1
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Avila B, Augusto P, Zimmer M, Serafino M, Makse HA. Fibration symmetries and cluster synchronization in the Caenorhabditis elegans connectome. ARXIV 2024:arXiv:2305.19367v2. [PMID: 37396607 PMCID: PMC10312817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Capturing how the Caenorhabditis elegans connectome structure gives rise to its neuron functionality remains unclear. It is through fiber symmetries found in its neuronal connectivity that synchronization of a group of neurons can be determined. To understand these we investigate graph symmetries and search for such in the symmetrized versions of the forward and backward locomotive sub-networks of the Caenorhabditi elegans worm neuron network. The use of ordinarily differential equations simulations admissible to these graphs are used to validate the predictions of these fiber symmetries and are compared to the more restrictive orbit symmetries. Additionally fibration symmetries are used to decompose these graphs into their fundamental building blocks which reveal units formed by nested loops or multilayered fibers. It is found that fiber symmetries of the connectome can accurately predict neuronal synchronization even under not idealized connectivity as long as the dynamics are within stable regimes of simulations.
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Affiliation(s)
- Bryant Avila
- Levich Institute, Physics Department, City College of New York, New York, NY, USA
| | - Pedro Augusto
- Vienna Biocenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
- Department of Neuroscience and Developmental Biology, Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
| | - Manuel Zimmer
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
- Department of Neuroscience and Developmental Biology, Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
| | - Matteo Serafino
- Levich Institute, Physics Department, City College of New York, New York, NY, USA
| | - Hernán A. Makse
- Levich Institute, Physics Department, City College of New York, New York, NY, USA
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2
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Avila B, Serafino M, Augusto P, Zimmer M, Makse HA. Fibration symmetries and cluster synchronization in the Caenorhabditis elegans connectome. PLoS One 2024; 19:e0297669. [PMID: 38598455 PMCID: PMC11006206 DOI: 10.1371/journal.pone.0297669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 01/11/2024] [Indexed: 04/12/2024] Open
Abstract
Capturing how the Caenorhabditis elegans connectome structure gives rise to its neuron functionality remains unclear. It is through fiber symmetries found in its neuronal connectivity that synchronization of a group of neurons can be determined. To understand these we investigate graph symmetries and search for such in the symmetrized versions of the forward and backward locomotive sub-networks of the Caenorhabditi elegans worm neuron network. The use of ordinarily differential equations simulations admissible to these graphs are used to validate the predictions of these fiber symmetries and are compared to the more restrictive orbit symmetries. Additionally fibration symmetries are used to decompose these graphs into their fundamental building blocks which reveal units formed by nested loops or multilayered fibers. It is found that fiber symmetries of the connectome can accurately predict neuronal synchronization even under not idealized connectivity as long as the dynamics are within stable regimes of simulations.
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Affiliation(s)
- Bryant Avila
- Physics Department, Levich Institute, City College of New York, New York, NY, United Stated of America
| | - Matteo Serafino
- Physics Department, Levich Institute, City College of New York, New York, NY, United Stated of America
| | - Pedro Augusto
- Vienna Biocenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
- Department of Neuroscience and Developmental Biology, Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
| | - Manuel Zimmer
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
- Department of Neuroscience and Developmental Biology, Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
| | - Hernán A. Makse
- Physics Department, Levich Institute, City College of New York, New York, NY, United Stated of America
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3
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Ripoll-Sánchez L, Watteyne J, Sun H, Fernandez R, Taylor SR, Weinreb A, Bentley BL, Hammarlund M, Miller DM, Hobert O, Beets I, Vértes PE, Schafer WR. The neuropeptidergic connectome of C. elegans. Neuron 2023; 111:3570-3589.e5. [PMID: 37935195 PMCID: PMC7615469 DOI: 10.1016/j.neuron.2023.09.043] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 08/02/2023] [Accepted: 09/29/2023] [Indexed: 11/09/2023]
Abstract
Efforts are ongoing to map synaptic wiring diagrams, or connectomes, to understand the neural basis of brain function. However, chemical synapses represent only one type of functionally important neuronal connection; in particular, extrasynaptic, "wireless" signaling by neuropeptides is widespread and plays essential roles in all nervous systems. By integrating single-cell anatomical and gene-expression datasets with biochemical analysis of receptor-ligand interactions, we have generated a draft connectome of neuropeptide signaling in the C. elegans nervous system. This network is characterized by high connection density, extended signaling cascades, autocrine foci, and a decentralized topology, with a large, highly interconnected core containing three constituent communities sharing similar patterns of input connectivity. Intriguingly, several key network hubs are little-studied neurons that appear specialized for peptidergic neuromodulation. We anticipate that the C. elegans neuropeptidergic connectome will serve as a prototype to understand how networks of neuromodulatory signaling are organized.
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Affiliation(s)
- Lidia Ripoll-Sánchez
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK; Department of Psychiatry, Cambridge University, Cambridge, UK
| | - Jan Watteyne
- Department of Biology, KU Leuven, Leuven, Belgium
| | - HaoSheng Sun
- Department of Biological Sciences/HHMI, Columbia University, New York, NY, USA; Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Robert Fernandez
- Department of Biological Sciences/HHMI, Columbia University, New York, NY, USA
| | - Seth R Taylor
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Alexis Weinreb
- Departments of Genetics and Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Barry L Bentley
- Cardiff School of Technologies, Cardiff Metropolitan University, Cardiff, UK
| | - Marc Hammarlund
- Departments of Genetics and Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - David M Miller
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Oliver Hobert
- Department of Biological Sciences/HHMI, Columbia University, New York, NY, USA
| | - Isabel Beets
- Department of Biology, KU Leuven, Leuven, Belgium
| | - Petra E Vértes
- Department of Psychiatry, Cambridge University, Cambridge, UK
| | - William R Schafer
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK; Department of Biology, KU Leuven, Leuven, Belgium.
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4
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Sineshchekov OA, Govorunova EG, Li H, Wang Y, Spudich JL. Sequential absorption of two photons creates a bistable form of RubyACR responsible for its strong desensitization. Proc Natl Acad Sci U S A 2023; 120:e2301521120. [PMID: 37186849 PMCID: PMC10214203 DOI: 10.1073/pnas.2301521120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 04/18/2023] [Indexed: 05/17/2023] Open
Abstract
Channelrhodopsins with red-shifted absorption, rare in nature, are highly desired for optogenetics because light of longer wavelengths more deeply penetrates biological tissue. RubyACRs (Anion ChannelRhodopsins), a group of four closely related anion-conducting channelrhodopsins from thraustochytrid protists, are the most red-shifted channelrhodopsins known with absorption maxima up to 610 nm. Their photocurrents are large, as is typical of blue- and green-absorbing ACRs, but they rapidly decrease during continuous illumination (desensitization) and extremely slowly recover in the dark. Here, we show that long-lasting desensitization of RubyACRs results from photochemistry not observed in any previously studied channelrhodopsins. Absorption of a second photon by a photocycle intermediate with maximal absorption at 640 nm (P640) renders RubyACR bistable (i.e., very slowly interconvertible between two spectrally distinct forms). The photocycle of this bistable form involves long-lived nonconducting states (Llong and Mlong), formation of which is the reason for long-lasting desensitization of RubyACR photocurrents. Both Llong and Mlong are photoactive and convert to the initial unphotolyzed state upon blue or ultraviolet (UV) illumination, respectively. We show that desensitization of RubyACRs can be reduced or even eliminated by using ns laser flashes, trains of short light pulses instead of continuous illumination to avoid formation of Llong and Mlong, or by application of pulses of blue light between pulses of red light to photoconvert Llong to the initial unphotolyzed state.
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Affiliation(s)
- Oleg A. Sineshchekov
- Department of Biochemistry and Molecular Biology, Center for Membrane Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX77030
| | - Elena G. Govorunova
- Department of Biochemistry and Molecular Biology, Center for Membrane Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX77030
| | - Hai Li
- Department of Biochemistry and Molecular Biology, Center for Membrane Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX77030
| | - Yumei Wang
- Department of Biochemistry and Molecular Biology, Center for Membrane Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX77030
| | - John L. Spudich
- Department of Biochemistry and Molecular Biology, Center for Membrane Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX77030
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5
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Melnikov K, Kucharíková S, Bárdyová Z, Botek N, Kaiglová A. Applications of a powerful model organism Caenorhabditis elegans to study the neurotoxicity induced by heavy metals and pesticides. Physiol Res 2023; 72:149-166. [PMID: 37159850 PMCID: PMC10226405 DOI: 10.33549/physiolres.934977] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 02/03/2023] [Indexed: 08/27/2023] Open
Abstract
The expansion of industry and the use of pesticides in agriculture represent one of the major causes of environmental contamination. Unfortunately, individuals and animals are exposed to these foreign and often toxic substances on a daily basis. Therefore, it is crucial to monitor the impact of such chemicals on human health. Several in vitro studies have addressed this issue, but it is difficult to explore the impact of these compounds on living organisms. A nematode Caenorhabditis elegans has become a useful alternative to animal models mainly because of its transparent body, fast growth, short life cycle, and easy cultivation. Furthermore, at the molecular level, there are significant similarities between humans and C. elegans. These unique features make it an excellent model to complement mammalian models in toxicology research. Heavy metals and pesticides, which are considered environmental contaminants, are known to have affected the locomotion, feeding behavior, brood size, growth, life span, and cell death of C. elegans. Today, there are increasing numbers of research articles dedicated to this topic, of which we summarized the most recent findings dedicated to the effect of heavy metals, heavy metal mixtures, and pesticides on the well-characterized nervous system of this nematode.
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Affiliation(s)
- K Melnikov
- Department of Laboratory Medicine, Faculty of Health Care and Social Work, University in Trnava, Slovakia.
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Seidenthal M, Vettkötter D, Gottschalk A. WormRuler: A software to track body length used to characterize a super red-shifted channelrhodopsin in Caenorhabditis elegans. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000607. [PMID: 35903772 PMCID: PMC9315411 DOI: 10.17912/micropub.biology.000607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/06/2022] [Accepted: 07/15/2022] [Indexed: 11/13/2022]
Abstract
Manipulation of neuronal or muscular activity by optogenetics or other stimuli can be directly linked to the analysis of Caenorhabditis elegans ( C. elegans ) body length. Thus, WormRuler was developed as an open-source video analysis toolbox that offers video processing and data analysis in one application. Utilizing this novel tool, the super red-shifted channelrhodopsin variant, ChrimsonSA, was characterized in C. elegans . Expression and activation of ChrimsonSA in GABAergic motor neurons results in their depolarization and therefore elongation of body length, the extent of which providing information about the strength of neuronal transmission.
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Affiliation(s)
- Marius Seidenthal
- Buchmann Institute for Molecular Life Sciences, Goethe-University, Max-von-Laue-Strasse 15, D-60438 Frankfurt, Germany
,
Department of Biochemistry, Chemistry, and Pharmacy, Institute for Biophysical Chemistry, Goethe-University, Max-von-Laue-Strasse 9, D-60438 Frankfurt, Germany
| | - Dennis Vettkötter
- Buchmann Institute for Molecular Life Sciences, Goethe-University, Max-von-Laue-Strasse 15, D-60438 Frankfurt, Germany
,
Department of Biochemistry, Chemistry, and Pharmacy, Institute for Biophysical Chemistry, Goethe-University, Max-von-Laue-Strasse 9, D-60438 Frankfurt, Germany
| | - Alexander Gottschalk
- Buchmann Institute for Molecular Life Sciences, Goethe-University, Max-von-Laue-Strasse 15, D-60438 Frankfurt, Germany
,
Department of Biochemistry, Chemistry, and Pharmacy, Institute for Biophysical Chemistry, Goethe-University, Max-von-Laue-Strasse 9, D-60438 Frankfurt, Germany
,
Correspondence to: Alexander Gottschalk (
)
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7
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Driesschaert B, Temmerman L. The Q system for conditional gene expression is leaky and lacks dynamic range in C. elegans neurons. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000573. [PMID: 35601753 PMCID: PMC9115586 DOI: 10.17912/micropub.biology.000573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/11/2022] [Accepted: 05/16/2022] [Indexed: 11/18/2022]
Abstract
The Q system allows for conditional gene expression in several organisms, including
C. elegans
. We aimed to apply this system in
C. elegans
neurons to obtain temporally-resolved, tissue-specific expression of a fluorescent reporter. We report that, in our hands, there is undesired expression of the reporter in conditions where expression is supposed to be repressed. In addition, in this setup, the signal‑to‑noise ratio of the Q system is unfavorable. We conclude that the Q system is far from optimal in the
C. elegans
nervous system, and advise cautious use.
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Affiliation(s)
| | - Liesbet Temmerman
- Katholieke Universiteit Leuven, Leuven, Belgium
,
Correspondence to: Liesbet Temmerman (
)
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8
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Yu B, Wang Y, Gao S. Motor Rhythm Dissection From the Backward Circuit in C. elegans. Front Mol Neurosci 2022; 15:845733. [PMID: 35370545 PMCID: PMC8966088 DOI: 10.3389/fnmol.2022.845733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 01/26/2022] [Indexed: 11/28/2022] Open
Abstract
Motor rhythm is initiated and sustained by oscillatory neuronal activity. We recently discovered that the A-class excitatory motor neurons (MNs) (A-MNs) function as intrinsic oscillators. They drive backward locomotion by generating rhythmic postsynaptic currents (rPSCs) in body wall muscles. Molecular underpinning of the rPSCs, however, is not fully elucidated. We report here that there are three types of the rPSC patterns, namely the phasic, tonic, and long-lasting, each with distinct kinetics and channel-dependence. The Na+ leak channel is required for all rPSC patterns. The tonic rPSCs exhibit strong dependence on the high-voltage-gated Ca2+ channels. Three K+ channels, the BK-type Ca2+-activated K+ channel, Na+-activated K+ channel, and voltage-gated K+ channel (Kv4), primarily inhibit tonic and long-lasting rPSCs with varying degrees and preferences. The elaborate regulation of rPSCs by different channels, through increasing or decreasing the rPSCs frequency and/or charge, correlates with the changes in the reversal velocity for respective channel mutants. The molecular dissection of different A-MNs-rPSC components therefore reveals different mechanisms for multiplex motor rhythm.
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Affiliation(s)
- Bin Yu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Ya Wang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Shangbang Gao
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- Department of Geriatrics, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Shangbang Gao,
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9
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Bergs A, Henss T, Glock C, Nagpal J, Gottschalk A. Microbial Rhodopsin Optogenetic Tools: Application for Analyses of Synaptic Transmission and of Neuronal Network Activity in Behavior. Methods Mol Biol 2022; 2468:89-115. [PMID: 35320562 DOI: 10.1007/978-1-0716-2181-3_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Over the past 15 years, optogenetic methods have revolutionized neuroscientific and cell biological research, also in the nematode Caenorhabditis elegans. In this chapter, we give an update about current optogenetic tools and methods to address neuronal activity and inhibition, as well as second messenger signaling, based on microbial rhodopsins. We address channelrhodopsins and variants thereof, which conduct cations or anions, for depolarization and hyperpolarization of the membrane potential. Also, we cover ion pumping rhodopsins, like halorhodopsin, Mac, and Arch. A recent addition to rhodopsin-based optogenetics is voltage imaging tools that allow fluorescent readout of membrane voltage (directly, via fluorescence of the rhodopsin chromophore retinal, or indirectly, via electrochromic FRET). Last, we report on a new addition to the optogenetic toolbox, which is rhodopsin guanylyl cyclases, as well as mutated variants with specificity for cyclic AMP. These can be used to regulate intracellular levels of cGMP and cAMP, which are important second messengers in sensory and other neurons. We further show how they can be combined with cyclic nucleotide-gated channels in two-component optogenetics, for depolarization or hyperpolarization of membrane potential. For all tools, we present protocols for straightforward experimentation to address neuronal activation and inhibition, particularly at the neuromuscular junction, and for combined optogenetic actuation and Ca2+ imaging. We also provide protocols for usage of rhodopsin guanylyl and adenylyl cyclases. Finally, we list a number of points to consider when designing and conducting rhodopsin-based optogenetic experiments.
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Affiliation(s)
- Amelie Bergs
- Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany
- Institute of Biophysical Chemistry, Goethe University, Frankfurt, Germany
| | - Thilo Henss
- Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany
- Institute of Biophysical Chemistry, Goethe University, Frankfurt, Germany
| | - Caspar Glock
- Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany
- Institute of Biophysical Chemistry, Goethe University, Frankfurt, Germany
- Max-Planck-Institute for Brain Research, Frankfurt, Germany
| | - Jatin Nagpal
- Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany
- Institute of Biophysical Chemistry, Goethe University, Frankfurt, Germany
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Alexander Gottschalk
- Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany.
- Institute of Biophysical Chemistry, Goethe University, Frankfurt, Germany.
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10
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Fölsz O, Lin CC, Task D, Riabinina O, Potter CJ. The Q-system: A Versatile Repressible Binary Expression System. Methods Mol Biol 2022; 2540:35-78. [PMID: 35980572 DOI: 10.1007/978-1-0716-2541-5_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Binary expression systems are useful genetic tools for experimentally labeling or manipulating the function of defined cells. The Q-system is a repressible binary expression system that consists of a transcription factor QF (and the recently improved QF2/QF2w), the inhibitor QS, a QUAS-geneX effector, and a drug that inhibits QS (quinic acid). The Q-system can be used alone or in combination with other binary expression systems, such as GAL4/UAS and LexA/LexAop. In this review chapter, we discuss the past, present, and future of the Q-system for applications in Drosophila and other organisms. We discuss the in vivo application of the Q-system for transgenic labeling, the modular nature of QF that allows chimeric or split transcriptional activators to be developed, its temporal control by quinic acid, new methods to generate QF2 reagents, intersectional expression labeling, and its recent adoption into many emerging experimental species.
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Affiliation(s)
- Orsolya Fölsz
- Department of Biosciences, Durham University, Durham, UK
| | - Chun-Chieh Lin
- Department of Pathology and Laboratory Medicine, Giesel School of Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Darya Task
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | | | - Christopher J Potter
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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11
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Müller M, Gräbnitz F, Barandun N, Shen Y, Wendt F, Steiner SN, Severin Y, Vetterli SU, Mondal M, Prudent JR, Hofmann R, van Oostrum M, Sarott RC, Nesvizhskii AI, Carreira EM, Bode JW, Snijder B, Robinson JA, Loessner MJ, Oxenius A, Wollscheid B. Light-mediated discovery of surfaceome nanoscale organization and intercellular receptor interaction networks. Nat Commun 2021; 12:7036. [PMID: 34857745 PMCID: PMC8639842 DOI: 10.1038/s41467-021-27280-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 11/09/2021] [Indexed: 12/18/2022] Open
Abstract
The molecular nanoscale organization of the surfaceome is a fundamental regulator of cellular signaling in health and disease. Technologies for mapping the spatial relationships of cell surface receptors and their extracellular signaling synapses would unlock theranostic opportunities to target protein communities and the possibility to engineer extracellular signaling. Here, we develop an optoproteomic technology termed LUX-MS that enables the targeted elucidation of acute protein interactions on and in between living cells using light-controlled singlet oxygen generators (SOG). By using SOG-coupled antibodies, small molecule drugs, biologics and intact viral particles, we demonstrate the ability of LUX-MS to decode ligand receptor interactions across organisms and to discover surfaceome receptor nanoscale organization with direct implications for drug action. Furthermore, by coupling SOG to antigens we achieved light-controlled molecular mapping of intercellular signaling within functional immune synapses between antigen-presenting cells and CD8+ T cells providing insights into T cell activation with spatiotemporal specificity. LUX-MS based decoding of surfaceome signaling architectures thereby provides a molecular framework for the rational development of theranostic strategies. The spatial organization of cell surface receptors is critical for cell signaling and drug action. Here, the authors develop an optoproteomic method for mapping surface protein interactions, revealing cellular responses to antibodies, drugs and viral particles as well as immunosynapse signaling events.
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Affiliation(s)
- Maik Müller
- Department of Health Sciences and Technology (D-HEST), ETH Zurich, Institute of Translational Medicine (ITM), Zurich, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Fabienne Gräbnitz
- Department of Biology, ETH Zurich, Institute of Microbiology, Zurich, Switzerland
| | - Niculò Barandun
- Department of Biology, ETH Zurich, Institute of Microbiology, Zurich, Switzerland
| | - Yang Shen
- Institute of Food Nutrition and Health, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Fabian Wendt
- Department of Health Sciences and Technology (D-HEST), ETH Zurich, Institute of Translational Medicine (ITM), Zurich, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Sebastian N Steiner
- Department of Health Sciences and Technology (D-HEST), ETH Zurich, Institute of Translational Medicine (ITM), Zurich, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Yannik Severin
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | | | - Milon Mondal
- Chemistry Department, University of Zurich, Zurich, Switzerland
| | | | - Raphael Hofmann
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Marc van Oostrum
- Department of Health Sciences and Technology (D-HEST), ETH Zurich, Institute of Translational Medicine (ITM), Zurich, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Roman C Sarott
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Erick M Carreira
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Jeffrey W Bode
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Berend Snijder
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.,Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - John A Robinson
- Chemistry Department, University of Zurich, Zurich, Switzerland
| | - Martin J Loessner
- Institute of Food Nutrition and Health, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Annette Oxenius
- Department of Biology, ETH Zurich, Institute of Microbiology, Zurich, Switzerland
| | - Bernd Wollscheid
- Department of Health Sciences and Technology (D-HEST), ETH Zurich, Institute of Translational Medicine (ITM), Zurich, Switzerland. .,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
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12
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Byrd DT, Jin Y. Wired for insight-recent advances in Caenorhabditis elegans neural circuits. Curr Opin Neurobiol 2021; 69:159-169. [PMID: 33957432 PMCID: PMC8387325 DOI: 10.1016/j.conb.2021.02.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/16/2021] [Accepted: 02/22/2021] [Indexed: 11/15/2022]
Abstract
The completion of Caenorhabditis elegans connectomics four decades ago has long guided mechanistic investigation of neuronal circuits. Recent technological advances in microscopy and computation programs have aided re-examination of this connectomics, expanding our knowledge by both uncovering previously unreported synaptic connections and also generating models for neural networks underlying behaviors. Combining molecular information from single cell transcriptomes with elegant tools for cell-specific manipulation has further enhanced the ability to precisely investigate individual neurons in behaving animals. This mini-review aims to provide an overview of new information on connectomics and progress toward a molecular atlas of C. elegans nervous system, and discuss emerging findings on neuronal circuits.
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Affiliation(s)
- Dana T Byrd
- Neurobiology Section, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Yishi Jin
- Neurobiology Section, University of California San Diego, La Jolla, CA, 92093, USA; Kavli Institute of Brain and Mind, University of California San Diego, La Jolla, CA, 92093, USA.
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13
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Inhibition Underlies Fast Undulatory Locomotion in Caenorhabditis elegans. eNeuro 2021; 8:ENEURO.0241-20.2020. [PMID: 33361147 PMCID: PMC7986531 DOI: 10.1523/eneuro.0241-20.2020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 10/20/2020] [Accepted: 12/01/2020] [Indexed: 12/21/2022] Open
Abstract
Inhibition plays important roles in modulating the neural activities of sensory and motor systems at different levels from synapses to brain regions. To achieve coordinated movement, motor systems produce alternating contractions of antagonist muscles, whether along the body axis or within and among limbs, which often involves direct or indirect cross-inhibitory pathways. In the nematode Caenorhabditis elegans, a small network involving excitatory cholinergic and inhibitory GABAergic motoneurons generates the dorsoventral alternation of body-wall muscles that supports undulatory locomotion. Inhibition has been suggested to be necessary for backward undulation because mutants that are defective in GABA transmission exhibit a shrinking phenotype in response to a harsh touch to the head, whereas wild-type animals produce a backward escape response. Here, we demonstrate that the shrinking phenotype is exhibited by wild-type as well as mutant animals in response to harsh touch to the head or tail, but only GABA transmission mutants show slow locomotion after stimulation. Impairment of GABA transmission, either genetically or optogenetically, induces lower undulation frequency and lower translocation speed during crawling and swimming in both directions. The activity patterns of GABAergic motoneurons are different during low-frequency and high-frequency undulation. During low-frequency undulation, GABAergic VD and DD motoneurons show correlated activity patterns, while during high-frequency undulation, their activity alternates. The experimental results suggest at least three non-mutually exclusive roles for inhibition that could underlie fast undulatory locomotion in C. elegans, which we tested with computational models: cross-inhibition or disinhibition of body-wall muscles, or neuronal reset.
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14
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Olivares E, Izquierdo EJ, Beer RD. A Neuromechanical Model of Multiple Network Rhythmic Pattern Generators for Forward Locomotion in C. elegans. Front Comput Neurosci 2021; 15:572339. [PMID: 33679357 PMCID: PMC7930337 DOI: 10.3389/fncom.2021.572339] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 01/21/2021] [Indexed: 12/04/2022] Open
Abstract
Multiple mechanisms contribute to the generation, propagation, and coordination of the rhythmic patterns necessary for locomotion in Caenorhabditis elegans. Current experiments have focused on two possibilities: pacemaker neurons and stretch-receptor feedback. Here, we focus on whether it is possible that a chain of multiple network rhythmic pattern generators in the ventral nerve cord also contribute to locomotion. We use a simulation model to search for parameters of the anatomically constrained ventral nerve cord circuit that, when embodied and situated, can drive forward locomotion on agar, in the absence of pacemaker neurons or stretch-receptor feedback. Systematic exploration of the space of possible solutions reveals that there are multiple configurations that result in locomotion that is consistent with certain aspects of the kinematics of worm locomotion on agar. Analysis of the best solutions reveals that gap junctions between different classes of motorneurons in the ventral nerve cord can play key roles in coordinating the multiple rhythmic pattern generators.
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Affiliation(s)
- Erick Olivares
- Cognitive Science Program, Indiana University Bloomington, Bloomington, IN, United States
| | - Eduardo J. Izquierdo
- Cognitive Science Program, Indiana University Bloomington, Bloomington, IN, United States
- Luddy School of Informatics, Computing, and Engineering, Indiana University Bloomington, Bloomington, IN, United States
| | - Randall D. Beer
- Cognitive Science Program, Indiana University Bloomington, Bloomington, IN, United States
- Luddy School of Informatics, Computing, and Engineering, Indiana University Bloomington, Bloomington, IN, United States
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15
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Maertens T, Schöll E, Ruiz J, Hövel P. Multilayer network analysis of C. elegans: Looking into the locomotory circuitry. Neurocomputing 2021. [DOI: 10.1016/j.neucom.2020.11.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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16
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Targeted Central Nervous System Irradiation of Caenorhabditis elegans Induces a Limited Effect on Motility. BIOLOGY 2020; 9:biology9090289. [PMID: 32937967 PMCID: PMC7564402 DOI: 10.3390/biology9090289] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 09/09/2020] [Accepted: 09/10/2020] [Indexed: 12/29/2022]
Abstract
To clarify the tissue responsible for a biological function, that function can be experimentally perturbed by an external stimulus, such as radiation. Radiation can be precisely and finely administered and any subsequent change in function examined. To investigate the involvement of the central nervous system (CNS) in Caenorhabditis elegans’ locomotion, we irradiated a limited 20-µm-diameter area of the CNS with a single dose and evaluated the resulting effects on motility. However, whether irradiated area (beam size)-dependent or dose-dependent effects on motility occur via targeted irradiation remain unknown. In the present study, we examined the irradiated area- and dose-dependent effects of CNS-targeted irradiation on the motility of C. elegans using a collimating microbeam system and confirmed the involvement of the CNS and body-wall muscle cells around the CNS in motility. After CNS-targeted microbeam irradiation, C. elegans’ motility was assayed. The results demonstrated a dose-dependent effect of CNS-targeted irradiation on motility reflecting direct effects on the irradiated CNS. In addition, when irradiated with 1000-Gy irradiation, irradiated area (beam size)-dependent effects were observed. This method has two technical advantages: Performing a series of on-chip imaging analyses before and after irradiation and targeted irradiation using a distinct ion-beam size.
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17
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Towlson EK, Barabási AL. Synthetic ablations in the C. elegans nervous system. Netw Neurosci 2020; 4:200-216. [PMID: 32166208 PMCID: PMC7055645 DOI: 10.1162/netn_a_00115] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 11/12/2019] [Indexed: 01/03/2023] Open
Abstract
Synthetic lethality, the finding that the simultaneous knockout of two or more individually nonessential genes leads to cell or organism death, has offered a systematic framework to explore cellular function, and also offered therapeutic applications. Yet the concept lacks its parallel in neuroscience—a systematic knowledge base on the role of double or higher order ablations in the functioning of a neural system. Here, we use the framework of network control to systematically predict the effects of ablating neuron pairs and triplets on the gentle touch response. We find that surprisingly small sets of 58 pairs and 46 triplets can reduce muscle controllability in this context, and that these sets are localized in the nervous system in distinct groups. Further, they lead to highly specific experimentally testable predictions about mechanisms of loss of control, and which muscle cells are expected to experience this loss. “Synthetic lethality” in cell biology is an extreme example of the effects of higher order genetic interactions: The simultaneous knockout of two or more individually nonessential genes leads to cell death. We define a neural analog to this concept in relation to the locomotor response to gentle touch in C. elegans. Two or more neurons are synthetic essential if individually they are not required for this behavior, yet their combination is. We employ a network control approach to systematically assess all pairs and triplets of neurons by their effect on body wall muscle controllability, and find that only surprisingly small sets of neurons are synthetic essential. They are highly localized in the nervous system and predicted to affect control over specific sets of muscles.
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Affiliation(s)
- Emma K Towlson
- Network Science Institute and Department of Physics, Northeastern University, Boston, MA, USA
| | - Albert-László Barabási
- Network Science Institute and Department of Physics, Northeastern University, Boston, MA, USA
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18
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Pathak A, Chatterjee N, Sinha S. Developmental trajectory of Caenorhabditis elegans nervous system governs its structural organization. PLoS Comput Biol 2020; 16:e1007602. [PMID: 31895942 PMCID: PMC6959611 DOI: 10.1371/journal.pcbi.1007602] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 01/14/2020] [Accepted: 12/11/2019] [Indexed: 11/22/2022] Open
Abstract
A central problem of neuroscience involves uncovering the principles governing the organization of nervous systems which ensure robustness in brain development. The nematode Caenorhabditis elegans provides us with a model organism for studying this question. In this paper, we focus on the invariant connection structure and spatial arrangement of the neurons comprising the somatic neuronal network of this organism to understand the key developmental constraints underlying its design. We observe that neurons with certain shared characteristics-such as, neural process lengths, birth time cohort, lineage and bilateral symmetry-exhibit a preference for connecting to each other. Recognizing the existence of such homophily and their relative degree of importance in determining connection probability within neurons (for example, in synapses, symmetric pairing is the most dominant factor followed by birth time cohort, process length and lineage) helps in connecting specific neuronal attributes to the topological organization of the network. Further, the functional identities of neurons appear to dictate the temporal hierarchy of their appearance during the course of development. Providing crucial insights into principles that may be common across many organisms, our study shows how the trajectory in the developmental landscape constrains the structural organization of a nervous system.
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Affiliation(s)
- Anand Pathak
- The Institute of Mathematical Sciences, CIT Campus, Taramani, Chennai, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai, India
| | | | - Sitabhra Sinha
- The Institute of Mathematical Sciences, CIT Campus, Taramani, Chennai, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai, India
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19
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Steuer Costa W, Van der Auwera P, Glock C, Liewald JF, Bach M, Schüler C, Wabnig S, Oranth A, Masurat F, Bringmann H, Schoofs L, Stelzer EHK, Fischer SC, Gottschalk A. A GABAergic and peptidergic sleep neuron as a locomotion stop neuron with compartmentalized Ca2+ dynamics. Nat Commun 2019; 10:4095. [PMID: 31506439 PMCID: PMC6736843 DOI: 10.1038/s41467-019-12098-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 08/21/2019] [Indexed: 11/09/2022] Open
Abstract
Animals must slow or halt locomotion to integrate sensory inputs or to change direction. In Caenorhabditis elegans, the GABAergic and peptidergic neuron RIS mediates developmentally timed quiescence. Here, we show RIS functions additionally as a locomotion stop neuron. RIS optogenetic stimulation caused acute and persistent inhibition of locomotion and pharyngeal pumping, phenotypes requiring FLP-11 neuropeptides and GABA. RIS photoactivation allows the animal to maintain its body posture by sustaining muscle tone, yet inactivating motor neuron oscillatory activity. During locomotion, RIS axonal Ca2+ signals revealed functional compartmentalization: Activity in the nerve ring process correlated with locomotion stop, while activity in a branch correlated with induced reversals. GABA was required to induce, and FLP-11 neuropeptides were required to sustain locomotion stop. RIS attenuates neuronal activity and inhibits movement, possibly enabling sensory integration and decision making, and exemplifies dual use of one cell across development in a compact nervous system.
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Affiliation(s)
- Wagner Steuer Costa
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Max-von-Laue-Strasse 15, 60438, Frankfurt, Germany.,Institute for Biophysical Chemistry, Goethe University, Max-von-Laue-Strasse 9, 60438, Frankfurt, Germany
| | - Petrus Van der Auwera
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Max-von-Laue-Strasse 15, 60438, Frankfurt, Germany.,Institute for Biophysical Chemistry, Goethe University, Max-von-Laue-Strasse 9, 60438, Frankfurt, Germany.,Functional Genomics and Proteomics Group, Department of Biology, KU Leuven, Naamsestraat 59 - box 2465, 3000, Leuven, Belgium
| | - Caspar Glock
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Max-von-Laue-Strasse 15, 60438, Frankfurt, Germany.,Institute for Biophysical Chemistry, Goethe University, Max-von-Laue-Strasse 9, 60438, Frankfurt, Germany.,Max-Planck-Institute for Brain Research, Max-von-Laue-Strasse 4, 60438, Frankfurt, Germany
| | - Jana F Liewald
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Max-von-Laue-Strasse 15, 60438, Frankfurt, Germany.,Institute for Biophysical Chemistry, Goethe University, Max-von-Laue-Strasse 9, 60438, Frankfurt, Germany
| | - Maximilian Bach
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Max-von-Laue-Strasse 15, 60438, Frankfurt, Germany.,Institute for Biophysical Chemistry, Goethe University, Max-von-Laue-Strasse 9, 60438, Frankfurt, Germany
| | - Christina Schüler
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Max-von-Laue-Strasse 15, 60438, Frankfurt, Germany.,Institute for Biophysical Chemistry, Goethe University, Max-von-Laue-Strasse 9, 60438, Frankfurt, Germany
| | - Sebastian Wabnig
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Max-von-Laue-Strasse 15, 60438, Frankfurt, Germany.,Institute for Biophysical Chemistry, Goethe University, Max-von-Laue-Strasse 9, 60438, Frankfurt, Germany.,od green GmbH, Passauerstrasse 34, 4780, Schärding am Inn, Austria
| | - Alexandra Oranth
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Max-von-Laue-Strasse 15, 60438, Frankfurt, Germany.,Institute for Biophysical Chemistry, Goethe University, Max-von-Laue-Strasse 9, 60438, Frankfurt, Germany
| | - Florentin Masurat
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Henrik Bringmann
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany.,Department of Biology, University of Marburg, Karl-von-Frisch-Strasse 8, 35043, Marburg, Germany
| | - Liliane Schoofs
- Functional Genomics and Proteomics Group, Department of Biology, KU Leuven, Naamsestraat 59 - box 2465, 3000, Leuven, Belgium
| | - Ernst H K Stelzer
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Max-von-Laue-Strasse 15, 60438, Frankfurt, Germany.,Institute of Cell Biology and Neuroscience, Goethe University, Max-von-Laue-Strasse 13, 60439, Frankfurt, Germany
| | - Sabine C Fischer
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Max-von-Laue-Strasse 15, 60438, Frankfurt, Germany.,Institute of Cell Biology and Neuroscience, Goethe University, Max-von-Laue-Strasse 13, 60439, Frankfurt, Germany.,Center for Computational and Theoretical Biology (CCTB), University of Würzburg, Campus Hubland Nord 32, 97074, Würzburg, Germany
| | - Alexander Gottschalk
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Max-von-Laue-Strasse 15, 60438, Frankfurt, Germany. .,Institute for Biophysical Chemistry, Goethe University, Max-von-Laue-Strasse 9, 60438, Frankfurt, Germany.
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20
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Hughes S, Celikel T. Prominent Inhibitory Projections Guide Sensorimotor Computation: An Invertebrate Perspective. Bioessays 2019; 41:e1900088. [DOI: 10.1002/bies.201900088] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/17/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Samantha Hughes
- HAN BioCentreHAN University of Applied Sciences Nijmegen 6525EM The Netherlands
| | - Tansu Celikel
- Department of Neurophysiology, Donders Institute for Brain Cognition and BehaviourRadboud University Nijmegen 6525AJ The Netherlands
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21
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Barkan CL, Zornik E. Feedback to the future: motor neuron contributions to central pattern generator function. ACTA ACUST UNITED AC 2019; 222:222/16/jeb193318. [PMID: 31420449 DOI: 10.1242/jeb.193318] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Motor behaviors depend on neural signals in the brain. Regardless of where in the brain behavior patterns arise, the central nervous system sends projections to motor neurons, which in turn project to and control temporally appropriate muscle contractions; thus, motor neurons are traditionally considered the last relay from the central nervous system to muscles. However, in an array of species and motor systems, an accumulating body of evidence supports a more complex role of motor neurons in pattern generation. These studies suggest that motor neurons not only relay motor patterns to the periphery, but directly contribute to pattern generation by providing feedback to upstream circuitry. In spinal and hindbrain circuits in a variety of animals - including flies, worms, leeches, crustaceans, rodents, birds, fish, amphibians and mammals - studies have indicated a crucial role for motor neuron feedback in maintaining normal behavior patterns dictated by the activity of a central pattern generator. Hence, in this Review, we discuss literature examining the role of motor neuron feedback across many taxa and behaviors, and set out to determine the prevalence of motor neuron participation in motor circuits.
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Affiliation(s)
| | - Erik Zornik
- Biology Department, Reed College, Portland, OR 97202, USA
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22
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Rhodopsin-based voltage imaging tools for use in muscles and neurons of Caenorhabditis elegans. Proc Natl Acad Sci U S A 2019; 116:17051-17060. [PMID: 31371514 PMCID: PMC6708366 DOI: 10.1073/pnas.1902443116] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Neuronal and other excitable cell activity is characterized by alteration in membrane voltage, while intracellular Ca2+ levels and transmitter release are affected downstream of electrical activity. Thus, the most direct way of monitoring neuronal activity is by membrane voltage. Electrophysiology is demanding for multiple cells or cell ensembles and difficult to use in live animals, thus imaging methods are desirable. Yet, genetically encoded voltage indicators fell behind Ca2+ indicators until recently, when microbial rhodopsins and derivatives were introduced as genetically encoded voltage indicators. We evaluated rhodopsin tools for voltage imaging in muscles and neurons of Caenorhabditis elegans, a prime animal model in neuro- and cell biology, showing robust performance and the ability to characterize genetic mutants. Genetically encoded voltage indicators (GEVIs) based on microbial rhodopsins utilize the voltage-sensitive fluorescence of all-trans retinal (ATR), while in electrochromic FRET (eFRET) sensors, donor fluorescence drops when the rhodopsin acts as depolarization-sensitive acceptor. In recent years, such tools have become widely used in mammalian cells but are less commonly used in invertebrate systems, mostly due to low fluorescence yields. We systematically assessed Arch(D95N), Archon, QuasAr, and the eFRET sensors MacQ-mCitrine and QuasAr-mOrange, in the nematode Caenorhabditis elegans. ATR-bearing rhodopsins reported on voltage changes in body wall muscles (BWMs), in the pharynx, the feeding organ [where Arch(D95N) showed approximately 128% ΔF/F increase per 100 mV], and in neurons, integrating circuit activity. ATR fluorescence is very dim, yet, using the retinal analog dimethylaminoretinal, it was boosted 250-fold. eFRET sensors provided sensitivities of 45 to 78% ΔF/F per 100 mV, induced by BWM action potentials, and in pharyngeal muscle, measured in simultaneous optical and sharp electrode recordings, MacQ-mCitrine showed approximately 20% ΔF/F per 100 mV. All sensors reported differences in muscle depolarization induced by a voltage-gated Ca2+-channel mutant. Optogenetically evoked de- or hyperpolarization of motor neurons increased or eliminated action potential activity and caused a rise or drop in BWM sensor fluorescence. Finally, we analyzed voltage dynamics across the entire pharynx, showing uniform depolarization but compartmentalized repolarization of anterior and posterior parts. Our work establishes all-optical, noninvasive electrophysiology in live, intact C. elegans.
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23
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Yamanashi T, Maki M, Kojima K, Shibukawa A, Tsukamoto T, Chowdhury S, Yamanaka A, Takagi S, Sudo Y. Quantitation of the neural silencing activity of anion channelrhodopsins in Caenorhabditis elegans and their applicability for long-term illumination. Sci Rep 2019; 9:7863. [PMID: 31133660 PMCID: PMC6536681 DOI: 10.1038/s41598-019-44308-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 05/14/2019] [Indexed: 11/15/2022] Open
Abstract
Ion pumps and channels are responsible for a wide variety of biological functions. Ion pumps transport only one ion during each stimulus-dependent reaction cycle, whereas ion channels conduct a large number of ions during each cycle. Ion pumping rhodopsins such as archaerhodopsin-3 (Arch) are often utilized as light-dependent neural silencers in animals, but they require a high-density light illumination of around 1 mW/mm2. Recently, anion channelrhodopsins -1 and -2 (GtACR1 and GtACR2) were discovered as light-gated anion channels from the cryptophyte algae Guillardia theta. GtACRs are therefore expected to silence neural activity much more efficiently than Arch. In this study, we successfully expressed GtACRs in neurons of the nematode Caenorhabditis elegans (C. elegans) and quantitatively evaluated how potently GtACRs can silence neurons in freely moving C. elegans. The results showed that the light intensity required for GtACRs to cause locomotion paralysis was around 1 µW/mm2, which is three orders of magnitude smaller than the light intensity required for Arch. As attractive features, GtACRs are less harmfulness to worms and allow stable neural silencing effects under long-term illumination. Our findings thus demonstrate that GtACRs possess a hypersensitive neural silencing activity in C. elegans and are promising tools for long-term neural silencing.
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Affiliation(s)
- Taro Yamanashi
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan
| | - Misayo Maki
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan
| | - Keiichi Kojima
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan
| | - Atsushi Shibukawa
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan
| | - Takashi Tsukamoto
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan.,Faculty of Advanced Life Science and Global Station for Soft Matter, Global Institution for Collaborative Research and Education, Hokkaido University, Kita-10 Nishi-8, Kita-ku, Sapporo, 060-0810, Japan
| | - Srikanta Chowdhury
- Department of Neuroscience II, Research Institute of Environmental Medicine, Nagoya University, Nagoya, 464-8601, Japan
| | - Akihiro Yamanaka
- Department of Neuroscience II, Research Institute of Environmental Medicine, Nagoya University, Nagoya, 464-8601, Japan
| | - Shin Takagi
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan
| | - Yuki Sudo
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan.
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24
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