Optogenetics articles within Nature Communications

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  • Article
    | Open Access

    Cas13 systems suffer from a lack of spatiotemporal control. Here the authors report paCas13, a light-inducible Cas13 system created by fusing Magnet with fragment pairs; they also report padCas13, a light-inducible base-editing system by fusing ADAR2 to catalytically inactive paCas13 fragments.

    • Jeonghye Yu
    • , Jongpil Shin
    •  & Won Do Heo

  • Article
    | Open Access

    Rhodopsins are ubiquitous light-driven membrane proteins that have diverse functions in nature, and value as optogenetics tools. Here the authors characterise type 1 viral channelrhodopsins, showing that they regulate intracellular calcium and can be used for the photocontrol of muscle contraction in vivo.

    • Ana-Sofia Eria-Oliveira
    • , Mathilde Folacci
    •  & Michel Vivaudou

  • Article
    | Open Access

    Microbial communities are the siege of complex metabolic interactions including cooperation and competition. Here, the authors report the utilization of optogenetics and spatial light-patterning to activate the expression of the invertase SUC2 at selected locations and selectively switch cooperation and competition roles of the yeast cells.

    • Matthias Le Bec
    • , Sylvain Pouzet
    •  & Pascal Hersen

  • Article
    | Open Access

    Tools for high spatiotemporal control of cell-cell adhesions are lacking. Here, authors propose an optogenetic tool, opto-E-cadherin, that allows reversible control of E-cadherin-mediated cell-cell adhesions with blue light.

    • Brice Nzigou Mombo
    • , Brent M. Bijonowski
    •  & Seraphine V. Wegner

  • Article
    | Open Access

    Virtual optical waveguide can be potentially utilised in variety of applications that require in situ light steering yet the efficacy is still unclear. Here, the authors show that ultrasonically-sculpted virtual gradient-index waveguides are effective in guiding and confining light inside tissue and other scattering media, and significantly outperform external lenses at this task.

    • Adithya Pediredla
    • , Matteo Giuseppe Scopelliti
    •  & Ioannis Gkioulekas

  • Article
    | Open Access

    The ability to independently control the expression of different genes is important for quantitative biology. Here, the authors report kinetic parameters, noise scaling, impact on growth, and the fundamental leakiness of a wide range of inducible transcriptional systems, including a new, highly light sensitive LOV-transcription factor.

    • Vojislav Gligorovski
    • , Ahmad Sadeghi
    •  & Sahand Jamal Rahi

  • Article
    | Open Access

    Light-switchable variants are only available for a limited subset of proteins and pathways. Here the authors adapt strategies for protein domain insertion and mammalian-cell expression to generate and screen a library of potential optogenetic tools directly in mammalian cells.

    • Liyuan Zhu
    • , Harold M. McNamara
    •  & Jared E. Toettcher

  • Article
    | Open Access

    Tools for the spatiotemporal control of protein abundance are valuable in studying diverse complex biological processes. Here, authors engineered a protein tag which is stabilized upon light induction but which quickly degrades the protein of interest in the dark, demonstrating control of protein stability in yeast and zebrafish.

    • Miaowei Mao
    • , Yajie Qian
    •  & Yi Yang

  • Article
    | Open Access

    Optogenetic actuation regimes are often static, which allows perturbation, but not true control of neuronal activity. Here, the authors describe an all-optical method for bidirectional steering of membrane potential, in closed loop, in C. elegans muscles and neurons, and rat hippocampal slice culture. The ‘optogenetic voltage clamp’ uses two microbial rhodopsin actuators and the rhodopsin voltage indicator QuasAr.

    • Amelie C. F. Bergs
    • , Jana F. Liewald
    •  & Alexander Gottschalk

  • Article
    | Open Access

    PIEZO proteins are large, mechanically-activated trimeric ion channels. Here the authors report a light-gated mouse PIEZO1 channel, mOP1, whereby an azobenzene-based photoswitch covalently localised at the extracellular apex of a transmembrane helix, rapidly triggers channel gating on light irradiation.

    • Francisco Andrés Peralta
    • , Mélaine Balcon
    •  & Thomas Grutter

  • Article
    | Open Access

    The mechanical properties of biological tissues are key to their integrity and function. Here, the authors engineer 3D microtissues from optogenetically modified fibroblasts and use light to quantify tissue elasticity and strain propagation using their own constituent cells as internal actuators.

    • Adrien Méry
    • , Artur Ruppel
    •  & Thomas Boudou

  • Article
    | Open Access

    To date, no Ca2 + -selective channelrhodopsins have been characterized. In this study, Fernandez Lahore et al. report two calcium-permeable channelrhodopsins (CapChR1 and 2) for the photocontrol of calcium signalling in excitable tissue.

    • Rodrigo G. Fernandez Lahore
    • , Niccolò P. Pampaloni
    •  & Peter Hegemann

  • Article
    | Open Access

    Existing optogenetic silencing methods affect membrane potential, biochemistry or protein integrity. Here, the authors demonstrate an approach for silencing synaptic transmission that combines fast activation and reversibility, by using nondisruptive, reversible, light-evoked clustering of synaptic vesicles, which they validate in Caenorhabditis elegans, zebrafish, and murine cell culture.

    • Dennis Vettkötter
    • , Martin Schneider
    •  & Alexander Gottschalk

  • Article
    | Open Access

    The neurophysiological mechanisms of deep brain stimulation remain poorly understood. Through fluorescence voltage imaging of individual hippocampal neurons in awake mice, the authors show that deep brain stimulation causes membrane depolarization that impairs a neuron’s ability to respond to intrinsic network activity patterns and optogenetic somatic depolarization, thereby creating an informational lesion.

    • Eric Lowet
    • , Krishnakanth Kondabolu
    •  & Xue Han

  • Article
    | Open Access

    Achieving spatial control of gene expression is important. Here the authors report an optimised photoactivatable Cre recombinase system, doxycycline- and light-inducible Cre recombinase (DiLiCre), and generate a DiLiCre mouse line which they use for mutagenesis in vivo and positional cell-tracing.

    • Miguel Vizoso
    • , Colin E. J. Pritchard
    •  & Jacco van Rheenen

  • Article
    | Open Access

    The induction of long-term systemic immunosurveillance can protect against post-surgery tumor recurrence. Here the authors describe the design of optogenetic-controlled cytokine secreting (IFN-β, TNF-α, and IL-12) engineered mesenchymal stem cells loaded into a hydrogel scaffold, eliciting long-term immune memory and preventing post-operative recurrence in preclinical cancer models.

    • Yuanhuan Yu
    • , Xin Wu
    •  & Haifeng Ye

  • Article
    | Open Access

    Wireless delivery of both light and pharmacological agents is important for optogenetic and other mechanistic experiments in the brain. Here the authors present a wireless real-time programmable optofluidic platform that enables optogenetics and photopharmacology experiments that require real-time precise control of light and drug delivery.

    • Yixin Wu
    • , Mingzheng Wu
    •  & John A. Rogers

  • Article
    | Open Access

    Apical constriction is a force-generating process required during embryonic development; there is a lack of tools to manipulate 3D shapes of mammalian tissues. Here the authors report the optogenetic method, OptoShroom3, to achieve fast spatiotemporal control of apical constriction in mammalian epithelia.

    • Guillermo Martínez-Ara
    • , Núria Taberner
    •  & Miki Ebisuya

  • Article
    | Open Access

    Communities of microbes play important roles in natural environments and hold great potential for deploying division-of-labor strategies in synthetic biology and bioproduction. Here, in a community of two competing E. coli strains, the authors show that the relative abundances of the strains can be stabilized and steered dynamically with remarkable precision by coupling the cells to an automated computer-controlled feedback-loop.

    • Joaquín Gutiérrez Mena
    • , Sant Kumar
    •  & Mustafa Khammash

  • Article
    | Open Access

    Optogenetic tools can be used as in vivo imaging probes. Here the authors generate a loxP-BphP1 transgenic mouse to enable Cre-dependent temporal and spatial targeting of BphP1 expression in vivo; they show photoacoustic tomography of BphP1 expression in developing embryos and regenerating livers.

    • Ludmila A. Kasatkina
    • , Chenshuo Ma
    •  & Vladislav V. Verkhusha

  • Article
    | Open Access

    The design of feedback biomolecular controllers is essential to synthetically regulate biological processes in a robust and timely fashion. Here the authors introduce a wide array of biomolecular Proportional-Integral-Derivative (PID) controllers that are capable of enhancing stability and dynamic performance, and also reducing stochastic noise.

    • Maurice Filo
    • , Sant Kumar
    •  & Mustafa Khammash

  • Article
    | Open Access

    Gq proteins are one of four major classes of G proteins; optogenetic receptors for selective and repetitive activation of Gq proteins with fast kinetics are lacking. Here the authors report UV light-dependent Gq signalling using human Neuropsin (hOPN5) and demonstrate its potential as an optogenetic tool.

    • Ahmed Wagdi
    • , Daniela Malan
    •  & Tobias Bruegmann

  • Article
    | Open Access

    Parathyroid hormone (PTH) plays a role in maintaining calcium and phosphorus homeostasis, and in secondary hyperparathyroidism excess PTH secretion contributes to bone loss. Here the authors report an optogenetic approach to inhibit PTH secretion in human hyperplastic parathyroid cells, and prevented hyperplastic parathyroid tissue-induced bone loss in mice.

    • Yunhui Liu
    • , Lu Zhang
    •  & Fan Yang

  • Article
    | Open Access

    During pyroptosis, gasdermin D (GSDMD) forms plasma membrane pores that initiate cell lysis. Here, the authors develop optogenetically activatable human GSDMD to assess GSDMD pore behavior and show that they are dynamic and can close, which can be a pyroptosis regulatory mechanism.

    • Ana Beatriz Santa Cruz Garcia
    • , Kevin P. Schnur
    •  & Gary C. H. Mo

  • Article
    | Open Access

    The authors present a viral vector-delivery optrode system to integrate optogenetics and electrophysiology. The flexible microelectrode filaments and fiber optics self-assemble in a nanoliter-scale, viral vector-delivery polymer carrier for localized delivery and expression of opsin genes at microelectrode-tissue interfaces.

    • Liang Zou
    • , Huihui Tian
    •  & Ying Fang

  • Article
    | Open Access

    Current cardiac mapping systems provide either electrical or optical readouts. Here the authors report a panoramic opto-electrical measurement and stimulation (POEMS) system which embraces the entire ventricular surface of mouse hearts, allowing flexible combinations of optical and electrical recording and stimulation modalities.

    • Michael Rieger
    • , Christian Dellenbach
    •  & Stephan Rohr

  • Article
    | Open Access

    Conventional upconversion nanoparticles (UCNPs) cannot activate multiple neuron populations independently using optogenetics. Here the authors report trichromatic UCNPs with excitation-specific luminescence to allow activation of three distinct neuronal populations in the brain of awake mice.

    • Xuan Liu
    • , Heming Chen
    •  & Fan Zhang

  • Article
    | Open Access

    Practical implementation of genetic circuits is difficult due to low predictability and time-intensive troubleshooting. Here the authors present Cyberloop, which interfaces a computer with single cells to enable cell-in-the-loop testing and optimization of circuit designs before they are built.

    • Sant Kumar
    • , Marc Rullan
    •  & Mustafa Khammash

  • Article
    | Open Access

    Molecular tethers physically bridge transport vesicles to their target membranes as a prerequisite step for fusion. Here the authors control vesicle tethering using optogenetic approaches to study the interplay between vesicle tethering and fusion.

    • Seong J. An
    • , Felix Rivera-Molina
    •  & Derek Toomre

  • Article
    | Open Access

    Currently, bidirectional control of activity in the same neurons in the same experiment is difficult. Here the authors report a Bidirectional Pair of Opsins for Light-induced Excitation and Silencing, BiPOLES, which they use in a range of organisms including worms, fruit flies, mice and ferrets.

    • Johannes Vierock
    • , Silvia Rodriguez-Rozada
    •  & J. Simon Wiegert

  • Article
    | Open Access

    Scintillators emit visible luminescence when irradiated with X-rays and may enable remote optogenetic control of neurons deep in the brain. The authors inject an inorganic scintillator to activate and inhibit midbrain dopamine neurons in freely moving mice by X-ray irradiation to modulate place preference behavior.

    • Takanori Matsubara
    • , Takayuki Yanagida
    •  & Takayuki Yamashita

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