with electrodes and biomolecules at the Institute of Biophysics of the CAS

2025-06-25

Miroslav Fojta , Jan Paleček | European Biophysics Journal

Eureka! The brain science behind lightbulb moments

2025-06-25

Humberto Basilio | Nature

Visible-Light-Responsive Organic Synaptic Devices Based on Rhodamine B-Doped Source-Gated Transistors

2025-06-23

Yonghee Kim , Chang Min Lee , Eun Kwang Lee | ACS Applied Materials & Interfaces

Organic artificial synaptic devices replicating biological neurons in sensing, transporting, and storing information with energy efficiency are gaining attention to next-generation computing circuits. Previous studies report that organic electrochemical transistors … Organic artificial synaptic devices replicating biological neurons in sensing, transporting, and storing information with energy efficiency are gaining attention to next-generation computing circuits. Previous studies report that organic electrochemical transistors (OECTs) with polymeric semiconductors show inconsistent structure-synaptic properties. Also, OECTs with small molecular semiconductors demonstrate performance degradation by hydrophilic ions. This study develops low-power and high-performance organic photoneuromorphic devices based on n-type small molecular semiconductor of BPE-PTCDI doped with Rhodamine B (RhoB, an organic cationic dye) and a source-gated transistor (SGT) structure. Organic SGTs (OSGTs) with RhoB exhibit a high photoresponsivity of 2.07 × 103 A W-1 induced by charge transfer from RhoB in visible light and a low-power operation induced by the Schottky barrier. OSGTs exhibit 3.70 × 103 times higher photoresponsivity per drive power (4.92 × 108 A W-2) than typical field-effect transistors. The OSGTs achieve synaptic properties at 1 V electrical pulsed stimulation by thinning the Schottky barrier of the SGT, high paired-pulse facilitation per driving power (3.20 × 1011% W-1), and pulsed photo-synaptic properties using hole trap by RhoB doping. These findings suggest potential technology for low-power auxiliary electronics for glaucoma patients and light trauma treatment and thus contribute to improving the quality of human life.

Projection-Specific Intersectional Optogenetics for Precise Excitation and Inhibition in the Marmoset Brain

2025-06-22

Luke Shaw , Krishnan Padmanabhan , Amy Bucklaew +2 more | bioRxiv (Cold Spring Harbor Laboratory)

The primate cerebral cortex relies on long-range connections to integrate information between functionally specialized areas. Investigating these processes requires tools that can selectively modulate specific projection pathways. While cell-class-specific optogenetics … The primate cerebral cortex relies on long-range connections to integrate information between functionally specialized areas. Investigating these processes requires tools that can selectively modulate specific projection pathways. While cell-class-specific optogenetics can modulate local circuits, these approaches often lack pathway specificity. Projection-specific optogenetics offers greater precision, especially in primates, where cortical areas are spatially and functionally well-separated. To address challenges in translating this approach from rodents to primates, we developed a mouse-to-marmoset pipeline. We first validated that optogenetic targeting of inhibitory neurons (AAV9-Dlx-ChR2) effectively silenced local cortical areas in marmosets. We then tested selective excitation and inhibition of defined projection pathways. By intersecting retrogradely delivered Cre-recombinase (AAVretro-Cre) with locally injected Cre-dependent opsins (AAV8-FLEx-ChR2 or Jaws), we achieved efficient, direction-specific labeling of both callosal and longitudinal projections. This intersectional strategy enabled precise excitatory and inhibitory control of cortical activity using distinct light wavelengths, advancing projection-specific optogenetics for investigating primate brain circuit function.

Ultrastructural analysis of synapses after induction of spike-timing-dependent plasticity

2025-06-21

Rui Wang , Michaela Schweizer , Margarita Anisimova +2 more | bioRxiv (Cold Spring Harbor Laboratory)

Repeated sequential activation of connected neurons causes lasting changes in synaptic strength, a process known as spike-timing-dependent plasticity (STDP). Recently, sequential spike patterns have been induced without electrodes, using two … Repeated sequential activation of connected neurons causes lasting changes in synaptic strength, a process known as spike-timing-dependent plasticity (STDP). Recently, sequential spike patterns have been induced without electrodes, using two spectrally separated channelrhodopsins. However, due to the difficulty of labeling and localizing the few connecting synapses between the stimulated pre and postsynaptic neurons (~1-5 per neuron pair), ultrastructural analysis after STDP has not been reported. Here, we optogenetically induce STDP at CA3-CA1 hippocampal synapses and identify stimulated boutons and spines in CA1 using transmission electron microscopy (TEM). Presynaptic CA3 neurons express vesicle-targeted horseradish peroxidase, cre recombinase and cre-dependent ChrimsonR, a red light activatable channelrhodopsin. Postsynaptic neurons express violet light activatable CheRiff and dAPEX2, an enhanced ascorbate peroxidase. In transmission electron microscopy, presynaptic boutons and postsynaptic spines are readily identifiable with well-preserved ultrastructural features. Our labeling strategy allows ultrastructural analysis of optogenetically manipulated neurons and their synapses.

Algal Optics

2025-06-21

Raymond E. Goldstein , Sumit Kumar Birwa , Ming Yang | bioRxiv (Cold Spring Harbor Laboratory)

Nearly a decade ago it was discovered that the spherical cell body of the alga Chlamydomonas reinhardtii can act as a lens to concentrate incoming light onto the cell's membrane-bound … Nearly a decade ago it was discovered that the spherical cell body of the alga Chlamydomonas reinhardtii can act as a lens to concentrate incoming light onto the cell's membrane-bound photoreceptor and thereby affect phototaxis. Since many nearly transparent cells in marine environments have complex, often non-axisymmetric shapes, this observation raises fundamental, yet little-explored questions in biological optics about light refraction by the bodies of microorganisms. There are two distinct contexts for such questions: the absorption problem for incoming light, typified by photosynthetic activity taking place in the chloroplasts of green algae, and the emission problem for outgoing light, where the paradigm is bioluminescence emitted from scintillons within dinoflagellates. Here we examine both of these aspects of ``algal optics" in the special case where the absorption or emission is localized in structures that are small relative to the overall organism size, taking into account both refraction and reflections at the cell-water boundary. Analytical and numerical results are developed for the distribution of light intensities inside and outside the body, and we establish certain duality relationships that connect the incoming and outgoing problems. For strongly non-spherical shapes we find lensing effects that may have implications for photosynthetic activity and for the angular distribution of light emitted during bioluminescent flashes.

A Constructive Study Based on Gloeobacter Rhodopsin to Explore the Origin of Extreme Redshift and Nontypical Isomerization of Bestrhodopsin

2025-06-20

Takashi Nagata , Yuma Kawasaki , Masae Konno +1 more | The Journal of Physical Chemistry Letters

Bestrhodopsins are recently discovered microbial rhodopsins comprising one or two photosensitive rhodopsin domains and an ion channel. Their rhodopsin domains exhibit extremely red-shifted absorption spectra and a nontypical all-trans-to-11-cis photoisomerization … Bestrhodopsins are recently discovered microbial rhodopsins comprising one or two photosensitive rhodopsin domains and an ion channel. Their rhodopsin domains exhibit extremely red-shifted absorption spectra and a nontypical all-trans-to-11-cis photoisomerization of the retinal chromophore. To determine the origin of these characteristics, we reconstituted a bestrhodopsin-like retinal-binding pocket in a prototypical microbial rhodopsin, Gloeobacter rhodopsin (GR). A triple mutation, D121E/T125D/A256M, in GR induced a 70-nm redshift of its absorption maximum and a pH-dependent spectral shift mirroring Tara-RRB, the best-characterized bestrhodopsin. The D121E/T125D/A256M substitutions also changed the isomerization position on the retinal chromophore from the typical C13=C14 to the C9=C10 bond, whereas an additional mutation, V126A, was found to be critical for efficient photoreaction. Thus, the present study identified four amino acid residues from bestrhodopsin that partially confer unique bestrhodopsin-like spectroscopic and photochemical properties on GR, providing insights into the mechanisms determining the photoisomerization pattern among rhodopsins.

Effects of taurine, brimonidine and betaxolol on oscillation modulation and stimulation efficiency in degenerated rd10 mouse retinas

2025-06-20

Kim Schaffrath , Claudia Ingensiep , Frank Müller +2 more | Scientific Reports

Abstract The rd10 mouse is a widely used model for degenerative retinal diseases such as retinitis pigmentosa (RP). Its retina shows rhythmic spontaneous activity at a frequency of three to … Abstract The rd10 mouse is a widely used model for degenerative retinal diseases such as retinitis pigmentosa (RP). Its retina shows rhythmic spontaneous activity at a frequency of three to seven Hz, and the retinal ganglion cells (RGCs) are less electrically excitable. We hypothesize that the electrical excitability can be improved by suppressing the oscillations using the neuroprotective drugs 2-aminoethanesulphonic acid (taurine), brimonidine and betaxolol. These are involved in calcium homeostasis and may play a crucial role in neuroprotection and excitotoxicity by preventing Ca 2+ overload. Spontaneous activity and responses to electrical stimulation of isolated retinas from 3- to 4-month-old rd10 mice were recorded using multielectrode arrays. At defined times, the neuroprotectants were repeatedly added to the medium according to a standardized protocol to analyze the reproducibility and reversibility of their effects. Taurine and betaxolol significantly reduced oscillations and bursting behavior and ameliorated electrical efficiency. Brimonidine only reduced the frequency of oscillations. The effects on oscillation, spontaneous firing frequency, bursting behavior and stimulation efficiency were reproducible and reversible. The drugs tested appear to be promising therapeutic candidates for improving the residual function of RGCs. They will be further investigated and combined with other RP treatments, such as retinal prostheses, in the future.

A New Optogenetic Tool to Investigate the Role of Dopamine Signaling in the Basal Ganglia

2025-06-18

Gabriel S. Rocha , Marco Aurélio M. Freire | Journal of Neuroscience

Cryo-EM structure of a blue-shifted channelrhodopsin from Klebsormidium nitens

2025-06-18

Y. Wang , Koki Natsume , Tatsuki Tanaka +7 more | Nature Communications

Reciprocal interaction between cortical SST and PV interneurons in top–down regulation of retinothalamic refinement

2025-06-18

Qiufen Jiang , Sherry Jingjing Wu , Gord Fishell +1 more | Proceedings of the National Academy of Sciences

Refinement of thalamic circuits is crucial for the proper maturation of sensory circuits. In the visual system, this process is regulated by corticothalamic feedback during the experience-dependent phase of development. … Refinement of thalamic circuits is crucial for the proper maturation of sensory circuits. In the visual system, this process is regulated by corticothalamic feedback during the experience-dependent phase of development. Yet the cortical circuits modulating this feedback remain elusive. Here, we demonstrate opposing roles for cortical somatostatin (SST) and parvalbumin (PV) interneurons in shaping retinogeniculate connectivity during the thalamic sensitive period (P20-30). Early in the refinement process, SST interneurons promote the strengthening and pruning of retinal inputs in the thalamus, as evidenced by disrupted synaptic refinement following their ablation. In contrast, PV interneurons, which mature later, act as a brake on this refinement, with their ablation leading to enhanced pruning of retinogeniculate connections. Notably, manipulating the relative balance between these inhibitory circuits can regulate sensory deprivation-induced retinogeniculate remodeling. Taken together, our findings show that cortical SST and PV interneuron circuits drive experience-dependent reciprocal antagonism that gates cortical feedback regulation of feedforward thalamic refinement.

Distinct Protochromic Mechanisms Driving Green/Red Absorption in Phycocyanobilin-Binding Proteins

2025-06-18

Tomoyasu Noji , Keisuke Saito , Hiroshi Ishikita | Biochemistry

RcaE, a phycocyanobilin (PCB)-binding protein, undergoes a reversible structural conversion, shifting light absorption between red (Pr-state) and green (Pg-state). Using a quantum mechanical/molecular mechanical approach combined with a linear Poisson-Boltzmann … RcaE, a phycocyanobilin (PCB)-binding protein, undergoes a reversible structural conversion, shifting light absorption between red (Pr-state) and green (Pg-state). Using a quantum mechanical/molecular mechanical approach combined with a linear Poisson-Boltzmann equation, we reveal the molecular mechanisms underlying this 130 nm blue shift. The experimentally measured Pg-RcaE absorption wavelength is reproduced only when ring B of PCB is deprotonated. While the low-dielectric chromophore environment remains unchanged during the Pr-to-Pg conversion, Lys261 deprotonation in Pg-RcaE is driven by the loss of key electrostatic interactions, specifically the loss of salt bridges with PCB propionic groups. Unlike Slr1393g3, where a 110 nm blue shift arises from PCB conformational changes, RcaE employs a distinct mechanism, leveraging proton-mediated electrostatic changes while maintaining a low-dielectric environment. This Pr-to-Pg conversion is triggered by ring B deprotonation via Glu217, facilitated by water molecules forming a Grotthuss-like proton transfer pathway. This unique strategy achieves efficient photochromic switching and a large spectral shift without PCB structural rearrangements.

Widespread Changes in the Immunoreactivity of Bioactive Peptide T14 After Manipulating the Activity of Cortical Projection Neurons

2025-06-17

Augustė Vadišiūtė , Sara Garcia‐Ratés , Clive W. Coen +2 more | International Journal of Molecular Sciences

Previous studies have suggested that T14, a 14-amino-acid peptide derived from acetylcholinesterase (AChE), functions as an activity-dependent signalling molecule with key roles in brain development, and its dysregulation has been … Previous studies have suggested that T14, a 14-amino-acid peptide derived from acetylcholinesterase (AChE), functions as an activity-dependent signalling molecule with key roles in brain development, and its dysregulation has been linked to neurodegeneration in Alzheimer's disease. In this study, we examined the distribution of T14 under normal developmental conditions in the mouse forebrain, motor cortex (M1), striatum (STR), and substantia nigra (SN). T14 immunoreactivity declined from E16 to E17 and further decreased by P0, then peaked at P7 during early postnatal development before declining again by adulthood at P70. Lower T14 immunoreactivity in samples processed without Triton indicated that T14 is primarily localised intracellularly. To explore the relationship between T14 expression and neuronal activity, we used mouse models with chronic silencing (Rbp4Cre-Snap25), acute silencing (Rbp4Cre-hM4Di), and acute activation (Rbp4Cre-hM3D1). Chronic silencing altered the location and size of intracellular T14-immunoreactive particles in adult brains, while acute silencing had no observable effect. In contrast, acute activation increased T14+ density in the STR, modified T14 puncta size near Rbp4Cre cell bodies in M1 layer 5 and their projections to the STR, and enhanced co-localisation of T14 with presynaptic terminals in the SN.

Non-Gaussianity of neurotransmitters co-released from mammalian adrenal chromaffin cells

2025-06-17

Ziheng Xu , Jingxiao Huo , Yanmei Kang +1 more | Cognitive Neurodynamics

Microstate in rats EEG: a proof of concept study

2025-06-17

Václava Piorecká , Čestmír Vejmola , Petra Pešková +5 more | bioRxiv (Cold Spring Harbor Laboratory)

The electroencephalogram (EEG) reflecting brain activity can be characterized through brief periods of stable neural activity patterns that recur over time and are referred to as microstates. Microstates are related … The electroencephalogram (EEG) reflecting brain activity can be characterized through brief periods of stable neural activity patterns that recur over time and are referred to as microstates. Microstates are related to a range of cognitive processes, and their analysis has become an increasingly popular tool for studying human brain function. While microstates have been extensively studied in humans, their presence and characteristics in animal models have yet to be as thoroughly investigated. This study aims to address this gap by detecting and characterizing microstates in EEGs of rats collected using a superficial electrode system corresponding to homological areas of the human 10-20 system. Specifically, we demonstrate the presence of microstates in rats EEG; those can be captured by the same metrics as in humans. We define these microstates, describe them through topology and parameters, and identify the EEG frequency bands and intracranial sources that predominantly determine microstate topography. These findings have important implications for the use of microstates as a preclinical tool for investigating brain functions, detecting new biomarkers of brain diseases, and translating this knowledge to humans.

Two-color laser control of photocurrent and high harmonics in graphene

2025-06-17

NULL AUTHOR_ID | Physical review. B./Physical review. B

Evidence for the acquisition of a proteorhodopsin-like rhodopsin by a chrysophyte-infecting giant virus

2025-06-17

Petra Byl , Christopher R. Schvarcz , Julie Thomy +6 more | bioRxiv (Cold Spring Harbor Laboratory)

Abstract Chrysophytes are widespread nanoflagellate protists in aquatic ecosystems with diverse trophic strategies ranging from phototrophy to heterotrophy. Here, we report the first isolation of a chrysophyte-infecting virus, Chrysophyceae clade-H … Abstract Chrysophytes are widespread nanoflagellate protists in aquatic ecosystems with diverse trophic strategies ranging from phototrophy to heterotrophy. Here, we report the first isolation of a chrysophyte-infecting virus, Chrysophyceae clade-H virus SA1, referred to hereafter as ChrysoHV, on a sympatric mixotrophic chrysophyte. Both host and virus were isolated from surface waters in the subtropical North Pacific. The ChrysoHV capsid (291 ± 42 nm diameter) is associated with a loose, sac-like membrane that extends its effective diameter (716 ± 115 nm), and presents a long, thin tail extending 1,202 (± 243) nm. This unique morphology has not been previously observed in other isolates or environmental surveys. The sequenced, assembled genome is 1.19 Mbp, and phylogenetic analysis places ChrysoHV as the third cultivated member of the Aliimimivirinae subfamily in the Mimiviridae family of giant viruses. ChrysoHV is the first cultivated member of Aliimimivirinae to encode a rhodopsin, which has high phylogenetic relatedness and structural similarity to proteorhodopsin sequences retrieved from the same subtropical research site. The most closely related sequences from cultivated organisms derive from bacteria in the genus Pelagibacter . This suggests that ChrysoHV acquired the proteorhodopsin-like protein through lateral gene transfer from the chrysophyte’s bacterial prey.

Autonomous Dynamic Control of Crown Ether Cargo Release from [2]Rotaxane Carriers in a Piperidine Oscillator

2025-06-17

Kamil D. Petryczkiewicz , Johanan Kootstra , Maëlle Le Cacheux +4 more | Journal of the American Chemical Society

Chemical oscillations play a fundamental role in biological systems, yet their synthetic counterparts remain challenging to implement with functional outputs. Here, we report a piperidine-based chemical oscillator that autonomously drives … Chemical oscillations play a fundamental role in biological systems, yet their synthetic counterparts remain challenging to implement with functional outputs. Here, we report a piperidine-based chemical oscillator that autonomously drives periodic cleavage of a [2]rotaxane carrier, leading to controlled cargo release. The system operates through self-sustained oscillations, triggering rotaxane cleavage and the release of a crown ether cargo. Crown ethers were selected for their reactivity distinct from piperidine, while Fmoc-protected benzylamine rotaxane structures allowed for straightforward carrier modification. For all tested carriers, a piperidine pulse is present and occurs simultaneously with carrier cleavage, yielding up to 95% cargo release. Under flow conditions, periodic cargo release was sustained without extensive reoptimization, demonstrating the robustness of the system. Additionally, by adjusting space velocity, trigger concentration, and inhibitor levels, the oscillation period was varied by up to 2.5 h, with cargo release amplitude changing more than 3-fold. This work demonstrates the potential of catalytic oscillators to regulate downstream processes, paving the way toward construction of complex dynamic chemical systems.

Minimally invasive upconversion optogenetics for Parkinson’s disease treatment

2025-06-17

X Li , Xiaoran Wang , Ting Zhou +5 more | Biomaterials

A Photophosphorylation Nanobot for Restoring Anabolism of Myocardial Injury

2025-06-16

Yue Li , Ying Chen , Yingjie Wu +3 more | Journal of the American Chemical Society

Myocardial injury poses a significant obstacle due to the limited capacity for self-repair or dysfunction in ATP generation, leading to mortality risks worldwide. Here, we present a photophosphorylation nanobot capable … Myocardial injury poses a significant obstacle due to the limited capacity for self-repair or dysfunction in ATP generation, leading to mortality risks worldwide. Here, we present a photophosphorylation nanobot capable of actively targeting therapeutics for myocardial injury in zebrafish larvae by accelerating the supply of ATP. Janus photophosphorylation nanobots are created through mechanical extrusion-assisted phase separation, forming asymmetric FoF1-ATPases embedded in a proteoliposome. Light-induced synergistic rotation of FoF1-ATPase significantly enhances the effective translational diffusion of nanobots by 89%, accompanying the photophosphorylation for generating ATP. The photophosphorylation nanobots display cell-like adaptive positive phototaxis motion and a phototactic swarm. These programmable phototactic nanobots can actively target the heart, improve intracellular ATP concentration to restore cellular metabolism, and finally repair myocardial injury. Such self-propelled and maneuverable nanobots that can actively modulate cellular energy metabolism in vivo hold considerable promise for advancing the targeted regulation of diseases associated with bioenergy metabolism in the future.

Selective octopaminergic tuning of mushroom body circuits during memory formation

2025-06-16

Ulrike S. Franke , Alexandra Großjohann , Samantha Aurich +6 more | bioRxiv (Cold Spring Harbor Laboratory)

The catecholamines octopamine and tyramine undoubtedly have a major impact on the life of an insect. A wide range of physiological processes and behaviours are regulated by these neurotransmitters/hormones. Octopamine … The catecholamines octopamine and tyramine undoubtedly have a major impact on the life of an insect. A wide range of physiological processes and behaviours are regulated by these neurotransmitters/hormones. Octopamine and tyramine act homologous to the adrenergic system of vertebrates, primarily adapting the organism to the given situation, by switching between the states of alertness and rest. Interestingly, higher brain functions like learning and memory are also regulated by octopamine and tyramine. About 30 years ago, initial work in Drosophila has demonstrated that dopaminergic neurons signal punishment, while octopaminergic neurons signal reward during olfactory associative learning and memory. In the meantime, however, it has become clear that distinct types of dopaminergic neurons convey both reward and punishment signals to the mushroom bodies, a central brain region responsible for the formation and storage of associative memories. Although some conflicting data remain, these findings challenge the previously established model of functional segregation and may limit the proposed role of octopamine neurons as teaching neurons during memory formation. We have therefore re-examined the role of octopamine in learning and memory in Drosophila larvae. Through a combination of Ca2+ imaging, anatomical studies and gain-of-function and loss-of-function behavioural approaches, we demonstrate that octopamine signalling plays a crucial role in larval learning by modulating dopaminergic neurons across distinct cell clusters to orchestrate memory processes.

Solvent-Dependent Ultrafast Photochemical Dynamics of N-Methyl Oxindole Overcrowded Alkene Molecular Motors

2025-06-15

C.S. Harris , Beatrice S. L. Collins , Andrew J. Orr‐Ewing | The Journal of Physical Chemistry A

Overcrowded alkenes are a class of rotational molecular motors that operate via alternating photochemical and thermal relaxation processes. Although the performances of various designs of molecular motors have been extensively … Overcrowded alkenes are a class of rotational molecular motors that operate via alternating photochemical and thermal relaxation processes. Although the performances of various designs of molecular motors have been extensively studied, in general, their photoinduced isomerization efficiencies remain low. Ultrafast time-resolved spectroscopy can explore the excited-state dynamics and investigate the photoisomerization mechanisms. Herein, we study a series of visible-light-activated overcrowded alkene motors with N-methyl oxindole functionality using transient absorption and time-resolved infrared (TRIR) spectroscopies. The motors are examined in cyclohexane, DMSO, and methanol to probe the solvent environmental effects on the photoisomerization, paying particular attention to polarity and viscosity. Four dynamical processes are identified: relaxation from the Franck-Condon region of the bright excited state to a region of different electronic character (<120 fs) that is not directly optically accessible from the ground state; prompt (0.5-4 ps) and indirect (4-14 ps) depopulation of this dark state via conical intersections with the ground state; and vibrational cooling of hot ground-state molecules (10-15 ps). The time scales for decay of the dark state are both solvent polarity and viscosity-dependent. In nonpolar cyclohexane solutions, only direct depopulation of the dark state is observed, but in the DMSO and methanol solutions, both prompt and indirect depopulation are identified. Greater solvent viscosity increases the average excited-state lifetimes of the dark states by inhibiting rotation of the alkene bond. Oscillations observed in the excited-state absorption bands are attributed to coherent vibrations of the excited-state wave packet. Density functional theory (DFT) calculations of the stable (P,P)-E and metastable (M,M)-Z diastereomer structures, optimized at the ωB97XD/6-31+G(d,p) level of theory and interpolated between the two geometries using internal coordinates, are used to approximate the geometrical change of the isomerization reaction in the excited state. For each interpolated structure, the vertical excitation energies are calculated using time-dependent DFT calculations at the same level of theory to track the adiabatic potential energy surfaces of the S0, S1, and S2 electronic states. This interpolation study shows that the excited-state dynamics are dictated by the S1 state, with no involvement of higher-lying singlet states. The poor quantum yield of isomerization is confirmed using the degree of ground-state bleach recovery of the carbonyl stretch in the recorded TRIR spectra, finding an upper estimate of the quantum yield for isomerization of the five molecular motors studied to range from 0.4-8.7%.

RubyACRs Enable Red-Shifted Optogenetic Inhibition in Freely Behaving Drosophila

2025-06-15

Daniel Bushey , Hiroshi Shiozaki , Yichun Shuai +5 more | bioRxiv (Cold Spring Harbor Laboratory)

Optogenetic neuronal activators with red-shifted excitation spectra, such as Chrimson, have significantly advanced Drosophila neuroscience. However, until recently, available optogenetic inhibitors required shorter activation wavelengths, which do not penetrate tissue … Optogenetic neuronal activators with red-shifted excitation spectra, such as Chrimson, have significantly advanced Drosophila neuroscience. However, until recently, available optogenetic inhibitors required shorter activation wavelengths, which do not penetrate tissue as effectively and are stronger visual stimuli to the animal, potentially confounding behavioral results. Here, we assess the efficacy of two newly identified anion-conducting channelrhodopsins with spectral sensitivities similar to Chrimson: A1ACR and HfACR (RubyACRs). Electrophysiology and functional imaging confirmed that RubyACRs effectively hyperpolarize neurons, with stronger and faster effects than the widely used inhibitor GtACR1. Activation of RubyACRs led to circuit-specific behavioral changes in three different neuronal groups. In glutamatergic motor neurons, activating RubyACRs suppressed adult locomotor activity. In PPL1-γ1pedc dopaminergic neurons, pairing odors with RubyACR activation during learning produced odor responses consistent with synaptic silencing. Finally, activation of RubyACRs in the pIP10 neuron suppressed pulse song during courtship. Together, these results demonstrate that RubyACRs are effective and reliable tools for neuronal inhibition in Drosophila, expanding the optogenetic toolkit for circuit dissection in freely behaving animals.

Entirely synthetic memory inception via dual optogenetic activation of sensory and dopaminergic neurons

2025-06-15

Tayfun Tumkaya , Xianyuan Zhang , Yishan Mai +2 more | bioRxiv (Cold Spring Harbor Laboratory)

Associative conditioning is a fundamental learning paradigm that links salient stimuli to appropriate behavior. The vinegar fly is an important memory model that can associate odors with rewarding or punishing … Associative conditioning is a fundamental learning paradigm that links salient stimuli to appropriate behavior. The vinegar fly is an important memory model that can associate odors with rewarding or punishing reinforcement stimuli via distinct sets of dopaminergic neurons. While much is known about learning, a crucial question remains: is the simple co-activation of sensory and neuromodulatory dopaminergic neurons sufficient to induce memory formation? To address this, we systematically replaced natural stimuli, namely odor-evoked activity, punishment, and reward signals, with optogenetic activation of corresponding neurons, both individually and in combination. In all cases, including a full-substitution paradigm where both olfactory activity and reinforcement dopamine signals were replaced, optogenetic activation successfully implanted synthetic memories. These findings provide a clear answer: simple coincident, rectangular-pulse sensory and neuromodulatory stimulation can instruct associative memory formation. We conclude that associative memory does not have strict requirements for temporal or ensemble activity patterns in olfactory or dopaminergic neurons that are specific to natural stimuli (e.g. odorants, sugar, or pain); rather, simple coincidence is an effective driver of memory inception. These findings open new avenues for manipulating and studying memory formation with all-optical control.

Protocol for closed-loop optogenetic manipulation of cortical activity following hippocampal sharp-wave ripples in freely behaving rats

2025-06-14

Hanna den Bakker , Jyh‐Jang Sun , M. Guyot +1 more | STAR Protocols

Hydrogen-Bonding-Dependent Water-Responsive Actuation of Bacillus subtilis Cell Walls

2025-06-13

S. O. Kim , Haozhen Wang , Darjan Podbevšek +2 more | Langmuir

Water-responsive (WR) materials can exert significant forces when they deform in response to changes in the relative humidity. Recent studies on biological WR materials have brought attention to the potential … Water-responsive (WR) materials can exert significant forces when they deform in response to changes in the relative humidity. Recent studies on biological WR materials have brought attention to the potential influence of nanoconfined water on high-energy WR actuation. Here, we investigated the effects of nanoconfined liquids on the WR actuation of Bacillus subtilis cell walls by introducing chaotropic or kosmotropic solutes, known for their impact on the H-bonding network and biomolecule stabilities in aqueous solutions. We discovered that cell walls treated with low-concentration kosmotropic solutes exhibited a significant increase in the WR actuation energy density, reaching 103.3 MJ m-3, surpassing that of existing actuators. However, higher concentrations of kosmotropic or chaotropic solutes led to decreased WR performance. These findings could be explained by the impact of the solutes on hydration forces and intermolecular interactions, which affect the ultimate WR pressure. This, in turn, provides a pathway toward achieving superior WR actuation performance and advancing the development of high-work-density actuator materials.

Instant noninvasive near-infrared deep brain stimulation using optoelectronic nanoparticles without genetic modification

2025-06-13

Shuang Jin , Jiazhi Li , Luyue Jiang +7 more | Science Advances

Noninvasive transcranial neuromodulation of deep brain regions is a longstanding goal in neuroscience. While optogenetics enables remote neural control, it is constrained by shallow tissue penetration of visible light and … Noninvasive transcranial neuromodulation of deep brain regions is a longstanding goal in neuroscience. While optogenetics enables remote neural control, it is constrained by shallow tissue penetration of visible light and delayed onset due to required opsin expression. Here, we introduce a neuromodulation technique using hybrid upconversion and photovoltaic (HUP) nanoparticles, which eliminates the need for genetic modification and affords near-infrared (NIR) activation of neurons in wild-type mice. This method converts deeply penetrating NIR light into localized electrical stimuli, enabling immediate and precise modulation in deep brain. In vitro patch-clamp experiments confirm neuronal activation upon HUP application. In vivo, we achieve remote NIR neuromodulation in the medial septum and ventral tegmental area 7 days postinjection, effectively modulating neuronal activity, suppressing seizures, and triggering dopamine release. This minimally invasive approach offers a versatile tool kit for investigating neural processes in mammals, with potential applications across diverse brain regions through customizable nanoparticle engineering.

New effect of stimulated Raman scattering laser induced by diffusion and its application in signal synchronisation transmission

2025-06-13

Ling Lü , Huixiu Li , Hongfeng Hou | Pramana

Flexible modeling of large-scale neural network stimulation: electrical and optical extensions to The Virtual Electrode Recording Tool for EXtracellular Potentials (VERTEX)

2025-06-13

Anne F. Pierce , Larry Shupe , Julien Bloch +2 more | Journal of Neuroscience Methods

Switchable client specificity in a dual functional chaperone coordinates light-harvesting complex biogenesis

2025-06-13

Alex Siegel , Gerard Kroon , Changqi Zhao +3 more | Science Advances

The proper assembly of light-harvesting complexes (LHCs) is critical for photosynthesis and requires the biogenesis of light-harvesting chlorophyll a , b -binding proteins (LHCPs) to be coordinated with chlorophyll (Chl) … The proper assembly of light-harvesting complexes (LHCs) is critical for photosynthesis and requires the biogenesis of light-harvesting chlorophyll a , b -binding proteins (LHCPs) to be coordinated with chlorophyll (Chl) biosynthesis. The mechanism underlying this coordination is not well understood. Here, we show that a conserved molecular chaperone, chloroplast signal recognition particle 43-kDa protein (cpSRP43), provides a molecular thermostat that helps maintain this coordination. cpSRP43 undergoes a conformational rearrangement between a well-folded closed state and a partially disordered open state. Closed cpSRP43 is dedicated to the biogenesis of LHCPs, whereas open cpSRP43 protects multiple Chl biosynthesis enzymes from heat-induced destabilization. Rising temperature shifts cpSRP43 to the open state, enabling it to protect heat-destabilized Chl biosynthesis enzymes. Our results reveal the molecular basis of a posttranslational mechanism for the thermoadaptation of LHC biogenesis. They also demonstrate how an adenosine triphosphate–independent chaperone uses conformational dynamics to switch its activity and client selectivity, thereby adapting to different proteostatic demands under shifting environmental conditions.

Intermediate light adaptation induces oscillatory phototaxis switching and pattern formation in Chlamydomonas

2025-06-12

Zhao Wang , Alan Cheng Hou Tsang | Proceedings of the National Academy of Sciences

Biological microswimmers exhibit intricate taxis behaviors in response to environmental stimuli and swim in complex trajectories to navigate their environment. How microswimmers respond to stimulus instantaneously, and how adaptation to … Biological microswimmers exhibit intricate taxis behaviors in response to environmental stimuli and swim in complex trajectories to navigate their environment. How microswimmers respond to stimulus instantaneously, and how adaptation to stimulus influences their long-term behavioral changes, remains largely unclear. Here, we report an oscillatory phototaxis observed in Chlamydomonas reinhardtii at intermediate light intensities, where cells swim back-and-forth under a constant, unidirectional light stimulus due to alternation between positive and negative phototaxis. The phototaxis switching can be captured by the change in phase relationship between eyespot and helical swimming. Oscillatory phototaxis of individual cells leads to a global pattern of millimeter-scale propagating density bands that persists for <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline" id="i1" overflow="scroll"> <mml:mo>∼</mml:mo> </mml:math> 30 min. High-speed imaging and long-time tracking experiments at single-cell level verify a unified phototaxis mechanism that couples light detection, light adaptation, flagella responses, and behavioral switching. By experimentally tracking steady swimming and transient turning states, we verify that phototaxis transition is achieved via the modulation of flagella waveforms and flagella phase difference, which can be captured by a hydrodynamic model accounting for photoresponses. Adaptation acts effectively as an oscillator damper to mediate multipurpose tasking across multiple system levels (subcellular flagella beats, oscillatory phototaxis, colonial pattern formation) and timescales (from milliseconds to over 30 min). This adaptive phototaxis mechanism provides a comprehensive understanding of how microswimmers achieve complex behavioral changes across multiple temporal scales with a single sensor–actuator circuit featuring relatively simple adaptive feedback responses.

Structural Changes in the Retinal Chromophore and Ion-Conducting Pathway of an Anion Channelrhodopsin GtACR1

2025-06-12

Keisei Shibata , Yuma Kawasaki , Shunki Takaramoto +6 more | The Journal of Physical Chemistry Letters

Guillardia theta anion-conducting channelrhodopsin 1 (GtACR1) is a light-gated anion channel and is widely used as a representative optogenetic tool for neuronal silencing. However, its gating mechanism is unclear due … Guillardia theta anion-conducting channelrhodopsin 1 (GtACR1) is a light-gated anion channel and is widely used as a representative optogenetic tool for neuronal silencing. However, its gating mechanism is unclear due to the lack of insight into its structural changes and kinetics. Here, we measured the structural changes in the retinal chromophore of GtACR1 throughout its photocycle using time-resolved resonance Raman spectroscopy. Moreover, we investigated the rate-limiting factors of the gating through transient absorption spectroscopy and laser patch clamp electrophysiology. Our results provided the following understanding: the retinal chromophore keeps planar structure even in the open state. The ion-conducting pathway extends to the retinal Schiff base (RSB) as the channel opens. The channel closes in a two-step process, rate-limited by the RSB deprotonation and reprotonation. These findings reveal that the gating mechanism of GtACR1 differs markedly from that of a cation channelrhodopsin C1C2 and contribute to the development of next-generation optogenetic tools.

Smart Materials in Ophthalmic Applications

2025-06-11

Joaquín J. Jiménez , E. Phelps , Morgan V. DiLeo | Royal Society of Chemistry eBooks

Advanced materials, such as polymers with functional groups that change in response to temperature or light, present the opportunity to develop next-generation ophthalmic therapeutic and diagnostic tools. This chapter will … Advanced materials, such as polymers with functional groups that change in response to temperature or light, present the opportunity to develop next-generation ophthalmic therapeutic and diagnostic tools. This chapter will summarize advances in stimuli-responsive materials and devices suited for applications in different tissues within and around the eye. It will also provide context for these novel materials and systems in the broader landscape of clinical applicability and patient needs.

Blue light‐induced stomatal opening is associated with species‐specific changes in primary metabolism but not with starch breakdown in guard cells

2025-06-11

Humaira Bahadar , Eva Gomes Morais , Francisco Bruno S. Freire +5 more | New Phytologist

Blue light (BL)-induced stomatal opening has been associated with starch breakdown within Arabidopsis guard cells (GCs). However, whether this mechanism is conserved in angiosperms and which metabolic pathways are activated … Blue light (BL)-induced stomatal opening has been associated with starch breakdown within Arabidopsis guard cells (GCs). However, whether this mechanism is conserved in angiosperms and which metabolic pathways are activated downstream of BL perception and/or starch degradation, remains unknown. Here, we performed stomatal and metabolomics analyses to investigate how BL stomatal responses are associated with GC starch and primary metabolisms in Arabidopsis, cowpea, and tobacco. The stomatal aperture increased, but no starch degradation was observed in all species under BL. Guard cell primary metabolism was altered by BL exposition in a species-specific and time-dependent manner. Sucrose was negatively correlated with stomatal aperture in both Arabidopsis and cowpea, resembling previous results during white light (WL)-induced stomatal opening. However, contrasting metabolic changes were observed in tobacco under BL and WL. For instance, malate and fumarate accumulated preferentially in tobacco GCs under BL and WL, respectively. Despite the species-specific BL metabolic responses, sugars were positively correlated with tricarboxylic acid cycle-related metabolites in all species under BL, similar to those previously observed under WL-induced stomatal opening. Our study highlights that both starch breakdown and the changes in primary metabolism within GCs triggered by light depend on the species, environmental condition, and/or light quality.