Optogenetics articles within Nature Communications

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  • Article
    | Open Access

    Current near-IR optogenetic systems to regulate transcription consist of a number of large protein components. Here the authors report a smaller single-component near-IR system, iLight, developed from a bacterial phytochrome that they use to control gene transcription in bacterial and mammalian cells.

    • Andrii A. Kaberniuk
    • , Mikhail Baloban
    •  & Vladislav V. Verkhusha

  • Article
    | Open Access

    Here, the authors present DisCo (Disassembly of Condensates), a method that allows the fast, inducible, and specific disruption of tagged condensates in mammalian cells. DisCo uses chemical dimerizers to induce the recruitment of a ligand into condensates leading to condensate disassembly.

    • Carmen N. Hernández-Candia
    • , Sarah Pearce
    •  & Chandra L. Tucker

  • Article
    | Open Access

    Optogenetic control of molecules is important in cell biology and neuroscience. Here, the authors describe an optogenetic tool to control the Ca²+/calmodulin-dependent protein kinase II and use it to control plasticity at the single synapse level.

    • Akihiro C. E. Shibata
    • , Hiromi H. Ueda
    •  & Hideji Murakoshi

  • Article
    | Open Access

    Although wireless optogenetic technologies enable brain circuit investigation in freely moving animals, existing devices have limited their full potential, requiring special power setups. Here, the authors report fully implantable optogenetic systems that allow intervention-free wireless charging and controls for operation in any environment.

    • Choong Yeon Kim
    • , Min Jeong Ku
    •  & Jae-Woong Jeong

  • Article
    | Open Access

    Existing optogenetic methods to induce calcium mobilisation lack selectivity and specificity. Here, the authors design and engineer a single-component light-operated calcium channel to provide optical control over calcium signals and calcium-dependent physiological responses: LOCa.

    • Lian He
    • , Liuqing Wang
    •  & Yubin Zhou

  • Article
    | Open Access

    Existing neural interfaces are limited in accessing one, small brain region. Here, the authors introduce a scaffold with helix hollow channels, which direct multisite multifunctional fibre probes into the brain at different angles, allowing for simultaneous recording and stimulation across distant regions.

    • Shan Jiang
    • , Dipan C. Patel
    •  & Xiaoting Jia

  • Article
    | Open Access

    Current media for neuronal cell and organoid cultures are suboptimal for functional imaging and optogenetics experiments, owing to phototoxicity and unphysiological performance. Here the authors formulate an optimised neuronal medium to support live cell imaging and electrophysiological activity.

    • Michael Zabolocki
    • , Kasandra McCormack
    •  & Cedric Bardy

  • Article
    | Open Access

    Short hairpin RNAs can be used to modulate and regulate gene expression. Here the authors generate chimeric RNAs that interact with the photoreceptor PAL, allowing for optoribogenetic control of cell physiology.

    • Sebastian Pilsl
    • , Charles Morgan
    •  & Günter Mayer

  • Article
    | Open Access

    The ability to reversibly control monobody binding affinity would find use in biotechnology and research applications. Here the authors fuse the light-sensitive AsLOV2 domain to a monobody against the Abl SH2 domain to obtain a light dependent monobody and apply it in vitro and in mammalian cells.

    • César Carrasco-López
    • , Evan M. Zhao
    •  & José L. Avalos

  • Article
    | Open Access

    The ability to regulate nanobody affinity with light would expand the applications toolbox for these reagents. Here the authors insert an optimised photoswitchable AsLOV2 domain into multiple nanobodies and demonstrate photoswitchable binding to fluorescent proteins and endogenous proteins in cells.

    • Agnieszka A. Gil
    • , César Carrasco-López
    •  & Jared E. Toettcher

  • Article
    | Open Access

    The type III secretion system (T3SS) of bacteria can be used to inject cargo into eukaryotic cells but its lack of target specificity is a disadvantage. Here the authors place the T3SS under the regulation of light by engineering optogenetic switches into the dynamic cytosolic T3SS component SctQ.

    • Florian Lindner
    • , Bailey Milne-Davies
    •  & Andreas Diepold

  • Article
    | Open Access

    During development, organs undergo large scale forces driven by the cytoskeleton but the precise molecular regulation of cytoskeletal networks remains unclear. Here, the authors report a Cdc42-dependent supracellular cytoskeletal network integrates local actomyosin contraction at tissue scale and drives global tissue elongation.

    • Anna Popkova
    • , Orrin J. Stone
    •  & Xiaobo Wang

  • Article
    | Open Access

    The ability to manipulate and monitor calcium signaling in cells in vivo would provide insights into signaling in an endogenous context. Here the authors develop a two-photon-responsive calcium actuator and reporter combination to monitor the effect of calcium actuation on T cell migration, adhesion and chemokine release in vivo.

    • Armelle Bohineust
    • , Zacarias Garcia
    •  & Philippe Bousso

  • Article
    | Open Access

    Optogenetic approaches to control protein-protein interactions usually require overexpression of the target proteins. Here the authors integrate intrabodies into near-infrared- and blue-light activatable optogenetic tools to control endogenous proteins in mammalian cells.

    • Taras A. Redchuk
    • , Maksim M. Karasev
    •  & Vladislav V. Verkhusha

  • Article
    | Open Access

    Optogenetic applications in the brain of live animals often require the use of optic fibers due to poor tissue-penetration of blue light. Here the authors present monSTIM1, an improved high sensitivity optogenetic tool able to modulate Ca2+ signaling in the brain of awake mice using non-invasive light stimulation.

    • Sungsoo Kim
    • , Taeyoon Kyung
    •  & Won Do Heo

  • Article
    | Open Access

    Detailed characterization of large-scale hemodynamic responses linked to specific neural activity remains to be elucidated at the single-vessel level across the subcentimeter scale hippocampal vasculature in vivo. Here, authors use a novel multi-modal fMRI platform to characterize distinct spatiotemporal patterns of hippocampal hemodynamic responses that were correlated to the optogenetically evoked Ca2+ events and to further demonstrate the significantly reduced neurovascular coupling efficiency upon spreading depression-like Ca2+ events.

    • Xuming Chen
    • , Filip Sobczak
    •  & Xin Yu

  • Article
    | Open Access

    Protein phosphatases play an essential role in signal transduction, but are understudied due to the difficulties in detecting phosphate removal and the lack of good inhibitors. Here the authors develop a light-activated protein phosphatase using photocaged, unnatural amino acids and use it to study ERK nuclear translocation.

    • Taylor M. Courtney
    •  & Alexander Deiters

  • Article
    | Open Access

    The nature of the signals that propagate through feedforward networks is not well understood. Here, the authors combine microfabrication, multilayer cortical cultures, and optogenetic stimulation to show that NMDA-mediated synaptic current generates a sustained phase of activity that propagates firing rate signals.

    • Jérémie Barral
    • , Xiao-Jing Wang
    •  & Alex D. Reyes

  • Article
    | Open Access

    Bacillus subtilis has complex spatial and temporal gene expression patterns but currently lacks optogenetic tools to explore these processes. Here the authors import and debug a cyanobacterial green light sensor pathway and show that it enables precise optical control of gene expression.

    • Sebastian M. Castillo-Hair
    • , Elliot A. Baerman
    •  & Jeffrey J. Tabor

  • Article
    | Open Access

    Optogenetic stimulation of damaged peripheral nerves has advantages over electrical stimulation but it’s limited to single-site stimulation. Here the authors develop a spiral-shaped LED implant for precise optogenetic stimulation of peripheral nerve bundles at multiple sites and use it to induce distinct limb movements in mice.

    • Hao Zheng
    • , Zhitao Zhang
    •  & Jiayi Zhang

  • Article
    | Open Access

    Fiber optic implantation in deep areas of the rodent’s brain for MRI combined with optogenetics is challenging. Here the authors use an MRI-guided robotic arm as the navigation method for accurate fiber optic placement and precise microinjection during multi-modal fMRI, optogenetics and calcium recordings.

    • Yi Chen
    • , Patricia Pais-Roldan
    •  & Xin Yu

  • Article
    | Open Access

    Autophagic degradation of mitochondria (mitophagy) is a key quality control mechanism in cellular homeostasis, and its misregulation is involved in neurodegenerative diseases. Here the authors develop an optogenetic system for reversible induction of mitophagy and validate its use in cell culture and zebrafish embryos.

    • Pasquale D’Acunzo
    • , Flavie Strappazzon
    •  & Francesco Cecconi

  • Article
    | Open Access

    Optical control over receptor tyrosine kinase (RTK) activity can find application in both basic biology and synthetic biology. Here the authors combine the photosensory module of DrBphP bacterial phytochrome with the Trk family of RTKs to obtain Trks that are reversibly switchable with near-infrared and far-red light.

    • Anna V. Leopold
    • , Konstantin G. Chernov
    •  & Vladislav V. Verkhusha

  • Article
    | Open Access

    A steep gradient of Cdc42 is at the front of migrating cells, whereas the active Rac1 gradient is graded. Here the authors show that Cdc42 gradients follow the distribution of GEFs and govern direction of migration, while Rac1 gradients require the activity of the GAP β2-chimaerin and control cell speed.

    • S. de Beco
    • , K. Vaidžiulytė
    •  & M. Coppey

  • Article
    | Open Access

    Cellular ERK activation occurs as discrete pulses but their relationship to upstream Ras signaling is still under debate. Here, the authors show that Ras signaling associated with cellular protrusions triggers pulsed ERK activation, thereby enabling cells to integrate chemical and mechanical stimuli.

    • Jr-Ming Yang
    • , Sayak Bhattacharya
    •  & Chuan-Hsiang Huang

  • Article
    | Open Access

    Optogenetic tools enable precise experimental control of the behaviour of cells. Here, the authors introduce a genetically-encoded two-protein system that enables silencing of excitable cells such as neurons and cardiomyocytes using blue light, and demonstrate its utility both in vitro and In vivo.

    • Yinth Andrea Bernal Sierra
    • , Benjamin R. Rost
    •  & Dietmar Schmitz

  • Article
    | Open Access

    Designing split protein approaches is time consuming and often results in high background activity due to spontaneous assembly. Here the authors present an automated approach which uses a split energy scoring function to identify optimal protein split sites and reduces spontaneous assembly.

    • Onur Dagliyan
    • , Andrey Krokhotin
    •  & Nikolay V. Dokholyan

  • Article
    | Open Access

    The International Synthetic Yeast Sc2.0 project has built Cre recombinase sites into synthetic chromosomes, enabling rapid genome evolution. Here the authors demonstrate L-SCRaMbLE, a light-controlled recombinase tool with improved control over recombination events.

    • Lena Hochrein
    • , Leslie A. Mitchell
    •  & Bernd Mueller-Roeber

  • Article
    | Open Access

    G-protein coupled receptors (GPCRs) represent the largest receptor family and are prime drug targets, but many orphan GPCRs are poorly characterized. Here authors engineer human orphan GPCRs to be activated by light which allows studying the receptors ligand identity and downstream signaling.

    • Maurizio Morri
    • , Inmaculada Sanchez-Romero
    •  & Harald Janovjak

  • Article
    | Open Access

    Optogenetic applications would benefit from channelrhodopsins (ChRs) with faster photostimulation, increased tissue transparency and lower phototoxicity. Here, the authors develop fast red-shifted ChR variants and show the abilities for temporal precise spiking of cerebral interneurons and restoring auditory activity in deaf mice.

    • Thomas Mager
    • , David Lopez de la Morena
    •  & Ernst Bamberg

  • Article
    | Open Access

    Changes to subsets of dendritic spines are thought to be important for memory formation. Here, the authors develop a hybrid RNA/protein tool that allows for optogenetic stimulation of single synapses that have been tagged in an activity-dependent manner

    • Francesco Gobbo
    • , Laura Marchetti
    •  & Antonino Cattaneo

  • Article
    | Open Access

    Optogenetics, the optical stimulation of neurons, suffers from many technical challenges that limit the number of neurons that can be excited as well as their relative positions. Here, Pégard et al. develop a method to simultaneously stimulate an arbitrary number of neurons in 3D space with single neuron resolution.

    • Nicolas C. Pégard
    • , Alan R. Mardinly
    •  & Hillel Adesnik

  • Article
    | Open Access

    Cryptochrome 2 (CRY2) can form light-regulated CRY2-CRY2 homo-oligomers or CRY2-CIB1 hetero-dimers, but modulating these interactions is difficult owing to the lack of interaction mechanism. Here the authors identify the interactions facilitating homo-oligomers and introduce mutations to create low and high oligomerization versions.

    • Liting Duan
    • , Jen Hope
    •  & Bianxiao Cui

  • Article
    | Open Access

    Cryptochrome 2 (CRY2) from A. thaliana can be used to control light-dependent protein homo-oligomerization, but the molecular mechanism of CRY2 clustering is not known, limiting its application. Here the authors identify determinants of CRY2 clustering and engineer fusion partners to modulate clustering efficiency.

    • Hyerim Park
    • , Na Yeon Kim
    •  & Won Do Heo

  • Article
    | Open Access

    Osteoclasts induce chemotaxis of osteoblasts during bone remodelling, but maintain spatial segregation. Here the authors show that osteoclasts repel osteoblasts via contact inhibition of locomotion mediated by Semaphorin-Plexin signalling and develop an optogenetic tool for Plexin-B1 to show how this signalling axis induces cell repolarization.

    • Abhijit Deb Roy
    • , Taofei Yin
    •  & Yi I. Wu

  • Article
    | Open Access

    Current approaches to thermogenetic manipulation of neuronal activity lack sufficient spatiotemporal resolution. Here the authors show that neurons expressing snake TRPA1 channels are activated at high temporal resolution with IR light and this technique can be used to elicit behaviour in zebrafish larvae.

    • Yulia G. Ermakova
    • , Aleksandr A. Lanin
    •  & Vsevolod V. Belousov

  • Article
    | Open Access

    Light-sensitive regulators of protein kinases could offer valuable insights into intracellular signalling. Here the authors design an optogenetic inhibitor of c-Jun N-terminal kinase (JNK) and show evidence for resonance in JNK signalling circuits in neurons, and use the same design principle to develop an inhibitor for p38MAPK.

    • Raquel M. Melero-Fernandez de Mera
    • , Li-Li Li
    •  & Michael J. Courtney

  • Article
    | Open Access

    Pulsatile actomyosin contractility during tissue morphogenesis has been mainly studied in apical domains but less is known about the contribution of the basal domain. Here the authors show differential influence of cell-matrix and cell-cell adhesions in regulating oscillations and tissue elongation.

    • Xiang Qin
    • , Byung Ouk Park
    •  & Xiaobo Wang

  • Article
    | Open Access

    Cellular mechanical forces are regulated by Rho GTPases. Here the authors develop an optogenetic system to control the spatiotemporal activity of RhoA, and show that directing a RhoA activator to the plasma membrane causes contraction and YAP nuclear localization, whereas directing it to the mitochondria causes relaxation.

    • Léo Valon
    • , Ariadna Marín-Llauradó
    •  & Xavier Trepat

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